National Park Service

U.S. Department of the Interior

Natural Resource Stewardship and Science

Cave Ecology Inventory and Monitoring Framework

Natural Resource Report NPS/NRSS/NRR—2015/948
ON THE COVER

Cave-adapted crayfish in Mammoth Cave (Rick Olson), Pseudoscorpion (Gretchen Baker), Millipede (David Hunter), Cave 

Cricket (Gretchen Baker), microbes (Hazel Barton), and Townsend’s big-eared bats (Shawn Thomas).
Cave Ecology Inventory and Monitoring Framework

Natural Resource Report NPS/NRSS/NRR—2015/948

Gretchen M. Baker

Ecologist

Great Basin National Park

100 Great Basin National Park

Baker, Nevada 89311

Gretchen_Baker@nps.gov

Steven J. Taylor

Illinois Natural History Survey

University of Illinois at Urbana-Champaign

1816 S. Oak Street (MC-652)

Champaign IL 61820-6953 USA

sjtaylor@illinois.edu

Shawn Thomas

Formerly Physical Science Technician

Carlsbad Caverns National Park

3225 National Parks Highway

Carlsbad, NM 88220

sthomas@batcon.org

Kathy Lavoie

Professor of Biology

Dean, Faculty of Arts and Science

101 Ward Hall

SUNY-Plattsburgh

Plattsburg, NY 12901

lavoiekh@plattsburgh.edu

Rick Olson

Ecologist

Mammoth Cave National Park

P.O. Box 7

Mammoth Cave, KY 42259

Rick_Olson@nps.gov

Hazel Barton

Associate Professor

Department of Biology

University of Akron

Akron, OH 44325-1901

bartonh@uakron.edu

Marie Denn

Regional Aquatic Ecologist

Pacific West Region

333 Bush Street, Suite 500

San Francisco, CA 94104-2828

Marie_Denn@nps.gov

Marie Denn

Regional Aquatic Ecologist

Pacific West Region

333 Bush Street, Suite 500

San Francisco, CA 94104-2828

Marie_Denn@nps.gov

Steven C. Thomas

Monitoring Program Leader

Cumberland Piedmont Network

P.O. Box 8

Mammoth Cave, KY 42259

Steven_Thomas@nps.gov

Rene Ohms

Formerly Physical Science Technician

Jewel Cave National Monument

11149 US Highway 16 #B12

Custer, SD 57730

Rene_Ohms@nps.gov

Kurt Lewis Helf

Ecologist

Cumberland Piedmont Network

P.O. Box 8

Mammoth Cave, KY 42259

Kurt_Helf@nps.gov

Joel Despain

Formerly Cave Specialist

Sequoia & Kings Canyon National Parks

47050 Generals Highway

Three Rivers, California 93271-9700

jddespain@fs.fed.us

Jim Kennedy

Formerly Habitat Protection Coordinator

Bat Conservation International 

P.O. Box 162603 

Austin, TX 78716-3302

cavercrash@gmail.com

David Larson

Chief of Resource Management

Big Bend National Park

P.O. Box 129

Big Bend National Park, TX 79834

David_Larson@nps.gov

April 2015

U.S. Department of the Interior

National Park Service

Natural Resource Stewardship and Science 

Fort Collins, Colorado
ii

The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, 

Colorado, publishes a range of reports that address natural resource topics. These reports are of 

interest and applicability to a broad audience in the National Park Service and others in natural 

resource management, including scientists, conservation and environmental constituencies, and the 

public.

The Natural Resource Report Series is used to disseminate comprehensive information and analysis 

about natural resources and related topics concerning lands managed by the National Park Service. 

The series supports the advancement of science, informed decision-making, and the achievement of 

the National Park Service mission. The series also provides a forum for presenting more lengthy 

results that may not be accepted by publications with page limitations. 

All manuscripts in the series receive the appropriate level of peer review to ensure that the 

information is scientifically credible, technically accurate, appropriately written for the intended 

audience, and designed and published in a professional manner. 

This report received formal peer review by subject-matter experts who were not directly 

involved in the collection, analysis, or reporting of the data, and whose background and expertise 

put them on par technically and scientifically with the authors of the information.

Views, statements, findings, conclusions, recommendations, and data in this report do not necessarily 

reflect views and policies of the National Park Service, U.S. Department of the Interior. Mention of 

trade names or commercial products does not constitute endorsement or recommendation for use by 

the U.S. Government.

This report is available in digital format from the NPS Cave and Karst Program at 

(http://www2.nature.nps.gov/geology/caves/cave_parks.cfm) and the Natural Resource Publications 

Management website (http://www.nature.nps.gov/publications/nrpm/). To receive this report in a 

format optimized for screen readers, please email irma@nps.gov.

Please cite this publication as:

Baker, G. M., S. J. Taylor, S. Thomas, K. Lavoie, R. Olson, H. Barton, M. Denn, S. C. Thomas, R. 

Ohms. K. L. Helf, J. Despain, J. Kennedy, and D. Larson. 2015. Cave ecology inventory and 

monitoring framework. Natural Resource Report NPS/NRPC/NRR—2015/XXX. National Park 

Service, Fort Collins, Colorado.

NPS 999/128378, April 2015
iii

Contents 

Page

Figures..................................................................................................................................................vii

Tables...................................................................................................................................................vii

Appendices...........................................................................................................................................vii

Executive Summary..............................................................................................................................ix

Acknowledgments.................................................................................................................................xi

List of Abbreviations and Acronyms....................................................................................................xi

Cave Ecology Glossary........................................................................................................................xii

1.0 Introduction......................................................................................................................................1

1.1 Background...............................................................................................................................1

1.1.1 Definitions of Caves and Karst.........................................................................................2

1.2 Why Caves are Important.........................................................................................................2

1.2.1 Importance of caves as habitats........................................................................................3

1.2.2 Threats to Cave Ecosystems.............................................................................................5

1.3 Introduction to Cave Ecology...................................................................................................8

1.3.1 Ecological Classification of Cave Organisms..................................................................8

1.3.2 Cave Habitats....................................................................................................................9

1.3.3 Ecosystem trophic structure and energy sources............................................................11

1.4 Overview of NPS Cave Resources.........................................................................................16

1.4.1 Solution Caves................................................................................................................16

1.4.2 Lava Caves .....................................................................................................................16

1.4.3 Erosion Caves.................................................................................................................17

1.4.4 Tectonic Caves ...............................................................................................................17

1.4.5 Talus Caves ....................................................................................................................17

1.4.6 Glacier Caves..................................................................................................................18

1.4.7 Sea Caves........................................................................................................................18
iv

Contents (continued)

Page

1.4.8 Epikarst...........................................................................................................................18

1.5 Overview of NPS Cave Ecosystem Management Practices...................................................18

1.5.1 Authority and Policies....................................................................................................18

1.5.2 Categories of Cave Management....................................................................................20

1.6 General Considerations for Inventory and Monitoring ..........................................................21

1.6.1 Setting Goals and Objectives..........................................................................................21

1.6.2 Inventory or Monitoring? ...............................................................................................23

1.6.3 Sampling Design Considerations ...................................................................................23

1.7 Cave Ecological Inventory and Monitoring Currently in Place .............................................25

1.7.1 Mammoth Cave National Park .......................................................................................25

1.7.2 Lava Beds and Oregon Caves National Monuments......................................................25

1.7.3 Lehman Cave (Great Basin National Park)....................................................................26

1.7.4 Jewel Cave National Monument and Wind Cave National Park....................................27

1.7.5 Chickamauga and Chattanooga National Military Park, Cumberland Gap 

National Historical Park, and Russell Cave National Monument ...........................................27

2.0 Potential Monitoring Targets for Cave Ecology Inventory and Monitoring....................................1

2.1 Overview ..................................................................................................................................1

2.1.1 Flagship, Umbrella, and Keystone Species......................................................................1

2.1.2 Listed or other special interest species that are not keystones .........................................2

2.2 Terrestrial Cave Ecosystem......................................................................................................3

2.2.1 Bats...................................................................................................................................6

2.2.2 Woodrats.........................................................................................................................16

2.2.4 Birds ...............................................................................................................................18

2.2.3 Cave Crickets..................................................................................................................20

2.2.5 Cave obligate invertebrates ............................................................................................24
v

Contents (continued)

Page

2.2.6 Other wildlife use of caves.............................................................................................28

2.3 Aquatic Cave Ecosystem........................................................................................................30

2.4 Plants......................................................................................................................................38

2.4.1 Cave Entrance Flora .......................................................................................................38

2.4.2 Lamp flora ......................................................................................................................40

2.4.3 Habitat above Caves.......................................................................................................41

2.5 Microbes.................................................................................................................................42

3.0 General Guidance for Inventory and Monitoring of Cave Ecology...............................................48

3.1 Deciding What to Monitor (Decision Tree) ...........................................................................48

3.2 Best Management Practices for Work in Caves.....................................................................51

3.3 Personnel Requirements and Training....................................................................................53

3.4 Safety......................................................................................................................................53

3.5 Scheduling Work ....................................................................................................................54

3.6 Monitoring Surrogates............................................................................................................54

3.7 Lab and Office Methods.........................................................................................................55

3.7.1 Specimen Vouchers, Tissue Samples, and Photo Vouchers...........................................55

3.7.2 Proper Preservation of Specimens..................................................................................55

3.7.3 Shipping to Taxonomic Experts.....................................................................................56

4.0 Data Management ..........................................................................................................................57

5.0 Data Analysis.................................................................................................................................58

5.1 Power Analyses......................................................................................................................58

5.2 Quality Assurance/Quality Control ........................................................................................58

5.3 Preliminary Data Analysis......................................................................................................59

5.4 Presence/Absence—Occupancy Estimation...........................................................................59

5.5 Trend Analysis........................................................................................................................59
vi

Contents (continued)

Page

5.5.1 Visual Assessment..........................................................................................................59

5.5.2 Parametric vs. Non-Parametric Trend Testing ...............................................................59

5.3.3 Trend-Testing Methods..................................................................................................59

5.5.4 Generalized Linear Mixed Models.................................................................................60

5.6 Reports....................................................................................................................................60

5.7 Resource Briefs ......................................................................................................................60

6.0 Roles, Resources, and Partners......................................................................................................61

6.1 National Park Service Roles and Resources...........................................................................61

6.1.1 Parks...............................................................................................................................61

6.1.2 Networks.........................................................................................................................61

6.1.3 Regions...........................................................................................................................61

6.1.4 Natural Resource Stewardship and Science Directorate ................................................62

6.2 Interagency Cooperation ........................................................................................................62

6.3 Partnerships............................................................................................................................63

6.3.1 National Cave & Karst Management Symposium .........................................................63

6.3.2 Cooperative Ecosystem Studies Units............................................................................63

6.3.3 Academic institutions.....................................................................................................64

6.3.4 Nonprofit and nongovernmental organizations..............................................................64

6.4 Online Resources....................................................................................................................65

7.0 Conclusions....................................................................................................................................66

8.0 Literature Cited ..............................................................................................................................67
vii

Figures 

Page

Figure 1. Cave/karst areas and NPS units with cave/karst resources in the contiguous U.S. ................1

Figure 2. Cave obligate fauna in the United States................................................................................4

Figure 3. Summary of threats to cave ecosystems. ................................................................................6

Figure 4. Energy entering cave by action of trogloxenes. ...................................................................12

Figure 5. Energy entering caves, excluding trogloxenes (Figure 4). ...................................................13

Figure 6. Illustration of cave food pyramid. ........................................................................................14

Figure 7. Diagram of general relationships between cave ecosystems and the landscape. .................15

Figure 8. Cave cricket distribution by HFL (Hind Femur Length) at entrance and deep 

cave sites. .............................................................................................................................................21

Figure 9. Decision Tree for Monitoring Cave Ecology. ......................................................................50

Tables 

Page

Table 1. Cave Organism Classification from least cave adapted to most cave adapted. .......................8

Table 2. Species List of Bats that Use Mines (adapted from Table 1 in Bats and Mines

[Tuttle and Taylor 1988]).......................................................................................................................7

Appendices 

Page

Appendix A: Cave Parks......................................................................................................................76

Appendix B: Example of Cave Classification Scheme........................................................................80

Appendix C: Process for Selecting Caves to Monitor .........................................................................82

Appendix D: Protocols and Standard Operating Procedures...............................................................84

Appendix E: Job Hazard Analysis.......................................................................................................88

ix

Executive Summary

The Cave Ecology Inventory and Monitoring Framework (Framework) is intended to assist National 

Park Service (NPS) cave managers to better understand what lives in the caves that they are 

responsible for managing and how they interact with the cave environment. For many NPS units 

where cave resources have not emerged as a vital sign in their NPS Inventory and Monitoring (I&M) 

Network, additional guidance would be helpful. Designing inventory and monitoring programs for 

cave ecosystems poses particular challenges: many cave species are rare and/or cryptic, and their 

distributions can be highly patchy and variable over time. Logistics of accessing sites can be 

complex, and observers must take unusual care to avoid damaging the ecosystems they are tasked 

with monitoring.

The guidance in this document can aid managers in deciding what to inventory and monitor and ways 

that can be done. It also helps provide a national context, which may help parks conduct inventory 

and monitoring in a more cohesive manner. Due to the wide geographical scope of NPS caves and 

their many different types, the document is not an I&M protocol and it also does not prescribe exact 

protocols. Instead, this document provides peer-reviewed guidance for what types of inventory and 

monitoring are possible, a framework for deciding how to prioritize inventory and monitoring 

activities, and references to specific protocols that are already in place at other caves.

The principal goal of this Cave Ecology Inventory and Monitoring Framework is to encourage cave 

managers to understand as much as possible about local cave ecology and threats to cave biota in 

order to make informed decisions geared towards cave conservation and protection of cave 

ecological systems. In order to do this, the Framework provides managers with tools to determine 

variability and long-term trends in cave biota. Additional objectives of the Framework include 

helping cave managers prioritize monitoring activities and providing guidance on conducting in-cave 

monitoring work by promoting safe and sustainable methods. 

Section 1.0 provides a background of the importance of caves, an introduction to cave ecology, an 

overview of NPS cave resources and what cave ecological I&M programs are already in place, as 

well as some general considerations for inventory and monitoring.

Section 2.0 provides cave managers with examples of what can be monitored, divided into four main 

areas: terrestrial cave ecosystems, aquatic cave ecosystems, plants, and microbes. Within each of 

these areas, potential targets are described and consideration is given to monitoring questions, focal 

species, techniques, sampling locations, and appropriate data analysis. In addition, references, related 

studies, and links to relevant monitoring protocols are provided.

Section 3.0 covers how to decide what to monitor. Before monitoring can proceed, data mining and 

inventories must first be conducted. Data mining will help managers decipher past efforts and 

understand the current state of knowledge on potential monitoring targets. This is an important step 

for planning inventories and avoiding duplication of efforts. Basic inventories include specific biota, 

cave habitats, and threats to caves. Specific biota inventories may focus on something the park is 

known for, such as bats, or for more obscure biota, like microbes or springtails. Park managers need 
x

to know something about the cave habitats in their areas. Conducting assessments may also be a 

valuable use of time and money to better understand cave resources.

Section 4.0 includes basic information on data management, while section 5.0 concentrates on data 

analysis. Due to the rare and cryptic characteristics of some cave biota, additional and/or different 

data analysis techniques from what are used to analyze surface fauna may be required.

Developing and implementing a long-term cave ecological monitoring program is a complex and 

challenging prospect. National Park Service cave managers are well situated to act as catalysts for 

initiating and carrying out monitoring programs, however, they cannot, and should not act alone. 

Monitoring programs will be stronger and more likely to succeed with the input of other cave 

managers, resource specialists, researchers, cave conservation organizations, the NPS I&M Program

and more. Section 6.0 outlines options for collaboration and partnerships, both within and outside of 

the NPS, in order to achieve monitoring goals.
xi

Acknowledgments 

This multi-year national endeavor would not have been possible without the initial enthusiasm of 

Denis Davis and Dale Pate. Reviews of this document by Don Seale, Greg Eckert, Rod Horrocks, 

and Cyndee Watson greatly benefited the manuscript. Help from the National Inventory and 

Monitoring office by Bruce Bingham and Steve Fancy and regional I&M coordinator Penny Latham 

guided the production of this report. Additional information was contributed by Chuck Bitting, Scott 

House, Nancy Nordensten, Emily Ring, Tom Strong, Steve West, and Kevin Wilson.

List of Abbreviations and Acronyms

BRMD Biological Resource Management Division

CESU Cooperative Ecosystem Studies Unit

CFR Code of Federal Regulations

CRF Cave Research Foundation

EIAF Ecological Integrity Assessment Framework

FCRPA Federal Cave Resources Protection Act

FOIA Freedom of Information Act

GIS Geographical Information System

GLMM Generalized Linear Mixed Model

GRD Geological Resources Division

I&M Inventory and Monitoring

KWI Karst Waters Institute

MKT Mann Kendall Test

NCKMS National Cave & Karst Management Symposium

NCKRI National Cave and Karst Research Institute

NPS National Park Service

NRSS Natural Resource Stewardship and Science

NSS National Speleological Society

QA Quality Assurance

QAPP Quality Assurance Project Plan

QC Quality Control

RH Relative Humidity

RPRS NPS Research Permit and Reporting System

SCC Servicewide Comprehensive Call

SKT Seasonal Kendall Test

SOPs Standard Operating Procedures

T&E Threatened and Endangered

TAC Technical Assistance Call

USFWS United States Fish and Wildlife Service

WNS White Nose Syndrome
xii

Cave Ecology Glossary

Accidentals – Animals that find themselves in caves by accident.

Biodiversity – Degree of variation of life.

Cave – The Federal Cave Resources Protection Act (1988) defines a cave as "any naturally occurring 

void, cavity, recess, or system of interconnected passages beneath the surface of the earth or within a 

cliff or ledge, including any cave resource therein, and which is large enough to permit a person to 

enter, whether the entrance is excavated or naturally formed." For the purposes of the Framework, 

caves chosen for ecological inventory and monitoring should be of sufficient length or depth that 

environmental parameters differentiate it from surface habitats. 

Cave Ecosystem – Community of living organisms in conjunction with the nonliving components of 

their environment that include both organisms that live entirely in the cave (e.g., cave obligate 

invertebrates) as well as those that may only come in contact with the cave periodically (e.g., bats) or 

in a small way (e.g., tree roots).

Dark Zone – The area of a cave that is perpetually without light.

Detritovore – An organism that eats detritus to receive its nutrients, for example a millipede. 

Edaphic systems – Soil systems, especially as they affect living organisms.

Edaphobites – Soil inhabiting organisms that may also be encountered in caves, but which are more 

typical of the general soil environment.

Endemic - An organism found only in that particular area and nowhere else in the world.

Entrance Zone – The area of a cave closest to the surface that experiences a greater range of light, 

humidity, and temperature, and generally a higher level of nutrient input.

Epigean – Surface, or above cave.

Epigenic Cave – Caves formed by acids generated at or near the surface (Palmer 2007).

Epikarst – Area under the soil and above the bedrock; this transition zone is often fractured, 

providing an MSS (see below).

Erosion Cave – Cave that forms by the mechanical forces of moving water, and to a lesser extent, 

wind. 

Flagship species – A species chosen to represent an environmental cause, such as an ecosystem in 

need of conservation.

Glacier Cave – A cave that is formed by the melting of channels in ice caps or glaciers.

Guanophiles – Animals associated with accumulations of guano, but not normally found in other 

settings. 

Hypogenic Cave – Caves formed by acids generated partly or entirely at depth below the surface 

(Palmer 2007).

Karst – Landform that is often characterized by a landscape of soluble rock, containing depressions, 

sinkholes, and caves that provide a conduit for subsurface water. 

Keystone species – A species that has a disproportionate effect on its environment relative to its 

abundance.

Lamp Flora – Algae, mosses, and fungi that grow near artificial light sources in caves.

Lava tube – A subterranean void formed when flowing lava begins to cool and subside.

Lentic – Still water, or a body of water.
xiii

Littoral Caves – See sea caves.

Lotic – Flowing water.

MSS – Milleu souterrain superficial, or mesovoid shallow substratum; a transition zone where you 

can often find both epigean and cave adapted animals

Obligate – An organism that is restricted to a particular environment; in this document we speak of 

cave obligate organisms.

Phreatic zone – Zone in the ground, below the water table, in which all the openings are filled with 

water (Palmer 2007).

Pseudokarst – Landform that can contain many of the same resources as karst systems but have a 

very different mechanism of development (e.g., lava tubes, talus caves). 

Sea Cave – A cave formed by erosive wave action in ocean coastal areas and sometimes along the 

shorelines of large lakes.

Sinkhole – A depression or hole in the ground caused by some form of collapse of the surface layer.

Solution Cave – A cave that forms by the dissolving action of subsurface water, as it seeps or flows 

through voids or cracks in soluble bedrock.

Stygobites – An aquatic troglobite.

Stygophiles – An aquatic troglophile.

Talus Cave – A cave that is a void between boulders that accumulate on steep slopes. Or Voids 

within slabs of rock that have separated from the cliff face and accumulated at the base of the cliffs in 

piles are also considered talus caves.

Tectonic Cave – A cave that forms when large slabs of rock move apart during ground movement.

Troglobite – An organism that is limited to caves and similar environments. The most extreme forms 

show adaptations to the cave environment such as reduced eyes and pigmentation. They complete 

their entire life cycle within the cave. 

Troglomorphic – An organism showing adaptations to the cave environment such as reduced eyes 

and pigmentation.

Troglophile – An organism that uses the cave for most parts of its life cycle, but has to return to the 

surface for some purpose, like feeding or reproduction.

Trogloxene – A species that uses caves, but is also found in other locations.

Trophic structure - Refers to the way in which organisms use food resources and how they provide 

energy for other organisms in the food web.

Twilight zone – Area of the cave between the Entrance Zone and the Dark Zone. It has 

characteristics of both.

Umbrella species – Species selected for making conservation related decisions, typically because 

protecting these species indirectly protects the many other species that make up the ecological 

community of its habitat.

Vadose zone – Zone above the water table in which water moves by gravity and capillarity. Water 

does not fill all the openings and does not build up pressures greater than atmospheric (Palmer 2007).

Water table – Upper surface of the phreatic zone (Palmer 2007).

Cave Ecology Inventory and Monitoring Framework 1

1.0 Introduction 

1.1 Background

Cave and karst resources occur in over 125 National Park Service (NPS) units, most of which are 

within the contiguous U.S. (Figure 1). In late 2008 the NPS Cave and Karst Office held a meeting in 

Lakewood, Colorado to discuss how national protocols could be written to address a variety of NPS 

units containing cave resources. It was decided to divide into smaller groups to focus on visitor 

impacts to caves, cave paleontology, cave inventory, cave air quality, cave water quality, and cave 

ecology. This document is the product of the cave ecology group, which communicated 

intermittently by email and teleconference for six years. 

Figure 1. Cave/karst areas and NPS units with cave/karst resources in the contiguous U.S. Adapted from 

Croskrey 2012 and Tobin and Weary 2004.

Cave biological monitoring and inventory is a huge topic with great variety across the units of the 

National Park System. It may include studies on roots in lava tubes at Hawaii Volcanoes National 

Park, bats in talus caves at Pinnacles National Park, endemic microbes in Lechuguilla Cave at 

Carlsbad Caverns National Park, and Endangered Species Act-listed aquatic invertebrate species at 

Mammoth Cave National Park. Due to the large diversity of cave biological and ecological resources 

within the System, the project team determined that specific, one-size-fits-all protocols for all cave 

biological and ecological inventory and monitoring efforts were not practical or desirable. Rather, the 
Cave Ecology Inventory and Monitoring Framework 2

team has worked to develop a decision-making tool that NPS units can use to determine their own 

local cave biology and ecology inventory and monitoring priorities and needs. 

The Cave Ecology Inventory and Monitoring Framework (Framework) is intended to assist NPS cave 

managers to better understand what lives in the caves that they are responsible for managing and how 

they interact with the cave environment. For many NPS units where cave resources have not emerged 

as a vital sign in their NPS Inventory and Monitoring (I&M) Network, additional guidance would be 

helpful. This guidance can aid managers in deciding what to inventory and monitor and ways that can 

be done. It also helps provide a national context, which may help parks conduct inventory and 

monitoring in a more cohesive manner.

This document is called a “Framework” rather than a “Protocol.” Framework is intended to mean a 

guiding document that outlines what is possible, how to decide what to do, and what is already being 

done. This approach is more appropriate for this document, which is national in scope and thus must 

be applicable to many different types of caves and habitats. Protocols, on the other hand, offer 

specific ways to conduct inventory and monitoring. Protocols are referenced in this document so that 

readers can find what has been done at specific parks and borrow or adapt methods where 

appropriate. This document provides a guideline of what can be done, followed by references to 

specific protocols. This organization may be sufficient information for managers to accomplish their 

objectives. In other cases, it may just be a starting point, as the unique nature of each cave park may 

require protocols tailored to that park.

1.1.1 Definitions of Caves and Karst 

The Federal Cave Resources Protection Act (1988) defines a cave as "any naturally occurring void, 

cavity, recess, or system of interconnected passages beneath the surface of the earth or within a cliff 

or ledge, including any cave resource therein, and which is large enough to permit a person to enter, 

whether the entrance is excavated or naturally formed." For the purposes of the Framework, caves 

chosen for ecological inventory and monitoring should be of sufficient length or depth that 

environmental parameters differentiate it from surface habitats. 

Karst is often characterized by a landscape of soluble rock, containing depressions, sinkholes, and 

caves that provide a conduit for subsurface water. This definition can be expanded to include 

pseudokarst, such as lava tubes or talus caves, which can contain many of the same resources as karst 

systems but have a very different mechanism of development. The karst landscapes of the National 

Park Service vary greatly, and are not always easily recognizable. For example, while some NPS 

sites contain vast sinkhole plains, others are known for submerged caves, deeply buried paleokarst or 

high-alpine cave systems. 

1.2 Why Caves are Important

Worldwide, caves have always been of interest and fascination to people. Many great discoveries 

relating to our understanding of paleontology, human evolution, and human cultural evolution have 

been made in caves. The unique conditions in caves preserve records of animal and human activity, 
Cave Ecology Inventory and Monitoring Framework 3

including burials, and clastic sediments and speleothems provide insights into past climates and 

surface conditions. Originally of interest to geologists and biologists as oddities, studies now 

appreciate caves as simplified natural ecosystems of interest to scientists in many disciplines and 

resource managers in many areas (LaMoreaux 2004).

Nearly 20% of the surface of the Earth is carbonate rock suitable for cave formation, including 40% 

of land east of the Mississippi River (White et al. 1995). Carbonate rocks are also important sources 

of oil and gas. Caves provide a window into the subsurface and can allow humans direct access to the 

groundwater system, including the Edwards Aquifer in Texas and the Floridian aquifer, both major 

reserves of fresh water for millions of people. These systems are dynamic, balancing water flow and 

solution of rock, while also being very susceptible to contamination from pollution and spills. 

Many natural areas managed by the National Park Service include caves as the major attraction. 

These include Carlsbad Caverns National Park, Mammoth Cave National Park, Wind Cave National 

Park, Jewel Cave National Monument, Oregon Caves National Monument, and Timpanogos Cave 

National Monument. Parks that are more well known for their surface resources but also contain 

significant cave and karst resources include Great Basin National Park, Sequoia-Kings Canyon 

National Park, Grand Canyon National Park, Lava Beds National Monument, Craters of the Moon 

National Monument, El Malpais National Monument, Buffalo National River, Ozark National Scenic 

Riverways, and others.

1.2.1 Importance of caves as habitats

Caves are important as a distinct ecological resource that varies in substrate, biotic and abiotic 

components, and role in the ecological landscape. Caves provide subterranean habitat for many 

species, some of which are wholly dependent on caves to survive. The unique characteristics of cave 

environments offer the specific conditions required by many animals, as well as some plants that 

utilize cave entrances. At first, these habitats may appear to be isolated from the outside world, with 

a layer of rock separating the underground from sunlight, precipitation, and wind. However, a closer 

look finds that the surface and subsurface are connected in a variety of ways, as described in more 

detail in section 1.3. 

Many caves contain cave-obligate biota (Figure 2), and without caves, these species would cease to 

exist. In North America there are over 1,100 known troglobites and stygobites (see section 1.3.1 for 

definitions of these terms or the glossary at the beginning of the document), with many more likely 

present in other subterranean environments, like aquifers and epikarst. Most cave species are largely 

unknown; they have small populations, restricted ranges, and low rates of reproduction, making field
Cave Ecology Inventory and Monitoring Framework 4

studies difficult, and few can be raised successfully in the lab. 

Figure 2. Cave obligate fauna in the United States. Each dot represents one cave obligate species. From 

Culver et al. (1999), used with permission.

In general, biodiversity in caves is low compared to surface habitats. There are generally fewer food 

resources, reduced subterranean habitat diversity, and decreased boundary ecotones between 

different habitats. Culver and Sket (2000) identified subterranean biodiversity “hot spots” with 

exceptional biodiversity, which they defined as having 20 or more species of both terrestrial 

troglobites and aquatic stygobites. Compare this to surface environments which may support many 

thousands of endemic species. Terrestrial cave environments are dominated by insects and arachnids, 

and the aquatic cave environments by crustaceans. The United States has three hotspots of 

subterranean biodiversity: San Marcos Springs (a phreatic environment) with 27 species, Shelta Cave 

in Alabama with 24 species, and Mammoth Cave in Kentucky with 41 species as of the year 2000. 

There are 14 hotspots in Europe, one in Australia, and one in Bermuda. The Sistem Rostojna Plania

in Slovenia has a stunning 84 species of troglobites. What do these biodiversity hotspots have in 

common? Culver and Sket identified four main factors: 1) high levels of primary productivity, 

usually by chemolitotrophic bacteria or root mats; 2) rich organic inputs of energy; 3) large size, 

which usually means a good diversity of habitats; and 4) permanent groundwater. The majority of 

these sites are threatened by human activity. 
Cave Ecology Inventory and Monitoring Framework 5

Understanding regional patterns is very important in studying subterranean biodiversity. Caves are 

often highly fragmented and separate from one another. For example, in West Virginia the maximum 

number of troglobites in any one cave is 14, but across the state there are 76 known troglobites, many 

considered to be threatened and endangered. 

1.2.2 Threats to Cave Ecosystems

In order to protect cave ecosystems it is important to understand how external factors impact the 

system across local and regional scales. Damage or distortion to cave ecosystems can come from a 

myriad of sources, near and far (Figure 3). Starting with far out sources, air pollution from regional 

and even global sources can impact vegetation that trogloxenes such as bats or woodrats or crickets 

rely upon directly or indirectly for food supply. Such a negative change in vegetation status could 

then reduce the flow of food resources into caves that many cave-adapted organisms rely upon. 

Atmospheric contaminants have direct and indirect effects on cave ecosystems. Ozone causes foliar 

damage to vegetation (Carson 2001), and mercury from coal combustion is toxic to surface and cave 

wildlife, including some listed as endangered. Acid deposition linked to coal combustion causes 

direct damage to vegetation, leaches cations from soil, and mobilizes aluminum, which is toxic to 

plants and aquatic life such as fish (Olson 2001). All component ecosystems within the karst 

landscape, including those in caves, are generally dependent upon the primary productivity of 

vegetation communities. Other sources of impacts to vegetation include exotic insects such as the 

gypsy moth, emerald ash borer, wooly adelgids, and also exotic diseases such as chestnut blight, 

butternut canker, and dogwood anthracnose. Fire obviously affects vegetation, and there can be 

negative impacts from either fire suppression or excessive fire to both water budget and foraging 

habitat for trogloxenes. Excessive vegetative growth over a cave can also impact the subsurface.

Moving to a regional and local scale, water resources in karst and pseudokarst aquifers can be 

impacted by pumping that lowers the water table. For example, at Great Basin National Park, a 

proposal to pump massive amounts of groundwater from the adjacent valleys could lower the water 

table in cave and karst areas according to hydrology studies and aquifer modeling work (Elliot et al. 

2006, BLM 2012). Several of the caves in Great Basin National Park are connected to the water 

table, which if lowered, could affect species both in and above caves, including the newly discovered 

amphipod Stygobromus albapinus.

Surface runoff from agricultural or industrial operations, urban areas, and also routine runoff from 

transportation corridors (highways and railroads) can be significant sources of water pollution. Spills 

along transportation corridors can be catastrophic for cave life (Brucker 1979) if these pollutants are 

carried into caves where they can affect both aquatic and terrestrial cave ecosystems. Trash-filled 

sinkholes can cause toxins to be dumped directly into cave systems. Impoundments on rivers for 

navigation or flood control can have far-reaching and major impacts not only on the river itself, but 

to cave aquatic habitats. For instance, Lock and Dam #6 on Green River adjoining Mammoth Cave 

National Park degrades habitat for seven aquatic species listed as endangered, including the 

Kentucky cave shrimp (Olson 2005). Dams on rivers can alter water levels, flow velocity, and flow
Cave Ecology Inventory and Monitoring Framework 6

Figure 3. Summary of threats to cave ecosystems.

