Research Priorities for Tropical Ecosystems 

Under Climate Change Workshop

June 4–5, 2012

Convened by

U.S. Department of Energy

Office of Science

Office of Biological and Environmental Research

This report is available at science.energy.gov/ber/news-and-resources/ and tes.science.energy.gov.

Mission

The Office of Biological and Environmental Research (BER) advances world-class fundamental research programs and scientific user 

facilities to support the Department of Energy’s energy, environment, and basic research missions. Addressing diverse and critical 

global challenges, the BER program seeks to understand how genomic information is translated to functional capabilities, enabling 

more confident redesign of microbes and plants for sustainable biofuel production, improved carbon storage, or contaminant 

bioremediation. BER research advances understanding of the roles of Earth’s biogeochemical systems (the atmosphere, land, oceans, 

sea ice, and subsurface) in determining climate so that it can be predicted decades or centuries into the future, information needed 

to plan for future energy and resource needs. Solutions to these challenges are driven by a foundation of scientific knowledge and 

inquiry in atmospheric chemistry and physics, ecology, biology, and biogeochemistry.

Jeffrey Chambers, Ph.D

Lawrence Berkeley 

National Laboratory

Co-Chairs

Rosie Fisher, Ph.D.

National Center for 

Atmospheric Research

Jefferson Hall, Ph.D. 

Smithsonian Tropical 

Research Institute

Richard J. Norby, Ph.D 

Oak Ridge National Laboratory

Steven C. Wofsy, Ph.D. 

Harvard University

Images. Front cover: NASA tropical forest map by Robert Simmon, using Moderate Resolution Imaging Spectroradiometer land cover classification data. 

Second and fourth images on top row courtesy of Yadvinder Malhi, University of Oxford, and Jeffrey Chambers, Lawrence Berkeley National Laboratory, 

respectively. Other images from iStockphoto.com. Back cover: First and fourth images courtesy of Sassan Saatchi, NASA/JPL-Caltech, and Biqing Liang, Cornell 

University and Academia Sinica, respectively. Other images from iStockphoto.com. Appendices image courtesy of Tana E. Wood, USDA Forest Service.

Suggested Citation for this Report. U.S. DOE. 2012. Research Priorities for Tropical Ecosystems Under Climate Change Workshop Report, DOE/SC-0153. 

U.S. Department of Energy Office of Science. science.energy.gov/ber/news-and-resources/ .

Organizers

Climate and Environmental Sciences Division

Daniel Stover, Ph.D.

Daniel.Stover@science.doe.gov 

301-903-0289

Dorothy Koch, Ph.D. Mike Kuperberg, Ph.D. Patrick Horan, M.Sc. 
i

Research Priorities for Tropical Ecosystems 

Under Climate Change Workshop Report

U.S. Department of Energy

Office of Science

Office of Biological and Environmental Research

Published: October 2012

DOE/SC-0153
ii Research Priorities for Tropical Ecosystems Under Climate Change DOE Office of Science

Preface and Acknowledgements

The goal of the Research Priorities for 

Tropical Ecosystems Under Climate Change 

Workshop was to engage the scientific 

community in an open discussion to identify critical 

scientific gaps that limit the ability to represent 

tropical ecosystems in Earth system models (ESMs) 

and that demand immediate field investigations. The 

results of this workshop will inform the Department 

of Energy’s Office of Biological and Environmental Research (BER) as it plans and prepares for a 

tropical Next-Generation Ecosystem Experiment 

(NGEE). The NGEE approach uses model-informed 

and -inspired field studies resulting in iterative 

refinement of high-resolution, predictive ESMs. 

The overall goal of BER’s decade-long investment 

will be to investigate tropical ecosystems and their 

vulnerabilities to climate change and to improve the 

representation of these systems in ESMs. Specifically, the workshop (1) summarized past and current 

tropical terrestrial field and modeling research 

related to tropical climate change; (2) identified 

critical sensitivities and uncertainties in the systems; 

and (3) discussed the state of the science in tropical 

land modeling, processes poorly captured in models, and potential experiments that would test and 

improve tropical land model fidelity. These issues 

were discussed with an emphasis on three major 

tropical ecosystem locations that may be candidate 

regions for NGEE Tropics field studies: the Amazon 

Basin, Congo Basin, and Southeast Asia.

BER would like to thank all participants who 

energetically took part in workshop discussions 

and generously contributed their time and ideas 

during the two-day meeting. The workshop would 

not have been possible without the scientific vision 

and leadership of the workshop co-chairs. We are 

thankful for the dedicated efforts of the following members of the workshop writing team who 

did an exceptional job of stimulating a productive 

discussion and capturing new ideas and concepts 

that emerged: Scott Brooks, Molly Cavaleri, Jeffrey 

Chambers, Nick Chappell, Robin Chazdon, Mary 

Firestone, Rosie Fisher, Jefferson Hall, Terry Hazen, 

Alex Johs, Michael Keller, Charlie Koven, Liyuan 

Liang, Scot Martin, Melanie Mayes, Patrick Meir, 

Richard J. Norby, Sasha Reed, Peter Thornton, Sue 

Trumbore, Maria Uriarte, Steven C. Wofsy, Tana 

Wood, Joe Wright, and Xiaojuan Yang.

Additional contributions from Patrick Baker, 

Lucas Cernusak, William Hoffmann, Ariel Lugo, 

Yadvinder Malhi, Alistair Rogers, and Whendee 

Silver are greatly appreciated. We also are 

thankful for the excellent work of the staff from 

Oak Ridge National Laboratory’s Biological and 

Environmental Research Information System who 

served as rapporteurs, edited, and prepared this 

report for publication.
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change iii

Table of Contents

Executive Summary ...............................................................................................................................................................v

Background

1 Introduction ..............................................................................................................................................................1

2 Regional Differences in Tropical Forest Response to Climate Change .........................................................................7

Responses to External Forcings

3 Responses of Tropical Forests to Elevated CO2........................................................................................................... 13

4 Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes......................................................................23

5 Drought and Drought-Induced Mortality in Tropical Forests .................................................................................... 33

6 Natural Disturbance and Recovery...........................................................................................................................43

7 Anthropogenic Disturbance and Land Use...............................................................................................................51

Integrating Processes

8 Biosphere-Atmosphere Interactions: Greenhouse Gases, Reactive Chemicals, and Aerosols ...................................55

9 Nutrient Limitations................................................................................................................................................63

10 Belowground Processes: Roots and Soil Biogeochemistry........................................................................................69

11 Hydrology Within Tropical Natural Forests: Implications for Large-Scale Ecosystem Modeling.................................77

12 Summary of Key Uncertainties and Research Opportunities.........................................................................................85

Appendices

Appendix 1. Next-Generation Ecosystem Experiment: Integrating Modeling and Experimentation ............................92

Appendix 2. Workshop Agenda, Breakout Sessions, and Participants..........................................................................95

Appendix 3. Bibliography..........................................................................................................................................101

Acronyms and Abbreviations.........................................................................................................................Inside back cover
iv Research Priorities for Tropical Ecosystems Under Climate Change DOE Office of Science
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change v

Executive Summary 

Understanding Connections 

Between Tropical Forests 

and Climate

The Tropics, with approximately 40% of 

Earth’s land surface area, critically regulate 

many Earth system processes. Containing 

great stores of biomass, tropical ecosystems represent 

the largest reservoir of terrestrial carbon. The Tropics 

also cycle more carbon dioxide (CO2) and water than 

any other biome and play important roles in determining Earth’s energy balance, which drives global 

systems of temperature and precipitation. Overall, 

wet tropical forests contain about 25% of the carbon 

in the terrestrial biosphere and account for 34% of 

Earth’s gross primary production. This vast area, 

which includes the world’s driest deserts and wettest 

forests, also harbors a large fraction of Earth’s biodiversity. Despite the negative impact of widespread 

deforestation, tropical ecosystems continue to benefit 

Earth’s atmosphere and climate system by mitigating 

climatic warming through carbon sequestration and 

evaporative cooling. Of great concern, however, is 

the vulnerability of tropical ecosystems to rapid shifts 

resulting from a changing climate. Significant potential thus exists for important feedbacks with CO2, 

water, and energy exchange from tropical ecosystems 

due to climatic change.

Tropical forests are thought to be especially vulnerable to climate change compared to other regions of 

Earth. Unlike in temperate forests where temperatures fluctuate widely during the course of a year, 

temperatures in tropical forests (at a given elevation) 

vary little, with trees adapted to thrive in a relatively 

narrow thermal range. Hence, the relative impact of 

climatic warming likely will be greater in the Tropics 

because predicted changes in temperature are large 

compared to normal interannual variation. Moreover, 

increasing atmospheric temperatures may push 

tropical forests into climate regimes beyond those 

ever experienced by existing forests. Also, highbiomass tropical forests require sufficient moisture to 

maintain a closed canopy, and changing precipitation 

patterns such as a shift toward more extreme events 

and extended droughts potentially could push forests 

beyond a moisture threshold, causing widespread 

tree mortality. Catastrophic loss of tropical forests 

may be a key feedback in tropical ecosystems because 

widespread tree mortality would release large quantities of CO2 back to the atmosphere, accelerating the 

influence of this primary driver of global warming. 

Major disruptions in hydrologic cycles affecting large 

tropical regions also would be expected.

Improving Climate Model 

Representation of Tropical Systems

The ability to reliably predict interactions between 

the Tropics and climate is imperative, given the 

large potential impacts of a changing climate on the 

structure and function of tropical forests and on the 

direct and indirect feedbacks they provide to the 

climate system. Although understanding of tropical 

systems is improving, their representation in climate 

models lags significantly behind that of temperate 

systems. Tropical ecosystems are responsible for 

numerous biases in ESMs, which currently disagree 

on the direction or degree of climate–carbon cycle 

feedbacks in tropical forests. Improving ESMs will 

require a coordinated effort by scientists from many 

disciplines. This urgently needed effort involves 

integrating new data, experimental results, and 

process knowledge into a fully coupled global climate 

model. This robust, fully coupled community model 

must incorporate diverse sources of information 

that describe the physical, chemical, and biological 

processes by which tropical terrestrial ecosystems 

affect and are affected by climate.

The U.S. Department of Energy (DOE) is strategically committed to improving the representation of 

terrestrial ecosystem processes in ESMs—and thereby 

enhancing the robustness of their climate projections—by coupling models with experimental and 

observational studies across relevant spatial and temporal scales. These improved predictive capabilites can 

then be used, for example, to better inform U.S. energy 

policy and climate adaptation strategies. The scientific 

community has determined that tropical forests are a 

Executive Summary
vi Research Priorities for Tropical Ecosystems Under Climate Change DOE Office of Science

Executive Summary

key biome for comprehensive study, given their global 

and regional significance, expected sensitivity to a 

changing climate with large potential feedbacks to the 

Earth system, and inadequate representation in modeling efforts (IPCC 2007; Christensen et al. 2007; 

Hanson et al. 2008). Model-informed field studies in 

the most climate-sensitive tropical geographies can 

result in iterative refinement of high-resolution predictive models. These improvements can be achieved 

by identifying key processes from the bedrock to the 

top of the canopy, improving their representation in 

models, and exploring the vulnerabilities of tropical 

ecosystems to a changing climate.

Identifying Uncertainties and Gaps 

in Tropical Ecosystem Research

This report documents the results of the Research 

Priorities for Tropical Ecosystems Under Climate 

Change Workshop held June 4–5, 2012, in Bethesda, 

Maryland. The workshop’s overall goal was to 

identify critical scientific gaps that limit the ability to 

represent tropical forests in ESMs and that demand 

immediate field investigations. Nearly 40 researchers 

representing a large range of tropical forest expertise 

participated in the meeting. During the workshop, 

these experts addressed key unanswered questions 

that are critical for determining how tropical ecosystems interact with and feed back to the climate 

system. The workshop featured a series of plenary 

talks, four breakout sessions with three parallel 

groups focused on broad research areas, and activities to integrate discussions among groups. Breakout sessions focused on soil biogeochemistry and 

hydrology, natural and anthropogenic disturbance, 

tropical forest ecophysiology, and cross-cutting 

issues. During the breakouts, participants were 

charged with summarizing and discussing current 

knowledge and understanding of these topics, the 

largest associated uncertainties, and general strategies for resolving those uncertainties. Underlying all 

topics was the recognition that they must be considered within the context of high-level constraints, 

such as energy and mass balance and regional-scale 

measurements of terrestrial-atmosphere fluxes, so 

that experimental results can be leveraged for modeling and simulation. Workshop participants identified 

a number of critical uncertainties. Considerable 

overlap was recognized among these broad themes, 

and several additional questions were discussed 

during the breakout sessions. The broad themes 

identified include:

•	 Soil Biogeochemistry and Hydrology. How 

are tropical soils characterized, including soil 

structure, soil carbon pools, and biogeochemical cycling? How will forests on different soils, 

saprolite, and rock respond to the same climate 

change drivers? How do differences in hydrology 

and soil, saprolite, and rock (i.e., geochemical 

and geomorphological) properties influence tree 

susceptibility to drought-induced mortality? How 

will, for example, local and regional soil nutrient 

availability respond to rising atmospheric temperature and changing precipitation combined with 

unique local characteristics of soil geochemistry, 

microbiology, ecology, and geomorphology?

•	 Natural and Anthropogenic Disturbance. How 

do changes in land use affect mass and energy 

fluxes to the atmosphere? How does fire interact 

with other environmental factors to affect closedcanopy forests and transitions to other states? 

What are other major natural disturbances, and 

how will they vary with climate change?

•	 Tropical Forest Ecophysiology. What are the 

direct effects of elevated atmospheric CO2 on 

leaf physiology and plant and ecosystem carbon 

cycling and metabolism? How do tropical trees 

and forests respond to drought, what are the 

thresholds for drought-induced tree mortality, 

and will these responses and thresholds change as 

atmospheric CO2 rises? How will trees and forest 

ecosystems respond to rising atmospheric temperature with a changing climate?

•	 Cross-Cutting Issues. What aspects of tropical 

ecosystem diversity and demography are most 

important for constraining ESMs? What are the 

physiological and climatic factors that control 

forest-atmosphere interactions, processes, convection, and emissions (e.g., biogenic volatile organic 

compounds and carbon)? What kinds of remotesensing datasets and products, at relevant scales 

(landscape, regional, and continental), could 

inform uncertainties related to carbon energy 

fluxes and climate change in the Tropics?
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change vii

Executive Summary

Based on these workshop discussions, this report 

is broadly organized into three sections including 

background information (introduction and regional 

differences across the Tropics); responses to external 

forcings (elevated atmospheric CO2, elevated temperature, drought, natural disturbances, and anthropogenic disturbance); and integrating processes 

(biosphere-atmosphere interactions, nutrient limitations, roots and soil biogeochemistry, and hydrology). 

Summary key points from these chapters include:

•	 How will tropical ecosystems respond to 

increasing temperatures? In the Intergovernmental Panel on Climate Change’s (IPCC) Fourth 

Assessment Report A1B scenario, temperatures are 

predicted to increase by 2 to 5°C over the tropical 

region by 2100, representing a substantial warming 

(IPCC 2007; Christensen et al. 2007). The change 

in temperature relative to weather patterns in the 

1900s is particularly important because tropical 

species have adapted to a very narrow thermal 

range. Because the current climate is at the upper 

end of this range, projected temperature increases 

during this century will increasingly expose tropical forest systems to conditions that are beyond 

their natural operating regime. Thus, there are no 

analogue environments with which to compare 

tropical climates in a warmer world. To improve 

ESM predictions of tropical ecological response to 

increasing temperatures, more research is required 

to understand temperature thresholds and sensitivities of photosynthesis and respiration, temperature-induced changes in plant carbon allocation, 

impacts on soil biogeochemical processes, and 

interactions between functional diversity and temperature. More insight is needed on how long-term 

responses to increased temperature relate to those 

observed in the short term and on the importance 

of temporal variation in these responses.

•	 How will tropical ecosystems respond to 

changes in rainfall? Atmospheric processes 

are among the best developed aspects of current 

models. Projections from these models indicate 

reduced precipitation patterns and regimes across 

large tropical regions (such as the southern and 

eastern Amazon) and increased rainfall seasonality, raising concerns over the vulnerability of 

tropical forests to drought-induced changes in 

ecosystem structure and functioning. These 

projections also show increased rainfall over other 

regions such as tropical Africa. To improve the 

representation of tropical forests in these models, 

a better understanding is needed of the response 

of these systems to changes in water supply and, 

most importantly, the spatial and temporal drivers 

and feedbacks of drought stress and tree mortality. 

Similar improvements are needed for representations of soil depth, structure, and hydraulic 

properties; root systems; and stomatal regulation.

•	 How will natural disturbance events and 

tree mortality increase as a result of climate 

forcings? Relatively small directional shifts in 

tree mortality rates can significantly affect the 

global carbon cycle and net forest-atmosphere 

CO2 exchanges. The potential for increased tree 

mortality from drought, fire, temperature, and 

windthrow is a primary concern. A major gap 

in the ability of models to predict disturbance 

regimes is the insufficient understanding of the 

dominant mechanisms and risks of vegetation 

mortality, the relationship between atmospheric 

convection patterns and extreme events, and 

functional compositional shifts related to disturbance events.

•	 How will tropical ecosystems respond to 

increasing atmospheric CO2 concentrations?

Although the increase in atmospheric CO2 is 

unambiguous and short-term physiological 

responses are universal, the integrated response 

of forest ecosystems and the feedbacks to the 

atmosphere are harder to predict. Research is 

needed to understand the response of tropical 

forests to elevated CO2, including the study of 

critical interactions among CO2, water, and nutrient cycles. ESMs cannot predict the response 

of tropical forests to elevated CO2 without new 

data on leaf-level gas exchange under tropical 

conditions; the role of nutrient limitations; and 

large-scale biomass dynamics, carbon allocation 

patterns, and belowground responses that alter 

the longer-term fate of carbon. A particularly 

important uncertainty is whether elevated atmospheric CO2 will ameliorate drought responses of 

tropical ecosystems and alter their plant community composition.

Executive Summary
viii Research Priorities for Tropical Ecosystems Under Climate Change DOE Office of Science

Executive Summary

•	 What are the interactions between climate 

change and aerosols, particulates, and other 

trace gas emissions from tropical forests?

Tropical forests are large sources of biological 

aerosols and trace gases such as methane, nitrous 

oxide, and biogenic volatile organic compounds 

(BVOCs), which all have significant roles in the 

Earth system. Many unanswered questions about 

these compounds and their roles limit current 

understanding and representation of tropical 

ecosystems in ESMs. Key uncertainties include 

physiological and climatic factors that control 

production and emission of plant and soil methane, nitrous oxide, and BVOCs. Also needed is 

improved understanding of the environmental 

influence of forest ecosystem properties and 

processes including light quality, storm intensity, 

cloud-aerosol interactions (e.g., fire- and fungalderived aerosols), nutrient deposition, and 

ozone effects.

•	 How will tropical forest interactions with the 

Earth system shift as a result of anthropogenic 

disturbance and land-use change? A significant 

fraction of the tropical forest cover lies in areas 

recovering from logging or in secondary forests 

and land abandoned from agriculture (FAO 

2010). The consequences of this land-use change 

on ecosystem function remain uncertain. Thus, 

a key need is understanding the relationships 

between changes in land use (e.g., deforestation, 

use conversion, and recovery) and hydrology, 

sensible and latent heat fluxes, and impacts on 

soil biogeochemistry. Such insights are essential 

for capturing the magnitude of land-atmosphere 

feedbacks across a range of spatial scales in ESMs.

Addressing Research Uncertainties, 

Gaps, and Opportunities

Many of these questions are critical and relevant 

across the Tropics—including the Amazon, Central 

America and the Caribbean, the Congo Basin of 

Africa, and Southeast Asia—but some may be more 

applicable to one region than another. Choosing the 

best place to study these questions requires balancing 

numerous factors, such as the region’s impact on the 

global system; its perceived vulnerability to climate 

change; the representativeness of a site relative to a 

larger region; and the degree to which an area has 

been studied, whether little or extensively. Studying 

one region intensively holds great value, but so too 

does conducting extensive research across all of the 

Tropics. Regardless of the geographic approach, careful coordination of the implementation, goals, and 

outcomes of the proposed research will be necessary 

to achieve the intended objectives. Science drivers 

are paramount, but practical issues of infrastructure 

support and accessibility cannot be ignored. Ultimately, good hypothesis-driven science carried out 

anywhere in the Tropics will be valuable in informing 

models about critical processes that can improve 

their predictive capacity.

Although the questions and uncertainties identified at 

the workshop and in this report are challenging, the 

scientific community is committed to tackling them. 

Research networks established across the Tropics, as 

well as projects led by single investigators, have elucidated many critical processes that must be studied 

more extensively. Observations of forest productivity, responses to periodic drought, or recovery after 

disturbance reveal areas in which models currently fail 

and require improvement. Important processes missing from models iteratively guide decisions about new 

knowledge to be pursued and datasets to assemble. 

Using these models to predict an uncertain future—

one with climatic conditions never experienced by 

extant tropical forests—may require experimental 

systems that simulate those future conditions and 

provide a platform for model testing. A rigorous 

scaling framework is needed so that process studies, 

experiments, plot-level observations, and regional 

to continental scaling approaches can inform and be 

constrained by their simulated representation in a 

global land-ocean-atmosphere model. Together, these 

considerations describe the broad goals of a concentrated and multidisciplinary research program—such 

as DOE’s Next-Generation Ecosystem Experiment 

(NGEE) in the Tropics—that closely integrates 

experimental approaches and modeling to maximize 

research investments in ecosystem science.
Introduction

CHAPTER 1
2 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 1 – Introduction

DOE Office of Science

The Tropics—the region of Earth between 

23.4° latitude north and south of the equator—have widely diverse ecosystems, including some of the driest deserts and wettest forests on 

the planet. Tropical forests, which comprise about 

half of Earth’s total forest area, are characterized by 

their warm and wet climate, generally nutrient-poor 

soils, and high biological diversity. These forests hold 

more biomass and cycle more carbon and water than 

any other biome and play critical roles in determining Earth’s energy balance. Land-use activities in the 

Tropics are responsible for most of the net nonfossil 

flux of carbon dioxide (CO2) to the atmosphere. 

These fluxes, along with significant emissions of 

aerosols and other compounds from tropical forests, 

play important roles in determining the atmospheric 

chemical environment. The potential for extreme 

drought with a warming climate over large portions 

of the tropical forest biome could lead to significant 

carbon fluxes to the atmosphere associated with tree 

mortality. Moreover, because the Tropics occur at the 

high temperature extremes of the current climate, a 

warmer climate will push these ecosystems toward 

states not experienced in recent history. These critical 

features result in strong potential feedbacks among 

tropical forests, the atmosphere, and global cycles of 

carbon and water. The ability to better predict these 

feedbacks under a changing climate requires improving the representation of tropical forests in Earth 

system models (ESMs).

Report Structure and Organization

To identify critical scientific gaps that limit the ability 

to represent tropical ecosystems in ESMs, the U.S. 

Department of Energy’s (DOE) Office of Biological 

and Environmental Research (BER) held the 

Research Priorities for Tropical Ecosystems Under 

Climate Change Workshop in June 2012. Nearly 40 

experts in tropical ecosystem science addressed key 

questions important for determining how tropical 

forests interact with and feed back to the climate 

system. The workshop featured a series of plenary 

talks, four breakout sessions with three parallel 

Introduction

groups focused on broad research areas, and activities 

to integrate discussions among groups. Breakout 

sessions focused on soil biogeochemistry and 

hydrology, natural and anthropogenic disturbance, 

tropical forest ecophysiology, and cross-cutting 

issues. This report summarizes these discussions and 

presentations and is broadly organized into three 

sections:

•	 Background Information, including this Introduction and a description of regional differences 

across the Tropics (Chapter 2, p. 7).

•	 Responses of Tropical Forests to External 

Forcings, such as elevated atmospheric CO2

(Chapter 3, p. 13), temperature (Chapter 4, p. 23), 

drought (Chapter 5, p. 33), natural disturbance 

(Chapter 6, p. 43), and anthropogenic disturbance 

and land use (Chapter 7, p. 51).

•	 Integrating Processes, such as biosphereatmosphere interactions (Chapter 8, p. 55), 

nutrient limitations (Chapter 9, p. 63), belowground processes including roots and soil biogeochemistry (Chapter 10, p. 69), and hydrology 

(Chapter 11, p. 77).

Also featured in this report is a summary section 

reiterating the main workshop themes (Chapter 12, 

p. 85), followed by a description of BER’s NextGeneration Ecosystem Experiment (NGEE) 

approach (Appendix 1, p. 92). Next are the workshop agenda, breakout session details, participants 

list, (Appendix 2, p. 95), and bibliography (Appendix 3, p. 101).

Because of the focus on improving ESMs mechanistically, this report emphasizes understanding 

ecosystems at a functional scale. Ecosystem-scale 

carbon balance is an emergent property, representing the sum total of all processes. Since it is not 

represented directly, this report does not have a section devoted to the subject, even though measurements of net carbon fluxes could be very important 

as integral constraints.
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change 3

Chapter 1 – Introduction

Background

Significance of Tropics to Earth 

System and Climate

Tropical forests are a central component of the Earth 

system. Global gross primary productivity (GPP) 

is estimated at 122 Pg of carbon per year (C yr−1), 

and of that total, 41 Pg (34%) are assimilated by 

tropical forests, with an additional 31 Pg (25%) 

taken up by tropical savannahs and grasslands (Beer 

et al. 2010). Total aboveground carbon storage in 

terrestrial ecosystems is about 560 Pg (Schlesinger 

1997), with 190 Pg (34%) in tropical forests alone 

(Saatchi et al. 2011). Deforestation and forest 

degradation in the Tropics account for 12 to 20% of 

total global anthropogenic CO2 emissions, reducing 

tropical forest carbon stocks annually by 1 to 2 Pg 

in the 1990s and early 2000s (DeFries et al. 2002; 

Houghton 2003; van der Werf et al. 2009).

Given the importance of tropical forests to the global 

carbon cycle, any changes in their extent, structure, 

or functioning will have consequences for the 

trajectory of atmospheric CO2 and associated climate 

forcing. Carbon flux studies using observations from 

permanent forest plots indicate that mature tropical 

forests represent a net global sink of 1.3 Pg C yr−1

(Lewis et al. 2009a), or more than 50% of the total 

estimated global terrestrial carbon sink (Canadell 

et al. 2007). However, because plot networks sample 

only a small fraction of vast regions over a limited 

period of time, disturbances at timescales of decades 

or longer may not be adequately sampled, potentially 

leading to overestimates of biomass increase 

(Davidson et al. 2012; Chambers et al. 2009; Lloyd, 

Gloor, and Lewis 2009). Tower-based eddy flux 

studies show contrasting carbon balance estimates 

for Amazon forests (Pyle et al. 2008; Gatti et al. 

2010; Araújo et al. 2002; Malhi et al. 1998; Kruijt 

et al. 2004) that are highly dependent on a number of 

data-processing assumptions (Miller et al. 2004).

Tropical forests also are large sources of biogenic volatile organic compounds (BVOCs) and aerosols from 

biomass burning, which both play significant roles in 

Earth system functioning (Andreae et al. 2002; Martin 

et al. 2010). Changes in forest flooding and soil moisture associated with seasonal changes in precipitation 

and under drought cause biogeochemical shifts in 

reduction-oxidation (redox) conditions and related 

emissions of non-CO2 greenhouse gases (GHGs) such 

as methane and nitrous oxide (Melack et al. 2004; 

Silver 1998; Davidson 1993).

Tropical forests have other impacts on the climate 

system in addition to their indirect effects through 

the carbon cycle and GHG emissions. For example, 

climate model simulations indicate that tropical 

forests decrease air temperature and increase regional 

precipitation compared to pastureland (Bonan 

2008; Shukla, Nobre, and Sellers 1990). The cooling 

effect of high rates of evapotranspiration offsets the 

warming associated with low albedo (Bala et al. 

2007). Furthermore, the influence of tropical forests 

on climate may extend to other regions through 

atmospheric teleconnections (Bonan 2008; Avissar 

and Werth 2005; Nepstad et al. 2008). Land-use 

changes and forest fragmentation in the Tropics can 

alter atmospheric circulation patterns and cloud 

formation processes (Cox et al. 2004; Laurance 2004; 

Wang et al. 2009).

Vulnerability of Tropical Forests 

to Climate Change

Several aspects of tropical ecosystems suggest they 

will be particularly vulnerable to climate change. First, 

high-biomass tropical forests occur where sufficient 

precipitation, warm temperatures, and adequate soil 

fertility enable tall trees (exceeding ~20 m) to form 

relatively contiguous crowns, reducing understory 

light levels to a small fraction of incoming solar 

radiation. Because this forest type generally requires 

more than 1,000 mm per year to maintain a closedcanopy state, shifts in precipitation regimes with 

a warming climate may draw some forests below 

this threshold. This would result in structural and 

compositional shifts toward more open or lowerstatured forests with less biomass as susceptible trees 

succumb to drought-induced mortality.

Secondly, since many tropical forests already are 

among the warmest and wettest environments on 

Earth, projected warming scenarios indicate that 

these ecosystems will be pushed to new states that 

have no current analogs (Williams et al. 2007). 

The predicted changes in temperature are large 

compared to normal interannual variation in the 
4 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 1 – Introduction

DOE Office of Science

Tropics, further exacerbating potential adverse 

effects of warming. Nonlinear shifts in ecosystem 

structure and atmosphere-biosphere exchanges of 

GHGs, aerosols, water, and energy could be the 

result. Changes in temperature, precipitation regimes, 

nitrogen deposition, and the quantity and quality 

of organic matter inputs to soils likely will alter 

rates of GHG production and consumption. The 

sensitivity of photosynthetic metabolism and the 

acclimation of plants to temperature extremes are 

emerging as critical processes for modeling tropical 

forests (Booth et al. 2012). However, there is no clear 

consensus on the response of tropical tree species 

to the temperature regimes expected this century 

(Corlett 2011).

Shifts in precipitation and higher temperatures 

can affect numerous ecosystem processes and 

their interactions, including soil nutrient cycling, 

soil organic matter turnover, heterotrophic and 

autotrophic respiration, and plant carbon allocation 

patterns (Wood, Cavaleri, and Reed 2012). 

Moreover, many of these processes will interact with 

increased land use and fire frequency in the Tropics, 

intensifying climate change effects (Davidson et al. 

2012; Nepstad et al. 1999). Ultimately, current 

understanding of tropical ecosystems indicates that 

a warming climate will significantly affect ecosystem 

processes. Changes in these processes in turn could 

alter the role tropical forests play in critical global 

biogeochemical cycles, resulting in potentially 

strong feedbacks to the climate system.

Representation of Tropical Forests 

in Earth System Models

Although the understanding of tropical forests is 

improving, their representation in ESMs lags 

significantly behind that of temperate forests, as 

evidenced by, for example, the wide variation in 

estimates of tropical forest productivity (Beer et al. 

2010). The Coupled Climate–Carbon Cycle Model 

Intercomparison Project (C4MIP) compared 11 

coupled ESMs and found differences among the 

models in land uptake of CO2 for 2100, ranging from a 

large sink of 10 Pg C yr−1 to a source of 6 Pg C yr−1

(Friedlingstein et al. 2006). Most of this variability 

arose from differences in how tropical forests 

responded to CO2 fertilization, increased temperature, 

and changing precipitation patterns. In particular, 

widespread drought-driven tree mortality in the 

Amazon Basin (Cox et al. 2004) was a conspicuous 

difference among models. With respect to modeling 

trees, treatment of key processes is poor even for 

temperate forests, challenging efforts to understand 

how carbon allocation, root deployment, nutrient 

uptake, and tree mortality will affect ecosystem 

structure and functioning and atmospheric exchanges. 

A fundamental reason for this limitation is that ESMs 

traditionally have used a “big-leaf ” approach with 

specified parameters for photosynthesis, allocation, 

turnover, and other processes. This approach does not 

resolve the dynamics of individuals and therefore can 

only treat mortality and competitive vegetation 

interactions in a rudimentary way. These issues are 

magnified in tropical forests with tall deep canopies, 

high diversity, and complex ecosystem processes. 

Further uncertainty arises because tropical forests are 

near potential thresholds such as the high-temperature 

photosynthesis optimum, leading to widely divergent 

model behavior (Booth et al. 2012). Additionally, 

representation of the long-term ecosystem-scale effects 

of environmental forcings (e.g., temperature and CO2) 

typically is based on results from short-term 

physiological studies. This introduces biases into 

models by not accounting for potential acclimation 

responses or interactions with other environmental 

resources such as nitrogen or phosphorus. Thus, 

tropical ecosystems are responsible for large 

uncertainties in ESMs. In fact, models even disagree on 

the direction of the climate–carbon cycle feedback for 

tropical forests (Friedlingstein et al. 2006).

Another particular problem for model development 

in tropical systems is the absence of many important 

model validation products available for temperate 

ecosystems. For example, results from large-scale 

manipulation experiments in the Tropics are only 

sparsely available for some drivers (e.g., drought and 

nutrients) and completely lacking for others (e.g., 

CO2 and temperature). Although improvements in 

model structure are possible and ongoing, additional 

datasets with which to test models also are needed. 

This need is typified by studies associated with the 

Large-Scale Biosphere-Atmosphere Experiment 

in Amazonia (LBA) flux tower program, which 

unambiguously illustrated that the majority of 

models erroneously represented moisture-stressed 
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change 5

Chapter 1 – Introduction

Background

behavior in the dry season for Amazonian forests. 

The LBA research led to significant changes to the 

parameterization and structure of multiple ESM land 

surface schemes.

Similar problems arise when considering the lack of 

representation of key soil and ecosystem processes in 

ESMs, particularly for tropical forests. Critical redox 

processes, nutrient availability (especially phosphorus), soil organic matter dynamics, and soil structure 

and rooting depth are absent or poorly represented in 

most models. These limitations hinder the ability to 

model and predict how climate and land-use changes 

will affect net productivity and GHG fluxes from 

these ecosystems. Fully coupled, well-tested ESMs 

ultimately are needed to better understand global 

climate change during the 21st century, and improving the treatment of tropical forests in these models 

is essential for enhancing predictions at regional, 

continental, and global scales.

Geographical Considerations

Within the broader Tropics occupying latitudes 

between the Tropic of Cancer (23.4°N) and Tropic 

of Capricorn (23.4°S) are three regions with unique 

biota and geological history:

•	 Neotropic (NEO) ecozone of South America, 

Central America, and the Caribbean.

•	 Afrotropic (AFR) ecozone of sub-Sahara Africa.

•	 Indo-Malay-Australasia (IMA) tropic ecozone 

including regions of India, Southeast Asia, and 

southern China separated from Australia and 

New Guinea by Wallace’s Line.

Within these zones are large, relatively contiguous 

areas of tropical forest in the Amazon, Congo, and 

Southeast Asia. The soils in these regions are diverse, 

with Oxisols (a soil type absent in temperate zones) 

dominating the tropical forests of the Amazon and 

Congo and Ultisols dominating those of Southeast 

Asia (for details, see Chapter 8, Belowground 

Processes: Roots and Soil Biogeochemistry, p. 55). 

Because of their large potential feedbacks with the 

climate system, this report primarily is focused on the 

high-biomass forests in these three regions (hereafter 

referred to as “tropical forests”) and the areas that may 

shift toward or away from this high-biomass state.

Neotropical Region

Among the forests in this area (South America, 

Central America, and the Caribbean), those of the 

Amazon Basin represent the single largest block of 

intact tropical forests and alone comprise ~40% of 

total tropical forest biomass (Saatchi et al. 2011). 

The Amazon Basin also includes vast floodplains 

with remarkable seasonal variation in spatial extent. 

In several studies, the inundated areas along the 

Amazon River varied from a minimum of 25,000 

km2 in November to a maximum of 65,000 km2 in 

June. Flooded forests increased from 5,000 to 35,000 

km2, accompanied by a large increase in associated 

methane emissions (Melack et al. 2004; Hess et al. 

2003). Ter Steege et al. (2006) describe two major 

floristic gradients across Amazonia. The first stretches 

from the Guianan Shield to southwestern Amazonia 

and corresponds with a soil fertility gradient; the 

second spans from Columbia to southeastern 

Amazonia, representing a broad moisture gradient 

that corresponds with increasing dry season length. 

