U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2011–1066

Benthic Habitat Classification in Lignumvitae Key Basin, 

Florida Bay, using the U.S. Geological Survey Along-Track 

Reef Imaging System (ATRIS)
Cover. Bottom types classified in the ATRIS survey of Lignumvitae Key Basin. (See figure 5.)
Benthic Habitat Classification in Lignumvitae Key Basin, 

Florida Bay, using the U.S. Geological Survey Along-Track 

Reef Imaging System (ATRIS)

By C.D. Reich, D.G. Zawada, P.R. Thompson, C.E. Reynolds, A.H. Spear, D.K. Umberger, and R.Z. Poore

Open-File Report 2011–1066

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011

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reproduce any copyrighted materials contained within this report.

Suggested citation:

Reich, C.D., Zawada, D.G., Thompson, P.R., Reynolds, C.E., Spear, A.H., Umberger, D.K., and Poore, R.Z., 2011, 

Benthic habitat classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey Along-Track 

Reef Imaging System (ATRIS): U.S. Geological Survey Open-File Report 2011–1066, 12 p.
iii

Contents

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

Setting .............................................................................................................................................................1

Methods...........................................................................................................................................................2

Results and Summary....................................................................................................................................4

Area 1 ....................................................................................................................................................6

Area 2 ....................................................................................................................................................7

Area 3 ....................................................................................................................................................8

Area 4 ....................................................................................................................................................9

Conclusions...................................................................................................................................................12

Acknowledgments.......................................................................................................................................12

References Cited..........................................................................................................................................12

Figures

1. Map showing location of Florida Bay and study area in south Florida ...............................1

2. Graph showing salinity and temperature from January 2005 to February 2010, 

C-MAN (NOAA) station LONF1 located in Florida Bay near Long Key, FL ..........................2

3. ATRIS system setup aboard the R/V Halimeda........................................................................3

4. Screen-capture image of the ATRIS Data Analysis and Processing Tool (ADAPT) 

classification process..................................................................................................................3

5. Bottom types classified in the ATRIS survey of Lignumvitae Key Basin .............................4

6. Bottom-type map showing all surveyed areas in Lignumvitae Key Basin and 

Lower Matecumbe Key................................................................................................................5

7. Bottom-type map for Area 1........................................................................................................6

8. Bottom-type map for Area 2........................................................................................................7

9. Bottom-type map for Area 3........................................................................................................8

10. Bottom-type map for Area 4........................................................................................................9

11. Interpolation (Thiessen polygon) map of the survey data for a portion of area 4 

near Lignumvitae Key overlaid on high-resolution aerial photography. ...........................10

12. Classified bottom-type map of area 4 near Lignumvitae Key superimposed on 

bottom-type map of Prager and Halley (1997)........................................................................11
iv

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

mile, nautical (nmi) 1.852 kilometer (km)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) 

as follows:

 °F = (1.8 × °C) + 32

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) 

as follows:

 °C = (°F – 32) / 1.8
Introduction

The Comprehensive Everglades Restoration Plan 

(CERP) funded in partnership between the U.S. Army Corps 

of Engineers, South Florida Water Management District, and 

other Federal, local and Tribal members has in its mandate 

a guideline to protect and restore freshwater flows to coastal 

environments to pre-1940s conditions (CERP, 1999). Historic 

salinity data are sparse for Florida Bay, so it is difficult for 

water managers to decide what the correct quantity, quality, 

timing, and distribution of freshwater are to maintain a healthy 

and productive estuarine ecosystem. Proxy records of seasurface temperature (SST) and salinity have proven useful in 

south Florida. Trace-element chemistry on foraminifera and 

molluscan shells preserved in shallow-water sediments has 

provided some information on historical salinity and temperature variability in coastal settings, but little information is 

available for areas within the main part 

of Florida Bay (Brewster-Wingard and 

others, 1996).

Geochemistry of coral skeletons 

can be used to develop subannually 

resolved proxy records for SST and 

salinity. Previous studies suggest corals, specifically Solenastrea bournoni, 

present in the lower section of Florida 

Bay near Lignumvitae Key, may be 

suitable for developing records of SST 

and salinity for the past century, but the 

distribution and species composition of 

the bay coral community have not been 

well documented (Hudson and others, 

1989; Swart and others, 1999). Oddly, 

S. bournoni thrives in the study area 

because it can grow on a sandy substratum and can tolerate highly turbid water. 