 I. Cave Aquatic Ecosystem 

 

A. Altered Hydrology

 1. Flooding and siltation caused by dam impoundments and increased nearby impervious cover

 2. Lowered water table caused by excessive pumping

 3. Excessive or inadequate fire frequency in fire-adapted vegetation

4. Drying of caves from vegetation clearing (including timbering)

5. Drying of caves by excessive vegetation growth over a cave

6. Drying of caves by paving and surface development

 

B. Toxins and Nutrients

1. Acute Input

a. Spills along transportation corridors

b. Industrial dumping

2. Chronic Input

a. Agricultural chemicals

b. Runoff from roads and parking lots

c. Sinkhole dumps

d. Atmospheric deposition

e. Animal waste from feedlots or large operations

f. Leaking sewer lines

g. Leaking storage tanks

C. Organic Enrichment

1. Animal Wastes

2. Human Wastes

3. Overflow from Eutrophic Sinkhole Ponds

4. Wood Debris (Construction in Cave, Sawmill Waste)

D. Siltation (Other than from impoundments)

1. Erosion from agricultural land and logging sites

2. Erosion from construction sites

 II. Terrestrial Cave Ecosystem

A. Entrance Modifications

1. Natural entrances blocked for security

2. Artificial entrances opened for convenience

3. Poorly designed cave gates that affect microclimate and nutrient flow

B. Disturbance to wildlife

1. Bats awakened from hibernation

2. Migration pathways between cave and surface disrupted

3. Unsustainable levels of human disturbance

4. Substrate (sediment) compaction and alteration

C. Lighting impacts

 1. Lampflora growth and chemical treatment

 2. Heat generation and atmospheric effects

 3. Toxins from broken fluorescent lamps 

4. Behavioral disruption of dark-loving fauna

D. Introduction of exotic species 

1. Fire ants

2. White Nose Syndrome

3. Feral cats, pigs, mice, etc.

 E. Climate Change/Fire

 1. Changes to vegetation affecting surface foraging and water budget

 2. Impacts from weather extremes

I. Cave Aquatic Ecosystem 

 

A. Altered Hydrology

 1. Flooding and siltation caused by dam impoundments and increased nearby impervious 

cover

 2. Lowered water table caused by excessive pumping

 3. Excessive or inadequate fire frequency in fire-adapted vegetation

4. Drying of caves from vegetation clearing (including timbering)

5. Drying of caves by excessive vegetation growth over a cave

6. Drying of caves by paving and surface development

 

B. Toxins and Nutrients

1. Acute Input

a. Spills along transportation corridors

b. Industrial dumping

2. Chronic Input

a. Agricultural chemicals

b. Runoff from roads and parking lots

c. Sinkhole dumps

d. Atmospheric deposition

e. Animal waste from feedlots or large operations

f. Leaking sewer lines

g. Leaking storage tanks

C. Organic Enrichment

1. Animal Wastes

2. Human Wastes

3. Overflow from Eutrophic Sinkhole Ponds

4. Wood Debris (Construction in Cave, Sawmill Waste)

D. Siltation (Other than from impoundments)

1. Erosion from agricultural land and logging sites

2. Erosion from construction sites

 II. Terrestrial Cave Ecosystem

A. Entrance Modifications

1. Natural entrances blocked for security

2. Artificial entrances opened for convenience

3. Poorly designed cave gates that affect microclimate and nutrient flow

B. Disturbance to wildlife

1. Bats awakened from hibernation

2. Migration pathways between cave and surface disrupted

3. Unsustainable levels of human disturbance

4. Substrate (sediment) compaction and alteration

C. Lighting impacts

 1. Lampflora growth and chemical treatment

 2. Heat generation and atmospheric effects

 3. Toxins from broken fluorescent lamps 

4. Behavioral disruption of dark-loving fauna

D. Introduction of exotic species 

1. Fire ants

2. White Nose Syndrome

3. Feral cats, pigs, mice, etc.

 E. Climate Change/Fire

 1. Changes to vegetation affecting surface foraging and water budget

 2. Impacts from weather extremes
Cave Ecology Inventory and Monitoring Framework 7

direction in base-level cave streams. Unnatural sediment deposition may result in the decline in both 

the diversity and abundance of species in the cave aquatic ecosystem due to burial of vital 

rock-gravel habitats and preventing transport of organic matter from headwater inputs (Poulson 

1992). Potential exists for contaminants to be introduced during hydrocarbon extraction.

In developed areas, including within parks, parking lot runoff laden with oil and heavy metals can 

pose a significant threat. Barr (1976) documented such contaminants entering Mammoth Cave’s 

Historic Entrance from the Visitor Center parking lot. In response, the park installed parking lot 

filters in 2001, and these were moderately effective at reducing copper and zinc. Removal of diesel 

fuel from parking lot runoff was very effective (McMillan et al. 2013). 

Most water borne contaminant transfer occurs during flood pulses; at low flow cave waters often 

have no detectable pollution. This makes contaminant monitoring difficult in many cases. For 

monitoring purposes, a distorted cave community composition expresses a "memory" that provides a 

signature of the contaminant class that predominates during floods and indicates the extent of overall 

degradation. 

An overarching threat is climate change. Climate changes can affect the nutrient input into caves, and 

thus the life in them. In addition, many cave species have adapted to live in a habitat with very small 

fluctuations in temperature and humidity. Climate change may cause caves to become warmer and 

drier. It could also increase flooding and erosion, as well as other disturbance events. Climate change 

may even cause shifts in the range of bat species, which could have a direct effect on nutrient input 

and cave ecosystems.

Over time there have been many changes made to cave entrances in park caves for a variety of 

reasons. These have been classified using the best available information (Olson et al. 1997). 

Disturbance to wildlife, especially hibernating bats, can have serious effects from depletion of fat 

reserves1. For this reason, bat hibernacula are off limits for human entry, except for monitoring, 

during the hibernation period. Disturbance to other keystone species such as woodrats could affect 

not only these species, but the communities that are supported by their guano.

 

1 Bats are highly adapted to particular temperatures for successful hibernation. Changes in airflow and temperature 

can often drive out bats. Rafinesque Hall in Historic Mammoth Cave used to be home to a large number of 

hibernating bats, particularly Indiana bats and little brown bats, as evidenced by bones, paleofeces, and staining on 

walls and ceilings. Changes to the entrance to accommodate saltpeter mining and tourism, and possible blockage of 

a small natural entrance in the area, caused the temperature to increase 4-10° C making the roost unsuitable for these 

bats; they abandoned what had been a very successful roost to perhaps a million bats.
Cave Ecology Inventory and Monitoring Framework 8

Heat from high intensity lighting can dry areas that would have remained moist. As the temperature 

rises, relative humidity drops. Adapted to humidity near saturation, cave life is highly vulnerable to

desiccation compared to similar surface species, and mineral deposition may also be altered. Another 

major consideration in cave lighting design is the growth of photosynthetic organisms, alien to cave 

ecosystems. Their presence and the chemical measures used to control their growth constitute a 

major distortion to cave ecosystems (Olson 2002, Olson 2006).

1.3 Introduction to Cave Ecology 

Cave ecology is the study of how cave biota interacts with each other and their environment.

1.3.1 Ecological Classification of Cave Organisms

There are numerous systems that have been developed for classifying cave organisms. The most 

widespread system, and most familiar to natural resources managers, classifies organisms into four 

categories (Table 2). 

Table 1. Cave Organism Classification from least cave adapted to most cave adapted.

Accidentals Accidentals are organisms that find themselves in caves by accident. These include everything 

from a turtle being washed in during a spring flood to an unfortunate cow falling into a pit. They 

have no adaptations to the cave and usually die, contributing nutrients to the food base.

Trogloxenes Trogloxenes (cave-foreigners or cave-guests) are species that use caves, but are also found in 

other locations. Common trogloxenes include bats and some cave crickets, like Ceuthophilus

spp., which only use caves as a roost or to overwinter, and a frog or snake seeking the cool of 

an entrance on a hot summer day,

Troglophiles Troglophiles (cave-lovers) are animals that use the cave for most parts of their life cycle, but 

have to return to the surface for some purpose, like feeding or reproduction. Some cave 

crickets, like Hadenoecus spp., are troglophiles. They reproduce entirely within the cave, but 

leave at night to feed on the surface.

Troglobites Troglobites (cave-life) are limited to caves and similar environments. The most extreme forms 

show adaptations to the cave environment such as reduced eyes and pigmentation. They 

complete their entire life cycle within the cave. We sometimes separate terrestrial troglobites 

and aquatic stygobites.

These four categories are simplistic, arbitrary boxes that facilitate better understanding of cave 

ecology, and also are somewhat dated terminology. Nonetheless, we will use these terms as they are 

most efficient for communicating basic cave ecology concepts.

Some other classifications of cave organisms cave resource managers may encounter include:

Edaphobites -- Soil inhabiting organisms that may also be encountered in caves, but which are more 

typical of the general soil environment.

Guanophiles -- Animals associated with accumulations of guano, but not normally found in other 

settings – most typically, we think of the large numbers of invertebrates that accumulate on mounds 

of bat guano below larger bat roost sites in caves.
Cave Ecology Inventory and Monitoring Framework 9

Stygophiles & Stygobites -- These terms are sometimes used to refer to aquatic troglophiles and 

troglobites.

An entirely different approach to classifying cave organisms is based upon their trophic position: 

detritovores, omnivores, carnivores, etc. We’ll take this up a little later in discussing trophic 

structure.

1.3.2 Cave Habitats

Many habitat types occur in caves. A variety of environmental parameters that influence the nature of 

specific habitats overlay the structural habitat types discussed below.

Zonation

Physical conditions change as you move deeper into a cave. As you enter a cave there is often a 

noticeable increase in humidity and a change in temperature. It gets darker quickly until there is 

complete darkness. This zonation begins with the entrance zone, with surface-modified conditions,

through a twilight or transition zone into the deep cave, where we encounter true cave conditions of 

nearly constant temperature and high humidity in total darkness. The transition zone has greater 

species diversity since it includes organisms found in both entrance and deep cave zones.

The constant-temperature zone tends to closely mirror the mean annual surface temperature. Between 

the constant temperature zone and the ambient surface temperature exists the dynamic variable 

temperature zone. This zone is generally thought of as a continuous gradient of temperatures between 

the constant temperature zone and the ambient surface temperature; however, this may not be the 

case when strong weather patterns rapidly alter ambient surface temperature. Passage morphology 

and types of cave winds (chimney effect vs. barometric) will influence the shape and extent of this 

zone. Populations of animals may change in the entrance and variable temperature transition zone 

depending on the season, while the species in the deep or constant temperature zone do not change 

much. Because surface conditions in more tropical areas are much more constant, tropical caves also 

have fewer seasonal differences.

In aquatic environments, temperature zonation is much less extreme since water temperature changes 

slowly. In summer, water may enter the cave only a few degrees warmer, and may adjust to match 

ambient cave temperature as quickly as the twilight zone. In winter, the water entering the cave may 

be slightly cooler, but is at cave temperature by the end of the twilight zone. Because water flow is 

quick and turbulent over long distances, there are only subtle physical differences and gradients in 

aquatic environments in caves. The phreatic zone (deep, constant water) includes permanent 

groundwater environments that are often accessible only by wells or diving . In upper level vadose 

(temporary and/or shallow water) pools and seeps we find short-lived species like isopods, 

amphipods, and planarians. In lower level vadose zones there are longer lived crayfish, shrimp, and 

cavefish. In general, animal species using the same foods in water are less diverse, but larger, and 

with more troglomorphic adaptations for energy conservation than species in adjacent terrestrial 

environments.
Cave Ecology Inventory and Monitoring Framework 10

Light

Moving from the cave entrance to the deep cave environment, available light changes from 

conditions similar to the surface, through very dim light, to complete darkness (if the cave is long 

and/or deep enough). In the entrance and twilight zones, the presence of light allows some plant 

species to persist, with cyanobacteria (blue-green bacteria) growing in areas with the lowest levels of 

light. Similarly, in commercial caves, lighting used to highlight cave features for visitors may 

produce sufficient light to allow the growth of mosses and algae. Even in the deep twilight zone, the 

dim light may be enough for certain animal species to take advantage of the protected cave 

environment. For example, in many cave entrances, birds may be found nesting in sheltered areas. 

When colonial birds nest in cave entrances, their guano can also be an important source of nutrient 

inputs into caves. The complete darkness deeper in the caves give an advantage to those species, 

especially troglobites, which have adaptations that allow them to better sense their surroundings and 

detect food, mates, and preferred habitats.

Humidity

Just as light varies from the entrance to the deep cave, humidity also varies. Generally (and there are 

a variety of exceptions), deep cave environments tend to have very stable humidity levels, and 

relative humidity routinely exceeds 99%. Adaptations needed to maintain moisture may not be 

retained by troglobites, making these species vulnerable to abrupt changes in the humidity of their 

environment. For example, when a new entrance to a cave is created (e.g., valley wall collapse, new 

sinkhole formation, or excavation by humans) the change in airflow could result in a drastic 

reduction in relative humidity and subsequent impact to the cave biota. Small changes have effects 

over a long distance. Smaller caves and caves with more than one entrance tend to be much drier than 

similar caves with only a single entrance.

Temperature

Temperature is another environmental parameter affecting cave habitats. In a “typical” cave, the deep 

cave temperature is about equal to the mean annual surface temperature where the cave is located. 

Caves in southern Arizona are thus much warmer than caves in Montana, and, similarly, higher 

elevation caves tend to be colder than lower elevation caves. Moving closer to the cave entrance, 

however, cave temperatures increasingly fluctuate with surface temperatures. Some species of bats, 

such as the big brown bat, select overwintering sites particularly close to the cave entrance where 

temperatures are cold, therefore habitat requirements may vary. Other species have differing thermal 

requirements. The structure of the cave also influences the cave temperature. A high dome may serve 

as a warm air trap, which can be further warmed by colonial bats. Pits or low areas with no airflow 

outlet may create cold air traps, resulting in the presence of ice year round and providing habitat for 

cold-adapted animals.

Gases

Oxygen and carbon dioxide, as well as other gases, may also vary throughout caves. Where large 

quantities of organic debris accumulate in dead-end pits or are washed up against a sump or 

sediment plug where there is little air circulation, carbon dioxide (and potentially, but less likely, 

hydrogen sulfide and methane) can build up to levels that may be lethal to humans and other 
Cave Ecology Inventory and Monitoring Framework 11

mammals. Invertebrates, with their reduced metabolic demands, may find such habitats perfectly 

suitable. 

Water

As for all life forms, water is very important for cave organisms. Water defines many habitats, 

including cave streams, drips, drip pools, and seeps. These all form habitats for aquatic organisms. 

Seasonal inundation and flooding also help define the parameters of subterranean existence. Water or 

moisture levels help determine who can and cannot live in a particular setting – too dry, for example, 

and a cave cricket egg laid in the substrate may fail to hatch. Too wet and the same egg suffocates. In 

addition, even the smallest amount of water, such as drip water, can bring carbon and nitrogen into 

caves.

Morphology of the cave passage

The form (or morphology) of the cave passage also affects the distribution of species. An abundance 

of wall ledges and ceiling cracks might mean there is suitable habitat for woodrats to nest in areas 

relatively inaccessible to potential predators. Low ceiling heights commonly make for poor roost 

sites for bats – threats from predators such as raccoons (which could easily reach up and grab 

hibernating bats) and from flooding make these sites unsuitable. Cave domes can make excellent

microenvironments for bats.

Substrate

The substrate of the cave floor can also provide a variety of habitats. For example, dry, rocky areas 

with sufficient organic debris provide shelter for spiders under rocks, waiting to prey upon smaller 

animals feeding on organic debris. Bare bedrock substrates, perhaps scoured by floodwaters in the 

past, may provide few microhabitats and appear fairly uninteresting; however exposed bedrock 

provides essential nutrients to the cave ecosystem that can be mobilized by microbial activity. Tiny 

drip pools less than an inch across may contain ostracods (seed shrimp, commonly less than 1/16th of 

an inch long) swimming in their relative depths, and springtails and mites may be found on the 

surface of such tiny pools.

Connectivity

In some caves that are developed near the land surface with relatively little overburden, the 

connectivity of the cave with the surface influences habitat and cave life. For example, tree roots can 

penetrate into the cave through cracks in the overlying bedrock, providing an unusually direct 

connection between sunlight energy captured by living plants and deep cave troglobites. Hawaiian 

lava tube caves are well known for this type of habitat, which harbors several endemic troglobitic 

species. Seepage of overlying or nearby water through tiny cracks may add nutrients to a cave. 

1.3.3 Ecosystem trophic structure and energy sources

Typical cave ecosystems are decomposer ecosystems (Figures 3 & 4). In the absence of solar energy, 

these ecosystems depend upon organic materials which fall, blow, wash, wander, or are otherwise 

brought into caves. This plant and animal material dies (if it has not already), and a variety of fungi 

and bacteria begin the process of breaking down this material. This surface-derived organic material, 
Cave Ecology Inventory and Monitoring Framework 12

perhaps a larger vertebrate that has fallen into a pit entrance or washed into a stream cave, can be 

consumed by larger organisms, such as invertebrates. The bacteria and fungi are fed upon by small 

invertebrates such as springtails and millipedes, which feed at the lowest trophic levels. These, in 

turn may fall prey to larger invertebrates – spiders, harvestmen, beetles, etc., and in situations where 

still larger predators – vertebrates such as cave fish or salamanders – are present, the various 

invertebrates can fall prey to these larger organisms (Figure 6). In most cave settings, larger animals 

which would form still higher trophic levels do not exist. It should be emphasized again that 

compared to surface habitats, caves have low biodiversity and a simplified trophic structure.

The above paragraph describes a typical trophic structure, but there are many variations. A few caves 

have novel energy sources. For example, upwelling deep waters may contain high levels of sulfur, 

which can be broken down by certain microorganisms that oxidize sulfur compounds. In turn, aquatic 

and terrestrial invertebrates can graze upon these microbes as an energy source, forming an 

ecosystem based on an energy source other than sunlight.

Figure 4. Energy entering cave by action of trogloxenes. Illustration by Steve Taylor.

1. Energy from sunlight converts to plant biomass; 

2. Energy transfer to above-ground animals as they eat plants; 

3. Surface foraging trogloxenes feed on plants, organic debris; 

4. Surface foraging animals feed on animals (such as bats feeding on flying insects); 

5. Nesting material, feces (guano), &/or food stores or caches transfer nutrients to the cave; 

6. Other animals in the caves feed on the organic material brought into the cave by trogloxenes, or on the 

fungi & bacteria growing on organic materials; 

7. Bodies, eggs, & young of trogloxenes serve as energy for other cave animals; 

8. Foraging range is how far trogloxenes travel from cave to feed; 
Cave Ecology Inventory and Monitoring Framework 13

9. We expect higher numbers of trogloxenes closer to cave entrances; 

10. Sometimes cave entrances are too small for humans to notice, but these can be used by some 

trogloxenes (mice, crickets, etc.); 

11. Abundance and diversity of cave animals drops with increasing distance from guano &/or nest 

materials; 

12. High concentrations of guano, such as at bat roosts, provide lots of energy, but the available energy 

decreases with increasing distance from the source.

Figure 5. Energy entering caves, excluding trogloxenes (Figure 4). Illustration by Steve Taylor.

1. Energy from sunlight converts to plant biomass; 

2. Energy transfer to above-ground animals; 

3. Plant material falls, blows or is washed into caves, or may be brought in by animals. animals fall or 

wander into caves, or may be washed in during floods or brought in by other animals;

4. Plant and animal material broken down by fungi and bacterial; 

5. Roots trees and other larger plants above cave may penetrate into cave; 

6. Fungi, bacterial and cave animals feed on live and dead roots penetrating into cave; 

7. Water percolates through leaf litter and soil, and may transport organic molecules and fine particulates 

into cave as drip water; 

8. Fungi and bacterial utilize organic material in drip water as an energy source; 

9. Inorganic energy sources, such as high-sulfur groundwater, are occasionally available in caves –

bacteria can utilize these as a source of energy; 

10. Small cave animals feed on bacterial and fungi, larger cave animals may feed on the smaller species.
Cave Ecology Inventory and Monitoring Framework 14

Figure 6. Illustration of cave food pyramid. 

Cave ecosystems do not occur in isolation from the surrounding landscape as diagramed in Figure 7. 

Each component is shown as an oval which overlaps adjacent components, providing transition zones 

that have conditions and populations from all overlapping areas. Cave terrestrial ecosystems interact 

with adjacent cave aquatic systems, which can be influenced by underlying groundwater, epigean 

(surface) flowing water (lotic) and bodies of water (lentic). Between the cave terrestrial system and 

surface terrestrial systems are edaphic or soil systems. Soils modify water seeping through them 

before it enters the cave. Formation of caves is more rapid in areas with overlying organic soils due 

to production of more acids by microorganisms. Under the soil is the epikarst (“upon the karst”) with 

a transition between soil and bedrock. This transition zone is often fractured bedrock, providing an 

MSS (Milleu souterrain superficial, as described in French who were the first to study it, or 

mesovoid shallow substratum 

(www.nsm.buffalo.edu/Research/SPELEOBIOLOGY_NOTES/index.php/Speleo/article/view/19/21)

The MSS is a transition zone where you can often find both epigean- and cave-adapted animals. 
Cave Ecology Inventory and Monitoring Framework 15

Figure 7. Diagram of general relationships between cave ecosystems and the landscape.
Cave Ecology Inventory and Monitoring Framework 16

1.4 Overview of NPS Cave Resources

NPS sites contain a wide variety of cave types, and not all are part of a karst system. Non-karst caves 

include lava tubes, erosion caves, tectonic caves, talus caves, ice caves, and sea caves. This section 

describes the genesis of various types of caves as well as the ecology within them.

1.4.1 Solution Caves

Solution caves, sometimes called karst caves, form by the dissolving action of subsurface water as it 

seeps or flows through voids or cracks in soluble bedrock. The openings are enlarged over time into 

cave passages. These caves form by dissolution, a geochemical process by which water dissolves the 

rock and carries away the dissolved material. The water that forms solution caves usually has acidic 

or weakly acidic properties, which allows it to dissolve the bedrock more readily. The acidity comes 

from the natural acidity of rainwater, enhanced by microbial activity of the overlying soils or driven 

by microbial interactions with local geochemistry, as in the case of hypogenic caves. 

Epigenic caves are formed by surface water sinking underground and dissolving rock. In solution 

caves with epigenic origins, the oldest passages are closer to the surface, and newer passages are 

closer to the water table. Hypogenic caves are formed by groundwater rising from below. The 

dissolving action in hypogenic systems is oftentimes enhanced by the mixing of waters of different 

chemistries.

Solution caves may also be formed by the action of sulfuric acid. The sulfuric acid is usually formed 

from hydrogen sulfide present in groundwater or seepage from fossil fuels. The H2S is converted to 

sulfuric acid abiotically or through the growth of sulfur oxidizing bacteria using it as a source of 

energy (Engel, Stern, and Bennet 2004). This sulfuric acid speleogenesis is present in caves like 

Carlsbad Caverns and Lechuguilla Cave.

Solution caves are often found in limestone, but can also exist in dolomite, gypsum, marble, or any 

other soluble rock. In the National Park System, there are over 2,000 documented solution caves, 

distributed widely across the United States. Notable examples of NPS units containing solution caves 

include Buffalo National River, Carlsbad Caverns National Park, Grand Canyon National Park, Great 

Basin National Park, Jewel Cave National Monument, Mammoth Cave National Park, Oregon Caves 

National Monument, Ozark National Scenic Riverways, Sequoia & Kings Canyon National Parks, 

and Wind Cave National Park.

The ecology of solution caves varies greatly from region to region. Solution caves often contain 

streams or pools that can provide optimal habitat for species that depend on water. The generally 

stable temperature and humidity regimes of most solution caves provide a sheltered environment for 

several species. For instance, bats, invertebrates, and microbiota are often found in solution caves.

1.4.2 Lava Caves

Lava caves (sometimes called lava tubes) form when flowing lava begins to cool. The outer lava 

cools and solidifies first, and as the molten lava within continues to flow and ultimately subsides, a 

hollow tube is formed. Lava caves are often quite shallow, with multiple skylight entrances where the 
Cave Ecology Inventory and Monitoring Framework 17

flowing lava failed to form a continuous ceiling or the roof-rock collapsed after cooling completely. 

The structure of lava tubes can resemble that of some solutional caves, since the passages follow the 

course of the lava flow much as a stream cave will follow stream channels. In the National Park 

Service, lava caves are found in western NPS units such as Craters of the Moon National Monument,

El Malpais National Monument, Lava Beds National Monument, and parks on the islands of Hawaii 

and Guam.

Lava tube ecology is very different from solution caves because the youngest passages are nearest the 

surface, whereas in a typical karst system, deeper passages are younger. Fauna in lava tubes are also 

transitory compared to karst caves. The shallow nature of most lava caves can provide for greater 

input of surface nutrients and more crossover between surface and subsurface species. Many lava 

caves contain extensive root systems that grow through cracks and pores in the ceiling, as surface 

plants seek out moisture in the caves below. The roots can themselves provide habitat for 

microorganisms and invertebrates.

1.4.3 Erosion Caves

Erosion caves form by the mechanical forces of moving water, and to a lesser extent, wind. They can 

be found in almost any rock type, but are most commonly found in rock highly vulnerable to erosion, 

such as sandstone. Erosion caves in the NPS units are found in the desert southwest, in coastal parks, 

and in parks with highly-erodible rock such as Badlands National Park and Death Valley National 

Park.

Erosion caves are generally not extensive systems, and are often small pockets or rock shelters. They 

can provide significant habitat for trogloxene species looking to escape harsh environmental 

conditions outside the caves.

1.4.4 Tectonic Caves

Tectonic caves form when large slabs of rock move apart during ground movement. They most 

commonly form during land sliding or subsidence events in jointed rock and can form large fissures.

Tectonic caves can form in any type of rock, since their formation processes are unrelated to erosion 

or dissolution. In the National Park System, tectonic caves are typically found in high alpine regions 

of the West.

Tectonic caves are usually not extensive, but can form deep fissure pits in excess of 200 feet. They 

can be cold sinks, providing cool habitat in the summer for trogloxenes. They often hold ice and 

snow year round.

1.4.5 Talus Caves

Talus caves (or boulder caves) are voids between boulders that accumulate on steep slopes. Slabs of 

rock that have separated from the cliff face and accumulated at the base of the cliffs in piles are also 

considered talus caves. They are generally not extensive, but some very complex talus caves that are 

multiple kilometers in length have been documented. In the National Park System, talus caves are 
Cave Ecology Inventory and Monitoring Framework 18

found in parks with large boulder slopes, such as Pinnacles National Park, Yosemite National Park, 

and other mountainous regions of the West where vegetation is sparse.

Talus caves can provide habitat for a variety of species, including bats and ground-dwelling 

mammals such as marmots and pikas.

1.4.6 Glacier Caves

Glacier caves are caves that are formed by the melting of channels in ice caps or glaciers. The term 

“ice cave” is often applied more broadly to any cave that contains ice. The glacier caves referred to in 

this cave ecology framework are caves that are formed in ice. In the National Park System, glacier

caves are found in Alaska and Washington.

The ecology of glacier caves is limited to adaptive species that can survive freezing temperatures and 

changing conditions. Microorganisms are known to inhabit many glacier caves worldwide, but life in 

NPS glacier caves has not yet been widely studied.

1.4.7 Sea Caves

Sea caves (also called littoral caves) are formed by erosive wave action in ocean coastal areas and 

sometimes along the shorelines of large lakes. Sea caves can have impressively large entrances, but 

usually are not long or extensive. Exceptions to this include Painted Cave in Channel Islands 

National Park, which is nearly a quarter-mile long and 100 feet wide. NPS sea caves have been 

documented in several coastal NPS units.

Sea caves can provide habitat for a wide variety of species that inhabit the littoral zone, including 

crabs, urchins, barnacles, and mussels. Sea cave species must be resistant to forceful wave action, 

and must be able to survive during periods of high and low tide.

1.4.8 Epikarst 

The epikarst is a boundary between surface soils, underlying bedrock, and the cave. The epikarst 

often has a mixture of species found in both environments. The epikarst is also very important in 

aquatic habitats in caves because it is the source of most of the water from ceiling drips and in pools 

and seeps. Infiltration is slow, and the water chemistry is influenced by conditions in the epikarst.

1.5 Overview of NPS Cave Ecosystem Management Practices

NPS units follow overarching documents to manage the caves within their jurisdictions.

1.5.1 Authority and Policies

The management of caves and karst areas in the National Park System follows the NPS Mission and 

the 2006 NPS Management Policies, as well as the Federal Cave Resources Protection Act of 1988.
Cave Ecology Inventory and Monitoring Framework 19

The National Park Service Mission

"...to conserve the scenery and the natural and historic objects and the wildlife therein and to provide 

for the enjoyment of the same in such manner and by such means as will leave them unimpaired for 

the enjoyment of future generations." (1916 Organic Act)

"The authorization of activities shall be construed and the protection, management, and 

administration of these areas shall be conducted in light of the high public value and integrity of the 

National Park System and shall not be exercised in derogation of the values and purposes for which 

these various areas have been established..." (1978 Redwood Act amending the Organic Act)

The Federal Cave Resources Protection Act of 1988

The NPS follows the Federal Cave Resources Protection Act (FCRPA) of 1988, which in part, states: 

(1) significant caves on federal lands are an invaluable and irreplaceable part of the nation’s natural 

heritage; and (2) in some instances, these significant caves are threatened due to improper use, 

increased recreational demand, urban spread, and a lack of specific statutory protection. The FCRPA 

regulations at 43 CFR § 37.11(d) state that "The policy of the National Park Service, pursuant to its 

Organic Act of 1916 (16 U.S.C. 1, et seq.) and Management Policies (Chapter 4:20, Dec. 1988), is 

that all caves are afforded protection and will be managed in compliance with approved resource 

management plans. 

Accordingly, all caves on National Park Service administered lands are deemed to fall within the 

definition of 'significant cave.'" The purposes of the FCRPA are to: (1) secure, protect and preserve

significant caves on federal lands for the perpetual use, enjoyment, and benefit of all people; and (2) 

foster increased cooperation and exchange of information between governmental authorities and 

those who use caves located on federal lands for scientific, educational, or recreational purposes. The 

FCRPA establishes that "It is the policy of the U.S. that Federal lands be managed in a manner which 

protects and maintains, to the extent practical, significant caves." In order to comply with the intent 

of the FCRPA, cave resources must be inventoried, or existing inventories used, to determine the 

significance of individual caves.

The FCRPA also contains a Freedom of Information Act (FOIA) exemption, addressing the 

confidentiality of information concerning the specific location of significant caves to ensure 

protection of the resource. The FCRPA states: "Information concerning the specific location of any 

significant cave may not be made available to the public under section 552 of Title 5, United States 

Code [FOIA] unless the Secretary determines that disclosure of such information would further the 

purposes of this chapter and would not create a substantive risk of harm, theft, or destruction of such 

cave." 16 U.S.C. § 4304(a).

Management Policies 2006 

NPS units have management policies that guide management of caves:
Cave Ecology Inventory and Monitoring Framework 20

Section 4.8.2.2

“As used here, the term “caves” includes karst (such as limestone and gypsum caves) and nonkarst 

caves (such as lava tubes, littoral caves, and talus caves). The Service will manage caves in 

accordance with approved cave management plans to perpetuate the natural systems associated with 

the caves, such as karst and other drainage patterns, air flows, mineral deposition, and plant and 

animal communities. Wilderness and cultural resources and values will also be protected. 

Many caves or portions of caves contain fragile nonrenewable resources and have no natural 

restorative processes. In these cases, most impacts are cumulative and essentially permanent. As a 

result, no developments or uses, including those that allow for general public entry (such as 

pathways, lighting, and elevator shafts), will be allowed in, above, or adjacent to caves until it can be 

demonstrated that they will not unacceptably impact natural cave resources and conditions, including 

subsurface water movements, and that access will not result in unacceptable risks to public safety. 

Developments already in place above caves will be removed if they are impairing or threatening to 

impair natural conditions or resources. 

Parks will manage the use of caves when such actions are required for the protection of cave 

resources or for human safety. Some caves or portions of caves may be managed exclusively for 

research, with access limited to permitted research personnel. In accordance with the Federal Cave 

Resource Protection Act of 1988, recreational use of undeveloped caves will be governed by a permit 

system, and cave use will be regulated or restricted if necessary to protect and preserve cave 

resources. Under 43 CFR Part 37 regulations for the act, all caves in the national park system are 

deemed to be significant. As further established by this act, specific locations of significant cave 

entrances may be kept confidential and exempted from FOIA requests.”

1.5.2 Categories of Cave Management

Caves may be classified to help managers better understand at a glance what the cave contains. One 

such system is found in NPS-77, developed originally for use in Lincoln National Forest by Jerry 

Trout and for use in Carlsbad Caverns National Park by Ronal Kerbo. This system is in use by some 

cave parks, such as Sequoia/Kings Canyon (Sequoia and Kings Canyon National Parks Cave 

Management Plan 1998), while other classifications are used by some parks such as desired future 

conditions at Carlsbad Caverns National Park (Carlsbad Caverns National Park Cave and Karst 

Management Plan 2006).

The NPS-77 system consists of a three-element rating for each cave, which includes a) a numerical 

indication of management type, b) a capital letter indicating the resources in the cave, and c) a 

Roman numeral indicating a cave's hazard rating. The classifications may affect monitoring decisions 

such as prioritization of certain caves, not monitoring a cave due to hazard rating, or seasonal 

monitoring based on resource rating. See Appendix B for an example of cave classifications. 
Cave Ecology Inventory and Monitoring Framework 21

1.6 General Considerations for Inventory and Monitoring

Designing inventory and monitoring programs for cave ecosystems poses particular challenges: many 

cave species are rare and/or cryptic, and their distributions can be highly patchy and variable over 

time. Logistics of accessing sites can be complex, and observers must take unusual care to avoid 

damaging the ecosystems they are tasked with monitoring. Programs aimed at monitoring microbial 

species are particularly problematic, as the majority of microbial species (99.99%; (Amann et al. 

1996)) cannot be studied using traditional culture techniques and instead require expensive and timeconsuming molecular techniques. 

In addition to cave-specific considerations, a good long-term monitoring program for any habitat:

 is careful not to over-collect sensitive species;

 provides useful information to conservation managers; 

 can track either communities or single species; 

 doesn’t neglect rare species that are not protected under endangered species legislation, but also 

considers prioritizing common species for monitoring; 

 can focus on either charismatic species or inconspicuous-but-ecologically-critical biota; 

 doesn’t limit itself to tracking species that may become extirpated early or do not follow general 

trends; 

 addresses questions that have management solutions; 

 considers the possibility of a shifted baseline in altered habitats;

 tracks metrics that are of interest to the general public; and,

 creates ground-breaking, publishable ecological data. 