The forests of Central America and the Caribbean 

share many floristic similarities with those in the 

Amazon but occur on younger, more fertile soils 

with less overall diversity. With the exception of 

Panama, Central American and Caribbean forests 

experience regular hurricanes and more recently have 

been affected by forest fires that accompany severe 

El Niño drying periods (Cochrane 2002). Strong 

environmental gradients occur over relatively small 

spatial scales in Central America and the Caribbean, 

and forests are embedded in a complex matrix of 

human settlement.

Afrotropical Region

African forests include those of Madagascar, the 

Congo River and adjacent drainages in Gabon and 

neighboring countries, and West Africa located 

within several hundred kilometers of the coast. West 

African coastal forests are highly fragmented and 

degraded, but those of the Congo Basin represent the 

second-largest intact block of tropical forests after 

the Amazon (Pan et al. 2011). Within the center of 

the Congo Basin are approximately 220,000 km2

of swamp forest, and other forests dominated by a 

single tree species (Gilbertiodendron dewevrei) occupy 

large areas (Vande weghe 2004; Devers, Vande 

weghe, et al. 2006). Central African forests do not 
6 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 1 – Introduction

DOE Office of Science

experience tropical cyclones but are subject to large 

storm events. Additionally, African forests experience 

droughts and exceptionally wet years associated with 

El Niños and La Niñas. Lewis et al. (2009a) recently 

added a large set of plots to a pantropical network 

to monitor biomass in African tropical forests. They 

estimate that these forests accounted for 34% of a 

net 1.3 Pg C yr-1 tropical forest carbon sink (with 

NEO and IMA forests representing 47% and 19%, 

respectively).

Indo-Malay-Australasia Tropical Region

In contrast to all NEO and AFR forests where 

Leguminoseae is the dominant plant family, 

Southeast Asian forests are dominated by trees in 

the Dipterocarpaceae family, which are completely 

absent from NEO and AFR. Dipterocarps have a 

disproportionate influence on ecosystem properties 

and dynamics across the region because of their 

abundance and large size. Dipterocarps also are 

among the most highly prized timber species 

across much of the region, which has led to intense 

logging pressure in many IMA forests. Across the 

IMA region are steep gradients in total rainfall, 

rainfall seasonality, soil type and age, and land-use 

history. Drought is an important climatic feature 

of the region, particularly over the past 2,500 years 

with the onset of the El Niño–Southern Oscillation 

(ENSO). The intense ENSO-associated droughts of 

1982–83 and 1997–98 led to widespread fires and 

tree mortality even in the region’s wettest forests 

(Leighton and Wirawan 1986; Potts 2000; Phillips 

et al. 2010). Other remarkable features of this 

region are the peat swamps, primarily in Borneo and 

Peninsular Malaysia. Recent studies estimate that 

drainage and burning of peat forests in this area were 

responsible for a flux of ~0.3 Pg C yr−1, comprising 

~25% of total global carbon emissions from tropical 

forests (Harris et al. 2012; van der Werf et al. 2008; 

Hooijer et al. 2010).

DOE’s Role in Improving Predictions 

of Tropical Forest Response 

to Climate Change

BER includes programs focused on terrestrial 

ecosystems and ecological processes that are globally 

or regionally significant; expected to be sensitive 

to climate change; and insufficiently understood 

or inadequately represented in ESMs. Tropical 

ecosystems meet these criteria, and improving 

their representation in models is critically needed 

for enhancing the robustness of global climate 

predictions, which in turn will better inform future 

research, energy policy, and adaptation strategies. 

To achieve these advances, BER is strategically 

committed to coupling models with experimental 

and observational campaigns across relevant spatial 

and temporal scales. Developing a better predictive 

capacity for how climate feedbacks from tropical 

forests will respond to a changing climate will require 

an interdisciplinary approach such as BER’s NextGeneration Ecosystem Experiment activity. NGEE 

would serve as a powerful tool for understanding 

tropical ecosystems and provide the framework for 

their improved representation in climate modeling 

efforts. The NGEE program anticipates coupling 

focused manipulative experiments, extensive 

observational studies, and mechanistic forest 

ecosystem simulation models to ultimately improve 

ESMs. DOE is uniquely positioned to address this 

critical research need based on its (1) historical 

successes in developing long-term manipulation 

studies like the Free-Air CO2 Enrichment (FACE) 

experiments, (2) major investments in developing 

and assessing ESMs, and (3) leadership-class 

computational capabilities.
Regional Differences in 

Tropical Forest Response to 

Climate Change 

CHAPTER 2
8 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 2 – Regional Differences in Tropical Forest Response to Climate Change 

DOE Office of Science

Regional Differences in Tropical Forest Response 

to Climate Change

Tropical forests cover about 19.5 million km2

of Earth’s surface and are responsible for 34% 

of global terrestrial gross primary productivity 

(Beer et al. 2010). They can be broadly divided into 

wet, moist, and dry forests but also include significant 

areas in swamps or montane forests. Based on their 

geological history and floristic composition, tropical forests are broadly classified into the Neotropical 

(NEO) region of South America, Central America, 

and the Caribbean; the Afrotropical (AFR) region of 

sub-Sahara Africa; and the Indo-Malay-Australasia 

(IMA) tropical region that includes parts of India, 

Southeast Asia, southern China, and New Guinea. 

Although assessments of the extent of tropical forests 

vary substantially depending on the methodology 

and technologies used (Wright 2005), Saatchi et al. 

(2011) estimate that tropical forests with 10% to 30% 

minimum canopy-cover thresholds span about 2,500 

to 1,700 million hectares (Mha), respectively. Using 

the 30% canopy-cover threshold, NEO, AFR, and IMA 

forests comprise 890, 450, and 336 Mha, respectively. 

Saatchi et al. (2011) further define high-biomass 

tropical forests as those with aboveground biomass 

exceeding 100 Mg ha−1. The study notes that although 

high-biomass forests are less extensive than low-biomass ones, they contain 83%, 59%, and 82% of total 

biomass in NEO, AFR, and IMA forests, respectively 

(see Fig. 2.1, this page).

Particular differences among the three regions can 

influence tropical forest response to a warming climate and changing atmospheric conditions. Overall, 

the complex gradients in soil properties, total rainfall 

and seasonality, species composition, disturbance 

regimes, and land-use history among regions will 

affect forest response to climate change. These factors all contribute to a rich diversity of forest types 

across the Tropics and to complex aggregations of 

forest types within landscapes. Described below are 

a number of factors likely to have important effects 

on the differential responses of tropical forests at 

regional to continental scales.

Variations in Soil Fertility, 

Structure, Hydrology, Topography

A large range of soil types are found within tropical 

forests, including soils derived from volcanic origin 

Fig. 2.1. Distribution of Forest Aboveground Biomass. [From Saatchi, S. S., et al. 2011. “Benchmark Map of Forest Carbon Stocks in Tropical 

Regions Across Three Continents,” PNAS 108(24), 9899–904.]
Research Priorities for Tropical Ecosystems Under Climate Change 9

Chapter 2 – Regional Differences in Tropical Forest Response to Climate Change 

DOE Office of Science

Background

such as those in the Hawaiian Islands, widespread 

heavy clay Oxisols in Africa and South America, and 

white sand formations in the Amazon Basin. With 

other state variables such as precipitation, temperature, and topography held constant, differences in 

soil properties can drive dramatic changes in forest 

structure and ecosystem processes (Amundson and 

Jenny 1997). Within the Amazon Basin, for example, 

soils are highly complex, ranging from relatively 

fertile soils of anthropogenic origin to deep white 

sands (Quesada et al. 2011). Amazon forests on 

white sand formations vary from tall closed-canopy 

forests with a shallow saturated zone to low-biomass 

shrublands called “campinaranas” (“caatinga” and 

“heath forests”) when the water table occurs at 

depth (Anderson 1981). The soils of many forests in 

Central America and the Caribbean are younger and 

have been significantly affected by land-use activities. 

Overall, Oxisols and Ultisols are the dominant soil 

type among tropical regions globally but are relatively 

rare in extratropical ecosystems. Because tropical 

soils vary considerably from those in temperate forests 

(for which ecosystem models were largely developed), 

efforts to improve their treatment in terrestrial models 

should be a high priority.

A better understanding is needed of how regional 

variability in soil properties interacts with rising 

temperatures, shifts in precipitation, and elevated 

carbon dioxide (CO2) concentration to affect forest 

structure and ecosystem processes. These insights 

are essential for improving predictions of regional 

differences in the response of tropical forests to 

a changing atmosphere and warming climate. 

Achieving this understanding will require better 

regional mapping of key soil parameters (e.g., parent 

material, texture, hydraulic conductivity profiles, 

bedrock features, saprolite layers, and water table 

depth) as well as rigorous evaluation of terrestrial 

model representation of processes that change 

across key gradients in soil properties. For example, 

how does forest productivity and biomass density 

change along a gradient in soil texture from a heavy 

clay Oxisol to a deep white sand soil with all other 

factors held constant? Addressing this and other key 

tropical soil questions will be critical for improving 

terrestrial ecosystem components of Earth system 

models (ESMs).

Shifts in Precipitation and 

Temperature Patterns 

with a Warming Climate

Regional climate projections from the Intergovernmental Panel on Climate Change’s (IPCC) multimodel data (MMD) A1B scenario predict increased 

tropical surface temperatures ranging from ~3 to 5°C 

for Southeast Asia, the Amazon, and West Africa by 

2100 (IPCC 2007). This increase in temperature 

will push tropical forests into temperature regimes 

that do not currently exist, resulting in “no-analog” 

climates. The MMD A1B scenario also predicts 

generally increased annual precipitation for West 

Africa and Southeast Asia, though with decreases 

over some areas in Southeast Asia from December to 

February. Decreased precipitation also is projected 

over much of the southern and eastern Amazon, 

particularly from June to August, which corresponds 

to the region’s annual seasonal drought period. This 

potential intensification of the drought period across 

significant portions of the Amazon Basin is a critical 

topic for additional research. Increased severity of 

droughts also could lead to more frequent forest fires 

(Cochrane 2003), especially when associated with 

land-use forest fragmentation in the Amazon (Soares 

et al. 2012), Central America (Cochrane 2002), and 

West Africa (Hawthorne 1995). Both regular seasonal 

drought and intense episodic drought affect tropical 

forest ecosystem structure and functioning. Baltzer 

et al. (2008, 2009) demonstrated how drought variability drives plant species distributions in tropical 

Asia, with the transition from aseasonal to more seasonal environments. The intense droughts of 1982–83 

and 1997–98 associated with the El Niño–Southern 

Oscillation led to widespread fires and tree mortality, even in the most aseasonal forests in the region 

(Leighton and Wirawan 1984; Potts 2000). The 

interaction of human land-use change and increasing 

atmospheric temperatures may exacerbate the effects 

of drought in the coming decades and lead to widespread loss or degradation of tropical forests vulnerable to drought with a warming climate. The extent 

to which various regions will respond differently to 

the same drivers is unclear, as is current understanding of how changes in temperature, rainfall, and CO2

interact with variation in ecosystem properties such 

as soils and species composition. Addressing these 
10 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 2 – Regional Differences in Tropical Forest Response to Climate Change 

DOE Office of Science

uncertainties will require comprehensive multidisciplinary research approaches.

Functional and Phylogenetic 

Differences in Plant Species 

Responses

Other factors being equal, regional differences in 

tropical species composition, particularly trees, can 

affect regional responses to a warming climate. For 

example, many Southeast Asian forests are dominated 

by a single plant family (Dipterocarpaceae) that is 

virtually absent from Africa and Latin America, and 

Dipterocarps have a disproportionate influence on 

ecosystem properties and dynamics because of their 

abundance and large size. Thus, for a given set of conditions, Asian forests have higher biomass (Yamakura 

et al. 1986) and may respond differently to changes 

in temperature and precipitation. Tropical forests also 

vary dramatically in tree diversity. Although tree species are highly diverse in most tropical forests, typically 

averaging hundreds of tree species per hectare, there 

are some notable exceptions. For example, in equatorial forests of Africa, the tree species Gilbertiodendron

dewevrei can dominate thousands of square kilometers 

(Van de Weghe 2004). In the Neotropics, limited 

forest areas are mono-dominated by Dicymbe corymbosa, Eperua falcata, Mora gonggrijpii, and Peltogyne 

gracilipes (Henkel 2003). Finally, the tropical forests 

of Hawaii are dominated by a single tree species, 

Metrosideros polymorpha. In the Amazon, ter Steege 

et al. (2006) describe a number of floristic gradients 

that correspond with soil fertility, dry season length, 

and disturbance regimes. Overall, differences in community composition of plant species and phylogenies 

among tropical forest regions reflect a variety of factors 

that affect survivorship, including the potential for 

differential adaptation to potential stress factors such 

as drought and soil fertility. These differences should 

be considered in selecting sites for field studies and in 

developing robust models for improved prediction of 

tropical forest response to climate change.

Differences in species composition and functional 

types among tropical forests may partially explain 

some contrasting observations. Analysis of tree 

growth rates in Costa Rica, Panama and Malaysia, 

and the central Amazon found either decreases in tree 

growth rates or no discernible change (as yet) over 

the last two to three decades (Clark et al. 2003; Feeley 

et al. 2007; Laurance et al. 2009). These observations run counter to what might be expected if global 

changes are leading to increased forest biomass accumulation. Several authors have noted an increase in 

lianas (woody vines) in Neotropical forests in recent 

decades (Phillips et al. 2005; Schnitzer and Bongers 

2011; Wright et al. 2004), but limited evidence from 

Africa does not indicate an increase there (Schnitzer 

and Bongers 2011). Lianas compete with trees for 

light, nutrients, and moisture but store relatively little 

carbon. As such, the increased tree mortality and 

decrease in productivity associated with increasing 

lianas could profoundly affect tropical forest carbon 

cycling (Schnitzer and Bongers 2011). The effects of 

lianas may be particularly important early in forest 

development, during which lianas can rapidly attain 

high densities and significantly reduce tree recruitment, density, diversity, and survival (Schnitzer and 

Carson 2010). Research has yet to determine whether 

the observed increase in lianas results from a changing 

atmosphere or some other factor and whether they 

are increasing in tropical secondary forests. Regardless 

of the cause, lianas likely have a much stronger 

effect in tropical forests now than in recent history 

because their density, biomass, and productivity have 

increased considerably in some forests over the past 

30 years (Schnitzer and Bongers 2011).

Variation in Regional Disturbance 

Regimes

Natural disturbances that cause tree mortality 

in tropical forests include drought, storms (e.g., 

wind and lightning), fire, flooding, and other processes such as pest and pathogen outbreaks and 

monocarpy (for details, see Chapter 6, Natural 

Disturbance, p. 43). Each of these agents of mortality also exhibits regional variability and may 

respond differently to a changing climate. Examples 

of this variability are tropical forests affected by 

cyclonic storms, such as hurricanes in the Caribbean 

and Central America, typhoons in Southeast Asia, 

and tropical cyclones in the Southern Hemisphere 

including northeastern Australia. Several studies 

indicate an increase in the intensity of tropical 

cyclones with a warming climate (Emanuel 1987, 
Research Priorities for Tropical Ecosystems Under Climate Change 11

Chapter 2 – Regional Differences in Tropical Forest Response to Climate Change 

DOE Office of Science

Background

2005; Webster et al. 2005), although complex 

interactions with upper-atmosphere wind sheer can 

prevent cyclonic development (Hoyos et al. 2006). 

However, given conditions conducive to storm 

development, higher sea surface temperatures generally result in more intense tropical cyclones.

In addition to the expected intensification of tropical 

cyclones, a general increase in storm intensity and 

extremes in precipitation and wind speed are robust 

climate change predictions (IPCC 2007). More powerful storms under a warming climate may cause higher 

tree mortality rates and more dynamic disturbance 

regimes, leading to an increase in naturally regenerating secondary forests and shifts in ecosystem carbon 

balance toward lower biomass forests. However, little 

is known about how disturbance regimes of tropical forests will change regionally with a warming 

climate, and efforts are needed to quantify baseline 

regimes for different regions and to monitor changes 

in disturbance patterns. Important objectives include 

distinguishing among mortality processes in field 

and remote-sensing studies and developing mechanistic disturbance algorithms for terrestrial models.

The effects of land use in tropical forests also vary 

considerably among regions. In the Amazon, for 

example, a deforestation crescent from near the 

city of Belem in the northeast to Rio Branco in the 

southwest of Brazil represents most land-use activity and biomass burning (Skole and Tucker 1993). 

However, large tracts of tropical forests in the central 

and western Amazon are among those least disturbed by direct human activity. In Africa, western 

coastal forests are highly fragmented and degraded, 

but those in the Congo Basin are relatively intact. 

Similar regional variability in human disturbance 

occurs in Southeast Asian forests. The intensity 

of anthropogenic impacts on tropical forests also 

differs considerably across regions, ranging from 

low-level resource extraction to selective logging to 

widespread deforestation and biomass burning for 

agricultural activities. Atmospheric pollutants also 

exhibit strong regional variability. An important 

activity thus would be to determine which specific 

anthropogenic activities are affecting ecosystem 

processes among regions with respect to key interactions with the climate system.
12 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 2 – Regional Differences in Tropical Forest Response to Climate Change 

DOE Office of Science
Responses of Tropical 

Forests to Elevated CO2

CHAPTER 3
14 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

Responses of Tropical Forests to Elevated CO2

Moreover, substantial differences in the plant species, 

forest structure, soils, and climate of temperate and 

tropical forests severely limit the ability to use results 

from temperate-zone studies to predict tropical forest 

responses. The current generation of land surface 

models, as applied to tropical forests, highlights the 

gulf between what is known about tropical forest 

responses to rising CO2, what remains uncertain, and 

what must be done to resolve the uncertainty and 

improve predictive capacity.

Insights from Models

Forest inventory analysis has indicated increasing 

aboveground biomass and net primary productivity (NPP) in tropical forests over the past several 

decades. Some analyses suggest this increase may be 

attributable to rising CO2 (Lloyd and Farquhar 2008; 

Lewis et al. 2009b), but other studies conclude that 

different factors are the more likely cause of biomass 

increases observed at the plot scale (Chambers and 

Silver 2004; Clark, Clark, and Oberbauer 2010). 

Attributing the driver of past changes in forest 

biomass is never straightforward because of multiple, 

uncontrolled environmental and stand development 

factors that are confounded with past increases in 

atmospheric CO2. Adding to the difficulty is the 

problem of reliably estimating regional-scale changes 

in aboveground biomass and the potential divergence 

between changes in aboveground biomass and total 

NPP. Using an individual-based tree growth model, 

Chambers et al. (2004a) suggested that tree growth 

would need to be extremely sensitive to CO2 for 

stand-level increases in aboveground biomass to 

match observed increases in central Amazon forests 

over the past several decades. A more important 

challenge now for improving the ability to predict 

responses to future climate change is to understand 

and better represent in models the response of tropical forests to increases in atmospheric CO2 over the 

coming decades. 

Responses of temperate trees in FACE experiments make clear that aboveground biomass is not 

a sufficient metric for evaluating forest responses 

Overview

The rise in atmospheric carbon dioxide concentration [CO2] is unprecedented, rapid, 

and ubiquitous. Unlike some aspects of 

global change for which the magnitude, direction, 

and location of the change is uncertain, the rise in 

CO2 is global and, unfortunately, almost certain to 

continue for decades to come. Current projections—

based on assumptions about energy use, population 

growth, and other physical, biological, and socioeconomic factors—indicate that atmospheric [CO2] 

will increase from its present-day value of 392 parts 

per million (ppm) in 2011 to more than 800 ppm by 

2100 (Intergovernmental Panel on Climate Change 

A2 emissions scenario, www.ipcc-data.org/ddc_co2.

html). Because atmospheric CO2 is the primary substrate for all terrestrial productivity, this substantial 

increase undoubtedly will affect the metabolism of 

tropical forests worldwide. The qualitative and quantitative expression of the effects, however, is largely 

unknown, representing a major source of uncertainty 

that limits the capacity to understand tropical ecosystem processes, assess their vulnerabilities to climate 

change, and improve the representation of these systems in Earth system models. Much is known about 

the effects of elevated concentrations of CO2 (eCO2) 

on biochemical and physiological processes in leaves, 

including leaves of tropical trees under tropical conditions. However these primary responses (e.g., photosynthesis) do not necessarily reveal the integrated 

responses of ecosystem productivity, carbon cycling, 

and biotic interactions. Growth studies of tropical 

tree species have been conducted with seedlings 

and young saplings, but no single mature tropical 

tree has ever been exposed to eCO2 under natural 

forest conditions (Körner 2009). In temperate forest 

ecosystems, free-air CO2 enrichment (FACE) experiments have revealed many higher-order responses 

and emphasized the importance of interactions and 

feedbacks between CO2 and other environmental 

resources, stand development, and integration across 

time and space (Norby and Zak 2011). No such 

experiments have been conducted in tropical forests. 
Research Priorities for Tropical Ecosystems Under Climate Change 15

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

Responses to 

External Forcings

to eCO2 and their feedbacks to the atmosphere. 

Significant increases in NPP and carbon storage can 

occur without any increase in aboveground woody 

biomass (Norby et al. 2005; Iversen et al. 2012). 

Global models that incorporate a whole-ecosystem 

analysis illustrate the potential importance of eCO2

to tropical carbon cycling and the feedbacks from the 

Tropics to climate. Carbon cycle predictions of different dynamic global vegetation models (DGVMs) 

are consistent with contemporary global land carbon 

budgets but can diverge considerably when forced 

with the future climate predicted by general circulation models (GCMs) and emission scenarios. 

However, models agree that including effects of eCO2

in the simulations counteracts carbon losses caused 

by climate change, resulting in the land being a net 

sink for carbon rather than a net source over the 21st 

century (Sitch et al. 2008). The Tropics are especially 

important in such simulations, and the response 

of tropical forests has been explored in detail. One 

DGVM, the LPJ model, predicted a 35% increase 

in NPP for tropical forests at an atmospheric CO2

concentration of 550 ppm relative to that at 370 ppm 

(see Fig. 3.1, this page; Hickler et al. 2008). 

The effects of eCO2 on NPP of evergreen forests 

in the Amazon were simulated with two ecosystem 

models (Biome-BGC and LPJ) and compared with 

modeled effects of climate and increased shortwave 

radiation (Hashimoto et al. 2010). Both models 

showed a monotonous positive trend in NPP 

corresponding with increasing atmospheric CO2. 

However, observed trends of increasing normalized 

difference vegetation index (NDVI) had a distinct 

seasonal variation that was matched in the models 

by the response to increasing shortwave radiation 

but not by the response to increasing CO2. Hence, 

the authors concluded that the positive trend in 

Fig. 3.1. Geographic Pattern of NPP Enhancement Resulting from a Step Increase of CO2 from 

Ambient to 550 ppm as Simulated by the LPJ Model. [From Hickler, T., et al. 2008. “CO2 Fertilization in Temperate 

FACE Experiments not Representative of Boreal and Tropical Forests,” Global Change Biology 14(7), 1531–42. © 2008 Blackwell 

Publishing Ltd.]
16 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

shortwave radiation is most likely the driver of both 

the observed increasing trend in NDVI and the corresponding observed increases in aboveground biomass in the Amazon Basin for the period from 1984 

to 2002 (Hashimoto et al. 2010). The study, however, 

acknowledged that FACE experiments in temperate 

systems showed that increases in NPP under eCO2

occurred without increases in leaf area index (LAI) 

or, presumably, NDVI (Norby et al. 2005).

In addition to direct effects on NPP, eCO2 also could 

influence the trajectory of biome shifts. Scheiter and 

Higgins (2009) simulated the vegetation of the grassland-savanna-forest complex of Africa using a DGVM 

with process-based and adaptive modules for phenology, carbon allocation, and fire. C4 photosynthesis of 

tropical grasses is carbon saturated at ambient CO2

and C3 photosynthesis is not. Thus, with increases in 

CO2 concentration, the model simulates a change in 

the relative performance of grasses and trees resulting in a substantial increase in tree dominance and a 

replacement of savannas by deciduous woodlands. 

Lapola et al. (2009) used a potential vegetation model 

(CPTEC-PVM2) that performs well at delimiting the 

forest-savanna border in South America to analyze the 

effect of different scenarios of CO2 and climate. When 

a CO2 fertilization effect was fully considered, there 

were no substantial changes in Amazonia, but in the 

absence of CO2, climate change caused a pronounced 

shift to drier biomes, indicating that eCO2 could moderate the possibility of biome shifts caused by climate 

change. Numerous uncertainties were noted, however, 

giving rise to a call for long-term experimental studies 

exploring the effects of eCO2 on the productivity and 

canopy conductance of tropical ecosystems (Lapola 

et al. 2009). 

The possibility of climate change causing a substantial loss of Amazon rainforest cover and carbon 

stocks and amplifying the climate–carbon cycle 

feedback has been suggested (Cox et al. 2000). Galbraith et al. (2010) tested the importance of changes 

in precipitation relative to other environmental 

drivers, including CO2. Three DGVMs (HyLand, 

LPJ, and TRIFFID) agreed that modeled responses 

to increased temperature were as important, or more 

important, than reduced precipitation in causing 

loss of plant biomass carbon. Similar to the results of 

Lapola, eCO2 mitigated much of the climate-driven 

losses in the models (see Fig. 3.2, p. 17). Acknowledged uncertainties in the representation of the CO2

effect include nutrient limitations, which were not 

included in these models, and possible effects of 

eCO2 on species composition (Galbraith et al. 2010).

As discussed below, these model predictions are 

based on very limited information and omit what 

are likely to be critical modifying processes (e.g., the 

phosphorus cycle). At best, the model results represent testable hypotheses that can guide experimental 

design (Cernusak et al., in review). Understanding 

the critical points of uncertainty in the models with 

regard to representation of eCO2 responses will 

identify important research gaps.

Known Responses to Elevated CO2

The initial interaction between any green plant and 

CO2 occurs through the biochemical process of 

photosynthesis. Hence, most all terrestrial carbon 

cycling models appropriately start with an expression 

of leaf-level photosynthesis, employing a modified 

version of the Farquhar et al. photosynthesis model 

(Farquhar, Caemmerer, and Berry 1980; Collatz et al. 

1991). Photosynthetic responses to eCO2 are very 

well described. For example, eCO2 generally causes 

CO2 assimilation rate (A) to increase (Lloyd and 

Farquhar 1996; Drake et al. 1997), and the A of tropical woody plants has a larger potential to respond 

positively to eCO2 than that of plants in cooler 

climates. As temperature increases, the specificity 

of the primary carboxylating enzyme RuBisCO for 

fixing CO2 instead of O2 decreases along with the 

solubility of CO2, leading to increased photorespiration (Farquhar et al. 1980; Long 1991). Increasing 

the [CO2] around RuBisCO suppresses photorespiration, thereby stimulating A. In the abovementioned 

model by Hickler et al. (2008), the geographic 

difference in the simulated proportional stimulation 

of productivity largely was caused by variations in 

photorespiration. 

A second primary effect of eCO2 is to reduce stomatal 

conductance to water vapor through partial stomatal 

closure (Morison 1985; Ainsworth and Rogers 2007). 

This response has been observed in short-term studies 

and persists over time under field conditions. Stomatal 

conductance (gs) decreased 21% in eCO2 across all 
Fig. 3.2. Contribution of Environmental 

Factors to Simulated Changes in Amazonian 

Vegetation Carbon (Cveg) for Four Special 

Report on Emissions Scenarios (SRES) in 

Three Dynamic Global Vegetation Models.

Main effects and the sum of all interaction terms, as 

quantified in the factorial ANOVA, are shown. The overall 

net effect of including all factors is represented as the 

inner gray bar. [From Galbraith, D., et al. 2010. “Multiple 

Mechanisms of Amazonian Forest Biomass Losses in 

Three Dynamic Global Vegetation Models Under Climate 

Change,” New Phytologist 187(3), 647–65.]

Research Priorities for Tropical Ecosystems Under Climate Change 17

Chapter 3 – Responses of Tropical Forests to Elevated CO

2

DOE Office of Science

Responses to 

External Forcings

open-top chamber experiments with young, 

temperate-zone trees (Medlyn et al. 2001). 

FACE experiments have confirmed the persis-

tence of this primary physiological response to 

eCO

2 in some experiments, but the magni

-

tude of the response varied widely (4% to 

44%; Warren et al. 2011). Lower gs results in a 

lower transpiration rate, reducing the evapora-

tive cooling of the leaf and causing an increase 

in leaf temperature. Stomatal closure also 

occurs with unfavorable environmental condi-

tions, such as hot, sunny days that lead to a 

high leaf–to–air vapor pressure deficit. Under 

such conditions many tropical forest trees 

display a midday depression in both gs and 

A, 

responses that have been documented at both 

the leaf level (Koch, Amthor, and Goulden 

1994; Ishida et al. 1999; Kosugi et al. 2009) 

and canopy scale (Goulden et al. 2004). Thus, 

as atmospheric CO

2 rises over the coming 

century, higher vapor pressure deficit caused 

by higher leaf temperatures could curtail the 

positive response of A to eCO

2. However, no 

controlled experiments have investigated CO

2

and temperature interactions in the Tropics.

In young, rapidly growing tree seedlings, an 

increase in leaf-level photosynthesis under 

eCO

2 generally results in an increase in 

growth, especially when accompanied by 

increased leaf area (Curtis and Wang 1998; 

Norby et al. 1999). Although the number of 

observations of tropical trees under eCO

2

is much fewer than that of temperate trees 

(Körner 2009), results seem to be similar: 
18 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

eCO2 can stimulate growth of young tropical trees 

(e.g., Cernusak et al. 2011). Similar interactions 

between eCO2 and other resources have been 

observed in young tropical trees and temperate-zone 

trees. For example, the relative growth increase in two 

tropical tree species in response to eCO2 was larger for 

plants grown under water deficit than for well-watered 

plants (Cernusak et al. 2011). Growth of tropical trees 

grown in local soil and under local climatic conditions 

was strongly stimulated by eCO2 but only if fertilizer 

was added to the soil (Winter and Lovelock 1999).

In summary, the basic physiological responses of 

tropical trees to elevated CO2 are similar to widely 

observed responses of temperate-zone trees. However, based on the much more extensive experimentation done with temperate trees, the primary 

responses of leaf-level photosynthesis and stomatal 

conductance, along with growth responses of young, 

individual trees, are insufficient for informing predictions of the integrated response of a forest ecosystem 

to eCO2.

Major Uncertainties in Tropical 

Forest Response

FACE experiments in temperate forest ecosystems 

were valuable for testing hypotheses about forest 

response to eCO2 based on insights gained from 

earlier studies (Norby and Zak 2011). Although 

no FACE experiments have been conducted in the 

Tropics, the lessons from temperate FACE experiments can highlight some critical areas of uncertainty that must be resolved to improve predictions 

of tropical ecosystem responses to atmospheric and 

climatic change.

In four temperate closed-canopy tree plantations 

across a wide range of productivity, NPP increased 

23% (median response) in response to 550 ppm 

CO2 (Norby et al. 2005). In closed-canopy (nonexpanding) stands with relatively low LAI, much of 

the response to eCO2 was related to increased light 

absorption, whereas in high LAI stands, the increase 

in NPP under eCO2 was attributable to increased 

light-use efficiency. NPP represents the input of 

organic matter into an ecosystem but by itself does 

not predict ecosystem carbon storage, a process 

dependent on how carbon is partitioned to different 

plant and soil pools and the turnover times of those 

pools. FACE experiments have differed in this regard. 

For example, in one experiment, NPP stimulation 

occurred primarily in woody biomass, while in 

another forest, fine-root productivity was preferentially stimulated. Woody biomass has a substantially 

longer residence time (slower turnover) than fine 

roots (DeLucia, Moore, and Norby 2005), but some 

of the carbon deposited into soil by fine-root turnover may be retained in long-lived or protected pools 

(Iversen et al. 2012). Evaluation of tropical forest 

responses to eCO2 thus must include analysis of NPP 

distribution to all pools, not just aboveground biomass. Analyzing root system responses is particularly 

important because of the many intersection points 

between roots and carbon, water, and nutrient cycles 

in ecosystems.

Temperate-zone experiments revealed the importance of nutrient availability and feedbacks between 

carbon and nitrogen cycles in modifying response 

to eCO2. Even though nitrogen availability in three 

FACE experiments was demonstrably limiting to 

tree growth, nitrogen uptake increased in eCO2, 

and NPP increased commensurately (Finzi et al. 

2007). However, as one forest stand developed, 

nitrogen availability declined (especially in eCO2), 

as did the stimulation of NPP in eCO2 (Norby 

et al. 2010). Such interactions between eCO2 and 

nitrogen have been predicted by models (Comins 

and McMurtrie 1993). 

Many tropical forests may not be nitrogen limited, but 

strong evidence indicates that tropical photosynthesis 

is phosphorus limited (Vitousek 1984; Lloyd et al. 

2001; Reich, Oleksyn, and Wright 2009). Although 

many questions remain about how phosphorus affects 

plant metabolism, enough is known to develop a 

semimechanistic phosphorus model on photosynthesis. With additional data from tropical trees, the 

effects of leaf phosphorus concentration on photosynthesis can be incorporated into models using a linear 

function based on Reich et al. (2009). New modeling 

approaches also are needed to simulate phosphorus 

availability, including its potential increase to trees 

under eCO2 through stimulations of rhizosphere 

phosphatase activity (Wasaki et al. 2005), mycorrhizal 

establishment and activity (Lovelock et al. 1997), and 

deeper fine-root distribution (Iversen 2010). 
Research Priorities for Tropical Ecosystems Under Climate Change 19

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

Responses to 

External Forcings

Interactions between eCO2 and water availability and 

use have been investigated in temperate ecosystems 

and could be highly important to tropical forests in a 

future high-CO2 world. By increasing photosynthesis 

or decreasing water use via reduction in stomatal 

conductance (or both), water-use efficiency (WUE; 

carbon uptake per unit water loss) usually increases 

in response to eCO2. Depending on other factors, 

especially leaf area responses, increased WUE may 

or may not result in decreased water use (Norby and 

Zak 2011), but increased WUE potentially could 

confer increased drought tolerance to trees in eCO2

(Cernusak et al., in review). Increased soil moisture 

has been associated with eCO2 in some experiments, 

with subsequent effects on soil respiration and nutrient turnover (Hungate et al. 1997).

Interactions between CO2 and light derive from the 

effect of eCO2 to increase light-use efficiency and 

decrease the light compensation point (Long and 

Drake 1991). Although plants in the deep shade of 

a closed tropical forest will have slow growth, their 

relative response to eCO2 can be dramatic (Würth, 

Winter, and Körner 1998). Hence, eCO2 has the 

potential to facilitate the expansion of plants into 

deeper shade (Körner 2009) and alter the species 

composition that results after a canopy opening. 

This issue is critical in determining the response of 

LAI and the associated change in land-atmosphere 

interactions under high CO2 conditions. Controls on 

maximum LAI in vegetation models often are very 

crude “caps” on maximum leaf area and typically do 

not take into account the carbon balance of each leaf 

layer and the viability of leaf production in shade 

(Fisher et al. 2010). The models therefore generate 

highly varying responses to CO2 fertilization because 

of this issue and the highly variable rules governing 

model allocation to plant tissues. 

Despite details available on leaf-level photosynthesis, 

some remaining uncertainties could be particularly 

important in the Tropics. For example, stomatal and 

nonstomatal limitations on A are expected to increase 

with rising leaf temperatures in tropical canopies. 

However, the extent to which this temperature 

interaction will dampen the response of A and gross 

primary production (GPP) to rising [CO2] in tropical forests is not known. Some research also has suggested that eCO2 could enhance the heat tolerance of 

tropical tree leaves (Hogan, Smith, and Ziska 1991), 

but this hypothesis requires experimental testing. 

Leaf-scale studies on temperate species have consistently shown that mesophyll conductance strongly 

impacts photosynthesis with an effect comparable 

to that of gs (Niinemets et al. 2009). Sun et al. (in 

review) conducted a model simulation that suggested 

mesophyll conductance can cause a 24% reduction 

of model-estimated GPP in tropical rainforests. 

However, measurements of mesophyll conductance 

on tropical species are rare, and the validity of model 

parameters for such conductance in tropical species 

is unknown.

