U.S. Department of the Interior

U.S. Geological Survey

Fact Sheet 2006-3052

April 2006

Microbial Ecology in Reef Sediments of Biscayne National Park

Introduction— Biscayne National 

Park (BNP), located in south Florida, 

is unique from other national parks 

because more than 95% of its 172,000 

acres is located in the marine environment containing mangrove, seagrass, and 

coral reef ecosystems (http://www.nps.

gov/bisc/pphtml/nature.html). Recent 

declines in offshore coral reef health and 

shifts in nearshore biological communities may be linked to the quality and/or 

quantity of ground- and surface-water 

input to the park as well as to other 

ecosystem stress factors, such as chemical and nutrient pollution, sea level rise, 

or increased sea surface temperatures 

(Wingard and others, 2003). A critical 

component of the coral reef ecosystem 

that is typically overlooked during scientific investigations of reef productivity 

and health is the bacterial communities 

attached to sediment surfaces as well 

as in the pore water of those sediments. 

These bacterial communities regulate the 

mineralization and cycling of organic 

matter and produce environments 

(reductive or oxidative) that control 

nutrient and trace element speciation 

and concentrations in pore water. The 

transfer or flux of these pore-water 

constituents into the overlying water column provides a source of nutrients and 

trace elements to higher trophic levels. 

The relatively high carbon and nutrient 

cycling and flux rates that occur in reef 

sediment systems, which are driven by 

bacteria, support the high gross primary 

productivity rates of coral reefs (Wild 

and others, 2005). Conducting scientific 

investigations on these microbial and 

geochemical processes will undoubtedly further the scientific understanding of the processes that influence the 

overall productivity and health of our 

Nation’s coral reefs. The objectives of 

this project are to establish baseline data 

on (1) the abundance and productivity of 

microbial communities associated with 

pore water and reef sediments, and (2) 

dissolved trace metals and particulate 

Alina's pict

Alina's Reef site

f e

e R icfi caP

Anniversary Reef site

Area

Shown

a idr lo F

52 o

N' 32

80o80 09' W o10' W

0 km 1

Figure 1. The sample sites for this study are located in the southeastern tip of Florida within 

Biscayne National Park. The two coral reef sites selected are Alina’s and Anniversary Reefs, 

which are approximately 10 kilometers offshore. These reef systems are classified as patch reefs, 

with productive seagrass beds immediately outside the reef halo zone.
and dissolved nutrients in surface and 

pore water and their respective flux rates 

at the boundaries of selected reefs in the 

Florida Keys.

Methods— Two sites, Alina’s Reef and 

Anniversary Reef, were chosen based on 

previous investigations of in situ coral 

reef health (Yates and Halley, 2003; Fig. 

1). The aim of this project is to establish 

baseline data on (1) the abundance and 

productivity of microbial communities 

associated with reef sediments and the 

pore water and (2) dissolved trace metals 

and particulate and dissolved nutrients 

in surface and pore water and their 

respective flux rates at the boundaries of 

selected reefs in the Florida Keys.

SCUBA divers collected pore-water 

samples from carbonate reef sediments 

at two depths, 1.3 and 12.7 centimeters 

(cm). A round plate that can hold up to 

eight stainless steel samplers was used to 

stabilize the samplers at the two predetermined depths (Fig. 2 A, B). Each 

sampler has three slots at the tip that 

collect pore water at a vertical interval 

of 0.6 cm. Five 60-milliliter (mL) precleaned and autoclaved syringes, tubing, 

and 3-way valves were used for each 

depth: two for microbiology samples, 

two for nutrient and trace metal samples, 

and one for field parameter analyses. A 

surface-water sample was collected from 

approximately 30 cm above the seafloor 

in a sterile 1-Liter bottle. In addition, a 

2.5-cm-diameter, 16.3-cm-long core was 

collected from the adjacent reef sediments (Fig 2 C, D). Once the divers and 

samples arrived in the boat, all pore and 

surface water samples were placed in 

coolers containing ice. The one syringe 

collected for field parameters (specific 

conductivity, temperature, pH, and oxygen-reduction potential) was processed 

and analyzed immediately.