Solenastrea bournoni coral heads in this area should be ideally 

located to provide a record (~100–150 years) of past temperature and salinity variations in Florida Bay. 

The goal of this study was to utilize the U.S. Geological 

Survey’s (USGS) Along-Track Reef Imaging System (ATRIS) 

capability to further our understanding of the abundance, 

distribution, and size of corals in the Lignumvitae Key Basin. 

The study area was subdivided into four areas whereby corals 

and other benthic habitats were classified based on ATRIS 

imagery.

Setting

Lignumvitae Key Basin is located in the middle Florida 

Keys near Lower and Upper Matecumbe Keys in the south 

part of Florida Bay (fig. 1). The basin was surveyed from 

Benthic Habitat Classification in Lignumvitae Key Basin, 

Florida Bay, using the U.S. Geological Survey Along-Track 

Reef Imaging System (ATRIS)

By C.D. Reich, D.G. Zawada, P.R. Thompson, C.E. Reynolds, A.H. Spear, D.K. Umberger, and R.Z. Poore

Figure 1. Location of Florida Bay and 

study area in south Florida. -82o 25o 24.5o 25.5o

-81.5o -81o -80.5o

Gulf of Mexico

Atlantic Ocean

Miami

Biscayne

Bay

Study Area

Lignumvitae Key

Basin

Whipray Basin

Marathon

Long Key

Key West

Florida Bay

-30

-28.9

-27.8

-26.7

-25.6

-24.5

-23.4

-22.3

-21.2

-20.1

-19

-17.9

-16.8

-15.7

-14.6

-13.5

-12.4

-11.3

-10.2

-9.1

-8

-6.9

-5.8

-4.7

-3.6

-2.5

-1.4

-0.3

Water Depth (m)
2 Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey ATRIS

September 14 to 17, 2009. Two of the surveys were conducted 

near the Peterson Keys, one north of Lignumvitae Key, and the 

other along the north shore of Lower Matecumbe Key. These 

sites were chosen because of previous records of coral heads 

that were either cored or were large enough to be cored for 

potential paleo-environmental purposes (Hudson and others, 

1989; Swart and others, 1999). 

Surface waters of the south part of Florida Bay are 

subject to tidal mixing with the Gulf of Mexico and Atlantic Ocean. During the rainy season, June through October, 

freshwater flowing in from the Everglades, approximately 25 

kilometers (km) to the north, can lower the salinity at the study 

site from an average of 36 practical salinity units (psu) to 

near 27 psu (data from the National Oceanic and Atmospheric 

Administration, NOAA, Coastal-Marine Automated Network, 

C-MAN, station LONF1; fig. 2). Conversely, surface waters 

in this region can also escalate to above 40 psu due to evaporative effects. Salinity has been reported as high as 70 psu 

in the isolated basins of central Florida Bay (for example, 

Whipray Basin, fig. 1) and near 0 psu along the border of the 

Everglades and in the northern bay (Lee and others, 2006). 

Surface-water temperatures are also subject to drastic annual 

swings. Average water depth in Florida Bay is approximately 

1 m. The shallow waters have the capacity to get quite warm 

in the summer (~34 °C) and cool quickly during the passing of 

winter cold fronts (~8 °C; fig. 2). Because of the collocation of 

mixing waters from Everglades drainage and Gulf of Mexico 

and Atlantic Ocean waters, records from large coral heads in 

the Lignumvitae Key Basin should record annual swings in 

temperature and salinity patterns over the past ~100 years. 

Methods

The USGS developed the ATRIS imagery system to support mapping activities and to ground-truth remotely sensed 

data, such as acoustic, lidar, and satellite imagery of submerged coastal environments (Brock and Zawada, 2006). Two 

configurations are available for surveying benthic environments: (1) shallow, between 0 and 10 meters (m) and 

