Characterising fish habitat use of fringing oyster reefs using acoustic imaging
Robert P. Dunn
A B * , Matthew E. Kimball B , Caitlin G. O’Brien B and Nathan T. Adams B
+ Author Affiliations
- Author Affiliations
A North Inlet–Winyah Bay National Estuarine Research Reserve, Georgetown, SC 29440, USA.
B Baruch Marine Field Laboratory, University of South Carolina, 2306 Crabhall Road, Georgetown, SC 29440, USA.
Marine and Freshwater Research 74(1) 39-49 https://doi.org/10.1071/MF22081
Submitted: 7 April 2022 Accepted: 3 October 2022 Published: 28 October 2022
© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Context: Oysters provide structured habitat along coastal margins, but owing to the high turbidity of many estuaries, characterising the faunal communities that utilise oyster reefs typically requires direct capture, which is potentially lethal or destructive. Acoustic imaging sonar can non-destructively sample the abundance and size of swimming organisms (nekton), but collection of data from acoustic imaging files requires substantial processing time following field sampling.
Aims: We compared five alternate data examination protocols that could be applied to acoustic imaging files from intertidal oyster reefs and identified a protocol (analysing randomly chosen 3 of 5 min of imagery recordings) that reduces parameter estimation bias and processing time.
Methods: To demonstrate the utility of this protocol, we investigated diel differences in fish use of fringing oyster reefs.
Key results: During day-time and night-time sampling, we respectively recorded 4535 and 1924 fish across a size range of 1–52 cm. We found no difference between day and night in relative abundance, mean size, or size-spectra of the fish community inhabiting reefs.
Conclusions and implications: Active acoustic imaging can be an effective, non-destructive method to characterise faunal communities in shallow, turbid habitats and can be used to test hypotheses regarding the ecology of these ecosystems.
Keywords: active acoustics, ARIS, diel, estuarine fish, habitat utilisation, nekton, oyster reef, size-spectra.
References
Allen DM, Allen WB, Feller RF, Plunket JS (2014) ‘Site profile of the North Inlet–Winyah Bay National Estuarine Research Reserve.’ (North Inlet–Winyah Bay National Estuarine Research Reserve: Georgetown, SC, USA) p. 432.André, M, Solé, M, Lenoir, M, Durfort, M, Quero, C, Mas, A, Lombarte, A, van der Schaar, M, López-Bejar, M, Morell, M, Zaugg, S, and Houégnigan, L (2011). Low-frequency sounds induce acoustic trauma in cephalopods. Frontiers in Ecology and the Environment 9, 489–493.
| Low-frequency sounds induce acoustic trauma in cephalopods.Crossref | GoogleScholarGoogle Scholar |
Bahr LM, Lanier WP (1981) ‘The ecology of intertidal oyster reefs of the South Atlantic coast: a community profile.’ (US Fish and Wildlife Service)
Baker, R, Bilbrey, D, Bland, A, D’Alonzo, F, Ehrmann, H, Havard, S, Porter, Z, Ramsden, S, and Rodriguez, AR (2022). Underwater video as a tool to quantify fish density in complex coastal habitats. Diversity 14, 50.
| Underwater video as a tool to quantify fish density in complex coastal habitats.Crossref | GoogleScholarGoogle Scholar |
Beauchamp, DA, Byron, ER, and Wurtsbaugh, WA (1994). Summer habitat use by littoral-zone fishes in Lake Tahoe and the effects of shoreline structures. North American Journal of Fisheries Management 14, 385–394.
| Summer habitat use by littoral-zone fishes in Lake Tahoe and the effects of shoreline structures.Crossref | GoogleScholarGoogle Scholar |
Beck, MW, Brumbaugh, RD, Airoldi, L, Carranza, A, Coen, LD, Crawford, C, Defeo, O, Edgar, GJ, Hancock, B, Kay, MC, Lenihan, HS, Luckenbach, MW, Toropova, CL, Zhang, G, and Guo, X (2011). Oyster reefs at risk and recommendations for conservation, restoration, and management. BioScience 61, 107–116.
| Oyster reefs at risk and recommendations for conservation, restoration, and management.Crossref | GoogleScholarGoogle Scholar |
Becker, A, and Suthers, IM (2014). Predator driven diel variation in abundance and behaviour of fish in deep and shallow habitats of an estuary. Estuarine, Coastal and Shelf Science 144, 82–88.