Determination of microbial productivity 

presents two challenges in this environment: (1) the methods routinely used 

to determine these rates require that 

the analyses be initiated almost immediately, which prohibits the preservation, prolonged storage or shipping of 

samples; and (2) an additional logistical problem of determining microbial 

productivity measurements in the field 

is the required use of radioisotope 

Figure 2. Sediment pore-water and core sampler. (A) Pore water sampling devices were inserted to predetermined depths below the under surface of 

the weighted plate and secured by thumb screws. Each pore-water sampler (M.H.E. Products, East Tawas, Michigan) is 0.3 cm in diameter and 35.6 cm 

in length with a sampling interval of 0.6 cm. (B) Pore-water samples are collected by connecting a sterile 60 mL syringe, via tubing, to the pore-water 

sampler and gently extracting water samples from the predetermined sediment depths. (C,D) A sediment core (2.5 × 16.3 cm) was collected using a 

modified 60 mL syringe that had the distal end removed. The core was contained by sliding a sterile plug into the open end of the coring device.

A B

C D
labeled substrates. Both of these issues 

have been addressed and these types of 

samples are processed less than 2 hours 

after collection using a mobile laboratory that has been USGS certified for use 

of radioactive isotopes (i.e., 3H, 14C, 35S) 

in the field (Fig. 3). 

Sediment samples initially were processed in the mobile laboratory to 

remove bacteria from the sediments. The 

remaining sediments were processed for 

particle size analysis and to determine 

the percentage of sand, silt and mud. 

Surface and pore water, and extracted 

sediment samples were then processed 

to determine bacterial productivity rates 

by adding 3H-leucine (a radiolabeled 

amino acid) to each sample, followed 

by a 1-hour incubation period. After termination of the assay the samples were 

processed to recover radiolabeled bacterial biomass. The radioactivity in each 

sample was then measured and recorded 

using a scintillation counter. The resulting data were used to calculate the 

bacterial productivity rates in the water 

(μg C L-1 d-1) and sediment (μg C g-1 d-1) 

samples. 

Summary— Both reef sites had similar 

temperature profiles (Fig. 4). The pH 

profiles were also similar except for the 

March sample at Alina’s Reef, when it 

dropped to 6.97 at 1.3 cm. In general, 

the average pH of the pore water was 

0.50 (range: 0.16-1.32) pH units lower 

than the overlying water column. This 

decrease in pH is significant in regard 

to the rates of dissolution and precipitation of carbonate sediments and how 

the concomitant increase in alkalinity 

may influence buffering in the overlying 

water column. 

The oxygen-reduction potential data 

from both reefs followed a similar trend 

in that the sediment systems became 

more reduced as the water temperature 

increased (Fig. 4). The bacterial productivity rates in the sediment systems, 

which include pore water and sediments, 

also increased with increasing water 

temperature, with a 2 to 3 fold increase 

between the March and August sampling 

events (Fig. 4). On average, the bacterial productivity rates in the sediment 

systems were approximately 10 fold 

greater (range: 2.3-26.4 fold) than those 

measured in the overlying water column 

samples. 

With regard to two nutrients that are 

important to coral reef productivity, 

ammonium (NH4

+

) and silicate (SiO2), 

their respective concentrations in the 

sediment systems are between 5 to 175 

and 6 to 26 fold greater than in the water 

Figure 3. The USGS mobile field laboratory. Due to 

the requirement for rapid processing of samples, 

a mobile field laboratory was used to process 

and analyze the samples. The mobile laboratory 

is totally self-contained and powered, and easily 

transported and set up at field sites. One area of 

the mobile laboratory is designed for research 

that uses radioisotope-labeled substrates, which 

are necessary to determine the microbial ecology 

and productivity of coral reef systems.

Figure 4. Data summaries. The following datasets were collected from the overlying surface waters and two sediment depths at Alina’s and Anniversary Reefs during three sampling events. (b.d. = below detection limit)

Temperature (

o

C)

22 24 26 28 30

Depth (cm)

pH

6.8 7.2 7.6 8.0 8.4

ORP (mV)

-200 -100 0 100 200 0 5 10 15 20 25 30 1.0 2.0 3.0 4.0

NH4 (uM)

0 2 4 45 50

Productivity in Water

(ug C L-1 d-1) x103 Productivity in Sediment

(ug C L-1 d-1) x 103

Alina's Reef

Anniversary Reef

b.d.

22 24 26 28 30

Depth (cm)

7.4 7.6 7.8 8.0 8.2 8.4 -200 -100 0 100 200 0 2 4 6 8 10 12 14 0 1.0 2.0 3.0 4.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5

Temperature (

o

C) pH ORP (mV) NH4 (uM) Productivity in Water

(ug C L-1 d-1) x103 Productivity in Sediment

(ug C L-1 d-1) x 103

March 2005 June 2005 August 2005

-2

0

-4

-6

-8

-10

-12

-2

0

-4

-6

-8

-10

-12

SiO2

0 10 20 30 40 50 60

SiO2

0 2 4 6 8 10 12 14 16 18
columns adjacent to coral reefs. Accordingly, there was a flux of these nutrients 

from the sediments into the overlying 

water column at both reefs, with significant increases in the flux of ammonium 

and silicate at Alina’s Reef between the 

June and August sampling events (Fig. 