Of course, obtaining all of these ideals is almost always infeasible, but careful planning before 

initiating any inventory or monitoring program can maximize the benefit for the government funds 

dedicated to the program.is important that any Long-term monitoring program must be able to 

withstand changes in personnel and technology. Some critical steps for planning an inventory and 

monitoring program are:

1) identify management program goals and objectives, 

2) determine if inventory or monitoring is most appropriate, 

3) create a sampling design appropriate for the monitoring questions and objectives, 

4) discuss precautions for field observers to carry out to minimize habitat damage, 

5) describe appropriate staff qualification, and 

6) create procedures to record, verify, analyze, interpret, and store data.

1.6.1 Setting Goals and Objectives

The overall purpose of natural resource monitoring in parks is to develop scientifically sound 

information on the current status and long term trends in the composition, structure, and function of 

park ecosystems, and to determine how well current management practices are sustaining those 

ecosystems. Use of monitoring information will increase confidence in managers’ decisions and 

improve their ability to manage park resources, and will allow managers to confront and mitigate 
Cave Ecology Inventory and Monitoring Framework 22

threats to the park and operate more effectively in legal and political arenas. To be effective, the 

monitoring program must be:

 relevant to current management issues as well as anticipate future issues based on current and 

potential threats to park resources,

 scientifically credible, produce data of known quality that are accessible to managers and 

researchers in a timely manner, 

 be linked explicitly to management decision-making processes. 

One of the most critical steps in designing a monitoring program or protocol is to clearly define the 

goals and objectives of the monitoring effort. Developing good management objectives lays the 

foundation for all succeeding management and monitoring efforts. Management objectives need to be 

clearly written descriptions of a measureable stand, desired state, threshold value, amount of change, 

or trend that you are striving to achieve for a particular population or habitat characteristic (Elzinga 

et al. 1998). 

The Vital Signs Monitoring Program has been developed by the I&M Program to look at the most 

important focal resources to get a pulse of how the park unit is doing.

The five Goals of Vital Signs Monitoring are:

 Determine the status and trends in selected indicators of the condition of park ecosystems to 

allow managers to make better-informed decisions and to work more effectively with other 

agencies and individuals for the benefit of park resources.

 Provide early warning of abnormal conditions of selected resources to help develop effective 

mitigation measures and reduce costs of management.

 Provide data to better understand the dynamic nature and condition of park ecosystems and to 

provide reference points for comparisons with other, altered environments.

 Provide data to meet certain legal and Congressional mandates related to natural resource 

protection and visitor enjoyment.

 Provide a means of measuring progress towards performance goals.

Monitoring objectives provide additional detail about what the monitoring program or sampling 

protocol will do. The monitoring objectives explain 'what the protocol will do', and they often put 

boundaries or limits on what will be included in the monitoring by specifying particular study areas, 

species, or measures. The following checklist of questions should be applied to the set of monitoring 

objectives to see if they meet the test: 

 Are each of the objectives measureable? 

 Are they achievable? 

 Is the location or spatial bounds of the monitoring specified? 

 Is the species or attribute being monitored specified? 

 Will the reader be able to anticipate what the data will look like? 
Cave Ecology Inventory and Monitoring Framework 23

An effective set of monitoring objectives should meet the test of being realistic, specific, and 

measurable.

A primary objective of this Cave Ecology Inventory and Monitoring Framework is to 

determine variability and long-term trends in cave biota using summaries of descriptive 

statistics for selected parameters as explained in more detail in section 2.0.

Additional objectives of the Framework include helping cave managers prioritize monitoring 

activities and providing guidance on conducting in-cave monitoring work by promoting safe 

and sustainable methods. Ultimately, the principal goal of the Framework is to encourage cave 

managers to understand as much as possible about local cave ecology and threats to the biota 

supported by caves in order to make informed decisions geared towards cave conservation and 

protection of cave ecological systems.

1.6.2 Inventory or Monitoring?

Inventories are designed to determine the presence, spatial distribution, and/or abundance of a taxa or 

habitat, while monitoring programs seek to assess and detect change over time. Both of these efforts 

are different from traditional research, which typically seeks to unveil cause and effect relationships, 

and natural history studies, which seek to describe life histories of species or organizational structure 

of communities. While this document may suggest useful tools and references for conducting 

research or completing natural history studies for cave biota and habitats, inventory and monitoring 

are its primary foci.

Inventory and monitoring programs have different design criteria: while inventories often are 

designed to efficiently search for a target in space, monitoring programs must have a design that 

allows for successful detection of changes when they occur and minimize the chance that the 

program will conclude a change has taken place when no change has occurred. Both inventory and 

monitoring programs can focus on collecting qualitative data (for example, rapid assessment 

categorical “condition” information or photodocumentation), census data, or sampled data. For any 

of these types of data collection, articulated goals and objectives and attention to quality control are 

needed.

1.6.3 Sampling Design Considerations

Sampling designs answer questions such as: What metrics will be tracked? How many observations 

are needed each season to be able to track changes over time (keeping in mind that there seasonal 

variations may be muted or nonexistent in caves)? Where do staff make observations? How 

frequently and in what seasons should observations be made? What equipment or technique will be 

used to standardize observations?

The answer to the question What metrics will be tracked? depends, of course, on the inventory or 

monitoring question(s). However some metrics provide better information with fewer superfluous 

data points than others. Some considerations when choosing metrics for inventory and monitoring: 
Cave Ecology Inventory and Monitoring Framework 24

 metric should be sensitive to change with alterations in the environment; 

 metric response should be within management-relevant timeframes; 

 metric should be affordable to measure; 

 the potential for discrepancies between observers should be acceptable; 

 when or if the metric changes, the resulting data should be meaningful, biologically 

interpretable, and useful for formulating a management response. 

Questions include: 

 How many observations are needed? 

 Where and how frequently should observations be made? 

 Are observations dependent on the desired minimum detectable change, the tolerance for 

sampling error, and variability in the environment? 

 When do qualitative methods suffice rather than quantitative methods? 

In general, the higher the environmental variability, the less ability a monitoring program will have to 

be able to detect small changes with high confidence. The minimum detectable change desired by a 

monitoring program should be identified before finalizing a sampling design. This parameter should 

be set to be fiscally realistic, biologically significant, and sensitive enough to inform management. 

For example, detecting a 2% change in the abundance of a population may be both cost-prohibitive 

with respect to the number of samples needed (if feasible at all) and less than biologically significant. 

On the other hand, a protocol which could only detect an 80% or greater decline in a population may 

be inexpensive, but would be inadequate for providing timely information to managers. 

Similarly, tolerance for sampling error must be fiscally realistic and also provide managers with 

reasonable certainty about the results of the monitoring program. As a general guideline for a starting 

place, a 10% chance of error due to sampling bias (i.e., either a “type I” or “type II” statistical error)

is an acceptable risk for many monitoring objectives. However, this threshold may be lower for very 

high value resources (where the cost of making a poor management decision due to sampling error is 

high), or, more likely the threshold may be higher in cases for monitoring targets for which designing 

a monitoring program which will yield a 10% sampling error rate is infeasible, due to the high 

number of observations required.

The ability to design a sampling program to meet minimum detectable change and sampling error 

objectives is heavily dependent on data variability and available monitoring techniques: proposed 

monitoring programs will need to be evaluated through a pilot sampling period. If pilot data are 

highly variable then the stated objectives may not be achievable. In this case either objectives will 

need to be less stringent or the sampling protocol will need to be revised.

Because time and money are finite resources among all NPS units, resource managers will most 

likely have to monitor a representative sample of caves from their available pool of caves. Thus, each 

monitoring cave must be carefully chosen to maximize the amount of information gained as a 

function of time spent in the field while minimizing risks to personnel and resources. Caves with 
Cave Ecology Inventory and Monitoring Framework 25

existing monitoring programs that could be linked and/or co-located sampling sites are preferred over 

caves without extant monitoring programs. In Appendix C, we show a process to select monitoring 

caves that is useful to consider regardless of whether or not the NPS unit in question is densely 

populated with caves. In section 3.0, we provide a flowchart for managers to follow to help decide 

what to monitor.

1.7 Cave Ecological Inventory and Monitoring Currently in Place

Below are some examples of cave ecology currently being done in NPS units on a regular basis. 

These efforts are funded primarily by I&M, Servicewide Comprehensive Call, and park base funds. 

Many other NPS sites also have researchers actively studying cave ecology.

1.7.1 Mammoth Cave National Park

Cave ecological monitoring at Mammoth Cave National Park being conducted by the Cumberland 

Piedmont Inventory and Monitoring Network includes six “vital signs.” These include: 1) cave 

crickets, 2) Allegheny woodrats, 3) cave bats, 4) cave aquatic biota, 5) cave meteorology (in 

conjunction with cave crickets and cave bats), and 6) cave water quality and quantity (in conjunction 

with cave aquatic biota). The cave cricket and Allegheny woodrats monitoring protocols were peer 

reviewed, approved, and implemented from 2005-08 (woodrats) and 2006-08 (crickets). They are 

undergoing major revisions and subsequent peer review prior to resuming monitoring in 2014. Cave 

cricket populations will be monitored at six developed caves and seven undeveloped caves using 

strip adaptive cluster sampling. Woodrat populations will be monitored at 75 cave entrances 

(including nine developed caves) using live trapping and occupancy estimation. Development of the 

cave bats and cave aquatic biota protocols began in 2012. These protocols are scheduled for peer 

review, approval, and implementation in 2014. Summer population of cave-dwelling bats will be 

monitored via exit counts at approximately 20 cave entrances, while winter populations of bats will 

be monitored via internal counts with the use of photography at approximately 10 hibernacula caves. 

Cave aquatic biota will be monitored along 10 reaches of subterranean rivers using visual surveys 

and occupancy estimation and modeling. Cave water quality and quantity monitoring at Mammoth 

Cave National Park was included in a comprehensive water quality and quantity monitoring protocol 

peer reviewed, approved, and implemented in 2005 (ongoing). Elements of this protocol will be 

incorporated into the cave aquatic biota protocol. A protocol for monitoring cave meteorology was 

peer reviewed and approved for implementation in 2009. Portions of this protocol will be 

incorporated into the cave crickets and cave bats protocols. See 

http://science.nature.nps.gov/im/units/cupn/monitor/index.cfm for the most current protocols.

1.7.2 Lava Beds and Oregon Caves National Monuments

The Cave Entrance Community and Cave Environment Long-Term Monitoring Protocol is a peerreviewed protocol of the Klamath Inventory and Monitoring Network (Krejca et al. forthcoming).

The protocol is shared between Lava Beds National Monument and Oregon Caves National 

Monument, the two cave parks in the Klamath Network. This long-term cave monitoring effort was 

developed from 2008-2012 (after “cave entrance communities” and “environmental conditions in 

caves” were chosen as Vital Signs for the Klamath Network) and officially implemented starting in 
Cave Ecology Inventory and Monitoring Framework 26

2012. The protocol focuses on seven parameters that were chosen based on their significance as cave 

resources or their influence on the integrity of the cave ecological system. The parameters include 1) 

cave meteorology, 2) ice and water levels, 3) human visitation, 4) cave entrance vegetation, 5) bat 

populations, 6) scat and visible organics deposition, and 7) cave invertebrates. Monitoring is 

implemented in 31 caves at Lava Beds N.M. and in two caves at Oregon Caves N.M. The majority of 

the 31 Lava Beds caves were chosen through a stratified random sample (from over 700 caves), with 

the exception of a small set of hand-chosen caves selected to ensure inclusion of sample sites 

containing hibernating bat populations and year-round ice resources. The two Oregon Caves N.M. 

caves were subjectively (not randomly) chosen from the six caves in the monument, with a major 

monitoring focus on the approximately three-mile long Oregon Cave and a lesser focus on one of the 

five small caves (< 200 ft long) in the monument.

In addition to the Klamath Network cave monitoring protocol, Lava Beds and Oregon Caves have 

long histories of monitoring ecological parameters, including bat populations and cave invertebrates.

As of 2012, Lava Beds has an active bat monitoring program that includes Standard Operating 

Procedures (SOPs) specific to winter hibernacula surveys, summer maternity colony searches, 

evening emergence counts, and acoustic monitoring. These monitoring efforts primarily focus on 

Townsend’s big-eared bats (Corynorhinus townsendii), pallid bats (Antrozous pallidus), and 

Brazilian free-tailed bats (Tadarida brasiliensis), though acoustic methods are used to collect data on 

all 14 bat species at Lava Beds. Both monuments have engaged in short-term (1-2 years) cave 

invertebrate monitoring projects, though long-term monitoring of invertebrate communities will 

follow the Klamath Network protocol. Oregon Caves also conducts year-round “critter surveys” 

along the main tour trail in Oregon Cave. Critter surveys are conducted with varying frequency 

dependent on the season (ranging from weekly during summer to one survey per winter) and aimed 

at recording all detectable vertebrate and invertebrate biota (e.g., bats, moths, harvestmen, crickets) 

observed while walking the tour route.

1.7.3 Lehman Cave (Great Basin National Park)

Great Basin National Park had cave biologists Steve Taylor, Jean Krejca, and Mike Slay conduct a 

bioinventory of Lehman Cave in 2006 with the assistance of park staff. Following that initial effort, it 

was decided to monitor the cave monthly to determine the seasonality in the cave of different 

organisms. Those results are reported in Taylor et al. (2008). Park staff have continued monitoring 

cave biota on a quarterly basis at fourteen paired (on-trail and off-trail) stations in various areas of 

the cave that have been classified as high use, medium use, low use, and very low use. Bait is placed 

at each station, and 24 hours later, a 1-m radius is searched. Microhabit data including air 

temperature, soil temperature, relative humidity, dry bulb, and wet bulb, are recorded. Analysis of six 

plus-years of data has begun. 

During the summer of 2013, wildlife cameras were placed at the entrance of 11 caves to determine 

wildlife use of cave entrances. The most abundant species were Peromyscus spp., humans, 

chipmunks, packrats, and squirrels. In addition, other species observed in cave entrances included 
Cave Ecology Inventory and Monitoring Framework 27

cottontail rabbits, bats, skunks, foxes, insects, birds, and domestic dogs (Baker forthcoming). 

Additional cave entrance monitoring using wildlife cameras is planned.

1.7.4 Jewel Cave National Monument and Wind Cave National Park

John Moore conducted biological inventories in Jewel Cave and Wind Cave from 1992 to 1995

(1996). He concluded that due to their relative isolation from the surface (long cave systems with 

few, small entrances and little energy input), most macro-biota is found near sources of organic 

input, such as entrances and tour routes. However, the lakes in Wind Cave have been found to be 

teaming with unusual microbial life (Hazel Barton, pers. comm. 2013).

Jewel Cave National Monument conducts an annual hibernating bat count in passages near the 

Historic Entrance, using a methodology established in 1992 (Austin 2013). Bats are identified and 

counted by genus, and temperature and humidity measurements are recorded in each of the 24 search 

areas. The cave is one of the largest hibernacula in the world for Townsend’s big-eared bats, with an 

average of 832 individuals.

1.7.5 Chickamauga and Chattanooga National Military Park, Cumberland Gap National 

Historical Park, and Russell Cave National Monument

The Cumberland Piedmont Inventory and Monitoring Network Cave is in the process of initiating 

cave ecological monitoring at four network parks with significant cave resources. These units include 

Chickamauga and Chattanooga National Military Park, Cumberland Gap National Historical Park, 

Russell Cave National Monument, and Mammoth Cave National Park (previously mentioned). Vital 

Signs being monitored in the first three parks listed above include: 1) cave bats, 2) cave aquatic biota, 

3) cave meteorology (in conjunction with cave bats), and 4) cave water quality and quantity (in 

conjunction with cave aquatic biota). Development of the cave bats and cave aquatic biota protocols 

began in 2012. These protocols are scheduled for peer review, approval and implementation in 2014. 

Summer population of cave-dwelling bats will be monitored via exit counts at selected cave 

entrances at all three parks, while winter populations of bats will be monitored via internal counts 

with the use of photography at a subset of hibernacula caves on all three parks (Note: Cumberland 

Gap National Historical Park has an extant winter cave bat monitoring effort at two park caves that 

began in 1993). Cave aquatic biota will be monitored along subterranean rivers at Cumberland Gap 

National Historical Park and Russell Cave National Monument using visual surveys and occupancy 

estimation and modeling. Cave water quality and quantity monitoring at Cumberland Gap National 

Historical Park and Russell Cave National Monument was included in a comprehensive water quality 

and quantity monitoring protocol peer reviewed, approved, and implemented in 2005 (ongoing). 

Elements of this protocol will be incorporated into the cave aquatic biota protocol. A protocol for 

monitoring cave meteorology was peer reviewed and approved for implementation in 2009. Portions 

of this protocol will be incorporated into the cave bats protocol. 
Cave Ecology Inventory and Monitoring Framework 1

2.0 Potential Monitoring Targets for Cave Ecology Inventory 

and Monitoring

2.1 Overview

This section provides cave managers with examples of what can be monitored, divided into four 

main areas: terrestrial cave ecosystems, aquatic cave ecosystems, plants, and microbes.

Within each of these areas, potential targets are described and consideration is given to monitoring 

questions, focal species, techniques, sampling locations, and appropriate data analysis. In addition, 

references, related studies, and links to relevant monitoring protocols are provided. Appendix D 

provides an annotated list of protocols and SOPs already in place in parks. If using I&M funding, 

site specific I&M protocols resulting from the protocol framework (after review and approval), will 

still need to be reviewed according to procedures developed in each region. Well-developed methods 

identified in the protocol framework will not need additional review; however, requirements for 

review of developing methods and technologies will be up to the Regional I&M Program Manager.

2.1.1 Flagship, Umbrella, and Keystone Species

Terms often applied to species that are considered especially important are flagship, umbrella, and 

keystone species. These terms are not mutually exclusive.

A flagship species is a species chosen to represent an environmental cause, such as an ecosystem in 

need of conservation. These species are chosen for their vulnerability, attractiveness or 

distinctiveness in order to engender support and acknowledgment from the public at large. Thus, the 

concept of a flagship species holds that by giving publicity to a few key species, the support given to 

those species will successfully leverage conservation of entire ecosystems and all species contained 

therein. One example is the Indiana bat, a federally-endangered bat that hibernates in caves. By 

protecting it, the caves it uses are also protected, including the other lesser-known species that live in 

them. The bat is attractive to the public and helps to promote awareness of the importance of 

protecting hibernacula. Another example would be the Ozark hellbender (Cryptobranchus 

alleganiensis), a salamander found only in clear, cool waters in Missouri and Arkansas.

Umbrella species are species selected for making conservation related decisions, typically because 

protecting these species indirectly protects the many other species that make up the ecological 

community of its habitat. Two examples are predators that rely on prey they find in caves, the Tooth 

Cave pseudoscorpion (Tartarocreagris texana) and the cave crayfish (Cambarus aculabrum). If 

these predators are protected, then the habitat where they live and thus the prey they eat, are also 

protected.

A keystone species is a species that has a disproportionate effect on its environment relative to its 

abundance. Such species play a critical role in maintaining the structure of an ecological community, 

affecting many other organisms in an ecosystem and helping to determine the types and numbers of 

various other species in the community. An example is the woodrat (and in fact, many trogloxenes). 

Just one woodrat can provide a great deal of energy input for a cave, which then influences a great 

number of the biota that inhabit the cave.
Cave Ecology Inventory and Monitoring Framework 2

All three of the above environmental surrogates can be representative of a range of species and 

habitats. Nonetheless, they still suffer from the failing failure to embrace the full range of 

microhabitats utilized by small invertebrate species (Samways 2007). Recent assessment of available 

data suggests that such indicator species (flagship, umbrella, and keystone species) may actually be 

unreliable as surrogates for biodiversity, and it is recommended that several complementary 

surrogates for biodiversity and environmental conditions should be selected (Gerlach et al. 2013). 

2.1.2 Listed or other special interest species that are not keystones

Many cave and karst species have been listed by the US Fish and Wildlife Service as a Threatened or 

Endangered Species. Some of these include bats (e.g., Indiana bat, Ozark big-eared bat, Virginia bigeared bat), aquatic species (e.g., Alabama cavefish, Illinois cave amphipod, Kuai cave amphipod, 

Peck’s cave amphipod, Tumbling Creek cavesnail, cave crayfish, Texas blind salamander, Squirrel 

Chimney cave shrimp), and terrestrial invertebrates (e.g., Coffin Cave mold beetle, Bee Creek Cave 

harvestman, Tooth Cave pseudoscorpion). (See http://ecos.fws.gov/tess_public/pub/listedAnimals.jsp

for the complete list of threatened and endangered animals.) 

Individual states often have their own threated and endangered species lists that include additional 

species. Other species may be of special interest to managers, for example if they are endemic to a 

national park.

The NPS is mandated to monitor endangered species in most instances. Monitoring techniques for 

listed species usually follows the recovery plan for that species. If no recovery plan is available, as 

for species of special interest, managers should think about the best way to monitor with the least 

amount of impact. Often cave biologists with expertise in that area can provide advice.
Cave Ecology Inventory and Monitoring Framework 3

2.2 Terrestrial Cave Ecosystem

A terrestrial cave ecosystem can vary widely from one cave to another, and even within a single 

cave. Included in this section are taxa that are likely to be encountered, including bats, woodrats, 

birds, cave crickets, and cave obligate invertebrates. We also consider other wildlife use of caves.

Some inventory and monitoring components are nearly the same for all terrestrial taxa. We mention 

them here and then in the individual taxa sections point out any differences.

Dominant threats

Dominant threats to terrestrial cave organisms center around habitat (both in and above the cave). 

Habitat loss or impact may be caused by human disturbance (e.g., unmanaged visitation, intentional

vandalism), in-cave development (e.g., cave infrastructure, lighting, chemical use), land use changes 

above caves, vegetation structure changes above caves (e.g., wildfires alter infiltration), sudden 

environmental changes (e.g., freezes, flash floods), and food source contamination from heavy metals 

and/or pesticides. Some of these threats can be mitigated through land management actions, while 

others may be not be possible to control, such as major environmental changes driven by climate 

change or natural processes. Other threats include increased predators (e.g., more urbanization so 

more feral cats) and invasive species above ground or underground that could affect food sources or 

habitat (e.g., fire ants, fungi, springtails.)

Potential inventory and monitoring questions 

The list of questions related to terrestrial cave organisms and cave use is highly diverse and 

potentially endless, though most cave managers will likely find common ground in wanting to 

determine some basic information about local populations:

 What species are present in caves?

 What caves/sites do they use?

 When are they present (e.g., year-round vs. seasonally)?

 How many are there (population estimates)?

 What is their population status (e.g., stable, decreasing)?

 How does the population or activity change seasonally?

 What can be done to protect them?

More advanced questions may follow after managers have succeeded in answering some of the 

basics about local populations. Many of these questions may be beyond the scope of inventory and

monitoring and enter the realm of research. Additional questions may include:

 What microclimate parameters are the species of interest selecting for, and how does this 

vary based on season/use (e.g., summer maternity use or winter hibernation in bats)?

 What physical or morphological characters are species selecting for, and how does this vary 

based on season/use (e.g., cold sinks, single vs. multiple entrances)?

 Is there any correlation between the species of interest use and level of development of a 

particular cave or cave area?
Cave Ecology Inventory and Monitoring Framework 4

 How do changes in environmental factors (e.g., temperature, relative humidity, barometric 

pressure) due to development or modification (e.g., artificial entrances, trail construction, 

gates) affect species? 

 How does land use above caves impact species of interest populations?

 Have populations / species composition changed over time (decadal or century scale using 

paleontological data)?

Potential focal species/sites

The focal species for monitoring will depend on the species present in the area, as well as the status 

(state or federal protection), significance (relative local importance of that species and if they are 

facing threats), and feasibility of monitoring for a particular species. In addition, documentation of 

sites critical to the life cycle of a particular population should necessitate prioritized monitoring and 

protection for that site. In most localities, multiple species will be present. Priorities for inventory 

and monitoring often depend on available resources and trained staff; however, strong consideration 

should be given to endangered species, abundant/detectable species (easier to monitor), and sites that 

are used by multiple species. These priority monitoring categories will likely overlap, and 

implementation of robust, long-term monitoring efforts and proper data analysis may reveal proxies 

for estimating the status or trend of interrelated monitoring groups.

Potential inventory & monitoring strategies

Answering inventory and monitoring questions related to terrestrial species requires following a 

strategy or combination of strategies. Monitoring generally falls into three strategy levels or 

categories:

1. Presence/absence inventories/monitoring is used to develop faunal or species lists, is useful 

for determining site occupancy and informing species protection efforts, and may be used as 

a strategy to inform ecological monitoring efforts.

2. Population monitoring may be based on in-cave surveys, emergence counts, or acoustic 

monitoring and informs long-term trends in the status of populations.

3. Ecological monitoring attempts to understand the dynamics of species behavior and 

dispersal, including the habitat preferences of the species of interest, the life cycle needs that 

correspond to those habitat preferences, and the temporal patterns (daily or seasonal) 

associated with those habitats.

Potential inventory and monitoring techniques

When choosing inventory and monitoring techniques, consideration should be given to how much 

disturbance to the species a particular method would potentially cause. Long-term monitoring should 

aim to be as unobtrusive as possible to avoid the risk of impacting population stability. Species 

protection is an overarching goal that monitoring can and should inform; monitoring should never 

jeopardize the protection of populations. More obtrusive methods may be warranted for short-term 

projects such as inventories and research, as long as the projects are aimed at gaining valuable 

information and are conducted by qualified professionals with a vested interest in minimizing 

disturbance to the species. Methods justified for short-term needs, though, should be discontinued 

with the conclusion of the project, and the results should be used to inform the development of 
Cave Ecology Inventory and Monitoring Framework 5

sustainable long-term monitoring efforts that yield valuable data while minimizing disturbance. 

Additional important criteria of long-term monitoring includes producing quality, useful data based 

on methodology that is as consistent and repeatable as possible. These conditions are necessary for 

data collection and interpretation that yield results capable of answering monitoring questions with 

confidence. 
Cave Ecology Inventory and Monitoring Framework 6

2.2.1 Bats

Bats are strongly associated with caves, and cave-dwelling bats are indeed critical 

components of cave ecosystems. Bats are also extremely important contributors to 

terrestrial ecosystems. All bats utilize terrestrial environments for foraging and 

hunting, though only a portion of bat species occupies caves. Most cave-dwelling 

bats are generally considered trogloxenes, as they spend part of their life-cycle in caves. Of the 47 bat 

species that occur in the United States, a significant proportion are known to use caves during part of 

their life cycle for some purpose, though to varying degrees. The Bat Conservation International 

publication Bats and Mines (Tuttle and Taylor 1988) includes a list of bat species that use mines. 

While mine use and cave use are not necessarily interchangeable, the degree of habitat similarity and 

overlap of usage warrants inclusion of the table in this document (Table 6) and provides a starting 

point for determining potential for bat species to utilize caves. Uses of caves include maternity 

roosting, hibernation, night roosting, fall swarming, and/or mineral acquisition. The consistency of 

cave use among a species, however, may be quite variable regionally, depending on the availability 

and conditions of local cave habitat. For example, a species that exhibits a strong affinity for cave 

roosting in one geographic region may be entirely tree-dwelling in a different area. Even bat species 

that are usually classified as strictly tree-dwelling (e.g., hoary bats, silver-haired bats) may on rare 

occasions use cave habitat.

Cave-dwelling bats are important in providing nutrients to cave ecosystems that are generally 

nutrient poor. Bats introduce nutrients though guano deposition at roost sites and along flyways; bat 

guano may constitute the primary nutrient source for the system, providing the foundation for cave 

biological communities, including microbes, fungi, and invertebrates. In other caves, bat guano may 

be a minor, but still important, component of an already nutrient rich system. Given the energy 

contributions of bats to a cave ecosystem, bat protection efforts propagate down the food chain when 

biological communities are sustained through natural guano input. Cave-dwelling bats use caves for a 

significant part of their life cycle, but for feeding, bats must forage above ground, where they serve 

critical ecological roles. As part of the terrestrial ecosystem in the United States, bats are generally 

nocturnal and follow either insectivorous (insect-feeding) or nectarivorous (nectar-feeding) diets. In 

the tropics, frugivorous (fruit-eating) bats often use caves. Insectivorous bats are the most common 

types in the U.S., and their feeding behavior contributes to controlling certain insect populations and 

reducing agricultural pests, providing billions of dollars’ worth of ecosystem services annually 

(Boyles et al. 2011). Nectarivorous bats are important in the southwestern U.S. for their role as 

pollinators of many desert plants, including cacti and agaves (Horner et al. 1998; Fleming et al. 

2001). Given the importance of bats to both surface and subsurface ecosystems, and because many 

bat species rely on cave habitat for their survival, monitoring of bats and bat roosts is necessary for 

understanding the health of bat populations and protecting critical bat habitat. Bat monitoring can 

reveal the status and behavior of populations and contribute to bat protection efforts by identifying 

important bat sites and determining their time of use in bat life cycles. 
Cave Ecology Inventory and Monitoring Framework 7

Table 2. Species List of Bats that Use Mines (adapted from Table 1 in Bats and Mines [Tuttle and Taylor 

1988])

Species Group Size Range Use Time

Ghost-faced bat

Mormoops megalophylla

Dozens to hundreds AZ & TX Year-round

California leaf-nosed bat

Macrotus californicus

Dozens to over a thousand AZ & southern CA & NV Year-round

Mexican long-tongued bat

Choeronycteris mexicana

A dozen or fewer AZ & southern CA Summer

Lesser long-nosed bat

Leptonycteris yerbabuenae

Hundreds to thousands AZ & NM Summer

Greater (Mexican) long-nosed bat

Leptonycteris nivalis

Hundreds to thousands TX & NM Summer

Southeastern bat

Myotis austroriparius

Hundreds to thousands Southeastern U.S. Year-round 

California bat

Myotis californicus

Up to a hundred Western U.S. Year-round

Western small-footed bat

Myotis ciliolabrum

Up to a hundred Western U.S. Year-round

Long-eared bat Myotis evotis Dozens Western U.S. Year-round

Gray bat Myotis grisescens Hundreds to 50,000 or more Southeastern U.S. Year-round

Eastern small-footed bat

Myotis leibii

Dozens Eastern U.S. Winter

Little brown bat

Myotis lucifugus

Hundreds to a million + Northern U.S. Year-round

Arizona bat Myotis occultus Hundreds Southwestern U.S. Year-round

Northern long-eared bat

Myotis septentrionalis

Hundreds to thousands Eastern U.S. Winter

Indiana bat Myotis sodalis Hundreds to 100,000 or more Eastern U.S. Winter

Fringed bat Myotis thysanodes Dozens to hundreds Western U.S. Year-round

Cave bat Myotis velifer Hundreds to 100,000 or more Southwestern U.S. Year-round

Long-legged bat Myotis volans Hundreds Western U.S. Year-round

Yuma bat Myotis yumanensis Hundreds to thousands Western U.S. Year-round

Canyon bat Parastrellus hesperus Dozens Western U.S. Year-round

Tri-colored bat

Perimyotis subflavus

Dozens to thousands Eastern U.S. Winter

Big brown bat Eptesicus fuscus Dozens to hundreds North America Year-round

Allen’s big-eared bat

Idionycteris phyllotis

Dozens to about two hundred Mostly AZ, also parts of 

NV, CO

Year-round

Rafinesque’s big-eared bat

Corynorhinus rafinesquii

Dozens to several hundred Southeastern U.S. Year-round

Townsend’s big-eared bat

C. townsendii townsendii

Dozens to hundreds Western U.S. Year-round

Ozark big-eared bat C. t. ingens Dozens to hundreds Ozark Mountains Year-round

Western big-eared bat

C. t. pallescens

Dozens to thousands Western U.S. Year-round

Virginia big-eared bat

C. t. virginianus

Dozens to thousands KY, VA & WV Year-round

Pallid bat Antrozous pallidus Dozens to hundreds Western U.S. Year-round

Brazilian free-tailed bat

Tadarida brasiliensis

Hundreds of thousands Southwestern U.S. north to 

OR

Summer
Cave Ecology Inventory and Monitoring Framework 8

The recent emergence of white-nose syndrome (WNS) (Blehert et al. 2009, Cryan et al. 2010) has 

become the single greatest threat to North American bat populations. Since 2006 over six million 

bats have died from infection with Pseudogymnoascus destructans (formerly Geomyces destructans), 

the fungus responsible for WNS. The unparalleled wildlife impact of WNS has placed greater 

emphasis on the need for bat monitoring methods capable of detecting long-term population impacts, 

which will help cave managers understand the current status of bat resources and provide a reference 

for measuring the potential effects of WNS. Bat monitoring and surveillance will increase the 

possibility of early detection of WNS (Duchamp et al. 2010) and offer the greatest chance for 

conservation measures based on current scientific knowledge. The example of WNS is a reminder 

that cave managers must be diligent in emphasizing responsible caving practices among all users 

(e.g., staff, researchers, volunteers, visitors) in regard to preventing the spread of invasive species 

through regular cleaning and disinfecting of cave gear.

Potential focused inventory and monitoring questions 

In addition to the questions posed at the beginning of the Terrestrial Cave Ecology section, these 

questions may help managers better understand what bats are doing:

 Does roost switching occur during the winter hibernation season?

 Are seemingly separate summer maternity colonies actually distinct populations or do they 

interact with each other, and if so, to what degree?

 Does fall swarming occur, and if so, at what sites?