(2) deep, between 10 and 25 m. The shallow-ATRIS setup 

used in this study was operated from the 7.6-m-long USGS 

vessel R/V Halimeda (fig. 3). The shallow-water system 

houses a sensor package containing a gigabit Ethernet digital camera affixed to the submerged portion of an adjustable 

fiberglass pole. Attached directly above the camera at the top 

of the pole is a Global Positioning System (GPS) antenna. An 

Ashtech receiver collects GPS positioning from the antenna, 

which allows for accurate geo-location of the imagery. Each 

image was geo-located to within 5 m in real time, but after 

differential corrections, accuracy improved to ~50 cm. To 

improve the boat GPS data, a base station was established at 

the Keys Marine Laboratory on Long Key (fig. 1). The base 

station consisted of an Ashtech kinematic GPS receiver and 

antenna, identical to that used on the R/V Halimeda, and fixed 

at the same location throughout the study period. The base 

station GPS data were used to differentially correct each of the 

image locations. Camera-to-seafloor range and vessel-heading 

data were also collected for each image. Field conditions 

(water clarity and sea state) for much of the study limited the 

collection rate of imagery to 4 frames per second (fps; maximum of 20 fps). Approximately 20 linear km were surveyed 

Figure 2. Salinity (blue) and 

temperature (green) from 

January 2005 to February 2010. 

Note the consistent warm 

summer high temperatures 

and declining winter low 

temperatures during the 5-year 

record. Salinity also varies 

from a low of near 27 psu up to 

44 psu (normal marine salinity 

is 35 psu, dashed line). Data 

were recorded hourly from the 

C-MAN (NOAA) station LONF1 

located in Florida Bay near 

Long Key, FL. [psu is practical 

salinity units]

12/1/04 6/1/05 12/1/05 6/1/06 12/1/06 6/1/07 12/1/07 6/1/08 12/1/08 6/1/09 12/1/09

S alinity (psu)

0

10

20

30

40

50

Tem perature (degC)

0

10

20

30

40

50
Methods 3

each day at a boat speed of 4–5 km per hour (kph). The camera angular field-of-view in the x and y directions is 29° and 

22°, respectively. Images were displayed in real time and were 

written to a Level 1, mirrored redundant array of independent 

disks (RAID), enabling simultaneous storage and backup.

The ATRIS Data Analysis and Processing Tool (ADAPT) 

was utilized for post-processing of the imagery dataset. 

ADAPT allows for interactive geographic browsing, scaling, and extraction of specific substratum images for further 

quantitative analysis, as well as a classification tool that 

allows the user to define and classify the substratum in each 

image (fig. 4). The images for each of the surveyed areas 

were viewed in the ADAPT software and every third image 

classified, due to substantial overlap between frames. Five 

Figure 4. Screen-capture image of the ATRIS Data Analysis and Processing Tool (ADAPT) classification process. Various screens are 

displayed when classifying images: (A) Tool screen is used to help adjust the color or contrast of the image; (B) Image information screen 

displays the image number, time and date of acquisition, range of camera off the seafloor, and image dimensions; (C) Classification screen 

contains selectable buttons for possible bottom types; (D) Image screen; (E) Plotting screen shows the location of each image (red dot) 

along the boat track line.

E

B

A

C

D

Figure 3. ATRIS system setup aboard the R/V Halimeda. 

(I) Photograph displaying the (a) Along-Track Reef Imaging 

System (ATRIS) computer package and monitor showing 

real-time images, (b) depth sounder, and (c) computer screen 

showing navigation and boat track line. (II) Photograph of the 

R/V Halimeda with pole attached to side of boat. The pole has 

a GPS antenna mounted on top (a) and camera affixed to the 

bottom (b).

a

a

b b

c

I II
4 Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey ATRIS

categories were used in classifying the benthic habitats: 

seagrass (subcategories, dense and sparse), sand, hardbottom, coral, and unclassifiable. The classification files were 

merged with other data files that contained latitude, longitude, 

water depth, camera range, boat heading, and bottom type. 

This merged file was used to create benthic habitat products 

presented in this report.

Currently, progress is being made to increase the rate 

at which images can be viewed and classified. In the future, 

ATRIS images will be viewed in a Geographical Information 

System (GIS)-based format, allowing the scientist to view all 

images on a map, zoom in to particular areas, and potentially 

classify benthic habitats within the ArcGIS software. Within 

the ArcGIS program, world files (*.tfw) are generated from 

GPS, compass, and depth data associated with each image. 

The resulting world files are then used by the ArcGIS program 

to georeference, orient, and scale the images. The final step is 

to utilize an ArcGIS Image Server, which permits interactive 

browsing, dynamic mosaicking, and zooming within a given 

geographic region. The ATRIS images reside on a single GIS 

layer, making it easy to integrate with other geospatial data.