Few data are available describing differential sensitivity to eCO2 among tropical species, but if such 

differences exist, they could represent a significant 

influence on forest structure resulting from revegetation of a forest gap or abandoned agricultural land. 

Lianas (woody vines) are increasing in Neotropical forests, representing one of the first large-scale 

compositional changes documented for old-growth 

tropical forests. Some research indicates lianas may be 

particularly sensitive to eCO2 (Schnitzer and Bongers 

2011), but other explanations unrelated to global 

change also have been offered for why they may be 

increasing (Wright, Hernandez, and Condit 2007). 

Nevertheless, a specific liana response to eCO2 is an 

important hypothesis to test because more vigorous 

lianas—and their effects on tree mortality and growth 

suppression—would have far-reaching consequences 

for carbon storage (Phillips et al. 2002). The potential 

ramifications of increasing lianas are huge because 

these vines alter both tropical forest diversity and 

ecosystem functioning. At the community level, 

lianas affect tree species coexistence and diversity by 

competing more intensely with some tree species than 

others and thus will likely alter tree species composition. At the ecosystem level, lianas affect forest carbon 

and nutrient storage and fluxes. A decrease in forest 

carbon sequestration might be the most important 

consequence of liana increases. Lianas also reduce tree 

growth and increase tree mortality, thus reducing forest-level carbon storage. The increase in lianas, which 

have much less wood than trees, compensates only 

partially for the amount of carbon lost in the displaced 

trees. Because tropical forests contribute approximately one-third of global terrestrial carbon stocks 

and NPP, the effect of increasing lianas for tropical 
20 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

forest carbon cycles may have serious consequences at 

the global scale. 

Woody legumes are another plant functional type 

abundant in tropical forests and may be especially 

responsive to eCO2 (Thomas et al. 1991; Tissue, 

Megonigal, and Thomas 1997; Cernusak et al. 2011). 

Key Uncertainties and 

Research Opportunities

Underlying the need to gain a better understanding 

of CO2 effects on tropical forests are several factors: 

(1) the certainty of tropical forests growing in and 

responding to increasing atmospheric CO2 concentrations during this century, (2) importance of CO2

fertilization effects in land process models and the climate models to which they are coupled, and (3) high 

uncertainty and lack of data about CO2 effects and 

interactions in the Tropics. Efforts addressing these 

uncertainties are needed as part of a coordinated program to improve the ability to predict the responses of 

tropical forests to climate change and their feedbacks 

to the atmosphere and climate. Four research gaps are 

especially critical:

•	 Will NPP of tropical forests increase in response 

to future concentrations of CO2? Retrospective 

analyses of tropical forest carbon stocks and tree 

growth have been inadequate for answering this 

question. Such analyses considered just part of the 

carbon budget (aboveground biomass), and they 

attempted to detect a response to a much smaller 

increase in CO2 (e.g., from 330 to 380 ppm) than 

will be occurring in future decades. Furthermore, 

retrospective analyses cannot separate CO2 effects 

from the confounding responses to many other 

uncontrolled environmental variables. Hence, 

failing to unambiguously detect a response to past 

increases in CO2 says little about the potential for 

rising CO2 to affect the metabolism and ecology 

of tropical forests. Getting NPP responses right in 

models requires new data and understanding of 

leaf-level gas exchange under tropical conditions, 

modification of those responses by temperature 

and nutrient (especially phosphorus) interactions, and integration of leaf-level responses across 

complex canopies and landscapes.

•	 Will increased NPP increase ecosystems’ 

carbon storage? NPP is just the first, but necessary, step in addressing longer-term ecosystem 

carbon cycling questions. A critical uncertainty is 

how increased NPP is allocated to different plant 

and soil pools. The response of root production 

and turnover to elevated CO2 in tropical forests 

is completely unknown, yet root responses have 

many important interaction points with an ecosystem’s carbon, water, and nutrient budgets.

•	 Will eCO2 alter forest responses to drought?

Seasonal and episodic droughts are one of the 

most significant environmental factors affecting 

tropical forests, and drought is projected to be 

increasingly important in the future. Because 

eCO2 has a strong potential for ameliorating 

drought responses, predictions of tropical forest 

responses to future drought scenarios will be unreliable unless the effects of eCO2 are considered.

•	 Will eCO2 alter community composition? Tropical forests are dynamic and diverse. Establishment 

of a new forest—whether in a forest gap created by 

a tree fall, after a large-scale disturbance (e.g., wind 

or fire), on abandoned land previous managed for 

crops or pasture, or at the forest-savannah border—can entail intense competition among species with differing resource requirements. Because 

tree seedlings in an exponential growth phase can 

respond much more strongly to eCO2 than trees 

in a closed forest, eCO2 has the potential to alter 

competitive outcomes and influence the trajectory 

of forest development (Souza et al. 2010). This 

in turn has long-term consequences for carbon 

cycling and climate feedbacks. Although there 

are some indications of differential responses to 

eCO2 among tropical plant species or functional 

types, the effects of eCO2 on forest establishment 

are undetermined and a modeling framework for 

incorporating such effects does not yet exist.

Addressing these Uncertainties

Unlike other aspects of global change, there is no 

possibility of substituting space for time or taking 

advantage of interannual variation to better understand the response of the Tropics to rising CO2. 

Hence, intact tropical ecosystems are considered to 
Research Priorities for Tropical Ecosystems Under Climate Change 21

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science

Responses to 

External Forcings

be high-priority targets for a next-generation FACE 

experiment (Calfapietra et al. 2010). In temperate 

ecosystems, open-top chamber (OTC) and FACE 

studies enabled significant advances in mechanistic 

understanding and constrained estimates of the 

response of temperate plants and ecosystems to rising CO2 (Norby and Zak 2011). Results from temperate FACE experiments can be used to highlight 

critical uncertainties and guide hypotheses about 

possible tropical responses, but the inference space 

from these studies does not extend to tropical forests. CO2 manipulation experiments have been strikingly absent in the Tropics (see Fig. 3.3, this page), 

and new FACE or OTC studies certainly would be 

highly informative. Current understanding of the 

CO2 response in tropical systems is based on only 

a few experiments in which plants were rooted in 

soil and none in which the artifacts associated with 

enclosures were absent. FACE or OTC studies will 

be required to gain the process-level understanding, model algorithms, and scaling rules needed for 

integrating physiological processes with complex, 

whole-plant, and ecosystem feedbacks. These feedbacks are unique to the Tropics and undoubtedly 

will shape the response of tropical systems to rising 

CO2. Critical resource interactions (e.g., drought 

and nutrient limitations) can be part of a long-term 

experimental campaign on eCO2 by incorporating 

natural variability in precipitation, imposing extreme 

droughts, relieving nutrient limitations after baseline 

responses are established, or establishing experimental sites across resource gradients. 

Clearly, no experiment or small set of experiments can 

ever represent the full diversity of the tropical biome. 

Furthermore, many of the critical questions about 

the role of tropical forests in global carbon cycling are 

inherently long term (e.g., 50 to 100 years). Models 

well informed and constrained by experimental 

observations offer an opportunity to extrapolate 

through space and time. Hence, an important strategy 

for designing experiments that will provide the most 

useful and needed data and process understanding is 

to engage a modeling perspective from the start. Existing ecosystem models as described above can identify 

the most critical uncertainties that can be addressed 

in models and also define specific hypotheses to guide 

the experimental approach. 

Fig. 3.3. Global Distribution of Elevated [CO2] Experiments in Open-Top Chamber (OTC) and FreeAir CO2 Enrichment (FACE) Facilities where Plants Have Been Rooted in Soil. [Reprinted with permission 

by Elsevier from Leakey, A. D. B., K. A. Bishop, and E. A. Ainsworth. © 2012. “A Multi-Biome Gap in Understanding of Crop and 

Ecosystem Responses to Elevated CO2,” Current Opinion in Plant Biology 15(3), 228–36.]
22 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 3 – Responses of Tropical Forests to Elevated CO2

DOE Office of Science
Temperature Effects on 

Tropical Plant, Soil, and 

Ecosystem Processes

CHAPTER 4
24 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

Temperature Effects on Tropical Plant, Soil, 

and Ecosystem Processes

Overview

Earth system models (ESMs) predict temperature increases of 2 to 5°C in tropical 

regions by 2100 (A1B scenario; Christensen 

et al. 2007), and more recent work suggests tropical 

forests could be facing a sustained and significant 

shift toward a novel temperature regime within the 

next two decades (Anderson 2011; Diffenbaugh 

and Scherer 2011). Because lowland tropical forests 

typically maintain low seasonal and interannual 

variability in temperature, the majority of temperature research has focused on higher-latitude 

ecosystems where temperature changes are more 

apparent. The primary nonanthropogenic drivers of 

ecosystem change in tropical forests, however, often 

are thought to be carbon dioxide (CO2) fertilization, shifts in precipitation, and stronger storms 

with a warming climate (Davidson, Ishida, and Nepstad 2004; Lewis et al. 2004; da Costa et al. 2010; 

Elmendorf et al. 2012; Emanuel 2005; NegrónJuárez et al. 2010). Recent studies have challenged 

this view, suggesting that tropical forests could 

respond markedly to small increases in temperature 

(Clark et al. 2003; Lewis et al. 2009b). However, 

predicting the effects of increased temperature on 

the carbon balance in tropical forests is complicated 

by wide forest diversity (see Chapter 2, Regional 

Differences in Forest Response to Climate Change, 

p. 7). Given that most tropical forests are already 

quite warm [88% experience mean annual temperatures ≥ 20°C (FAO 2010)] and are responsible for 

cycling vast amounts of carbon, improving the ability to accurately predict their response to increased 

temperature is imperative (Booth et al. 2012). 

Presented in this chapter is an overview of the current understanding of temperature effects on key 

ecosystem processes and associated uncertainties. 

For more in-depth discussion of these topics see 

Wood, Cavaleri, and Reed (2012); Corlett (2011); 

and Reed et al. (2012).

Effects of Temperature 

on Plant Processes

Photosynthesis and Stomatal Conductance

Leaf-level photosynthesis experiments have shown 

that photosynthetic uptake rates increase with 

temperature until a thermal optimum is reached, 

beyond which rates begin to decline (Berry and 

Bjorkman 1980). Whether tropical forests are at or 

near a temperature threshold—leading to an overall 

decline in photosynthetic rates in the near future—is 

subject to debate (Doughty and Goulden 2008a; 

Lloyd and Farquhar 2008). At the leaf level, thermal 

optimums for photosynthesis of tropical tree species 

are between ~33 and 40°C, while eddy flux studies of 

tropical forests show overall declines in canopy-level 

photosynthesis at significantly lower temperatures 

(~20 to 27°C; Wood et al. 2012). Photosynthesizing 

leaves in tropical forests exist in two states: cool and 

light-limited vs. warm and light-exposed. Research 

indicates that the warm, illuminated leaves—which 

are most responsible for photosynthesis—are at 

the upper limit of the photosynthetic temperature 

optimum. This observation implies a strong 

possibility for reduced photosynthesis with warming 

(Doughty and Goulden 2008a). The disconnect 

between leaf- and canopy-level photosynthetic 

response to temperature, while crucial for accurately 

representing tropical forest carbon flux, is not well 

represented in current models.

Warming temperatures have both direct 

physiological effects on photosynthetic machinery 

and indirect stomatal effects, with increased 

temperature associated with decreased relative 

humidity and higher vapor pressure deficit (VPD) 

and thus reduced stomatal exchange (Sage and 

Kubien 2007; Lloyd and Farquhar 2008). Direct 

physiological effects of warming under expected 

elevated CO2 scenarios (>380 parts per million) 

include a decline in electron transport (Jmax) and 

irreversible denaturation of enzymes associated 

with photosynthesis (especially RuBisCO activase; 
Research Priorities for Tropical Ecosystems Under Climate Change 25

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

Responses to 

External Forcings

Sage and Kubien 2007). However, interactions 

between increased CO2 concentrations and 

increased temperature may attenuate much of this 

reduction (Taub, Seemann, and Coleman 2000). 

Many models represent the temperature sensitivity 

of Jmax, and whether indirect stomatal effects (Lloyd 

and Farquhar 2008) or direct effects of temperature 

on photosynthetic machinery (Doughty 2011) 

will dominate in tropical forests with increased 

temperatures is subject to debate. Data on either 

direct or indirect effects of temperature on tropical 

tree photosynthesis are quite sparse, and only a 

handful of potted seedling or branch- and leafwarming studies are available from which to glean 

model parameters for tropical forests (Cunningham 

and Read 2002; Cunningham and Read 2003a; 

Cunningham 2005; Doughty 2011; Tribuzy 2005).

Climate-induced warming is likely to be associated 

with constant relative humidity due to increased 

evaporation from higher surface temperatures (Held 

and Soden 2006). However, on diurnal timescales, 

absolute humidity is more constant so that relative 

humidity decreases with increasing temperature 

(Lloyd and Farquhar 2008). The resulting “midday 

depression” of photosynthesis that has been 

measured in tropical forest canopies (Koch et al. 

1994) may or may not hold true with longer-term 

warming. Furthermore, recent evidence suggests 

that tropical plants are unable to acclimate under 

longer-term warming conditions (Cunningham 

and Read 2003b; Doughty 2011). While these 

studies are limited to seedlings and branch-warming 

experiments, they suggest that tropical trees may 

not have the plasticity to respond to increasing 

temperatures because these plants develop under 

lower diurnal, seasonal, and interannual temperature 

variation. If photosynthesis is unable to thermally 

acclimate in the long term, tropical species may be 

more sensitive to climate change than temperate 

ones, potentially leading to an overall decrease in the 

strength of the carbon sink in tropical forests. Most 

models currently do not represent photosynthetic 

acclimation, and data on the thermal acclimation 

potential of tropical tree species are very limited 

because no in situ warming studies have been 

conducted in any tropical forest.

Autotrophic Respiration

The rates of autotrophic respiration (CO2 respired by 

stems, leaves, and roots) increase with temperature 

over the short term in a roughly exponential 

relationship. For tropical rainforest trees, mean foliar 

and woody respiration Q10 values (the proportional 

change in rate with a 10°C rise in temperature) range 

from 1.8 to 2.3 (Ryan et al. 1994; Meir, Grace, and 

Miranda 2001; Cavaleri, Oberbauer, and Ryan 2008). 

To our knowledge, no studies have investigated Q10

values of tropical tree roots despite the fact that root 

respiration is estimated to account for 24 to 38% of 

total soil respiration in some tropical forests (Silver 

et al. 2005a; Sayer and Tanner 2010). Accounting 

for this dynamic response of autotrophic respiration 

to temperature is now recognized as essential for 

properly quantifying ecosystem respiration on a 

diurnal basis (Wythers et al. 2005), and with all else 

held constant, future warming might be expected to 

increase autotrophic respiratory losses of CO2 to the 

atmosphere (Wythers et al. 2005; Atkin et al. 2008).

The temperature sensitivity of respiration is not 

constant with temperature (Tjoelker, Oleksyn, and 

Reich 2001; Atkin and Tjoelker 2003), and shortterm respiration-temperature responses are not 

necessarily applicable to predicting long-term change 

with warming because acclimation to sustained 

changes in temperature is typically observed (Atkin 

and Tjoelker 2003). Respiratory thermal acclimation 

of leaves, wood, or roots (decreasing Q10 with 

increasing growth temperatures) can result from 

limited substrate availability or changes in enzyme 

activity (Atkin and Tjoelker 2003). As production 

shifts in response to changing climate, the potential 

for respiration ultimately may be limited by carbon 

supply. If substrate (photosynthate) availability is 

the primary driving force behind respiratory thermal 

acclimation of plants, then the acclimation potential 

of photosynthesis becomes the ultimate driver of 

the response of tropical forests to a warmer world. 

However, there have been only limited studies on 

the short-term respiration-temperature responses 

of tropical plants and no investigations of the longterm thermal acclimation of foliar, wood, or root 

respiration of tropical trees. This lack of research 

makes determining or predicting respiratory 

acclimation difficult.
26 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

Volatile Organic Carbon Emission

In addition to respiratory losses, 30 to 50% of 

all tropical trees emit volatile organic carbon 

compounds (VOCs), especially isoprene (Lerdau 

and Keller 1997; Harley et al. 2004), which has 

been suggested to be the single largest global source 

of photochemically reactive compounds in the 

atmosphere (Lerdau and Keller 1997). Isoprene 

emissions typically are observed to increase with 

increasing temperature (Guenther et al. 2006) and 

at high temperatures may be important both for the 

net carbon balance of forests and for atmospheric 

chemistry and secondary organic aerosol formation 

(Clark 2004; Harley et al. 2004). While isoprene 

helps plants tolerate high temperatures in the short 

term, it may not be helpful under long-term sustained 

warming because production may be limited by 

substrate supply (Sharkey, Wiberley, and Donohue 

2008). These processes are beginning to be included 

into ESMs, though with great uncertainty (see 

Chapter 8, Biosphere-Atmosphere Interactions: 

Greenhouse Gases, Reactive Chemicals, and 

Aerosols p. 55).

Plant Water Use

Warming may have indirect effects on tropical 

forest water balance. For example, certain species 

with better-adapted hydraulic architecture may outcompete more poorly adapted species, or increased 

temperatures may affect whole-plant water use via 

changes in water supply or evaporative demand. 

Evidence from a Costa Rican lowland tropical forest 

shows that transpiration may be more responsive to 

air temperature than to precipitation when soils are 

saturated (O’Brien, Oberbauer, and Clark 2004). 

In a more seasonal tropical rainforest in Brazil, 

however, transpiration was primarily driven by 

soil and root hydraulic resistance (Williams et al. 

1998). Whole-canopy transpiration depends on the 

resistance of both stomata and the canopy boundary 

layer (Meinzer et al. 1997). While warming may 

greatly influence stomatal behavior, it will have little 

effect on boundary layer thickness (unless wind 

speed is affected indirectly). Some studies suggest 

that boundary layer conductance is actually a more 

important driver of canopy transpiration in tropical 

forests (Meinzer et al. 1997), but the opposite also 

may be true. The relative influence of boundary 

layer vs. stomatal conductance on whole-canopy 

transpiration is difficult to determine in the field.

Species-specific hydraulic architecture may greatly 

influence whole-forest response to warming. 

Trees that either have deep roots or are able to 

hydraulically redistribute water within soil profiles 

(as has been found among Amazonian species) 

may have a competitive advantage over other 

trees (Oliveira et al. 2005; Stork et al. 2007). For 

shallow-rooted species, hydraulic redistribution may 

be a mechanism that helps buffer the detrimental 

effects of increased evaporative demand with 

warming. Xylem architecture variation can greatly 

affect competitive advantage, as well. Lianas are 

more vulnerable to cavitation (disruption of the 

xylem water column by air emboli caused by high 

tension during transpiration) but also are able to 

transpire more water than a given tree of the same 

diameter (Fisher and Ewers 1995). Given the 

increasing abundance of lianas in the Neotropics 

(Phillips et al. 2002; Schnitzer and Bongers 2011), 

their high transpiration rates may increase the 

susceptibility of forests as a whole to water stress 

caused by increased warming. Alternatively, liana 

cover may buffer the responses of host tree sap flow 

to extreme temperatures, as was observed in Costa 

Rica (O’Brien et al. 2004). The diversity of root 

architecture, soil water partitioning, and hydraulic 

architecture is neither well explored in tropical 

forests nor well represented in modeling efforts. 

Nevertheless, including this type of data in models 

would be important for understanding how water 

balance may be affected by the increased evaporative 

demand resulting from warmer temperatures.

Individual Plant Growth 

and Carbon Allocation

Overall tree growth depends on the partitioning of 

assimilated carbon, but growth rates cannot always 

be predicted by photosynthesis rates. For example, 

tropical rainforest species in Australia had optimum 

growth under much higher temperatures than is 

ideal for photosynthesis, indicating that growth can 

continue to increase with rising temperatures even 

as photosynthesis declines (Cunningham and Read 

2003a). The apparent disconnect between photosynthesis and growth showed that carbon source 
Research Priorities for Tropical Ecosystems Under Climate Change 27

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

Responses to 

External Forcings

and sink activity could have more influence over a 

tree’s growth rate than CO2 exchange. In addition, 

achieving a mechanistic understanding of tropical 

tree growth response to warming requires investigating the effects of temperature on plant cell division and expansion (Ryan 2010). However, no such 

studies have yet been conducted for tropical species.

Few experiments have investigated warming effects 

on tropical tree growth or morphology, and no 

large-scale field warming manipulation study exists 

anywhere in the Tropics. A recent global metaanalysis found decreased root:shoot ratios and 

taller, thinner stems under increasing mean annual 

temperatures. However, the same study indicated that 

tree growth in tropical forests decreased overall with 

warming compared to boreal and temperate forests 

where growth increased (Way and Oren 2010). A 

study of tropical tree seedlings, on the other hand, 

showed increased biomass allocation to roots vs. 

leaves under warming treatments (Cunningham and 

Read 2003a). Accordingly, increased temperatures 

may affect not only growth rates but also tree 

morphology and above- vs. belowground allocation, 

both of which are largely missing from many 

modeling efforts. Nevertheless, understanding how 

temperature affects carbon allocation is critical to 

predicting how both carbon flux and storage respond 

to or change with warming in tropical forests.

Recognizing that forests may respond to warming 

differently over different timescales also is important. Plant acclimation to warming with respect to 

photosynthetic rates will vary over the lifetime of 

individual trees in addition to any adaptation that 

is expressed through the replacement of individuals 

and species with others that may be more competitive under a changed climate. Thus, ecosystem-level 

responses over longer timescales are likely to be 

quite different from individual responses. A further 

(theoretical but disputed) uncertainty is whether 

higher temperatures will lead to increased plant mortality as a result of metabolic limitation, a response 

(McDowell et al. 2011) that in turn could lead to 

changes in forest community structure and distribution of tree lifetimes.

Temperature Effects 

on Soil Processes

Tropical forest soils contain more carbon than any 

other terrestrial biome and about twice the amount 

found in the aboveground vegetation (Raich and 

Schlesinger 1992; Jobbágy and Jackson 2000). 

The capacity to predict and ameliorate the consequences of global warming thus depends, in part, 

on an improved understanding of the temperature 

sensitivity of processes controlling carbon cycling 

and storage in tropical forest soils. Although no in 

situ warming experiments have been conducted in 

tropical forest ecosystems, field warming studies in 

high-latitude ecosystems and tropical soil laboratory 

incubations (e.g., Holland et al. 2000) suggest that 

soil respiration will increase with warming in the 

short term (months to years) and ultimately acclimate 

over the longer term (2 to 15 years). Completely 

unknown, however, is the amount of time before 

thermal acclimation of soil respiration would occur 

and the amount of carbon that would be released to 

the atmosphere in that time frame. Various theories 

have been suggested to explain the observed thermal 

acclimation of soil respiration in higher-latitude ecosystems (Kirschbaum 2000; Davidson and Janssens 

2006; Bradford et al. 2008; Kleber 2010), yet how 

these theories will apply to tropical forests remains 

highly uncertain. Described in detail below are the 

current understanding of and evidence for temperature effects on tropical forest soil processes.

Heterotrophic Respiration

There are two types of respiration in soils: heterotrophic (CO2 respired by microbes) and autotrophic 

(CO2 respired by plant roots). Incubations of tropical 

forest soils would suggest that soil microbes respond 

positively to short-term exposure to elevated temperatures, with notably high soil respiration rates observed 

at temperatures as warm as 55°C when substrate is 

not limiting (Holland et al. 2000; Balser and Wixon 

2009). Although the longer-term responses of soil 

heterotrophic communities to elevated temperature 

remain uncertain, potential effects could include a shift 

in community composition, biochemical acclimation 

of respiration, and changes in carbon-use efficiency. 

Each result would significantly alter the trajectory of 

the temperature response of soil respiration in tropical 
28 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

forests (Balser and Wixon 2009; Allison, Wallenstein, 

and Bradford 2010; Bradford, Watts, and Davies 

2010). The role of the chemical complexity of soil 

carbon represents another challenge to quantifying the 

effect of temperature on soil heterotrophic respiration. 

Soil respiration responses to temperature are, in part, 

regulated by the quality of carbon the heterotrophs 

consume (Davidson and Janssens 2006). If elevated 

temperature alters soil organic carbon inputs or stocks, 

both soil respiration rates and responses to continued 

temperature change could be affected. However, the 

importance of different carbon chemical pools in regulating soil microbial respiration responses to changing 

temperature remains a topic of significant debate 

(Giardina and Ryan 2000; Fang et al. 2005; Conant 

et al. 2008; Kleber 2010). High variability among 

tropical forests in the size of the easily accessible 

labile carbon pool and in the depth profiles adds an 

additional layer of complexity ( Jobbágy and Jackson 

2000). Finally, plant photosynthesis and soil respiration are tightly linked (Högberg et al. 2008; Kuzyakov 

and Gavrichkova 2010). Not only is root respiration 

an important component of tropical soil CO2 efflux 

(see Autotrophic Respiration section, this page), but 

carbon allocated by plants to soils (via root exudates) 

also could supply key substrate for heterotrophic soil 

respiration. Thus, if warming reduced photosynthesis 

and carbon exudation belowground, it also could dramatically affect soil respiration rates (see the Plant-Soil 

Feedbacks section, this page). Research exploring soil 

microbial responses to increased temperature across 

a diversity of tropical soil types would be essential for 

accurately predicting the fate of tropical soil carbon in 

a warmer world. Because soil heterotrophic CO2 fluxes 

to the atmosphere are very large, determining their 

response to elevated temperature also would be important at the global scale.

Autotrophic Respiration

Root respiration is estimated to account for as 

much as 24 to 38% of total soil respiration in some 

tropical forests (Silver et al. 2005a; Sayer and Tanner 

2010). Studies that evaluate microbial responses 

alone thus exclude a significant component of soil 

respiration and consequently could lead to inaccurate 

representations of soil respiration in global models. 

Evidence from high-latitude systems suggests 

that temperature may influence root respiration 

via its effects on photosynthesis and allocation of 

photosynthate to roots. Changes in plant carbon 

allocation to roots and in the distribution of roots 

within the soil profile could further alter soil 

respiration rates (Davidson et al. 2000a; Sotta et al. 

2006; Metcalfe et al. 2007). Little is known about 

either the temperature sensitivity of tropical root 

respiration or the influence of temperature on the 

mass and distribution of roots in the soil profile.

Plant-Soil Feedbacks

As highlighted above, soil and plant processes are 

intricately linked, and the temperature response 

of carbon cycling in tropical forest soils cannot be 

accurately predicted without considering how temperature affects a variety of aboveground processes. 

For example, increases in litter and root inputs 

have been shown to stimulate additional CO2 loss 

from soils via a process known as “priming” (Sayer, 

Powers, and Tanner 2007; Kuzyakov 2010; Kuzyakov 

and Gavrichkova 2010). Priming occurs when soil 

heterotrophs respond to additional carbon inputs 

by respiring carbon well beyond the amount added. 

These litter and root inputs have primed the soil 

heterotrophic community to decompose soil organic 

carbon that otherwise would remain stabilized 

within the soil. Plants also may change belowground 

carbon allocation patterns under increasing temperature, potentially leading to differences in the 

amount and location of autotrophic respiration in 

the soil profile and also changes in soil heterotrophic 

respiration. Through these mechanisms, changes 

in the quality and quantity of litter and root inputs 

subsequently can determine the short- and longterm stability of that carbon in the soil profile (see 

Chapter 10, Belowground Processes: Roots and Soil 

Biogeochemistry, p. 69). The potential for plant temperature responses to have subsequent effects on soil 

processes is strong. High research priorities therefore include belowground studies investigating the 

effects of increased temperature on aboveground net 

primary productivity (NPP) and plant carbon allocation, as well as the linkage between photosynthesis 

and root respiration.

Nutrient Cycling

An exciting advance in recent modeling efforts is a 

focus on the significant role nutrient cycling could play 
Research Priorities for Tropical Ecosystems Under Climate Change 29

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

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Responses to 

External Forcings

in net carbon flux responses to warming (Thornton 

et al. 2009; Wang and Houlton 2009; Bonan and Levis 

2010). A robust inclusion of nutrient cycling could 

similarly improve tropical modeling efforts. The few 

tropical fertilization studies that exist support the 

conclusion that soil nutrient availability plays a large 

role in regulating carbon flux and storage in tropical forests (Vitousek and Farrington 1997; Tanner, 

Vitousek, and Cuevas 1998; Cleveland and Townsend 

2006). Temperature can dramatically affect the rates 

of various nutrient cycling pathways that regulate 

nutrient availability and loss (e.g., nitrogen mineralization, phosphorus mineralization, and nitrification). 

Accordingly, temperature effects on nutrient cycling 

and subsequent feedbacks to carbon cycling pathways, 

such as aboveground NPP, represent major uncertainties in predicting how increased temperature will influence ecosystem processes in tropical forests.

Effects of Temperature on 

Ecosystem Carbon Balance

Potential effects of warming on ecosystem carbon 

balance can be assessed using several approaches, 

such as elevation gradients, cross-site comparisons, 

eddy covariance, coupled carbon-climate models, 

and field warming experiments (Wood et al. 2012). 

Cross-site comparisons and elevation gradient studies 

suggest that forest NPP will increase enough to offset 

any additional loss in soil carbon caused by warming, 

leading to no net change in ecosystem carbon balance 

(Raich et al. 2006). However, these results probably 

will have limited applicability to understanding future 

responses, given the likelihood that most tropical 

forests will experience novel temperature regimes 

within the next two decades (Wright, Muller-Landau, 

and Schipper 2009; Anderson 2011; Diffenbaugh 

and Scherer 2011). Results from eddy covariance and 

ESMs predict that tropical forests will become a net 

source of carbon, but eddy covariance results vary 

among studies depending on the duration (Grace 

et al. 1996; Loescher et al. 2003; Hutyra et al. 2007; 

Doughty and Goulden 2008a), and models disagree 

on what the primary drivers of increased carbon loss 

will be (White, Cannell, and Friend 2000; Cramer 

et al. 2001). Interannual variability also can be used 

to infer relationships between temperature and 

tropical forest productivity. For example, warmer 

El Niño years are associated with reduced growth 

at the site level, as well as reduced overall carbon 

uptake from tropical forests (Clark et al. 2003). 

However, the hydrologic cycle co-varies strongly 

with temperature on this timescale, so inferring a 

strict temperature response from these relationships 

is difficult. Furthermore, we know of no studies that 

evaluate long-term variability (>10 years) of the net 

ecosystem carbon balance of tropical forests (i.e., both 

above- and belowground responses). Resolving the 

potential effects of temperature on the net carbon 

balance in these ecosystems will require an improved 

understanding of temperature controls on the flow of 

carbon into and out of the system over multiple spatial 

and temporal scales. Using a variety of approaches in 

concert would allow research questions to span these 

scales and could offer the richest insight and predictive power into how tropical forest carbon balance will 

respond to increased temperatures.

Representation in Global Models

Aboveground Representation

Model representation of foliar respiration currently 

is based on the hypothesis that tissue nutrient 

concentration dictates basal maintenance respiration 

rates (Ryan et al. 1994). If plant respiration acclimates 

to increased temperature, modelers may have cause (at 

least for tropical forest vegetation) to more explicitly 

represent the influence of plant-scale source and sink 

relationships on tissue basal respiration rates and 

temperature responses. These changes would have 

important consequences for global-scale carbonclimate feedbacks, although speculating the magnitude

of the effect at the global scale is not yet possible.

In ESMs, parameters describing carbon allocation are 

some of the most sensitive constraints on total growth 

and accumulation of vegetation and soil carbon stocks 

over time (White et al. 2000). However, such parameters are poorly defined for tropical forests, so research 

investigating temperature effects on these processes 

would provide critical new constraints on model performance. In turn, these improvements likely would 

have important consequences for predicting globalscale carbon balance and changes under a warming 

climate. ESMs currently have limited dynamic range 

for their allocation parameterization, partly because of 
30 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

a lack of both data and understanding of the fundamental processes guiding carbon allocation patterns 

in real ecosystems.

Belowground Representation

Current representation of soil carbon cycling in 

ecosystem-scale models does not effectively enable 

prediction of belowground tropical forest responses 

to climate change. Models parameterized with temperature functions developed for temperate systems 

are highly unlikely to adequately simulate tropical 

ecosystems, which harbor plants and microbes with 

specific carbon-use efficiencies and acclimation 

potentials (see Chapter 10, Belowground Processes: 

Roots and Soil Biogeochemistry, p. 69). Research 

that refines rate variables and temperature functions 

for key belowground processes in tropical forest 

soils (i.e., autotrophic and heterotrophic respiration) 

across diverse soil types is critical for accurately 

representing such processes in traditional and Tropicspecific soil carbon cycling models.

Few ESMs explicitly incorporate fundamental ecological interactions between carbon and nitrogen 

cycling in their land components. However, those 

that do suggest that nitrogen biogeochemistry can 

significantly affect the carbon cycle feedback in climate simulations (Randerson et al. 2009; Bonan and 

Levis 2010). Given that carbon cycling in lowland 

tropical forests is commonly considered phosphorus 

limited (Walker and Syers 1976; Vitousek 1984), 

phosphorus availability could constrain the response 

of organisms to changing temperature, and temperature-induced effects on this availability (e.g., via 

altered phosphorus mineralization rates) could affect 

carbon cycling in tropical ecosystems. Key research 

gaps include improved understanding of how soil 

nutrients regulate tropical carbon cycling, better 

insights into how temperature will affect soil nutrient 

availability, and effective incorporation of phosphorus cycling into ESMs.

Ecosystem Representation

Currently, the most widely used tropical simulations 

do not represent the full range of climate possibilities, nor do they account for the immense diversity 

of tropical forest ecosystems. These uncertainties are 

compounded by a general lack of understanding of 

the potential biological consequences of warming 

on tropical forest processes. Model experiments are 

needed that explore the range and variability of tropical forest responses to temperature change at multiple scales. Furthermore, multidimensional sensitivity 

analyses of models to variations in subcomponent 

temperature functions would help determine which 

pools, parameters, and processes can maintain subtle 

changes yet have large effects on carbon cycling and 

future climate.

Key Uncertainties and Research 

Opportunities

Research that simultaneously explores above- and 

belowground responses to temperature and the 

linkages between plants and soil is vital for accurately predicting the net response of tropical forests 

to increased temperature (Wood et al. 2012). For 

some areas of tropical forest research, however, 

almost no field data on temperature responses are 

available. These areas include nutrient cycling, 

heterotrophic vs. autotrophic respiration, thermal 

acclimation vs. substrate limitation of plant and 

soil microbial communities, belowground carbon 

allocation, temperature effects on plant and microbial species composition, hydraulic architecture of 

roots, sensitivity of soil carbon loss to temperature, 

and temperature effects on abiotic soil properties. 

Because of fundamental differences between tropical forests and other biomes and the large diversity 

among tropical forests themselves, knowledge about 

temperate systems may reveal little about the potential effects of increased temperature on tropical forests. ESMs require new data to correctly represent 

the effects of increased temperatures on tropical 

forest carbon balance across diverse landscapes. Key 

research uncertainties and gaps are:

•	 How will warming temperatures affect canopy 

gas exchange in tropical forests? Investigations 

of tropical tree responses to increased temperature 

reveal large uncertainties in understanding how 

photosynthesis and autotrophic respiration will 

respond to warming. These uncertainties, which 

greatly constrain the ability to predict future global 

carbon cycling and feedbacks to climate, include 

the following: Will tropical plant photosynthesis 
Research Priorities for Tropical Ecosystems Under Climate Change 31

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science

Responses to 

External Forcings

acclimate to long-term warming? If photosynthesis is reduced with warming, will plant respiration 

(leaf, wood, root) decline concomitantly via substrate limitation? Will the effects of warming on 

tropical plant photosynthesis be primarily stomatal or biochemical? How do long-term responses 

to increased temperature relate to those observed 

in the short term, and how does temporal variation in net photosynthetic responses drive overall 

carbon exchange between tropical forests and the 

atmosphere? How can canopy-level gas exchange 

be best modeled using leaf-level information? 

What are the long-term temperature responses 

(i.e., acclimation or substrate limitation) of volatile 

organic compounds in tropical forest canopies? 

