Marine Sanctuaries Conservation Series ONMS (ONMS-16-01)

Benthic Characterization of Deep-Water Habitat 

in the Newly Expanded Areas of Cordell Bank 

and Greater Farallones National

Marine Sanctuaries

U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Ocean Service

Office of National Marine Sanctuaries April 2016
About the Marine Sanctuaries Conservation Series

The Office of National Marine Sanctuaries, part of the National Oceanic and 

Atmospheric Administration, serves as the trustee for a system of 14 marine protected 

areas encompassing more than 170,000 square miles of ocean and Great Lakes waters. 

The 13 national marine sanctuaries and one marine national monument within the 

National Marine Sanctuary System represent areas of America’s ocean and Great Lakes 

environment that are of special national significance. Within their waters, giant 

humpback whales breed and calve their young, coral colonies flourish, and shipwrecks 

tell stories of our maritime history. Habitats include beautiful coral reefs, lush kelp 

forests, whale migrations corridors, spectacular deep-sea canyons, and underwater 

archaeological sites. These special places also provide homes to thousands of unique or 

endangered species and are important to America’s cultural heritage. Sites range in size 

from one square mile to almost 140,000 square miles and serve as natural classrooms, 

cherished recreational spots, and are home to valuable commercial industries.

Because of considerable differences in settings, resources, and threats, each marine 

sanctuary has a tailored management plan. Conservation, education, research, 

monitoring and enforcement programs vary accordingly. The integration of these 

programs is fundamental to marine protected area management. The Marine 

Sanctuaries Conservation Series reflects and supports this integration by providing a 

forum for publication and discussion of the complex issues currently facing the sanctuary 

system. Topics of published reports vary substantially and may include descriptions of 

educational programs, discussions on resource management issues, and results of 

scientific research and monitoring projects. The series facilitates integration of natural 

sciences, socioeconomic and cultural sciences, education, and policy development to 

accomplish the diverse needs of NOAA’s resource protection mandate. All publications 

are available on the Office of National Marine Sanctuaries Web site 

(http://www.sanctuaries.noaa.gov).
Benthic Characterization of Deep-Water Habitat in the Newly 

Expanded Areas of Cordell Bank and Greater Farallones 

National Marine Sanctuaries

K. Graiff1, D. Lipski1, P. Etnoyer2, G. Cochrane3, G. Williams4, and E. Salgado5

1 NOAA-NOS, Cordell Bank National Marine Sanctuary, Point Reyes Station, CA

2 NOAA-NOS, National Centers for Coastal Ocean Science, Charleston, SC

3 United States Geologic Survey, Santa Cruz, CA

4 California Academy of Sciences, San Francisco, CA

5 JHT, Inc., Orlando, FL

Silver Spring, Maryland

April 2016

U.S. Department of Commerce

Penny Pritzker, Secretary

National Oceanic and Atmospheric Administration

Kathryn Sullivan, Ph.D.

Under Secretary of Commerce for Oceans and Atmosphere

National Ocean Service

Russell Callender, Ph.D., Assistant Administrator

Office of National Marine Sanctuaries

John Armor, Acting Director
Disclaimer

Report content does not necessarily reflect the views and policies of the Office of 

National Marine Sanctuaries or the National Oceanic and Atmospheric Administration, 

nor does the mention of trade names or commercial products constitute endorsement or 

recommendation for use.

Report Availability

Electronic copies of this report may be downloaded from the Office of National Marine

Sanctuaries web site at http://sanctuaries.noaa.gov.

Cover

A sedimentary rock outcrop slope was a prominent feature at The Football and provided 

habitat for cup corals in the family Flabellidae, crinoids (Florometra serratissima), brittle 

stars and many other invertebrate and rockfish species (not shown in picture).

Suggested Citation

Graiff, K., D. Lipski, P. Etnoyer, G. Cochrane, G. Williams, E. Salgado. 2016. Benthic 

Characterization of Deep-Water Habitat in the Newly Expanded Areas of Cordell Bank

and Greater Farallones National Marine Sanctuaries. Marine Sanctuaries Conservation 

Series ONMS-16-01. U.S. Department of Commerce, National Oceanic and 

Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD. 

38 pp. 

Contact

Danielle Lipski, Research Coordintor

Cordell Bank National Marine Sanctuary

1 Bear Valley Rd.

Point Reyes Station, CA 94956

E-mail: danielle.lipski@noaa.gov

Phone: 415-464-5264
i

Abstract

A large area of the seafloor off northern California lies within the US National Marine 

Sanctuary System, but very little of the habitat has been explored and even less is 

characterized using visual survey techniques, especially deep-water habitats. Benthic 

surveys using a Phantom HD2 remotely operated vehicle (ROV) were conducted during

September 2-7, 2014 off the coast of Sonoma County, northern California at dive targets 

near Bodega Canyon and on a rocky feature informally named “The Football.” The 

targeted sites are within the northern areas recently added to Cordell Bank and Greater 

Farallones National Marine Sanctuaries. Information was collected to establish a baseline 

characterization of these areas that could inform researchers and the sanctuaries’

managers to better understand these deep-water ecosystems. The goals of the ROV 

surveys were to characterize deep-water benthic habitats, ground truth predicted habitat 

classifications, ground truth predictive habitat suitability models for coral and fish 

occurrence, and contribute to education and outreach about deep-water habitats. The 

sampling scheme was designed to characterize three classes of habitat predicted by 

multibeam sonar data: 1) hard-rugose (high-relief, hard bottom), 2) hard-flat (low-relief,

hard bottom), and 3) soft-flat (low relief, soft bottom). A total of 20 transects were 

conducted, 9 at the Bodega Canyon site and 11 at The Football site at depths ranging 

from 180 to 306 meters. Many species of fishes, corals and sponges were documented. At 

Bodega Canyon at least 30 taxa of fish, 6 coral taxa and 6 sponge taxa were observed. At 

The Football at least 34 taxa of fish, 5 coral taxa and 4 sponge taxa were observed. A 

large sedimentary rock outcrop slope with many ledges and overhangs providing an ideal

habitat for invertebrates and hundreds of rockfish were observed on The Football transect 

HC-30. A sea whip commonly seen while surveying The Football was collected and 

determined to be a new species Swiftia farallonesica. Other interesting observations 

included large aggregations of catshark and skate egg cases at The Football. Derelict 

fishing gear was observed at both sites.

Key Words

California continental shelf, deep-water benthic habitats, corals, sponges, rockfishes, 

National Marine Sanctuaries, remotely operated vehicle (ROV)
ii

Table of Contents

Topic Page

Abstract................................................................................................................................ i

Key Words........................................................................................................................... i

Table of Contents................................................................................................................ ii

List of Figures and Tables..................................................................................................iii

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

Methods............................................................................................................................... 4

Site Selection ................................................................................................................ 4

Field Survey.................................................................................................................. 6

Data Processing and Video Analysis............................................................................ 7

Results................................................................................................................................. 9

General Location and Dive Track – Bodega Canyon ................................................... 9

Transect Summary - Bodega Canyon ......................................................................... 10

Physical Habitat - Bodega Canyon ............................................................................. 11

Biological Environment – Bodega Canyon ................................................................ 12

Fishes .................................................................................................................... 12

Corals and Sponges............................................................................................... 14

Other Invertebrates................................................................................................ 16

Other Observations – Bodega Canyon........................................................................ 17

Fish-Invertebrate Associations.............................................................................. 17

Anthropogenic Items/Derelict Fishing Gear......................................................... 17

Collections............................................................................................................ 17

General Location and Dive Track –The Football ....................................................... 18

Transect Summary - The Football .............................................................................. 19

Physical Habitat – The Football.................................................................................. 20

Biological Environment – The Football ..................................................................... 21

Fishes .................................................................................................................... 21

Corals and Sponges............................................................................................... 23

Other Invertebrates................................................................................................ 25

Other Observations – The Football............................................................................. 26

Fish-Invertebrate Associations.............................................................................. 26

Anthropogenic Items/Derelict Fishing Gear......................................................... 26

Collections............................................................................................................ 27

Education and Outreach.................................................................................................... 29

Conclusions....................................................................................................................... 30

Acknowledgments............................................................................................................. 34

References......................................................................................................................... 35

Appendix A – Bodega Canyon Image Gallery ................................................................. 36

Appendix B – The Football Image Gallery....................................................................... 38
iii

List of Figures and Tables

Figure/Table Number and Title Page

Figure 1. Map showing the expansion of Greater Farallones and Cordell Bank National 

Marine Sanctuaries.............................................................................................................. 3

Figure 2. Locations of ROV dive targets near Bodega Canyon and The Football. ............ 5

Figure 3. Bodega Canyon ROV transect track lines overlaid on interpreted habitats. ....... 9

Figure 4. Percent habitat observed along quantitative segments from Bodega Canyon... 11

Figure 5. Percent composition of densities of fish groups from Bodega Canyon.. .......... 12

Figure 6. Percent composition of densities of coral and sponges from Bodega Canyon. .14

Figure 7. Total percent composition of other invertebrates from Bodega Canyon .......... 16

Figure 8. The Football ROV transect track lines overlaid on interpreted habitats........... 18

Figure 9. Percent habitat observed along quantitative segments from The Football........ 20

Figure 10. Percent composition of densities of fish groups from The Football.. ............. 21