5). Flux rate estimates were calculated 

using Fick’s law of diffusion and the 

appropriate constants as described 

by Rasheed and others, (2002). This 

approach to calculating flux rates does 

not account for advection, as described 

by Huettel and others, (1998). Therefore, 

the flux rate values from this study are 

conservative estimates.

Collectively, the data from this study 

show seasonal trends in the production 

and release of nutrients from sediments 

immediately adjacent to coral reefs. 

Bacterial activities directly alter sediment 

environments in ways that promote the 

production and cycling of these nutrients. 

The concentrations of these sedimentassociated nutrients are significantly 

greater than those found in the overlying 

water column and the flux rates of these 

nutrients contribute to the productivity of 

coral reefs. Bacterial cycling of carbon, 

nutrients, oxygen, and metals alters geochemical processes and, therefore, needs 

to be considered when assessing the ecology and health of coral reefs.

Figure 5. Diffusive flux rates of nutrients from the sediments. Nutrient concentration data from the 

overlying water columns and two sediment depths at Alina’s and Anniversary Reefs were used to 

calculate diffusive flux rates of ammonium, silicate, and phosphate into the overlying water column. 

Future research areas - Nutrient 

availability and the positive and negative effect that nutrients can have on 

coral reef health are major concerns 

of the USGS. The study described in 

this publication establishes a baseline 

dataset for how coral reef sedimentassociated microbial communities in 

the Florida Keys change spatially and 

temporally and how these changes may 

influence the quantity and quality of 

nutrients that are important to coral reef 

productivity. To address how sedimentassociated microbial activities affect 

nutrient cycling and coral reef health, 

future research areas of interest are: (1) 

determining how sediment-associated 

microbial productivity relates to coral 

reef productivity; (2) determining how 

oxygen transport and utilization in the 

sediments by the microbial communities 

alters geochemical processes, such as 

nutrient and metal cycling; (3) determining how different carbon and nutrient 

sources (e.g., phytoplankton biomass) 

from the overlying water column influences microbial productivity and nutrient cycling rates; and (4) how microbial 

activities in the sediments influence 

carbonate dissolution and precipitation in response to acidified pore water 

conditions.

Acknowledgments

This project was funded by the USGS 

Coastal and Marine Program. We 

acknowledge Richard Curry (Biscayne 

National Park) for onsite logistical support and Molly McLaughlin (USGS) 

and Kate Ciembronowicz (USGS) for 

their assistance in the field. We also 

acknowledge Bob Halley (USGS) for 

constructive and informative conversations that assisted in the guidance of this 

research effort.

References

Huettel, M., Ziebis, W., Forster, S., and 

Luther III, G., 1998, Advective transport 

affecting metal and nutrient distributions 

and interfacial fluxes in permeable 

sediments: Geochimica et Cosmochimica 

Acta, v. 62, p. 613-631.

Rasheed, M., Mohammed, I., Richter, C., 

and Huettel, M., 2002, Effect of reef 

framework and bottom sediment on 

nutrient enrichment in a coral reef of the 

Gulf of Aqaba, Red Sea: Marine Ecology 

Progress Series, v. 239, p. 277-285.

Wild, C., Rasheed, M., Jantzen, C., Cook, 

P., Struck, U., Huettel, M., and Boetius, 

A., 2005, Benthic metabolism and 

degradation of natural particulate organic 

matter in carbonate and silicate reef sands 

of the northern Red Sea: Marine Ecology 

Progress Series, v. 298, p. 69-78.

Wingard, G., Cronin, T., Willard, D., 

Murray, J., Stamm, R., Holmes, C., 

Dwyer, G., Ishman, S., and Williams, 

C., 2003, Ecosystem history of central 

Biscayne Bay based on sediment core 

analyses: US Geological Survey 

Open-File Report 03-54, p 213-214. 

Yates, K. and Halley, R., 2003, Measuring 

coral reef community metabolism using 

new benthic chamber technology: Coral 

Reefs, v. 22, p. 247-255.

Contact Information:

John Lisle, jlisle@usgs.gov

Chris Reich, creich@usgs.gov

600 4th Street South

St. Petersburg, FL 33701

727-803-8747

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