Potential inventory and monitoring techniques

Common techniques for inventory and monitoring of bats include:

 In-cave surveys

 Emergence counts

 Acoustic monitoring

 Capture and release

 Telemetry

 Other techniques

In-cave surveys 

In-cave or internal surveys are often the most efficient and accurate means of assessing bat 

populations, provided that counts are conducted in a consistent manner by trained surveyors. For 

population monitoring of bat species that hibernate, winter surveys are the most reliable way of 

understanding abundance and population trends of these species. During hibernation, bats are 

immobile and easiest to count; also, because the bats are in torpor, they are less likely to be disturbed 

relative to more active times of the year. It is important to note, however, that the consequences of 

disturbance during hibernation are likely to be greater, as a bat aroused from torpor increases its 

metabolism and raises its body temperature, which is costly to the stored energy reserves bats rely on 

to survive the winter. Therefore, winter surveys should be scheduled at most once annually to prevent 

additional arousals and disturbance, and surveys should be conducted by personnel that are capable 

of quickly, quietly, and safely moving through the cave environment to minimize the amount of time 
Cave Ecology Inventory and Monitoring Framework 9

in proximity to hibernating bats. For more cautionary guidance about bat censuses in caves, see 

Tuttle 2003.

In-cave surveys during summer months can also be valuable for tracking the activity and habitat 

preferences of maternity colonies (females and their pups) and individuals (often bachelor males). 

Because maternity colonies are extremely sensitive to intrusion and may even abandon their pups if 

disturbed repeatedly, in-cave summer surveys should not be utilized as a technique for population 

monitoring. Rather, these should be considered presence/absence surveys with the goal of tracking 

the movement and whereabouts of maternity colonies. Surveyors should always immediately leave 

the cave (or cave area) upon discovering a colony. The information gained from in-cave summer 

surveys is necessary for building an effective bat protection program centered around implementing 

cave closures for critical maternity sites. 

In-cave surveys provide opportunities for collection of limited environmental data, such as 

temperature and relative humidity, using handheld climate meters. Another advantage of actively 

searching caves for bats includes the ability to document the type of cave use (e.g., hibernation, 

maternity roosting, night roosting), which may be based on direct observation of bats or observation 

of other bat signs, such as guano piles and accumulations of moth wings or other insect parts. Of 

course, in-cave surveys also present the potential of identifying bat species that use the site. Direct 

in-cave observation may be enough to confidently identify some bat species with easily recognizable 

diagnostic features, however, many bat species require handling and measurement or acoustic 

recording for definitive taxonomic identification. If species identification is not possible, direct 

observation resulting in identification to the genus or family level is still valuable information. Other 

in-cave bat signs may provide clues to species identification or type of use. Bat guano can be 

identified to some taxonomic level based on observation alone (e.g., size, color, insect parts, 

associated roost characteristics); with funding and proper expertise, genetic analysis of guano can be 

used to identify species. Concentrations of moth wings or other insect parts may indicate maternity 

colony roosts or night roosts of solitary bats.

Photography during in-cave surveys may be used to increase accuracy of counts when dealing with 

large clusters of bats, as is common in the eastern U.S. In this case, photography likely also improves 

bat conservation efforts by minimizing time spent in a roost (since the actual counting is conducted 

later via photo analysis). Photography also provides data on bat health by recording visual condition 

of bats; photographs have been used to help diagnose and characterize the presence of white-nose 

syndrome, for instance. The benefits of photography, however, should be carefully weighed against 

the potential for disturbance, and photography should only be employed when necessary. In western 

U.S. caves where large aggregations of bats are rare, the need for photography to improve count 

accuracy is rare and limited to large clusters that cannot be confidently counted through visual 

observation alone. In many western hibernacula that are dominated by numerous solitary bats and 

small clusters, a complete census based on photography would actually increase disturbance potential 

through excessive use of flashes and additional time spent in the cave. 

All teams conducting in-cave surveys need to be experienced, organized, small, fast, and quiet. It is 

of utmost importance that bat disturbance be minimized to the degree possible while collecting 
Cave Ecology Inventory and Monitoring Framework 10

survey data. In accordance, the frequency of surveys conducted at a particular site should be limited 

and combined with bat protection efforts (such as cave closures and education) to provide for 

undisturbed bat habitat and long-term population viability.

Emergence surveys

Emergence surveys, also known as outflight counts, are most often used to gauge population 

estimates of known summer maternity colonies. These surveys are a low-impact alternative to 

estimating population size of maternity colonies during in-cave surveys, and they may sometimes be 

more accurate. As discussed above, summer in-cave surveys are valuable for determining presenceabsence of maternity colonies; however, it is nearly impossible to determine a reasonable colony 

population estimate via in-cave observation since colonies are easily disturbed and tend to disperse 

when approached. In-cave presence-absence surveys are important, though, for guiding site selection 

and timing of evening emergence surveys. 

Relatively small colonies of a few hundred bats or less can be counted with emergence surveys, using 

direct observation to manually record all exits/entries. Larger colonies numbering in the thousands 

exceed the threshold of manual counting ability and necessitate more complex methods involving 

standard photography (Humphrey 1971, Cross 1989, McCracken 2003) or thermal imaging/infrared 

videography (Betke et al. 2008, Hristov 2010). Though emergence surveys are more accurate than incave estimations of summer colonies (and cause less disturbance), they are still estimates. Many 

factors affect the confidence in emergence survey results, most notably bat behavior and visibility. 

Erratic flight behavior, swooping in and out of entrances, and traveling in clusters or dense streams 

increase the difficulty level for surveyors. Behavioral characteristics are often predictable based on 

the species in question. Bat outflights usually occur at or near dusk, making visibility a significant 

problem affecting survey quality. This factor may also vary predictably based on species and area. 

Margins of error resulting from these factors will generally increase in direct proportion to 

population size, duration of outflight, and number of cave entrances; these variables describe the 

complexity of the survey (Thomas 2011). 

Emergence surveys are generally most valuable when applied to a roost that is known to be occupied 

(or at least a roost in which occupancy is highly suspected), for the simple reason that some level of 

population data is guaranteed since a colony is known to be present. Surveying known roosts will 

ensure that colony size estimates for a particular site outnumber zero counts. Though zero counts 

confirm absence and add value to long-term knowledge of bat occupancy patterns and habitat 

preferences, they do not necessarily indicate that a cave is not ever utilized as a summer roost. Active 

summer bat colonies frequently roost switch among sites throughout the maternity season, and sites 

that may be used as critical habitat during a specific time of year or in response to specific climate 

conditions could be vacant for the rest of the year. For many summer roosts that are only occupied 

for a portion of the maternity season, random emergence surveys (without in-cave determination of 

occupancy) could yield zero counts, despite the importance of these sites as summer habitat. 

Repeated implementation and supplementation with in-cave surveys may be necessary to confirm a 

cave as a summer roost; therefore, management decisions related to summer bat monitoring and 

protection efforts should be based on conservative interpretations of data if site records are limited. 
Cave Ecology Inventory and Monitoring Framework 11

Acoustic monitoring

The field of acoustics has spurned major technological research and development in the application 

of acoustics for countless purposes, including wildlife monitoring, and monitoring of bats is certainly 

among the fields of wildlife study most buoyed by the assistance of acoustic technology. Current 

knowledge of bats throughout the world has grown substantially based on acoustic studies. All of the 

bat species occupying National Park Service sites in the U.S. (excluding some territories) rely on 

echolocation for navigation and feeding. This adaptation has rendered these bats well suited to their 

environment, and also well suited to be recorded by bat detectors and analyzed based on vocal 

characteristics. Acoustic monitoring of bats relies on identifying characteristic frequencies, shapes, 

and patterns of bat calls that are unique to species (or assemblage of species). Numerous acoustic 

devices have been developed and marketed for bat monitoring, along with software programs 

designed to analyze the calls recorded by acoustic bat detectors. These devices are widely divergent 

in application, data quality, cost, etc. In turn, comparing the results of acoustic monitoring efforts is 

extremely difficult due to the diversity of acoustic monitoring equipment and methods available. 

While acoustic data may be difficult to compare among sites and areas, nearly any acoustic device 

chosen may yield valuable data for a particular site, when implemented with consistent methodology 

and informed by a valid research or monitoring question. A great benefit of acoustic monitoring is 

that it is generally a non-invasive monitoring technique, causing little to no disturbance to bat 

populations. 

Acoustic bat detectors may be used for very specific applications, such as monitoring occupancy of a 

single, known bat roost over the course of a season or for conducting inventories by identifying 

species based on recorded bat calls. Acoustic monitoring technology can also be applied to assess 

landscape-scale patterns over many years. The possibilities are nearly endless but limited by practical 

considerations involving acoustic equipment and management of large datasets Provided that 

appropriate methods are used, acoustic monitoring can characterize the occurrence and activity levels 

(daily, seasonal, annual) of bat populations (Gorresen et al. 2008; Rodhouse et al. 2011). Multiple 

years of inventory and monitoring may be required to reveal natural variance in bat populations, 

making the practice of standard methodology and implementation absolutely critical to interpretation 

of long-term datasets.

In a general sense, acoustic monitoring methods can be classified as active or passive. Active 

monitoring occurs when surveyors are present and actively involved in the recording process. 

Examples of active monitoring include running a bat detector by hand while watching an emergence 

or driving a designated transect route at a consistent speed with a detector microphone mounted on 

the roof of a vehicle (Britzke & Herzog 2010, Thomas & Weller 2011). Conversely, passive 

monitoring occurs when detectors are deployed at a stationary location, usually for an extended 

period of time; surveyors are absent for the bulk of data collection. A major advantage of passive 

monitoring is the ability to collect large amounts of data with relatively little effort. Passive 

monitoring may be used to characterize a single site, or a network of sites may be established to 

understand landscape-scale bat activity. 
Cave Ecology Inventory and Monitoring Framework 12

Active and passive monitoring can both be used to collect data within caves or on the surface, 

depending on the monitoring goal. Bat calls recorded on the surface are often more diagnostic (based 

on foraging calls) and of better quality (less reflection) than those recorded within a cave. If the 

monitoring goal is related to a colony of a known species, then acoustic activity monitoring within a 

cave can be accomplished without concern for call quality; rather, a record of acoustic activity can be 

used to characterize occupancy (daily and seasonal) as well as daily emergence times and nighttime 

activity. Landscape-scale acoustic monitoring efforts are especially advantageous if designed with 

the purpose of being compatible across areas, based on shared methodology, allowing for monitoring 

data to be pooled and analyzed for regional patterns and trends. 

Capture and release

Capture and release of live bats can be a valuable inventory and monitoring technique. This 

technique utilizes mist nets and/or harp traps, which when properly deployed over water sources, are 

successful at ensnaring bats without causing injury. Live capture and release requires surveyors who 

are trained to handle bats, have received rabies vaccinations (usually pre-exposure), and have titer 

levels indicating rabies immunity. Furthermore, surveyors must be experienced not just with 

handling bats, but also with knowing how to identify, age, and sex bats With such specialized 

prerequisites and non-trivial costs associated with maintaining vaccinations, capture and release as a 

monitoring method is limited by the availability of surveyors with these qualifications. When 

utilized, though, mist netting or harp trapping can be an extremely valuable method for obtaining 

inventory and monitoring data. Used in conjunction with acoustic techniques, these are among the 

best methods for establishing species composition and reproductive status for an area. They are also 

among the best methods for characterizing general bat health through visual inspection and wing 

damage index analysis. While capture and release yields valuable data when conducted by trained 

surveyors, it is a highly invasive method relative to most other monitoring techniques. Using mist 

nets and harp traps is also very time-intensive, requiring late nights monitoring nets after dusk. Sites 

must be carefully chosen to be productive, usually requiring nets to be placed over water sources 

utilized by bats; site placement should be considered when interpreting capture results. Mist nets and 

harp traps should never be placed in cave entrances without first assessing the number of bats inside, 

as the net or trap could quickly become overwhelmed, leading to increased bat injuries and potential 

deaths. The equipment required for mist netting and harp trapping can be expensive, and nets and 

traps need to be carefully handled and stored to prevent tears and tangles. As an inventory method, 

capture and release is a simple and effective technique for determining species presence and 

reproductive status. Monitoring applications, as with all monitoring techniques, need to follow 

consistent methodology informed by long-term monitoring goals. 

Telemetry

Telemetry, or radio-tracking, is often used to locate bat roosts, as it is one of the most effective and 

practical means of tracking bats over landscapes. Another advantage of telemetry is its ability to 

estimate home ranges, or foraging ranges, of bats. Tracking bats with telemetry also yields 

information on habitat selection, including foraging habitat and possible day and night roosts. 
Cave Ecology Inventory and Monitoring Framework 13

Monitoring via telemetry must also, by necessity, incorporate mist netting. Though telemetry is 

extremely valuable for certain projects, it is often too costly and time intensive for routine 

monitoring. It can also be more invasive than other monitoring methods, as telemetry requires live 

capture of bats in order to place transmitters. The transmitter adds weight to the bat, which could 

affect flight ability and result in an energy cost to the bat; however, bats routinely survive telemetry 

projects, and studies suggest that little disturbance results from the transmitters, which eventually fall 

off.

Other techniques

PIT tags, wing bands, dyes, and other marking techniques have been used on many bat species over 

the years, each yielding information of varying utility. For a complete discussion, refer to Kunz and 

Parsons (2009).

Relevant Monitoring Protocols and Methods

National Park Service:

Cumberland Piedmont Network (Mammoth Cave National Park, Cumberland Gap National 

Historic Park): http://science.nature.nps.gov/im/units/cupn/monitor/cavebats.cfm

Klamath Network (Lava Beds National Monument, Oregon Caves National Monument): Krejca, 

J. K., G. R. Myers, III, S. R. Mohren, D. A. Sarr, and S. C. Thomas. forthcoming. Integrated cave 

entrance community and cave environment long-term monitoring protocol. Natural Resource 

Report NPS/KLM/NRR—2014/XXX. National Park Service, Fort Collins, Colorado. 

http://science.nature.nps.gov/im/units/klmn/publications.cfm

Upper Columbia Basin Network (Craters of the Moon National Monument): Rodhouse, T. J., T. 

Stefanic, S. Thomas, and G. Dicus. forthcoming. Protocol for monitoring bat use of lava caves 

during winter in Craters of the Moon National Monument and Preserve. Natural Resource Report 

NPS/UCBN/NRR—2014/XXX. National Park Service, Fort Collins, Colorado.

Other:

Kunz, T.H. and S. Parsons. 2009. Ecological and behavioral methods for the study of bats, second 

edition. Johns Hopkins University Press, Baltimore, Maryland.

O'Shea, T .J., and M. A. Bogan (eds.). 2003. Monitoring trends in bat populations of the United 

States and territories: problems and prospects: U.S. Geological Survey, Biological Resources 

Discipline, Information and Technology Report, USGS/BRD/ITR—2003-0003, 274 p. 

http://www.fort.usgs.gov/products/publications/pub_abstract.asp?PubID=21329

Bat Population Database:

https://www.fort.usgs.gov/search/content/bat%20population%20database
Cave Ecology Inventory and Monitoring Framework 14

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Boyles, J. G., P. M. Cryan, G. F. McCracken, and T. H. Kunz. 2011. Economic importance of bats in 

agriculture. Science 332(6025):41-42.

Britzke, E. R. and C. Herzog. 2010. Using acoustic surveys to monitor population trends in bats. U.S. 

Army Corps of Engineers, http://corpslakes.usace.army.mil/employees/bats/acoustic.cfm.

Cryan, P. M., C. U. Meteyer, J. G. Boyles, and D. S. Blehert. 2010. Wing pathology of white-nose 

syndrome in bats suggests life-threatening disruption of physiology. BMC Biology 8:135.

Cross, S. P. 1989. Studies of the Brazilian free-tailed bat, Bat Cave, Lava Beds National Monument: 

measuring population levels and influencing factors. Unpublished report, Lava Beds National 

Monument, Tulelake, CA.

Duchamp, J., E. Britzke, M. Bayless, P. Ormsbee, A. Ballmann, and C. Willis. 2010. White-nose 

syndrome surveillance and population monitoring for cave dwelling bats. Report for the WNS 

Surveillance and Monitoring Task Group. 

Fleming, T. H., C. T. Sahley, J. N. Holland, J. D. Nason, and J. L. Hamrick. 2001. Sonoran Desert 

columnar cacti and the evolution of generalized pollination systems. Ecological Monographs

71:511-530.

Gorresen, P. M., A. C. Miles, C. M. Todd, F. J. Bonaccorso, and T. J. Weller. 2008. Assessing bat 

detectability and occupancy with multiple automated echolocation detectors. Journal of 

Mammalogy 89:11-17.

Horner, M. A., T. H. Fleming, and C. T. Sahley. 1998. Foraging behaviour and energetics of a 

nectar-feeding bat, Leptonycteris curasoae (Chiroptera: Phyllostomidae). Journal of Zoology

244:575-586.

Hristov, N. I., M. Betke, D. E. H. Theriault, A. Bagchi, and T. H. Kunz. 2010. Seasonal variation in 

colony size of Brazilian free-tailed bats at Carlsbad Cavern based on thermal imaging. Journal of 

Mammalogy 91:183-192.

Humphrey, S. R. 1971. Photographic estimation of population size of the Mexican free-tailed bat, 

Tadarida brasiliensis. American Midland Naturalist 86:220-223.
Cave Ecology Inventory and Monitoring Framework 15

Kunz, T. H. 2003. Censusing bats: challenges, solutions, and sampling biases. pages 9-20 in O’Shea, 

T. J. and M. A. Bogan, eds. Monitoring trends in bat populations of the United States and 

territories: problems and prospects. USGS Information and Technology Report 2003-0003.

McCracken, G. F. 2003. Estimates of population sizes in summer colonies of Brazilian free-tailed 

bats (Tadarida brasiliensis). pages 21-30 in O’Shea, T. J. and M. A. Bogan, eds. Monitoring 

trends in bat populations of the United States and territories: problems and prospects. USGS 

Information and Technology Report 2003-0003.

Rodhouse, T. J., K. T. Vierling, and K. M. Irvine. 2011. A practical sampling design for acoustic 

surveys of bats. Journal of Wildlife Management 75:1094-1102.

Thomas, S. C. 2011. Building a diversified monitoring program for cave-dwelling bat populations. 

Proceedings of the 2011 National Cave and Karst Management Symposium, 2011. Midway, 

Utah.

Thomas, S. C. and T. J. Weller. 2011. Lava Beds acoustic transect protocol. Unpublished protocol, 

Lava Beds National Monument, Tulelake, CA.

Tuttle, M. D. 2003. Estimating population sizes of hibernating bats in caves and mines. pages

31–39, in Monitoring trends in bat populations of the United States and territories: problems and 

prospects. U.S. Geological Survey, Biological Resources Discipline, Information and 

Technology Report, USGS/BRD/ITR—2003-0003. 274 pp.

Tuttle, Merlin D., and Daniel A. R. Taylor. 1998. Bats and mines, Resource Publication No. 3. Bat 

Conservation International, Austin, Texas. 50 pp.
Cave Ecology Inventory and Monitoring Framework 16

2.2.2 Woodrats

About 20 species of woodrats (genus Neotoma), also known as pack rats, 

cave rats, cliff rats, and other common names, inhabit a wide variety of 

habitats throughout North America. Many of these species use caves. 

Woodrats are nest builders, using a variety of plant materials to make nests, called middens. Some of 

these middens have been important to paleoecologists. Woodrats are generally considered 

trogloxenes but, like some species of bats, can be troglophilic in certain locations using clifflines, 

hollow trees, debris piles, and man-made structures as shelter.

The most studied woodrats in NPS caves are Allegheny woodrats (Neotoma magister), a native 

species in the eastern United States. They are primarily nocturnal. They are a territorial species so 

they are usually solitary, except when mating and raising young. After a mother gives birth, the 

young stay for two to four months. Then the mother ejects the young, or a youngster may force the 

mother and other young out of the nest. Generally one or two woodrats may be found around a single 

cave entrance area. In the East they are found in the woods and often associated with rocky habitat. 

In the Midwest and Southeast where rocky habitat is scarce, they may be found near fence rows, 

shrubs, and trees. They can move long distances (3.5 km) to look for mates, but they usually forage 

within 200 m from the entrance to get food. Some stay even closer, only going less than 50 m to find 

the food they need. Males tend to have larger home ranges than females. In the last 35 years there has 

been a noted decline in the northeastern portion of their range. Several states have listed Allegheny 

woodrats as threatened or endangered, and the US Fish and Wildlife Service has them listed as 

species of concern (global rank of G3-G4). 

Woodrats, a facultative species that come and go, provide a good link between surface and 

subsurface ecosystems. They use caves primarily as shelter and incidentally supplement the cave 

environment with an input of organic material. Even one woodrat can greatly add to the organic 

material in a cave. Woodrats generally do not venture far into the cave, but have been known to 

travel hundreds of feet from an entrance. Fresh woodrat sign far from any known entrance usually

indicates that a woodrat-sized entrance is nearby. Woodrats build a nest (sometimes concealed by a 

house/den made of sticks or bark) out of vegetative material, such as finely shredded bark or grass. 

They distribute dried leaves around the nest, possibly so that anything that approaches the nest will 

make noise. Woodrats often gather bones and shiny objects from outside of caves, which they 

incorporate into their nests. Woodrats use the nest for sleeping and rearing young. In the West, 

woodrats sometimes use juniper which may have a repellant effect on some fleas and other 

organisms. Woodrats tear down and rebuild nests fairly frequently. Their food sources, including 

nuts, fruits, berries, flowers, fungi, green vegetation, along with any leaf litter and sticks they bring 

in, provide a food source for cave organisms. These food collections (caches), along with other 

materials, are called middens. Woodrats establish a separate latrine area, and guano deposited there is 

important. Several cave invertebrate communities have been found utilizing these latrine areas; these 

guano dependent organisms include fungus gnats, predatory beetles, bacteria, and more. Occasionally 

woodrats die in caves and provide a large nutrient input to cave organisms. Woodrats often use the 
Cave Ecology Inventory and Monitoring Framework 17

same middens and latrines over many generations. They are able to travel through dark cave passages 

by following urine trails. These trails can become polished when used for multiple generations.

In addition to the threats facing most terrestrial cave-dwelling creatures, woodrats face some 

additional ones. These include raccoon roundworm parasite; chestnut blight (at one time American 

chestnuts made up 25% of canopy in areas); sudden oak decline and gypsy moth infestation leading 

to a decrease in supply of key food sources (i.e., acorns).

Potential inventory and monitoring techniques

Both direct and indirect methods can be used to survey woodrats. The most common direct technique 

is to mark/recapture woodrats using live traps. Woodrats can then be ear tagged (although some ear 

tags may be lost) or have an ear tattooed. While the woodrat is in hand, it can be sexed, weighed, 

checked for age class, checked for ectoparasites, and assessed for overall health and reproductive 

condition. Woodrats are easily caught in live traps, but it should be noted that due to low density, a 

large number of traps must be used in order to get meaningful data (Woodman et al. 2007).

Indirect methods for surveying woodrats include:

 Scat monitoring, which is used by the Klamath Network (Krejca et al. forthcoming). For this 

protocol, they monitor scat deposition, mostly from rodents but also from other mammals and 

birds. The timed area searches used to detect scat are fairly simple, requiring minimal 

training or equipment, and they provide valuable information on the consistency and amount 

of nutrient inflows that support cave communities.

 UV light for looking at woodrat urine

 Tracking boards to determine if a woodrat is entering a cave

 Trail cameras to photograph woodrat use of a cave

References, Related Studies, and Relevant Monitoring Protocols

Cumberland Piedmont Network resource brief: 

http://science.nature.nps.gov/im/units/cupn/monitor/woodrats.cfm

Krejca, J. K., G. R. Myers, III, S. R. Mohren, D. A. Sarr, and S. C. Thomas. forthcoming. Integrated 

cave entrance community and cave environment long-term monitoring protocol. Natural 

Resource Report NPS/KLM/NRR—2014/XXX. National Park Service, Fort Collins, Colorado. 

Mengak, M. T., C. M. Butchkoski, D. J. Feller, and S. A. Johnson. Chapter 7: Lessons from longterm monitoring of woodrat populations in The Allegheny woodrat: ecology, conservation, and 

management of a declining, J. D. Peles and J. Wright (eds.). 109-132.

Woodman, Robert L., Steven C. Thomas, and Bill J. Moore. 2007. A protocol for monitoring 

Allegheny woodrats (Neotoma magister) at Mammoth Cave National Park, version 3.1. 

Cumberland Piedmont Network, National Park Service, U.S. Department of the Interior.
Cave Ecology Inventory and Monitoring Framework 18

2.2.4 Birds

Overall, birds are vagile animals that occupy a variety of habitats. A few species are 

dependent upon caves for habitat, particularly cave swallows. Additional species are 

found in cave entrances, using the structures for nesting and foraging. These species 

include purple martins, violet-green swallows, hummingbirds, lark sparrows, common 

ravens, Say’s phoebes (Lava Beds), turkey and black vultures (Mammoth Cave), and eastern phoebes 

and barn swallows (Russell Cave). Other bird species have the potential to use caves, such as redtailed hawks, great horned owls, and barn owls. In lava tube areas where trench collapse systems are 

present, approximately 30 more species can be found, including canyon wrens and rock wrens. In 

addition, various raptors, such as American kestrels, prairie falcons, peregrine falcons, merlins, and 

screech owls are found near cave entrances during bat out-flights.

Birds are important to cave ecosystems because they are a facultative species that come and go, 

providing a good link between surface and subsurface ecosystems. They use caves primarily as 

shelter and subsidize the cave environment with an input of organic material. Even one bird can 

greatly add to the organic material in a cave. Birds generally do not venture far into the cave. 

Common ravens are probably one of the biggest contributors of energy to a cave because of their 

large nest size, the amount of fecal matter they leave, and the chicks that fall out of the nest to the 

cave floor. 

Birds use caves for various reasons, including shelter (caves provide nesting areas and/or perches), 

foraging (insects and bats), escape predation, and possible refugia from parasitism (e.g., cowbirds). 

In some areas, birds may use caves differently than in other areas. For example, lava tubes in Lava 

Bed National Monument support the only known population of cave-roosting purple martins.

Dominant threats, in addition to those faced by most terrestrial cave fauna, include disturbance by 

humans, especially seasonal disturbance that coincides with breeding; natural predation by barn owls, 

along with other avian, reptilian, and mammalian predators; and habitat stability over time (i.e., are 

birds building themselves out of a nesting site?).

Potential inventory and monitoring techniques

Very few cave parks currently monitor bird use of caves. Lava Beds National Monument monitors 

purple martins via flight counts. They also conduct point counts that occur near cave entrances and 

are investigating ways of interpreting that data to understand how birds use caves. Carlsbad Caverns 

National Park has conducted cave swallow research for decades, using mist nests. The list below 

includes these techniques, as well as additional techniques that have the potential to be used.

 Nest counts—cave swallows build new nests each year (high collapse rate after a year)

 Pellet monitoring (e.g., owl presence/absence)

 Presence of nesting material in caves; whitewash on the walls

 Point counts near cave entrances/trench collapses

 Raptor surveys during bat outflights
Cave Ecology Inventory and Monitoring Framework 19

 Bird outflight counts

 Mist nets: identifying, weighing, measuring, and sexing birds caught

References, Related Studies, and Relevant Monitoring Protocols

Lava Beds National Monument. 2010. Purple martin survey protocol. Tulelake, California. 

West, S. 1995. Cave Swallow (Hirundo fulva). In the birds of North American, No.141 (A. Poole and 

F. Gill, eds.). The Academy of Natural Sciences, Philadelphia and the American Ornithologists 

Union. Washington, D. C. 18 pp.

West. S. 1998. Status of the Cave Swallow in New Mexico. New Mexico Ornithological Society 

Newsletter, pp 2-6. http://newmexicobirds.nfshost.com/wp-content/bu16-4.pdf
Cave Ecology Inventory and Monitoring Framework 20

2.2.3 Cave Crickets

Cave and camel crickets are a varied group of insects widely distributed in caves 

around the world. In the United States most cave “crickets” are actually 

grasshoppers (Rhaphidaphorids). True Gyrillid crickets are found in caves in Hawaii 

and in Mexico. For a review of the biology and ecology of North American cave 

crickets, see Lavoie, Helf, and Poulson (2007). Cave crickets are important keystone species in many 

caves. They provide energy inputs in the form of eggs, guano, and carcasses that support specialized 

communities. The foraging success of crickets is influenced by the weather, as seen in the amount of 

guano deposited and the diversity and abundance of invertebrate guano communities (Poulson, 

Lavoie, and Helf 1995). In caves without large bat colonies the population structure and dynamics of 

cave crickets are often a significant indicator of the integrity of terrestrial cave communities. These 

genera are typically the primary conduits for the active, regular input of organic matter into the 

subsurface habitat (Lavoie et al. 2007). Cave crickets feed in the relatively productive surface habitat 

and deposit nutrients--in the form of eggs, guano, and bodies--into the subsurface terrestrial habitat 

where primary productivity is nonexistent. Cave cricket eggs and feces support subsurface 

communities that may include rare, sometimes endemic, obligate cave-dwelling invertebrates (Culver 

et al. 2000). 

Cave and camel crickets show different degrees of troglomorphy in their metabolism and appearance. 

Elongation of legs is a good indicator of troglomorphy in crickets (Studier, Lavoie, and Howarth 

2002). In Mammoth Cave National Park, Ceuthophilus stygius camel crickets are trogloxenes, using 

the cave as a refuge. Meanwhile Hadenoecus subterraneus cave crickets are troglophiles, completing 

their entire reproduction and growth in the cave, but having to leave at night to feed on the surface 

when conditions are close to the temperature and high humidity levels found in the cave.

Dividing crickets into size classes allows for differentiation of their use of particular areas. Figure 7 

shows the distribution of Hadenoecus cave crickets by the length of their hind femurs (HFL). The 

smallest crickets (HFL 4-10 mm) are the ones recently hatched and through the first few molts. 

Mature adults have HFL greater than 20 mm. Entrance populations show mostly adults, and a fairly 

even distribution of younger size classes, reflective of species that live for several years. Deep cave 

sites that are suitable for egg laying show a distribution of the smallest and largest size classes. The 

intermediate size classes have moved out of the deep cave sites and closer to entrances to allow for 

surface foraging. In contrast, Ceuthophilus camel crickets would be graphed as a narrow curve that 

moves depending on the time of year because of their annual life cycle. They grow at the same rate, 

and all of them reach adult size in late August. Small, young crickets overwinter and begin growing 

in the spring.
Cave Ecology Inventory and Monitoring Framework 21

HFL (mm)

Figure 8. Cave cricket distribution by HFL (Hind Femur Length) at entrance and deep cave sites.

Cave crickets are relatively rare in most caves, although in some they can roost in large clusters. 

When crickets occur in clusters, more quantitative methods are available for monitoring. When 

crickets are solitary, presence/absence in conjunction with occupancy modeling may be more 

appropriate. It should also be noted that some cave crickets live for multiple years (e.g., Mammoth 

Cave), so multiple age/size classes can be found in the same area. Some species of crickets can 

mature at different times of year.

Potential inventory and monitoring techniques

Six primary techniques are used to conduct inventory and monitoring on cave crickets:

 Timed area searches – used to determine what is detectable and what organisms should be 

monitored. 

 Census by Transect -- The cave entrance is divided into appropriately spaced transects, and 

the total populations are counted within each transect. Crickets can also be easily separated 

by size class using estimations of the length of the hind femur. Seasonal movements and 

daily movement towards or away from entrances can be demonstrated. Census by transect 

works well both for clusters and individual crickets.

 Baited traps – Bait is placed for a specified amount of time. Used for areas of low occupancy.

 Adaptive cluster sampling -- If cave crickets are found in clusters, this method is robust. 

Randomized sample areas are chosen and transects are searched for clusters of cave crickets. 

If a cluster is found, more intense monitoring is focused at this location. 

0

5

10

15

20

25

4 5 6 7 8 9 10111213141516171819202122232425

Percent of the Population

Cave Crickets by HFL

Entrance

Deep
Cave Ecology Inventory and Monitoring Framework 22

 Photography – Photos are taken in raw mode, then processed in Photoshop to count 

individuals. Photography works for smaller clusters. For larger clusters, you can import 

photos into ArcGIS, mark individuals, and then the program counts them. The program can 

also be trained to recognize features of the organisms and then count them (good success 

with bats). Photocounts results in demographic data with less human error by using computer 

programs. 

 Exit counts – The number of cave crickets leaving the cave to forage are counted.

References, Related Studies, and Relevant Monitoring Protocols

Culver, D. C., L. L. Master, M. C. Christman, & H. H. Hobbs. 2000. Obligate cave fauna of the 48 

contiguous United States. Conservation Biology 14(2):386-401.

Helf, K. L. and R. Woodman. 2009. Utility of cave cricket monitoring methods developed by USGS 

and Cumberland Piedmont Network ecologists for Mammoth Cave National Park. Proceedings of 

the XVth International Congress of Speleology.

Lavoie, K. H., K. L. Helf, and T. L. Poulson. 2007. The biology and ecology of North American cave 

crickets. Invited paper, 65th Anniversary Special Issue, Journal of Cave and Karst Studies 69:114-

134.

Poulson, T., K. Lavoie, and K. Helf. 1995. Long-term effects of weather on the cricket (Hadenoecus 

subterraneus, Orthoptera, Rhaphidophoridae) guano communities in Mammoth Cave National 

Park. American Midland Naturalist 134:226-236.

Poulson, T. L., K. H. Lavoie, and K .L. Helf. 2000. NRPP entrance monitoring final report. 

University of Illinois at Chicago, Chicago, Illinois.

Studier, E. H., K. H. Lavoie, and F. G. Howarth. 2002. Attenuation and seasonal femur length:mass 

relationships in cavernicolous crickets (Insecta: Orthoptera). Journal of Cave and Karst Studies

642:127-132.

Studier, E. H., K. H. Lavoie, W. D. Wares Ii, and J. Linn. 1986. Bioenergetics of the cave cricket, 

Hadenoecus subterraneus. Comparative Biochemistry and Physiology 84A:431-436.