Figure 11. Percent composition of densities of coral and sponges from The Football.... 23

Figure 12. Total percent composition of other invertebrates from The Football.............. 25

Table 1. Transects completed for Bodega Canyon area.. ................................................. 10

Table 2. Abundance of fish taxa observed on Bodega Canyon transects. ........................ 13

Table 3. Abundance of corals and sponges observed on Bodega Canyon transects......... 14

Table 4. Percent composition of coral and sponge counts documented on Bodega Canyon 

qualitative segments.......................................................................................................... 15

Table 5. Associations of fish and invertebrates from Bodega Canyon transects.............. 17

Table 6. Specimen collection from Bodega Canyon. ....................................................... 17

Table 7. Transects completed for The Football area......................................................... 19

Table 8. Abundance of fish taxa observed on The Football transects. ............................. 22

Table 9. Abundance of corals and sponges observed on The Football transects.............. 23

Table 10. Percent composition of coral and sponge counts documented on The Football 

qualitative segments.......................................................................................................... 24

Table 11. Specimen collections from The Football.......................................................... 27
1

Introduction

In 2014, the National Oceanic and Atmospheric Administration (NOAA) proposed to expand the 

northern and western boundaries of Cordell Bank and Gulf of the Farallones National Marine 

Sanctuaries off the northern California coast. The proposal followed years of grass roots support 

starting in 2001, with Congressional legislation, research, and public comment in the intervening 

years. Support for this proposal resulted in NOAA’s decision (announced in the Federal Register 

[FR]; 80 FR 13078) to expand Cordell Bank National Marine Sanctuary (CBNMS) and Greater 

Farallones National Marine Sanctuary1 (GFNMS), effective June 9, 2015 (Figure 1).

The waters of CBNMS and GFNMS are influenced by the Point Arena upwelling center, which 

contributes to the highly productive waters (Halle and Largier 2011) that sustain rich and 

abundant underwater biological communities including a diversity of fishes and invertebrates 

such as deep-sea corals and sponges (Roberts et al. 2004, Anderson et al. 2009, Etnoyer et al. 

2014). Deep-sea corals and sponges are long-lived, slow-growing animals with structurally 

complex morphologies that can provide biogenic habitat for commercially important fishes and 

other invertebrates (Krieger and Wing 2002, Costello et al. 2005). Previous seafloor 

characterizations on the continental shelf and slope within the original boundaries of CBNMS 

and GFNMS have documented numerous species of deep-sea corals, sponges and fishes (Graiff 

et al. 2011, Etnoyer et al. 2014). ROV surveys over unconsolidated sand bottom in GFNMS 

documented the sea pen Halipteris californica as the dominant epifauna macroinvertebrate (de 

Marignac et al. 2008). However, there has been limited seafloor exploration and characterization 

within the newly established northern boundaries of CBNMS and GFNMS. Benthic surveys 

were needed to characterize the habitat and species in this area to inform management of the

resources in the expanded areas of the sanctuaries. 

During September 2-7, 2014, scientists from CBNMS, GFNMS, the National Centers for Coastal 

Ocean Science (NCCOS), the US Geological Survey (USGS) and the California Academy of 

Sciences (CAS) teamed up to characterize the seafloor habitats, fishes and invertebrates (with 

special focus on deep-sea corals and sponges), using a remotely operated vehicle (ROV) near 

Bodega Canyon and a rocky feature to the north informally named “The Football” (and referred 

to as such hereafter in this report) within CBNMS and GFNMS, respectively. The surveys were 

made possible, in part, by mapping activities conducted by NOAA Ship Okeanos Explorer in 

2009 which provided bathymetry and hardness of the underlying seafloor.

Bodega Canyon is a prominent submarine feature within CBNMS that cuts across the continental 

shelf and slope about 16 km north of Cordell Bank. The Canyon is about 20 km long and is over 

1,600 m deep. Submarine canyons provide areas of high bathymetric complexity, support deepwater communities, and affect local and regional circulation patterns. Physical and biological 

processes associated with Bodega Canyon make this a dynamic oceanographic area. Previous 

surveys in Bodega Canyon using an Autonomous Underwater Vehicle (AUV) revealed muddraped hard substrate on the canyon edges, deep-sea corals and sponges associated with the hard 

substrate and numerous fishes (Fruh et al. 2011). These AUV surveys within and near Bodega 

 1

NOAA changed the name from Gulf of the Farallones National Marine Sanctuary to Greater Farallones National 

Marine Sanctuary to reflect the new jurisdiction on June 15, 2015 (80 FR 34047).
2

Canyon included just a small area of this vast and complex underwater feature, making this 

region a priority for further characterization.

Underwater rocky features provide habitat for corals, sponges and fishes. Rocky banks in 

CBNMS and GFNMS include Cordell Bank, the focal point of CBNMS, and Rittenburg Bank 

and Cochrane Bank within GFNMS. The Football is a rocky feature, approximately 180 to 250 

meters deep, in northern GFNMS located on the continental shelf north of Bodega Canyon and 

approximately 33 km west of the Russian River. The Football was briefly explored with a ROV 

in 2010 (Stierhoff et al. 2011). The survey confirmed hard bottom habitat was present, and 

identified a moderate-relief (~1 m) sedimentary rock outcrop slope with many ledges, providing 

habitat for rockfish and cup corals. The extent of the feature was undetermined at the time, but 

multibeam bathymetry suggested the feature was semi-continuous. Scattered boulders and 

cobbles were also observed, supporting numerous rockfish species and invertebrates, however no 

habitat forming deep-sea corals were observed and only a few small sponges were documented 

(Stierhoff et al. 2011). Although The Football may not be as structurally complex as the banks to 

the south, The Football’s rocky habitats can be considered important as the area is large, but the 

habitat is relatively uncommon. The rocky area is mostly surrounded by expanses of low relief, 

soft sediments (as predicted from multibeam sonar data). Therefore, it was deemed important to 

continue and expand upon the characterization of The Football, particularly for deep-sea corals 

and sponges.

The goals and priorities of benthic characterization aboard the R/V Fulmar in 2014 were: (1) to 

use the sanctuary-owned Phantom HD2 ROV to characterize deep-water benthic habitats within 

the northern areas of Cordell Bank and Greater Farallones National Marine Sanctuaries, 

including fishes, corals, sponges, and physical habitat; (2) to contribute to outreach, education, 

and public awareness of deep-water habitats; (3) to ground truth interpreted habitat classification 

from multibeam sonar data; and (4) to ground truth habitat suitability models for corals and 

fishes. 
3

Figure 1. Expanded boundaries of Greater Farallones National Marine Sanctuary from 

approximately 1,282 sq. mi. to approximately 3,295 sq. mi., and Cordell Bank National Marine 

Sanctuary from approximately 529 sq. mi. to approximately 1,286 sq. mi. The northern area of 

Monterey Bay National Marine Sanctuary is shown in blue for reference but the boundaries of 

MBNMS were not expanded. 
4

Methods

Site Selection

Two areas were selected for exploration, one within each sanctuary, based on the availability of 

multibeam data to interpret geology and the ability of the ROV to access these sites. The depth 

limit of the ROV was 310 meters. ROV dive sites at Bodega Canyon were selected on a 

projecting plateau to the south of the head of the canyon. This area was selected because it is in 

close proximately to the canyon which is oceanographically and geologically influential to 

CBNMS. The Football was selected for dive targets because a previous ROV dive revealed some 

relief and hard substrate (Stierhoff et al. 2011) (Figure 2). 

Additionally, since one goal of the ROV surveys was to ground truth predictive fish and coral 

species models, some ROV transects were conducted in locations where the models predicted

rockfish and coral species to occur. Some of these transects were completed during the vessel 

transit to Bodega Canyon and The Football. These transects are denoted by the “MV” in their 

identifier.
5

Figure 2. Locations of ROV dive targets near Bodega Canyon and The Football on the continental shelf 

within Cordell Bank National Marine Sanctuary (CBNMS) and Greater Farallones National Marine 

Sanctuary (GFNMS), northern California.
6

Field Survey

ROV dive sites were planned near Bodega Canyon and at The Football to ground truth multiple 

habitat types as predicted by multibeam sonar data collected in 2009 on the NOAA Ship

Okeanos Explorer to produce a seafloor habitat characterization map. The sampling scheme 

targeted at least two transects in each of the three interpreted habitat categories: 1) hard-rugose 

(high-relief, hard bottom), 2) hard-flat (low-relief, hard bottom), and 3) soft-flat (low relief, soft 

bottom), at each of the two sites. In addition, transects were planned in areas to test habitat 

suitability models for corals and fishes. Planned transects were 500 to 750 meters in length and 

no deeper than 310 meters (maximum depth rating of the ROV). 