How will increased temperature interact with 

other environmental stresses (e.g., drought) and 

ecosystem characteristics (e.g., phosphorus availability) to affect aboveground carbon cycling?

•	 How will increasing temperature affect patterns 

of above- vs. belowground carbon allocation 

and overall morphology of tropical trees?

Changes to carbon allocation and source and sink 

relationships can greatly affect carbon storage, with 

direct implications for altering the net exchange 

of carbon between tropical forests and the atmosphere. Little is known about how increasing temperature will alter carbon allocation to above- vs. 

belowground pools (e.g., root biomass and exudation), and no research has been done to investigate 

the effects of increasing temperature on cell expansion and division of tropical plant species.

•	 How will temperature effects on both aboveand belowground processes regulate gross 

and net carbon fluxes? Strong evidence suggests that above- and belowground processes will 

respond to changing climate in concert. However, 

no studies simultaneously investigate canopy and 

soil warming, and a whole-system perspective 

may be difficult to gather from studies that do not 

explore above- and belowground effects concurrently. For example, reduced photosynthesis can 

quickly result in reduced belowground respiration 

without any change to root biomass.

•	 Will soil respiration (autotrophic and heterotrophic) acclimate to increased temperature?

No field warming experiments currently exist 

in the Tropics, but evidence from high-latitude 

experiments would suggest that soil respiration will 

acclimate to increased temperature. If so, what is the 

primary driver (e.g., substrate limitation, changes in 

microbial carbon-use efficiency) of this response? 

Over what timescales will this acclimation occur, 

and how will it vary among different tropical forests?

•	 How will nutrient availability interact with 

increased temperature to regulate carbon 

cycling and storage? Current model simulations suggest that temperature-nutrient interactions could strongly regulate carbon cycling and 

storage. For example, nutrient limitation to tree 

growth and soil respiration could help mediate 

forest responses to increased temperature. If so, 

temperature effects on soil nutrient availability 

(e.g., via changes to mineralization rates) could 

act as important indirect controls over tropical 

forest carbon exchange.

•	 How will increased temperature affect wholeforest water use? As temperature increases, so 

does vapor pressure deficit. Plants can respond to 

these changes through various mechanisms, each 

of which could differentially interact with other 

ecosystem processes related to carbon cycling and 

storage. Specific questions include: What is the 

relative importance of stomatal vs. boundary layer 

conductance in whole-forest water use? How does 

distribution of species-specific root architecture, 

xylem architecture, and hydraulic redistribution 

affect response to warming in tropical forests? 

Although characterized by relatively abundant rainfall, tropical forests depend greatly on the availability 

of water. Because of the tight coupling between 

water and carbon cycling, increased temperature has 

the potential to alter carbon cycling and storage via 

changes to water use.
32 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 4 – Temperature Effects on Tropical Plant, Soil, and Ecosystem Processes

DOE Office of Science
Drought and DroughtInduced Mortality in 

Tropical Forests 

CHAPTER 5
Fig. 5.1. Drought Intensity and Tree Mortality in the Amazon. The difference in the 12-month (October to September) 

maximum cumulative water deficit from the decadal mean (excluding 2005 and 2010) is shown for the two most extensive droughts of the 

21st century in Amazonia. This 

difference represents a measure 

of drought intensity that correlates with tree mortality. [From 

Lewis, S. L., et. al. 2011. “The 

2010 Amazon Drought,” Science

331(6017), 554. Reprinted with 

permission from AAAS.]

34 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Drought and Drought-Induced Mortality 

in Tropical Forests

The vulnerability of tropical forest trees to 

drought and drought-induced mortality is a 

function of climate risk and vegetation sensitivity (Meir and Woodward 2010). Both historical 

evidence and model predictions indicate increasing 

exposure of tropical forests to drought. In recent 

decades, severe episodic droughts have affected 

tropical forests globally in association with El Niño 

incidence, especially during 1982–83 and 1997–98. 

Unrelated to El Niño, two exceptionally severe (e.g., 

“1-in-100 year”) drought events occurred in Amazonia in 2005 and 2010 (see Fig. 5.1, this page; Cox et al. 

2008; Marengo et al. 2008, 2010; Lewis et al. 2011) 

during a period of increased weather extremes in 

several areas of South America (Marengo et al. 2012). 

Modeled future climate scenarios (IPCC 2007) indicate overall warming over the tropical biome and spatially nonuniform changes in rainfall. Climate models 

vary with respect to their fidelity in predicting 20th 

century rainfall in Amazonia (the region for which 

the most intensive analyses have been performed) 

and with their predictions of 21st century drought 

( Jupp et al. 2010). However, in an ensemble analysis 

by Malhi et al. (2008), models agreed on the scenario 

of an increased likelihood of drying and warming, 

especially in eastern and southern Amazonia (IPCC 

2007). Model analyses also indicate a likely increase 

in drought severity associated with increased deforestation and other land-use change (Werth and Avissar 

2002; Soares-Filho 2006).

Nonlethal Effects of Moisture Stress

Overview

Nonlethal physiological effects of drought on forest 

ecosystems include changes in photosynthetic 

uptake, alterations in plant and soil respiration rates, 

and subsequent shifts in growth rates. Thus, even if 

drought thresholds are not reached, drought may still 

induce significant changes in forest carbon storage 

(Phillips et al. 2009). Physiological responses to 

drought are known to depend on a combination of 

(1) climate patterns (with respect to prevailing past 

variability), (2) subsurface moisture storage capacity (in soil, saprolite, and rock aquifers), (3) plant 

adaptations (particularly rooting behavior and stem 

construction), and (4) plant physiological strategies. 

The interactions among these factors may be complex 

and are examined at both plant and ecosystem scales.

Establishing how intact rainforests respond to 

anomalously low rainfall is difficult because natural 

droughts are rare in space and time, and the logistics 

of making detailed physiological measurements 

typically precludes intense observations during these 

unpredictable events (although simpler measurements may be deployable, given appropriate planning). Current understanding of the long-term effects 

of moisture stress on plant physiology, ecology, and 

vegetation-atmosphere interactions remains limited because few ecosystem-scale datasets exist for 
Research Priorities for Tropical Ecosystems Under Climate Change 35

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Responses to 

External Forcings

periods of detectable moisture stress and such data 

have been collected only for relatively short periods 

(Malhi et al. 1998).

Although drought-related inventory data exist (e.g., 

Phillips et al. 2009, 2010), the main datasets available 

for constraining physiological responses to water 

stress in mature humid tropical forests derive from 

throughfall exclusion experiments. At large scales 

(e.g., 1 hectare), only two such studies have been 

implemented, both in eastern Amazonia, at Caxiuanã 

and Tapajós in Brazil (see Fig. 5.2, this page; Meir 

et al. 2008). A third, smaller-scale experiment has 

been implemented in Sulawesi in Southeast Asia 

(Schuldt et al. 2011; van Straaten, Veldkamp, and 

Corre 2011). Soil-only rainfall exclusion or irrigation experiments also have been performed at the 

scale of a few square meters (Vasconcelos et al. 2004; 

Cleveland et al. 2010; Wood and Silver 2012). These 

studies have the advantage of allowing more treatment replication, but the results are focused on soil 

biogeochemistry, considered in Chapter 10, Belowground Processes: Roots and Soil Biogeochemistry, 

p. 69. Some ecosystem flux measurements derived 

from eddy covariance are available for seasonally dry 

forests (Vourlitis et al. 2001, 2005). However, the 

vegetation in these ecosystems probably already possesses adaptive mechanisms for coping with reduced 

rainfall, and thus they are less useful for predicting 

the responses of intact rainforests to changes in 

climate regime.

Remote-sensing observations of the effect of both 

seasonal and episodic drought on forest reflectance 

properties (i.e., “greenness”) also are potentially useful 

(Asner et al. 2004; Huete et al. 2006; Myneni et al. 

2007; Doughty and Goulden 2008b). However, alternative interpretations of satellite-derived data streams 

during drought have indicated both increased and 

decreased greenness, for example, in response to the 

2005 Amazonia drought (Saleska et al. 2007; Samanta 

et al. 2010, 2011). Anderson et al. (2010) determined 

a positive correlation between increasing enhanced 

vegetation index (EVI) and ground-based mortality 

rates during the 2005 drought, suggesting that greenness per se is not indicative of resistance to drought 

events. Thus, a clear interpretation of changes in apparent greenness across Amazonia remains challenging 

(Samanta et al. 2012), and indeed Asner et al. (2010) 

have argued that improved satellite instrumentation is 

required to resolve this issue.

Fig. 5.2. Drought 

Experiment 

Infrastructure 

at Tapajós and 

Caxiuanã National 

Forests in Para, 

Brazil. [Drawing 

from From Nepstad, 

D.C. 2002. “The Effects 

of Partial Throughfall 

Exclusion on Canopy 

Processes, Aboveground 

Production, and 

Biogeochemistry of 

an Amazon Forest,” 

Journal of Geophysical 

Research 107, 8085. DOI: 

10.1029/2001JD000360. 

Photo courtesy of P. Meir, 

University of Edinburgh.]
36 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Representation of Physiological Effects 

of Water Stress in Land Surface Models

Water stress is represented as a simple and uniformly 

applied empirical function of either soil moisture 

content or soil water potential in every major land surface model. The “water stress” factor, applied directly 

to reduce either unstressed stomatal conductance or 

unstressed photosynthesis rates, is a function of soil 

moisture content relative to soil texture–specific “critical” and “wilting” points. Root depth (but not root 

quantity) typically influences water stress calculations 

via weighting of the water-stress factor by the fraction 

of root biomass in each vertical layer of soil.

Using flux tower data from the Large-Scale BiosphereAtmosphere Experiment in Amazonia study (LBA), 

several researchers have assessed how well the waterstress functions in land surface models capture the 

seasonal dynamics of observed gas exchange. In 

recent years, multiple studies have concluded that, in 

their default state, land surface models predict large 

reductions in gas exchange in the dry season (Saleska 

et al. 2003; Werth and Avissar 2004; Baker et al. 

2008; Verbeeck et al. 2011). This contradicts most 

tower observations, both in the Amazon and Borneo 

(e.g., Kumagai et al. 2004), that 

indicate largely constant evapotranspiration (or even slight 

increases) in the dry season and 

net ecosystem exchange between 

seasons. Many modeling groups 

subsequently have improved predictions by increasing the depth 

of soil available for water uptake 

by roots. This modification is 

consistent with evidence that, 

in the areas covered by the LBA 

project, trees typically have access 

to water from a soil profile more 

than 3 m deep (Markewitz et al. 

2010; Hodnett and Tomasella 

1997; R. A. Fisher et al. 2008) 

and draw moisture from underlying saprolite. Many models (e.g., 

Baker et al. 2008; Verbeeck et al. 

2011) thus have now resolved the 

problems of excessive water stress 

on gas exchange.

Predicting the correct average seasonality of the transpiration and photosynthesis observed by flux towers, however, does not actually improve confidence 

in model capacities to predict responses to rainfall 

reductions. This is because most forests observed to 

date are not subject to significant (if any) moisture 

stress in “normal” dry seasons, and so calibrating 

model water storage to generate conditions of “no 

drought stress under ambient conditions” leaves 

open the possibility of the models having too much 

buffering capacity in the event of a major drought. 

Testing models under conditions of imposed drought 

therefore is informative about whether or not this is 

indeed the case.

Drought Experiment Modeling Studies

Of the three mentioned ecosystem-scale drought 

experiments, more model-based validations have been 

conducted for the Caxiuanã site and are presently in 

review, along with validations and comparisons of the 

other Amazonian site. At Caxiuanã, R. A. Fisher et al. 

(2006, 2007, 2008) parameterized and tested a hydrodynamic model that simulates explicit water transport 

and the resistance of water transfer from soils to 

leaves (see Fig. 5.3, this page). Given an investment in 

Fig. 5.3. Modeled and Observed Forest Water Use (sap flow) at the 

Caxiuanã National Forest. [From Fisher, R. A., et al. 2007. “The Response of an 

Eastern Amazonian Rain Forest to Drought Stress: Results and Modelling Analyses from a 

Throughfall Exclusion Experiment,” Global Change Biology 13(11), 2361–78.]
Research Priorities for Tropical Ecosystems Under Climate Change 37

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Responses to 

External Forcings

collecting data on the hydraulic and photosynthetic 

traits of soil and plants, the emergent properties of the 

Soil-Plant-Atmosphere model (Williams et al. 1996) 

were in good agreement with observed componentand ecosystem-scale fluxes of water and carbon. However, further studies currently in preparation indicate 

that traditional land surface models do not yet simulate stressed fluxes well. According to these studies, 

this difficulty may arise from the absence of adaptive 

capacity in the average depth of water uptake, among 

other model differences such as explicit simulation of 

water transport to leaves. At a diurnal timescale, water 

stored overnight by many tropical trees supports gas 

exchange in the morning. Consequently, the stomatal 

response to vapor pressure deficit (VPD) is much 

stronger as the day progresses (Meinzer et al. 2008). 

This diurnal change in stomatal behavior severely 

limits carbon uptake in the afternoon, particularly on 

sunny days when potential carbon gain is greatest but 

evapotranspiration and the loss of stored water also 

are greatest (Doughty and Goulden 2008a). Absence 

of explicit water transport models also precludes 

accurate simulation of this behavior.

Leaf Litterfall

Most litterfall studies in tropical forests have demonstrated a strong seasonality of leaf litterfall, with the 

peak at the end of the dry (or drier) season (Hopkins 

1966; Klinge and Rodrigues 1968; Haines and Foster 

1977; Kunkel-Westphal and Kunkel 1979; Herbohn 

and Congdon 1993; Swamy and Proctor 1994; Wieder and Wright 1995; Lawrence and Foster 2002). 

Periods of drought therefore might be expected to 

drive temporary increases in leaf litter inputs also.

Evidence suggests that both the quantity and quality of leaf litterfall affect a variety of ecosystem 

processes (Sayer, Powers, and Tanner 2007; Wood 

et al. 2009). Litter manipulation experiments 

demonstrate potential feedbacks of leaf litter quality and quantity on forest productivity (Wood 

et al. 2009), soil nutrient availability (Wieder, 

Cleveland, and Townsend 2011), and greenhouse 

gas emissions (Sayer et al. 2007; Cleveland et al. 

2010; Wieder et al. 2011). As such, understanding 

how drought will affect the timing, quantity, and 

quality of leaf drop is vital. Interestingly, however, 

a dry season irrigation experiment in Panama did 

not result in significant changes in the timing of 

leaf litterfall (Wieder and Wright 1995), suggesting 

that the timing of leaf drop might be controlled by 

the canopy environment (e.g., light availability and 

vapor pressure deficit) rather than changes in soil 

moisture availability.

Drought-Induced Mortality 

in Tropical Forests

Overview

Drought and associated high temperatures are widely 

anticipated to be key drivers of tree mortality globally, and the reported frequency of such events has 

increased in recent decades (van Mantgem et al. 

2009; McDowell et al. 2011; Allen et al. 2010). 

Large-scale increases in the mortality rate of tropical 

forests would have significant impacts on the terrestrial carbon cycle and land-atmosphere energy 

exchange, yet adequate predictions of the drought 

sensitivity of tropical tree mortality are not currently 

available (Meir, Cox, and Grace 2006; Friedlingstein 

et al. 2006; White, Cannell, and Friend 1999; Sitch 

et al. 2008; Delbart et al. 2010).

Observations from long-term forest-monitoring 

networks from Amazonia to Borneo suggest that 

extreme drought events can result in rates of mortality 100 to 1200% above background (Phillips et al. 

2010), but the specific reasons for these increases, 

and particularly the differences among them, are 

not well understood (see Fig. 5.4, p. 38). Largescale drought experiments in the same region have 

demonstrated soil drought-mortality response 

surfaces empirically similar to those obtained from 

the plot network study in Amazonia (Brando et al. 

2008; da Costa et al. 2010). Where data have been 

combined globally, the sensitivity of rainforest tree 

mortality rates to soil moisture deficit appears to 

vary strongly by region, with the more perhumid 

rainforests of Southeast Asia showing substantially 

larger increases in mortality than those of Amazonia 

(Phillips et al. 2010). However, the data available 

for these analyses remain limited. An adequate 

representation of the similarities and differences in 

the climate sensitivity of tree mortality is needed if 

decadal to century drought responses in rainforest 

ecosystems are to be modeled convincingly in an 

Earth system context (Fisher et al. 2010).
38 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Representation of Tropical Forest Mortality 

in Land Surface Models

Some “dieback” of the Amazon rainforest is a recurring feature of various land surface models driven 

with the output of climate simulations. Several modeling studies have highlighted the importance of the 

response of tropical forest mortality to drought in 

future predictions (Cox et al. 2000; Sitch et al. 2008; 

Delbart et al. 2010; Fisher et al. 2010; Galbraith et al. 

2010). This modeled dieback response is ambiguous 

because of uncertainties in both climatic drivers and 

process representations in land surface models. The 

representations of mortality in these models were 

reviewed by McDowell et al. (2011) who found 

that most models included either no stress-induced 

mortality mechanisms or only very simple functions 

driven either by plant productivity or by the crossing 

of empirically defined climate thresholds.

Significant effort is being dedicated to developing 

improved algorithms for plant mortality. This development process reflects the general consensus, also 

expressed in McDowell et al. (2011), that a generic 

theory on the common causes of death in 

woody plants is not yet available. Emphasis 

has been placed on the need for gaining a 

greater understanding of preadaptations 

to drought (e.g., carbohydrate storage and 

hydraulic properties) and for representing 

the widely observed correlation among soil 

nutrient status, productivity, and turnover 

rates of tropical forests (Delbart et al. 2010). 

Multiple simultaneous laboratory studies are 

ongoing internationally, but so far none are 

concerned with tropical forest trees. Longterm field-scale manipulation studies likely 

will provide the best test of current understanding of tree mortality following environmental (i.e., climate) stress. However, none 

of the few such studies conducted thus far 

have included the detailed measurements 

required to investigate mortality physiology.

In addition, models also fail to represent 

known heterogeneity in contemporary mortality patterns because the drivers of these 

patterns, which are typically correlated with 

ecosystem productivity and soil nutrient 

status, are not understood (Delbart et al. 2010). Furthermore, there are known variations in the drought 

tolerance found among coexisting tropical tree species (Poorter and Kitajima 2007). Models that make 

no attempt to account for such variations in plant 

strategy are likely to predict exaggerated threshold 

behaviors.

Drought Effects on Soil Processes

Tropical forest soils are the largest natural source of 

both carbon dioxide (CO2; Raich and Schlesinger 

1992) and nitrous oxide (N2O) globally (Matson and 

Vitousek 1990), and wet tropical soils are a globally 

important source of methane (CH4) (Frankenberg 

et al. 2005; see also Chapter 8, Biosphere-Atmosphere 

Interactions, p. 55). Theory suggests that soil moisture is a key driver of biogeochemical processes in 

terrestrial ecosystems because of its effects on factors 

such as soil redox dynamics, diffusion, and soil carbon and nutrient pools (e.g., Conrad 1996; Vasconcelos et al. 2004; Holtgrieve, Jewett, and Matson 

2006). As such, projected changes in precipitation for 

tropical regions probably will have significant effects 

Fig. 5.4. Change in Mortality for Tropical Forests Under 

Varying Observed Soil Moisture Deficit. This change was 

determined by a simple bucket model (monthly cumulative water deficit, 

MCWD) assuming a transpiration rate of 100 mm per month. [From 

Phillips, O. L., et al. 2010. “Drought–Mortality Relationships for Tropical 

Forests,” New Phytologist 187(3), 631–46.]
Research Priorities for Tropical Ecosystems Under Climate Change 39

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Responses to 

External Forcings

on key biogeochemical processes, including trace 

gas production and nutrient availability that, in turn, 

could feed back on future climate change. The potential effects of drought (i.e., reduced soil moisture) 

on key biogeochemical processes in tropical soils are 

discussed below.

Trace Gas Consumption and Production 

(CO2 , CH4 , N2O)

Throughfall exclusion experiments investigating 

the effects of drought on trace gas emissions have 

been conducted in six tropical forests spanning a 

wide range of soil types and rainfall regimes. Results 

range from increased trace gas consumption to a 

net increase in emissions (see Table 5.1, p. 40). For 

CO2, the variable responses have been attributed to 

several factors: soil texture that led to deeper rooting 

(Davidson et al. 2008; Davidson, Ishida, and Nepstad 

2004); differential response of root, litter, and soil 

organic matter to drought (Sotta et al. 2007; Metcalfe 

et al. 2007; van Straaten et al. 2011); increase in the 

concentration of dissolved organic carbon (Cleveland et al. 2010); and soil nutrient availability (Wood 

and Silver 2012). The diversity of CH4 responses to 

drought has been attributed to a variety of factors, 

including an increase in termite activity (Cattânio 

et al. 2002); variability in soil texture, redox, and 

the soil microbial community (Teh et al. 2005); and 

variability in nutrients or carbon with topography 

(Wood and Silver 2012).

Like CH4, net N2O released from soils reflects both 

N2O production and consumption. Typically, N2O 

consumption in soils occurs in anaerobic microsites 

under low NO3–

 conditions (Cleveland et al. 2010). 

Net consumption of N2O in response to drought 

could occur as a result of net N2O consumption in 

deeper, wet soil (Wood and Silver 2012). Net emissions of N2O, in contrast, might result from increased 

concentrations of dissolved organic carbon (Wieder 

et al. 2011).

Overall, the highly variable responses of trace gas 

fluxes to drought both within and among tropical 

forest sites reflect the high degree of spatial heterogeneity and complexity of biogeochemical cycling in 

tropical forest ecosystems. These diverse responses 

create significant uncertainty in the ability to accurately predict how changes in precipitation will 

influence trace gas emissions and ultimately their 

concentration in the atmosphere.

Soil Nutrient Availability

Changes in soil moisture resulting from alterations 

in the precipitation regime could significantly affect 

a variety of factors that regulate nutrient availability 

and loss (e.g., mineralization rates, leaching, soil 

redox, and diffusion). In tropical forest ecosystems, 

drought is likely to increase soil redox potential and 

thus favor aerobic processes such as nitrification 

and iron oxidation (Silver, Lugo, and Keller 1999; 

Schuur and Matson 2001). This, in turn, affects 

the availability of exchangeable phosphorus, as the 

binding of iron oxide compounds with phosphorus 

is affected by redox potential (Chacon et al. 2006; 

Liptzin and Silver 2009). In keeping with this 

theory, soil drying in a Puerto Rican forest led to a 

significant reduction in exchangeable phosphorus, 

although such a response was not seen at other sites 

with lower iron concentrations (Silver et al. 1994, 

1999; Chacon et al. 2006; Liptzin and Silver 2009). 

Evaluating the importance of iron-phosphorus 

dynamics may enable further insight into tropical 

soil responses to drought. Furthermore, competition between plants and microbes for nutrients is 

expected to be an important factor in understanding soil nutrient dynamics (Lodge, McDowell, and 

McSwiney 1994).

The effects of drought on nitrogen cycling also 

are poorly understood. Tropical forests on highly 

weathered soils tend to be nitrogen rich (Vitousek 

and Sanford 1986) and cycle nitrogen rapidly 

(Templer et al. 2008). Drought is likely to increase 

soil O2 availability and thus decrease denitrification 

potential. However, drought also could increase 

nitrification rates, providing more substrate for 

denitrification during rainy periods. Experimental 

drought in Puerto Rico significantly increased NH4+

concentrations in the exclusion plots of the valley 

site, decreasing the ratio of NO3–

 to NH4+. Changes 

in the proportion of different soil nitrogen pools 

have been shown to affect a variety of ecosystem 

processes, such as decomposition rates, plant cover, 

and ultimately carbon cycling (Austin, Sala, and 

Jackson 2006).
40 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Key Uncertainties and Research 

Opportunities

In contrast to the simple empirical drought functions of existing land surface schemes, numerous 

ecosystem-scale models now explicitly simulate plant 

hydraulics, including the transport of water from soil 

to leaves, leaf water status, and associated control on 

stomatal conductance and gas exchange. Such models 

have been tested against observations from droughtstressed forests in temperate, Arctic, and subtropical 

ecosystems with encouraging results, but estimates of 

the ecosystem properties needed to properly specify 

them are only sparsely known at larger scales. Thus, 

predictions of tropical forest response to moisture 

stress could be improved by addressing the following 

critical gaps in knowledge on plant and soil traits:

•	 How do soil, saprolite, and rock aquifer 

depths vary across tropical forests? The 

potential size of the water store available to plants 

during the dry season is a function of soil depth 

and the presence of deep saprolite and rock aquifers below soils. As discussed, depths of porous 

media vary widely across the Tropics and can be 

Table 5.1. Comparison of Tropical Forest Throughfall Exclusion Experimentsa

Forest Location

Annual 

Rainfall 

(mm)

Plot Size 

(No. Exp. 

Reps.)

Months 

of 

Exclusion

No. Year 

Repeated

CO2

Response

CH4 

Response

N2O 

Response Citation

Fazenda Vitoria, 

Brazil 1800 100 m2 (1) 12 4 −16% 171% −25% Cattânio et al. 2002

Tapajós National 

Forest, Brazil 2000 1 ha (1) 6 5 No effect −206% −33%

Davidson, Ishida, 

and Nepstad 

2004; Davidson 

et al. 2008

Caxiuanã National 

Forest, Brazil 2300b 1 ha (1) 24c 1 −26% NA NA Doff Sotta et al. 

2007

Caxiuanã National 

Forest, Brazil 2300b 1 ha (1) 48c 4 Weak 

effectd NA NA Metcalfe et al. 2007

Central Sulawesi, 

Indonesia 2900 0.16 ha (3) 12c 2

−23%e

−48%f NA NA

van Straaten, 

Veldkamp, and 

Corre 2011

LEF, Puerto Rico: 

Ridge 3500 1.54 m2 (5) 3 1 −19% No effect −1788% Wood and Silver 2012

LEF, Puerto Rico: 

Slope 3500 1.54 m2 (5) 3 1 −26% No effect No effect Wood and Silver 2012

LEF, Puerto Rico: 

Valley 3500 1.54 m2 (5) 3 1 No effect −480% −108% Wood and Silver 2012

Osa Peninsula, 

Costa Rica 5000 5.76 m2 (10) 12c 1 25% NA 35%

Cleveland et al. 

2010; Wieder, 

Cleveland, and 

Townsend 2011

[Modified from Wood, T. E., and W. L. Silver. 2012. “Strong Spatial 

Variability in Trace Gas Dynamics Following Experimental Drought in 

a Humid Tropical Forest, Global Biogeochemical Cycles 26, GB3005.]

a For comparison purposes, the responses reported in this table are 

the mean percent difference between control and exclusion plots over 

the entire study period (e.g., drought and nondrought).

b 2300 ± 200 mm.

c Partial throughfall exclusion experiment (e.g., 50%).

d When total soil respiration was partitioned, soil organic matter and 

litter respiration declined in response to drought and root respiration 

increased.

e 9 months of 50% exclusion.

f

15 months of 80% exclusion.
Research Priorities for Tropical Ecosystems Under Climate Change 41

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science

Responses to 

External Forcings

deep and challenging to observe. Currently, no 

reliable maps of these depths exist, either globally 

or across the Tropics.

•	 How do the hydraulic properties of soil, saprolite, and rock aquifers vary below tropical 

forests? Within deeper strata, the soil water and 

moisture available to plants varies by a factor of 

4 to 5. The quantity of water available to plants 

depends on both water retention properties and 

how hydraulic conductivity varies with capillary 

potential. These combined datasets are very rare 

(n ~5) for the tropical rainforest biome.

•	 How does root function vary among forests, 

and how does it affect drought tolerance? Root 

biomass profiles are poorly understood despite 

the increasingly frequent finding that soil-to-root 

and within-root transport are critical bottlenecks 

in plant water supply (Sperry et al. 2002; Fisher 

et al. 2007; Williams et al. 2001; Plaut et al. 2012). 

The number of complete root profiles in tropical 

forests is very low (<10), and no published data 

exist that include possible taproots below trees in 

tropical rainforests.

•	 How do plant hydraulic strategies with respect 

to drought vary across the Tropics? Some 

evidence from Amazonia suggests that trees have 

conservative stomatal closure mechanisms. Other 

studies indicate less stomatal control of leaf water 

potential at sites where the climate is less seasonal 

(Kumugai et al. 2004, 2008; Kumugai and Porporato 2012). Alternative hydraulic strategies might 

be adaptive responses to hydraulic and competitive environments in different rainforests.

•	 How does plant allocation of carbon and nutrients respond to drought stress? Evidence from 

throughfall manipulation experiments suggests 

no short-term change in photosynthetic capacity 

with drought in tropical forests (Fisher et al. 2007). 

However, other studies from more persistently 

drought-affected nontropical ecosystems have indicated seasonal changes in photosynthetic capacity 

(Keenan et al. 2009). Over the longer term, there 

is evidence that leaf dark respiration increases 

under extended drought (Metcalfe et al. 2010), 

in contrast to the respiration reductions more 

frequently observed coincident with short-term 

drought (Atkin and Macherel 2009). This topic 

of carbon acquisition, use, and storage is poorly 

understood and may be critically important for 

modeling the ecosystem-scale outcomes of leaf-, 

stem- or tree-level processes. Similarly, allocation 

to reproduction is highly variable; most plants 

forgo reproduction under unfavorable conditions 

and instead allocate resources to functions ensuring survival. Models failing to incorporate this 

well-known plant stress response will systematically predict forest-level responses to unfavorable 

conditions that are too strong.

•	 What is the dominant mechanism of plant 

death under sporadic severe drought events?

Obtaining such knowledge would enable 

improved predictions of how this mechanism 

might or might not be affected by changes in 

climate and atmospheric composition. This challenge must incorporate knowledge of the existing 

functional diversity of plant responses to drought 

(Engelbrecht et al. 2007), how this diversity is 

related to specific plant traits, and how it affects 

the resistance and resilience of tropical forest communities to drought.

•	 What are the mechanisms driving spatial and 

temporal variability in the production and 

emission of trace gases in response to reduced 

soil moisture?

•	 How does reduced soil moisture influence 

processes related to soil nutrient availability?

Studies are needed that explicitly evaluate specific mechanisms and potential controls across a 

diversity of forest types.
42 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 5 – Drought and Drought-Induced Mortality in Tropical Forests

DOE Office of Science
Natural Disturbance 

and Recovery

CHAPTER 6
44 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 6 – Natural Disturbance and Recovery

DOE Office of Science

Natural Disturbance and Recovery

One of the least understood aspects of climate 

change is its potential effect on natural disturbance regimes. This lack of understanding 

results in part from the unpredictable ways natural disturbance interacts with human land use (Drury and 

Nisbet 1973; Paine et al. 1998; Foster, Motzkin, and 

Slater 1998; Platt et al. 2002; Uriarte et al. 2009), yet 

individual disturbance events can dramatically affect 

carbon, water, and energy fluxes to the atmosphere. 

For instance, a strong, single storm can convert a 

large portion of forest carbon stocks to dead biomass 

(McNulty 2002; Chambers et al. 2007a; NegrónJuárez et al. 2010). More importantly, these individual 

events add up to determine regional- to continentalscale disturbance regimes whose changes can affect 

mass and energy fluxes to the atmosphere, potentially 

resulting in important feedback processes (Frolking 

et al. 2009). Establishing regional baselines for these 

regimes is critical to evaluate potential shifts in disturbance with a warming climate.

Disturbance Effects on Tropical 

Tree Mortality and Climate Change

“Natural” disturbances are events not directly linked 

to human activities such as logging and deforestation. In tropical forests, these include drought, 

storms (e.g., wind, lightning, and flooding), fire, and 

other processes (e.g., pest and pathogen outbreaks 

and monocarpy). Each of these disturbances can 

lead to tree death and may respond differently to a 

changing climate. Thus, distinguishing among these 

mortality processes in field studies and developing 

improved disturbance algorithms for terrestrial 

models are important.

The death of an individual tropical tree can be a slow 

process resulting from a combination of factors. 

For example, a tree can be snapped midtrunk in a 

windstorm, yet many tropical tree species survive by 

sprouting, enabling more rapid access to a canopy 

position. Trees can regrow lost branches and repair 

damaged crowns within relatively short time periods 

(Walker 1991; Ostertag, Silver, and Lugo 2005). 

However, a damaged stem also can be colonized by 

pathogenic microbes and wood-boring organisms, 

resulting in a compromised tree potentially more 

vulnerable to other factors such as drought and 

windthrow. At the other extreme, high winds from 

tropical cyclones (Canham et al. 2010; Lugo 2008; 

Zimmerman et al.1994) or blowdowns in the Amazon (Negrón-Juárez et al. 2010, 2011) can lead to 

rapid mortality over large areas. In addition, cohorts 

of wind-damaged trees can experience elevated 

mortality for many years after the event (Lugo and 

Scatena 1996; Walker 1991; Uriarte et al. 2009).

Many types of natural disturbance including fires, 

cyclonic storms, and floods are expected to increase 

with climate change, and shifts in land use throughout the Tropics probably will exacerbate these effects 

(Allen et al. 2010; Frolking et al. 2009; Dale et al. 

2001). Cyclonic storms (hurricanes, typhoons, and 

cyclones) represent the dominant natural disturbance in temperate and tropical forests in coastal 

regions of North, Central, and South America; the 

Indian subcontinent; localized parts of Southeast 

Asia and Africa; and northern Australia (Gray 1975; 

Boose, Foster, and Fluet 1994; Everham and Brokaw 

1996; Mabry et al. 1998; Platt et al. 2002; McNab, 

Greenberg, and Berg 2004). In the past decade, 

the frequency and intensity of hurricanes in the 

North Atlantic have increased twofold and fourfold, 

respectively (Webster et al. 2005; Emmanuel 2005; 

Goldenberg et al. 2001). Since hurricanes derive 

their energy from ocean heat, this increase in activity 

has generated much debate on the role that humandriven global climate change has played in recent 

storms. In addition to changes in tropical cyclones 

and similar to predictions for temperate regions, a 

general increase in storm intensity also is expected 

for the Tropics (Shepherd and Knutson 2007; IPCC 

2007). Moreover, changes in storm intensity can 

interact with changes in the atmospheric aerosol 

environment caused by, for example, biomass burning in the Tropics. Such interactions could further 

intensify storm systems and alter precipitation patterns (Andreae et al. 2004; Li et al. 2011).
Research Priorities for Tropical Ecosystems Under Climate Change 45

Chapter 6 – Natural Disturbance and Recovery

DOE Office of Science

Responses to 

External Forcings

Increases in the frequency of extreme precipitation 

events coupled with deforestation also may amplify 

flood risk globally (Bradshaw et al. 2007; Bruijnzeel 

1990, 2004). The anoxic conditions created by floods 

not only can kill trees but also increase emissions 

of trace gases, including methane, in flooded areas 

(Hess et al. 2003; Melack et al. 2004). A considerable 

body of literature is devoted to the development of 

complex, catchment-specific models to predict the 

temporal frequency of floods (Cameron, Beven, and 

Naden 2000; Arnaud and Lavabre 2002; Cunderlik 

and Burn 2002; Prudhomme, Reynard, and Crooks 

2002). However, no attempts have been made to predict (1) flood frequency over broader spatial scales, 

(2) the influence of climate change on flood intensity 

and frequency, and (3) the effects of these changes on 

ecosystem fluxes and forest-atmosphere interactions.

Incorporating the vulnerability of tropical forests 

to shifts in disturbance regimes and the subsequent 

recovery of these ecosystems following disturbance 

requires the robust characterization of current disturbance regimes and a greater understanding of 

individual species responses. Tree species differ in 

their susceptibility to disturbance of varying intensities and in the nature of the damage they sustain 

from a given disturbance event. Their recovery also 

varies, at both the individual plant level through 

repair of damage and at the population level through 

reproduction, seedling establishment, and juvenile 

response to changes in resource conditions that typically follow disturbance events (Glitzenstein and 

Harcombe 1988; Peterson and Pickett 1991; You 

and Petty 1991; Walker 1991; Boucher et al. 1994; 

Zimmerman et al. 1994; Peterson and Rebertus 

1997; Cooper-Ellis et al. 1999). For instance, hurricanes tend to damage larger, slower-growing trees, 

so short-term productivity may increase as a result 

(Sanford et al. 1991). However, higher-production 

ecosystems do not necessarily store more carbon, 

and the loss of massive trees can shift ecosystems 

to lower biomass states as dead trees decompose. 