Results and Summary

We collected 363,960 seafloor images during the shallowATRIS survey from September 14 to 17, 2009. The 85-linekm survey over the 4 days revealed representative examples 

of Florida Bay bottom types. The bottom-type classifications 

used for this study are seagrass (subcategories, dense and 

sparse), sand, hardbottom, coral, and unclassifiable (fig. 5). 

Surveys did not cover areas near mud banks because the 

objective was to document areas likely to support coral growth 

(specifically, S. bournoni). In addition, S. bournoni occurrence was noted during classification of bottom types. Figure 6 

shows survey areas 1, 2, and 4 in Lignumvitae Key Basin and 

area 3 along the north shore of Lower Matecumbe Key. The 

highlights of each survey area are discussed below.

Figure 5. Bottom types classified in 

the ATRIS survey of Lignumvitae Key 

Basin: (A) sparse seagrass, (B) dense 

seagrass, (C) sand, (D) hardbottom, and 

(E) coral. Other possible organisims 

observed included algae, invertebrates 

(lobster, crabs), and larger animals 

such as fish and stingrays (F).
Results and Summary 5

80°42'0"W

80°42'0"W

80°44'0"W

80°44'0"W

24°56'0"N

24°56'0"N

24°54'0"N

24°54'0"N

24°52'0"N

24°52'0"N

Explanation

Bottom Type

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

0 0.5 1 2 3

Kilometers

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:42,677

Area 1

Area 2

Area 4

Area 3

Florida Bay

Atlantic Ocean

Lignumvitae

Key

Peterson Keys

Lower Matecumbe Key

Lignumvitae Key Basin

Figure 6. Bottom-type map showing all surveyed areas in Lignumvitae Key Basin and Lower Matecumbe Key.
6 Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey ATRIS

Area 1

Area 1 is located to the east of the Peterson Keys in Lignumvitae Key Basin and is the site where Hudson and others 

(1989) cored a S. bournoni coral head. Water depth ranged 

from 4.4 to 7.1 m. Area 1 was surveyed over a 2-day period 

(fig. 7). No large (>1 m) coral heads were observed in this 

region even though a detailed survey of the area surrounding 

the Hudson coordinates was conducted (inset, fig. 7). However, numerous small coral heads were observed ranging in 

size from 5 to 30 cm in diameter. The majority of area 1 was 

found to be seagrass (sparse and dense) and with interspersed 

sand. Sandy areas contained Penicillus sp., the predominate 

sediment-producing alga, and burrow mounds constructed by 

burrowing shrimp (Callianassia spp.). Hardbottom areas typically had a veneer of sediment, but were noticeable because 

they supported various species that require hardbottom habitat 

including gorgonians, primarily sea whips, small scleractinian corals (Siderastrea radians, Solenastrea bournoni, Porites 

porites), and occasionally hydrocorals (Millepora spp.).

80°44'0"W

80°44'30"W 80°44'0"W

24°55'30"N

24°55'30"N

24°55'0"N

24°55'0"N

Explanation

Bottom Type

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

0 0.1 0.2 0.4 0.6

Kilometers

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:12,000

Area 1

Florida Bay

Peterson Keys

inset 0 meters 80

Figure 7. Bottomtype map for area 1. 

Inset in upper right 

corner is the area 

where Hudson and 

others (1989) cored a 

Solenastrea bournoni

coral head. (See fig. 6 

for area 1 location.)
Results and Summary 7

Area 2

Area 2 is north of the most northerly Peterson Key and 

overlaps the north end of area 1. Water depth ranged from 4.4 

to 5.9 m. The area was dominated by hardbottom and seagrass 

(fig. 8). Numerous small corals (5–10 cm) were found in this 

area, but due to low-visibility water conditions resulting in 

blurry images, some of those corals on the map may have been 

misinterpreted and may in fact be the orange clionid sponges. 

There were also computer problems during the processing of 

the images that resulted in the omission of numerous classified 

images in the central section of the survey line.