Operations were conducted September 2-7, 2014 onboard the R/V Fulmar using the CBNMS 

Phantom HD2 ROV. The ROV was outfitted with three cameras to collect photographic and 

video images. A standard definition video camera (Deep Ocean Engineering) on a motorized tilt 

was mounted on the front center of the ROV to be forward-looking. During surveys the video 

camera angle was maintained at approximately 60 degrees from vertical. Standard definition 

(SD) video was continuously recorded to mini digital video (MiniDV) tapes. A pair of parallel 

lasers were used for scale, set 10 cm apart and positioned in the center of the video frame for 

sizing objects viewed in images. A high-definition still camera (Insite Pacific Scorpio Plus) on 

loan from the Undersea Vehicles Program at University of North Carolina at Wilmington was 

mounted on the top lateral bar of the ROV frame at an angle of approximately 60 degrees. Still 

images were manually captured approximately every 30 seconds using Insite Pacific custom user 

interface software on a topside laptop and stored on the camera’s storage card until they were 

downloaded to a hard drive after the ROV was recovered. A strobe light (Insite Pacific) 

illuminated the camera field of view when the still camera was triggered and three other lights 

(Deep Sea Power and Light) provided lighting for the video cameras. In addition, a GoPro Hero 

3 camera in a custom submersible housing was mounted facing forward on the lower front lateral 

bar of the ROV frame to capture wide angle high-definition video imagery for education and 

outreach.

Specimens of corals and other organisms of interest were collected as they were encountered 

using the ROV’s manipulator arm with a two-fingered pincher. Samples were preserved dry and 

in 95% ethanol, labeled, and bagged in plastic. The ROV was not equipped with storage 

compartments so specimens were held in the manipulator arm until the ROV surfaced and 

recovered on the ship deck. Only one collection was made per dive. 

The ROV dives each consisted of a series of pre-determined transects over a geological 

classification scheme with a series of transits to approach the start point(s) and maneuver 

between transects. While on transect, the ROV maintained a consistent height and speed from the 

bottom; about 1 meter off the bottom and at a speed of 0.5 to 1 knots. During the dive, the ROV 

position was tracked using an ORE Trackpoint II acoustic tracking system which provided 

bearing and range from the R/V Fulmar to the ROV. Trackpoint positions were integrated with 

the ship’s GPS and relative to the planned transect lines using Hypack software (Hypack, Inc., 

Connecticut, USA).
7

Data Processing and Video Analysis

ROV and ship tracking data were recorded at one second intervals. The locations were smoothed 

with a filter over a 20 point sampling window. Positions with a distance greater than 0.1 degrees 

from the previous position were removed.

MiniDV tapes from the forward facing SD video camera were converted to digital MPG files 

using a Diamond Multimedia VC500 Video Capture Device and these files were used for 

analysis. Survey distance and duration varied among transects so the MPG files were reviewed to 

subsample 15-minute segments that met specific criteria: the seafloor was in focus with clear 

visibility and the ROV moved at a consistent height and speed over bottom. These 15-minute 

segments were used for species identification and counts, which were later converted into 

quantitative densities of fishes and invertebrates based on the area of the transect. 

To estimate transect area, the length of the 15-minute segments was measured by summing the 

distance between successive UTM points in the segment. The width of the field of view of the 

video camera was estimated by measuring the distance between the laser points as they were 

observed on the video monitor and applying the ratio of the known laser distance (10 cm) with 

that measured on the video screen to calculate the width of the field of view. Since this value 

changed as the altitude of the ROV changed the width estimates were made every 30 seconds or 

when there was a large (> 1 m) change in ROV altitude and these estimates were applied to the 

entire 30 seconds of the segment. The total area of each 15-minute segment was the product of 

the total width measurements and total segment length. 

Subject matter experts separately reviewed videos for substrate, fishes, and invertebrates and 

each data set was imported into a Microsoft Access relational database. ROV transects ranged in 

duration from 17 minutes to more than an hour. Data were analyzed for substrate, invertebrates, 

species associations of fishes with corals or sponges, and marine debris. Fishes were identified 

within the 15-minute subsampled segments only because of the significant processing time 

required to review video to identify fishes. Densities of corals, sponges and fishes were 

estimated for the area of the 15-minute quantitative segments. Relative percent composition of 

corals and sponges and other invertebrates from the remainder of each transect (referred to as 

qualitative transects in this report) was also calculated. 

A fish was considered “associated” with a coral or sponge if it was located less than one body 

length away or in direct contact with a coral or sponge (Krieger and Wing 2002, Tissot et al. 

2006). The type of association, the taxa with which the fish was associated, and the coordinates 

were recorded. Fishes were identified to the lowest taxonomic level, enumerated, sized using the 

paired lasers, and georeferenced. Elasmobranch egg cases were also enumerated when image 

resolution was satisfactory. Egg cases and egg bundles were identified as Scyliorhinidae 

(catshark) or Rajiformidae (skate), based on their morphology. Individual skate egg cases could 

be counted because they were large and discernible, but many of the catshark egg cases occurred 

in large aggregations or bundles. Counts of catshark egg cases in bundles were estimated from in 

situ images based on laboratory counts of shark eggs from a single bundle collected by the ROV. 
8

Counts in images were estimates based on number of egg cases per unit volume from the 

collected shark egg bundle.

Macro invertebrates in the following categories were identified to the lowest taxonomic level, 

enumerated, and georeferenced: corals and sponges > 10 cm, Flabellidae cup-corals (usually < 

10 cm), anemones larger than 10 cm, sea pens (Halipteris spp.), sea stars, urchins, and spot 

prawns (Pandalus platyceros). Some invertebrates were recorded as presence only. These 

included: small sea pens (possibly Stylatula sp. or Virgularia sp.), octopus, crabs, brittle stars, 

and crinoids. Corals and sponges were measured within categories as follows: 10-20 cm 

(Category 1); 21-50 cm (Category 2); and larger than 50 cm (Category 3). Specimen collections 

were identified and cataloged at the California Academy of Sciences (CAS), San Francisco; one 

elasmobranch sample, a juvenile catshark in an egg case bundle, was cataloged at College of 

Charleston for mitochondrial DNA analysis by Dr. Gavin Naylor. 

Three classes of substratum types: 1) hard-rugose (high-relief, hard bottom), 2) hard-flat (lowrelief, hard bottom), and 3) soft-flat (low relief, soft bottom) were used to quantify distinct 

changes in substratum types greater than or equal to 30 seconds in duration along the transect, 

thus establishing “habitat patches” of uniform substrate type. Marine debris was also identified 

and georeferenced. 

The high-definition video collected by the GoPro camera was originally collected to be used for 

education and outreach. However, GoPro video and the high-definition still images were found 

to be useful in species detection and identification and were referenced alongside the lower 

quality SD video. The GoPro was battery powered and recorded in situ to a SD card so there 

were some instances when the GoPro would stop recording (battery died or SD card filled) 

before the end of the dive. Therefore, GoPro video does not exist for all transects or some 

portions of transects resulting in lower species detection and identification for those transects 

without GoPro video. All the GoPro video was made available to education staff at GFNMS and 

CBNMS to be used in education and outreach products. 
9

Results

General Location and Dive Track – Bodega Canyon

Figure 3. Bodega Canyon ROV transect track lines overlaid on interpreted habitat types predicted 

from multibeam data. 
10

Transect Summary - Bodega Canyon

Total transects: 9 Depth range (m): 273 to 306

Table 1. Transects completed for Bodega Canyon area. Predicted habitat type refers to the substrate type that was anticipated from the interpreted 

habitat model displayed in Figure 3 and model type refers to the predictive species model that the survey was ground truthing. 

Date Dive Transect Transect 

duration

Area of

15-minute 

Segment (m2)

Predicted 

Habitat or 

Model Type

Observed 

Habitat

Depth 

min (m)

Depth 

max (m)

Start 

Lat/Long

End 

Lat/Long

9/2/2014 1 HC-5 0:41:00 1,081 Hard-flat Hard-flat 273 283 38.1915

-123.4689

38.1878

-123.4687

9/3/2014 2 HC-12 0:32:50 950 Hard-rugose

Hard-rugose

Hard-flat 281 292 38.1894-123.4799

38.1876

-123.4799

9/3/2014 2 MV-BC-1 0:33:00 n/a Holaxonia 

model Hard-flat 282 292 38.1859-123.4813

38.1863

-123.4794

9/3/2014 2 HC-10 0:42:00 891 Soft-flat Soft-flat

Hard-flat 282 285 38.1862-123.4792

38.1834

-123.4761

9/3/2014 2 HC-6 0:32:50 641 Soft-flat Soft-flat

Hard-flat 277 280 38.1845-123.4728

38.1830

-123.4703

9/4/2014 3 HC-28 0:22:10 884 Hard-rugose Hard-flat 301 306 38.1947

-123.4579

38.1933

-123.4570

9/4/2014 3 MV-BC-3 0:17:15 736

Sablefish and

Thornyheads

models

Hard-flat 287 291 38.1929

-123.4587

38.1918

-123.4599

9/4/2014 3 HC-3 0:29:15 714 Hard-flat Hard-flat 283 289 38.1915

-123.4602

38.1881

-123.4581

9/4/2014 3 HC-1 0:41:00 914 Hard-rugose

Hard-rugose

Hard-flat 274 278 38.1885-123.4622

38.1847

-123.4601
11

Physical Habitat - Bodega Canyon

A total area of 6,811 m2 of seafloor was surveyed during the eight 15-minute quantitative 

segments conducted in the Bodega Canyon area. Area for transect MV-BC-1 could not be 

calculated because the ROV’s lasers were turned off and transect width could not be estimated. 

Habitat types were classified as (1) soft-flat (3% of the total area surveyed) comprised of sand 

and mud sediments were observed in small patches; (2) hard-flat (93% of the total area surveyed) 

comprised of sand mixed with cobbles, boulders or rocks, or a mix of cobbles, boulders and 

rocks; and (3) hard-rugose (4% of total area surveyed) rocky bottom was limited (Figure 4).