In an Amazon forest, 50% of the aboveground biomass was contained in 3% of the trees (Brown et 

al. 1995), and large Amazon trees can live for many 

hundreds of years (Chambers, Higuchi, and Schimel 

1998). Understanding the relative importance of 

these seemingly countervailing effects on long-term 

changes in forest composition and ecosystem fluxes 

requires the use of models. These models should 

be specifically designed to incorporate disturbance 

effects on the basic demographic processes (e.g., 

recruitment, growth, and mortality) that regulate forest community dynamics and the feedbacks between 

these changes and ecosystem processes.

Drought

The physiology of drought-induced mortality is 

described in more detail in Chapter 5, p. 33. To 

briefly summarize in the context of disturbance, little 

is known about the differential sensitivity of tropical 

forests to drought. In the Amazon, for example, forests span a broad range in precipitation seasonality, 

from those with a wet perhumid climate to others 

experiencing up to 4 to 5 months of drought (e.g., 

<100 m/month) while maintaining a closed canopy 

and high biomass density (Sombroek 2001). Another 

important feature of forest sensitivity to drought is 

water table depth. Amazon forests on white sand 

soils can vary, ranging from tall closed-canopy forests 

when the saturated zone is shallow to “campinaranas” 

(“caatinga” and “heath forests”) when the water table 

occurs at depth (Anderson 1981; Jordan 1985). Tall 

forests on white sand soils with shallow water tables 

may be particularly vulnerable to intense droughts 

that substantially lower the depth of the saturation 

zone. Overall, more research is needed to determine 

regional variability and tree mortality patterns associated with drought.

Drought also interacts with other modes of disturbance. For example, increasing numbers of standing 

dead trees eventually will topple during a subsequent 

event such as a storm. Moreover, standing dead trees 

decay more slowly than downed trees (Chambers 

et al. 2000), so the carbon fluxes to the atmosphere 

from drought-induced mortality may be delayed from 

mortality processes that transfer biomass to the forest 

floor. Standing dead trees represent a global process 

because they also are caused by insect outbreaks 

and drought in temperate forests and thus should be 

treated explicitly in terrestrial models that currently 

lack this mechanism.

Storms

Storm-induced mortality from wind, lightning, or 

flooding is one of the primary agents of disturbance 
46 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 6 – Natural Disturbance and Recovery

DOE Office of Science

in tropical forests. Wind and lightning result in 

uprooted, snapped, and shattered trees that may 

survive by sprouting. However, a tree snapped below 

the diameter measurement height (generally 1.3 m 

or above buttresses) that sprouts is still considered 

part of the mortality flux, and this nonlethal damage also results in significant transfer of biomass 

from live to dead carbon pools. Thus for terrestrial 

and Earth system models (ESMs), the combined 

disturbance flux from both mortality and damage is 

important to quantify.

Some studies, including ones in the Amazon and 

Puerto Rico, partition mortality into different modes 

(e.g., standing, uprooted, and snapped), which 

can be valuable in assigning causal agents of death 

(Uriarte et al. 2009; Chambers et al. 2000; Chao et 

al. 2009; Toledo 2002; Fontes 2012). For example, 

wind disturbance causes uprooted and snapped trees, 

whereas drought generally results in standing dead 

trees that can subsequently topple or snap. Individual 

variation in mortality damage is a function of species 

identity, tree size, and storm severity (Uriarte et al. 

2009). Overall, there are too few studies to draw generalizations useful for model development, and more 

field studies are needed on the agents and modes of 

mortality and their variation among tropical forests 

at a global scale. Downscaling natural disturbance in 

models to scales relevant to field observations of tree 

mortality also is a critical need.

Three studies of tree mortality in Central Amazon 

forests north of Manaus, Brazil, demonstrate some 

of these contrasting results. In 2011, a study from 

Brazil’s National Institute for Amazonian Research 

(INPA) examined agents of mortality with detailed 

field studies in two 5-hectare (ha) permanent plots, 

alternating monthly for a year (Fontes 2012). This 

study included six mortality classes and recognized 

both direct storm effects (e.g., wind and lightning), 

which accounted for 49% of tree mortality, and 

indirect effects (e.g., wind-damaged trees that eventually succumbed and senescing weakened trees that 

were windthrown), which represented 19%. The 

remaining deaths were attributed to direct effects of 

stress (e.g., standing dead trees from drought, flooding, and competition), which accounted for 30% of 

mortality, and other factors (2%). In contrast to the 

short-duration, detailed studies of Fontes (2012), 

research by Toledo (2002) found standing death was 

the predominant mode of mortality (54%) followed 

by snapping (26%) and uprooting (14%) for 72 1-ha 

permanent plots recensused twice (from 2003 to 2005 

and 2005 to 2008). Chambers et al. (2000) assessed 

18 ha of permanent plots monitored over an ~6-year 

period and found that wind disturbance (snapped and 

uprooted) was the dominant mode (54%) followed by 

treefalls (33%) and standing dead (13%). These studies illustrate the difficulties in determining regional 

disturbance patterns and their variation from year to 

year in association with changing environmental factors. To develop causal relationships among climate 

change variables and tree mortality, additional detailed 

mortality studies with high temporal resolution (at 

intervals of 1 year or less) are needed for tropical forests and should be considered a research priority.

Distinguishing among mortality agents at regional 

scales also is difficult in tropical forests (see Fig. 

6.1, this page). For example, Phillips et al. (2009) 

found an increase in Amazon mortality rates in 

Fig. 6.1. Distribution of IntermediateSize Tree Mortality Disturbance 

Events in Central Amazon North of 

Manaus, Brazil. [From Chambers, J. Q., et al. 

2009. “Lack of Intermediate-Scale Disturbance 

Data Prevents Robust Extrapolation of Plot-Level 

Tree Mortality Rates for Old-Growth Tropical 

Forests,” Ecology Letters 12(12), E22–25.]
Research Priorities for Tropical Ecosystems Under Climate Change 47

Chapter 6 – Natural Disturbance and Recovery

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Responses to 

External Forcings

2005 associated with a large basin-wide drought. 

However, some Amazon sites such as Manaus did 

not experience severe drought during this period, 

and Negrón-Juárez et al. (2010) demonstrated that 

a powerful squall line in 2005 also caused basinwide tree mortality that was particularly acute in 

the Manaus region. Detailed tree mortality studies 

would be useful for distinguishing among agents and 

would enable development of more mechanistic tree 

mortality algorithms for terrestrial ecosystem models. Additional measurements on modes and agents 

of mortality could be added to existing tropical plot 

networks to facilitate developing these disturbance 

baselines and could be coupled with remote sensing 

to scale from plots to regions.

Fire

Fire Disturbance and Tropical Forest Boundaries

Savanna and forest differ vastly in terms of biomass, 

flammability, and ecosystem fluxes, so climate-driven 

switches between these biomes have broad consequences for the Earth system. The structure, dynamics, and location of the savanna-forest boundary are 

emergent properties arising from the counteracting 

effects of fire and tree growth (Hoffmann et al. 2012), 

both of which are highly sensitive to climate. These 

opposing processes, combined with strong feedbacks between vegetation and flammability, result in 

complex dynamics (Beckage, Platt, and Gross 2009; 

Staver et al. 2011) that pose an ultimate test of the 

ability of ESMs to integrate physics and biology.

The savanna-forest boundary represents the natural 

limit of distribution of tropical forests and therefore 

offers a unique opportunity to understand how these 

forests will respond to changing climate and disturbance regimes. Fire and acute drought, two primary 

factors that threaten tropical forests under climate 

change, have acted for millennia at natural savannaforest boundaries. These factors can serve as model 

systems for obtaining a mechanistic understanding of 

climate change effects in tropical forests while allowing quantification of the long-term consequences of 

forest loss on ecosystem stocks and fluxes.

The extent of forest is particularly sensitive to any factor that influences ecosystem productivity (Lehmann 

et al. 2011) because of the importance of tree growth 

rates for determining ecosystem recovery between 

fires (Hoffmann et al. 2012). Post-fire recovery of 

resprouting trees is strongly sensitive to CO2 (Hoffmann et al. 2000; Kgope, Bond, and Midgley 2010), 

so forest margins should be more responsive to 

increasing CO2 than intact forests (Bond and Midgley 2012; Higgins and Scheiter 2012).

Fires and Anthropogenic Disturbance

The incidence of fires in many tropical regions has 

increased steeply (Sanford et al. 1985; Hammond 

et al. 2007; Cochrane 2003). Research has focused 

on causal or exacerbating physical factors such as 

drought (Mueller-Dombois 1981; Woods 1989; 

Setzer and Pereira 1991; Nepstad et al. 2004), 

including “deforestation-induced drought” (Nepstad 

et al. 2007), and also has emphasized the increased 

flammability of forests due to timber extraction 

(Verissimo et al. 1995; Uhl and Kauffman 1990; 

Holdsworth and Uhl 1997; Cochrane 2003) and 

repeated burning (Cochrane et al.1999; Nepstad 

et al. 1999; Uhl and Kauffman 1990). Increased 

agricultural use, whether large or small in scale, often 

results in more frequent use of fire, the planting or 

invasion of more flammable vegetation including 

grasses, creation of more fire-susceptible forest fragments and edges, and increased quantities of highly 

flammable woody debris (Cochrane and Schulze 

1999). The reduction of total regional rainfall, combined with large-scale deforestation and declines in 

evapotranspiration, also increases the probability 

of future drought. This effect suggests that positive feedbacks link deforestation, droughts, and 

fires with forest destruction, leading to decreased 

rainfall, increased probability of escaped fires, and 

yet more deforestation (Malhi et al. 2008; Baidya 

Roy and Avissar 2002; Oyama and Nobre 2003; 

Bala et al. 2007; Andreae et al. 2004; Nepstad et al. 

2007; Laurance and Williamson 2001; Hoffmann, 

Schroeder, and Jackson 2002). Beyond Amazonia, 

the conflagration of severe El Niño–Southern 

Oscillation events, road building, changes in the 

types and scales of land use, and increasing landscape fragmentation is expected to lead to pantropical increases in fire activity (Nepstad et al. 2001; 

Cochrane 2003; Cochrane and Laurance 2008).
48 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 6 – Natural Disturbance and Recovery

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Disturbance and Landscape 

Carbon Balance

Landscape carbon balance is estimated by summing 

tree recruitment and growth in permanent forest 

plots and subtracting mortality from the total 

(Baker et al. 2004; Phillips et al. 1998). A number 

of potential complicating factors emerge in making 

this calculation (Davidson et al. 2012; J. I. Fisher 

et al. 2008; Wright 2005), and accounting for 

spatially and temporally aggregated mortality losses 

from disturbance events is particularly challenging 

(Körner 2003). Additional remote-sensing studies 

are needed to augment plot-based approaches that 

account for mortality events with return frequencies 

> ~50 years (Chambers et al. 2009). Comprehensive 

landscape-scale carbon balance studies will be 

particularly useful in addressing regional variability in 

net biomass accumulation and in providing improved 

estimates of tropical forest carbon sinks that may be 

driven by carbon dioxide (CO2) fertilization.

Tropical forest plot-based studies aggregated at 

continental to global scales indicate an old-growth 

tropical forest carbon sink of ~0.5 Mg C ha–1 yr–1, or 

a global sink of ~1.3 Pg C yr–1 (Lewis et al. 2009a). 

Using a similar approach, Chave et al. (2008) studied 

ten larger globally distributed plots (16 to 52 ha 

each) and found a net sink of 0.24 Mg C ha–1 yr–1, or 

about half of that estimated from a network of smaller 

plots. These studies were focused on quantifying 

continental- to global-scale sink estimates, and efforts 

to determine the magnitude of the net forest carbon 

sink at individual sites using plot-based approaches 

are lacking. Studies to determine the strength of the 

tropical forest carbon sink as a function of factors 

such as soil fertility are needed to develop improved 

terrestrial models.

Also important to consider is that a net increase 

in biomass can occur from an increase in both tree 

recruitment and growth rates. However, since the 

biomass of a new 10 cm tree is less than ~48 kg, 

shifts in recruitment rates must lead to changes in 

stem density and size structure to result in significant 

changes in biomass. To more directly address the 

issue of the CO2 fertilization of productivity in tropical forests, increases in biomass caused by changes 

in recruitment and stand structure should be 

distinguished from biomass increases resulting from 

elevated growth rates. Feeley et al. (2007) examined 

tropical tree growth rates in two large (50-ha) forest 

dynamics plots in Panama and Malaysia and found 

that stem growth rates declined significantly for both 

forests, with growth rates negatively correlated with 

mean annual daily minimum temperature. Additional studies on tropical tree growth rates would 

help shed light on the CO2 fertilization hypothesis 

for old-growth forests.

Another complicating factor in addressing the oldgrowth tropical forest carbon sink is the observed 

increase in forest turnover (average of recruitment 

and mortality) rates (Phillips et al. 2004; Phillips 

and Gentry 1994). An increase in mortality rates 

will drive forest biomass lower, so simultaneous 

increases in biomass and mortality rates must be 

compensated by an even greater increase in growth 

rates (Chambers et al. 2004a) or recruitment rates 

and forest structure. To elucidate these complex 

interactions and develop an improved mechanistic 

understanding of the underlying processes, 

recruitment rates should be studied independently 

of mortality rates.

Tree Mortality in Terrestrial 

Ecosystem Models

Representation of Fire Disturbance in ESMs

There has been a proliferation of fire models in ESMs 

in recent years, reflecting an increased interest in 

feedbacks in the climate system. However, many of 

these models have very similar theoretical bases and 

thus have converged on comparable operating principles. For example, ignition sources and moisture conditions determine the number of fires simulated by 

the models. The rate of spread and area of elliptically 

shaped fires are determined using algorithms based 

on fire-service statistics from either the United States 

(Rothermel 1972), in the case of the SPITFIRE 

family of models (Thonicke et al. 2010; Lehsten et 

al. 2009), or Canada (van Wagner and Pickett 1985), 

in the case of the CTEM-derived family of models 

(Arora and Boer 2005; Kloster et al. 2010, 2011; 

Li, Zeng, and Levis 2012). Litter quality, humidity, 

and wind speed are typically the drivers of fire size. 
Research Priorities for Tropical Ecosystems Under Climate Change 49

Chapter 6 – Natural Disturbance and Recovery

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Responses to 

External Forcings

Neither of these baseline datasets is from the Tropics, 

so applicability to these ecosystems is seldom validated. One particular problem in these models is the 

assumption of homogeneous vegetated surfaces that 

include no element of landscape-level impedance 

to fire spread, which likely will be important both 

at natural forest boundaries and in deforestationdominated frontiers.

To predict fire effects on natural vegetation, capturing 

the variability in fire tolerance of different vegetation 

types is highly important. Differences in plant functional type (PFT) tolerances are represented in some 

models such as SPITFIRE and a dynamic global 

vegetation model (DGVM; Scheiter et al. 2012), 

but the resolution of such representations remains 

low. This situation could be improved by modeling 

studies that include higher-resolution representations of observed functional trade-offs between, for 

example, growth rates and bark thickness or resprouting capacity (Hoffmann et al. 2012). In addition to 

this challenge, no ESMs take into account other types 

of disturbance such as windstorms, floods, or pest 

outbreaks, all of which may be critical to understanding ecosystem fluxes in the Tropics. However, work in 

these areas is ongoing.

Representation of Post-Disturbance 

Succession, Regrowth, and 

Competition in ESMs

Traditional DGVMs typically represent portions of 

the land surface as tiles of continuous PFTs (e.g., LPJ; 

Sitch et al. 2001). Although this approach can simulate recovery after disturbance (Shevliakova et al. 

2009), representing shifts in community composition 

that arise from changing conditions across successional gradients is not possible using the traditional 

methodology. Second-generation DGVMs are being 

developed that can simulate horizontal heterogeneity in light availability using either the individualbased and stochastic “gap model” approach (Smith, 

Prentice, and Sykes 2001; Sato, Itoh, and Kohyama 

2007; Scheiter and Higgins 2008) or a statistically 

aggregated approach, typified by the Ecosystem 

Demography model (Moorcroft, Hurtt, and Pacala 

2001; Fisher et al. 2010). Both approaches enable the 

representation of succession, competition for light, 

multiple height classes, and potential coexistence of 

plant types at all phases of succession. This is a very 

active area of research, and many challenges remain, 

particularly in representing existing theories of vegetation competition, distribution, and coexistence in 

a quantitative manner. Clearly, the existing representation of tropical diversity in ESMs is insufficient and 

often consists of only one plant type to represent all 

tropical forest species. The next generation of models 

needs to represent at least the major axes of plant 

variation, especially with respect to plant responses 

to the major forcings discussed in this report. Empirically quantifying the basic trade-offs in plant form 

and function (e.g., Markesteijn et al. 2011; Baraloto 

et al. 2010; Paine et al. 2011) is particularly useful 

for generating hypotheses of vegetation distribution 

(which currently are mostly verbal arguments that 

have not been quantitatively tested) and should be 

considered a high priority for future efforts.

Disturbance Research Themes 

Relevant to ESMs

Four model developments are critical for representing disturbances in tropical landscapes and their 

influence on Earth system processes:

•	 Robust characterization of disturbance 

regimes, differing agents and modes of tree 

mortality across the Tropics, and their interactions with climate change. This will require 

understanding the frequency distribution of disturbance events of differing intensities (possibly 

using spatial extent as a proxy). Also needed is an 

understanding of return intervals for mortality 

events driven by different processes (e.g., drought, 

fire, and storms) and how these might shift with a 

changing atmosphere and warming climate.

•	 Improved representation of the diversity of 

species’ responses to disturbance. The range 

of PFTs currently in models does not adequately 

capture this diversity. Tree species differ in their 

susceptibility to disturbance of different types 

and intensities, the nature of the damage they 

sustain from a given disturbance event, and community recovery from disturbance. Understanding the links between tree community assembly 

processes and the trajectory of ecosystem fluxes 

remains a challenge.
50 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 6 – Natural Disturbance and Recovery

DOE Office of Science

•	 A better understanding of how landscape 

configuration (i.e., the distribution and size 

of different land cover types) influences the 

susceptibility of forests to fire and wind disturbance. Increased agricultural use and fragmentation often result in more frequent disturbance, a 

greater abundance of invasive species, creation of 

more disturbance-susceptible forest fragments and 

edges (Cochrane and Schulze 1999; Laurance et al. 

2002), and altered feedbacks to the atmosphere.

•	 Greater insight into how disturbance intensity 

interacts with soil fertility, precipitation, and 

rising atmospheric CO2 concentration to influence succession rates, shifts in species composition, and biomass recovery (Chazdon 2003; 

Zarin et al. 2005; Crk et al. 2009; Lawrence et al. 

2010; Aide et al. 2012; Poorter and Navas 2003).

Key Uncertainties and Research 

Opportunities

Three key uncertainties in the response of natural disturbance to climate change in tropical forests are:

•	 What are the biomass loss fluxes from tree 

mortality and damage? Addressing this question 

is critical for generating robust landscape-scale 

carbon balance estimates and determining the 

magnitude of the terrestrial carbon sink attributed 

to old-growth tropical forests. These insights in 

turn will improve the understanding of how forestatmosphere CO2 exchange may shift with a warming climate.

•	 How will natural disturbance processes 

change with a warming climate? Climate 

change predictions for the Tropics include the 

potential for increased incidence of regional 

drought, intensification of storm systems, and elevated temperature effects on tree ecophysiology. 

Each of these can result in elevated disturbance 

regimes and higher tree mortality rates that in 

turn can affect the forest-atmosphere exchange of 

CO2, moisture, and energy.

•	 How will atmospheric and climate change 

affect the successional trajectory following 

tree mortality disturbance? Biomass recovery 

rates and associated changes in species composition in tropical forests depend on the size and 

severity of disturbance, distribution of disturbed 

patches over the landscape, interval between 

subsequent disturbance events, and environmental constraints (Uriarte and Papaik 2007; 

Sousa 1984). The recovery pathway also will be 

influenced by competitive interactions among 

individual trees and how these interactions vary 

with increasing atmospheric CO2, changing precipitation regimes, and elevated temperature from 

a warming climate.
Anthropogenic Disturbance 

and Land Use

CHAPTER 7
Anthropogenic Disturbance and Land Use

Human Land Use and Forest 

Regeneration

Human land use can have direct and indirect 

effects on nutrient and energy fluxes to the 

atmosphere. For example, deforestation is 

the second largest anthropogenic source of carbon 

dioxide (CO2) emitted to the atmosphere, after fossil fuel combustion (van der Werf et al. 2009). This 

contribution is fairly well characterized, accounting 

for 12% of carbon emissions. Of these emissions, 

about half are attributed to forest fire, and the largest proportion come from the Tropics. Brazil alone 

accounts for an annual release of 0.28 (0.17 to 0.49) 

Pg of carbon to the atmosphere, representing 24% of 

the world’s carbon emissions from land cover change 

[1.15 (0.58 to 1.79) Pg of carbon per year].

Despite the strong focus of Earth systems research 

on emissions from deforestation and degradation of 

primary forests, most tropical landscapes are mosaics 

of forest, agricultural lands, and successional forest 

patches undergoing natural regeneration following 

abandonment from diverse land uses (Chazdon 

2003; Grau et al. 2003; Asner et al. 2009). Primary 

or old-growth forests represent less than 25% of the 

total area of tropical forests worldwide (FAO 2010). 

A significant fraction of the tropical forest cover lies 

in areas recovering from logging or in secondary 

forests and land abandoned from agriculture. Much 

remains to be learned about the processes involved in 

forest regeneration, their response to global change, 

and their ability to mitigate species loss and carbon 

emissions resulting from deforestation. Global 

estimates of the cover of regenerating forests and 

of “committed forest regrowth” are inaccurate and 

imprecise (Asner et al. 2009). All three aspects of forest attributes—biodiversity, structure, and ecosystem 

functions—change during forest regeneration but at 

different rates. Changes in species composition, vegetation structure, and biomass accumulation following 

land abandonment or large-scale natural disturbances 

are intricately linked and govern the recovery of 

carbon and nutrient stocks above- and belowground 

during secondary succession. Structure and ecosystem functions appear to recover more quickly than 

species composition (Chazdon et al. 2007). Although 

these coordinated changes are poorly understood, 

current knowledge suggests a high degree of functional redundancy of tree species in tropical forests 

(Chazdon and Arroyo-Mora, in press). During forest regeneration, the number of species in different 

functional groups of trees changes, but the number 

of functional groups remains constant (Zhang, Zang, 

and Qi 2008; Chazdon et al. 2010). Links between 

species composition and ecosystem processes in 

regenerating tropical forests are poorly understood.

Despite the high degree of uncertainty in estimating 

carbon sinks and rates of deforestation (Ramankutty 

et al. 2007), regenerating forests in the Tropics 

unquestionably are major sinks for carbon (Yang, 

Richardson, and Jain 2010). The carbon sink in 

regrowth forests varies considerably across tropical 

regions. Since 1990, the greatest increase in carbon 

stocks has been in the Americas, followed by Asia, 

and then Africa (Pan et al. 2011). However, the 

high potential for carbon sequestration in regenerating forests is not even close to being achieved on a 

global scale for two major reasons. First, regrowth 

vegetation in the Tropics is being recleared at high 

rates (Chazdon et al. 2009). Second, intensification 

of land use, reduction of fallow cycles, and multiple 

cycles of forest clearing and burning can arrest succession because degraded soils cannot support vegetation without management interventions (Chazdon 

2003; Zarin et al. 2005; Lawrence et al. 2010). 

These factors, should they become significant, could 

reduce future carbon storage in the Tropics. In addition to these anthropogenic disturbances, the effects 

of global climate change on tropical forests are major 

concerns. Growth and survival of trees in moist 

tropical second-growth forests are highly sensitive to 

seasonal drought conditions, particularly the severity 

of the relatively short dry season (Chazdon, Brenes, 

and Alvarado 2005). For example, severe drought in 

the Amazon in 2005 (Phillips et al. 2009) reduced 

the estimated decadal carbon sinks in the Tropics by 

15% (Pan et al. 2011).

52 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 7 – Anthropogenic Disturbance and Land Use

DOE Office of Science
Biomass estimation (and thus estimation of carbon 

in vegetation) is an imprecise science because robust 

data on allometric relationships are available for only 

a few vegetation zones and assemblages. Biomass 

estimation of second-growth forests in Rondonia, 

Brazil (Alves et al. 1997) and northeastern Costa 

Rica (Letcher and Chazdon 2009) varied substantially when different allometric equations were 

used. Species differences in specific wood gravity, 

tree height:diameter allometry, and tree damage are 

significant sources of error that have not been carefully assessed in most tropical forests. Estimates of 

carbon accumulation rates during forest regrowth 

therefore should be scrutinized carefully because 

many of these sources of error can lead to inaccurate 

estimates (Kauffman, Hughes, and Heider 2009; 

Nelson et al. 1999).

Tropical forests amass much more than carbon as 

they regenerate. They also accumulate nitrogen, 

phosphorus, calcium, and other nutrients in foliage, 

stems, branches, and roots and recycle these nutrients in litter and dead plant matter. Aboveground 

pools of nutrients were restored rapidly during the 

first 14 years of regrowth on abandoned pastures in 

Central Amazonia, with the bulk of nutrients stored 

in wood tissue (Feldpausch et al. 2004). Increased 

soil organic matter enhances soil fertility and waterholding capacity. Regrowth forests also pump water 

from soils into the atmosphere, influencing local 

rainfall and regulating flows within watersheds. In 

addition, these forests increase in height and structural complexity, creating arrays of microenvironments in the understory and canopy. Many of these 

ecosystem processes occur in actively restored tropical forests (Paul et al. 2010). During forest regeneration, nutrient limitations may shift seasonally, 

spatially, and temporally (Townsend et al. 2011). 

For example, in Amazonian forests, decreasing foliar 

concentrations of phosphorus with increasing forest 

age suggest that phosphorus becomes more limiting 

later in succession (Feldpausch et al. 2004; Davidson 

et al. 2007), although luxury consumption (Chapin 

1980; Attiwill and Leeper 1987) during early developmental stages may reduce soil nutrient requirements for mature trees.

Representation of Land-Use 

Processes in Earth System Models

The representation of land-use change in ESMs, 

such as the Community Land Model version 4 

(CLM4), remains rather limited. For instance, CLM4 

relies on harmonized land-use datasets (Hurtt et al. 

2006) to divide land surface into different land uses. 

Transitions between the different classes depend on 

potential vegetation and current CLM land surface 

parameters. Vegetation is further subdivided into 

crop, pasture, primary vegetation, and secondary vegetation land units (Bonan and Levis 2006; 

Oleson et al. 2010). The current dataset is based on 

the methodology of Lawrence and Chase (2007) 

and uses a variety of satellite products to develop 

present-day plant functional type (PFT) distributions with matching leaf area index values. The 

dataset initially derives fractions of bare ground and 

forest land cover from the Moderate Resolution 

Imaging Spectroradiometer (MODIS) continuous 

vegetation fields (Hansen et al. 2003). To further 

distinguish tree types, the tree fraction is divided into 

broadleaf or needleleaf and evergreen or deciduous 

types based on the Advanced Very High Resolution 

Radiometer (AVHRR) continuous fields tree cover 

(DeFries, Hansen, and Townsend 2000). The Hurtt 

et al. (2006) dataset is the de facto standard for ESM 

historical simulations (e.g., Shevliakova et al. 2009), 

but future land-use trajectories depend on the output 

of integrated assessment modeling efforts (Lawrence 

et al. 2012) that are highly uncertain.

Key Uncertainties and Research 

Opportunities

Addressing three significant research gaps is particularly important for representing forest succession in 

tropical landscapes and effects on Earth system processes. First, the range of PFTs currently in models 

does not capture the successional diversity of tropical forests, especially among shade-tolerant species. 

Although important for characterizing successional 

dynamics, species differences are significant sources 

of error in estimates of ecosystem fluxes and have 

not been carefully assessed in most tropical forests. Secondly, succession at the landscape scale 

Research Priorities for Tropical Ecosystems Under Climate Change 53

Chapter 7 – Anthropogenic Disturbance and Land Use

DOE Office of Science

Responses to 

External Forcings
occurs much faster in the Tropics than in temperate 

zones. Landscape configuration (i.e., the distribution and size of different land cover types) around 

individual landscape patches (i.e., cell grids) is an 

important predictor of succession rates (Crk et al. 

2009; Galanes and Thomlinson 2009). Finally, the 

intensity of land use interacts with soil fertility and 

precipitation to influence the rates of succession 

and biomass recovery (Chazdon 2003; Zarin et al. 

2005; Crk et al. 2009; Lawrence et al. 2010; Aide 

et al. 2012). Intensification of land use, reduction 

of fallow cycles, and multiple cycles of forest clearing and burning can prevent forest regeneration in 

degraded areas (Chazdon 2003; Zarin et al. 2005; 

Lawrence et al. 2010). Such factors thus will significantly reduce future carbon storage in the Tropics. 

Based on these three areas, key research gaps and 

uncertainties include:

•	 How does functional diversity in species 

composition influence forest regeneration 

processes in the Tropics? The ability to predict 

tropical forest and biomass recovery from natural 

disturbance and human land use will depend on 

plant functional type characterizations that accurately capture the successional diversity of tropical 

forests, especially among shade-tolerant species. 

Studies should examine species differences in specific wood gravity, tree height:diameter allometry, 

and hydraulic properties and focus on scaling up 

the effects of plant functional traits to the community and ecosystem levels.

•	 What are the links between functional 

diversity through succession and important 

climate parameters such as vulnerability to 

drought? Significant portions of tropical forests 

are recovering from some type of human activity. Understanding how species functional traits 

that determine vulnerability to drought change 

through succession is critical to predicting how 

recovering forests will respond to shifts in drought 

frequency and intensity.

•	 How do landscape- and stand-level processes 

interact to affect succession rates? The tempo 

and mode of stand-level successional dynamics are 

strongly affected by features of the surrounding 

landscape, including the composition and spatial 

configuration of habitat types and land-cover 

classes. Studies should examine how landscape 

characteristics influence rates of succession and 

biomass accumulation.

•	 How does biomass recovery and carbon storage resulting from succession vary with landuse intensity? Human land-use legacies greatly 

influence the ecosystem properties of successional 

forests. Carbon and nitrogen stocks, as well as 

the ability of successional forests to accumulate 

biomass, strongly decline as the duration, intensity, and frequency of prior agricultural land use 

increase. Understanding how these land-use legacies influence rates of succession processes and 

biomass accumulation is a critical research need.

54 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 7 – Anthropogenic Disturbance and Land Use

DOE Office of Science
Biosphere-Atmosphere 

Interactions: Greenhouse 

Gases, Reactive Chemicals, 

and Aerosols 

CHAPTER 8
Biosphere-Atmosphere Interactions: Greenhouse 

Gases, Reactive Chemicals, and Aerosols

Overview

Exchanges of mass and energy between tropical forests and the atmosphere are critical to 

the control of the Earth system. Among these 

exchanges, water and carbon dioxide (CO2) are the 

most significant and most studied. The release and 

uptake of greenhouse gases, reactive chemical compounds, and particles also are critically important for 

Earth system models (ESMs) due to the strong direct 

and indirect effects of these species on atmospheric 

chemistry, atmospheric radiation budgets, cloud 

processes, and precipitation. Atmospheric composition and energy fluxes in turn regulate tropical forest 

metabolism, creating a closely coupled, strong feedback system. For example, clouds and aerosols modulate the fluxes and direct:diffuse ratio of radiation 

received by the ecosystem. Aerosols derived from 

both the forest and biomass fires help control cloud 

lifetimes, droplet numbers, and convection. Several 

studies have suggested that human-caused changes in 

aerosol amounts and chemical properties in Amazonia can affect dry season length, rainfall amounts, and 

convective properties of clouds, with climate effects 

on regional and global scales.

This chapter will identify some critical science questions concerning biosphere-atmosphere exchanges 

(see Fig. 8.1, this page, for key features). First, the 

fluxes of gaseous compounds between the forest 

and atmosphere are discussed, focusing on the most 

important non-CO2 greenhouse gases: nitrous oxide 

(N2O) and methane (CH4). Next examined are 

biogenic volatile organic compounds (BVOCs) and 

NOx radicals that participate in chemical reactions 

regulating atmospheric oxidative capacity, controlling atmospheric ozone (O3) concentration, and 

generating secondary organic aerosols (SOA). The 

forest not only is a source of changes, it is a recipient 

as well. For example, land-use change, industrialization, and urbanization lead to increasing production 

of O3, whose negative effects on trees in temperate 

forests are well known but essentially unstudied 

in the Tropics. Also discussed in this chapter are 

atmospheric particles and aerosols, including both 

primary particles and SOA.

Fig. 8.1. Interactions 

Between Tropical Forest 

Ecosystems and the Global 

Atmosphere. This schematic 

emphasizes non-CO2 greenhouse 

gases, reactive hydrocarbons, NOx, 

O3, and aerosols.

56 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 8 – Biosphere-Atmosphere Interactions: Greenhouse Gases, Reactive Chemicals, and Aerosols

DOE Office of Science
Exchange of Gaseous Compounds 

with Tropical Forests

“People look at a tree and they think that it comes 

out of the ground ... but trees come out of the air.” 

— Richard Feynman

Tropical forests play a critical role in controlling 

the emission of two key greenhouse gases: N2O 

and CH4. They also influence exchanges of organic 

compounds including isoprene, monoterpenes, 

sesquiterpenes, and a wide range of oxygenated 

compounds collectively known as BVOCs. These 

oxygenated compounds influence climate indirectly 

through atmospheric chemical reactions that can 

generate or remove O3 or consume hydroxyl radical 

(OH). Hydroxyl is a main sink for CH4, and its atmospheric distribution determines the lifetime, and thus 

potency, of this greenhouse gas. BVOCs also may 

condense or react to form SOA, as discussed in the 

aerosols section on p. 59.

Direct Exchange of Greenhouse Gases

Nitrogen Oxides

Globally, humid tropical forests are the largest 

sources of N2O, a gas with strong radiative forcing 

(Zhuang, Lu, and Chen 2012; Bouwman et al. 1993). 

A recent estimate found that evergreen broadleaf 

forests and woody savannas emitted over 1.6 Tg of 

N2O-N in 2000, the vast majority of which comes 

from the Tropics. This amount equals the sum of all 

other cover types combined (Zhuang, Lu, and Chen 

2012). Warm and moist conditions, along with large 

ecosystem fluxes of organic and inorganic nitrogen, 

optimally position tropical forest soils to produce 

N2O (Davidson et al. 2000b). In these humid environments, N2O production occurs primarily via denitrification, a low redox process (Groffman and Tiedje 

1989; Silver, Herman, and Firestone 2001; Silver 

et al. 2005b; Templer et al. 2008). Increases in the 

severity and frequency of rainfall events could lower 

soil redox potential (Silver, Liptzin, and Almaraz, in 

press) and increase the amount of N2O emitted from 

tropical forests. Significant quantities of NOx radicals 

also are emitted by tropical forest soils, providing a 

key ingredient for the highly reactive photochemical environment (Bakwin, Wofsy, and Fan 1990). In 

the future, if changing land use causes tropical forest 

areas to contract, natural N2O and NOx emissions 

might diminish, possibly to be replaced or exceeded 

by emissions associated with fertilized agriculture 

(Reiners et al. 2002) in the same areas. The natural 

sources could be enhanced by future increases in 

temperature and precipitation as well as deposition of 

pollution-derived fixed nitrogen (e.g., NH3 or HNO3; 

cf. Hietz et al. 2011; Matson et al. 1999; Matson, 

Lohse, and Hall 2002). Alternatively, these sources 

could be suppressed by increased aridity (Davidson 

et al. 2000b). The overall ecosystem response of tropical soil N2O and NOx emissions to global changes 

in climate and chemistry is thus very uncertain and a 

high priority for investigation.

Methane

Humid tropical forests and wetlands also are important sources of CH4 emissions, which globally are 

dominated by anthropogenic sources such as fossil 

fuel extraction (coal and natural gas), rice agriculture, 

enteric fermentation, and the processing of human 

and animal wastes. As with N2O, methanogenesis 

typically proceeds under low redox conditions. 