80°44'30"W

80°44'30"W

80°45'0"W

80°45'0"W

24°55'30"N

24°55'30"N

24°55'0"N

24°55'0"N

Explanation

Bottom Type

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

0 0.1 0.2 0.3 0.4 0.5

Kilometers

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:9,600

Area 2

Florida Bay

Peterson Key

Figure 8. Bottom-type 

map for area 2. The 

absence of continuous 

data in the middle 

section of the survey 

line was the result of 

computer-related issues 

during the classification 

process. (See fig. 6 for 

area 2 location.)
8 Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey ATRIS

Area 3

Area 3 is located along the Florida Bay side of Lower 

Matecumbe Key. Area 3 was surveyed because of information that implied moderate to large coral heads were present (Harold Hudson [retired NOAA, Florida Keys National 

Marine Sanctuary], oral commun., 2008). Water depth ranged 

from 4.3 to 5.7 m. Four track lines were run offshore, but after 

noting that most of the area was seagrass, the survey lines 

were moved closer to the coastline of Lower Matecumbe Key 

(fig. 9). A 400-square-meter area of hardbottom and sand was 

discovered in the lower southwest corner of the survey area, 

coinciding with the presence of numerous (~33) S. bournoni

corals (inset, fig. 9). Solenastrea bournoni corals were concentrated in this small area and ranged in size from 10 cm to 

70 cm. The water was exceptionally clear during the survey, 

and numerous small corals were observed from the boat. 

80°42'30"W

80°42'30"W

80°43'0"W

80°43'0"W

80°43'30"W

80°43'30"W

24°52'30"N

24°52'30"N

24°52'0"N

24°52'0"N

24°51'30"N

24°51'30"N

Explanation

Bottom Type

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

Lower Matecumbe Key

Florida Bay

Atlantic Ocean

Area 3

inset

0 0.1 0.2 0.4 0.6

Kilometers

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:11,000

0 500

Meters

Figure 9. Bottom-type 

map for area 3. Majority of 

area 3 in this cove of Lower 

Matecumbe Key is sparse 

and dense seagrass. Inset in 

the figure shows an enlarged 

area in the elbow of the 

survey area characterized by 

sand and hardbottom. This 

area contained numerous 

small- (10 cm) to mediumsized (70 cm) Solenastrea 

bournoni coral heads. (See 

fig. 6 for area 3 location.)
Results and Summary 9

Area 4

The area 4 survey was conducted north of Lignumvitae 

Key. Water depth ranged from 4.8 to 6.1 m. Interpretation of 

aerial photography and results published by Prager and Halley 

(1997) indicated that this area was primarily hardbottom and 

sandy substratum and had high potential for the occurrence 

of Solenastrea sp. corals (fig. 10). A shallow-water ridge of 

hardbottom was discovered along the east part of the survey 

area. Lush gorgonians and numerous small (<10-cm-diameter) 

corals were revealed in this region. Overall, area 4 showed 

gradation from seagrass at the west end to hardbottom and 

sand along the east survey boundary. To help clarify the zonal 

patterns, an interpolation map, or Thiessen polygon (fig. 11), 

was created for a portion of area 4. This map helped visually 

identify and isolate those regions of dense and sparse seagrass 

as well as areas of sand and hardbottom. The combination 

of the contour map and high-resolution aerial photography 

80°42'0"W

80°42'0"W

80°43'0"W

80°43'0"W

24°55'0"N

24°55'0"N 24°54'0"N

Explanation

Bottom Type

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

0 0.25 0.5 0.75

Kilometers

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:14,053

Florida Bay

Lignumvitae Key

Area 4 Figure 10. Bottomtype map for area 4 near 

Lignumvitae Key. The aerial 

photograph shows a ridge 

(dotted line) along the 

northeast section of the 

survey that corresponds 

to a region of hardbottom 

species, such as gorgonians 

and small corals. (See fig. 6 

for area 4 location.)
10 Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey ATRIS

showed how spatially variable the benthic habitats can be 

in Florida Bay. The numerous, small seagrass patches and 

sand-bottom types can be difficult to discern from hardbottom 

areas in the imagery. Without the aid of ATRIS, area 4 could 

have been interpreted as sand and seagrass. It is important 

to include multiple in-situ observations and ground-truthing 

when interpreting benthic habitats from aerial photography. 

Prager and Halley (1997) interpreted much of Lignumvitae 

Key Basin as hardbottom based on limited visual (diver) 

interpretation and bottom grab samples. Results show that the 

area is much more heterogeneous than shown in the results 

published by Prager and Halley (1997), as seen in figure 12.