Figure 4. Percent of total habitat (soft-flat, hard-flat, hard-rugose) area observed along 

quantitative segments in the Bodega Canyon area
12

Biological Environment – Bodega Canyon

Fishes

A total of 589 fishes from at least 30 

different taxa were enumerated from the 

eight 15-minute quantitative segments 

conducted in the Bodega Canyon region 

(Table 2). A total density of 79 fish per 

1,000 m2 of seafloor was estimated. No 

density estimates were available from 

transect MV-BC-1 because the ROV’s 

lasers were turned off and transect area 

could not be calculated. 

Rockfishes (at least 12 Sebastes species 

and at least 1 Sebastolobus

species) comprised almost half (49%) of 

total fish density. Flatfishes (at least 5 

species) accounted for 27% of the total 

density and many individuals could not 

be identified to the species level due to 

them being mostly covered in soft 

sediment. Poachers accounted for 9% of 

total density. The remainder of the fish 

assemblage included eelpouts (4%), other taxa (3%), sculpins (3%), Pacific hagfish (3%), and 

lingcod (2%) (Figure 5). 

A small bundle of catshark egg cases was observed attached to a fishing net along transect HC-3. 

The total estimate was 13 catshark eggs. No catsharks were observed. Transect MV-BC-3 was 

designed to test a predictive model for sablefish (Anoplopoma fimbria) and thornyheads 

(Sebastolobus spp.). A total of 16 thornyheads were observed, but no sablefish.

Figure 5. Percent composition of densities of fish groups 

from Bodega Canyon. Colors in pie diagram match colors in 

list of fish taxa (Table 2).
13

Table 2. Abundance of fish taxa observed on Bodega Canyon transects. Colors in table match colors in pie 

diagram (Figure 5). 

Scientific Name Common Name Number

Fishes

Sebastes aurora Aurora rockfish 1

Sebastes babcocki Redbanded rockfish 1

Sebastes crameri Darkblotched rockfish 6

Sebastes diploproa Splitnose rockfish 5

Sebastes elongatus Greenstriped rockfish 2

Sebastes goodei Chilipepper rockfish 86

Sebastes helvomaculatus Rosethorn rockfish 31

Sebastes pinniger Canary rockfish 1

Sebastes rufus Bank rockfish 11

Sebastes saxicola Stripetail rockfish 9

Sebastes zacentrus Sharpchin rockfish 1

Sebastes spp. Unidentified rockfishes 42

Sebastolobus spp. Unidentified thornyheads 66

Sebastomus subgenus Unidentified rockfishes 25

Eopsetta jordani Petrale sole 6

Glytocephalus zachirus Rex sole 12

Lyopsetta exilis Slender sole 9

Microstomus pacificus Dover sole 43

Pleuronectiformes Unidentified flatfishes 86

Agonidae Unidentified poachers 56

Lycodes diapterus Black eelpout 1

Lyconema barbatum Bearded eelpout 20

Zoarcidae Unidentified eelpouts 1

Hydrolagus colliei Spotted ratfish 6

Merluccius productus Pacific hake 8

Raja rhina Longnose skate 4

Paricelinus hopliticus Thornback sculpin 4

Cottidae Unidentified sculpins 14

Eptatretus stoutii Pacific hagfish 18

Ophiodon elongatus Lingcod 14
14

Corals and Sponges

Findings from Quantitative 15-Minute Segments:

A total of 25 individual corals from 4 

taxa and 12 individual sponges from at 

least 5 taxa were enumerated from the 

eight 15-minute quantitative segments 

conducted in the Bodega Canyon region 

(Table 3). A total density of 5 corals and 

sponges per 1,000 m2 of seafloor was 

estimated. No density estimates were 

available from transect MV-BC-1 

because the ROV’s lasers were turned 

off and transect area could not be 

calculated. 

The mushroom coral (Heteropolypus 

ritteri) comprised 35% of the total 

density and sea pens accounted for 33% 

of the total density. Small sea pens 

(possibly Stylatula sp. or Virgularia

sp.) were not enumerated but were 

present on 3 of the 10 transects. Also 

noteworthy is the one primnoid octocoral, Plumarella sp., observed on transect MV-BC-1 but 

not included in density estimates as previously stated. Sponges accounted for 32% of total 

density of sessile benthic invertebrates (Figure 6). The structure forming barrel/boot sponges, 

Staurocalyptus sp. were most conspicuous, and ranged in size from 10 – 20 cm tall. 

Transect MV-BC-1 was designed to test a predictive model for Holaxonia gorgonian corals, 

however no corals in this suborder were observed on transect.

Table 3. Abundance of corals and sponges observed on Bodega Canyon transects. Colors in table match 

colors in pie diagram (Figure 6). 

Scientific Name Common Name Number

Corals and Sponges

Heteropolypus ritteri Mushroom coral 13

Halipteris californica Sea pen 8

Pennatulacea Sea pen 2

Ptilosarcus gurneyi Orange sea pen 2

Dysidea sp. Gray sponge 1

Euplectella sp. Glass sponge 2

Iophon sp. White sponge 1

Polymastia sp. Aggregated sponge 1

Staurocalyptus sp. Barrel/boot sponge 7

Figure 6. Percent composition of densities of corals and sponges 

from Bodega Canyon. Colors in pie diagram match colors in 

list of coral and sponge taxa (Table 3).
15

Findings from qualitative segments:

A total of 41 individual sponges from at least 6 taxa and 66 individual corals from 3 taxa were 

enumerated from the remaining Bodega Canyon transects that were not part of the 15-minute 

quantitative segments (Table 4a). Sponges accounted for 38% of species composition of sessile 

benthic invertebrates. Observations of mushroom corals (Heteropolypus ritteri) comprised 36% 

of the total species composition. Sea pens comprised 26% of species composition (Table 4b). 

Small sea pens (possibly Stylatula sp. or Virgularia sp.) were not enumerated but were present 

on 1 of the 10 transects. 

Table 4. (a) Abundance of corals and sponges documented on Bodega Canyon qualitative segments. (b) 

Percent composition of coral and sponge counts. Colors of corals and sponges in table (a) match colors in 

table (b).

a. Scientific Name Common Name Number

Corals and Sponges

Dysidea sp. Gray sponge 1

Euplectella sp. Glass sponge 5

Iophon sp. White sponge 2

Mycale sp. Yellow vase sponge 1

Porifera Unidentified sponges 7

Staurocalyptus sp. Barrel/boot sponge 25

Heteropolypus ritteri Mushroom coral 38

Halipteris californica Sea pen 23

Pennatulacea Sea pen 5

b. Corals and Sponges % Composition

Sponges 38

Mushroom coral 36

Sea pens 26
16

Other Invertebrates

A total of 2,324 other invertebrates such as sea stars (Ceramaster patagonicus, Rathbunaster 

californicus, other Asteroidea); sea urchins (Strongylocentrotus fragilis); spot prawns (Pandalus 

platyceros); and anemones (Corallimorphus pilatus, other Actiniaria) were counted along 

Bodega Canyon transects and total percent composition is displayed in Figure 7. Corallimorphus 

pilatus accounted for over half of the total percent composition of these taxa. 

Other invertebrates present in the Bodega Canyon area included unidentified octopus species, 

brachyurian crabs, brittle stars and crinoids (Florometra serratissima). Crinoids were commonly 

observed, and recorded as present on 9 of the 10 transects.

 

Figure 7. Total percent composition of other invertebrates from Bodega Canyon transects.
17

Other Observations – Bodega Canyon 

Fish-Invertebrate Associations

There were 11 fishes associated with a coral or sponge in the Bodega Canyon region. Three fish 

were documented in direct contact with three individual sponges. Eight fishes were documented 

within one body length of the coral or sponge (Table 5).

Table 5. Associations of fish and invertebrates from Bodega Canyon transects. *Association code: 1 = fish in 

contact with coral or sponge; 2 = fish within 1 body length of coral or sponge.

Transect Fish

Fish 

Count

Association 

Code* Invertebrate Latitude Longitude

MV-BC-1 Agonidae 1 1 Iophon sp. 38.1864 -123.4801

MV-BC-1 Ophiodon 

elongatus 1 2 Heteropolypus ritteri 38.1855 -123.4811

MV-BC-1 Lyconema 

barbatum 1 2 Heteropolypus ritteri 38.1863 -123.4797

MV-BC-1 Sebastes 

helvomaculatus 1 1 Staurocalyptus sp. 38.1863 -123.4797

HC-6 Sebastes goodei 1 2 Ptilosarcus gurneyi 38.1832 -123.4710

HC-5 Ophiodon 

elongatus 1 1 Staurocalyptus sp. 38.1889 -123.4682

HC-12 Hydrolagus 

colliei 1 2 Heteropolypus ritteri 38.1885 -123.4802

HC-10 Unknown 

flatfish 1 2 Heteropolypus ritteri 38.1842 -123.4770

HC-1 Sebastes rufus 3 2 Staurocalyptus sp. 38.1849 -123.4600

Anthropogenic Items/Derelict Fishing Gear

There were three observations of anthropogenic materials from the Bodega Canyon region, 

including: one trawl net; one large metal cylinder with a hole in middle about 100 cm long with 

crinoids (Florometra serratissima) and other inverts and an associated darkblotched rockfish

(Sebastes crameri); and one small pile of rope covered in sediment.