Taylor, S. J. K. Hackley, J. K. Krejca, M. J. Dreslik, S. E. Greenberg, and E. L. Raboin. 2004. 

Examining the role of cave crickets (Rhaphidophoridae) in central Texas cave ecosystems 

isotope ratios (δ13C, δ15N) and radio tracking. Illinois Natural History Survey, Center for 

Biodiversity Technical Report 2004(9):1-128.

Taylor, S. J., J. K. Krejca, & M. L. Denight. 2005. Foraging range and habitat use of Ceuthophilus 

secretus (Orthoptera: Rhaphidophoridae), a key trogloxene in central Texas cave communities. 

The American Midland Naturalist 154(1):97-114.
Cave Ecology Inventory and Monitoring Framework 23

Thompson, Steven K. 2012. Sampling. 3rd edition. Wiley Desktop Editions. Hoboken, New Jersey.

Woodman, Robert L., Kurt L. Helf, and Bill Moore. 2005. Cave Cricket (Hadenoecus subterraneus) 

monitoring protocol for Mammoth Cave National Park, Kentucky, version 2.0. Cumberland 

Piedmont Network, National Park Service, U.S. Department of the Interior.
Cave Ecology Inventory and Monitoring Framework 24

2.2.5 Cave obligate invertebrates 

Obligate, cave-limited (troglobitic) invertebrates, in particular those exhibiting obvious 

troglomorphies such as loss of pigment, loss of functional eyes, and elongate 

appendages, are indicative of subterranean habitats that have been relatively stable over 

recent geological time. Such species are commonly associated with stable conditions (temperature, 

humidity, etc.) and relatively low energy environments. Such animals typically mature more slowly 

than their above ground relatives and have a competitive advantage under conditions where food is 

scarce. These animals are typically found at lower densities relative to their surface cousins.

For cave-adapted invertebrates, monitoring generally requires having some basic inventory work, 

conducted by an appropriately trained biologist, done prior to monitoring. This allows the resource 

manager to have a list of most of the species to be expected. Where visual field identifications are to 

be made, it is helpful to have a collection of good macrophotos of the target taxa to facilitate field 

identification– a set of laminated identification cards with photos can greatly assist in field 

identifications. Bringing a camera with a good macro lens to photograph unusual taxa during 

monitoring, or a few vials to collect unusual organisms for later identification by an expert, keeping 

in mind protocols for the area, may be helpful. Various techniques can be used for documenting 

species, depending on the inventory and monitoring questions.

Potential focal species

For general monitoring, identifiable taxa may be target organisms – those relatively few distinctive 

looking troglobites or troglophiles which are reasonably abundant and which can readily be 

quantified, identified, and sampled by trained personnel. These might be larger organisms such as the 

large milliped Plumatyla humerosa at Lava Beds National Monument. Monitoring several such 

species, perhaps ones which function at differing trophic levels (spiders as predators, but then also a 

distinctive springtail, for example) or microhabitats, will produce more reliable results (Gerlach et al. 

2013) and will provide more complete coverage of fine-scale microhabitats and their associated 

biodiversity (Samways 2007).

Where sufficient invertebrate expertise is available, it may be appropriate to monitor invertebrate 

communities – assessing species richness and diversity across different areas with caves, across 

different caves, and across time (different monitoring events). Such studies might include timed area 

searches, perhaps with baiting (to attract invertebrates to search area). Lethal pitfall trapping is 

probably best restricted to inventory studies and specific research projects, so as not to deplete 

populations with repeated trapping.

Potential inventory and monitoring techniques and considerations

Several inventory and monitoring techniques have proven useful for cave obligate invertebrates:

 Timed areas searches

 Pitfall trapping

 Habitat & Environmental Parameters

 Photography
Cave Ecology Inventory and Monitoring Framework 25

Timed area searches

Timed area searches require delineating areas to be searched. The area is then searched for a fixed 

time period by appropriate personnel, with all target taxa (alternatively, all taxa) recorded by species 

(or morphospecies) and number of individuals. This effort can be converted to person/hours/m2to 

allow comparisons among sites and across survey periods. There are numerous ways to define search 

areas, and choice of approaches depends on the size and morphology of the cave or caves to be 

monitored, but also depends upon the likelihood of detecting target taxa. Search areas (zones, 

replicate plots) can be a segment of cave passage (X meters of passage, measured off with survey 

tape), or, where passage or rooms are more spacious, fixed size study plots, or linear transects (such 

as a survey tape laid out, with search covering 1 meter on either side of the tape for a distance of X 

meters). In most instances, size of search areas should be sufficiently large that numerous search 

areas are likely to detect the presence of the target taxa when the target(s) are present, but not so 

large that there is insufficient time to search the area, or there are too many of the target taxa to count 

in the allotted time. When particularly rare troglobites are the targets, sufficient numbers of search 

areas in appropriate habitat and at appropriate times of year (i.e., spatial and temporal considerations) 

should be used to have a reasonably good chance of detecting the species when present. A good cave 

map is extremely useful for marking search areas. Search areas can be fixed plots, randomly placed 

through the searchable portions of a cave, stratified (entrance, twilight, dark zones), or restricted to 

certain areas (dark zone only, or restricted to specialized habitats where species will only occur or 

where species are most likely to be detected). In caves with little energy and few invertebrates 

present, it may be advisable to set out bait stations to attract target taxa. If bait is used, care should be 

taken to remove it after each monitoring period, and considerations of possibility of other animals 

taking the bait away should be weighed. Placing baits in a well anchored cage or under a stone may 

work in some settings. Common baits include limburger cheese, rotting liver, peanut butter, etc. 

(consult with cave biologists familiar with your area). It should be noted that many species do not 

come to baits, especially predators like spiders, so you will not get a representative sample of those 

species. In addition, baits near the entrance could also attract surface species.

Pitfall trapping

Pitfall traps are more appropriate for inventories than for monitoring, as most implementations result 

in mortality. However, “dry” pitfall traps without a preservative may, in some instances, be 

appropriate. The bottom of these live traps should have paper towels or other “cover” for animals to 

hide under, and should not be left for more than a day or two. Pitfall traps are most useful for 

ambulatory invertebrates. Flies and web-building spiders are not likely to be caught in pitfall traps. 

This approach should probably be discontinued if mortality is observed in preliminary trials.

Habitat & Environmental Parameters

Terrestrial cave invertebrate monitoring should include associating each search area during each 

monitoring period with a standardized list of parameters. Standard environmental parameters include 
Cave Ecology Inventory and Monitoring Framework 26

relative humidity (RH), temperature, air velocity and direction, and light levels inside the cave, and 

temperature, relative humidity, and recent precipitation outside the cave. Pay special attention in 

selecting an instrument for measuring relative humidity to ensure the selected device is effective and 

accurate between 85 and 100% RH, a typical range for deep cave humidities. Calibration of meters 

should follow manufacturer’s recommendations. Substrate should be characterized in a standardized 

manner for each plot, with relative proportions of bedrock, calcite formations, organic debris, soil, 

clay, loose rocks, etc. In addition, a subjective measure of substrate moisture can be added, for 

example: dry, normal (damp to touch), wet (glistening).

Photography

Species-level identification may be possible in the field for some cave obligate invertebrates with 

appropriate training and a pictorial guide to area cave invertebrates. But in other situations, specieslevel identification requires the animals be collected and preserved so that tiny morphological 

structures can be examined by an expert under a microscope to determine species identity. Because 

of the slower maturation and low populations of these animals, collecting and preserving troglobites 

should not be a routine component of cave resource monitoring. However, in areas where cave 

resources have been well-studied, it may be possible to make reasonably accurate field 

identifications. A laminated set of identification cards, developed in consultation with an 

appropriately trained biospeleologist, may make this approach more feasible. Field identification 

requires that the field crew be reasonably aware of what other potentially similar-looking 

invertebrates might also be encountered.

Some obligate cave invertebrates, especially predatory species, such as spiders and pseudoscorpions, 

can be very reclusive and rare. A troglobitic pseudoscorpion might not be detected during each visit, 

even if the species is present in the subterranean habitat – such false negatives make it difficult to use 

such species for short term monitoring (Krejca and Weckerly 2007). However, data on these rarely 

encountered species collected over years may provide valuable insights into the condition of the cave 

ecosystem. Obviously, where extremely rare species are expected, their well-being needs to be 

carefully considered when lethal sampling methods may be implemented.

Considerations for locating monitoring/sampling sites

Monitoring troglophiles may be effective when monitoring considerations emphasize sample size. In 

many cave settings, several troglophilic species may be sufficiently numerous that one might expect 

to regularly encounter them during each cave visit. These species include some flies, springtails, and, 

closer to the cave entrance, a variety of other taxa. With sufficient training, it is possible to field ID 

springtails and flies to family, and with a few voucher specimens confirmed by an expert, it is 

feasible to assign presumptive generic or even species names to distinctive forms.

When monitoring cave invertebrates, it is important to keep in mind that for troglophiles, “more” is 

not necessarily “better.” Larger numbers of individuals of taxa which have a competitive advantage 

when energy is more abundant may indicate undesirable organic enrichment – septic leaks, excessive 

visitation, human waste, etc.
Cave Ecology Inventory and Monitoring Framework 27

Considerations for sampling interval

The interval between invertebrate monitoring events should balance several factors, including: 1) 

funding and resources available to conduct monitoring; 2) seasonality of both access to cave sites and 

activity of target organisms; 3) potential impacts of monitoring visits on the cave ecosystem and 

other cave resources; 4) statistical/data interpretation considerations such as variance in data, power, 

area of inference, sample size (number of caves, number of samples/cave, typical counts of animals 

in samples) and statistical significance; and 5) impact of visiting the cave.

Commonly, annual monitoring of terrestrial cave macroinvertebrates at a selected time of year is 

determined to be the best balance of the above factors, but this could vary greatly by the situation at a 

given Park.

References, Related Studies, and Relevant Monitoring Protocols

Gerlach, J., M. Samways, & J. Pryke. 2013. Terrestrial invertebrates as bioindicators: an overview of 

available taxonomic groups. Journal of Insect Conservation, 1-20.

Helf, K. L., R. L. Woodman, and B. J. Moore. 2005. Cave beetle (Neaphaenops tekklampfi) 

monitoring protocol for Mammoth Cave National Park, Kentucky. National Park Service report 

prepared for Mammoth Cave, National Park Service, U.S. Department of the Interior, Version 

2.00.

Hunt, M. and I. Millar. 2001. Cave invertebrate collecting guide. Department of Conservation 

Technical Series 26. Wellington, New Zealand. http://www.doc.govt.nz/Documents/science-andtechnical/docts26.pdf

Krejca, J. K., G. R. Myers, III, S. R. Mohren, D. A. Sarr, and S. C. Thomas. forthcoming. Integrated 

cave entrance community and cave environment long-term monitoring protocol. Natural 

Resource Report NPS/KLM/NRR—2014/XXX. National Park Service, Fort Collins, Colorado. 

Krejca, J. K. and F. W. Weckerly. 2007. Detection probabilities of karst invertebrates. Report 

prepared for Texas Parks and Wildlife Department and U.S. Fish and Wildlife Service. 

Samways, M. J. 2007. Insect conservation: a synthetic management approach. Annual Review of

Entomolology. 52:465-487.

USFWS. 2011. Karst preserve management and monitoring recommendations. Austin Ecological 

Services Field Office, Austin, TX. 

http://www.fws.gov/southwest/es/Documents/R2ES/Bexar_RP_Mgmt_module.pdf
Cave Ecology Inventory and Monitoring Framework 28

2.2.6 Other wildlife use of caves

While the above sections cover some of the most common terrestrial wildlife 

found in caves, many more species use caves, especially cave entrance areas. The 

cave entrance area can provide a refuge for animals seeking a more humid and 

moderate climate. In the Southwest U.S., over 81 species of vertebrates have been 

documented in 160 caves in the Chihuahua Desert, while in the Sonoran Desert, 

74 species of vertebrates have been documented in 13 caves and 52 mines (Strong 2010). Mammals 

were the most dominant group of vertebrates, followed by birds, reptiles, and amphibians in the 

Chihuahuan Desert, while in the Sonoran Desert the number of reptile species was slightly higher 

than bird species. The most common mammals were ringtails and porcupines, followed by mountain 

lions, Townsend’s big-eared bats, mule deer, and domestic goats. The most common birds were great 

horned owls, cave swallows, rock wrens, canyon wrens, and turkey vultures. The most common 

reptile species were three species of rattlesnakes. Other snake species, as well as lizard and turtle 

species were also found. Amphibians were infrequent, likely due to the arid nature of the region; of 

the three species found, tiger salamanders were the most common (Strong 2010). 

In the Great Basin, a cave entrance study using remote cameras at seven caves in Great Basin 

National Park found that the most abundant species were small mice (Peromyscus spp.), humans, 

chipmunks, woodrats, and squirrels. In addition, other species observed in cave entrances included 

cottontail rabbits, bats, skunks, foxes, insects, birds, and domestic dogs (Baker forthcoming). 

Vertebrate species may use the caves for roosting (e.g., great horned owls), denning (e.g., porcupines 

and mountain lions), nesting (e.g., woodrats and cave swallows), and hibernating (e.g., bats or bears).

Some species use the cave for foraging, such as white-footed mice feeding on crickets (Strong and 

Goodbar 2005) or snakes hunting rodents or bats. In the desert Southwest, many species may use 

cave habitats simply as a respite from arid and hot conditions.

Monitoring for these species could use techniques specific for those species (e.g., traps, mist nets, 

photography, scat and track techniques). This is an area that has not been widely studied, and many 

caves do not even have an inventory of what vertebrate species use them. Thus, an inventory would 

be the starting point for many cave managers desiring to know what wildlife species use the caves 

they manage.

References, Related Studies, and Relevant Monitoring Protocols

Baker, G. forthcoming. Quantifying wildlife use of cave entrances using remote cameras. Report. 

Great Basin National Park, Baker, NV.

O'Connell, A. F., Nichols, J. D., & Karanth, K. U. 2011. Camera traps in animal ecology: methods 

and analyses. Springer: Tokyo, Japan. 271 pp.

Strong, Thomas R. 2010. Vertebrate species in desert caves and mines – a comparison between the 

Chihuahuan and Sonoran deserts. in William Lee Halvorson, Cecil R. Schwalbe, Charles Van 
Cave Ecology Inventory and Monitoring Framework 29

Riper, III, Editors, Southwestern desert resources, University of Arizona Press, Phoenix, AZ, pp. 

93-106.

Strong, Thomas R. and James R. Goodbar. 2005. Vertebrate species use of caves in the Chihuahuan 

Desert. Pages 269-274 in 14th International Congress of Speleology Proceedings. Hellenic 

Speleological Society, Athens, Greece.
Cave Ecology Inventory and Monitoring Framework 30

2.3 Aquatic Cave Ecosystem

When subterranean voids contain water, we enter the aquatic cave ecosystem. This 

could be an underground stream, spring, pool, or the water table. It could also be lake 

water (e.g., Apostle Islands National Seashore) sea water adjacent to the ocean (e.g., 

Point Reyes National Seashore), or sea water that is landlocked but connected via subterranean 

passages, also called anchialine pools (e.g., Kaloko-Honokohau National Historical Park).

The habitats in which specific cave aquatic communities are reliably found can be roughly divided 

between the unsaturated or saturated zone (Poulson 1992, Ford and Williams 2009). The unsaturated 

zone lies above the water table and may contain both ephemeral (e.g., isolated pools and streams) and 

permanent aquatic habitats (e.g., the epikarst). The saturated zone is permanently flooded (Ford and 

Williams 2009). Both unsaturated and saturated zones may contain cave passages.

Inputs to aquatic cave ecosystems can vary considerably from one cave to the next. Some include a 

single river that sinks into a cave and later reemerges. Others include multiple inputs from numerous 

streams and sinkholes. Diffuse groundwater inputs can be a significant contributor to aquatic cave 

ecosystems, with springs emerging in caves or water tables dropping to allow more access to deeper 

parts of the cave and then rising and restricting access.

Research indicates physicochemical parameters can significantly affect the distribution and 

abundance of cave aquatic biota (Simon and Buikema 1997, Sket 1999, Graening and Brown 2003, 

Panno et al. 2006). The varieties of land use atop NPS caves contribute to the range of groundwater

quality, and thus, can affect habitat suitability for cave aquatic biota among its aquatic habitat.

Water quality monitoring data by itself tells resource managers at NPS units little about the impact of 

chronic and/or episodic stressors on cave aquatic biota. However, water quality monitoring creates a 

long-term data set for trend analysis and directly supports and aids the interpretation of aquatic 

biological monitoring. 

Primary reasons for monitoring biological communities within NPS cave aquatic ecosystems are: 

1. Monitoring cave aquatic community diversity, species richness, and relative abundance will yield 

information that can trigger targeted research, which will support future management actions aimed 

at preservation, protection, and restoration where needed.

2. Information on the baseline cave aquatic community may provide a basis for judging the 

effectiveness of efforts by park managers to conserve populations of the federally-listed species. For

instance, if abundance trends of a species declined beyond a threshold to be established, then 

research into causes could support negotiations on agricultural land management standards upstream 

of the park. 
Cave Ecology Inventory and Monitoring Framework 31

3. Monitoring data will help identify declines beyond acceptable limits (to be established over time) 

in sensitive cave aquatic species, which again would induce targeted research to support management 

actions for mitigating impacts.

4. Status and trend data coupled with limits of acceptable change, to be developed as enough data are 

acquired, could support park efforts to deal with water structures outside of caves.

The overriding question addressed by this framework is: Are biological communities within the 

cave’s aquatic ecosystem impaired by any biotic or abiotic stressor arising from within or beyond 

park boundaries?

Dominant threats

Dominant threats to aquatic cave organisms may be intensified any time the water they live in 

experiences a variation. Changing water levels, temperature, dissolved oxygen, pH, and nutrients 

may stress or even kill the cave organisms. Additional stressors include acute or chronic exposure to 

toxins, low level to extreme organic enrichment, mild to severe siltation, plus introduction and/or 

establishment of either exotic (such as rainbow trout) or epigean species (e.g., non-native ants at 

anchialine pools consuming native shrimp when pool waters recede during low tides). These 

stressors are often caused by changes in habitat (both in and above the cave). Habitat loss or impact 

may be caused by human disturbance (e.g., dumping in sinkholes, oil spills washing into storm drains 

that flow into caves), in-cave development (e.g., cave infrastructure, lighting, dams), land use 

changes above caves (especially urbanization and altered agricultural practices), vegetation structure 

changes above caves (e.g., wildfires alter infiltration), sudden environmental changes (e.g., flash 

floods, earthquake-induced waves (as seen in Devils Hole)), and food source contamination from 

heavy metals and/or pesticides. Some of these threats can be mitigated through land management 

actions, while others may not be possible to control, such as major environmental changes driven by 

climate change or natural processes. 

Potential inventory and monitoring questions

The list of questions related to aquatic cave organisms and cave use is highly diverse and potentially 

endless, though most cave managers will likely find common ground in wanting to determine some 

basic information about local populations:

 What species are present in caves?

 What caves/sites do they use?

 When are they present (e.g., year-round vs. seasonally)?

 How many are there (population estimates)?

 What is their population status (e.g., stable, decreasing)?

 How does the population or activity change seasonally or annually?

 How do water quantity and quality correlate with the status of the species of interest?

 What is the community composition of a particular aquatic habitat within the cave?

 What can be done to protect them?
Cave Ecology Inventory and Monitoring Framework 32

More advanced questions may follow after managers have succeeded in answering some of the 

basics about local populations. Many of these questions may be beyond the scope of inventory and 

monitoring and enter the realm of research. Additional questions may include:

 What water quality parameters are the species of interest selecting for, and how does this 

vary based on season/use (e.g., dissolved oxygen, nutrient availability)?

 What physical or morphological characters are species selecting for, and how does this vary 

based on season/use (e.g., water temperature, depth)?

 Is there any correlation between the species of interest use and level of development of a 

particular cave or cave area?

 How do floods/tidal extremes affect the species/community of interest?

 How do changes in environmental factors (e.g., temperature, relative humidity, barometric 

pressure) due to development or modification (e.g., artificial entrances, trail construction, 

dams) affect species? 

 How does land use above caves impact species of interest populations?

 Have populations / species composition changed over time (decadal or century scale using 

paleontological data)?

Potential focal species/sites

The focal species for monitoring will depend on the species present in the area, as well as the status 

(state or federal protection), significance (relative local importance of that species and if they are 

facing threats), and feasibility of monitoring for a particular species. In addition, documentation of 

sites critical to the life cycle of a particular population should necessitate prioritized monitoring and 

protection for that site. In most localities, multiple species will be present. Priorities for inventory 

and monitoring often depend on available resources and trained staff, however, strong consideration 

should be given to endangered species, abundant/detectable species (easier to monitor), and sites that 

are used by multiple species. These priority monitoring categories will likely overlap, and 

implementation of robust, long-term monitoring efforts and proper data analysis may reveal proxies 

for estimating the status or trend of interrelated monitoring groups. For aquatic species it cannot be 

emphasized enough that measuring water quantity and quality concurrently with inventory and 

monitoring of the aquatic cave species is critical.

Additional information is provided here about monitoring two broad categories: top predators, which 

are often flagship species, and detritovores, which may be representative of the system. In addition, 

many species within each of these categories are stygobites. Stygobites often have adapted to low 

nutrient systems and have a lower metabolism than their surface relatives or even stygophiles, and 

thus live longer lives (Wilhelm et al. 2006). They may be more susceptible to competition by 

stygophiles if nutrient inputs are high.

Top Predators

 Fish-Many fish have adapted to the subterranean environment. One example is the Northern 

cavefish Amblyopsis in Mammoth Cave, which can live up to 60 years. Devils Hole Pupfish 

may be some of the most monitored subterranean fish in the world.
Cave Ecology Inventory and Monitoring Framework 33

 Crayfish--Stygobiotic crayfishes can play a major role in aquatic cave ecosystems. They are 

found in the eastern United States, Mexico, and Cuba, with 41 species (Hobbs 2005). They 

are omnivores and highly-adapted to low-energy fluxes. They are able to persist for decades, 

and sometimes even to 100 years (Culver 1982). In Mammoth Cave, the cave crayfish 

Orconectes pellucidus may live up to 90 years.

 Amphibians-- a variety of amphibians use caves, but some of them, such as the Texas blind 

salamander (Eurycea rathbuni) are entirely aquatic. 

 Crabs and Shrimp--Although not often found in inland caves, crabs and shrimp can be the top 

of the food chain in tropical and anchialine caves found in the tropics. The Kentucky cave 

shrimp feed on biofilms in caves in several counties in Kentucky.

Detritovores

 Isopods-- Subterranean isopods occur in caves throughout the world, with about 1,000 

species described from 35 families (Hobbs 2005).

 Amphipods-- Amphipods are found in most aquatic subterranean habitats throughout the 

country. They are diverse, with 35 families, 133 genera, and over 800 species (Culver and 

Pipan 2009). 

 Snails-- Cave-adapted snails in the family Hydrobiidae are numerous, with more than 350 

species (Bole and Velkovrh 1986). They are often extremely tiny, with simplified body 

structures to adapt to the limited space. 

Potential inventory & monitoring strategies

Answering inventory and monitoring questions related to aquatic species requires following a 

strategy or combination of strategies. Monitoring generally falls into three strategy levels or 

categories:

1. Presence/absence inventories/monitoring is used to develop faunal or species lists, is 

useful for determining site occupancy and informing species protection efforts, and may 

be used as a strategy to inform ecological monitoring efforts.

2. Population monitoring may be based on in-cave surveys and informs long-term trends 

in the status of populations.

3. Ecological monitoring attempts to understand the dynamics of species behavior and 

dispersal, including the habitat preferences of the species of interest, the life cycle needs 

that correspond to those habitat preferences, and the temporal patterns (daily or seasonal) 

associated with those habitats. 

For all three of these strategy levels, monitoring water quantity and quality is recommended.

Potential inventory and monitoring techniques

As for terrestrial cave macroinvertebrate monitoring, aquatic cave macroinvertebrate monitoring 

should be preceded by basic inventory work conducted with an appropriately qualified biologist to 

develop a list of species likely to be encountered. Macrophotos of taxa can be helpful – a set of 

laminated identification cards with photos can greatly assist in field identifications. Bringing a 
Cave Ecology Inventory and Monitoring Framework 34

camera with a good macro lens to photograph unusual taxa during monitoring, or a few vials to 

collect unusual organisms for later identification by an expert, may be helpful.

Approaches to monitoring of aquatic cave invertebrates (isopods, amphipods, flatworms, snails, and 

microcrustaceans) varies by type of aquatic habitat. These include:

 Timed area search

 Drip traps

 Baited funnel traps

 Quadrats

 Census

Timed area search

In drier cave environments with isolated drip pools, visual timed area search of pools may be 

appropriate. Such searches might include calculating the area of each drip pool, then counting the 

invertebrates, by taxon, in each pool. Amphipods may be underestimated with this approach, as some 

spend considerable time buried in substrates or under stones.

Drip traps

For microcrustaceans, it may be possible to conduct monitoring using drip traps to live-capture 

copepods and other small organisms dripping down from the MSS. It may be appropriate to bring a 

dissecting microscope into the cave to count the microcrustaceans before releasing them into drip 

pools. Species level identifications are not feasible, but copepods can be classified as harpacticoid, 

cyclopoid, and calanoid with some training.

Baited funnel traps

Where cave streams are present, approaches may vary with scale, turbidity, flow rates, degree of 

natural organic enrichment, and pollution. In relatively large, flowing, turbid, high energy cave 

streams, baited funnel traps can be used to monitor isopods and, especially, amphipods. These should 

be left in place a rather short period of time (probably hours at most) so that larger numbers of 

individuals do not accumulate (resulting in specimen death from anoxia and predation). The best bait 

for such traps is raw (uncooked) shrimp that has been allowed to decay for a day at room temperature 

– only a small piece is needed. Prior inventories by a trained biologist are needed to be able to 

determine the range of likely species to be detected, and it is often not feasible to field identify 

amphipods and isopods to species level where more than one species occurs in the area. Multiple 

funnel traps should be placed to get some estimate of variance among samples.

Where streams are small, clear and/or low energy (few organics), baited funnel traps may introduce 

unacceptable levels of nutrients into the cave system (resulting in an increase in microbial growth). 

For the same reason, baited funnel traps should not be used in drip pools.

Quadrats
Cave Ecology Inventory and Monitoring Framework 35

In small, rocky, clear slow-moving streams, monitoring can be undertaken using quadrats constructed 

from PVC pipe. These quadrats are used to delineate search areas, and a pair of researchers (one 

searching, one data recording) can count all of the macroinvertebrates occurring within a quadrat. 

Concerns regarding the possible impacts of this activity, including trampling and substrate disruption 

caused by lifting stones, should be weighed prior to implementing monitoring.

Census 

Census methods are concentrated on macro-organisms which can be identified in the field, since 

wholesale collecting of specimens for later identification in the laboratory often is incompatible with 

the objectives of a Park. These macro-organisms censuses can include total counts along a stream 

segment for fishes, salamanders, and other vertebrates, plus crayfish and shrimp. Other macrofauna 

are noted as they are encountered in the field, but total counts are not attempted. These organisms 

may include isopods, amphipods, flatworms, snails, and copepods. Many of the organisms are 

captured with small dip nets, measured, and examined for signs of health, reproduction, and food 

intake. All organisms are returned to the stream as quickly as possible, without harm, and at the 

capture location. At those sites where the stream is one meter deep or less, the surveys can be made 

by walking along and in the stream. At locations where the water depths exceed 1-2 meters, however, 

it is necessary to use wet suits or dry suits, fins, masks and snorkels. 

At Mammoth Cave, vertebrates and larger macroinvertebrates are censused by two observers who 

either wade upstream or swim with mask and snorkel. All organisms are counted, and subsets of 

them are captured (with a dip net 10 x 20 cm with a 3mm mesh) and measured. The volume (by 

water displacement) of captured organisms may be determined, and various characteristics that might 

indicate the condition of individuals in the population are recorded. These characters include 

reproductive condition; the presence of food; the presence of deformities, eroded fins, lesions, and 

tumors; and regeneration or loss of limbs.

For sea cave monitoring, see http://jncc.defra.gov.uk/PDF/CSM_marine_sea_caves.pdf

References, Related Studies, and Relevant Monitoring Protocols

Bole, J. and Velkovrh, F. 1986. Mollusca from continental subterranean aquatic habitats, pages 177-

206. in L. Botosaneanu, ed. Stygofauna mundi. E.J. Brill, Leiden, The Netherlands.

Campbell Grant, E. H., W. H. Lowe, & W. F. Fagan. 2007. Living in the branches: population 

dynamics and ecological processes in dendritic networks. Ecology Letters 10(2):165-175.

Culver, D. C. 1976. The evolution of aquatic cave communities. American Naturalist, 945-957.

Culver, D. C. 1982. Cave life. Harvard University Press, Cambridge, MA.

Culver, D. C. 1985. Trophic relationships in aquatic cave environments. Stygologia 1.1:43-53.
Cave Ecology Inventory and Monitoring Framework 36

Culver, D. C. and T. Pipan. 2009. The biology of caves and other subterranean habitats. Oxford 

University Press, New York.

Eberhard, S. 1999. Cave fauna management and monitoring at Ida Bay, Tasmania. Parks and 

Wildlife Service.

Ford, D. and Williams, P. 2007. Karst hydrogeology and geomorphology. John Wiley & Sons, New 

York.

Graening, G. O., & A. V. Brown, A. V. 2003. Ecosystem dynamics and pollution effects in an ozark 

cave stream. Journal of the American Water Resources Association 39(6):1497-1507.

Graening, G. O., D. B. Fenolio, M. L. Niemiller, A. V. Brown, & J. B. Beard. 2010. The 30-year 

recovery effort for the Ozark cavefish (Amblyopsis rosae): Analysis of current distribution, 

population trends, and conservation status of this threatened species. Environmental biology of 

fishes, 87(1):55-88.

Graening, G. O., M. E. Slay, & C. Bitting. 2006. Cave fauna of the Buffalo National River. Journal 

of Cave and Karst Studies 68(3):153-163.

Graening, G. O., M. E. Slay, A. V. Brown, & J. B. Koppelman. 2006. Status and distribution of the 

endangered Benton cave crayfish, Cambarus aculabrum (Decapoda: Cambaridae). The 

Southwestern Naturalist 51(3):376-381.

Graening, G. O., & M. E. Tinkle. 2003. Subterranean Biodiversity of Arkansas, part 1: Bioinventory 

and bioassessment of caves in the Sylamore Ranger District, Ozark. Journal of the Arkansas 

Academy of Science, 57.

Hobbs, H. H., III. 2005. Crustacea. Pages 141-53. in D. C. Culver and W. B. White, eds. 

Encyclopedia of caves. Elsevier/Academic Press, Amsterdam, The Netherlands.

Panno, S. V., K. C. Hackley, W. R. Kelly, H. H. Hwang, F. M. Wilhelm, S. J. Taylor, & B. J. Stiff. 

2006. Potential effects of recurrent low oxygen conditions on the Illinois cave amphipod. Journal 

of Cave and Karst Studies 68(2):55-63.

Pearson, W. D., R. Olson, and B. Moore. 2006. Cave aquatic system monitoring protocol for 

Mammoth Cave National Park, Kentucky. National Park Service, U.S. Department of the 

Interior.

Poulson, T. 1992. The Mammoth Cave ecosystem. Pages 564-611 in The natural history of 

biospeleology, edited by A. I. Camancho, Monographs of the National Museum of Natural 

Sciences, Madrid, Spain.

Simon, K. S., & A. L. Buikema Jr. 1997. Effects of organic pollution on an Appalachian cave: 

changes in macroinvertebrate populations and food supplies. American Midland Naturalist:387-

401.
Cave Ecology Inventory and Monitoring Framework 37

Sket, B. 1999. The nature of biodiversity in subterranean waters and how it is endangered. 

Biodiversity and Conservation 8:1319-38.

Wilhelm, F. M., S. J. Taylor, and G. L. Adams. 2006. Comparison of routine metabolic rates of the 

stygobite, Gammarus archerondytes (Amphipoda: Gammaridae) and the stygophile, Gammarus 

troglophilus. Freshwater Biology 51:1162-1174.
Cave Ecology Inventory and Monitoring Framework 38

2.4 Plants 

Plants are often not considered at first when thinking about monitoring cave ecology, but they can be 

an important part of the cave ecosystem. Vegetation near the cave entrance can influence what lives 

in the entrance and twilight zones. Ferns, mosses, and lichens are common within cave entrances, and 

the microclimate of some entrances may support rare and/or specialized plant species. In addition, 

the vegetation above the cave can have an impact on the cave environment via its roots, 

evapotranspiration, amendments to the soil, and more. 

Lamp flora, or flora growing near artificial lights in the cave, often supports its own ecological 

communities. Since lamp flora is unnatural to the cave, eradication is usually the goal of cave 

managers, though short-term inventory and monitoring may be useful for quantifying impacts and 

determining mitigations.

2.4.1 Cave Entrance Flora

Cave entrance flora are plants that grow in and near cave entrances, and may be 

different from surrounding vegetation depending upon air flow direction, slope 

position, and aspect. There are two basic scenarios for caves with chimney effect 

airflow. If air exits the cave during the growing season at a particular entrance, 

then the plants there may be part of the ecotone between cave ecosystems and 

surface ecosystems. A particularly cool and moist microclimate may be noticeable if the entrance is 

in a sinkhole and cave air pours over the lowest lip of the sink. This will yield a thermocline at the 

level of the spillway where plants that prefer cool moist conditions will be found below this level and 

more typical plants will dominate above that “pool” of cool moist air. It may be possible at night to 

see waves at the interface of these two air masses, sometimes with a layer of fog above the 

thermocline. Shining a light almost parallel to the thermocline brings out the boundary layer structure 

best. The second scenario happens in winter at upper entrances with chimney-effect airflow. The 

relatively warm and moist air may facilitate mosses and other small plants. Potentially, this “moss” 

community could be very rich in non-vascular plant species. 