Research in Puerto Rico found that rates of CH4

oxidation were more sensitive to redox than CH4

production, largely because of the strong aggregation 

and aggregate stability of tropical soils, leading to an 

abundance of anaerobic microsites (Teh, Silver, and 

Conrad 2005) that facilitate methanogenesis even 

when bulk soil conditions are aerobic.

Prior to agricultural intensification and industrialization, wetland emissions likely accounted for most of 

the global CH4 budgets, with strong contributions 

from Amazonia. Even now, natural wetland variability 

may control the interannual variability of CH4 flux 

to the atmosphere (Gedney, Cox, and Huntingford 

2004). Tropical wetlands, including areas of peat 

deposits with very high (and potentially vulnerable) 

carbon stocks, cover vast areas in tropical forest 

regions (Page, Rieley, and Banks 2011). Studies of 

wetland areas during the Large-Scale BiosphereAtmosphere Experiment in Amazonia (LBA) project 

revealed that about 20% (more at the end of the wet 

season) of the Amazon Basin has wetland character 

and may contribute 5% of global CH4 emissions 

(Hess et al. 2003; Melack et al. 2004). Fluxes of CH4

from Amazon Basin wetlands have been measured 

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Integrating Processes
almost exclusively near the main stem of the Amazon River, although other environments such as 

the interfluvial wetlands in the Upper Rio Negro 

Basin recently have been studied (Belger, Forsberg, 

and Melack 2011). Vast areas of seasonally flooded 

forests may be potent sources of CH4 during particular phases of the cycle. These processes would be 

expected to shift markedly in response to an altered 

hydrograph resulting from changes in climate and 

land use.

Methane emissions from wetlands depend primarily on the availability of organic substrate and the 

extent of anaerobic environments. Thus, the extent 

and duration of flooding are the primary controls on 

CH4 emission (Walter and Heimann 2000). These 

factors change seasonally and interanually and can 

potentially shift with rainfall under climate change 

(Gedney et al. 2004). Temperature, availability of 

labile carbon, and route of methane to the atmosphere (e.g., transport through plants, ebullition, 

or diffusion) also are important controls on CH4

emissions. Measurements that can help improve representations of wetland areas and temporal extent of 

flooding are critical for accurately modeling present 

and future wetland emissions.

Upland forest soils have long been known to consume 

CH4 (Harriss and Sebacher 1981; Keller, Kaplan, and 

Wofsy 1986), representing a relatively small methane 

sink. Hence, upland forests have been assumed to 

represent a net sink for methane. But atmospheric 

data from Amazon forest sites recently suggest that 

there is a net source of CH4 in upland forests (Carmo 

et al. 2006). While this source is relatively small on 

a per-unit-area basis, it may be comparable to the 

wetland source if present throughout the Amazon 

forest area. Research in Ecuador suggests that tank 

bromeliads represent a potentially important source 

of CH4 in tropical forest canopies (Martinson et al. 

2010), along with termites ( Jamali et al. 2011) and 

anaerobic aggregates in wet clay soils (Blagodatsky 

and Smith 2012). A recent paper by Covey et al. 

(2012) suggests that colonization of wood by archeae 

may produce significant aerobic CH4.

Both N2O and CH4 fluxes have been studied in 

relatively few tropical forest locations, and most measurements have been made using chamber techniques 

subject to a variety of artifacts and challenging to 

scale up (Rochette and Eriksen-Hamel 2008). New 

measurement technologies using robust, portable 

laser-based sensors make wider-area measurements 

accessible even under relatively primitive conditions. 

Expanding greenhouse gas measurements to the 

ecosystem scale and larger in tropical forests is an 

important research priority.

Deposition fluxes of nitrogen oxides (NOx, HNO3) 

and O3 to forest canopies can significantly affect 

both the ecosystem and atmosphere. Foliar uptake of 

fixed nitrogen is an efficient way to deliver fertilizer 

to the forest, leading to stimulation, and potentially 

overstimulation, of growth (Bryan et al. 2009). 

Ozone uptake is efficient and damaging to the photosynthetic organs of the plant (Lindroth 2010). 

Conversely, uptake of these species by tropical forests 

lowers concentrations available for photochemistry 

(Wu et al. 2011). Few observations of these processes 

have been made at the ecosystem scale, limiting guidance for their representation in ESMs.

Biogenic Volatile Organic Compounds

BVOCs include a very diverse set of molecules, hundreds of which have been identified and thousands 

that have yet to be. The most important by mass are 

relatively low-molecular-weight compounds such as 

isoprene, monoterpenes, methanol, acetone, acetaldehyde, formaldehyde, and formic and acetic acids 

(Lathiere et al. 2006). Isoprene accounts for about 

40% of this flux by mass (Guenther et al. 2006) and 

provides the dominant chemical reactivity. BVOCs 

drive chemical reactions that lead to a sink for atmospheric hydroxyl radical (OH). This regulation of 

atmospheric oxidative capacity can affect the lifetime 

of CH4, which primarily is consumed by reactions 

with OH (Wuebbles et al. 1989). Under conditions 

in which the NOx concentration is sufficiently high 

(>5 to 30 ppt), as is typical in tropical forests due to 

endogenous biogenic emissions ( Jacob and Wofsy 

1988; Wu et al. 2011), BVOC oxidation contributes 

to the production of O3, a greenhouse gas and potent 

toxin for plants (Lombardozzi et al. 2012). Another 

critical role of BVOCs is the formation of SOA when 

organic compounds react or condense to form aerosol particles as discussed in the following section.

Most global models that simulate BVOCs adopt 

some variation of G95, the Guenther algorithm 

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(Guenther et al. 1995, 2006; Rinne et al. 2002; 

Greenberg et al. 2004). This algorithm is based 

on empirical equations parameterized in terms of 

temperature, sunlight, leaf age, and plant functional 

type using data from studies of midlatitude plants. 

Translation of G95 to ESMs requires that parameters 

be assigned to plants in completely different environments with very diverse chemistry and life histories. 

Relevant information is known for only a few species 

and thus is approximated very crudely in current 

models (e.g., Lathiere et al. 2006).

Leaf temperature is a critical variable because BVOC 

emissions increase exponentially with temperature 

(Guenther et al. 1995). A key research need is to 

improve modeling of both leaf temperature distributions in complex tropical forest canopies and the 

covariance of temperature with physiological and 

metabolic parameters. Better simulation of leaf temperatures not only will improve estimates of BVOC 

emissions, but also will be important for modeling 

photosynthesis and the mortality of leaves that may 

exceed a critical temperature threshold under water 

stress (Doughty 2011). This is a high-priority issue 

for ESMs in the near term, requiring data on shortand longwave absorption, reflection, and emission in 

a three-dimensional canopy, plus determination of 

the sensible and latent heat fluxes and water limitation affecting leaf elements in the same domain.

Recent research has questioned the basic framework 

of the G95 approach because it employs a “basal 

emission factor (Es)” that is an emergent property of 

an ecosystem, divorced from basic leaf- or plant-level 

biophysics. Es may vary seasonally, by species, by 

leaf age, with CO2 concentration, and with previous 

light and temperature environments (Niinemets et al. 

2010a). G95 provides an empirical fit such that the 

model responds only to instantaneous physical inputs 

of light and temperature. Recent reviews suggest 

that future models should more closely simulate the 

biological and biochemical controls on BVOC production, storage, and emission (Monson et al. 2007; 

Niinemets et al. 2010b), possibly including circadian 

control of isoprene emissions (Wilkinson et al. 2009; 

Loivamäki et al. 2007). Understanding how the 

inferred circadian control of these emissions functions (whether it is general to all isoprene emitters) is 

a strong research need, along with determining how 

this control should be accounted for in leaf-, ecosystem-, and global-scale models.

In the future, BVOC emissions may increase with 

temperature and decrease with CO2, as appears to be 

the case for isoprene. To understand the future emissions from tropical forests, quantifying these tradeoffs for tropical plants and the associated ecosystems 

is critical. Moreover, BVOC emissions are species 

specific, and hence large-scale changes in community 

composition will affect fluxes in the future.

Aerosol Particles and Tropical 

Forests

With the exception of some urbanized areas and transportation corridors, aerosol sources located within 

the Amazon Basin are dominated by natural and 

anthropogenic (fire-related) emissions from the biosphere (Martin et al. 2010). Sources include (1) low 

but consistent production of primary and secondary 

biological aerosol particles and components (Pöschl 

et al. 2010) and (2) high but intermittent natural 

and anthropogenic emissions from biomass burning 

(Andreae et al. 2004; see Fig. 8.2, p. 60). Primary biological particles (PBA) are produced both deliberately 

by flora (e.g., through the release of pollen and fungal 

spores) and incidentally (e.g., in leaf and soil debris 

or as suspended microbes; see Fig. 8.3, p. 60; Elbert 

et al. 2007) and are especially relevant as ice nuclei in 

the Amazon Basin (Prenni et al. 2009). Substantial 

production of secondary aerosols occurs by the 

atmospheric oxidation of trace gases to low-volatility 

compounds (Chen et al. 2009). These products can 

deposit on pre-existing particles or possibly nucleate 

new particles. This particle mode dominates the spectrum of cloud condensation nuclei (CCN).

Once in the atmosphere, particles undergo continuous transformations. Processes include photochemical reactions occurring within particles, reactions 

involving the gas phase such as the condensation of 

low-volatility compounds, and reactions with highly 

reactive gaseous species like the OH radical. Clouds 

are ubiquitous in the Amazon Basin, and aerosol particles may undergo several cycles of cloud processing 

during their residence in the region. Cloud processing 

can modify particle properties by chemical reactions 

in the liquid phase and by interactions among droplets 

Research Priorities for Tropical Ecosystems Under Climate Change 59

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(e.g., collision and coagulation). Aerosols 

in turn can modify clouds by changing, for 

example, droplet number and single scattering 

albedo. Particles leave the Amazonian atmosphere by dry deposition to the vegetation 

surface, cloud scavenging and precipitation, 

and advection out of the region.

During the wet season, the Amazon is one 

of the few continental regions where atmospheric aerosol particles and their effects on 

climate are not dominated by anthropogenic 

sources. During this period, particles are 

removed relatively quickly by wet deposition, and anthropogenic sources such as 

biomass burning are weak throughout the 

basin. Because of this combination of circumstances, natural processes (including contributions from marine and African sources) 

Fig. 8.2. Aerosol and Water Cycling 

over a Pristine Rainforest. Secondary 

organic aerosols (SOA) formed by photooxidation of volatile organic compounds (VOCs) 

and primary biological aerosols (PBA) emitted 

from plants and microbes in rainforests serve as 

biogenic nuclei for cloud condensation nuclei 

(CCN) and ice nuclei (IN). These nuclei induce 

warm or cold rain formation, precipitation, and 

wet deposition of gases and particles. [Adapted 

from Pöschl, U., et al. 2010. “Rainforest Aerosols 

as Biogenic Nuclei of Clouds and Precipitation 

in the Amazon,” Science 329(5998), 1513–16.

Reprinted with permission from AAAS.]

Fig. 8.3. Scanning Electron Micrographs of 

Primary Biological Particles Collected in 

the Amazon Basin. [Adapted from Martin, S. T., 

et al. 2010. “Sources and Properties of Amazonian 

Aerosol Particles,” Review of Geophysics 48, RG2002.]

60 Research Priorities for Tropical Ecosystems Under Climate Change

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in the Amazon Basin (e.g., pristine, low NOx)—and, 

more generally, of organic peroxy radicals. Finally, 

models (validated by measurements) need to represent 

how efficiently particles (e.g., over the Amazon Basin) 

are removed by precipitation and how this sink term 

is affected by the processing and alteration of particles 

during their residence in the atmosphere.

Despite many technological advances in the past 10 years 

for characterizing aerosol particles globally, many of the 

new instruments have yet to be deployed in the Amazon 

Basin. Logistical difficulties have constrained measurements temporally, spatially, and technically to levels 

insufficient for obtaining fully accurate descriptions of 

Amazonian aerosol particles and the processes affecting 

them. New instruments should be deployed to provide 

information on aerosol properties, especially related to 

particle chemical composition. Chemical information 

can be employed, in conjunction with models, to understand mechanisms of particle formation and subsequent 

aging processes.

The ideal field program for understanding particles, 

ecosystems, and climate would span several dry and 

wet seasons in the Amazon Basin. It would involve in 

situ and remote-sensing measurements from multiple 

ground-based and airborne platforms and be complemented by satellite observations from which particle 

and trace gas properties are derived.

In summary, the Amazon Basin can be pictured as a 

biogeochemical reactor that uses a feedstock of plant 

and microbial emissions in an environment with 

high water vapor, solar radiation, and photo-oxidant 

levels to produce SOA and PBA (Pöschl et al. 2010). 

Biogenic aerosol particles serve as nuclei for clouds 

and precipitation, sustaining the hydrological cycle 

and biological reproduction in the ecosystem. Aerosolchemistry-ecosystem interactions are important in 

the Amazonian rainforest and also may be generally 

relevant for the evolution of ecosystems and climate 

on global scales and in Earth’s history.

Key Uncertainties and Research 

Opportunities

Important research gaps for studying the exchange 

of greenhouse gases, reactive chemical compounds, 

and atmospheric particles in tropical forests and for 

become the dominant contributors to ambient particle populations over large expanses of the Amazon 

Basin during a significant part of the year. Particle 

concentrations measured during these conditions 

are among the lowest found on any continent and are 

similar to those over remote oceans (Andreae 2009). 

Consequently, the Amazon Basin has been dubbed 

the “green ocean” because of the similarities in particle concentrations and cloud microphysics between 

it and these remote oceanic regions (Williams et al. 

2002). This may be the only region on the tropical 

continents where there remains the possibility of 

finding at times populations of nearly pristine aerosol 

particles free of direct anthropogenic influences.

In stark contrast to the green-ocean conditions of the 

wet season are those associated with the dry season 

for large areas of the Amazon Basin. Vast numbers 

of deforestation fires burn during the dry season, 

especially along the peripheries of the forest, and large 

parts of the region become among the most polluted 

places on Earth (Artaxo et al. 2002). Consequently, 

the regional energy balance is changed because high 

particle concentrations affect the amount and location 

of solar radiation absorbed by the planet. Simulations 

using regional climate models show that the changes in 

energy delivery significantly influence regional patterns 

of atmospheric circulation and meteorology. The high 

particle concentrations change cloud microphysics and 

rainfall, significantly influencing the overall water cycle 

(Rosenfeld et al. 2008). They also affect air quality by 

degrading visibility and affecting human health.

Aerosol Measurement and Modeling Needs

The current generation of land-atmosphere models 

does not adequately capture important aerosol particle dynamics, specifically in the Amazon region. To 

improve the representation of PBA aerosol emissions 

in modeling efforts, a number of important research 

gaps must be overcome. Specifically needed are investigation and implementation of models at the scale necessary to capture how vegetative heterogeneity within 

the rainforest canopy affects BVOC and PBA particle 

emissions. Modeling advances also should include all 

BVOC emissions (at the level of compounds or families) that contribute to the secondary components of 

particles. Another major research gap is model incorporation of new BVOC chemistry—such as the reactions of isoprene in the chemical regimes prevailing 

Research Priorities for Tropical Ecosystems Under Climate Change 61

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understanding their connections with ecosystems 

and climate are summarized below.

•	 What are the controls of greenhouse gas emissions from tropical forests, and how can they 

be better represented in ESMs? Many studies 

have examined the magnitude of current emissions 

of biogenic greenhouse gases (N2O and CH4) and 

precursors (e.g., NOx and BVOC) at the ecosystem 

scale in tropical forests. However, large uncertainties remain regarding which components of the 

ecosystem produce these gases. For example, a significant upland source for CH4 has been identified, 

but there are only hints of the underlying sources 

(e.g., tank bromeliads and arboreal termites) and 

their potential response to climate change. Because 

most measurements have been made using small 

chambers focused on soil emissions, information 

that can be used to validate models at ecosystem 

and regional scales still is lacking. Chamber studies have been valuable for understanding physical 

and some chemical controls on greenhouse gas 

emissions, but more research is needed to elucidate 

the underlying biological and biochemical pathways. To test and enhance ESMs, future studies 

need to combine both improved quantification of 

ecosystem exchanges and better understanding of 

biological controls. A motivating question is, “How 

will future changes in temperature, precipitation, 

and nitrogen deposition affect N2O, NOx, and CH4

fluxes from tropical forests?”

•	 How will the effects of changing climate and 

hydrology affect the future emissions of CH4

from wetlands? Flooding conditions (e.g., extent, 

duration, and oxidation status of floodwaters) 

are the key controls on CH4 emissions in tropical 

forested wetlands. Wetland extent and duration 

of flooding will change under future climates in 

tropical forest regions.

•	 How do the deposition fluxes of NOx, HNO3, 

and O3 affect tropical forests? These fluxes are 

poorly quantified, demanding research to determine the origin of these gases and their effects 

on tropical forest ecosystems. Deposition of 

atmospheric nutrients and oxidants represents a 

possibly strong, human-mediated factor in changing the structure, composition, and function of 

tropical forests. How might this factor change in 

the future, and how should deposition processes 

be represented in ESMs?

•	 What are the underlying biological and biochemical controls on BVOC production, storage, and emissions, and how should these be 

represented in ESMs? Tropical vegetation diversity 

and the multiple biochemical pathways controlling 

BVOC production and emissions present formidable 

challenges to scaling the underlying mechanisms 

from the cellular to the leaf, canopy, ecosystem, and 

global levels. Nonetheless, recent studies have shown 

many new insights into biochemical and cellularlevel controls. Two decades of studies have mapped 

current emission distributions globally. How can the 

mapping of basal emission factors to plant functional 

types be tested to determine if ecosystem emissions 

are adequately represented in ESMs? How will the 

competing effects of increasing temperature and elevated CO2 affect isoprene emissions in tropical forest 

communities? Canopy temperature is a key control 

on BVOC emissions and therefore must be carefully 

measured to enable future ESMs to simulate the nonlinear effects of temperature on BVOC emissions.

•	 How might plausible future changes (e.g., 

large-scale forest loss, anthropogenic pollution, and changes to land cover) influence the 

large-scale characteristics of Amazonian aerosol particles? How might aerosols, in turn, affect 

aerosol-cloud-climate interactions in the Amazon 

Basin, providing a feedback to rainfall, vegetation, 

and climate change, all of which constrain and force 

ecosystem development? If large-scale vegetation 

change occurs in the Amazon Basin, the concentrations and properties of particles and their links 

to meteorology, cloud type, and rainfall intensity 

might change greatly. To what extent can these possible changes be predicted beforehand and thus be 

available for planning scenarios, including economic 

assessments? To what degree will increasing future 

anthropogenic pollution in the Amazon Basin 

enhance oxidant levels and thereby alter prevailing 

BVOC oxidation pathways, including the fraction 

of low-volatility products formed (i.e., those that 

eventually become particle components)? To what 

extent do past and anticipated future changes in 

land cover influence the abundance and properties 

of PBA particles and components?

62 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 8 – Biosphere-Atmosphere Interactions: Greenhouse Gases, Reactive Chemicals, and Aerosols

DOE Office of Science
Nutrient Limitations

CHAPTER 9
Nutrient Limitations

Over the coming century, tropical forest 

ecosystems will, with very high certainty, 

be subjected to anthropogenically forced 

increases in atmospheric carbon dioxide (CO2) 

concentration. There is consensus in the climate 

modeling community that this change in atmospheric 

composition will drive global-scale increases in nearsurface air temperature, including significant temperature increases over tropical forests in Central and 

South America, Central Africa, and Southeast Asia. 

Climate models agree that relative humidity remains 

stable as temperatures increase under radiative forcing, including over tropical forest regions (Soden 

et al. 2005). Compared to predictions of current 

temperature and future temperature change, models 

have lower fidelity in reproducing current distributions of precipitation over tropical forest, and there 

is less agreement among model projections regarding 

future changes in precipitation patterns.

Role of Nutrient Dynamics in 

Predicting Terrestrial Carbon Sink

The terrestrial biosphere is estimated to act as a sink 

for carbon released to the atmosphere from fossil fuel 

combustion, and models consistently show that a 

significant fraction of the current sink is occurring as 

increased carbon stocks in tropical forests, although 

direct observations do not consistently support this 

model result. Future predictions of the magnitude 

and spatial distribution of the terrestrial sink for fossil 

fuel carbon emissions differ widely among models, 

with estimates at the century scale varying by at least 

a factor of three among multiple models (Thornton 

et al. 2007). A robust pattern emerging from the 

current generation of models is that predicted sink 

strength is related to the models’ representation of 

nutrient dynamics. Models that include coupled 

carbon-nutrient dynamics as a component of the 

land biosphere predict a weaker land sink than those 

that do not (Zaehle et al. 2010). The mechanism 

responsible for this difference in model behavior is 

limitation on plant growth imposed by the availability of nutrients, which constrains the response of the 

carbon-nutrient models to CO2 fertilization. There 

is some experimental evidence for this mechanism, 

with declining CO2 fertilization associated with signs 

of increasing nutrient limitation in a temperate forest 

(Norby et al. 2010). Nutrient limitation in the same 

forest has been demonstrated experimentally through 

significant response of net primary production to 

nitrogen fertilization (Iversen and Norby 2008). 

However, nutrient addition experiments (using 

various combinations of nitrogen, phosphorus, and 

potassium) in tropical forests demonstrate contrasting results, with varying responses of root allocation, 

tree growth, and litter production among studies and 

no clear process-level understanding of what drives 

the differences (Wright et al. 2011).

Although changes in CO2 and climate co-occur in 

nature, models can be used to estimate the independent effects of CO2, temperature, humidity, precipitation, and other dimensions of climate change. 

Evaluating the influence of radiatively forced climate 

change (in the absence of the physiological effects of 

higher CO2 concentration), models generally agree 

that global land carbon stocks are reduced, although 

there is little agreement on the magnitude of the 

reduction. (Friedlingstein et al. 2006; Thornton et al. 

2009). One general prediction of these models is that 

inclusion of carbon-nutrient interactions may result 

in a smaller climate-driven reduction in carbon stocks 

(Bonan and Levis 2010). The mechanism hypothesized to cause these differences is increased mineralization of nutrients from litter and soil organic 

matter under warmer soil conditions, with important 

spatial variability introduced through changes in soil 

moisture status. Warming-induced increases in nutrient mineralization are maximized over tropical forest 

regions, as are associated increases in gross primary 

production. Temperature and substrate-induced 

increases in autotrophic respiration lead to a complex 

spatial pattern of increased and decreased vegetation 

carbon stocks over tropical forests. Soil organic matter stocks are predicted to be uniformly depleted by 

radiatively forced climate change over the tropical 

forest region.

64 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 9 – Nutrient Limitations

DOE Office of Science
Representation of carbon-nutrient dynamics in the 

current generation of Earth system models is incomplete and lacking in many mechanistic details. However, results summarized here suggest that improved 

predictive capability for future CO2 concentrations 

and associated climate change depends in part on 

realistically representing carbon-nutrient interactions, with tropical forests significantly contributing 

to the globally integrated dynamics.

Improving Model Representation 

of Nutrient Limitation

An important deficiency in the current generation of 

nutrient-enabled models, particularly pertinent to tropical forests, is that only nitrogen and carbon-nitrogen 

coupling have been included. Plant growth probably 

is limited more by phosphorus than nitrogen in many 

tropical forests, and recent empirical (Domingues 

et al. 2010) and modeling studies (Mercado et al. 

2011) have underlined the likely importance of phosphorus availability. Moreover, phosphorus-nitrogen 

co-limitation also appears to be common (Elser et al. 

2007; LeBauer and Treseder 2008). By including only 

nitrogen as a limiting nutrient, current models have 

defined, at best, an upper envelope for current and 

future growth responses. In other words, introducing 

phosphorus as a further limiting nutrient can only 

reduce modeled estimates of current and future growth 

fertilization by CO2 or future growth stimulation from 

increased mineralization under warming (Thornton 

et al. 2009) unless mechanisms are introduced in 

the models whereby current phosphorus limitation 

is alleviated under future conditions. For example, 

under elevated CO2, phosphorus mineralization and 

availability could be stimulated through increased 

carbohydrate supply, exudation, and rhizosphere 

activity (Norby, O’Neill, and Luxmoore 1986; Lloyd 

and Farquhar 1996).Other nutrients also have been 

demonstrated to limit growth in some places, and 

with each new limitation introduced in the models, a 

further constraint on predicted CO2 fertilization and 

predicted warming responses through mineralization would be expected. Therefore, although current 

nutrient-enabled models are incomplete, they have 

provided a compelling case for additional efforts to 

incorporate better mechanistic understanding and 

more comprehensive process representations.

Another important target for model improvement is 

representing disturbance processes and their effects 

on biogeochemical cycles, including interactions 

with nutrient limitation and carbon-nutrient-climate 

feedbacks. Chronosequence studies have demonstrated the importance of including “time since 

disturbance” and disturbance type as constraints on 

predicted net fluxes of carbon and carbon allocation 

patterns (Malhi et al. 2009a). Such studies also have 

highlighted the interactions of these disturbance and 

disturbance recovery dynamics with other forcings 

like increased CO2 and climate trends (Law et al. 

2001; Thornton et al. 2002). Model experiments 

suggest that nutrient limitation plays a critical role in 

disturbance recovery dynamics. The availability of 

nutrients for new growth is higher immediately after 

a stand-replacing disturbance because overall plant 

demand is low. As a new stand is established, nutrient 

availability becomes more limiting, partly resulting 

from both increased demand and from diminished 

labile litter and soil organic matter stocks reduced 

over the period of low vegetation inputs. Models 

predict that the responses of vegetation growth to 

CO2 fertilization and climate change are sensitive 

to disturbance history, with nutrient dynamics and 

varying nutrient limitation playing important roles. 

To the extent that disturbance processes are affecting large areas in the Tropics—or are increasing or 

decreasing in prominence over time—inclusion of 

more mechanistic representations of disturbance and 

recovery in nutrient-enabled models should lead to 

improved model predictions of CO2 and associated 

climate change. The rapid decomposition of fresh 

litter in tropical forests could make accurate model 

representation of time since disturbance even more 

critical in these forests than in the temperate zone.

Yet another deficiency in the structure of current 

nutrient-enabled models is the simplistic representation of soil heterotrophs and microbial community 

processes. Base rates for decomposition and respiration fractions are specified as global constants and 

are based on multiple exponential decay representations that ignore the influence of soil structure and 

microbe-mineral associations. Carbon-to-nitrogen 

ratios for microbes and microbial byproducts also are 

specified as global-scale constants. Several models 

represent nitrification and denitrification with some 

level of mechanistic detail but none currently include 

Research Priorities for Tropical Ecosystems Under Climate Change 65

Chapter 9 – Nutrient Limitations

DOE Office of Science

Integrating Processes
explicit representations of the microbial communities 

responsible for these processes. Insects are known to 

contribute significantly to litter decomposition rates 

in tropical forests, but no global-scale model incorporates this process. Current knowledge is adequate 

to support model improvements in these areas, but 

additional research is needed to quantify differences 

across the tropical forest biome.

The expression of plant and microbial demand for 

nutrients as well as their competition for available nutrient resources are poorly understood and 

very simply represented in current models. Plant 

demand and nutrient uptake are closely related to 

allocation, another critical area identified for model 

improvement in several previous analyses. For 

example, plant nutrient demand depends in part 

on fractional allocation among tissues with higher 

nutrient concentrations (e.g., leaves, fine roots, and 

phloem) and lower concentrations (e.g., stems and 

coarse roots). Plant nutrient uptake and competition with microbes depend on the structure and 

function of fine root systems. Current understanding of the mechanistic controls on allocation and 

functional relationships among rooting distribution, 

root function, and nutrient uptake in tropical forests 

is not adequate to constrain models at the global or 

pantropical scale.

Interactions among nutrient availability, heterotrophic activity, and plant physiology in experimental 

manipulations can provide multidimensional 

constraints to test and improve model performance. 

For example, greater availability of both nitrogen 

and phosphorus has been shown to increase soil 

respiration in a lowland tropical forest (Cleveland 

and Townsend 2006). This research indicates 

that increased phosphorus affects soil respiration 

through heterotrophic activity, while the influence 

of increased nitrogen on soil respiration seems to be 

related to more production of fine roots. However, 

sites vary significantly in responses to experimental 

nutrient additions among tropical forests (Wright et 

al. 2011). Current models predict the influence of 

nutrient availability on heterotrophic activity (e.g., 

Thornton and Rosenbloom 2005), but combined 

laboratory, field, and modeling experiments at additional sites could lead to improved model prediction 

of these complex interactions.

Key Uncertainties and Research 

Opportunities

Nutrient dynamics in tropical forest ecosystems are 

important points of interaction among radiatively 

forced climate change, rising CO2 concentrations, 

anthropogenic and natural disturbance, and plant and 

microbial community ecology. Current knowledge of 

these interactions still is quite limited, lacking both 

empirical and theoretical understanding. The following uncertainties and research gaps help frame the 

key opportunities related to these interactions:

•	 Will radiatively forced warming induce 

changes in tropical forest nutrient dynamics that influence carbon-climate feedbacks?

Warming experiments in the temperate zone and 

global-scale modeling studies suggest that warming 

of soil can accelerate organic matter decomposition 

and increase rates of nutrient mineralization. Shifting nutrient dynamics could influence net greenhouse gas fluxes, thereby driving carbon climate 

feedbacks. Interactions with the hydrologic cycle 

through changes in precipitation and humidity also 

are likely to play a critical role in these feedbacks. 

These mechanisms could be explored through a 

variety of in situ and laboratory warming and environmental modification experiments, accompanied 

by modeling explorations.

•	 Will the fertilization effect of rising atmospheric CO2 concentration interact with nutrient dynamics in tropical forests in ways that 

modify the net land sink for anthropogenic 

carbon emissions? Both field experiments and 

modeling studies strongly indicate that nitrogen 

availability and rising CO2 interact to regulate 

the CO2 fertilization feedback in temperate 

systems. Empirical knowledge of these interactions in tropical systems is limited, but modeling 

studies suggest the importance of both nitrogen 

and phosphorus as limiting nutrients that could 

interact strongly with rising CO2 to affect net 

land uptake of anthropogenic CO2 emissions. 

New field experiments in tropical forest systems 

could begin to explore these interactions.

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Chapter 9 – Nutrient Limitations

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•	 Will disturbances associated with anthropogenic land use and changes in land cover 

interact with nutrient dynamics in a way that 

modifies the post-disturbance trajectories 

of net greenhouse gas emissions in tropical 

forests? Land-use history, including disturbance type and time since disturbance, has been 

observed to play a significant role in determining net greenhouse gas fluxes, with important 

interactions between disturbance history and 

response of forests to changing climate and 

rising CO2. Modeling studies suggest that these 

interactions are regulated in part by the influence 

of land-use disturbance on nutrient dynamics. 

Additional empirical studies in tropical systems 

are needed to establish the relevant timescales 

and interaction effects.

•	 Are plant and microbial community dynamics 

influenced by the availability of nutrients in 

ways that affect climate system feedbacks?

Current theoretical understanding of soil 

microbial dynamics presents the interaction of 

microbial communities and nutrient dynamics as 

a dichotomy between (1) nutrient immobilization 

in the early stages of plant matter decomposition 

and (2) nutrient mineralization in the later stages 

of decay and in turnover of older soil organic 

matter. The theoretical outcome of these interactions depends strongly on assumptions about 

plasticity in microbial community stoichiometry 

and carbon-use efficiency and also on assumed 

dynamics for mechanisms linking the nitrogen 

and phosphorus cycles. Creating the potential for 

complex interactions are competition between 

plants and microbes for available nutrients and 

feedbacks between plant supply of fresh litter 

input (fueling microbial growth) and microbial 

supply of mineralized nutrients (fueling both 

plant and microbial growth). Laboratory and field 

studies are needed in tropical forest ecosystems to 

resolve these interactions and perhaps may best be 

accomplished with labeled tracer studies.

Research Priorities for Tropical Ecosystems Under Climate Change 67

Chapter 9 – Nutrient Limitations

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Integrating Processes
68 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 9 – Nutrient Limitations

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Belowground Processes: 

Roots and Soil 

Biogeochemistry

CHAPTER 10
Belowground Processes: Roots and Soil Biogeochemistry

Importance of Belowground 

Biogeochemical Cycling

Much research in tropical forests has concentrated on the easily accessible aboveground 

vegetation and its diversity, standing 

biomass, and productivity. However, factors such as 

nutrient and water availability that shape aboveground 

characteristics are inextricably linked to belowground 

biogeochemical cycling. Across a range of spatial 

scales, variation in soil depth, age, mineralogy, and 

indigenous microbial and faunal communities provides critical constraints on productivity and diversity 

in the aboveground components of ecosystems.

Belowground biogeochemical cycling is driven 

primarily by the delivery of organic matter (ranging 

from detritus to root exudates) to the soil decomposer community. The breakdown of organic matter 

provides the major source of energy to soil microorganisms, fueling large fluxes of carbon dioxide 

(CO2) and causing soil to serve as sources or sinks 

of important non-CO2 trace gases (e.g., methane, 

oxides of nitrogen, and carbon monoxide). Except 

for the initial stages, understanding of the decomposition cascade and how it reflects local physical, 

chemical, and biological conditions is limited. The 

belowground biodiversity and biogeography of soil 

organisms also are still poorly explored, particularly 

in the Tropics.

Physicochemical interactions of decomposition 

products with minerals and recycling through 

belowground food webs result in the persistence 

of some organic compounds in the soil structure 

over periods of centuries to millennia. These insufficiently understood stabilization mechanisms are 

represented in models using empirical correlations 

with properties like soil texture rather than process 

understanding. Because soil organic matter controls 

key soil properties—particularly those associated 

with overall nutrient availability, water holding 

capacity, redox, fertility, and trace gas balance—its 

importance extends far beyond its role in the global 

carbon cycle.

Future changes in climate, CO2, nitrogen deposition, and community composition will affect soils in 

several ways. Changes in productivity, allocation, and 

disturbance will alter the fluxes of detrital components (wood, leaf, and root litter) to the forest floor 

and soil. Changes in soil climate conditions and the 

rate or timing of substrate supply in turn will affect 

the cascade of processes involved in decomposition 

of detrital material. Roots and microbes interact to 

recycle limiting nutrients such as nitrogen, phosphorus, potassium, and other base cations. Therefore, 

changes in decomposition will feed back to further 

alter the aboveground portion of the ecosystem. In 

addition, nitrogen deposition is increasing in tropical 

regions (Matson et al. 1999) and can alter patterns 

in carbon storage and turnover times (Cusack et al. 

2010). Even in the absence of climate change, Earth 

system models (ESMs) that do not incorporate nitrogen deposition and plant nutrient limitations due to 

soil processes may inaccurately predict net primary 

productivity (NPP), carbon storage, and atmospheric 

CO2 concentrations.

Soils underlying tropical forests vary widely, but their 

responses to changes in climate, CO2, or nitrogen 

deposition are uncertain because little has been done 

to synthesize belowground-aboveground interactions 

in a way that will aid prediction of such responses. 

Also unclear is how the responses of these different 

systems will feed back to atmospheric concentrations 

of greenhouse gases and aerosols. Given these uncertainties and the influence of belowground processes 

on ecosystem dynamics, investigation of subsurface 

biogeochemistry must be a strong component of 

any future experiments simulating future climate or 

vegetation change.

Root Productivity, Dynamics, 

and Function

The factors controlling tropical root biomass, productivity, lifetimes, and decomposition rates—all the 

components of the root carbon cycle—are poorly 

understood. Detailed studies of root dynamics in 

70 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 10 – Belowground Processes: Roots and Soil Biogeochemistry

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tropical forests are few, though the importance of roots 

in redistributing water vertically in soils profiles and 

enhancing nutrient availability to plants is unquestioned (Trumbore et al. 2006; Silver et al. 2005a; 

Silver and Vogt 1993). For example, forests growing 

in the deeply weathered, nutrient-poor soils of the 

eastern Amazon extend roots deep into soils to access 

water sufficient for maintaining a transpiring canopy 

during the dry season (Nepstad et al. 1994). The role 

of deeper roots has been demonstrated in central and 

eastern Amazon forests, where about 20% of water 

uptake (Markewitz et al. 2010) and 10 to 20% of soil 

respiration (Davidson and Trumbore 1995) occur at 

depths greater than normally measured in soil studies. 