Collections

Table 6. Specimen collection from Bodega Canyon.

Specimen 

No. Species Date Coordinates Transect Depth CAS Cat. No.

S1 Halipteris californica 

(Sea Pen) 3-Sep-14 38.1818-123.4707 HC6 282 m 196928
18

General Location and Dive Track –The Football

Figure 8. The Football ROV transect track lines overlaid on interpreted habitat types predicted from 

multibeam data. Quality of the multibeam data was compromised by rough sea conditions during the 

survey, therefore causing the striped appearance classified as hard-flat habitat. These habitats are 

more likely to be soft-flat based on the classification of the surrounding habitats.
19

Transect Summary - The Football

Total transects: 11 Depth range (m): 180 to 279

Table 7. Transects completed for The Football area. Predicted habitat type refers to the substrate type that was anticipated from the 

interpreted habitat model displayed on Figure 8 and model type refers to the predictive species model that the survey was ground truthing. 

Date Dive Transect Transect 

duration

Area of

15-minute 

Segment (m2)

Predicted Habitat

or Model Type

Observed 

Habitat

Depth 

min (m)

Depth 

max (m)

Start 

Lat/Long

End 

Lat/Long

9/5/2014 5 MV-FB-7 0:22:40 702 Darkblotch model Soft-flat 268 279 38.4552

-123.6151

38.4589

-123.6150

9/5/2014 5 HC-15 0:35:40 598 Soft-flat Soft-flat 262 269 38.4592

-123.6150

38.4642

-123.6170

9/5/2014 5 HC-19 0:51:00 305 Hard-flat Hard-flat

Soft-flat 235 251 38.4643-123.6132

38.4617

-123.6074

9/5/2014 6 HC-14 1:06:50 397 Hard-rugose

Hard-rugose

Hard-flat

Soft-flat

223 240 38.4601

-123.6070

38.4583

-123.6028

9/6/2014 7 HC-16 0:57:00 630 Hard-rugose

Hard-rugose

Hard-flat 181 189 38.4266-123.5558

38.4301

-123.5589

9/6/2014 7 HC-17 0:35:45 627 Hard-flat Hard-flat

Soft-flat 185 186 38.4327-123.5599

38.4374

-123.5619

9/6/2014 7 HC-21 0:35:42 893 Hard-rugose

Hard-rugose

Hard-flat 180 184 38.4359-123.5648

38.4388

-123.5698

9/6/2014 8 HC-30 0:33:30 388 Hard-flat Hard-flat

Hard-rugose

191 192 38.4482

-123.5836

38.4461

-123.5822

9/6/2014 8 MV-FB-6 0:25:00 523 Canary model Hard-flat

Hard-rugose

184 188 38.4408

-123.5799

38.4429

-123.5762

9/7/2014 9 MV-FB-2 0:40:40 283 Chilipepper model Soft-flat

Hard-flat 243 274 38.4283-123.5989

38.4297

-123.5930

9/7/2014 9 HC-20 0:47:20 286 Soft-flat

Soft-flat

Hard-flat

Hard-rugose

234 245 38.4298

-123.5931

38.4275

-123.5901
20

Physical Habitat – The Football

A total area of 5,632 m2 of seafloor was surveyed during the eleven 15-minute quantitative 

segments conducted in The Football area. Habitat types were classified as (1) soft-flat (40% of 

the total area surveyed) comprised completely of sand or sand with a few boulders primarily on 

transects to the west of The Football feature; (2) hard-flat (25% of the total area surveyed) 

comprised of sand mixed with cobbles, boulders or rocks, or a mix of cobbles, boulders and 

rocks; and (3) hard-rugose (35% of the total area surveyed) primarily composed of a mix of 

larger rocky substrata like boulders, rock, cobbles. A large sedimentary rock outcrop slope that 

was eroded, forming many rock ledges and overhangs, on transect HC-30 was originally 

predicted to be hard-flat habitat, was later included in hard-rugose category (Figure 9).

Figure 9. Percent of total habitat (soft-flat, hard-flat, hard-rugose) area observed along 

quantitative segments at The Football.
21

Figure 10. Percent composition of densities of fish 

groups from The Football. Colors in pie diagram match 

colors in list of fish taxa (Table 8).

Biological Environment – The Football

Fishes

A total of 2,038 fishes from at least 34 

different taxa were enumerated from the 

eleven 15-minute quantitative segments 

conducted on The Football (Table 8). A total 

density of 362 fish per 1,000 m2 of seafloor

was estimated. 

Rockfishes (at least 16 Sebastes species and 

at least 1 Sebastolobus species) comprised

83% of total fish density. Flatfishes (from at 

least 6 species) accounted for 9% of total 

density and many individuals could not be 

identified to the species level because they 

were mostly covered in soft sediment. The 

remainder of the fish assemblage included 

lingcod (5%), other taxa (2%) and poachers 

(1%) (Figure 10).

Transects MV-FB-7 and MV-FB-2 were 

designed to test predictive models for 

darkblotched rockfish (Sebastes crameri) 

and chilipepper rockfish (Sebastes goodei)

respectively, however neither of these species were observed on transect. Transect MV-FB-6 was 

designed to test a predictive model for canary rockfish (Sebastes pinniger); two individuals were 

observed on transect. 

A total of 986 catshark and skate egg cases were observed during surveys at The Football. A 

total of 254 skate egg cases were observed on transects HC-14 and HC-19. A large number of 

catshark egg cases were observed in beehive-shaped bundles attached to rocks on transects HC14, HC-19 and HC-20. The total estimate was 732 catshark egg cases in a total of 11 bundles at 

The Football. Laboratory examination of one bundle revealed 164 egg cases of which 35% 

contained yolk sacs and 65% were empty (presumably hatched or predated). Egg cases with yolk 

sacs were exterior, empty egg cases were interior. One juvenile hatched on deck. Tissue samples 

revealed mDNA sequences suggesting the species to be Apristurus brunneus (brown 

catshark). This species of Scyliorhinid shark is common from Baja to southeastern Alaska 

(Flammang et at. 2008). No adult cat sharks were observed during quantitative transects.
22

Table 8. Abundance of fish taxa observed on The Football transects. Colors in table match colors in pie 

diagram (Figure 10).

Scientific Name Common Name Number

Fishes

Sebastes chlorostictus Greenspotted rockfish 79

Sebastes elongatus Greenstriped rockfish 35

Sebastes entomelas Widow rockfish 684

Sebastes goodei Chilipepper rockfish 2

Sebastes helvomaculatus Rosethorn rockfish 93

Sebastes hopkinsi Squarespot rockfish 8

Sebastes jordani Shortbelly rockfish 2

Sebastes levis Cowcod 3

Sebastes paucispinis Bocaccio 1

Sebastes pinniger Canary rockfish 3

Sebastes ruberrimus Yelloweye rockfish 15

Sebastes rufus Bank rockfish 7

Sebastes saxicola Stripetail rockfish 100

Sebastes wilsoni Pygmy rockfish 64

Sebastes zacentrus Sharpchin rockfish 93

Sebastes spp. Unidentified juvenile rockfish 90

Sebastes spp. Unidentified rockfishes 375

Sebastolobus spp. Unidentified thornyheads 2

Sebastomus subgenus Unidentified rockfishes 28

Atheresthes stomias Arrowtooth flounder 1

Glyptocephalus zachirus Rex sole 10

Lyopsetta exilis Slender sole 9

Microstomus pacificus Dover sole 32

Parophrys vetulus English sole 6

Pleuronectiformes Unidentified flatfishes 131

Ophiodon elongatus Lingcod 101

Eptatretus stoutii Pacific hagfish 3

Hydrolagus colliei Spotted ratfish 11

Lyconema barbatum Bearded eelpout 7

Raja rhina Longnose skate 5

Raja sp. Unidentified skate 7

Ophidiidae Unidentified cuskeel 1

Cottidae Unidentified sculpins 8

Agonidae Unidentified poachers 22
23

Figure 11. Percent composition of densities of coral and 

sponges from The Football. Colors in pie diagram 

match colors in list of coral and sponge taxa (Table 9).

Corals and Sponges

Findings from Quantitative 15-minute Segments:

A total of 22 individual corals from 4 taxa 

and 10 individual sponges from at least 4 

taxa were enumerated from the eleven 15-

minute quantitative segments conducted on 

The Football (Table 9). A density of 6 corals 

and sponges per 1,000 m2 of seafloor was 

estimated. Flabellidae cup-corals accounted 

for 31% of overall density. All were 

observed on a single transect (HC-30) on the 

ledges and overhangs of the sedimentary 

rock outcrop slope. Sponges comprised 31% 

of total density. A new species of gorgonian 

sea whip, Swiftia farallonesica, was observed 

and comprised a quarter of the total density 

of corals and sponges. Swiftia farallonesica

was observed on transects HC-16 and HC-21. 

Sea pens accounted for 13% of overall 

density (Figure 11). Small sea pens 

(possibly Stylatula sp. or Virgularia sp.)

were not enumerated but were present on 

1 of the 11 transects.

Table 9. Abundance of corals and sponges observed on The Football transects.

Colors in table match colors in pie diagram (Figure 11). 