| Predator driven diel variation in abundance and behaviour of fish in deep and shallow habitats of an estuary.Crossref | GoogleScholarGoogle Scholar |
Becker, A, Cowley, PD, Whitfield, AK, Järnegren, J, and Næsje, TF (2011a). Diel fish movements in the littoral zone of a temporarily closed South African estuary. Journal of Experimental Marine Biology and Ecology 406, 63–70.
| Diel fish movements in the littoral zone of a temporarily closed South African estuary.Crossref | GoogleScholarGoogle Scholar |
Becker, A, Whitfield, AK, Cowley, PD, Järnegren, J, and Næsje, TF (2011b). An assessment of the size structure, distribution and behaviour of fish populations within a temporarily closed estuary using dual frequency identification sonar (DIDSON). Journal of Fish Biology 79, 761–775.
| An assessment of the size structure, distribution and behaviour of fish populations within a temporarily closed estuary using dual frequency identification sonar (DIDSON).Crossref | GoogleScholarGoogle Scholar |
Becker, A, Holland, M, Smith, JA, and Suthers, IM (2016a). Fish movement through an estuary mouth is related to tidal flow. Estuaries and Coasts 39, 1199–1207.
| Fish movement through an estuary mouth is related to tidal flow.Crossref | GoogleScholarGoogle Scholar |
Becker, A, Whitfield, AK, Cowley, PD, Cole, VJ, and Taylor, MD (2016b). Tidal amplitude and fish abundance in the mouth region of a small estuary. Journal of Fish Biology 89, 1851–1856.
| Tidal amplitude and fish abundance in the mouth region of a small estuary.Crossref | GoogleScholarGoogle Scholar |
Becker, A, Whitfield, AK, Cowley, PD, Cole, VJ, Becker, A, Whitfield, AK, Cowley, PD, and Cole, VJ (2017). Does water depth influence size composition of estuary-associated fish? Distributions revealed using mobile acoustic-camera transects along the channel of a small shallow estuary. Marine and Freshwater Research 68, 2163–2169.
| Does water depth influence size composition of estuary-associated fish? Distributions revealed using mobile acoustic-camera transects along the channel of a small shallow estuary.Crossref | GoogleScholarGoogle Scholar |
Bennett, MA, Becker, A, Gaston, T, and Taylor, MD (2021). Connectivity of large-bodied fish with a recovering estuarine tidal marsh, revealed using an imaging sonar. Estuaries and Coasts 44, 1579–1587.
| Connectivity of large-bodied fish with a recovering estuarine tidal marsh, revealed using an imaging sonar.Crossref | GoogleScholarGoogle Scholar |
Boswell, KM, Kimball, ME, Rieucau, G, Martin, JGA, Jacques, DA, Correa, D, and Allen, DM (2019). Tidal stage mediates periodic asynchrony between predator and prey nekton in salt marsh creeks. Estuaries and Coasts 42, 1342–1352.
| Tidal stage mediates periodic asynchrony between predator and prey nekton in salt marsh creeks.Crossref | GoogleScholarGoogle Scholar |
Carvalho, PG, Setiawan, F, Fahlevy, K, Subhan, B, Madduppa, H, Zhu, G, and Humphries, AT (2021). Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes. Ecological Applications 31, e02345.
| Fishing and habitat condition differentially affect size spectra slopes of coral reef fishes.Crossref | GoogleScholarGoogle Scholar |
Cole, VJ, Harasti, D, Lines, R, and Stat, M (2022). Estuarine fishes associated with intertidal oyster reefs characterized using environmental DNA and baited remote underwater video. Environmental DNA 4, 50–62.
| Estuarine fishes associated with intertidal oyster reefs characterized using environmental DNA and baited remote underwater video.Crossref | GoogleScholarGoogle Scholar |
Cook, D, Middlemiss, K, Jaksons, P, Davison, W, and Jerrett, A (2019). Validation of fish length estimations from a high frequency multi-beam sonar (ARIS) and its utilisation as a field-based measurement technique. Fisheries Research 218, 59–68.
| Validation of fish length estimations from a high frequency multi-beam sonar (ARIS) and its utilisation as a field-based measurement technique.Crossref | GoogleScholarGoogle Scholar |
Dame, R, Alber, M, Allen, D, Mallin, M, Montague, C, Lewitus, A, Chalmers, A, Gardner, R, Gilman, C, Kjerfve, B, Pinckney, J, and Smith, N (2000). Estuaries of the South Atlantic coast of North America: their geographical signatures. Estuaries 23, 793–819.