Including this access to water sources extending deeper 

than a meter improved climate models (Kleidon and 

Heimann 2000). However, exactly how the deep 

rooting system offers 

advantages to emergent versus subcanopy 

trees remains unclear. 

Also uncertain is how 

forests in shallower or 

inundated soils differ 

from the terra firme 

Ultisols and Oxisols 

where deep rooting 

has been found. Root 

distributions and 

strategies for maintaining water availability 

during the dry season 

obviously will vary in 

tropical forests with 

different patterns of 

nutrient and water 

availability. The lack 

of basic understanding of plant allocation 

patterns belowground 

in the Tropics and of 

factors controlling the 

balance between root 

and heterotrophic respiration severely limits 

the ability to model 

whole-ecosystem 

carbon and nitrogen 

dynamics.

Soil Carbon Storage, Nutrient 

Bioavailability, and NPP

Stabilization mechanisms for soil organic matter vary, 

but the amount and age of stabilized carbon can be 

partly predicted from the mineralogy of the soil (Torn 

et al. 1996; Masiello et al. 2000). Approximately 

70% of tropical soils are Ultisols and Oxisols (see 

Fig. 10.1, this page) with variable-charge iron- and 

aluminum-(hydr)oxide and 1:1 clay (e.g., kaolinite) 

minerals (Oades et al. 1989). These minerals have 

minimal capacity for chemical protection via sorption 

(Feller and Beare 1997) and shorter residence times. 

Tropical Andisols, in contrast, tend to weather initially 

into highly reactive short-range-order minerals with 

Fig. 10.1 Global Distributions of Ultisols (A) and Oxisols (B). [U.S. Department of 

Agriculture’s Natural Resources Conservation Service.]

A

B

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Integrating Processes
a much higher capacity to stabilize carbon over long 

periods of time.

Tropical Ultisols and Oxisols together contain 

around one-fifth of the phosphorus present in 

temperate soils, and of that amount, “organic” phosphorus makes up a much larger proportion (60 to 

80%; Duxbury et al. 1989). Ortho phosphate forms 

extremely strong bonds and insoluble precipitates 

with amorphous iron and aluminum oxides, soil 

minerals that thus exert major limitation on phosphorus bioavailability (Duxbury et al. 1989; Yang 

and Post 2011). Phosphorus limitation, therefore, 

is typical of tropical systems, although it may be 

masked during periods of extreme nitrogen limitation. Pulses of low redox conditions may temporarily liberate iron-bound phosphorus (Chacon et al. 

2006) and are likely to play a critical role in nutrient 

availability in tropical forests (Liptzin and Silver 

2009). Mycorrhizae (root-fungus associations) also 

can strongly affect plant access to soil phosphorus, 

but little is known about the importance and functioning of these associations in tropical systems. 

In addition, production of the microbial enzyme 

phosphatase can offset phosphorus limitations by 

independently releasing the element from organic 

matter, but enzyme production also depends on 

nitrogen availability. Although not often considered, 

potassium can be a co-limiting nutrient as well, so 

both soil pH status and cation exchange capacity are 

important aspects of soil fertility.

Rates and Stoichiometry of Nutrient 

Decomposition and Competition 

Between Soil Biota and Plants

Large-scale comparisons of common litter decomposition (e.g., the Long-Term Inter-site Decomposition Experiment Team, or LIDET) and cross-site 

comparisons show that decomposition rates for fresh 

plant litter and dead trees (i.e., coarse woody debris) 

in tropical forests are among the highest known 

(Parton et al. 2007; Cusack et al. 2010; Chambers 

et al. 2000). Many tropical forests experience only 

small variations in site temperature, so litter moisture 

and quality (especially nutrient content) often are 

used to explain local differences in decomposition 

rates of fresh surface litter. Cross-site comparisons 

demonstrate temperature effects along gradients, but 

these may not be applicable for estimating short-term 

warming effects, especially since overall soil conditions are likely to vary along elevation gradients. To 

date, no soil or ecosystem experimental warming 

study has been performed in tropical forests. Soil 

organic matter incubation experiments—though 

often confounded by substrate limitation in longterm studies—have demonstrated that short-term 

heterotrophic respiration rates increase with temperature, even up to 55°C (Holland et al. 2000). 

The short-term character of these studies, however, 

likely misses evolutionary adaptation of microbial 

communities to changing temperature, which would 

modulate the response of decomposition rates to 

temperature change.

Because of the large amounts of carbon in detrital 

layers and the faster-cycling organic matter pools 

that support heterotrophic respiration, the response 

of these pools (both production and decomposition) to future change is critical for carbon balance 

in the next decades. In the short term, increasing 

temperatures may be expected to increase carbon 

and nutrient mineralization, as they do in incubation studies. However, considerable uncertainty 

remains about the fate of released nutrients, 

particularly regarding whether plants will outcompete microbial communities or even leaching losses 

for those nutrients. In the longer term, microbial 

communities (and their allocation patterns) also 

can shift in response to changing temperatures, with 

concomitant alterations in decomposition rates or 

soil conditions (e.g., pH and oxygen solubility). 

Current ESMs that couple nitrogen, phosphorus, 

and carbon cycling disagree on the future trajectory 

of productivity and carbon storage because they 

implement nutrient dynamics differently, emphasizing the importance of understanding ecosystem 

stoichiometry for microbes and plants.

Saturated Soils and Wetlands

The Tropics contain about half of the world’s wetland 

area and an estimated 250 gigatons of organic carbon 

(Neue et al. 1997). Tropical wetlands also are globally important sources of methane. Drainage and 

fire in Indonesia’s large peat complexes have been 

implicated in episodic, substantial, and net additions 

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of CO2 to the atmosphere, especially in the El Niño–

Southern Oscillation year of 1998 (Tosca et al. 

2011). Recently, new information has demonstrated 

the existence of extensive peatlands in the Neotropics 

in subsiding basins in lowland Peru and the Orinoco 

delta (Lahteenoja et al. 2012). Large amounts of 

carbon are sequestered in Histosols and Spodosols in 

these and other areas subject to periodic or seasonal 

inundation. Figure 10.2, this page, demonstrates that 

the area of inundation in the Amazon Basin varies 

tremendously on both a seasonal and interannual 

basis. The spatial extent of saturated soils probably is highly variable as well and will be critical for 

understanding how future changes in the hydrologic 

regimes of different tropical forest regions may alter 

belowground biogeochemical cycling. Over the past 

decade, the Amazon Basin already has experienced 

the lowest (2005) and highest (2012) recorded levels 

of the Amazon River at Manaus.

Saturation of soils can play a pivotal role in terms of 

nutrient availability because formerly stabilized nitrogen, phosphorus, and carbon can be released during 

seasonal waterlogging common to wet tropical forests. 

Growth rates decline in high rainfall years (da Silva et 

al. 2002), though whether this is due to limitation of 

light or saturation in soils is unclear. In saturated soils, 

or even in microsites in upland soils, oxygen can be 

depleted because it is consumed faster than it can be 

replaced by diffusion from the overlying air. Oxygen 

depletion leads to reduction of minerals including 

iron, which frees the associated nutrients for use and 

yields electrons for microbial mediation of reductive 

processes (Liptzin, Silver, and Detto 2011; 

Chacon et al. 2006; Silver, Lugo, and Keller 

1999). Released nutrients may be incorporated 

by plants, leached into deep groundwaters and 

surface waters, or re-adsorbed to soil mineral 

surfaces. Even partly saturated soils can switch 

from net consumption to net production of 

methane and can become large sources of 

nitrogen oxide gases (including N2O). The 

fate of mobilized nutrients, leaching, plant 

uptake, microbial respiration, or adsorption 

may depend on several factors. These include 

the timescale of oxygen limitation, spatial configuration of roots, age of vegetation, location 

of microbial biomass and exo-enzymes, availability of mineral surfaces for re-adsorption, 

and soil hydrologic properties.

Thus, carbon cycle feedbacks in tropical forests are sensitive to the combined mechanisms 

of the entire integrated ecosystem including, specifically, the intense competition for 

nutrients by soil minerals, plants, transport 

advection, and the microbial community. 

No current models represent key aspects 

of microbes, enzymes, vegetation, redox, 

and soil minerals or the role of hydrology in 

nutrient removal via leaching. Consequently, 

predicting the effects of shifts in soil moisture 

content resulting from climate change in the 

Tropics poses a major challenge.

Fig. 10.2. Interannual and Seasonal Variation in 

Flooded Areas in the Amazon Basin. [Reprinted by 

permission from Macmillan Publishers Ltd. from Davidson, E. A., 

et al. 2012. “The Amazon Basin in Transition,” Nature 481, 321–28. 

DOI: 10.1038/nature10717.]

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Integrating Processes
Current Models and 

Their Limitations

Coupled land-atmosphere ESMs use extremely 

simplified processes for the soil carbon cycle, yet the 

process understanding needed to improve models still 

is lacking. For example, soil carbon cycling appears 

to be much faster in the Tropics versus temperate 

climates, partly because of high temperatures and high 

microbial biomass (Dubinsky, Silver, and Firestone 

2010). Significant and ad hoc modifications to rate 

variables are required for traditional and detailed 

soil carbon cycling models (e.g., CENTURY and 

ROTHC; Parton et al. 1989; Diels et al. 2004). This 

suggests that the models or model parameters developed for temperate systems are not adequate to simulate tropical ecosystems. Some of these soil carbon 

cycling models are much more detailed than those 

used in ESMs. Regardless, research now indicates that 

these detailed models inaccurately or inadequately 

represent a number of relevant processes, including (1) preservation of labile carbon (Sollins et al. 

2009), (2) sorption of dissolved carbon (Conant et 

al. 2011), (3) the nature of biochemical recalcitrance 

(Kleber et al. 2010), (4) enzyme-facilitated degradation (Sinsabaugh, Antibus, and Linkins 1991; Allison, 

Wallenstein, and Bradford 2010), and (5) functional 

pools of soil carbon (Schmidt et al. 2011). One 

example of an area of uncertainty involves enzymes 

that catalyze the depolymerization of inputs, which 

produces small soluble oligomers and monomers as 

bioavailable substrates for microbial metabolism. Key 

factors controlling enzymatic degradation of organic 

matter and the subsequent release of bioavailable 

nutrients are largely unknown, limiting the ability to 

model ecosystem processes under current and future 

climates (Wallenstein et al. 2011). Additionally, 

changes in moisture and redox regimes may impart 

significant shifts in microbial community structure 

and function (Lawrence, Neff, and Schimel 2009) and 

in nutrient flow and transport through the subsurface. 

However, neither process is included in current soil 

carbon models at either the plot or ESM scales.

The absence in models of most key interactions 

among microbes, plants, and soil minerals that 

control dissolved carbon, nitrogen, and phosphorus 

dynamics seriously undermines realistic rendition 

of response to change. An important contribution 

would be determining how to tractably include into 

larger-scale climate models the key controllers of 

process-level nutrient interactions, including deterministic aspects of microbial community function. 

Key soil functional traits that can be successfully 

scaled in space and time must be identified.

Oversimplification in models can give very misleading results. For example, Falloon et al. (2007) predicted a large net loss of carbon in the Amazon Basin 

with climate change alone because drying reduced 

carbon gained in forest productivity to less than that 

of carbon lost through organic matter decomposition. However, the magnitude of their estimated 

carbon loss (a decline from 45 to 23 petagrams 

between 2000 and 2100 in the Amazon Basin) is too 

large to be credible given that >70% of the carbon 

in the 0- to 30-cm soil layer is in soil organic matter 

fractions with turnover times longer than centuries 

(Telles et al. 2003). The prediction of large losses 

likely results from using a single pool model for 

soil carbon that overpredicts carbon changes in the 

short term (Knorr et al. 2005). With more realistic 

models of carbon dynamics that have been highly 

parameterized for local conditions, losses from soils 

are small to minimal compared to changes in aboveground biomass that occur with deforestation and 

reforestation (Cerri et al. 2007). Far more important 

is the fate of nutrients like nitrogen, phosphorus, and 

potassium that rely on recycling through decomposition to be sustained.

There is a growing consensus that model structures 

using empirically defined “pools” of carbon with 

different intrinsic decomposition rates are not 

adequate to describe carbon and nutrient cycling in 

soils (Schmidt et al. 2011). However, improved formulations, which might be specific for different soil 

types, have yet to be developed and tested. Within 

the next several years, though, modeling approaches 

that include biological processes more explicitly are 

expected. As part of a coordinated research effort in 

the Tropics, a belowground experimental component 

could supply critical tests for this new generation of 

models that include soil biology more explicitly.

Detailed data for tropical forests soils, while increasing rapidly, are concentrated in only a few soil types 

and regions. Key tests for the new models will be 

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their ability to make predictions across a range of soil 

types in the Tropics, which will require collecting 

new types of data at diverse field sites.

Key Uncertainties and Research 

Opportunities

Gaining better insights into belowground processes in the Tropics is an important component of 

strengthening model predictions of tropical forest 

response to climate change. Workshop participants 

identified several research gaps, including improved 

process understanding and model representation of 

how soil biogeochemistry interacts with vegetation 

to determine overall ecosystem response to disturbance (e.g., moisture, temperature, CO2 increase, 

and vegetation loss). Also needed is a better understanding of how root and mycorrhizal production 

(including rates and controls), vertical distribution, 

turnover, and function affect the uptake and redistribution of water and nutrients in different tropical 

forests and under disturbance. The significance of soil 

redox and pH as critical elements in biogeochemical 

cycling needs to be quantified, as well. This includes 

understanding the spatial and temporal importance 

of low redox and its relationship to (1) ecosystem 

productivity, (2) soil and wetland carbon storage, 

(3) phosphorus and nitrogen cycling, and (4) microbial mediation of atmospherically important gases. 

Indigenous microbial communities across the range 

of tropical soils should be investigated, along with 

how shifts in community function or allocation 

patterns (enzymes vs. growth) could modulate 

system response to changing conditions. Finally, the 

cross-disciplinary interactions necessary to identify 

and scale key belowground characteristics should be 

fostered. Research gaps and uncertainties in belowground processes include:

•	 What controls spatial and temporal patterns 

of root production, and how will root production shift with changes in climate and atmospheric inputs? Understanding gained from 

temperate systems cannot be directly extrapolated 

to the Tropics because of substantial differences 

in plant communities, soil characteristics, climate, 

and soil biology. What factors (e.g., nutrient 

availability and soil hydrology, redox, pH, texture, 

depth, and biology) control spatial and temporal 

patterns in root productivity? What traits are 

important for modeling root function, and are 

they predictable from aboveground plant traits 

or soil characteristics? How will root allocation 

depend on or reflect changes in soil fauna and 

microbial communities?

•	 How will changes in root inputs alter belowground biogeochemistry and carbon stabilization? Improved understanding of the processes 

involved in the transformation of root carbon 

to stabilized soil carbon is the focus of intense 

interest. A high priority is investigating microbial 

and mineralogical mediation of carbon stabilization in tropical soils and the ways that root inputs 

alter these processes. Also important are efforts to 

identify and distinguish factors critical for stabilizing soil organic matter on short (decades or less) 

and long (decades to centuries) timescales. The 

soils near roots are important zones of carbon, 

nitrogen, iron, and phosphorus (hydrolysis) transformation. Changes in the inputs of root carbon 

likely will alter the transformation and resulting 

availability of these nutrients.

•	 How will components of a changing climate 

alter critical soil characteristics? More information is needed on the extent of tropical Histosols 

(peatlands) and their vulnerability to drying, 

land-use change, and fire. Changing patterns of 

leaching, soil redox, and soil organic carbon will 

alter the rates of release and recycling of potentially limiting nutrients (e.g., nitrogen, phosphorus, and potassium).

•	 To what degree will changes in microbial 

community composition and function alter 

nutrient availability (e.g., mycorrhizae and 

mineralization), trace gas production (e.g., of 

methane, nitric and nitrous oxide, and CO2), 

and carbon stabilization? Current understanding of the response of soil microbial communities 

to climate change is derived largely from studies of 

Arctic and, to some extent, temperate systems. The 

marked differences in tropical soils, plants, and 

climate make extrapolations from these studies 

tenuous at best. A number of important aspects 

of soil biology are poorly understood in tropical 

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Integrating Processes
systems, including the role of biological nitrogen 

fixation in different tropical forests (disturbed and 

undisturbed) and the importance of mycorrhizae 

in phosphorus-limited tropical forests.

•	 How can the biological controls of belowground biogeochemistry be best represented 

in models? In temperate systems, basing decomposition models on enzyme parameters has been 

a topic of interest, but how can models most 

accurately represent control of decomposition in 

tropical systems? In the next decade, a wealth of 

information will emerge from molecular characterizations of soil communities. Are there components of these huge datasets that will be useful in 

large-scale models? Are there indices of microbial 

community function that can be scaled up in time 

and space in tractable and robust ways?

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Hydrology Within 

Tropical Natural Forests: 

Implications for Large-Scale 

Ecosystem Modeling

CHAPTER 11
Hydrology Within Tropical Natural Forests: 

Implications for Large-Scale Ecosystem Modeling

The discipline of hydrology when focused on 

issues pertinent to tropical natural forests 

(sometimes described as “tropical forest 

hydrology”; Bonell 1999) may be divided into the 

study of (1) canopy hydrology and (2) hydrologic or 

“runoff ” pathways (Bonell 2004; Wohl et al. 2012).

Canopy Hydrology: Water Interactions 

Among the Atmosphere, Forest 

Canopy, and Land

Two central concerns for studying canopy hydrology within forests are (1) the effect of the vegetation 

canopy on the magnitude and distribution of rainfall 

reaching the ground surface and (2) the flux of water 

to the atmosphere by evapotranspiration mechanisms, also described as “latent heat flux” or simply 

“evaporation” (Penman and Schofield 1951).

Rainfall received by the canopy of a tropical natural 

forest is a fundamental component of the regional 

(and global) water cycle and is the key driver for:

•	 The rate of wet-canopy evaporation (a component 

of evapotranspiration).

•	 Rates and location of water flows on and below 

the ground surface.

•	 Rates of nutrient and carbon mobilization and 

transport within watersheds.

•	 River behavior (including nutrient and carbon 

losses).

When compared to temperate biomes, the higher 

rainfall intensities characteristic of tropical forests 

can have a disproportionate effect (due to nonlinearities in the hydrological system) on the dynamics of wet-canopy evaporation (Calder 1996) and 

the preferential pathways of water, nutrients, and 

particles (mineral or organic) toward tropical rivers 

(Chappell 2010; Walsh et al. 2011; Zimmermann, 

Francke, and Elsenbeer 2012). This is particularly the 

case in natural forest areas beneath tropical cyclone 

tracks—including the Caribbean, Queensland (Australia), Madagascar, and the Philippines—given their 

even greater rainfall intensities (Bonell, Callaghan, 

and Connor 2004; Howard et al. 2010; Chappell et 

al. 2012). Because of the impact of these regional 

differences in rainfall characteristics, large-scale ecosystem models must be able to capture how nonlinearities affect the hydrologic pathways and associated 

subsurface nutrient and carbon flows within small, 

low-order watersheds that contribute most riverflow 

and hence aquatic (chemical and particulate) flux 

within tropical natural forests.

Evapotranspiration is the summation of flux by wetcanopy evaporation (sometimes ambiguously called 

“interception loss”), transpiration, soil evaporation, 

and open-water evaporation. Recent advances in 

the direct measurement of evapotranspiration over 

subminute to interannual timescales using the eddy 

covariance (EC) method give observations over 

areas up to a few square kilometers that can assist 

parameterization and evaluation of regional or global 

ecosystem models (Mueller et al. 2011). Synchronous measurement of latent heat, sensible heat, and 

carbon dioxide (CO2) fluxes with EC systems allows 

study of the interactions among key variables of the 

global water and carbon budgets. This is an essential 

aspect of intrinsically interdisciplinary ecosystem 

models, such as Community Land Model (CLM) 4.0 

(Barron-Gafford et al. 2012). Though the number of 

tower-based EC systems is increasing within tropical natural forests, (Fisher et al. 2009), it is only a 

fraction of the number of published studies on basin 

water balance across this biome (Bruijnzeel 1990).

A key uncertainty arising from the extensive 

basin studies within forested and adjacent land 

uses—whether in the Humid Tropics or across all 

global biomes—is the large variability in change to 

evapotranspiration with forest cutting or establishment. With the same proportion of forest being 

cut, observed evapotranspiration changes lie 

within a huge range of values, whether expressed 

as a depth of evaporation (mm) or a proportion 

of rainfall (Andréssian 2004; Brown et al. 2005). 

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This variability makes it difficult to generalize how 

regional evapotranspiration is affected by various intensities of tropical natural forest cutting. 

The Zhang et al. (2001) generalization (so-called 

“Zhang curves”) is based on 250 global studies, 

including 35 basin studies from tropical latitudes. It 

indicates that forests have significantly higher evaporation rates compared to grasslands where annual 

precipitation is high (>2000 mm per year), but the 

rates are comparable in low rainfall areas (<500 mm 

per year). Important to note is that some of the variability in the evapotranspiration difference between 

forests and herbaceous vegetation arises from errors 

in basin water-balance studies. Many studies use 

basins that are too small (<0.5 km2) to discount the 

effects of deep seepage (so called “basin leakage”), 

resulting in overestimation of evapotranspiration 

totals from annual rainfall minus river discharge 

balances (Bruijnzeel 1996). In addition, many reforestation studies are not monitored long enough to 

show peak (or average) water-use effects (Vertessy, 

Zhang, and Dawes 2003), and studies monitoring 

the effects of forest cutting for only a few years 

emphasize maximum rather than longer-term differences between forests and herbaceous vegetation 

(Kuczera 1987; Andréssian 2004).

Earlier general circulation model (GCM) studies 

indicated that severe droughts within the Amazon 

produced by anthropogenically forced climate 

change could so deplete the subsurface moisture 

available to tropical natural forests that extensive 

tree mortality could occur (Cox et al. 2004). More 

recent studies, however, have demonstrated that 

Amazonian rainforests can maintain high transpiration rates during severe droughts, a finding that 

suggests tree roots are much deeper than specified 

in earlier GCM simulations (Canadell et al. 1996; 

Fisher et al. 2007). This in turn indicates that the 

subsurface moisture stores (accessible to deep tap 

roots) are often much deeper than the few meters 

specified in many GCM simulations. Consequently, 

an understanding of the subsurface hydrology and 

associated hydrologic pathways is fundamental for 

accurately simulating moisture availability in the 

dry season to support transpiration and associated 

tree hydraulic functions.

Hydrologic Pathways: Regulating 

Moisture Availability and 

Nutrient-Carbon Migration

The hydrologic (or water) pathways within watersheds of tropical natural forests can be defined the 

most unambiguously as the lateral flow routes toward 

a stream or river. These routes comprise:

•	 Lateral flow on slopes by infiltration- or saturationexcess overland flow mechanisms, both including 

lateral flow within the litter layer (Hewlett 1982).

•	 Lateral flow within the solum (i.e., A and B soil 

horizons).

•	 Lateral flow within deep saprolite (sometimes 

called the C soil horizon including, for example, 

deep granite saprolite).

•	 Lateral flow within rock aquifers (or localized 

rock fractures).

All of these terms have precise definitions within the 

discipline of scientific hydrology (Kirkby 1978), and 

much ambiguity and misinterpretation arise when 

used incorrectly.

The magnitude of water flow within these paths and 

the moisture states along them (e.g., soil moisture 

content, soil-water potential, and water-table depth) 

govern (1) the availability of moisture for consumptive use by trees within the rooting zone (including 

deep tap roots), (2) rates of soil organic matter 

decomposition, (3) rates of nutrient release and 

transformation, (4) weathering rates, and (5) transport of nutrients and carbon from the land system 

to rivers and oceans (Anderson and Spencer 1991; 

Proctor 2004; Buss et al. 2010; Shanley, McDowell, 

and Stallard 2011; Eaton et al. 2012). All these 

hydrologically mediated processes will need to be 

simulated within the next generation of regional (or 

global) ecosystem models.

Observations of the difference between mean annual 

rates of rainfall and evapotranspiration are insufficient 

to judge the accuracy and role of hydrologic (and 

hence associated nutrient) pathways represented 

within regional ecosystem models. Observations of 

the flows in each of the four lateral pathways (where 

present locally) through sequences of storm-events 

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Chapter 11 – Hydrology Within Tropical Natural Forests: Implications for Large-Scale Ecosystem Modeling

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Integrating Processes
are needed for robust validation. While infiltrationand saturation-excess overland flows can be directly 

measured relatively easily (at least at very small, 

subhectare scales), quantifying the proportion of 

infiltrated water that travels laterally within the solum, 

saprolite, and rock aquifer is extremely difficult to 

do without introducing artificial and very unrealistic 

boundary conditions (Knapp 1970; McDonnell 

2003).

Particulate, carbon, nitrogen, and phosphorus fluxes 

within both overland or subsurface flows and then 

small, low-order streams of tropical natural forests 

are equally dynamic through individual storm 

events, though they are imperfectly correlated with 

water flow (Wilcke et al. 2009; Walsh et al. 2011). 

This is partly because of the highly dynamic nature 

of water flows within shallow hydrologic pathways 

(over subhourly time intervals). Flux associated with 

particulate transport is particularly episodic, being 

dominated by extreme (rare) storm events (Douglas 

et al. 1999). Thus, ecosystem model simulations of 

observed time series of nutrients and aquatic carbon 

must be based on very high frequency sampling 

(often subhourly) of concentration and flow within 

the low-order tropical watersheds where most of the 

load is sourced. Although there are significantly fewer 

river gauging stations within tropical forests compared to temperate biomes, those with frequently 

sampled water-quality data are extremely sparse. 

Hence, observed evidence of linkages between locally 

dominant hydrologic pathways and resultant physicochemical flux (even integrated at the small watershed 

scale via stream-based observations) is very limited 

within tropical forest systems (Wohl et al. 2012).

In terms of observational knowledge of the hydrologic 

pathways across tropical natural forests, detailed 

hillslope and microbasin studies have been conducted 

throughout the region and summarized within several 

publications, notably Bonell et al. (2004). However, 

there is no real consensus on how the presence of 

particular pathways can be identified at large scales 

relevant to global climate models or on their volumetric significance when present. This is partly because 

few studies have been conducted within the Tropics 

and the volumetric significance of each pathway 

at specific sites in any climatic region is debated 

(McDonnell 2003). Some conclusions, however, can 

be drawn from available experimental evidence.

Widely believed outside the tropical hydrological community is that infiltration-excess overland flow—also 

called Hortonian overland flow (HOF)—generates 

a significant proportion of flow within rivers. HOF is 

defined precisely as surface flow (including flow in the 

litter layer) generated outside channels and produced 

by rainfall intensities (in units of mm per hour) greater 

than the saturated hydraulic conductivity of the 

ground surface (also in mm per hour). Contrary to 

popular view, experimental studies show that, except 

for a few isolated examples (e.g., Zimmermann et al. 

2012), HOF per unit basin area is only a few percent 

of the riverflow per unit basin area (Norcliff, Thornes, 

and Waylen 1979; Chappell et al. 2006). The popular 

misconception partly arises from misinterpreting 

the results of inclined-line, hydrograph separation 

into “stormflow” or “quickflow” and “baseflow” (or 

“delayed flow”; Hewlett and Hibbert 1967). This 

method is very useful in deriving a single number (i.e., 

quickflow percent) that characterizes the flashiness of a 

river’s response (Hewlett 1982). However, this proportion should not be used to infer the percentage of the 

total hydrograph sourced from a particular hydrologic 

pathway (e.g., overland flow), as was originally envisaged by Robert Horton (Beven 1991, 2012). When 

such inferences are made, the volumetric importance 

of the (infiltration- or saturation-excess) overland flow 

pathway is grossly exaggerated. For example, quickflow 

is approximately 46% of the total hydrograph in the 

Danum basins within tropical natural forests in Borneo 

(Bidin and Greer 1997), but measured overland flow is 

only 4% of the total hydrograph (Chappell et al. 2006). 

The volumetric insignificance of this pathway does not 

mean that its role in transporting particulates (erosion) or nutrients from the organic surface horizons of 

tropical soils is unimportant. In fact, this small volume 

of water does much work redistributing particles (and 

organic solutes) across slopes to streams. Certain soil 

types found within the Humid Tropics typically have a 

lower ground-surface saturated hydraulic conductivity, 

Ks, (also called infiltration capacity), notably Gleysols 

and Vertisols (Chappell and Ternan 1992; Bonell et al. 

2010). Consequently, these soils should have a greater 

propensity for generating overland flow (whether by 

HOF or saturation overland flow). However, studies 

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that quantify ground-surface Ks, overland flow per 

unit area, and riverflow per unit area are largely absent 

within the Humid Tropics.

With forest disturbance, soils can be affected by localized compaction from vehicles or by trampling from 

domesticated animals, causing ground-surface Ks to 

decrease locally (Bonell et al. 2010) and recover relatively slowly (Hassler et al. 2011). Within landscapes 

that remain forested, however, marked Ks reductions 

are highly localized and any HOF generated often 

reinfiltrates as it moves to less disturbed soils before 

reaching a river, an often unappreciated effect called 

the runoff–runon phenomenon (Bonell and Williams 1986). Even with better data on the proportion 

of rainfall generating HOF, an open question remains 

about how that process should be represented within 

finite element meshes of ecosystem models in which 

element size is so large (i.e., several square kilometers 

or larger) that overland flow cannot be separated 

from channel flow.

Given that almost all rainfall penetrating a tropical forest canopy infiltrates the ground, research 

into hydrologic pathways should be focused on 

subsurface pathways. Most streamflow-generation 

studies conducted within tropical natural forests 

have focused on examining the subsurface A and 

B soil horizons. However, few studies have been 

conducted on the role of deeper strata, notably 

saprolite and rock aquifers (Bonell et al. 2004). 

Underlying small experimental watersheds in, for 

example, northern Thailand (Kog Ma), Peninsular 

Malaysia (Bukit Tarek), Cambodia (O Toek Loork), 

and the central Amazon (Reserva Ducke) are many 

meters of deep saprolite (C soil horizon) with 

high saturated hydraulic conductivity. As a result, 

the lateral flow deep within the saprolite becomes 

a dominant pathway, subsequently damping the 

riverflow hydrograph (i.e., hydrograph recessions 

extending several days after a storm event; Lesack 

1993). There are even fewer small experimental 

watersheds established on rock aquifers within 

tropical natural forests. Large areas of the central 

Amazon and Congo basins, however, are underlain 

by major rock aquifers (Struckmeier and Richts 

2006; www.whymap.org). Where percolation 

readily penetrates both the solum and saprolite to 

recharge deep rock aquifers (“deep groundwater”), 

then river hydrograph recessions extending over 

several months clearly demonstrate the dominance 

of lateral flow within rock aquifers (Ockenden 

and Chappell 2011). Capturing in new ecosystem 

models the subsurface strata having root-available 

moisture storage and the transport of dissolved 

nutrients or carbon (e.g., dissolved organic carbon and CO2) within tropical natural forests will 

require identifying the presence and role of deep 

saprolite and rock aquifers at a pantropical scale; 

where present, hydraulic properties also will need 

to be characterized. Initially, this would serve as 

a basis for classifying tropical hydrologic systems 

into those with a deep rock aquifer (Type IV), a 

deep saprolite (Type III), a solum developed on 

impermeable bedrock and limited saprolite (Type 

II), and steep mountains only supporting an A soil 

horizon (Type I). Areas observed to be dominated 

by HOF (where infiltration is severally restricted) 

might be classified as shallow Type I systems also. 

In very simplistic terms, Type I to IV systems might 

be seen to have active hydrologic depths of 0.2 m, 2 

m, 20 m, and 200 m, respectively, with corresponding hydrograph time constants. Such constants are 

based on the recession characteristics associated 

with the dominant hydrologic pathways (Box, Jenkins, and Reinsel 2008) of minutes, hours, days, and 

months, respectively (see Fig. 11.1, p. 82; Chappell 

et al. 2007).

Although this conceptual model exists, it does 

require pantropical mapping using a combination of existing soil and hydrogeological map data 

combined with hydrograph recession analyses 

(Peña-Arancibia et al. 2010), plus further evaluation against observations from experimental basins 

in the Humid Tropics (Bonell et al. 2004). Such 

work potentially would provide the necessary 

pantropical parameterization for next-generation 

ecosystem models that would simulate (1) locations 

where deep rooting in deeper subsurface hydrologic 

systems affect transpiration and resilience against 

tree mortality (Fisher et al. 2007) and (2) locations where deep hydrologic pathways regulate the 

biogeochemistry of tropical natural forests (Buss 

et al. 2010).

Research Priorities for Tropical Ecosystems Under Climate Change 81

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Integrating Processes
Key Uncertainties and Research 

Opportunities

The preceding synthesis has highlighted several 

key research gaps and uncertainties related to both 

canopy hydrology and hydrologic pathways:

•	 How can water budgets derived from eddy 

correlation and catchment balances be integrated to give a better understanding of the 

changes in forest evapotranspiration following disturbance and reforestation at tropical 

macroscales? Understanding the evapotranspiration component of the tropical water cycle is of 

fundamental importance to ecosystem modeling. 

Although increasing, the number of locations with 

eddy flux observations above tropical forests still 

is limited. Consequently, most evapotranspiration 

estimates for tropical forests, in undisturbed and 

disturbed states, are derived from catchment water 

budgets (i.e., the difference between annual rainfall and annual stream flow per unit area) or the 

analysis of automatic weather station data (Zhang 

et al. 2001; Roberts et al. 2005). All these methods are now known to be prone to considerable 

error (Drexler et al. 2004; Burba and Anderson 

2010). Error analysis and method intercomparisons thus are necessary for all new observational 

studies and as integral parts of any new data 

assimilation studies. Such analyses enable confidence within the findings of new syntheses of 

long-term estimates of evapotranspiration or the 

effects of forest disturbance or reforestation on 

regional evapotranspiration.

•	 What is the depth of the dominant hydrological 

path mapped at each 100 km2 location across 

the Humid Tropics? What saturated hydraulic 

conductivity distribution can be associated 

with this dominant path for each mapped 

location? The pathways of water over and below 

the land surface regulate which strata (soil horizons, 

saprolite, and solid rock) provide the water and 

chemical resources that support tropical forests and 

associated faunal communities (including microbiology) and how nutrients are leached to rivers. In 

steep mountain environments, the dominant hydrological path may extend only to decimeters below 

the ground surface, but, within areas underlain by 

rock aquifers, it may be hectometers deep. Although 

I

II

Type

III

IV

topsoil

topsoil

topsoil

topsoil

0 m

0.2 m

2 m

20 m

200 m

subsoil

subsoil

subsoil

saprolite

saprolite

rock

aquifer

DELTA-model

Fig. 11.1. Schematic Representation 

of Hydrologic Systems in Tropical 

Natural Forests. This figure indicates where 

different pathway systems dominate, including 

near-surface hydrologic pathways (Type I), lateral 

hydrologic pathways in the solum (A and B soil 

horizon; Type II), lateral hydrologic pathways 

in the saprolite (Type III), or lateral hydrologic 

pathways in a rock aquifer (Type IV). Example 

depths and the logarithmic depth scale are given. 

[Adapted with kind permission from Springer 

Science+Business Media: Chappell, N.A., et al. 

2007. “Runoff Processes in Southeast Asia: 

Role of Soil, Regolith and Rock Type.” In Forest 

Environments in the Mekong River Basin, 3–23. 

Eds. H. Sawada, M. Araki, N. A. Chappell, J. V. 

LaFrankie, and A. Shimizu, Springer Verlag, Tokyo. 

© 2007 Springer.]

82 Research Priorities for Tropical Ecosystems Under Climate Change

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maps of the soil types covering the Humid Tropics 

are available, the hydrological functioning of each 

soil type (e.g., whether the flow is predominantly 

vertical or horizontal) is much debated, and there 

is often much variability within each soil type (e.g., 

McDonnell 2003; Chappell and Sherlock 2005; 

Chappell et al. 2007). Maps showing the presence 

of rock aquifers across the Humid Tropics are available (www.whymap.org), but maps of the extent 

of shallow saprolite layers are incomplete. Physicsbased models of catchment hydrology that can 

predict the dominant hydrological paths normally 

are most sensitive to the model parameter of the 

saturated hydraulic conductivity. Within the Humid 

Tropics, observations of the saturated hydraulic 

conductivity typically are available only for very 

small volumes of soil or saprolite. It is now known 

that the values needed to parameterize models 

with grid elements much larger than the measured 

volumes are not easily derived from direct observations (Brooks, Boll, and McDaniel 2004). Much 

research is needed to understand how saturated 

hydraulic conductivity values appropriate for the 

parameterization of regional or global ecosystem 

models can be derived for the mapped soil, saprolite, and rock types across the Humid Tropics.