Scientific Name Common Name Number

Corals and Sponges

Flabellidae Cup-coral 10

Swiftia farallonesica * Gorgonian sea whip 8

Pennatulacea Sea pen 2

Ptilosarcus gurneyi Orange sea pen 2

Dysidea sp. Gray sponge 3

Poecillastra sp. Shelf sponge 4

Porifera Unidentified sponges 2

Staurocalyptus sp. Barrel/boot sponge 1

* new species
24

Findings from qualitative segments:

A total of 57 individual corals from 3 taxa and 32 individual sponges from at least 4 taxa were 

enumerated from transects that were not considered the 15-minute quantitative segments (Table 

10a). The new species of gorgonian sea whip (Swiftia farallonesica) accounted for nearly half of 

the coral and sponge observations (48% of total species composition). Thirty-seven S.

farallonesica individuals ranged in size from 10-20 cm and 6 individuals ranged in size from 21-

50 cm. Sponges comprised 36% of species composition of the sessile structure forming fauna. 

The structure forming barrel/boot sponges, Staurocalyptus sp., ranged in size from 21-50 cm tall. 

The pennatulacean sea pen, Halipteris californica, made up 9% of coral and sponge species 

composition. Small sea pens (possibly Stylatula sp. or Virgularia sp.) were not enumerated but 

were present on 1 of the 11 transects. Flabellidae cup corals accounted for 7% of total species 

composition and were all observed on one transect (HC-30) at the sedimentary rock outcrop 

slope with many ledges and overhangs (Table 10b).

Table 10. (a) Abundance of corals and sponges documented on The Football qualitative segments. (b) Percent 

composition of coral and sponge counts. Colors of corals and sponges in table (a) match colors in table (b).

a. Scientific Name Common Name Number

Corals and Sponges

Swiftia farallonesica * Gorgonian sea whip 43

Dysidea sp. Gray sponge 7

Poecillastra sp. Shelf sponge 11

Porifera Unidentified sponges 9

Staurocalyptus sp. Barrel/boot sponge 5

Halipteris californica Sea pen 8

Flabellum sp. Cup-coral 6

* new species

b. Corals and Sponges % Composition

Gorgonians 48

Sponges 36

Sea pens 9

Cup-corals 7
25

Other Invertebrates

A total of 4,077 other invertebrates such as sea stars (Ceramaster patagonicus, Rathbunaster 

californicus, other Asteroidea); sea urchins (Strongylocentrotus fragilis); spot prawns (Pandalus 

platyceros); and anemones (Corallimorphus pilatus, Metridium farcimen, and other Actiniaria) 

were counted along The Football transects and total percent composition is displayed in Figure 

12. Strongylocentrotus fragilis accounted for over half of the total percent composition of these 

taxa.

Other invertebrates present at The Football included unidentified octopus species, brachyurian 

crabs, dungeness crab (Cancer magister), brittle stars and crinoids (Florometra serratissima).

Crinoids were commonly observed, and recorded as present on 9 of the 11 transects.

 

Figure 12. Total percent composition of other invertebrates from The Football transects.
26

Other Observations – The Football

Fish-Invertebrate Associations

There was one fish-invertebrate association observed, a rockfish (Sebastes sp.) darting into a 

barrel sponge (Staurocalyptus sp.) that was approximately 50 cm tall.

Anthropogenic Items/Derelict Fishing Gear

There were nine observations of anthropogenic materials documented at the Football, including: 

two lines, two nets (possibly gillnet or trawl net), four rubbish items (tire, glass bottle, etc.); and 

one derelict crab trap with many associated fish species, including a cowcod (Sebastes levis)

resting on top of the trap.
27

Collections

Table 11. Specimen collections at The Football.

** Hand collected off bottom rail of ROV

*** NOAA/College of Charleston material (not CAS)

  Found in S4G egg case mass

Cat shark egg cases (S4). One juvenile hatched on deck. Tissue samples revealed mDNA 

sequences suggesting the species to be Apristurus brunneus (brown catshark) This species 

of Scyliorhinid shark is common from Baja to southeastern Alaska (Flammang et at. 2008)

Specimen 

No. Species Date Coordinates Transect Depth

CAS 

Cat. 

No.

S3 Sea Star Arm**  5-Sep-14

38.4553

-123.6150

38.4617

-123.6074

MVFB7, HC19 281-242 m 196927

S4 Cat shark egg

cases*** 5-Sep-14 38.4585

-123.6029 HC14 230 m ---

S4A Brittle Star   5-Sep-14 (same as S4) HC14 230 m 196921

S4B Brittle Stars** ** 5-Sep-14 (same as S4) HC14 230 m 196939

S4C Polychaetes  5-Sep-14 (same as S4) HC14 230 m 196931

S4D Decapod** ** 5-Sep-14 (same as S4) HC14 230 m 196935

S4E Gastropods  5-Sep-14 (same as S4) HC14 230 m 196925

S4F Brachiopods** ** 5-Sep-14 (same as S4) HC14 230 m 196937

S5 Swiftia farallonesica

(Sea Whip) 6-Sep-14 38.4388

-123.5698 HC21 182 m 196930

S6 Cup Coral 6-Sep-14 38.4472

-123.5827 HC30 194 m 196940

S7 Holothurian (Sea 

Cucumber)** 7-Sep-14 38.4442

-123.5904 HC20 241 m 196938

S8 Decapod (Crab)** 7-Sep-14 38.4276

-123.5904 HC20 241 m 196933
28

Cup Coral (S6): A solitary hard coral in the family Flabellidae.

Brachiopod (S4F): Terebratulina unquicula (family Cancellothyrididae); known between 10 and 

850 m in depth.

Holothurian (S7): A deep-sea sea cucumber (family Stichopodidae). 

Swiftia farallonesica (S5): A new species of whip-like gorgonian coral described by Williams 

and Breedy (2016), California Academy of Sciences. 
29

Education and Outreach

The high-definition video and still imagery collected from Bodega Canyon and The Football was 

used by West Coast sanctuaries education staff to create a classroom activity and accompanying 

poster about deep-sea habitats in all five West Coast National Marine Sanctuaries. The activity 

and poster are entitled “Deep Coral Communities: Sentinels of a Changing Ocean.” The unit 

allows high school students to explore species abundance and diversity in different habitats 

(rocky and soft bottom). Students also examine threats to deep-sea corals such as ocean 

acidification, harmful fishing methods, and marine debris/derelict fishing gear and discuss action 

items that individuals and communities can take part in to help mitigate the impacts. The activity 

is available online for free download (http://sanctuaries.noaa.gov/education/teachers/deep-coralcommunities/) and it is estimated it may be used by over 50,000 students. The program meets

National ‘Next Generation Science Standards’ (http://www.nextgenscience.org) as well as 

California State Science Standards and Washington State Science Standards. Additionally, an inschool outreach program, titled ‘Diving Deep: Exploration of Deep-Sea Coral Communities’ was 

developed from the video and still images collected from The Football. The target audience is 

9th-12th grade students within the San Francisco Bay Area, reaching 1,000-2,000 students per 

year, and each program will be taught by a sanctuary educator. Additionally, some of the video 

footage was used to produce a narrated 5-minute video titled “Exploring Deep-Sea Coral 

Communities of West Coast National Marine Sanctuaries” that is available on the web for the 

general public (http://sanctuaries.noaa.gov/education/teachers/deep-coral-communities/). Future 

projects using the video and still images include: exhibits at partner institutions and/or sanctuary 

visitor centers, outreach presentations and social media.
30

Conclusions

The benthic characterization of Bodega Canyon and The Football provided details about the 

habitats and associated fish and invertebrate species in these areas, and revealed some expected 

and new findings. Collectively, a total of 12,443 m2 of seafloor was surveyed for quantitative 

analysis at both sites, and more was surveyed for qualitative analysis. The quantitative surveys 

for both sites together enumerated 2,627 individual fishes, 47 corals, and 22 sponges. In the 

qualitative segments, a total of 123 corals, 73 sponges and 6,401 other invertebrates were 

recorded. The surveys also revealed skate and catshark nursery habitat, and a new species of 

octocoral. For further detailed analysis, we examined each of the two sites separately given the 

disparate qualities and distance separating the sites. The information will be used by CBNMS 

and GFNMS to establish a baseline characterization of the habitat and species present, and to 

evaluate management efforts to protect these areas which have been recently added to the 

sanctuaries’ boundaries. 

At Bodega Canyon, the sampling scheme was designed to sample transects in each of three predetermined habitat categories (hard-rugose, hard-flat, and soft-flat) as predicted from multibeam 

sonar data. However, the observed habitat was primarily hard-flat with very little hard-rugose 

habitat. The observed assemblages of corals and sponges were not very diverse or abundant. All 

coral taxa, except for one observation of the primnoid, Plumarella sp., were soft bodied species 

such as mushroom coral (Heteropolypus ritteri) and small pennatulacean sea pens that can 

establish on soft bottom or low relief habitats of mixed rocks and soft sediments. The limited 

availability of rugose rocky habitat can also explain the few observations and low diversity of 

sponges. Although counts were relatively low, the most abundant sponge species was the 

barrel/boot sponge, Staurocalyptus sp., ranging in height from 10-50 cm, providing additional 

habitat and refuge for some fish species. Findings from a previous AUV survey in Bodega 

Canyon also found a relatively low abundance of corals and sponges, because the majority of 

habitat was soft sediment or when hard rock was present it was usually draped with mud (Fruh et 

al. 2011). The AUV surveys estimated a higher density of corals (mostly gorgonian octocorals -

Parastenella spp., Plumerella spp. and Swiftia spp.) and sponges than our ROV surveys. The 

difference could be attributed to the availability of exposed rock such as boulders and cobbles 

and deeper depths (to 500 m) as the highest density of sponges and second highest density of 

corals were found during the deepest AUV dive (Fruh et al. 2011). These deeper habitats may be 

providing the corals and sponges with colder and more stable water temperatures, greater 

availably of prey, or a natural refuge from disturbances from bottom contact fishing gear than 

available in shallower water habitats. 