In the driftless area (where ice age glaciers did not arrive) of the Midwest, steep limestone bluffs 

have cracks that open up to a talus slope. Snow settles down into the talus and can even form ice. 

This persistent cold creates its own down-draft, and where the cooled air exits, it can help support 

relict Pleistocene flora. Relict species may also occur in some cave entrance communities.

Algae and cyanobacteria (blue-green bacteria) will grow with any light source, natural or man-made. 

One will often see a transition in entrance sinkholes from surface vegetation to ferns, then mosses, 

then algae and liverworts, and finally dusky-green cyanobacteria. The plant growth is rich in 

invertebrates that have been little studied.

There is an earthy smell associated with most cave entrances due to the growth of actinomycete 

bacteria. These bacteria are normal soil microbes that also grow well in caves. They grow as colonies 

of white, yellow, pink, or other hues, close to entrances or in locations close to the surface where 
Cave Ecology Inventory and Monitoring Framework 39

organic nutrients seep into the cave. You will often see them as discrete “dots”, but in lava tube caves 

they may form a dense coating on the walls and ceiling of the cave.

Cave entrances and twilight zones can serve as refugia for plants, often providing cooler and/or 

moister conditions. 

Skylight communities

A skylight is an opening in a cave ceiling that opens up due to collapse, surface erosion, or water 

capture above an underlying cave. A skylight is a new entrance into a cave and may provide access to 

humans. It can develop a complete entrance community over time. Skylights are particularly 

common in lava tube caves and have been identified on the surface of Mars. Caves provide 

protection from ionizing radiation, and caves on other planets may harbor life and serve as a refuge 

for humans who might visit those planets.

Tree roots in caves may play an important role for invertebrates. Trees in karst areas may use water 

and reduce the amount that reaches a cave. Roots can fracture rocks in caves and around entrances. 

Vegetation is a source of energy and can be brought into caves by animals, washed into the cave, or 

falls into the cave (e.g., pinecones in entrances pits). Vegetation also attracts animals, which are 

additional energy sources for caves.

Dominant threats to cave entrance vegetation are those that also face terrestrial cave ecosystems 

(section 2.2). Monitoring/sampling sites should be located in a manner to minimize disturbance to the 

plant communities.

Potential inventory and monitoring questions for cave entrance flora are similar to those found in 

section 2.2 for terrestrial cave ecosystems. Potential focal species include relict flora/relict flora; 

sensitive species, especially those sensitive to changes in humidity and temperature; threatened and 

endangered species; natural heritage species; lichens; and fungi. Sites may need to be stratified based 

on entrance habitats. Temperature and humidity readings should be taken in conjunction with 

assessing vegetation.

Potential inventory and monitoring techniques

Depending on the monitoring objectives, several techniques are possible:

 Point-line intercept method if enough habitat is present

 Map area of focal species at a regular interval

 Count the number of cave entrances that contain the focal species

 Take samples of algae for identification

 Photomonitoring, with several techniques possible

 Mapping of social trails through thick vegetation
Cave Ecology Inventory and Monitoring Framework 40

References, Related Studies, and Relevant Monitoring Protocols

To find the Lava Beds National Monument Cave Entrance Vegetation SOP, go to the following link, 

click on the Cave Entrance Communities & Environments tab, and then click on Final Report.pdf: 

http://science.nature.nps.gov/im/units/klmn/publications.cfm?tab=2

2.4.2 Lamp flora

Cyanobacteria (formerly known as blue-green algae), algae, mosses, and other 

plants induced by the lights we place in cave passages are called lamp flora in 

Europe (or lampenflora). The term lamp flora has been adopted in the United 

States. These photosynthetic-based species displace the natural microflora

associated with the dark habitats of artificially-lighted caves. Such distortion of 

the cave ecosystem is often severe in passages decorated with calcite speleothems.

Lamp flora have been killed or removed by a variety of means including herbicides in Lehman Caves 

and steam in Mammoth Cave, Kentucky (Harris 1981). At Kartchner Caverns in Arizona, a 12% 

solution of hydrogen peroxide was used with limited success. Growths returned in a month compared

with three to six months for areas treated with diluted bleach (RS Toomey III, personal 

communication 2002). However, Aley (1976) found even 30% hydrogen peroxide to be ineffective, 

and such high concentrations are dangerous. For many years, these unwanted growths have been 

controlled through periodic spraying of 0.5% sodium hypochlorite, which is household bleach. In 

Hungarian caves, 5% formaldehyde has been used successfully (Rajczy et al. 1987). However, use of 

manufactured chemicals can create ecological, aesthetic, and safety issues. Light management may 

be one of the best solutions, as wavelengths can be chosen that do not allow lamp flora to flourish. In 

addition, it should be a regular practice in caves with artificial lighting to use that lighting only when 

necessary, turning it off when that part of the cave is not being visited.

Potential inventory and monitoring questions for lamp flora are similar to those found in section 2.2 

for terrestrial cave ecosystems. Focal species will depend on what is found during the inventory. 

Lamp flora not only differs from cave to cave, but also changes through time in the same cave. 

Monitoring/sampling sites can be located in a variety of ways depending on what question is being 

asked. Lamp flora will differ by moisture level, type of light, and area of cave 

(entrance/twilight/dark). Some areas may be too sensitive to conduct regular monitoring, especially 

wet formations. In addition to monitoring near lights, reference sites away from lights should also be 

included. When conducting an inventory or monitoring of lamp flora, be sure to document the past 

history of the area, particularly when it was last cleaned and the method used to clean it. An annual 

monitoring schedule may be adequate for most caves.

The primary inventory and monitoring technique used for lamp flora at this time is photomonitoring. 

An area near the light is photographed, and a GIS or photo program is used to calculate the area 

affected by lamp flora. This could be a good citizen science project using local caving grottoes.
Cave Ecology Inventory and Monitoring Framework 41

References, Related Studies, and Relevant Monitoring Protocols

Aley, T. J. 1976. Hydrology and surface management. Pages 44-45 in The National Cave 

Management Symposium Proceedings. Speleo-books, Albuquerque, NM. 

Harris, D. 1981. The control of nuisance plant growth in Mammoth Cave, KY. Mammoth Cave 

National Park, National Park Service.–1981.

Olson, R. 2008. Lampflora research update: This just in. Inside Earth, volume 11, no. 1.

http://www.nature.nps.gov/geology/caves/newsletters/INSIDE_EARTH_summer_08_v_11_n_1_

Finalscreen.pdf.

Olson, R. 2002. Control of lamp flora in Mammoth Cave National Park. Page 131 in Hazslinszky T, 

editor. International conference on cave lighting proceedings. Budapest: Hungarian Speleological 

Society. 

Rajczy, M., Buczkó, K. & P.-Komáromy, Zs. 1987. Contributions to the flora of the Hungarian

caves. I. Flora of the entrances of the caves Lõk-völgyi-barlang and Szeleta-barlang. – Studia bot. 

hung. 19 (1986):79-88.

Toomey, R., R. Olson, S. Kovar, M. Adams, and R. Ward. 2009. Relighting Mammoth Cave's new 

entrance: improving visitor experience, reducing exotic plant growth, and easing maintenance. 

Proceedings 15th International Congress of Speleology. Edited by W. White, V. 2, Part 2, 

Kerrville, TX. P. 1223-1228.

2.4.3 Habitat above Caves

Caves do not exist in isolation from their surroundings, as previously discussed (Figure 7). Habitat 

above caves is critical to caves. Trogloxenes, such as bats, cave crickets, and woodrats, shift 

resources from the habitat above the cave into the cave. Preservation of sufficient surface area, 

vegetation, stream flow, and other factors is a critical component of recovery plans under the 

Endangered Species Act. We know that changes on the surface have direct impacts on the underlying 

caves and populations of trogloxenes. Changes in surface habitat over thousands of years have been 

documented by studying middens in caves (Betancourt et al. 1990). Even habitat farther from caves 

can play an important role in the cave ecosystem, such as when bats leave the cave to go forage for 

insects. The number of insects available for bats is influenced by the vegetation types present, as well 

as water sources, development, and other factors.
Cave Ecology Inventory and Monitoring Framework 42

2.5 Microbes

Microorganisms are ubiquitous in all environments, including caves, although their 

small size means they are often overlooked despite their important role in recycling 

nutrients, decomposition, geomicrobiology, and primary productivity. 

Microorganisms are the most diverse group of organisms in terms of numbers of species and 

metabolic activities, and include bacteria, archaea, fungi, single-celled protozoa and algae (although 

such photosynthetic species are limited to the entrance zone). Despite their small size, visible growth 

of bacteria can often be seen in the form of colonies, or in the case of fungi, reproductive structures 

(mushrooms and molds) may be seen. For an introduction to cave microbiology for non-specialists, 

see Barton 2006.

The interrelations among microorganisms and geological processes is studied in the field of 

Geomicrobiology (Barton and Northup 2006, Barton et al. 2005, Northup and Lavoie 2001). 

Microorganisms play important roles in formation of some secondary minerals in caves, such as 

saltpeter; in the deposition of carbonates, including moonmilk, helectites, pool fingers, cave pearls, 

and carbonate speleothems; silicate speleothems; deposition of ferromanganese deposits (Northup et 

al. 2003, Spilde et al. 2005); sulfur compounds; and larger scale biokarst (Cunningham et al. 1995).

At the entrance, photosynthetic microorganisms such as algae and Cyanobacteria will be 

encountered. Once you proceed beyond the entrance, non-light dependent microorganisms thrive, 

particularly in areas of nutrient input, such as drip water coming into the cave or hydrogen-sulfide 

rich springs. These microbes can be observed by their paint splash-like white and yellow colonies on 

the wall, and from their distinctive earth-like smell. This smell is associated with production of 

geosmin by Actinomycete bacteria. In some lava tube caves, Actinomycete growth can completely 

coat the walls and ceilings of cave entrances with a white, dusty appearance (Garcia et al. 2009; 

Northup et al. 2008), or form a reflective surface known as “cave silver” when water beads up on 

hydrophobic colonies. Actinomycetes are important microorganisms in industry and have provided 

the majority of antibiotics currently in use. 

Additional indicators of microbial activity in caves (Barton et al. 2005) include colonies on surfaces, 

indicated by unusual coloration; precipitation; ferromanganese deposits, usually as coatings; 

structural changes such as dissolutional pitting; and gooey biofilms and white filaments. Typical

microbes use organic matter (all fungi, protozoa, and most bacteria) which is usually limited in most 

caves. In cave locations where organic matter does not enter the system, such as very deep caves and 

caves where little surface water enters the system, microbial ecosystems will rely on the 

geochemistry of the rock, including such elements as sulfur, iron, or manganese as a source of 

energy.

Microorganisms are often studied in the laboratory by culturing them on growth media. Cultivation is 

a powerful tool in medical and food microbiology, but less than 0.1% of environmental microbes can 

be grown using this technique, a number which reaches 0.01% in cave ecosystems (Angert et al., 

1998, Barton and Northup 2006). In doing cultural studies from oligotrophic cave environments it is 
Cave Ecology Inventory and Monitoring Framework 43

important to use low-nutrient media, such as diluted media and soil extract media, even water-agar, 

in an attempt to grow microbes of environmental interest (Pemberton et al. 2008). When studying 

fungi or indicators of human activity it is appropriate to use standard culture media (Vaughn et al. 

2007). Another important consideration in cultivation is incubation temperature; attempting to isolate 

environmental microbes from a 15° C cave when you incubate at the standard 37° C is a common 

error.

Environmental microbiologists usually have to rely on non-culture techniques primarily using genetic 

analysis (Angert et al 1998: Barton et al 2004; Chelius and Moore 2004), which are costly and highly 

technical (Barton et al. 2004). It is important to use procedures and kits designed for isolation of 

environmental microbes, not those designed for medical samples. Other laboratory techniques such 

as fluorescence microscopy, electron microscopy (see Spilde et al. 2005), and enzyme and lipid 

analysis can also be useful.

A common concern in microbiological studies is presence vs. activity. Since microbes are ubiquitous, 

you will isolate microbes that may be present but not active. Another important consideration is 

quantification. When collecting samples, it is best to swab a standard surface area, measure the gram 

dry mass of soil, or measure the milliliters of water so that useful comparisons may be made.

Dominant threats to microbes are similar and overlap with threats to other cave biota. These threats 

include anthropogenic energy input, such as human detrital input (e.g., vomit in Lascaux Cave in 

France, lint, human waste); changes to cave infrastructure (in particular lighting and the introduction 

of decomposable substrates, such as untreated wood); introduction of chemicals (e.g., cleaning with 

bleach, chemical residues from WNS decontamination); and land use changes above the cave (e.g., 

development, roads), that could increase the likelihood of pollution or nutrients entering the cave.

Potential inventory and monitoring questions 

Microbes differ from previously discussed organisms in that thousands can make up a community. 

These communities are often dependent on microniches, and a mere centimeter shift in any direction 

could result in finding a very different community of microorganisms (Macalady et al. 2008). 

Traditionally we thought cave microbes were a subset of microbes washed or carried in from the 

surface, but studies are showing widely distributed communities of what may be endemic microbes, 

adapted to grow best under cave conditions (Northup et al. 2008, Garcia et al. 2009).

With that said, microbes can still be useful in inventory and monitoring.

1. If fecal contamination is suspected, they can be used to track water pollution (e.g., 

coliforms). Changes over time will show the success of clean-up operations.

2. What is the trend in human impacts in a cave on a microbial level?

3. How is the microbial community changing over time and/or before-after some event?

Potential focal species

Human impacts (for example, Staphylococcus aureus, coliforms, and other species)
Cave Ecology Inventory and Monitoring Framework 44

can be indicative of human impact; however, it should be noted that a number of native cave species 

express many of the characteristics that could confuse them with introduced species. Because of this, 

it is critical that researchers are experienced in cave microbiology techniques and do not use tools 

and techniques that were developed for the medical setting, which can often lead to confusing and 

sometimes incorrect conclusions. 

Potential inventory and monitoring techniques

1. To measure fecal contamination, fecal coliforms can be identified by water filtration 

followed by lactose fermentation assays and confirmatory tests. There are simple and 

effective kits available for quantifying fecal contaminants.

2. If cultivation is desired, culture media must be made that reflects the geochemistry of the 

cave environment being examined, reduced nutrient levels, and appropriate incubation 

conditions. Quantification of area/mass/volume of samples allows for comparisons.

3. Direct cell counting can be carried out to determine the size of microbial populations. Direct 

cell counting is best done by the filtration of water and staining. It is possible to count 

microbial cells in sediments, provided that fluorescent markers are used to allow 

differentiation of the microbial cells from particulate matter, which requires the use of a 

fluorescent microscope.

4. Electron microscopy can be used to reveal microbial presence, density, and physical 

appearance.

5. The best method of examining microbial communities in cave environments is through a 

molecular phylogenetic analysis of the 16S ribosomal RNA gene sequences, although nextgeneration sequencing technologies are rapidly increasing the types of analyses that can be 

carried out. 

6. Measurement of microbial activities. Hach® test kits are available for on-site testing of many 

parameters, such as hydrocarbons, hydrosulfides, and dissolved methane (test for fracking); 

but the testers need to be aware that petrochemicals or methane presence are natural in some 

areas and may not be indicative of human impact.

Considerations for locating monitoring/sampling sites

Because of the large diversity of previously uncultivated microorganisms from caves, it is critically 

important that the intention of microbial surveillance is thoroughly established prior to beginning 

measurement. Microbial communities change greatly throughout the cave (Ikner et al 2007), so a 

cave manager must have a specific question in mind for investigating an area, such as looking at 

water pollution or human impacts (Vaughn et al 2011). Successful microbial sampling in caves often 

requires identifying the potential energy source for microbial growth in the cave and determining its 

impact(s) on microbial populations.

Considerations for data analysis and interpretation

Data analysis and interpretation is generally done by highly experienced cave microbiologists. 

Fortunately for cave managers, the number of these individuals is increasing, despite the science of 

cave microbiology still being relatively new. For instance, cave microbiologists know that in a cave 

about 40% of all species may be lactose-positive coliforms and test positive for E. coli but most are 
Cave Ecology Inventory and Monitoring Framework 45

really a different organism; secondary and tertiary tests (for example mTec at 42° C) will show the 

real E. coli. They will also know the limitations of direct cultivation on assessing the microbial 

communities in caves, and can provide advice on the correct culture media to use. For example, if the 

community growing on plant detritus is to be examined, then a media that contains this material will 

provide a better growth media.

When using tools developed for use in the medical setting, such as BBL and API metabolic tests, it is 

unclear whether previously uncultivated cave species have the same metabolic profiles as human 

pathogens. If this is the case, the use of such medically relevant techniques can often lead to incorrect 

information, often biasing results toward finding human infectious organisms when they are not 

present. It should also be noted that many human bacterial and fungal pathogens share nonpathogenic relatives in the cave environment, and therefore their identification does not necessarily 

indicate the presence of human impact. A much more reliable technique is to use the 16S ribosomal 

RNA sequence and genetic comparisons; however, this is an expensive proposition, especially given 

the likelihood of tens-of-thousands of different microbial species present in each cave system.

Considerations for monitoring regime

Microbe communities can change from sampling event to sampling event and over short distances. 

Long-term monitoring most likely will not be feasible or effective, except for water quality/pollution 

assays. Inventories, however, may be useful if an NPS unit finds something very unusual in the cave 

and wants to learn what it is. 

Discussion

Although microbial communities may be invisible, it is still important to preserve them. Using 

minimum impact caving techniques such as avoiding unnecessary touching, cleaning cave gear 

between trips, not leaving any crumbs or any other evidence that you’ve been in the cave will help 

keep the microbes in the most natural state possible; one crumb is enough to feed a million microbes 

for weeks or even months (Barton 2006). 

One goal is to decrease lint from visitors, as the natural, organic fibers from clothing and skin and 

hair normally shed by people provide an external source of food for microorganisms. Microbial 

growth results in production of organic acids that can damage underlying rock and speleothems. Lint 

input could be limited by advising visitors of the best types of clothing to wear, having visitors walk 

through blowers before entering the cave to remove lint, or even by limiting access to the cave.

References, Related Studies, and Relevant Monitoring Protocols

Angert, E.R., D.E. Northup, A.-L. Reysenbach, A. S. Peek, B. M. Goebel, and N.R. Pace. 1998. 

Molecular phylogenetic analysis of a bacterial community in Sulphur River, Parker Cave, 

Kentucky: American Mineralogist 83:1583–1592.

Barton, H.A. 2006. Introduction to cave microbiology: a review for the non-specialist. Journal of 

Cave and Karst Studies 68:43-54.
Cave Ecology Inventory and Monitoring Framework 46

Barton, H. A. and D.E. Northup. 2006. Geomicrobiology in cave environments: Past, current and 

future perspectives Journal of Cave and Karst Studies 69:163-178.

Barton, H. A., M. R. Taylor, and N. R. Pace. 2004. Molecular phylogenetic analysis of a bacterial 

community in an oligotrophic cave environment: Geomicrobiology Journal 21:11–20.

Barton, H. A., N. M. Taylor, M. P. Kreate, S. A. Oehrle, and J. L. Bertog. 2005. The impact of 

organic load on bacterial community structure and geomicrobial transformation in oligotrophic 

cave environments. International Journal of Speleology 36:93-104.

Barton, H. A., N. M. Taylor, M. P. Kreate, A. C. Springer, S. A. Oehrle, and J. L. Bertog. 2007. The 

impact of host rock geochemistry on bacterial community structure in oligotrophic cave 

environments. International Journal of Speleology 36:93–104.

Chelius, M. K., and J. C. Moore. 2004. Molecular phylogenetic analysis of Archaea and Bacteria in 

Wind Cave, South Dakota: Geomicrobiology Journal 21:123–134.

Cunningham, K. I., D. E. Northup, R. M. Pollastro, W. G. Wright, and E. J. LaRock. 1995. Bacteria, 

fungi and biokarst in Lechuguilla Cave, Carlsbad Caverns National Park, New Mexico: 

Environmental Geology 25:2–8.

Garcia, M. G., M. Moya, M. N. Spilde, F. D. Stone, and D. E. Northup. 2009. Discovering new 

diversity in Hawaiian lava tube microbial mats. Proceedings of the 15th International Congress of

Speleology 1:364–369.

Ikner L. A., R. S. Toomey, G. Nolan, J. W. Neilson, B. M. Bryan, and R. M. Maier. 2007. Culturable 

microbial diversity and the impact of tourism in Kartchner Caverns, Arizona. Microbial Ecology 

53:30-72.

Macalady, J. L., S. Dattagupta, I. Schaperdoth, D. S. Jones, G. K. Druschel, and D. Eastman. 2008.

Niche differentiation among sulfur-oxidizing bacterial populations in cave waters. ISME J 

2:590–601.

Northup D. E., S. M. Barns, L. E. Yu, M. N. Spilde, R. T. Schelble, K. E. Dano, L. J. Crossley, C. A. 

Connolly, P.A. Voston, D. O. Natvig, and C. N. Dahm. 2003. Diverse microbial communities 

inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environmental 

Microbiology 5(11):1071-1086.

Northup, D.E., and K. H. Lavoie. 2001, Geomicrobiology of Caves: A Review: Geomicrobiology 

Journal 18:199–222.

Northup, D.E., C. A. Connolly, A. Trent, V. M. Peck, M. N. Spilde, W. C. Welbourn, and D. O. 

Natvig. 2008. The nature of bacterial communities in Four Windows Cave, El Malpais National 

Monument, New Mexico, USA. AMCS Bulletin 19:119–125.
Cave Ecology Inventory and Monitoring Framework 47

Pemberton, A., J. Millette, and H. A. Barton. 2005. Comparative study of oligotrophic bacterial 

species cultivated from Jack Bradley Cave, Kentucky: 14th International Congress of Speleology, 

Athens, Greece.

Spilde, M.N., D. E. Northup, P. J. Boston, R. T. Schelble, K. E. Dano, L. J. Crossey, and C. N. 

Dahm. 2005. Geomicrobiology of cave ferromanganese deposits: A field and laboratory 

investigation: Geomicrobiology Journal 22:99–116.

Vaughn M. J., R. M. Maier, and B. M. Pryor. 2011. Fungal communities on speleothem surfaces in 

Kartchner Caverns, Arizona, USA. International Journal of Speleology 4(1):65-77.
Cave Ecology Inventory and Monitoring Framework 48

3.0 General Guidance for Inventory and Monitoring of Cave 

Ecology

3.1 Deciding What to Monitor (Decision Tree)

Section 2.0 discussed potential targets for cave managers to monitor to better understand their cave 

ecosystems. However, monitoring everything mentioned in that chapter would clearly be unfeasible 

given time, money, and staff constraints. So how does a manger decide what to monitor? Here we 

provide a path for determining just that.

It should be noted that although this document concentrates on the Inventory and Monitoring 

Framework that is in place throughout the NPS, another method may be useful for managers. The 

Ecological Integrity Assessment Framework (EIAF) provides a detailed characterization of a 

resource or site as a precursor to identifying management strategies (Unnasch et al. 2008). The EIAF 

uses three steps: identifying what’s important, developing metrics to characterize the integrity of the 

focal ecological resources and shifting to the management of focal ecological resources. The EIAF is 

currently being used in some Natural Resource Condition Assessments (e.g., Great Basin National 

Park). 

When using the Inventory and Monitoring Framework, before monitoring can proceed, data mining 

and inventories must first be conducted. Data mining will help managers decipher past efforts and 

understand the current state of knowledge on potential monitoring targets. This is an important step 

for planning inventories and avoiding duplication of efforts. Basic inventories include specific biota, 

cave habitats, and threats to caves. Specific biota inventories may focus on something the park is 

known for, such as bats, or for more obscure biota, like microbes or springtails. Park managers need 

to know something about the cave habitats in their areas. Are the caves wet, dry, vertical, horizontal? 

Do they contain ice, bad air, or any other special features that could affect cave ecosystems? A 

threats inventory can begin with the basic question: What do we know or suspect is altered from the 

natural condition that would have negative effects on cave life?

Following inventories, managers can prioritize monitoring. Several categories of biota to monitor 

may appear:

 Threatened and Endangered (T&E) Species -- Often parks must meet goals for monitoring 

these species. They also have additional regulatory protections that go beyond those provided 

for other species. T&E species may not always reflect the overall health of the ecosystem. 

However, T&E species are generally more vulnerable to climatic changes or human 

disturbance, so a change in their population levels could be an early indicator of a problem 

with overall ecosystem health. 

 Keystone Species -- Species which have a disproportionately large effect relative to their 

abundance. They play a critical role in determining and maintaining community structure of 

an ecosystem. 
Cave Ecology Inventory and Monitoring Framework 49

 Representative Species -- Species that can represent all or a portion of a cave ecosystem are 

cost-effective targets.

 Sensitive Species -- Species that are sensitive to change, where monitoring might be most 

likely to detect changes. In part this requires an assessment of what likely/possible changes 

might occur: wildfires? climate change? changing vegetation structure? new construction? 

changing hydrological regimes? oil & gas prospecting?

 Rare Species -- Rare and unique species that are vulnerable, and thus awareness of their 

condition is important; State Natural Heritage Programs are an excellent resource.

 Indicator Species – Species that indicate a problem, for example, coliforms indicate fecal 

contamination of water supplies. An indicator species can represent the health of the entire 

ecosystem.

 Special threats -- Species which already have known potential/impending threats, such as 

White-nose Syndrome in bats, might be particularly appropriate monitoring targets.

Below is a suggested flowchart for deciding what to monitor. Starting at the top, managers need 

to ask if inventories have been conducted. If not, that needs to occur before monitoring. Once 

results for inventories are available, managers can prioritize monitoring. We suggest that T&E 

species be considered first, as often there are mandates for their monitoring. Then we suggest 

monitoring for keystone species, as they will often give you the most bang for your buck. If 

resources are available, then proceed to monitoring representative/sensitive species. If more 

funding is needed, see Chapter 6.0 for partnering and funding opportunities.

Other considerations for what to monitor:

 What level of identification expertise is available in-house? 

 Would it be feasible (time, money, personnel, resources) to obtain appropriate expertise?

 What would be the recurring, yearly cost incurred in monitoring?

 Will funding sources support long-term continuation of monitoring? 

 How much time would it take to conduct the monitoring?

 How likely is it that the findings of the monitoring will have substantive impacts on 

management practices?

 If change or a "problem" is detected, what procedures do we have in place to decide what 

actions will be taken? What is the potential for actions to improve the situation?

 Will monitoring produce data that are of sufficient quality and quantity to allow for statistical 

analyses?

 Is the monitoring capable of detecting actual change, as opposed to variation within 

confidence intervals of the methodology? 

 To what extent will the life history of the organism impact results of the monitoring?

 Could the monitoring cause damage (to the cave, to the organisms being studied) which 

exceeds the benefits of monitoring?
Cave Ecology Inventory and Monitoring Framework 50

 What kinds of baseline data (perhaps inventory data) are needed prior to beginning a 

monitoring program? 

 What kinds of data are needed prior to determining what should be monitored?

Splitting up funding priorities can be done in multiple ways. Finding ways to monitor various 

categories would be advantageous. Otherwise, if a cave might have several T&E species, and all of 

the funding goes to those, the representative species would never be monitored. One solution could 

be to base funding on rough percentages, with the top category receiving X% of available funds, the 

second receiving Y%, and if additional funding can be found, rare species would be monitored.

Figure 9. Decision Tree for Monitoring Cave Ecology.
Cave Ecology Inventory and Monitoring Framework 51

Following prioritizing monitoring, it is essential to develop monitoring questions so that the proper 

methodology can be used. How many data loggers, how many caves, and for how long are all 

important considerations in designing an environmental monitoring program, along with 

considerations of cost and effort. The answer to all questions is: It depends. What are you trying to 

learn or what question will you try to answer? Is it for a specific location or specific cave, or parkwide to detect a small scale trend over 1-3 years, a system wide tend in 5-10 years, or decadal trends 

within 30 years (E. Ring, personal communication)?

3.2 Best Management Practices for Work in Caves

Caves are fragile environments. Speleothems, or cave formations, are often delicate features which 

have formed over thousands to millions of years. Many such formations are vulnerable to breakage if 

touched or inadvertently bumped into. Unlike a flower in a field which may grow back next year, a 

cave formation, once damaged, may take thousands of years to recover, if ever. Thus, monitoring of 

resources and specific areas selected for monitoring must be weighed carefully against the possibility 

of essentially irreversible damage to cave resources. 

More subtle damage also can be caused by humans. Dirt and dust raised during resource management 

activities may settle on actively growing formations and become embedded in them as calcite is 

deposited. The ground underfoot is home to a wide variety of tiny organisms which may be trampled 

and crushed; even if these small animals escape immediate death, the footsteps of resource managers 

and other cave visitors can cause substrate compaction which may make formerly available habitat 

unusable to the organisms in the caves. Permanently marking sampling sites in caves may cause 

damage. 

Due to the sensitive nature of the cave environment and the ease with which irreversible damage can 

occur, working in caves requires strict adherence to low-impact caving techniques. Anyone working 

in caves needs to be provided with proper training and knowledge regarding travel etiquette and 

preventative practices. If cave-specific guidelines have been established for a site, workers need to 

understand and adhere to these guidelines. If no specific guidelines have been established, workers 

should take a conservative approach to cave travel with the goal of minimizing impact.

Travel through caves may in some cases require following an established trail that may be delineated 

by flagging or reflective markers. Travel should generally proceed in a single-file line to confine 

impact to a narrow path. While traveling, cavers should maintain a pace that is comfortable to all 

members of the group. Traveling slowly and deliberately through particularly fragile cave sections is 

necessary to minimize the chances of impact, such as breaking cave formations or contaminating 

pristine cave pools. When resting, cavers should stay within the boundaries of the trail (if delineated) 

or find suitable surfaces within the travel route that avoid fragile formations or delicate substrates. 

When eating, cavers should hold all food items over a sealable bag to catch crumbs. When leaving a 

rest area, cavers should inspect the area to ensure that no trash is inadvertently left behind (Tuohy 

1998). 
Cave Ecology Inventory and Monitoring Framework 52

Occasionally, caves may contain both “clean” and “dirty” areas. Clean areas are generally 

characterized by flowstone surfaces and calcite/aragonite deposits on walls and ceilings, whereas 

dirty areas may contain mud or silt deposits on the cave floor. To avoid tracking sediment from dirty 

to clean areas, alternate routes that bypass clean areas, if available, should first be considered. If 

alternate routes do not exist or are unsafe, changing areas will be required. In this situation, cavers 

will need to bring a tarp to change on and a set of “clean gear” to change into for crossing or working 

in clean areas. At a minimum, clean gear should include aqua socks or other suitable, non-marking 

footwear, an extra set of clothing, and an extra pack for containing dirty gear. Wet wipes can be used 

to clean durable items, such as helmets.

White-Nose Syndrome

White-nose Syndrome (WNS) is a disease new to North American bats that is devastating 

populations of seven hibernating bat species in North America. The cause is a fungus, 

Pseudogymnoascus detructans, that was confirmed as the causative agent of WNS in 2011. WNS 

was first reported from caves in New York State during the winter of 2006-07. It is now reported in 

or immediately adjacent to ten National Parks. The disease continues to spread through the 

movement of bats and possibly by humans, and has been confirmed in 25 states and 5 Canadian 

provinces. Since 2006 over six million bats have died.

Of the 45 species of bats found in North American, more than half hibernate and are potentially at 

risk of infection. To date seven species and subspecies of cave-hibernating bats are affected by WNS, 

including the Gray bat and the Indiana bat. Based on population-level studies, two species of bats are 

predicted to be extinct in 20 years, Indiana bats and Northern long-eared bats.

The fungus, Pseudogymnoascus destructans, was new to science. It grows best under low 

temperatures of 5-14° C (40-55° F) and high humidity typically found in caves used by hibernating 

bats. Infection changes the behavior of bats, with many flying during the day and during the winter in 

search of food. The bats rouse from hibernation, using up fat reserves at a higher rate than normal, 

causing them to leave the cave during the winter in search of food. The fungus is likely an invasive 

species from Europe. Genetic studies have confirmed that the fungi from both continents are the 

same. WNS was not known in Europe. 

WNS has spread along bat flyways, showing the natural spread of the disease, but there are concerns 

that humans may also spread the disease and could move it long distances in a short time. The U.S. 

Fish and Wildlife Service (USFWS) recommends avoiding direct contact with bats, contaminated 

environments, or objects. Wear barriers, and disinfect yourself, clothing, boots, and any objects

brought into the cave. Also important is to use covers to prevent contamination of your vehicle, 

allowing spread of the fungus.

With the spread of WNS in many NPS units, it is imperative that all working in NPS caves be 

familiar with the USFWS guidelines for WNS decontamination, as well as the most up-to-date 
Cave Ecology Inventory and Monitoring Framework 53

information on White Nose Syndrome. This link contains the most current news: 

http://www.WhiteNoseSyndrome.org

3.3 Personnel Requirements and Training

Personnel designated to conduct cave ecology inventory and monitoring will need to be trained and 

capable of entering cave environments. For monitoring programs, in order to avoid biased data due to 

discrepancies between observers, staff must be consistently trained. Training should seek to 

standardize observations in different lighting conditions, in different habitats, and, perhaps most 

difficult, between years. Training should also ensure that all observers identify targets correctly. 

Training is necessary at the beginning of every field season, and recalibration is needed mid-season 

as well. Some monitoring targets discussed in this document will require employment of observers 

with more experience. Other protocols may be accomplished by staff with less experience and/or 

may be adaptable for implementation by dedicated volunteer groups.