•	 Can hydrograph shape be used to help determine the dominant hydrological path, (i.e., 

a lateral path via the soil, a saprolite layer, a 

fractured rock, or a rock aquifer) at gauged 

locations throughout the Humid Tropics?

The recession of a river hydrograph is an areaintegrated expression of the dominant hydrological path or paths within a watershed. Watersheds 

where the water movement is dominated by shallow water pathways through the soil have rapid 

hydrograph recessions (i.e., minutes to hours). 

In areas underlain by major rock aquifers, the 

hydrological pathways are much deeper and the 

hydrograph recessions much longer (i.e., months). 

In areas where saprolite pathways or shallow rock 

fractures dominate, then the intermediate duration 

recessions dominate (Ockenden and Chappell 

2011). Analysis of recession constants for many 

watersheds across the Humid Tropics should be 

undertaken systematically (Peña-Arancibia et al. 

2010), as these findings have the potential to help 

develop the pantropical map of the dominant 

hydrological paths.

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Chapter 11 – Hydrology Within Tropical Natural Forests: Implications for Large-Scale Ecosystem Modeling

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Integrating Processes
84 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 11 – Hydrology Within Tropical Natural Forests: Implications for Large-Scale Ecosystem Modeling

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Summary of Key 

Uncertainties and 

Research Opportunities

CHAPTER 12
Summary of Key Uncertainties and Research Opportunities

Research Gaps for Improving 

Representation of Tropical Forests

Large differences in Earth system model (ESM) 

prognoses of future climates are driven by land 

model variations in tropical forest response 

to temperature, precipitation, natural disturbances 

and associated tree mortality, CO2 fertilization, shifts 

in species community composition, and land-use 

change. Given these large uncertainties, the current 

suite of models is able to suggest testable hypotheses 

that can help guide experimental design. As a major 

contributor to national climate change research, the 

U.S. Department of Energy (DOE) is committed 

to enhancing these models to better determine the 

effects of climate change on tropical forests and the 

role of ecological change in feedbacks on the climate 

system. Identifying important research uncertainties 

for achieving this objective was the overarching goal 

of the Research Priorities for Tropical Ecosystems 

Under Climate Change Workshop. Research gaps and 

uncertainties discussed throughout this report were 

examined as independent forcings and responses. In 

reality, the individual themes and variables described 

herein likely will be interactive by nature. For example, temperature and precipitation forcings will be 

co-dependent, requiring a complex systems approach 

to understand the adaptive rates of ecosystems and 

their feedbacks. The following highlights from this 

workshop report summarize important research 

questions critical for improving the representation of 

tropical forest ecosystems in ESMs.

•	 How will tropical ecosystems respond to 

increasing temperatures? In the Intergovernmental Panel on Climate Change’s (IPCC) Fourth 

Assessment Report A1B scenario, temperatures 

are predicted to increase by 2 to 5°C over the 

tropical region by 2100, representing a substantial 

warming (IPCC 2007; Christensen et al. 2007). 

The change in temperature relative to weather 

patterns in the 1900s is particularly important 

because tropical species have adapted to a very 

narrow thermal range. Because the current climate 

is at the upper end of this range, projected temperature increases during this century will increasingly expose tropical forest systems to conditions 

that are beyond their natural operating regime. 

Thus, there are no analogue environments with 

which to compare tropical climates in a warmer 

world. To improve ESM predictions of tropical 

ecological response to increasing temperatures, 

more research is required to address several uncertainties including:

− Are there temperature thresholds beyond which 

photosynthesis significantly decreases? If so, 

what are they?

− Will the temperature sensitivity of respiration 

change with warming, and to what extent can 

plant respiration acclimate to this warming?

− How will plant carbon allocation and related 

respiration patterns change with warming?

− Will warming lead to sustained increases in 

heterotrophic respiration, reductions in soil 

and litter carbon content, and changes to soil 

nutrient availability?

− What is the functional diversity among tree 

species in temperature responses, and how does 

it vary across tropical regions?

•	 How will tropical ecosystems respond to 

changes in rainfall? Atmospheric processes 

are among the best developed aspects of current 

models. Projections from these models indicate 

reduced precipitation patterns and regimes across 

large tropical regions (such as the southern and 

eastern Amazon) and increased rainfall seasonality, raising concerns over the vulnerability of 

tropical forests to drought-induced changes in 

ecosystem structure and functioning. These 

projections also show increased rainfall over 

other regions such as tropical Africa. To improve 

model representation of tropical forests, a better 

understanding is needed of the response of these 

systems to changes in water supply and, most 

importantly, the spatial and temporal drivers and 

86 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 12 – Summary of Key Uncertainties and Research Opportunities

DOE Office of Science
feedbacks of drought stress and tree mortality. 

Specific uncertainties include:

− How do soil depth, structure, and hydraulic 

properties affect tropical ecosystem responses 

to moisture stress?

− What roles do root structure (e.g., taproots) 

and soil profiles play in responding to drought?

− What is the functional diversity in stomatal 

control strategies among tropical species that 

help prevent desiccation?

− How does the response of plant resource allocation to drought stress vary among tropical species?

− What role does deep subsurface hydrology 

play in the prevalence of deep-rooting in tropical forests, and how does it vary among sites 

and regions?

•	 How will natural disturbance events and tree 

mortality increase as a result of climate forcings? Relatively small directional shifts in tree 

mortality rates (e.g., 1 to 1.5%) can significantly 

affect the global carbon cycle and net forestatmosphere CO2 exchanges. The potential for 

increased tree mortality from drought, fire, temperature, and windthrow is a primary concern. 

To improve model predictions of disturbance 

regimes, several research gaps must be addressed:

− What are the dominant mechanisms of vegetation mortality in tropical forests, and how do 

they vary among tropical regions?

− How does mortality risk from climate forcings 

vary as a function of geography and vegetation 

composition?

− What is the relationship between atmospheric 

convection patterns and the distribution of 

forest blowdown events? How will this change 

through time?

− What vegetation, soil, and climate characteristics define the current edges of the tropical 

forest biome, and how are they likely to shift 

with changes in climate regimes?

− Under what conditions will intact tropical 

forests become susceptible to burning?

− How will forest functional composition shift in 

response to altered disturbance regimes?

•	 How will tropical ecosystems respond to 

increasing atmospheric CO2 concentrations?

Although the increase in atmospheric CO2 is 

unambiguous and short-term physiological 

responses are universal, the integrated response of 

forest ecosystems and the feedbacks to the atmosphere are harder to predict. Research is needed 

to understand the response of tropical forests to 

elevated CO2, including the study of critical interactions among CO2, water, and nutrient cycles. 

Large-scale biomass dynamics and belowground 

responses are also important for understanding the 

longer-term fate of carbon. ESMs cannot predict 

the response of tropical forests to elevated CO2

without new data that address critical uncertainties, including:

− How will increasing atmospheric CO2 affect leaflevel gas exchange under tropical conditions?

− How do nutrient limitations affect tropical forest response to elevated atmospheric CO2, do 

these limitations vary spatially at present, and 

how will they change with predicted environmental forcings?

− How will water-use efficiency and drought 

tolerance respond to rising atmospheric CO2?

− How will ecosystem allocation patterns change 

in response to increased CO2?

− Will elevated atmospheric CO2 alter plant species composition?

− How will belowground biogeochemical cycles 

respond to increasing CO2 and affect the 

longer-term fate of carbon?

− Will elevated atmospheric CO2 ameliorate 

drought responses of tropical ecosystems and 

alter their plant community composition?

•	 What are the interactions between climate 

change and aerosols, particulates, and other 

trace gas emissions from tropical forests?

Tropical forests are large sources of biological 

aerosols and trace gases such as methane, nitrous 

oxide, and biogenic volatile organic compounds 

Research Priorities for Tropical Ecosystems Under Climate Change 87

Chapter 12 – Summary of Key Uncertainties and Research Opportunities

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Summary of Key 

Uncertainties
(BVOCs), which all have significant roles in the 

Earth system. Many unanswered questions about 

these compounds and their roles limit the understanding and representation of tropical ecosystems 

in ESMs. Key uncertainties include:

− What are the physiological and climatic factors 

that control plant and soil methane, nitrous 

oxide, and BVOC emissions?

− How does a changing aerosol environment 

affect forest ecosystem properties and processes, such as light quality, storm intensity, 

cloud-aerosol interactions, nutrient deposition, 

and ozone effects on plant physiology?

− How does climate affect production of forest 

aerosols, including those derived from fungi?

•	 How will tropical forest interactions with the 

Earth system shift as a result of anthropogenic 

disturbance and land-use change? A significant 

fraction of the tropical forest cover lies in areas 

recovering from logging or in secondary forests and 

land abandoned from agriculture (FAO 2010). The 

consequences of this land-use change on ecosystem 

function remain uncertain. Addressing the following gaps would help improve model predictions:

− What are the hydrological changes in sensible 

and latent heat fluxes associated with deforestation, logging, and the conversion of forest to 

agricultural activities?

− How does land-use change affect soil biogeochemistry and the ability of forests to recover 

on abandoned agricultural land?

− What are the spatial scales and magnitudes of 

feedbacks among land-use change, climate patterns, and forest fire frequency?

− How will climate change affect aerosol and particulate emissions from biomass burning and 

the interactions among fire-derived aerosols 

and atmospheric processes?

− How do secondary succession and biomass 

accumulation trajectories in abandoned agricultural areas vary with factors such as the intensity of land use or the proximity of seed sources 

for tree establishment?

− What are the key differences in potential climate 

feedbacks between managed and unmanaged 

systems?

Geographical Considerations for 

Large-Scale Project in the Tropics

Geographical constraints need to be considered 

when developing a large comprehensive scientific 

effort to address interactions among tropical forests 

and Earth’s climate system. The high-biomass forests 

of the Amazon, Congo Basin, and Southeast Asia on 

Oxisol and Ultisol soils comprise the bulk of climaterelevant fluxes and potential feedbacks in the Tropics. 

The Amazon and portions of Southeast Asia take on 

added importance with the expectation of decreased 

precipitation, increased prevalence of widespread 

drought, and the potential for elevated tree mortality 

over large eastern and southern portions of the basin 

(Lewis et al. 2011; Marengo et al. 2011; IPCC 2007).

Another consideration is that key mechanisms ubiquitous across the tropical forest biome probably can 

be studied at a variety of sites. For example, although 

tropical forests in Hawaii are quite unique compared 

to others, numerous studies of ecosystem development there have shed light on important processes 

(Chadwick et al. 1999; Vitousek et al. 1997).

Logistical constraints and past research efforts also 

should be taken into account. Central America, the 

Caribbean, and the Brazilian Amazon offer wellestablished infrastructure and decades of outstanding 

tropical forest research activities. The Brazilian-led 

Large-Scale Biosphere-Atmosphere Experiment in 

Amazonia (LBA) project—which had substantial 

support from the National Aeronautics and Space 

Administration’s Terrestrial Ecosystem program—

carried out high-quality research relevant to ESMs at 

a variety of spatial and temporal scales (Davidson et 

al. 2012; Keller et al. 2004). Alternatively, there may 

be compelling reasons to focus new research efforts in 

less-studied regions for which there is a dearth of data.

Leveraging existing small-scale research networks 

and efforts also should be considered to maximize 

representation of all tropical regions. Ultimately, 

good hypothesis-driven science carried out anywhere 

in the Tropics will be valuable in informing models 

88 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 12 – Summary of Key Uncertainties and Research Opportunities

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about critical processes that can improve their predictive capacity. Several approaches could be used to 

address the research gaps and uncertainties described 

throughout this report, including:

•	 Experimental manipulations and detailed observational studies at intensive study sites.

•	 Extensive studies at sites spanning important 

functional gradients in collaboration with existing 

networks such as RAINFOR and the Center for 

Tropical Forest Science within the Smithsonian 

Tropical Research Institute (Condit 1995; Malhi 

et al. 2002).

•	 Extension of these studies using remote sensing and 

geographic information systems for extrapolating 

site-level results to regional and continental scales 

and ensuring adequate sampling of key ecosystem 

gradients (Asner et al. 2005; Chambers et al. 

2007b; DeFries et al. 2002; Saatchi et al. 2011).

Need for Integrated Multidisciplinary 

Effort Examining Tropical Ecosystems

A changing climate has the potential to significantly 

affect the structure and function of tropical forests 

and the direct and indirect feedbacks they provide 

to the climate system. Efforts to predict these effects 

and thus inform future research, energy policy, and 

adaptation strategies are challenged by numerous 

uncertainties discussed throughout this report. 

Robust climate predictions therefore will require 

both a better understanding of how climate forcing factors influence critical ecosystem processes 

and improved representations of these processes in 

ESMs. Given their scope and complexity, addressing these knowledge gaps and model limitations 

demands a coordinated effort by scientists from 

many disciplines. This urgently needed effort will 

leverage existing resources and information and 

also integrate new data, experimental results, and 

process knowledge into fully coupled global climate 

models. These robust, fully coupled community 

models must incorporate diverse sources of information that describe the physical, chemical, and 

biological processes by which tropical ecosystems 

affect and are affected by climate. Coordination and 

stewardship of data from existing and future research 

activities also should be carefully considered as part 

of an integrated modeling-experimental approach to 

predictively understand the Tropics. Together, these 

needed improvements in both process and modeling 

research represent the broad goals of a concentrated 

multidisciplinary effort that closely integrates 

experimental approaches and modeling to maximize 

research investments in ecosystem science.

Research Priorities for Tropical Ecosystems Under Climate Change 89

Chapter 12 – Summary of Key Uncertainties and Research Opportunities

DOE Office of Science

Summary of Key 

Uncertainties
90 Research Priorities for Tropical Ecosystems Under Climate Change

Chapter 12 – Summary of Key Uncertainties and Research Opportunities

DOE Office of Science
Appendices

Appendix 1. Next-Generation Ecosystem Experiment: 

Integrating Modeling and Experimentation................. 92

Appendix 2. Workshop Agenda, Breakout Sessions, 

and Participants.................................................................. 95

Appendix 3. Bibliography .............................................. 101
92 Research Priorities for Tropical Ecosystems Under Climate Change DOE Office of Science

Next-Generation Ecosystem Experiment: 

Integrating Modeling and Experimentation

Appendix 1

DOE Builds on Legacy in 

Ecosystem Science

The U.S. Department of Energy (DOE) is 

responsible for the nation’s energy policy and 

energy futures, and DOE’s Office of Science 

(SC) supports the fundamental scientific research 

needed to meet this responsibility. Within SC, the 

Office of Biological and Environmental Research 

(BER) includes the Climate and Environmental 

Sciences Division (CESD). This division seeks to 

advance a robust predictive understanding of Earth’s 

climate and environmental systems and to inform 

development of sustainable solutions to U.S. energy 

and environmental challenges. In particular, CESD 

seeks to synthesize new process knowledge and 

innovative computational methods advancing nextgeneration integrated models of the human-Earth 

system. These models integrate the state of the science, help inform future research, and form the basis 

for decisions on energy policy.

CESD has a long history in the ecological sciences, 

including sponsoring a number of large-scale, longterm ecosystem experiments that manipulate critical 

environmental parameters including: precipitation 

(Oak Ridge Throughfall Displacement Experiment; 

tde.ornl.gov), temperature, CO2 (public.ornl.gov/

face/global_face.shtml), and combinations thereof. 

In 2007, as the most recent generation of these 

studies neared completion, BER began planning 

for the next generation of ecosystem experiments. 

The goal of this planning activity was to develop an 

approach that closely and iteratively connects modeling and process research. In this approach—aptly 

named Next-Generation Ecosystem Experiment, or 

NGEE—model structure and needs are considered 

in the development of process studies, and process 

outcomes are designed to directly inform and challenge models at appropriate scales. Planning for the 

NGEE activity involved a series of workshops ranging from large community meetings to small focused 

groups. Emerging from a large community workshop 

held in spring 2008 was the concept of focusing on 

systems that are globally (or regionally) 

important, climatically sensitive, and 

understudied or 

underrepresented 

in Earth system 

models (ESMs). 

Details of the workshop are summarized in 

the report Ecosystem Experiments: Understanding Climate Change Impacts on Ecosystems and Feedbacks to the Physical Climate (science.

energy.gov/~/media/ber/pdf/ecosystem_experiments.pdf). Based on these scientific considerations 

and practical limitations, Arctic tundra was found to 

best meet these criteria for the first next-generation 

ecosystem project: NGEE Arctic.

NGEE Approach Bridges Process 

and Modeling Research

The field of climate science has been advanced from 

two important perspectives: process research and 

modeling research. For purposes of this discussion, 

process research involves experiments, observations, 

and measurements performed in the field or laboratory. Modeling research describes the development, 

evaluation, and exercising of computer models that, 

in this case, simulate these same processes.

In many areas of science, models have become 

powerful tools to capture, scale, and describe process 

understanding of complex systems. For climate 

science, models are critical mechanisms that consolidate current understanding of the many processes 

and their interactions that create “climate.” Models 

enable testing of system understanding by conducting computerized experiments that in some cases 

would be impossible to reproduce in nature. The 

analysis of such experiments suggests needed model 

developments and identifies areas of process understanding that are insufficient (or missing altogether). 
Research Priorities for Tropical Ecosystems Under Climate Change 93

Next-Generation Ecosystem Experiment: Integrating Modeling and Experimentation

DOE Office of Science

Models also can be used prognostically to project the 

outcome of future conditions like climate change. 

Such applications are extremely valuable for exploring potential future scenarios but are limited by the 

system knowledge underpinning the model.

Climate models must consider the myriad processes 

that drive the Earth system and its climate. These 

models are extremely complex and challenge the 

capabilities of the most advanced computer systems 

in the world. Such modeling is an exercise in compromise as decisions are made about which processes to 

include (and at what level of detail). Climate modeling has become a highly technical and specialized 

field, demanding specialists with advanced knowledge 

and capabilities in the science of modeling and highperformance computing. This specialization often 

leads to a separation between experts in the processes 

being modeled and the modelers themselves. This 

separation means that process research and climate 

modeling are often independent activities, even 

when they address the same topics. Process research 

is conducted and published in topical or disciplinespecific journals. Modelers mine these journals for 

insights into pertinent processes and data to support 

parameterization or model validation. Significant time 

and effort are invested in consolidating and formatting 

disparate datasets and making them compatible with 

model needs. The process scientists who produced 

the original publications are often unaware that their 

research has been used, missing the opportunity to 

contribute to model development or gain insights 

from model representations of their processes.

This separation is inefficient for developing and 

validating models and improving the process science 

needed to support them. As a major contributor to 

the national climate change research activity, DOE 

has unique capabilities in the process understanding of clouds, aerosols, and terrestrial ecosystems; 

regional, global, and integrated assessment modeling; 

and the high-performance computing expertise and 

hardware needed to implement those models. NGEE, 

which leverages these capabilities, is designed as an 

integrated activity whereby the separation between 

modeling and process research is closed as models 

are exercised to evaluate the impacts of new parameterizations or representations and then the results 

are applied to inform further process research. This 

approach is implemented at both the program level 

as DOE program managers cooperate to design and 

initiate projects and at the project level where large 

efforts (such as NGEE Arctic) incorporate modeling 

and process research components.

The concept of model-experimental (ModEx) 

integration is now fundamental to NGEE. ModEx 

recognizes that improved collaboration between 

modeling and process scientists is needed to develop, 

test, and implement process representations in 

models of all scales. Strongly coupling modeling 

and process-science research ensures that models 

incorporate state-of-the-science knowledge about 

critical systems, reducing the steps between traditional process research and modeling as described 

above. Process studies can advance understanding 

in weak or unrepresented areas, and the resulting 

improved models can be used to guide field and 

laboratory research and to inform future decisions. 

This approach more efficiently meets DOE’s goals of 

predictive understanding but also leverages its investments and national leadership in climate process 

and modeling science, scientific user facilities, and 

high-performance computing.

NGEE Goals, Mechanisms, 

and Implementation

Based on DOE’s mission needs and unique capabilities, NGEE Arctic has been designed to deliver a 

“process-rich ecosystem model, extending from the 

bedrock to the top of the vegetative canopy, in which 

the evolution of target ecosystems in a changing climate can be modeled at the scale of a high-resolution 

ESM grid cell (i.e., 30x30 km grid size).” This concept 

is recognized as being applicable to any target system 

(ecosystem or otherwise) where close coupling of 

process and modeling research could benefit the 

system’s representation in ESMs. BER envisions other 

possible NGEE projects focused on critical ecosystems (e.g., the Tropics), climate systems (e.g., precipitation and clouds), or processes such as water cycling.

The NGEE process is informed by community 

input, guided by the three criteria described previously (globally or regionally important, climatically 

sensitive, and understudied), and directed by BER to 

best match the science direction with DOE mission 

Appendix 1
94 Research Priorities for Tropical Ecosystems Under Climate Change

Next-Generation Ecosystem Experiment: Integrating Modeling and Experimentation

DOE Office of Science

needs. An NGEE project begins by interactions and 

discussions between process and modeling scientists 

to understand the needs and limitations of each 

side. Target models are then exercised and evaluated 

to identify obvious areas of weakness and poor or 

missing process representation. NGEE incorporates 

and considers processes and scales, recognizing that 

processes critical to one scale may be much less 

important at higher (or lower) scales. Myriad small 

processes shape the function of a larger-scale process. 

The scaling challenge in modeling is deciding which 

small-scale processes must be represented and how to 

include them. Models address this challenge through 

parameterization—describing complex, smaller-scale 

processes as simplified, mathematical representations 

in larger-scale models. Parameterization requires 

understanding both the systems in question and the 

target model. Observations and process understanding need to be developed at scales that correspond 

to the modeling goal (or parameterization). Close 

and improved collaboration between modeling and 

process scientists is needed to develop, test, and 

implement parameterizations.

Based on this goal, NGEE works carefully to facilitate 

collaborations between process and model scientists. 

For example, modelers work with process scientists 

to understand how state-of-the-art models represent 

various processes. Process scientists in turn work 

with modelers to capture the complexity of natural 

systems in ways feasible for model representation. 

These partnerships provide opportunities to identify 

and address omissions and insufficiencies in process 

or modeling science; understand the needs and 

constraints of large-scale, coupled models; and tailor 

process science to the needs of models, resulting in 

more robust process representations. Ultimately, 

NGEE evaluates a model, designs experiments and 

observations, confronts the model, and then iterates. The final goal is significant improvement in 

representing the NGEE topic of interest (e.g., Arctic 

permafrost in the case of NGEE Arctic) in coupled, 

community-based ESMs.

DOE national laboratories are uniquely qualified 

to design, implement, and manage large long-term 

research projects such as NGEE. NGEE efforts have 

broad input from the scientific community, including direct and indirect collaborations involving 

other national laboratories, universities, and private 

research entities as appropriate. NGEE projects also 

welcome collaborators from many institutions, providing opportunities for field research in established 

and characterized areas and serving as a resource for 

sample collection. For the initial geography-based 

NGEE projects, DOE anticipates a 10-year duration for field experiments and observations. This 

time frame balances the need for answering critical 

questions with the timescales necessary to examine 

change in terrestrial ecosystems.

Appendix 1
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change 95

Appendix 2

Workshop Agenda, Breakout Sessions, and Participants

Agenda

Hyatt Regency Bethesda, Bethesda, Maryland

Monday, June 4

7:00 a.m. Breakfast (Lobby)

8:00 a.m. Welcome and Introductory Comments (Cabinet/Judiciary Room)

8:00 a.m. Welcome Workshop Organizers

8:05 a.m. Welcome and Workshop Charge Dan Stover (DOE)

8:15 a.m. CESD Investments in the Tropics Gary Geernaert (DOE) 

8:25 a.m. BER and NGEE Sharlene Weatherwax (DOE)

8:35 a.m. NGEE Philosophy Mike Kuperberg (DOE)

8:45 a.m. Plenary Sessions (Cabinet/Judiciary)

8:45 a.m. Introductions and Workshop Discussion Organizing Committee

9:15 a.m. Tropical Forests and Climate Change Joe Wright (Smithsonian Tropical 

Research Institute)

9:45 a.m. Break

10:00 a.m. Modeling Tropical Ecosystems Peter Thornton (Oak Ridge National 

Laboratory) and Marcos Costa (Federal 

University of Viçosa)

10:30 a.m. Modeling Tropical Ecosystems Rosie Fisher (National Center for 

Atmospheric Research) and Jeffrey Chambers 

(Lawrence Berkeley National Laboratory)

11:00 a.m. Breakout Session

11:00 a.m. Breakout logistics Workshop Organizers

11:05 a.m. Breakout Session 1: Tree Ecophysiology

Group A (Cabinet/Judiciary) Lead: Rosie Fisher 

Group B (Waterford) Lead: Richard Norby (Oak Ridge National 

 Laboratory)

Group C (Congressional) Lead: Jeffrey Chambers 

12:30 p.m. Working Lunch (Lobby)

1:00 p.m. Breakout Session Outbrief (Cabinet/Judiciary)

1:45 p.m. Breakout Session 2: Soil Biogeochemistry and Hydrology

Group A (Cabinet/Judiciary) Lead: Jefferson Hall (Smithsonian Tropical 

Research Institute)

Group B (Waterford) Lead: Steven C. Wofsy (Harvard University)

Group C (Congressional) Lead: Sue Trumbore (Max Planck Institute 

for Biogeochemistry)

3:15 p.m. Breakout Session Outbrief (Cabinet/Judiciary)

3:45 p.m. Break

4:00 p.m. Plenary Session (Cabinet/Judiciary)

4:00 p.m. LBA and NGEE Michael Keller (U.S. Forest Service)

4:30 p.m. Open Discussion (Cabinet/Judiciary)

4:50 p.m. Summary and Closing (Cabinet/Judiciary)

5:30 p.m. Writing Teams Collaborate
96 Research Priorities for Tropical Ecosystems Under Climate Change

Workshop Agenda, Breakout Sessions, and Participants

DOE Office of Science

Tuesday, June 5

7:00 a.m. Breakfast (Lobby)

8:00 a.m. Welcome and Reconvening Comments (Cabinet/Judiciary)

8:30 a.m. Plenary Session (Cabinet/Judiciary)

8:30 a.m. Tropical Landscapes Yadvinder Malhi (University of Oxford)

9:00 a.m. Drought Experiments, Ecophysiology Patrick Meir (University of Edinburgh)

9:20 a.m. CO2 and Tropical Forests Lucas Cernusak (Australian National 

 University)

9:40 a.m. Temperature Effects on Tropical Forests Molly Cavaleri (Michigan Technological 

 University)

10:00 a.m. Forest-Atmosphere Interactions Paulo Artaxo (University of São Paulo)

10:30 a.m. Break

10:45 a.m. Breakout Session 3: Disturbance and Forest-Atmosphere Interactions

Group A (Cabinet/Judiciary) Lead: Maria Uriarte (Columbia University)

Group B (Waterford) Lead: Michael Keller 

Group C (Congressional) Lead: Peter Thornton

12:15 p.m. Working Lunch (Lobby)

1:00 p.m. Breakout Session Outbrief (Cabinet/Judiciary)

1:30 p.m. Breakout Session 4: Brainstorming of Additional Topics

Group A (Cabinet/Judiciary) Lead: Charlie Koven (Lawrence Berkeley 

National Laboratory)

Group B (Waterford) Lead: Richard Norby 

Group C (Congressional) Lead: Jeffrey Chambers 

3:00 p.m. Breakout Session Outbrief (Cabinet/Judiciary)

3:30 p.m. Break

3:45 p.m. Open Discussion (Cabinet/Judiciary)

4:45 p.m. Synthesizing the Major Themes (Cabinet/Judiciary)

5:15 p.m. Summary and Closing (Cabinet/Judiciary)

6:00 p.m. Writing Teams Collaborate

Wednesday, June 6

7:00 a.m. Breakfast (Lobby)

8:00 a.m. Writing and Finalization of Workshop Report (writing team)

Appendix 2
Research Priorities for Tropical Ecosystems Under Climate Change 97

Workshop Agenda, Breakout Sessions, and Participants

DOE Office of Science

Workshop Breakout Sessions

Monday, June 4

Breakout Session 1: Tree Ecophysiology 

11:05 a.m. — What are the direct effects of CO2 on leaf physiology and plant carbon metabolism?

11:20 a.m. — How does drought affect tree ecophysiology, and what are the drought-induced 

 mortality thresholds?

11:40 a.m. — How will trees respond to rising atmospheric temperature with a changing climate?

12:00 p.m. — Open discussion on other key tree ecophysiology questions.

Breakout Session 2: Soil Biogeochemistry and Hydrology

1:45 p.m. — How will forests on different soils respond to the same climate change drivers?

2:05 p.m. — How do differences in soil properties and hydrology influence tree susceptibility to 

 drought-induced mortality?

2:25 p.m. — How will soil nutrient availability respond to rising temperature and changes in 

 precipitation?

2:45 p.m. —  Open discussion on other key soil biogeochemistry and hydrology questions.

Tuesday, June 5

Breakout Session 3: Disturbance (Natural and Anthropogenic) and Forest-Atmosphere Interactions

10:45 a.m. — How does land use and land-use change affect mass and energy fluxes to the 

 atmosphere?

11:05 a.m. — How does fire interact with other environmental factors to affect closed-canopy 

 forests and transitions to other states?

11:25 a.m. —  What are other major natural disturbances, and how will they change with climate?

11:45 a.m. —  Open discussion on other key disturbance questions.

Breakout Session 4: Brainstorming of Additional Topics

1:30 p.m. — Diversity and demography.

1:50 p.m. — Forest-atmosphere interactions (e.g., biogenic volatile organic compounds and 

 convection).

2:10 p.m. — Remote sensing and landscape-, regional-, and continental-scale questions.

2:30 p.m. — Open discussion.

Appendix 2
98 Research Priorities for Tropical Ecosystems Under Climate Change

Workshop Agenda, Breakout Sessions, and Participants

DOE Office of Science

Appendix 2

Organizing Committee

Jeffrey Chambers

Lawrence Berkeley National Laboratory

Rosie Fisher

National Center for Atmospheric Research

Jefferson Hall

Smithsonian Tropical Research Institute

Richard J. Norby

Oak Ridge National Laboratory

Steven C. Wofsy

Harvard University

Participants

Ane Alencar

Amazon Institute of Environmental Studies

Paulo Artaxo

University of São Paulo

Patrick Baker

Monash University

Joseph Berry

Stanford University

Molly Cavaleri

Michigan Technological University

Lucas Cernusak

Australian National University

Nick Chappell

Lancaster University

Michael Coe

Woods Hole Research Center

Marcos Costa

Federal University of Viçosa

Stuart Davies

Smithsonian Tropical Research Institute

Mary Firestone

University of California, Berkeley

Guillermo Goldstein

University of Miami

Workshop Participants

Michael Goulden

University of California, Irvine

Lars Hedin

Princeton University

David Hilbert

Commonwealth Scientific and Industrial Research 

Organisation

Forrest Hoffman

Oak Ridge National Laboratory

William Hoffmann

North Carolina State University

Valeriy Ivanov

University of Michigan

Michael Keller

U.S. Forest Service

Charlie Koven

Lawrence Berkeley National Laboratory

Tomo’omi Kumagai

Nagoya University

Ariel Lugo

U.S. Forest Service

Yadvinder Malhi

University of Oxford

Antonio Manzi

National Institute of Amazonian Research

Nate McDowell

Los Alamos National Laboratory

Patrick Meir

University of Edinburgh

Lina Mercado

University of Exeter

Paul Moorcroft

Harvard University

Akira Osawa

Kyoto University

Sasha Reed

U.S. Geological Survey
Research Priorities for Tropical Ecosystems Under Climate Change 99

Workshop Agenda, Breakout Sessions, and Participants

DOE Office of Science

Appendix 2

Alistair Rogers

Brookhaven National Laboratory

Scott Saleska

University of Arizona

Whendee Silver

University of California, Berkeley

Peter Thornton

Oak Ridge National Laboratory

Sue Trumbore

Max Planck Institute for Biogeochemistry

Maria Uriarte

Columbia University

Joe Wright

Smithsonian Tropical Research Institute

Soenke Zaehle

Max Planck Institute for Biogeochemistry

U.S. Department of Energy

Office of Biological and Environmental Research

Sharlene Weatherwax

Associate Director of Science

Gary Geernaert

Director, Climate and Environmental Sciences 

Division

Paul Bayer

Program manager, Climate and Environmental 

Sciences Division

Patrick Horan

Science Assistant, Climate and Environmental 

Sciences Division

Renu Joseph

Program manager, Climate and Environmental 

Sciences Division

Arthur Katz

Program manager, Biological Systems Science 

Division

Dorothy Koch

Program manager, Climate and Environmental 

Sciences Division

Mike Kuperberg

Program manager, Climate and Environmental 

Sciences Division

David Lesmes

Program manager, Climate and Environmental 

Sciences Division

Rick Petty

Program manager, Climate and Environmental 

Sciences Division

Daniel Stover

Program manager, Climate and Environmental 

Sciences Division

Bob Vallario

Program manager, Climate and Environmental 

Sciences Division

Observers

Tony Janetos

Pacific Northwest National Laboratory

Robin Graham

Argonne National Laboratory

Jennifer Pett-Ridge

Lawrence Livermore National Laboratory

Report Preparation

Biological and Environmental Research Information 

System, Oak Ridge National Laboratory

Kris Christen, LeJean Hardin, Holly Haun, Brett 

Hopwood, Betty Mansfield, Sheryl Martin, Marissa 

Mills, and Judy Wyrick
100 Research Priorities for Tropical Ecosystems Under Climate Change

Workshop Agenda, Breakout Sessions, and Participants

DOE Office of Science

Appendix 2
DOE Office of Science Research Priorities for Tropical Ecosystems Under Climate Change 101

Appendix 3

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Appendix 3
AFR Afrotropic

ANOVA analysis of variance

AVHRR Advanced Very High Resolution Radiometer

BER Office of Biological and Environmental 

Research

Biome-BGC Biome–BioGeochemical Cycles model

BVOC biogenic volatile organic compound

C4MIP Coupled Climate–Carbon Cycle Model 

Intercomparison Project

CCN cloud condensation nuclei

CESD Climate and Environmental Sciences Division

CLM Community Land Model

DGVM dynamic global vegetation model

DOE U.S. Department of Energy

EC eddy covariance

ENSO El Niño–Southern Oscillation

ESM Earth system model

EVI enhanced vegetation index

FACE free-air CO2 enrichment

GCM general circulation model

GHG greenhouse gas

GPP gross primary productivity

HOF Hortonian overland flow

HyLand Hyperspectral remote sensing for the 

assessment of crop and soil parameters 

in precision farming and yield estimation 

model

IMA Indo-Malay-Australasia

IN ice nuclei

INPA Instituto Nacional de Pesquisas da Amazônia 

(National Institute for Amazonian Research)

IPCC Intergovernmental Panel on Climate Change

LAI leaf area index

LBA Large-Scale Biosphere-Atmosphere 

Experiment in Amazonia

LIDET Long-Term Inter-site Decomposition 

Experiment Team

LPJ Lund-Potsdam-Jena dynamic global 

vegetation model

MCWD monthly cumulative water deficit

MMD multimodel data

ModEX model-experimental

MODIS Moderate Resolution Imaging 

Spectroradiometer

NDVI normalized difference vegetation index

NEO Neotropic

NGEE Next-Generation Ecosystem Experiment

NPP net primary productivity

OTC open-top chamber

PBA primary biological aerosols

PFT plant functional type

ppm parts per million

SC U.S. Department of Energy Office of Science

SOA secondary organic aerosols

SRES special report on emissions scenarios

TRIFFID top-down representation of interactive 

foliage and flora including dynamics model

VOC volatile organic compound

VPD vapor pressure deficit

WUE water-use efficiency

Acronyms and Abbreviations