Similarly, majority of fish species documented at Bodega Canyon were those that prefer mixed 

rock and soft sediment habitats. Rockfishes accounted for about half of the fishes observed, the 

majority were thornyheads (Sebastolobus spp.) and chillipepper (Sebastes goodei) resting on the 

seafloor. About a quarter of the fishes observed were flatfishes, many could not be identified to 

the species level because they were buried in sediment. The 2011 AUV surveys in Bodega 

Canyon also observed a high abundance of thornyheads and flatfishes; comprising over 75% of 

the total fish density. Species composition of other fishes observed by the AUV was very similar 

to those species observed by the ROV with the exception of a relatively high number of sablefish 
31

(Anoplopoma fimbria) as this species is most common deeper than 600 m (Love 1996, Fruh et al. 

2011).

Observations from The Football revealed habitat types consistent with the predicted habitats. The 

Football is a low-relief rocky feature (with some areas of hard-rugose habitat) surrounded by 

soft-flat sediments. The availability of rocky substrate provided habitat for Flabellidae cup 

corals, the only stony coral observed in our surveys, and numerous (n=51) gorgonian sea whips

determined from a sample collection to be a new species Swiftia farallonesica (Williams and 

Breedy, 2016). Abundance of sponges on both quantitative and qualitative segments was about a 

third of the total sessile benthic invertebrate observations. A few large habitat‐forming sponges 

were observed such as the shelf sponge (Poecillastra sp.) and barrel/boot sponge (Staurocalyptus

sp.). As suggested by Stierhoff et al. (2011), the multiple ROV dives on The Football resulted in 

a greater density and diversity of corals and sponges than was observed during their one ROV 

dive in 2011. This survey confirms and better quantifies the hard substrate, and resulting growth 

and recruitment of habitat forming benthic invertebrates at this location. 

Rockfishes at The Football were the most abundant group of fishes, mostly dominated by large 

schools of widow rockfish (Sebastes entomelas) swimming in the water column above rocky 

bottom. Widow rockfish was federally designated by NOAA as an "overfished" species in 2001

(which means that less than 25 percent of their estimated pre-fishery population existed), but was 

declared “rebuilt” (population at a biomass to support maximum sustainable yield) in 2011 

(NMFS 2012). Numerous yelloweye rockfish (S. ruberrimus) were observed on transects and the 

stock is currently listed as overfished. A few canary rockfish (S. pinniger) were observed on 

transect and the stock was listed as overfished until 2015 when it was declared rebuilt (NMFS 

2015). Bocaccio (S. paucispinis) and cowcod (S. levis) were observed on transects and both

stocks had previously been listed as overfished and are currently in rebuilding phases (PFMC

2014). More than one hundred very large lingcod (Ophiodon elongatus) were observed on 

transects. Lingcod was once listed as overfished, but populations have now recovered and the 

species was declared rebuilt in 2005 (PFMC 2014). On one transect (HC-30) there was a large 

sedimentary rock outcrop slope with many ledges and overhangs providing an ideal habitat for 

invertebrates and hundreds of rockfishes including sharpchins (S. zacentrus) and other adult and 

juvenile rockfishes (Sebastes spp.). Many of the fishes taking refuge within the rock layers were 

so well hidden they could not be identified to species. Stierhoff et al. (2011) also observed this

outcrop slope in their ROV survey transect at The Football in 2011. The high abundance and 

diversity of associated invertebrates and fishes highlights the value the rock outcrop serves as 

habitat. 

Our research team made significant discoveries in the hundreds of skate egg cases on the 

seafloor, and in the many bundles of catshark egg cases attached to rocks. One of the catshark 

eggs hatched a juvenile Apristurus brunneus, but the identity of the other egg cases is still 

unverified. The Football location represents an unusual nursery area because, to our knowledge, 

catshark nurseries have not previously been reported in the same area as skate nurseries. 

Catshark nurseries have been identified among gorgonian octocorals in the deep Gulf of Mexico 

(Etnoyer and Warrenchuk 2007) and in Lophelia pertusa corals in the North Atlantic (Henry et 

al. 2013). Nursery grounds are also reported locally in Northern California (Flammang et al. 

2008) and in Southern California (Cross 1988). No catsharks were observed in the vicinity of the 
32

catshark egg cases, but our surveys did observe five longnose skates (Raja rhina) and seven 

other skates in the vicinity of the skate egg cases at The Football. Abundance and diversity of 

skates tend to reach a peak at the continental shelf break. Several species of skates lay eggs in 

association with rocky substrates, including high-relief habitats (Bizarro et al. 2014). Migration 

patterns for skates are poorly understood, but may represent seasonal movements to the breeding 

grounds and/or egg deposition sites (Frisk 2010). The Football appears to be one of these 

breeding ground locations. This confers value on the habitat and supports the need for protection 

from anthropogenic bottom disturbance.

The discovery of a new species of coral (Swiftia farallonesica) is an indication that there is still 

much to be learned about these underexplored habitats (Williams and Breedy, 2016). In most 

cases it is not possible to make positive identifications of deep-sea invertebrates with images or 

video footage alone. It is necessary to examine collected specimens to make identifications, to 

acquire tissue samples for molecular analysis, and to preserve and properly curate specimens for 

future study. Several examples of this occurred during the 2014 survey. The white sea pen and 

white sea whip that were photographed and collected (Halipteris californica and Swiftia 

farallonesica respectively) could only be properly identified after examining the specimens that 

were collected by the ROV. Without specimens to study for identification purposes, deep-sea 

studies regarding biodiversity of the benthic fauna are necessarily limited in scope as well as 

scientific merit and importance. Therefore, all future ROV expeditions destined for deep-sea 

biodiversity studies should be equipped for the collection of benthic specimens.

There was evidence of human impacts on many of the transects at Bodega Canyon and The 

Football. Marine debris in the form of derelict fishing gear, included longlines, nets (gillnets 

and/or trawl nets) and other human rubbish was observed. In some cases, the derelict fishing gear 

provided additional habitat for fishes and invertebrates, however the initial loss of the gear most 

likely had negative impacts to the seafloor and associated species (particularly corals and 

sponges). Indeed, lost fishing gear presents hazards to habitat, wildlife, and humans. On the last 

day of the surveys the ROV became entangled in marine debris (pot and line) that we were 

observing, but was eventually successfully freed. 

Data collected to inform model validation of corals and rockfishes were too limited for a 

complete analysis. When more observations of these species become available through other 

studies, data from our study can be combined to inform a more robust model validation. 

The imagery collected was used in four education and outreach products to date. The curriculum 

and poster, available online, will reach thousands of high school students. The footage from the 

ROV is an exciting and novel tool for marine science education. It is visually engaging and 

represents a unique and important marine habitat that students otherwise know very little about. 

It provides the opportunity to learn about conducting marine research, and to talk about specific 

threats to habitats in National Marine Sanctuaries and realistic actions people can make to 

mitigate these threats. In addition, a large audience was informed about the ROV surveys and 

discovery of a new coral species, Swiftia farallonesica, through a press release in November 

2014 that was widely distributed by news media in 431 outlets worldwide, providing over 80 

million “media impressions” (opportunities to view the feature). 
33

Planned upgrades to the CBNMS ROV including improved cameras and lighting will allow us to 

collect high definition still images and video to enhance our capabilities to detect and identify 

more species than was possible with the standard definition video collected on this cruise. 

Although one of this mission’s goals was to use the CBNMS Phantom HD2 ROV, this class of 

ROV has depth, sampling and power limitations so a larger, deep depth rated ‘science class’ 

ROV is necessary to explore and characterize larger expanses of the deep-water habitats within 

CBNMS and GFNMS. Another needed upgrade is a suite of sensors to measure physical 

parameters. The ability to record environmental data concurrently with imagery through use of a 

Conductivity-Temperature-Depth (CTD) sensor mounted on the ROV would contribute to our 

knowledge of the physical environment species experience in the deep sea and how that affects 

their distribution and abundance. 

One of the limitations to benthic surveys in CBNMS and GFNMS is lack of high quality 

multibeam sonar data necessary to produce reliable habitat maps for the sanctuary. Future 

benthic surveys in CBNMS and GFNMS are dependent on acquiring high quality continuous 

multibeam data and habitat maps and this will be a priority in the coming years. As this study has 

shown, reliable interpretations of these data depend upon supervised visual surveys in order to 

evaluate and ground truth habitat classes. 

Based on the work presented in this report, recommendations for future missions include the 

equipment upgrades and new mapping data mentioned above so that surveys of other unexplored 

areas in the sanctuaries can be completed. Results from this work will assist in planning future 

surveys which should focus on data collection needed to inform analysis of initial 

characterization of new areas, as well as community composition, habitat-species associations, 

and changes to habitats and species over time and in response to stressors and protections.