Personnel must be aware of safe caving practices (e.g., Jones 2009), including vertical caving 

techniques where necessary. They must be able to follow minimum-impact caving practices, 

including packing out garbage and human wastes (Tuohy 1998). They must also receive training for 

the inventory and monitoring component that they are completing. 

Qualified crew members may include park staff, researchers, grotto members, students, and 

volunteers. These crew members should be experienced in coping with the cave environment of that 

area, which may be wet, dusty, cold, hot, small, or vertical. Team members need to be physically fit 

and able to function in a variety of cave environments.

The project leader and experienced personnel will maintain their qualifications for monitoring. For 

new crew members, training sessions will include an orientation to the monitoring protocol, surface

demonstrations, and on the job training. 

3.4 Safety

Safety is the first priority for all NPS activities. Before beginning any caving, a Job Hazard Analysis 

(JHA) should be conducted. A sample one JHA is included in Appendix E. Prior to entering a cave, 

the plan for the cave trip should be established and appropriate for the task at hand and the available 

people for the trip. The trip leader should notify a surface contact of where field personnel are 

planning on going each day and when they will be back. Volunteer field crews should be trained on 

park check-in and check-out processes. 

In addition to practicing low-impact caving, cave work requires careful attention to safe caving 

practices and use of proper caving equipment. Though responsible, experienced cavers rarely have 

accidents or injuries, proper training is required for those that may be new to the cave environment or 

out of practice. All personnel working in caves need to be equipped with a helmet (UIAA and/or CE 

certified), helmet-mounted light with adequate illumination, rugged ankle-supporting boots and 

clothing, kneepads, gloves, and a cave pack containing water, food, spare headlamps, extra batteries, 
Cave Ecology Inventory and Monitoring Framework 54

medical kit, and containers for capturing human waste. Dependent on specific cave conditions (e.g., 

cold temperatures, presence of water, tight spaces), additional protective items such as cave suits, 

insulating layers, or elbow pads may be required. Vertical caving equipment, including descending 

and ascending gear, ropes, and rigging gear, may be required for negotiating caves that contain 

vertical drops and/or traverses. It is imperative that anyone performing work in a vertical cave be 

adequately equipped for vertical obstacles, and most importantly, be skilled and knowledgeable in 

vertical caving techniques. Additional safety measures need to be taken for wet caves and for caves 

with suspected bad air, such as taking an oxygen or carbon dioxide meter. 

3.5 Scheduling Work 

Scheduling cave inventory and monitoring will depend on many factors, including:

 when are caves most accessible,

 life history of the targeted species, 

 availability of personnel,

 visitation of targeted cave, and/or

 recommendations of experts for that taxa.

If in doubt, it is best to consult experts in that field to determine when the work should be scheduled.

3.6 Monitoring Surrogates

If the species of interest is too delicate or too difficult to monitor, it may be possible to monitor it 

using surrogates. Surrogates could include abiotic factors such as temperature, humidity, 

precipitation; monitoring a closely-associated species (something that is prey or predator to the 

species of interest); or monitoring signs that the species leaves behind (e.g., scat or tracks). For 

instance, surrogates are used in monitoring water for fecal contamination. There are too many 

potential pathogens to test for, so we monitor E. coli, which is always present if there is fecal 

pollution, numbers are quantifiable with the amount of pollution, it does not multiply in water, and 

lives longer than other pathogens. 

One example of monitoring surrogates is looking at the long-term effects of weather on cave crickets, 

which is done by monitoring guano community invertebrates (Poulson et al. 1995). Numbers and 

diversity of invertebrates change with the amount of cricket guano input, which is controlled by the 

weather, and which determines success of foraging by cave crickets.

The surrogate does not have to be a specific species. Schneider and Culver (2004) established 

subterranean species richness using intensive sampling and rarefaction curves in a cave-dense region 

of West Virginia. They calculated that 89% of species richness could be determined by sampling the 

largest 7 caves out of the 65 caves sampled. Using cave length as a surrogate for species richness 

gave nearly the same result as intensive sampling. Knowing the status and vulnerability of cave 

species facilitates their preservation, and many species, including rare ones, could be protected and 

monitored by focusing on study and preservation of the largest caves. But Schneider and Culver’s 
Cave Ecology Inventory and Monitoring Framework 55

(2004) estimates suggested that only half of the species were collected, showing the need for caution 

in interpreting the results, and the need of intensive sampling to establish a useful baseline.

An example of surrogate monitoring is at Tumbling Creek Cave in Missouri, which is the only 

known habitat for the Tumbling Creek Cavesnail. In 1975 about 15,000 snails were found, and 

numbers steadily dropped to about 150. The snail was listed as Endangered in 2002. They have used 

a surrogate snail species to develop effective techniques and identify problems in raising the snails. 

The snail propagation facility uses water from a deep well, so it could serve as an emergency refuge 

for cave invertebrates in the event of a pollutant spill that would impact the cave 

(http://www.tumblingcreekcave.org/4_protection.html).

3.7 Lab and Office Methods

3.7.1 Specimen Vouchers, Tissue Samples, and Photo Vouchers

Answering some questions about cave biota and habitats may require collection of specimen 

vouchers and/or tissue samples. All research and collections in NPS areas require a NPS Scientific 

Research and Collecting Permit. Collections can assure future researchers and managers that 

identifications are correct. In addition they can have unforeseen benefits, such as retroactively 

determining when invasive species arrived at network parks or evaluating the relationships between 

species. Applications for NPS research permits are made online at: https://irma.nps.gov/rprs/Home

Although photography in cave environments can be challenging, regular photography of observed 

biota is essential; photographs should focus on species-distinguishing features, as many species are 

difficult to differentiate. 

Final protocols for any monitoring program should include species verification procedures such as: 

 voucher collection procedures,

 procedures for avoiding harm to populations while conducting verification,

 procedures for collection of incidental mortality vouchers, 

 voucher documentation and storage procedures,

 photography guidelines, and

 photography and document archive procedures.

3.7.2 Proper Preservation of Specimens 

For species that could not be identified in the field, care should be taken to photograph the unknown 

species at multiple angles both in-hand and in the natural environment. The camera should have a 

macro lens so field crews can zoom into unique features of the organism. A photographic scale bar or 

ruler should be included in the photos. Once out of the field, the images should be reviewed by park 

staff to see if it can be identified; if not, a specialist should be contacted. Once the species is 

identified, datasheets, databases, and the photographic key should be updated. For many 

invertebrates, photographs will not suffice for species-level identifications, especially where detailed 

invertebrate bioinventory work has not been completed.
Cave Ecology Inventory and Monitoring Framework 56

For species that are deemed to be new records for that site, the team should determine if one of the 

people present has a collecting permit to make collections, and if so, they should collect the 

specimens in 95% Ethanol. Use the forceps, paintbrush, and/or eyedropper to handle them as 

delicately as possible to avoid breaking off setae, antennae or legs. Because many caves have been 

visited infrequently by invertebrate biologists, and the detectability of cave organisms is extremely 

low, there is a high likelihood that the researchers performing this SOP have the potential to record 

new localities, range extensions, or even new species. For this reason, the team should be prepared to 

make collections that can later be sent to taxonomic specialists for identification. Any specimens 

collected should have a label (often pencil on Rite-in-Rain paper) inserted in the vial with the 

following minimum information: Location in cave, Name of Cave, NPS unit, Date, and Collectors.

3.7.3 Shipping to Taxonomic Experts

It is important to contact taxonomic experts in advance. Taxonomic experts for some taxa are few 

and far between, as many are retiring. Each taxonomic expert may have a preferred way and 

timeframe for receiving material.
Cave Ecology Inventory and Monitoring Framework 57

4.0 Data Management

We encourage cave managers to consider data management as an integral component of monitoring.

Development of databases and data sheets should be tightly integrated with monitoring protocols to 

improve the efficiency and success of the monitoring program. This Cave Ecology Framework is not 

mandating that any park or region must follow one specific data management plan. Although it 

would be advantageous in many ways to have a nationwide cave ecology database, at this time 

neither funding nor time is available for such an endeavor. However, if all parks conducting cave 

ecology projects consider the recommendations herein, the potential for assembling a large 

nationwide database in the future, if desired, will be improved. We refer readers to the Klamath I&M 

Network protocols (Krejca et al. forthcoming) for specifics in data management with regards to a 

cave ecology program. For more general information, see 

http://science.nature.nps.gov/im/datamgmt/assets/docs/DMPlans/National_DM_Plan_v1.2.pdf.

Data management for a monitoring project is a cyclic process that begins during the planning phase 

of a project and continues until the close-out of the season. This process is then repeated each year 

the project is implemented and includes planning, training, data collection and entry, validation and 

verification processes, documentation, distribution of project products, storage, and archiving 

(Mohren 2007). 

It is important to ensure that project personnel understand all necessary data management 

methodologies, including who is responsible for implementing the methods and the timelines they 

are expected to follow when conducting data management. 

Important components of a Data Management Program for cave ecology include:

 Overview of Database Design

 Data Entry

 Photographic Data

 Map Data

 Quality Review

 Metadata Procedures

 Sensitive Information

 Data Certification and Delivery

 Data Archival Procedures
Cave Ecology Inventory and Monitoring Framework 58

5.0 Data Analysis 

Analysis of cave ecology data can be varied. Before any data are collected it is recommended that a 

statistician or someone with a great deal of experience with statistics be contacted. This person can 

help ensure that the data gathering will result in meaningful data. A word of caution, however; 

statisticians should be familiar with ecological principles and work closely with ecologists to ensure 

ecologically sound conclusions are reached. 

Pilot data, or data gathered during a short-term or small-area pilot testing period, can help inform 

whether the data being gathered are useful. It can also be used to help conduct a power analysis to 

establish the sample size needed to determine an effect of a given size with a specified level of 

confidence.

We encourage the use of R as an integral component of any monitoring project. R is a powerful 

language and environment for statistical computing and graphics, runs on Windows, Mac, and Unix 

computers, and is freely available at http://www.r-project.org/index.html. The R Wiki provides an 

online forum at: http://wiki.rproject.org/rwiki/doku.php. R is rapidly becoming the analytical 

environment of choice for ecologists.

Many cave ecology projects target very rare species that are not conducive to data analysis used for 

surface ecology projects. This section touches on some of these considerations, as well as 

overarching considerations. 

5.1 Power Analyses

In statistics, power is the proportion of times that the null hypothesis is rejected in favor of the 

alternative hypothesis given that the alternative hypothesis is true. Power analyses are used to 

determine the statistical power of sampling scheme given natural variability. 

Examples of questions related to monitoring cave climate variables at Oregon Caves National 

Monument and Lava Beds National Monument (Krejca et al. forthcoming) include:

1) How many data loggers are needed to determine annual trends in temperature and relative 

humidity for the cave? How many years are needed to detect annual trends in both parameters? 

2) How many caves are needed to monitor park-wide annual trends in temperature and relative 

humidity for each zone (deep, middle, entrance, outside)? How many years are needed to detect 

annual trends in both parameters? 

5.2 Quality Assurance/Quality Control

Quality assurance (QA) refers to the overall management system which includes the organization, 

planning, data collection, quality control, documentation, evaluation, and reporting activities of the 

group. QA provides the information needed to ascertain the quality of data and whether it meets the 
Cave Ecology Inventory and Monitoring Framework 59

requirements of the program. QA ensures that data will meet defined standards of quality with a 

stated level of confidence. Quality control (QC) refers to the routine technical activities whose 

purpose is, essentially, error control. The procedures carried out specifically for QA/QC purposes

should be fully described in a Quality Assurance Project Plan (QAPP). More information on 

developing a QAPP can be found at: http://epa.gov/region9/qa/projplans.html.

5.3 Preliminary Data Analysis

A large suite of statistical parameters (for example, mean, standard error, median, mode, standard 

deviation, sample variance, kurtosis, skewness, range, minimum, maximum, sum, and t-distribution 

confidence interval) could be calculated for continuous data (such as temperature data). The protocol 

lead should then inspect these parameters and determine whether any of them have changed 

significantly over time or differ more than expected between locations. Box-and-whisker plots may 

be useful in identifying outliers, both those that are true representations of the conditions of the vital 

sign and those caused by measurement errors. 

5.4 Presence/Absence—Occupancy Estimation

Due to the need for reliable inference in monitoring programs and the high potential for imperfect 

detection of target organisms during monitoring, occupancy estimation and modeling can be a useful 

tool (Mackenzie et al. 2006).

5.5 Trend Analysis

It will take several years of data before it can be analyzed for trends using statistical methods. Below 

is information that may be helpful to perform trend analysis, based on other I&M Protocols (Caudill 

et al. 2012).

5.5.1 Visual Assessment

The first step in trend analysis is to plot the data that will be analyzed and look for apparent trends. If 

the data are highly variable, then use a smoothed line generated using an algorithm such as LOWESS 

(Helsel and Hirsch 2002). While trends observed in the visual assessment step may not be 

statistically significant, they can provide an overview of how a parameter has changed over time. For 

example, if the smoothed trend lines hint that a trend has been up for 10 years and then down for 10 

years, a typical monotonic trend test might conclude “no trend” (Manly 2001). This conclusion might 

be less helpful to a resource manager than a conclusion that might be had by looking at a simple plot 

of values vs. time.

5.5.2 Parametric vs. Non-Parametric Trend Testing 

There are two general types of trend analyses that can be performed: mixed-model parametric trendtesting and non-parametric trend testing using various Kendall tests. 

5.3.3 Trend-Testing Methods

The Mann Kendall Test (MKT) is a statistical method used to assess trends in data sets. The 

advantages of this test are that it is widely-used, non-parametric, and applicable to any type of 

monotonic trend (i.e., not just linear changes). 
Cave Ecology Inventory and Monitoring Framework 60

The Seasonal Kendall Test (SKT) is used to detect trends in seasonally-variable data (e.g., Hirsch et 

al. 1982). The data are binned into seasons by the user, and MKT is performed for each season. The 

results from all seasons are then combined into a single test. Refinements to the SKT are corrections 

for serial correlation if 10 or more years of data are available (Hirsch and Slack 1984) and 

modifications to allow data from multiple sampling locations to be combined into a single test of 

regional trend (Helsel and Frans 2006). 

The statistical analyses using MKT, Regional Kendall Testing, and SKT can be conducted using 

kendall.exe, a software program available from the USGS (Helsel et al. 2006).

5.5.4 Generalized Linear Mixed Models

Count data and, with manipulation, percentages and proportions are not amenable to traditional 

statistical analysis wherein the variance is assumed to be constant and the errors normally distributed. 

For example, data on proportions (e.g., the proportion of small cave crickets in an entrance 

population), where all categories of the data are known, exhibit variance that is an inverted U-shaped 

function of the mean (Crawley 2002). Thus, for example, to determine whether there are differences 

in the proportion of juvenile cave crickets among entrance populations, and the factors that might 

significantly affect those differences, the data can be analyzed using Generalized Linear Mixed 

Models (GLMM). GLMMs are similar to Generalized Linear Models but provide a more flexible 

approach when analyzing nonnormal data because the explanatory variables can be both random and 

fixed (Bolker et al. 2008). Random effects are factors whose interest lies in the variation among 

them, such as surveys replicated across sites or time, rather than the specific effects of each level.

5.6 Reports

Regular reports for any cave ecology monitoring will help managers better understand what is 

happening in the cave. Reports may follow standard scientific format (abstract, introduction, 

methods, analysis, results, discussion, literature cited), but will vary in length and focus depending 

upon the core topic addressed. 

To the degree possible, efforts should attempt to summarize the status, trends, and dynamics in the 

diversity, distribution, and compositional changes in cave biological communities over time. We 

expect the report will have broad relevance to general management and interpretive planning at each 

park, as well as general interest to the public. 

Periodical reports on the results of monitoring activities should be drafted following the guidelines

provided on the “Natural Resource Publications Management Report Submission Procedures” 

website: http://www.nature.nps.gov/publications/nrpm/

5.7 Resource Briefs 

Resource briefs are one to two page summaries about the current monitoring effort. These reports are 

designed to quickly inform resource managers about the work that has been completed and any 

significant results related to this effort. In addition, these reports are written in a non-technical 

manner so they can be delivered to all park staff who may be interested in our efforts. 
Cave Ecology Inventory and Monitoring Framework 61

6.0 Roles, Resources, and Partners

Developing and implementing a long-term cave ecological monitoring program is a complex and 

challenging prospect. National Park Service cave managers are well situated to act as catalysts for 

initiating and carrying out monitoring programs, however, they cannot, and should not act alone. 

Monitoring programs will be stronger and more likely to succeed with the input of other cave 

managers, resource specialists, researchers, cave conservation organizations, and more. This section 

outlines options for collaboration and partnerships, both within and outside of the NPS, in order to 

achieve monitoring goals.

6.1 National Park Service Roles and Resources

The NPS management of cave and karst resources operates through a complex, integrated web of 

parks, networks, regions, and national divisions that collaborate at multiple levels of involvement. 

Policy is shaped at upper management levels with input from parks, while the needs of parks steer 

the involvement and direction of national program support. Usually, inventory and monitoring of 

cave resources necessitates a park-based approach due to the unique character of local caves and cave 

biota. However, regional and/or national support and guidance is often appropriate when choosing 

monitoring parameters, developing methodology, soliciting reviews, and other programmatic needs. 

6.1.1 Parks

Parks have the primary responsibilities for determining what the needs are for their management 

areas in order to fulfill the NPS mission. This may include periodic inspections of their cave 

resources, awareness of incoming threats, management of cave watersheds, and more. Parks then 

face the task of finding funding for the efforts they deem necessary. Fortunately, parks have many 

resources to turn to for assistance with cave and karst monitoring, including specialists at other cave 

parks and oversight from regional and national levels.

6.1.2 Networks

Parks with significant natural resources (270+ NPS units) are assigned to one of 32 ecoregional 

inventory & monitoring (I & M) networks that are drawn geographically. I & M networks share 

professional staff and funding to support natural resource baseline inventories and long-term 

monitoring of natural resource vital signs taking place within network parks, as well as associated 

data management. I & M networks are a valuable source for guidance and steering of natural 

resource projects. Networks encourage and facilitate collaboration among NPS units, and they often 

help parks develop relationships with researchers and partners that have mutual interest in natural 

resources occurring in the parks. More information on I & M networks and programs, including 

reports and protocols, is available through the NPS I & M website: http://science.nature.nps.gov/im/

6.1.3 Regions

The NPS is divided into seven Regions (Alaska, Intermountain, Midwest, National Capitol, 

Northeast, Pacific West, Southeast) that provide oversight to parks within their boundaries. NPS 

Regions employ natural resource specialists, ecologists, geologists, hydrologists, and geographic 

information systems (GIS) specialists who may be able to assist with cave monitoring questions. 
Cave Ecology Inventory and Monitoring Framework 62

Many regions also have funding available for park-sponsored projects. Contact information and links 

to additional resources are available through the Regions section of the NPS intranet. 

6.1.4 Natural Resource Stewardship and Science Directorate 

At the national level, the NPS operates several science-based divisions through the Natural Resource 

Stewardship and Science (NRSS) Directorate. These divisions specialize in natural resources such as 

air resources, biological resources, geologic resources, natural sounds and night skies, and water 

resources. Parks can request technical assistance and funding for natural resource projects by using 

the Technical Assistance Call (TAC) and the Servicewide Comprehensive Call (SCC), which are 

managed through this directorate. More information and contacts are available through the NRSS 

section of the NPS intranet. 

The NPS Cave & Karst Program is a national program within the Geological Resources Division 

(GRD), and in most cases, this program will be the appropriate source for seeking assistance with 

cave ecological monitoring activities. Based in Lakewood, Colorado, the Cave & Karst Program 

offers support to all NPS units with cave and karst resources. The program may provide advice or 

referrals for simple requests or may suggest routing requests through the TAC if more complex 

support is required. Communication between NPS cave managers is essential, and the program 

supports this need by managing a listserve that is available by subscribing at: 

http://webmail.itc.nps.gov/mailman/listinfo/cave-karst. The listserve provides an avenue for 

managers to share cave-related information or request help on cave-related topics. More information 

and links to publications can be found on the Cave & Karst Program’s website: 

http://nature.nps.gov/geology/caves/index.cfm. 

GRD also houses a number of other programs, including paleontology, energy/minerals, and soils, 

that could potentially overlap with cave resources. Another NPS division, the Biological Resource 

Management Division (BRMD), provides general support for biological resources in the NPS. The 

BRMD is not usually cave-focused but does work with cave parks on cave-related wildlife issues, 

most notably white-nose syndrome (WNS). Other natural resource divisions are available to provide 

assistance to parks on cave-related matters if their areas of specialty are relevant. The National 

Inventory & Monitoring (I & M) Program is also a division of the Natural Resource Stewardship and 

Science Directorate and provides oversight to the 32 I & M networks. 

6.2 Interagency Cooperation

Some caves extend beyond park boundaries, and certainly many karst watersheds do. There are many 

established precedents of the NPS working with adjoining land management agencies in the 

management and monitoring of cave resources. Agencies can also benefit from general cooperation 

across greater distances, ranging from specialized technical assistance with field activities to remote 

cooperation on policy development or general exchanges of information.
Cave Ecology Inventory and Monitoring Framework 63

The Interagency Agreement for Collaboration and Coordination in Cave and Karst Resources 

Management was updated and signed in 2012. The agreement provides guidance for cooperation 

between federal agencies in the Department of the Interior (Bureau of Land Management, U.S. Fish 

and Wildlife Service, U.S. Geological Survey, National Park Service) and the Department of 

Agriculture (U.S. Forest Service). The agreement recognizes that agency cooperation can increase 

the effectiveness and efficiency of cave and karst management, provides agency authority and policy 

summaries, and identifies areas of cooperation. The agreement is available from several sources,

including the NPS Cave & Karst Program website: 

http://nature.nps.gov/geology/caves/2012%2002%2024%20FINAL%20SIGNED%20CAVE%20KA

RST%20IA%20-%20FEB%2024,%202012.pdf

6.3 Partnerships

Parks across the country engage in innumerable partnerships to help achieve the NPS mission. 

Partners have become increasingly critical in assisting the NPS with implementing short-term 

projects, maintaining long-term monitoring programs, and responding to new challenges. Entering 

into partnerships often requires administrative and financial commitments from parks; however, the 

ability to acquire specialized assistance, the flexibility of arranging and scheduling activities, and 

oftentimes long-term cost savings may make partnerships an appealing and enduring path for 

advancing cave monitoring goals. 

6.3.1 National Cave & Karst Management Symposium

The National Cave & Karst Management Symposium (NCKMS) provides a venue for cave and karst 

managers, professionals, researchers, and cavers to present on cave-related topics and share ideas and 

methods. This gathering of cave managers and cave enthusiasts is an ideal opportunity to form 

partnerships and advance the goals of cave conservation and monitoring. The first NCKMS was held 

in 1975, and they have occurred regularly since that time, generally every other year in rotating 

venues. The 2013 Symposium in Carlsbad, NM represented the 20th NCKMS. The National Cave 

Management Steering Committee provides oversight and organization of the symposia. The Steering 

Committee is primarily composed of representatives from federal agencies and independent cave 

conservation organizations. Papers and abstracts delivered at the symposia are published as 

Proceedings of the NCKMS. The NCKMS hosts a website at www.nckms.org/index.shtml

6.3.2 Cooperative Ecosystem Studies Units

The Cooperative Ecosystem Studies Units (CESU) National Network is comprised of national and 

local partners working to support resource stewardship by bringing together scientists, land

managers, conservation professionals, students, and others to address shared resource issues. Federal 

agencies, tribes, academic institutions, nongovernmental organizations, and state and local 

governments represent some of the 300+ partners belonging to seventeen distinct CESUs. These 

regional CESU networks represent unique biogeographic areas that cover the U.S. and its territories. 

The NPS is a partner of the CESU National Network through a signed Memorandum of 

Understanding (MOU), and the NPS has a designated representative for each of the seventeen 

CESUs. More information is available through the CESU website: www.cesu.psu.edu
Cave Ecology Inventory and Monitoring Framework 64

6.3.3 Academic institutions

While CESUs represent one avenue to potentially engage with academic institutions, assistance can 

also occur directly through an NPS Research Permit. Researchers, professors, post-doctoral students, 

and graduate students at colleges and universities often contact parks directly to request permits for 

conducting scientific research. Researchers working in cave parks or attending cave conferences 

provide a good source of specialized information, and cave monitoring programs can benefit from 

review by researchers with overlapping interests. In some cases, cave monitoring methodology may 

be developed in tandem with related research projects under an approved research permit. The NPS 

Research Permit and Reporting System (RPRS) is an online system for managing research permit 

applications, approved permits, specimen collections, and investigator annual reports. The system 

can also be used by parks to advertise research needs and indicate park-specific research guidelines. 

The RPRS can be accessed at https://irma.nps.gov/rprs/Home

6.3.4 Nonprofit and nongovernmental organizations

The NPS can seek assistance, guidance, and/or information from organizations that promote cave 

conservation and specialize in cave-related work. These partnerships are mutually beneficial and 

contribute to a wide network of professionals collaborating on cave management, monitoring, and 

research projects. A partial list of organizations that the NPS collaborates with on cave-related 

projects follows:

National Cave and Karst Research Institute

www.nckri.org

The National Cave and Karst Research Institute (NCKRI) is a nonprofit government-supported 

institute headquartered in the City of Carlsbad, New Mexico. Its goals are to conduct, support, 

facilitate, and promote programs in cave and karst research, education, environmental management, 

and data acquisition and sharing. 

National Speleological Society

www.caves.org

The mission of the National Speleological Society (NSS) is to study, explore, and conserve cave and 

karst resources; protect access to caves; encourage responsible management of caves and their unique 

environments; and promote responsible caving.

Cave Research Foundation

www.cave-research.org

The Cave Research Foundation (CRF) is a private, nonprofit organization dedicated to facilitating 

research, management, and interpretation of caves and karst resources; forming partnerships to study, 

protect, and preserve cave resources and karst areas; and promoting the long-term conservation of 

caves and karst ecosystems.

Karst Waters Institute

www.karstwaters.org
Cave Ecology Inventory and Monitoring Framework 65

The Karst Waters Institute (KWI) is a nonprofit institution whose mission is to improve the 

fundamental understanding of karst water systems through sound scientific research and the 

education of professionals and the public. 

Geological Society of America

www.geosociety.org

The Geological Society of America (GSA) provides access to elements that are essential to the 

professional growth of earth scientists at all levels of expertise and from all sectors: academic, 

government, business, and industry. The Society’s membership unites thousands of earth scientists 

from every corner of the globe in a common purpose to study the mysteries of our planet and share 

scientific findings.

Bat Conservation International

www.batcon.org

Bat Conservation International (BCI) is conducting and supporting science-based conservation 

efforts around the world. Working with many partners and colleagues, these innovative programs 

combine research, education, and direct conservation to ensure bats will be helping to maintain 

healthy environments and human economies far into the future.

6.4 Online Resources 

In addition to the online presence and resources of the National Park Service and many of the 

partners listed above, there are numerous other websites that provide education and tools that can be 

of value to cave and karst management and monitoring. A partial list of online sites that specialize in 

topics relevant to caves and karst follows:

Karst Information Portal 

www.karstportal.org

The Karst Information Portal is a digital library linking scientists, managers, and explorers with

quality information resources concerning karst environments.

Speleogenesis

www.speleogenesis.info

Speleogenesis is a scientific network promoting scientific research and cooperation in karst 

hydrogeology with a special emphasis on speleogenesis.

White-Nose Syndrome

www.whitenosesyndrome.orgThis website is the central location for the coordinated North American 

interagency response to the devastating bat disease white-nose syndrome (WNS).

GIS for Caves & Karst

www.esri.com/industries/cavekarst

GIS offers a variety of tools and capabilities used in the management, analysis, and visualization 

of cave and karst information.
Cave Ecology Inventory and Monitoring Framework 66

7.0 Conclusions

This Cave Ecology Inventory and Monitoring Framework is not an I&M protocol but provides peerreviewed guidance for developing protocols. The background information and references provided 

are intended to give managers a solid starting point for pursuing inventory and monitoring of their 

resources. The Decision Tree will ideally guide managers through the process for deciding what to 

monitor. 

It takes more than an idea and a framework to accomplish a project; it also takes funding and 

dedicated staff. The NPS Cave and Karst Program is currently conducting a data gaps analysis of 

cave and karst parks. This will help determine the greatest needs for additional cave ecology work 

and help direct funding to deserving parks. In addition, funding sources are available from a variety 

of sources as mentioned in Chapter 6.0. 

The more we understand about cave ecology, the better we can protect the unique ecosystems that 

thrive below our feet.
Cave Ecology Inventory and Monitoring Framework 67

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Appendix A: Cave Parks

The following NPS units have caves reported in them. This table was originally constructed by David Ek in 2001, and later updated by him, 

then by Gretchen Baker in 2008-13, followed by the National Cave and Karst Office in 2014. Yellow highlighted boxes indicate the most 

recent updates.

Park

Total

Caves Solution Lava Erosion Tectonic Talus Glacier Data Source

Abraham Lincoln Birthplace National Historic 

Site 1 1 0 0 0 0 0

Acadia National Park 12 0 0 12 0 0 0

Amistad National Recreation Area 30 30 0 0 0 0 0

Aniakchak National Monument or Preserve 1 0 1 0 0 0 0

Apostle Islands National Lakeshore 75 0 0 75 0 0 0

Arches National Park 1 0 0 0 1 0 0 Karen Henker

Badlands National Park 50 0 0 50 0 0 0

*0 caves but thousands of 

pipes

Bandelier National Monument 2 0 2 0 0 0 0

Bering Land Bridge National Preserve 113 0 100 13 0 0 0

Big Bend National Park 7 7 0 0 0 0 0

Big South Fork National River and Recreation 

Area 1 1 0 0 0 0 0

Bighorn Canyon National Recreation Area 1 1 0 0 0 0 0

Bryce Canyon National Park 1 1 0 0 0 0 0

Buffalo National River 360 350 0 0 10 0 0 Chuck Bitting

Canyonlands 1 1 0 0 0 0 0 Karen Henker

Capulin Volcano National Monument 3 0 3 0 0 0 0 GRI Report

Carlsbad Caverns National Park 117 117 0 0 0 0 0 Dale Pate

Catoctin Mountain National Park 2 0 0 0 2 0 0

Cedar Breaks National Monument 1 1 0 0 0 0 0

Channel Islands National Park 369 0 0 369 0 0 0
Cave Ecology Inventory and Monitoring Framework 77

Park

Total 

Caves Solution Lava Erosion Tectonic Talus Glacier Data Source

Chesapeake and Ohio Canal National Historical 

Park 25 25 0 0 0 0 0 Michelle Carter

Chickamauga & Chattanooga National Military 

Park 16 16 0 0 0 0 0 Steve Thomas

Colorado National Monument 2 0 0 2 0 0 0 GRI Report

Coronado National Memorial 9 9 0 0 0 0 0 Dean Schlinchting

Crater Lake National Park 51 0 0 51 0 0 0 Greg Holm

Craters of the Moon National Monument 344 0 342 0 0 2 0 Doug Owen email

Cumberland Gap National Historical Park 33 33 0 0 0 0 0 Jenny Beeler

Cuyahoga Valley National Park 2 0 0 0 0 2 0 GRI Report

Death Valley National Park 79 61 0 18 0 0 0

Denali National Park 3 1 0 0 0 0 2

Dinosaur National Monument 5 3 0 2 0 0 0

El Malpais National Monument 290 290 0 0 0 0 Kayci Cook

Everglades National Park 1 1 Inside Earth, Lee Florea

Fort Donelson National Battlefield 1 1

Gates of the Arctic National Park 7 7 0 0 0 0 0

Gila Cliff Dwellings National Monument 7 0 0 7 0 0 0 Steve Riley

Glacier National Park 16 16 0 0 0 0 0

Glacier Cave Management 

Plan

Glacier Bay National Park 21 21 0 0 0 0 1 Wayne Howell

Golden Gate National Recreation Area 119 0 0 119 0 0 0

Golden Spike National Historic Site 3 3 0 0 0 0 0 Cami McKinney

Grand Canyon National Park 511 511 0 0 0 0 0 Steve Rice email

Grand Teton National Park 17 17 0 0 0 0 0

Great Basin National Park 46 46 0 0 0 0 0 Ben Roberts

Great Smoky Mountains National Park 10 10 0 0 0 0 0

Guadalupe Mountains National Park 27 27 0 0 0 0 0 GRI Report

Haleakala National Park 24 0 24 0 0 0 0
Cave Ecology Inventory and Monitoring Framework 78

Park

Total 

Caves Solution Lava Erosion Tectonic Talus Glacier Data Source

Harpers Ferry National Historical Park 2 2 0 0 0 0 0

Hawaii Volcanoes National Park 155 0 155 0 0 0 0

Jewel Cave National Monument 10 10 0 0 0 0 0 Rene Ohms

Kalaupapa National Historical Park 16 0 16 0 0 0 0

Kaloko-Honokohau National Historical Park 4 0 4 0 0 0 0

Kenai Fjords National Park 12 0 0 12 0 0 0

Kings Canyon National Park 12 12 0 0 0 0 0

Lake Mead National Recreation Area 2 2 0 0 0 0 0

Lava Beds National Monument 700+ 0 700+ 0 0 0 0 Shane Fryer

Mammoth Cave National Park 384 384 0 0 0 0 0 Lillian Scoggins

Mojave National Park 44 40 4 0 0 1 0 Ted Weasma

Montezuma Castle National Monument 2 2 0 0 0 0 0 GRI Report

Mount Rainier National Park 5 0 0 0 0 0 5

Natchez Trace Parkway 5 5 0 0 0 0 0

Noatak National Preserve 4 4 0 0 0 0 0

Obed Wild and Scenic River 1 0 0 1 0 0 0

Olympic National Park 3 0 0 3 0 0 0

Oregon Caves National Monument 12 12 0 0 0 0 0

Ozark National Scenic Riverways 320 320 0 0 0 0 0

Parashant National Monument 35 35 0 0 0 0 0

Pecos National Historic Part 2 2 0 0 0 0 0 Paul Burger and Stan Allison

Pea Ridge National Military Park 1 1 0 0 0 0 0

Pictured Rocks National Lakeshore 1 0 0 1 0 0 0 Tom Richer

Pinnacles National Monument 8 0 0 0 0 8 0 GRI Report

Point Reyes National Seashore 139 0 0 139 0 0 0

Pu’uhonua o Honaunau NHP 6 0 6 0 0 0 0

Redwood National and State Parks 2 0 0 2 0 0 0
Cave Ecology Inventory and Monitoring Framework 79

Park

Total 

Caves Solution Lava Erosion Tectonic Talus Glacier Data Source

Rocky Mountain National Park 1 0 0 0 0 0 1

Russell Cave National Monument 10 10 0 0 0 0 0

Saint Croix National Scenic Riverway 12 0 0 12 0 0 0

San Juan Island National Historic Site 1 1 0 0 0 0 0

Sequoia National Park 240 240 0 0 0 0 0 GRI Report

Shenandoah National Park 2 2 0 0 0 0 0 GRI Report

Stones River National Battlefield 2 2 0 0 0 0 0 GRI Report

Sunset Crater Volcano National Monument 1 0 1 0 0 0 0

Theodore Roosevelt National Park 6 0 0 6 0 0 0

Timpanogos Cave National Monument 8 8 0 0 0 0 0 Cami Pulham McKinney

Valley Forge National Historical Park 6 6 0 0 0 0 0 GRI Report

War in the Pacific National Historical Park 12 12 0 0 0 0 0

Wilson's Creek National Battlefield 3 3 0 0 0 0 0 GRI Report

Wind Cave National Park 44 44 0 0 0 0 0 Marc Ohms/ GRI Report

Wrangell-St. Elias National Park 4 3 0 0 0 0 1

Wrangell-St. Elias National Preserve 4 4 0 0 0 0 0

Wupatki National Monument 12 0 0 0 12 0 0

Yellowstone National Park 6 5 1 0 0 0 0

Yosemite National Park 11 1 0 0 3 6 1

Yukon-Charley Rivers National Preserve 6 6 0 0 0 0 0

5095 2496 1649 894 28 19 11
Cave Ecology Inventory and Monitoring Framework 

Appendix B: Example of Cave Classification Scheme

One way to classify caves is with a three-part rating, including management (Table 1), resource 

classes (Table 2), and hazards (Table 3).