80°42'0"W

80°42'0"W

80°42'30"W

80°42'30"W

80°43'0"W

80°43'0"W 24°55'0"N

24°55'0"N

24°54'30"N

24°54'30"N

Explanation

Trackline

Bottom Type

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

0 115 230 460 690 920

Meters

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:14,053

High resolution aerial photography

Area 04 Florida Bay

Figure 11. Interpolation (Thiessen polygon) map of the survey data for a portion of area 4 near 

Lignumvitae Key overlaid on high-resolution aerial photography. The interpolation plot reveals the 

zonation of seagrass, sand, and hardbottom types. Jagged edges result from the interpolation process 

during the Thiessen polygon creation.
Results and Summary 11

80°42'0"W

80°42'0"W

80°43'0"W

80°43'0"W

24°55'0"N

24°55'0"N

24°54'0"N

24°54'0"N

Explanation

ATRIS (2009) Prager and Halley (1997)

Seagrass, Sparse

Seagrass, Dense

Hardbottom

Sand

Coral

Unclassifiable

Sparse Seagrass

Intermediate Seagrass

Dense Seagrass

Hardbottom

Mud Bank Suite

Open Sand

Water

Land

0 0.10.2 0.4 0.6 0.8

Kilometers

Map Projection: Transverse Mercator

Datum: NAD 1983, UTM Zone 17N

Scale: 1:14,646

Lignumvitae Key

Figure 12. Area 4 classified bottom-type map near Lignumvitae Key superimposed on bottom-type map 

of Prager and Halley (1997). ATRIS results show high variability in benthic types in a small area when 

compared to large-scale benthic habitat surveys.
12 Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey ATRIS

Conclusions

Numerous corals were located during the ATRIS surveys in Florida Bay. Whereas the Solenastrea sp. corals were 

widespread across the areas surveyed, there were no corals of 

significant size (>1 m) along our track lines that would provide historical records of surface-water salinity or temperature 

reaching beyond instrumental records from Florida Bay. However, ATRIS proved to be a productive tool for developing 

high-resolution benthic habitat maps. In addition to producing 

detailed habitat maps, ATRIS has potential as a valuable monitoring tool, as for example, for monitoring seagrass recovery 

from propeller scars or storm damage or for mapping expansion or contraction of seagrass beds. The post-processing of 

hundreds of thousands of images is time consuming, but the 

products of the system are highly detailed and provide important information on benthic habitat.

Acknowledgments

This study was made possible through funding from the 

U.S. Geological Survey Greater Everglades Priority Ecosystems Science Program. We thank the Florida Institute of 

Oceanography’s Keys Marine Laboratory on Long Key for 

logistical support. Thanks to Ilsa Kuffner, Ginger Garrison, 

Barbara Lidz, and John Watson for diligent reviews, which 

greatly improved the final version of this report.

References Cited

Brewster-Wingard, G.L, Ishman, S.E., Edwards, L.E., and 

Willard, D.A., 1996, Preliminary report on the distribution 

of modern fauna and flora at selected sites in north-central 

and northeastern Florida Bay: U.S. Geological Survey 

Open-File Report 96–0732, 36 p.

Brock, J., and Zawada, D., 2006, Along-Track Reef Imaging System (ATRIS): U.S. Geological Survey Fact Sheet 

2006–3051, 4 p.

Comprehensive Everglades Restoration Plan (CERP), 1999, 

Central and Southern Florida Comprehensive Review Study 

Final Integrated Feasibility Report and Programmatic Environmental Impact Statement - April 1999: CERP, available 

at http://www.evergladesplan.org/docs/comp_plan_apr99/

the-plan-complete_web.pdf.

Hudson, H., Powell, G., Robblee, M., and Smith, T., III, 

1989, A 107-year-old coral from Florida Bay: Barometer of 

natural and man-induced catastrophes?: Bulletin of Marine 

Science, v. 44, no. 1, p. 283–291.

Lee, T.N., Johns, E., Melo, N., Smith, R.H., Ortner, P., and 

Smith, D., 2006, On Florida Bay hypersalinity and water 

exchange: Bulletin of Marine Science, v. 79, no. 2, p. 301–

327.

Prager, E., and Halley, R., 1997, Florida Bay bottom types: 

U.S. Geological Survey Open-File Report 97–526, 1 p.

Swart, P.K., Healy, G., Greer, L., Lutz, M., Saied, A. 

Anderegg, D., Dodge, R.A. and Rudnick. D., 1999, The use 

of proxy chemical records in coral skeletons to ascertain 

past environmental conditions in Florida Bay: Estuaries, 

v. 22, p. 384–397

Reich and others—Benthic Habitat Classification in Lignumvitae Key Basin, Florida Bay, using the USGS ATRIS—Open-File Report 2011–1066