Although the sites surveyed are a small portion of The Football and Bodega Canyon and more 

surveys are needed to comprehensively characterize the benthic habitat of the sanctuaries, overall 

the new information about species and habitats collected from this characterization of Bodega 

Canyon and The Football greatly expands our knowledge of the habitat and species present in 

these areas. This and future expeditions to CBNMS and GFNMS will assist researchers and the 

sanctuaries’ managers to better understand and protect benthic habitats in the newly expanded 

Cordell Bank and Greater Farallones National Marine Sanctuaries.
34

Acknowledgments

We thank Dave Minard and Sean Swing, the captain and mate of the R/V Fulmar, and Ian 

Griffith (Deep Ocean Exploration and Research, DOER) and Michael Carver (CBNMS), the 

pilots of the ROV, for their operation, maintenance and quick repair of the ROV. Laughlin 

Siceloff and Brian Kinlan from National Centers for Coastal Ocean Science (NCCOS), Center 

for Coastal Monitoring and Assessment (CCMA) Biogeography Branch developed the survey 

design and transect planning. Robert McGuinn (NCCOS) participated on the cruise and provided 

data management onboard. We also thank National Marine Sanctuary staff, Dan Howard, Jan 

Roletto, Rietta Hohmann, Carol Preston, Justin Holl, and Tim Reed and volunteer Darrell Gregg 

for participating and helping out on the cruise. Tom Laidig, NMFS-SWFSC, Santa Cruz 

Laboratory assisted with fish identifications. Thanks to Gavin Naylor and Elisabeth Rochel of 

College of Charleston for genetic analyses of catshark mitochondrial DNA. Jan Roletto, GFNMS 

Research Coordinator, reviewed this report and provided significant edits. Jenny Stock, CBNMS 

Education Coordinator, and Rietta Hohmann, GFNMS Marine Science Educator, provided 

content about the education and outreach products created by the West Coast National Marine 

Sanctuaries education staff. Comments from three reviewers improved the final report. Funding 

was provided by NOAA’s Office of National Marine Sanctuaries and the National Center for 

Coastal Ocean Sciences. 
35

References

Anderson, T.J., C. Syms, D.A. Roberts, D.F. Howard. 2009. Multi-scale fish-habitat associations 

and the use of habitat surrogates to predict the organization and abundance of deep-water fish 

assemblages. Journal of Experimental Marine Biology and Ecology 379(1-2): 34-42.

Bizzarro, J.J., K.M. Broms, M.G. Logsdon, D.A. Ebert, M.M. Yoklavich, L.A Kuhnz. 2014.

Spatial Segregation in Eastern North Pacific Skate Assemblages. PLoS ONE 9(10).

Costello, M.J., M. McCrea, A. Freiwald, T. Lundalv, L. Jonsson, B.J. Bett, T.V. Weering, H. de 

Haas, J.M. Roberts, D. Allen. 2005. Functional role of deep-sea cold-water Lophelia coral

reefs as fish habitat in the north-eastern Atlantic. Pages 771–805 in Freiwald A, J.M. Roberts 

(eds.), Cold-water corals and ecosystems. Springer-Verlag Berlin Heidelberg.

Cross, J.N. 1988. Aspects of the biology of two scyliorhinid sharks, Apristurus brunneus and 

Parmaturus xaniurus, from the upper continental slope off southern California. Fish Bull 

86(4):691–702.

de Marignac, J., J. Hyland, J. Lindholm, A. DeVogelaere, W.L. Balthis, D. Kline. 2008. A 

comparison of seafloor habitats and associated benthic fauna in areas open and closed to 

bottom trawling along the central California continental shelf. Marine Sanctuaries 

Conservation Series ONMS-09-02. U.S. Department of Commerce, National Oceanic and 

Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD. 44 

pp.

Etnoyer, P.J., G. Cochrane, E. Salgado, K. Graiff, J. Roletto, G. Williams, K. Reyna, J. Hyland. 

2014. Characterization of deep coral and sponge communities in the Gulf of the Farallones 

National Marine Sanctuary: Rittenburg Bank, Cochrane Bank and the Farallon Escarpment. 

NOAA Technical Memorandum NOS NCCOS 190. NOAA National Centers for Coastal 

Ocean Science, Charleston, SC. 32 pp.

Etnoyer, P. and J. Warrenchuk. 2007. A catshark nursery in a deep gorgonian field in the 

Mississippi Canyon, Gulf of Mexico. Bulletin of Marine Science, 81(3), 553.

Flammang, B.E., D.A. Ebert, G.M. Cailliet. 2008. Reproductive biology of deep-sea catsharks 

(Chondrichthyes: Scyliorhinidae) in the eastern North Pacific. Environmental Biology of 

Fishes, 81(1), 35-49.

Frisk M.G. 2010. Life history strategies of batoids In: Carrier JC, Musick JA, Heithaus MR, 

editors. The biology of sharks and their relatives II. Boca Raton: CRC Press. pp. 283–316.

Fruh, E., E. Clarke, C. Whitmire, 2011. A characterization of the deep-sea coral and sponge 

community in Bodega Canyon off the coast of California from a survey using an 

Autonomous Underwater Vehicle. Report to NOAA Deep-Sea Coral Research and 

Technology Program, pp. 40.
36

Graiff, K., D. Roberts, D. Howard, P. Etnoyer, G. Cochrane, J. Hyland, J. Roletto. 2011. A 

characterization of deep-sea coral and sponge communities on the continental slope west of 

Cordell Bank, using a remotely operated vehicle. Report to NOAA Deep-Sea Coral Research 

and Technology Program, pp. 21. 

Halle, C.M., and J.L. Largier. 2011. Surface Circulation downstream of the Point Arena 

upwelling center. Continental Shelf Research 31: 1260-1272. 

Henry, L.A., J.M Navas, S.J. Hennige, L.C. Wicks, J. Vad, J.M. Roberts. 2013. Cold-water coral 

reef habitats benefit recreationally valuable sharks. Biological conservation, 161, 67-70. 

Krieger, K.J. and B.L. Wing. 2002. Megafaunal associations with deepwater corals (Primnoa

sp.) in the Gulf of Alaska. Hydrobiologia 471:83−90.

Love, M. 1996. Probably More Than You Want to Know About The Fishes of The Pacific 

Coast. Really Big Press, Santa Barbara, California.

National Marine Fisheries Service (NMFS) 2012. Annual Report to Congress on the Status of 

U.S. Fisheries-2011, U.S. Department of Commerce, NOAA, Natl., Mar. Fish. Serv., Silver 

Spring, MD, 20 pp.

National Marine Fisheries Service (NMFS). 2015. Quarter 3 Update through September 30, 

2015, http://www.nmfs.noaa.gov/sfa/fisheries_eco/status_of_fisheries/. Accessed November 

2, 2015.

Pacific Fisheries Management Council (PFMC). 2014. Status of the Pacific Coast Groundfish 

Fishery: Stock Assessment and Fishery Evaluation (SAFE). Pacific Fishery Management 

Council, Portland, OR. 

Roberts, D.A., T.J. Anderson, D. Howard. 2004. Fish-habitat relationships at Cordell Bank 

(California) National Marine Sanctuary. Western Groundfish Conference, Victoria, British 

Columbia. Poster presentation.

Stierhoff, K. L., P.J. Etnoyer, D.W. Murfin, J.L. Butler. 2011. A survey of deep-water coral and 

sponge habitats along the West Coast of the US using a remotely operated vehicle. NOAA 

Technical Memorandum NOS NCCOS 138. NOAA Center for Coastal Environmental 

Health and Biomolecular Research, Charleston, SC. 38 pp.

Tissot, B.N., M.M. Yoklavich, M.S. Love, K. York, M. Amend. 2006. Benthic invertebrates that 

form habitat structures on deep banks off southern California, with special reference to deep 

sea coral. Fisheries Bulletin 104: 167-

Williams, G.C. and O. Breedy. 2016. A new species of whip-like gorgonian coral in the 

genus Swiftia from the Gulf of the Farallones in central California, with a key to eastern 

Pacific species in California (Cnidaria, Octocorallia, Plexauridae). Proceedings of the 

California Academy of Sciences 63 (1): 1-14.
37

Appendix A – Bodega Canyon Image Gallery

a) Derelict fishing net with invertebrates and catshark egg cases; b) Lingcod (Ophiodon elongatus) 

and crinoids (Florometra serratissima) on mud-cobble habitat; c) Mushroom coral (Heteropolypus 

ritteri) and unknown sea pen; d) Primnoid octocoral Plumarella sp. (circled in red); e) Barrel

sponge (Staurocalyptus sp.) with crinoids (F. serratissima) f) Cobble-mud habitat with bank 

rockfish (Sebastes rufus) and crinoids (F. serratissima).

a. b.

c. d.

e. f.
38

Appendix B – The Football Image Gallery

a) New species of gorgonian: Swiftia farallonesica; b) Flabellidae cup corals on rock ledge; c)

Catshark egg cases; d) Poecillastra sp. sponge with brittle stars e) rock ledge providing habitat for 

fishes and invertebrates; f) Cowcod (Sebastes levis) perched on derelict trap.

b.

d.

a.

c.

e. f.