Table 1. Cave classification of management type of cave.

Class Description

1 Caves or passages which are developed. Developed caves provide an opportunity for most visitors to 

tour a cave without special clothing, equipment, knowledge, or skills.

2 Caves or passages which are undeveloped, and which may be visited only with an NPS, or NPSdesignated or approved trip leader, and an approved permit. Such caves contain particularly sensitive 

geologic or cultural features.

3 Caves are undeveloped caves that may be visited by caving groups without an NPS, or NPS-approved 

guide.

4 Class 4 caves are closed to general use pending further evaluation or research.

5 Caves are closed to general use because they contain paleontological, archeological, geological, 

biological or other resources of special scientific value that would be easily altered, even by careful use of 

the cave.

6 Class 6 caves are closed to all use except the absolute minimum required for administrative purposes. 

These caves are closed because of extreme, unavoidable hazards for even the most skilled caver, 

(rockfall, disease, poisoned or dangerous atmosphere, etc.) or because entering them would cause 

irreparable harm to a fragile resource or to an endangered species, which is threatened by use of the 

cave.

Table 2. Cave classification by resource classes.

Class Description

A Class A Caves contain few or no features presently recognized to be unique. Mineral deposits would only 

include durable types such as flowstone and large stalactites or stalagmites. No historic or significant 

biological resources would be present in Class A caves. These caves can withstand frequent visitation 

from cavers with little or no resource degradation.

B Class B Caves contain only mildly delicate speleothems including smaller stalactites or stalagmites than 

Class A Caves, short soda straws and large curtains. In general speleothems are of such a size or are 

located where they are unlikely to be damaged by normal cave use. Biological resources are not unique 

and are not sensitive to the activity of people. Class B caves have no paleontological or archaeological 

resources.

C Class C caves may contain delicate speleothems such as rimstone dams, soda straws over 6 inches in 

length, narrow columns, stalagmites and stalactites, small helictites and thin curtains. In general 

speleothems are of such a size or are located where damage or vandalism is likely. Biological activity may 

include several viable interdependent species, all of which can withstand the activity of people. 

Paleontological and archaeological resources are limited and not significant.

D Class D Caves contain speleothems that are of unusual quality and/or are extremely delicate and 

susceptible to breakage, or resources of value that could be seriously disturbed or destroyed by cavers. 

Examples of Class D speleothems include selenite needles, aragonite crystals, gypsum flowers or hair, 

dog-tooth spar crystals, long (over 12 inches) soda straws, moonmilk speleothems and large helictites. 

Other delicate resources could include pictographs, materials of archaeological value, soft sedimentary 

deposits, animal remains or a sensitive species of animal.

E Class E caves contain resources of exceptional scientific value that would be seriously disturbed by 

frequent visits or by the visits of cavers unfamiliar with the cave's unique resources (resources may not be 

obvious). Such resources may be biological, geological, hydrological, archeological, ethnographical, or 

paleontological in nature. They may include rare or unusual speleothems.
Cave Ecology Inventory and Monitoring Framework 

Table 3. Cave classification by hazard classes.

Class Description

I Class I Caves are commercialized and feature a paved trail, handrails, a lighted route to follow, and a 

minimum of stooping or narrow passages, which can be easily negotiated by the average park visitor. 

II Class II Caves offer only minimal hazard to the caver. Characteristics include well-defined and obvious 

passage or passages; no passageways less than 60 centimeters (24 inches) in diameter that are used 

as the main route through a cave; no sudden drops over 1 meter (3 feet) high; no danger of flooding; 

small risk of hypothermia based upon the cave's air temperature, air flow and the temperature and 

amount of water in the cave; no known loose ceiling rock and few loose, floor rocks.

III Class III Caves offer some potential hazard to cavers. They are mostly horizontal in structure and do not 

require rope work. Their characteristics include passages which may wind, curve and interconnect, but 

which are straight-forward and obvious; no passageways less than 45 centimeters (18 inches) in height 

or diameter that are used as the main route through a cave; no sudden drops over 3 meters (10 feet) 

and which are easily climbable; limited risk of flooding and hypothermia on the basis of the cave's 

temperature, air flow and the presence of water; no known loose ceiling rock; floor materials may be 

loose.

IV Class IV Caves contain more extensive hazards than caves in Class I, II, or, III. Their characteristics 

include potentially confusing passages, which may exist on more than one level; passageways as small 

as 30 centimeters (12 inches) in height or diameter that are used as the main route through a cave; 

vertical drops less than 15 meters (50 feet) in depth some of which may require rope work; potential risk 

of flooding and/or danger of hypothermia based upon cave temperature, air flow and quantity of water in 

the cave; loose ceiling rock in larger passages and potentially unstable floors.

V Class V Caves are the most hazardous from a structural standpoint. Their characteristics may include 

areas of confusing maze-type passages and multiple levels; passages less than 30 centimeters (12 

inches) in height or diameter along main routes; vertical drops of more than 15 meters (50 feet) requiring 

ropes; a risk of flooding or a strong danger of hypothermia for the unprepared due to low cave 

temperatures and/or strong air flow and/or the presence of water; loose ceiling rocks in small passages 

and crawlways.

VI Class VI caves contain extreme hazards due to unusual cave characteristics. This includes airborne 

diseases, dangerous gases, unpredictable flooding and the presence of unstable rocks of a size or in a 

location that is dangerous to cavers. Class VI caves should only be entered by highly skilled cavers 

employing specialized equipment and who have a compelling reason. Extra safety precautions such as 

special communications and pre-arranged rescue capabilities should be considered.
Cave Ecology Inventory and Monitoring Framework 

Appendix C: Process for Selecting Caves to Monitor

NPS units with an extant, searchable computer database with information on the caves within its 

boundaries make the process of selecting monitoring caves simpler. If the data are contained in paper 

files, the process is obviously slowed somewhat but the search criteria still largely apply. The 

following criteria may be considered more or less a sequential winnowing process to produce a short 

list of potential monitoring caves prior to field vetting. This example uses cave crickets at Mammoth 

Cave to describe the process of selecting caves to monitor.

1. If the cave database is searchable, an initial keyword search for files that contain the word 

“cave crickets” should greatly reduce the number of files that must be examined closely. 

Examine the resultant files for any description of relative abundance of cave crickets and use 

this as part of your decision matrix as to whether or not a particular cave should be included 

in monitoring.

2. Examine the file’s notes regarding ease of access to the cave. If getting to the cave is 

particularly arduous it should be included only if there is no alternative. Further, if the cave’s 

morphology is such that access can only be obtained by field assistants with technical skills 

(e.g., rope climbing) or tight spots that would complicate rescue it should likely be rejected.

3. Consult park maps to determine cave location with respect to the starting point of monitoring 

teams (i.e., offices). Location of the cave with respect to offices is an important criterion to 

consider beforehand because it will determine driving and/or walking distance. Travel time to 

and from the caves will likely have the largest effect on the amount of time monitoring crews 

spend in the field. GPS coordinates, if available from the file, should be downloaded or 

programmed into a GPS unit to facilitate finding the cave.

Through information gained from data mining, many of the same criteria used in the pre-vetting 

process are mentioned below. Often field notes on file can be vague and so clearly there is some 

value to confirming, in the field, the information gained during the data mining process. Field vetting 

is particularly useful if the notes from the database suggest a cave is marginally promising. The 

following criteria may be considered more or less a sequential winnowing process to produce a short 

list of potential monitoring caves to include in the scoring process. Standardized data sheets should 

be created for the field vetting process.

1. Trip times from base, including drive time/walking time, should be recorded on the field data 

sheet. Travel time may be an especially important criterion due to its potential to significantly 

increase time in the field. Potential monitoring caves can and should be considered with 

reluctance, and scored accordingly, if travel time is too great. Obviously, determining what 

constitutes a long journey is subjective but a long travel time could, all things being equal, 

result in rejection of a potential monitoring cave.
Cave Ecology Inventory and Monitoring Framework 

2. Ease of access, safety hazards, and sensitive resources should be noted on the field data sheet. 

Safety is an especially important criterion and any safety concerns about a potential 

monitoring cave should result in its rejection from the list.

3. The relative abundance of the monitoring subject in a potential cave is a significant criterion 

to note in the field vetting process. Notes on relative abundance of monitoring subjects

should be recorded on vetting data sheets and cave maps. Cave maps are a useful part of field 

equipment in this part of the field vetting process. Cave maps can be marked, in pencil, 

where monitoring subjects found. Cricket guano deposits are particularly informative in 

determining where cave crickets regularly roost because roosts must be used over time to 

build guano deposits whereas clusters of cave crickets can be transient as they cycle to and 

from the cave entrance. A semi-quantitative method should be used to indicate relative 

abundance of cricket clusters on the map, e.g., circles of increasing size and numerical value, 

to facilitate scoring among caves during the Monitoring Cave Rating Process.

Prospective monitoring caves should be ranked from best to worst according to the criteria evaluated 

in the field vetting process. The ranking process involves assigning each criterion a weighted 

numerical value and using the sums of these values to rank the caves. The weights and importance 

assigned to each criterion in the rating process reflects their importance in obtaining adequate data 

during the sampling process. Not surprisingly, the semi-quantitative data on cave cricket 

abundance/population structure and cave ceiling height/relief obtained during the vetting process is 

weighted more heavily in the rating process than trip time and ease of access; this is because the 

farthest, most difficult to access caves were eliminated during the field vetting process. The cave 

with the highest summed value is ranked the best prospective monitoring cave and the rankings 

decrease sequentially to the worst ranked cave. The list generated in the rating process provides the 

user with defensible reasons why lower ranked caves may be excluded from a proposed sampling 

plan.
Cave Ecology Inventory and Monitoring Framework 

Appendix D: Protocols and Standard Operating Procedures

Monitoring Protocols and Standard Operating Procedures (SOPs) for specific protocols can be 

helpful to review for those considering similar work. 

Here is an annotated list of Protocols and SOPs already in use:

SOP: Bats 

Integrated Cave Entrance Community and Cave Environment Long-Term Monitoring Protocol, 

Klamath Network 

This SOP gives instructions for surveying known small colonies (<1,000) of bats using a noncontact method: in-cave counts. These methods can be used any time of year, but are prescribed 

here for counting during the winter hibernation season at ORCA and LABE in order to focus on 

monitoring long-term population trends of the Townsend’s Big-eared bat, Corynorhinus 

townsendii. Once at this website, click on Draft Long-term Monitoring Protocol and Sampling 

Procedures:

http://science.nature.nps.gov/im/units/klmn/monitor/caves.cfm

Protocol: Allegheny Woodrat Monitoring Protocol

Cumberland Piedmont Network

The Allegheny woodrat, Neotoma magister, is a native small mammal of interest on Mammoth 

Cave National and across the eastern USA, due, in part, to recent dramatic population declines. 

Woodrats are frequent visitors to the cave ecosystem and are important importers of organic matter, 

in the form of nesting materials, food caches, and fecal and urine deposition, into caves. These 

organic nutrients are known to support a specialized invertebrate cave community Richards 1989, 

1990). Cave management and visitor activity may impact or inhibit woodrat access into and use of 

caves through imposition of physical barriers, such as cave doors, and various disturbance factors 

(noise, lighting, etc.). Woodrats, as surface foragers feeding on a wide variety of plant materials and 

parts (e.g., fruit, nuts and seeds, fungi, leaves, etc.) also relate to the terrestrial ecosystem, and may 

reflect larger-scale changes in vegetation communities through long-term changes in population 

performance and structure. The combination of being relatively widespread, important to the cave 

ecosystem, potentially sensitive to cave management and visitation impacts, and a strong dependent 

relationship with surface vegetation-based ecosystem performance make woodrats a useful indicator 

for park-level monitoring.

http://www1.nrintra.nps.gov/im/units/CUPN/monitor/woodrats/docs/MACA_Woodrat_Protocol

_v3.1.pdf (access to NPS only)

SOP: Scat and Visible Organics, 

Integrated Cave Entrance Community and Cave Environment Long-Term Monitoring Protocol, 

Klamath I&M Network

Scat monitoring detects and gauges the potential flow of surface nutrients into caves via waste from 

terrestrial mammals (especially rodents), bats, and birds. Caves will be divided into zones and the 
Cave Ecology Inventory and Monitoring Framework 

number of rodent scats in each zone will be noted by assigning it to one of four categories: None, 1–

10, 10 – 100, or >100 scats. Other sources of organic input will also be noted such as nests, deceased 

organisms, and litter. Little training is required to implement this protocol. The KLMN will have 

primary responsibility for scat monitoring. To find this file go to:

http://science.nature.nps.gov/im/units/klmn/publications.cfm?tab=3

Click on 2010 Draft integrated cave entrance community and cave environment long-term 

monitoring protocol Multiple Files (Zip). Scroll down to SOP10_Scat_and_Visible_Organics and 

download.

Protocol: Cave Cricket Monitoring Protocol, Mammoth Cave National Park

Cumberland Piedmont Network

This monitoring protocol was written with emphasis on the cave-dwelling Orthopteran species, 

i.e., Hadenoecus subterraneus, inhabiting most caves found within Mammoth Cave National 

Park (MACA) boundaries. However, two cave cricket genera, i.e., Ceuthophilus spp. and 

Hadenoecus spp., are keystone species in caves throughout Department of Interior, Department 

of Defense, and United States Department of Agriculture land holdings in the southwest, 

including Carlsbad Caverns National Park, Fort Hood, and Lincoln National Forest, and in the 

southeast, including MACA, Russell Cave National Monument, Cumberland Gap National 

Historic Park and Chickamauga-Chattanooga National Military Park, respectively (Campbell 

1976, Hubbell and Norton 1978, Studier et al. 1987, Studier and Lavoie 1990, Hobbs III 1994, 

Cokendolpher et al. 2001, Mays 2002, Taylor et al. 2003b). Thus, with modification, this 

monitoring protocol could be adapted for use in any government land holding with significant 

cave cricket populations of either genera.

http://www1.nrintra.nps.gov/im/units/CUPN/monitor/cavecrickets/cavecrickets.cfm (access to 

NPS only)

SOP: Cave Invertebrates

Integrated Cave Entrance Community and Cave Environment Long-Term Monitoring Protocol, 

Klamath I&M Network

This SOP gives step-by-step instructions for surveying invertebrates bait stations. To find this file, go 

to: http://science.nature.nps.gov/im/units/klmn/publications.cfm?tab=3

Click on 2010 Draft integrated cave entrance community and cave environment long-term 

monitoring protocol Multiple Files (Zip). Scroll down to 

SOP11_Invertebrates_V1.00_DRAFT_20100624.pdf

SOP: Cave Swallow (Petrochelidon fulva) Banding Project, 

Carlsbad Caverns National Park, Eddy County, New Mexico
Cave Ecology Inventory and Monitoring Framework 

The Cave Swallow (Petrochelidon fulva) banding project has been conducted for over 20 years 

at the entrance of Carlsbad Caverns National Park. The main objective is to band Cave Swallows 

to study their winter range. During handling, the birds are also weighed, wings and tail are 

measured, and checked if brood patch is present, for maturity status, ectoparasites, and more. 

Over the years, additional data has been taken on birds handled and the data set for this 

population is very large. 

Standard mist nets are used, about 3 m tall and 12 m long. Volunteers hold the nets in place, and 

the net covers about 40% of the cave entrance. Up to 14 volunteers help at any one time.

As of 31 December 2011, 21,049 Cave Swallows have been banded at the entrance to Carlsbad 

Cavern and 17,111 retraps have been handled. Retraps are birds that have already been banded 

previously. To date, no birds have been captured with bands placed there by other banders. 

Fewer than 25 of these retraps have been banded at other locations by this project. 

Protocol: Integrated Cave Entrance Community and Cave Environment Long-Term Monitoring 

Protocol, Klamath I&M Network 

This long-term cave monitoring protocol was created according to NPS and Klamath Inventory 

and Monitoring Network (KLMN) guidance and standards. It concerns two parks, Lava Beds 

National Monument (LABE) and Oregon Caves National Monument (ORCA), and provides the 

rationale and methods for monitoring cave climate; ice and water levels; human visitation; 

coverage of ferns, mosses, and lichen; bat colonies; scat deposition; and invertebrate 

communities in caves. The protocol consists of a descriptive narrative, Standard Operating 

Procedures (SOPs) for various tasks, and appendices of relevant information. These procedures 

were designed for long-term use by each park so that data could be collected consistently and 

provide defensible results for management of park resources, public interpretation, and scientific 

research. To find this publication, go to:

http://science.nature.nps.gov/im/units/klmn/publications.cfm?tab=3

Click on 2010 Draft integrated cave entrance community and cave environment long-term 

monitoring protocol Multiple Files (Zip).

Protocol: Cave Aquatic Ecosystem Monitoring Protocol, Mammoth Cave National Park

Cumberland Piedmont Network

The overriding question addressed by this protocol is: Are biological communities within 

Mammoth Cave’s aquatic ecosystem impaired by any biotic or abiotic stressor arising from 

within or beyond park boundaries?

Stressor effects that could be detected by this protocol are acute or chronic exposure to toxins, 

low level to extreme organic enrichment, mild to severe siltation, plus introduction and/or 

establishment of either exotic (such as rainbow trout ) or epigean species.

http://www1.nrintra.nps.gov/im/units/CUPN/monitor/aquaticfauna/aquaticfauna.cfm (access to 

NPS only)
Cave Ecology Inventory and Monitoring Framework 

SOP: Cave Entrance Vegetation

Integrated Cave Entrance Community and Cave Environment Long-Term Monitoring Protocol, 

Klamath I&M Network 

Plant communities near caves can be distinctive, due to the unique environment offered by a cave 

entrance. For instance, some ferns at cave entrances in Lava Beds are biologically unique for being 

disjunct from the rest of the species’ range. Mosses and lichen that grow at many cave entrances in 

Lava Beds are an interesting and appreciated park resource but are vulnerable to human impacts. 

This SOP is intended to quantitatively describe the flora at cave entrances so that impacts can be 

detected.

The methods in this SOP are designed to be implemented in less than 1 hour per cave. It is, therefore, 

a rapid assessment approach that outlines simple vegetation classes and employs a quick, repeatable 

means of gaining accurate abundance information.

To find this publication, go to:

http://science.nature.nps.gov/im/units/klmn/publications.cfm?tab=3

Click on 2010 Draft integrated cave entrance community and cave environment long-term 

monitoring protocol Multiple Files (Zip). Scroll down to 

SOP09_Cave_Entrance_Vegetation_Monitoring_v1.00_DRAFT_20100608.pdf
Cave Ecology Inventory and Monitoring Framework 88

Appendix E: Job Hazard Analysis

JOB HAZARD ANALYSIS

Job Description:

Caving for the purposes of monitoring

Date of last update:

April 2013

NPS Division with primary responsibility for this 

JHA:

Last updated by: Reviewed by: Approved by:

Required standards 

& general notes:

Cave entry permits must be obtained and approved prior to any caving activity. Surface watch and call-in time must 

also be established prior to the trip; surface watch should be informed of party exiting cave ASAP (e.g., via cell phone 

or radio). LE informed of trip plan when conducting surveys in remote sections of cave. Trip leaders must be 

appropriately trained and prepared for the type of trip they are leading. Each team member must be prepared for the 

type of trip and familiar with first aid kit locations along the nearest travel route. All PPE will be inspected and tested 

prior to using, and all equipment will be adequate for the type of trip. Always cave with an appropriate party size for 

activity and cave area; caving alone is usually not appropriate.

Personal protective 

equipment:

UIAA approved helmet with four-point suspension chin strap, three reliable independent light sources, knee-pads (as 

needed), elbow-pads (as needed), gloves, treaded boots with good soles and ankle support, sufficiently warm clothing, 

chemical heat pack, compact first aid kit.

Typical tools, 

equipment & 

supplies:

Side-mounted pack, adequate drinking water, adequate quick-energy food supply, extra batteries, watch, cave maps, 

compass, hand-line.

Activity Potential Hazards Safe Action or Procedure

Planning Cave Trip

Lack of leadership, and

communication, or training. Failing

to establish a reliable surface watch 

and reasonable call-in time. 

Planning a caving trip that will 

exceed the abilities of any team 

member. These abilities include 

physical condition, technical skills 

One person for each trip will be designated as the trip leader. This 

person is responsible for providing leadership and clear 

communication concerning safety, minimizing impact to the cave 

resource and achieving the trip goals. Ensure that trip plans are within 

the range of all team members.

Discuss trip plans with team members and make sure each member 

understands the trip plans, is prepared to meet the challenges of the 

trip in terms of physical condition, technical skills and psychological 
Cave Ecology Inventory and Monitoring Framework 89

and psychological aspects. aspects.

Establish a reliable surface contact person and reasonable call-in 

time.

Ensure designated surface watch and LE informed when conducting 

surveys in remote sections of cave and/or backcountry caves.

Preparing Equipment

Not bringing proper equipment to 

achieve the planned objectives.

Trip members will make sure they have the proper personal 

equipment for the trip. Trip leader will supply protocol-specific 

checklist of necessary equipment.

Equipment worn, broken or 

inoperable due to lack of proper 

maintenance.

Each trip member is responsible for regularly checking, cleaning and 

ensuring their caving equipment is in proper working order. Each trip 

leader is responsible for verifying that equipment is in working order.

Team member not knowing how to 

properly use caving equipment.

All team members will have the training and knowledge as to proper 

usage of each piece of equipment used for their specific trip.

Activity Potential Hazards Safe Action or Procedure

Entering Cave

Entrance Zone Animals

While in the entrance area of a cave all team members should be alert 

and aware that skunks, venomous snakes, spiders, and other 

potentially hazardous animals may be found. Avoid treading on 

accumulated guano or middens.

Rock fall

Due to high fluctuation in temperature and moisture near cave 

entrances, some entrances areas can be particularly prone to loose 

rocks. Move carefully and thoughtfully so as not to dislodge rocks.

Horizontal Caving (general)

Exposed climbs

Always use three points of body contact on cave surfaces to minimize 

risk of falling. Where feasible, use a hand-line or belay.

Slippery surfaces / Falling

Everyone will wear footwear with good traction and a caving helmet 

with a chinstrap. Everyone should move in a careful, controlled 

manner to avoid falling. When climbing, test all holds to ensure that 

they can withstand the force being placed upon them. 

Low/small areas

Trip leaders should ensure all members are able to negotiate 

low/small areas on caving route. Remaining calm and thinking 
Cave Ecology Inventory and Monitoring Framework 90

through what one must do to get through low/small areas is key. 

Team members will not travel head-first through low/small areas that 

slope steeply downward.

Exertion / Exhaustion

Each team member should have adequate knowledge of the length 

and duration of trip prior to heading into the cave, and should have 

cave-specific physical conditioning. People in good physical 

condition need less water and are less prone to injury. Push your 

endurance limit in gradual increments. Avoid overloading your pack; 

be creative to reduce weight and bulk. Prior to the trip, the trip leader 

should inquire about people with known physical conditions and 

treatment needs. Groups should avoid overexertion, and should stop 

at least every hour to eat and drink. Group speed should be tailored to 

the slowest person on the team. Should the trip become too much for 

one trip member, the whole trip plan will be modified to achieve a 

safe trip.

Temperature related issues 

Ensure team members are appropriately dressed for continued 

movement – a lightweight long-sleeved shirt and lightweight, durable 

pants are usually sufficient and prevent overheating.

Ensure team members have adequate cold-weather clothing in their 

packs if needed, such as a balaclava and long-sleeved polypropylene 

shirt. Explain to team members about the colder temps while not 

moving and the necessity of wearing these items to prevent 

hypothermia. Keeping clothing dry is important.

Overdue party 

Trip leaders should always establish a reliable surface watch prior to 

embarking on a trip. This person should be briefed on what time to 

expect the team to return (or call-in) and whom to contact in the 

event the team does not exit on time. Location of the team, number of 

participants and travel route description or maps will be made 

available to the surface watch. Trip leaders will allow a reasonable 
Cave Ecology Inventory and Monitoring Framework 91

amount of time for the team to exit the cave. If the team becomes 

lost, they will remain where they are and wait for the surface watch to 

notify search & rescue.

Dehydration All team members will be properly hydrated before entering the cave 

and drink sufficient water or electrolyte replacement drinks during 

the trip to maintain a proper hydration and avoid cramps.

Minor injuries

Self-rescue using compact first aid kit in pack or in caches.

Major injuries

When possible, at least one team member stays with injured party 

while other team member(s) goes for help. When surveying remote 

locations the contact info of LE Ranger on duty should be known 

beforehand. 

Rock fall

Cavers should locate themselves in places where they will not be 

exposed to rockfall from team members above them. Cavers will 

move carefully and thoughtfully so as not to dislodge rocks. Should a 

team member accidentally dislodge a rock or drop equipment they 

will clearly yell “Rock!” to inform team members below of the 

impending danger. Team members below should be alert and step 

away (not look up). All team members will wear a UIAA approved 

helmet with four-point suspension chin strap caving helmet with a 

chinstrap. This helmet should not be removed when in an area with a 

potential for rockfall.

Activity Potential Hazards Safe Action or Procedure

Wading Total submersion 

When possible, monitoring in cave streams and rivers should be 

performed during the dry season so that water levels and flooding 

potential are low (and visibility high). Always check weather reports 

before performing monitoring in cave streams or rivers. Be aware of 

antecedent conditions: consider current soil saturation. If there is a 

high chance of heavy rain in the surrounding area the trip should be 
Cave Ecology Inventory and Monitoring Framework 92

postponed. Always work in areas with adequate air space between the 

water surface and the cave ceiling. Know alternative exit routes. 

Hypothermia

When wading use neoprene socks and shorts to keep warmed film of 

water in contact with skin. Chemical heaters that last for 8-10 hours

are highly recommended to deal with hypothermia. They can be 

wrapped in a rag and inserted into the exposure suit to supply heat to 

the person’s snorkeler’s core. A heat tab stove can be used to heat up 

a hot meal (e.g., beef stew) for energy and warmth. Performing 

physical exercise, e.g., hands and knees crawling, is a good way to 

warm someone up.

Vertical Caving

Additional required 

equipment:

Rope of adequate length, 

harness outfitted with 

standard (or preferred) 

ascending and descending 

gear, and Quick Attachment 

Safety. 

Miscommunication resulting in 

someone entering the rockfall zone 

while another team member is in a 

position to dislodge rocks or while 

another team member is still on 

rope. 

Clear signals will be used to avoid miscommunications. “On Rope!” 

will be clearly shouted when entering the rockfall zone with the 

intent to rappel or ascend a rope. “Off Rope!” will be clearly shouted 

after getting off rope and exiting the rockfall zone. A clearly shouted 

“OK!” from the other team members should acknowledge either of 

these commands.

Ropes and or rigging materials worn 

or damaged.

All ropes and rigging materials will be inspected for wear or damage 

before use. If necessary damaged or worn materials will be retired.
Cave Ecology Inventory and Monitoring Framework 93

Unsafe Rigging.

All rigging will be inspected before use to ensure that it is safe. If 

determined not to be safe, the rigging will be modified if possible or 

the trip halted until the rigging can be made safe. During rigging, a 

figure eight knot will be tied at the end of the rope prior to the first 

rappel to prevent accidental “short-roping”.

Not conducting a thorough check 

prior to rappelling.

All vertical caving participants will go through a pre-rappel checklist; 

often called “Checking the Chain”.

Rope damage encountered while 

on rope.

A butterfly knot will be used to eliminate the damaged section of 

rope from the life supporting rope. A note will be left both at the top 

and bottom of the rope informing cavers of the situation.

Incident occurs where caver is 

forced to change over to ascent 

while descending or to descent 

while ascending.

Everyone participating in vertical caving will be required to have the 

equipment, training and knowledge to perform changeovers from 

ascent to descent and descent to ascent.

Object becomes jammed in rappel 

device.

Everyone participating in vertical caving will be required to have the 

equipment, training and knowledge to safely lock off their rappel 

device and remove the jammed object without using a knife.

Difficulty in passing a rebelay, 

traverse or other complex rigging 

situation.

All persons traveling to sections of cave with complex riggings will 

be required to have the equipment, training and knowledge to safely 

negotiate these complex riggings.

Caver becomes exhausted, 

unconscious or injured resulting in 

immobilization on rope.

When someone becomes immobilized on rope, it is critical to remove 

that person from rope as soon as possible, usually by talking them 

through the problem, or lowering them to the ground. Ideally every 

trip should have at least one person knowledgeable of small-party 

vertical rescue techniques. Single-rope pickoffs are a last resort.
Cave Ecology Inventory and Monitoring Framework 94

JHA Instructions 

The JHA shall identify the location of the work project or activity, the name of employee(s) involved in the process, the date(s) of acknowledgment, and the 

name of the appropriate supervisor approving the JHA. The supervisor acknowledges that employees have read and understand the contents, have received the 

required training, and are qualified to perform the work project or activity. Identify all tasks and procedures associated with the work project or activity that have 

potential to cause injury or illness to personnel and damage to property or material. Include emergency evacuation procedures (EEP). Identify all known or 

suspect hazards associated with each respective task/procedure listed. 

For example: 

a. Research past accidents/incidents. 

b. Research the Health and Safety Code, or other appropriate literature. 

c. Discuss the work project/activity with participants. 

d. Observe the work project/activity. 

e. A combination of the above.

Identify appropriate actions to reduce or eliminate the hazards identified. 

Abatement measures listed below are in the order of the preferred abatement method: 

a. Engineering Controls (the most desirable method of abatement). For example, ergonomically designed tools, equipment, and furniture. 

b. Substitution. For example, switching to high flash point, non-toxic solvents. 

c. Administrative Controls. For example, limiting exposure by reducing the work schedule; establishing appropriate procedures and practices. 

d. PPE (least desirable method of abatement). For example, using hearing protection when working with or close to portable machines (chain saws, rock drills, 

and portable water pumps). 

e. A combination of the above. 

Emergency Evacuation Instructions 

Work supervisors and crewmembers are responsible for developing and discussing field emergency evacuation procedures (EEP) and alternatives in the event a 

person(s) becomes seriously ill or injured at the worksite. The items listed above serve only as guidelines for the development of emergency evacuation 

procedures.

Be prepared to provide the following information: 

a. Nature of the accident or injury (avoid using victim's name). 

b. Type of assistance needed, if any (ground, air, or water evacuation). 

c. Location of accident or injury, best access route into the worksite (road name/number), Identifiable ground/air landmarks. 

d. Radio frequencies. 

e. Contact person. 

f. Local hazards to ground vehicles or aviation. 

g. Weather conditions (wind speed & direction, visibility, temperature). 

h. Topography. 

i. Number of individuals to be transported. 

j. Estimated weight of individuals for air/water evacuation. 
Cave Ecology Inventory and Monitoring Framework 95

JHA and Emergency Evacuation 

Procedures Acknowledgment 

We, the undersigned work leader 

and crewmembers, acknowledge 

participation in the development 

of this JHA (as applicable) and 

accompanying emergency 

evacuation procedures. We have 

thoroughly discussed and 

understand the provisions of each 

of these documents: 

PRINT NAME SIGNATURE DATE

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________

_________________________________ _________________________________ _________________
The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific 

and other information about those resources; and honors its special responsibilities to American Indians, Alaska Natives, and 

affiliated Island Communities.

NPS 999/128378, April 2015
National Park Service

U.S. Department of the Interior

Natural Resource Stewardship and Science

1201 Oakridge Drive, Suite 150

Fort Collins, CO 80525

www.nature.nps.gov

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