| Estuaries of the South Atlantic coast of North America: their geographical signatures.Crossref | GoogleScholarGoogle Scholar |
Dunn RP, Kimball ME, O’Brien CG, Adams NT (2022) Data from: characterizing fish habitat use of fringing oyster reefs using acoustic imaging. Available at
| Crossref |
Edwards, AM, Robinson, JPW, Plank, MJ, Baum, JK, and Blanchard, JL (2017). Testing and recommending methods for fitting size spectra to data. Methods in Ecology and Evolution 8, 57–67.
| Testing and recommending methods for fitting size spectra to data.Crossref | GoogleScholarGoogle Scholar |
Fodrie, FJ, Yeager, LA, Grabowski, JH, Layman, CA, Sherwood, GD, and Kenworthy, MD (2015). Measuring individuality in habitat use across complex landscapes: approaches, constraints, and implications for assessing resource specialization. Oecologia 178, 75–87.
| Measuring individuality in habitat use across complex landscapes: approaches, constraints, and implications for assessing resource specialization.Crossref | GoogleScholarGoogle Scholar |
Fraser, KM, Stuart-Smith, RD, Ling, SD, and Edgar, GJ (2021). Small invertebrate consumers produce consistent size spectra across reef habitats and climatic zones. Oikos 130, 156–170.
| Small invertebrate consumers produce consistent size spectra across reef habitats and climatic zones.Crossref | GoogleScholarGoogle Scholar |
Gagnon, K, Rinde, E, Bengil, EGT, Carugati, L, Christianen, MJA, Danovaro, R, Gambi, C, Govers, LL, Kipson, S, Meysick, L, Pajusalu, L, Tüney Kızılkaya, İ, van de Koppel, J, van der Heide, T, van Katwijk, MM, and Boström, C (2020). Facilitating foundation species: the potential for plant–bivalve interactions to improve habitat restoration success. Journal of Applied Ecology 57, 1161–1179.
| Facilitating foundation species: the potential for plant–bivalve interactions to improve habitat restoration success.Crossref | GoogleScholarGoogle Scholar |
Grabowski, JH, and Peterson, CH (2007). Restoring oyster reefs to recover ecosystem services. Theoretical Ecology Series 4, 281–298.
| Restoring oyster reefs to recover ecosystem services.Crossref | GoogleScholarGoogle Scholar |
Grabowski, JH, Gouhier, TC, Byers, JE, Dodd, LF, Hughes, AR, Piehler, MF, and Kimbro, DL (2020). Regional environmental variation and local species interactions influence biogeographic structure on oyster reefs. Ecology 101, e02921.
| Regional environmental variation and local species interactions influence biogeographic structure on oyster reefs.Crossref | GoogleScholarGoogle Scholar |
Graham, NAJ, and Nash, KL (2013). The importance of structural complexity in coral reef ecosystems. Coral Reefs 32, 315–326.
| The importance of structural complexity in coral reef ecosystems.Crossref | GoogleScholarGoogle Scholar |
Gross, C, Ruesink, JL, Pruitt, C, Trimble, AC, and Donoghue, C (2019). Temporal variation in intertidal habitat use by nekton at seasonal and diel scales. Journal of Experimental Marine Biology and Ecology 516, 25–34.
| Temporal variation in intertidal habitat use by nekton at seasonal and diel scales.Crossref | GoogleScholarGoogle Scholar |
Hanke, MH, Posey, MH, and Alphin, TD (2017). The influence of habitat characteristics on intertidal oyster Crassostrea virginica populations. Marine Ecology Progress Series 571, 121–138.
| The influence of habitat characteristics on intertidal oyster Crassostrea virginica populations.Crossref | GoogleScholarGoogle Scholar |
Harding, JM, and Mann, RL (2001). Oyster reefs as fish habitat: opportunistic use of restored reefs by transient fishes. Journal of Shellfish Research 20, 951–959.
Heggie, K, and Ogburn, MB (2021). Rapid video assessment detects qualitative differences in oyster reef habitat. Marine Ecology Progress Series 667, 219–224.
| Rapid video assessment detects qualitative differences in oyster reef habitat.Crossref | GoogleScholarGoogle Scholar |
Humphries, AT, La Peyre, MK, and Decossas, GA (2011). The effect of structural complexity, prey density, and ‘predator-free space’ on prey survivorship at created oyster reef mesocosms. PLOS ONE 6, e28339.
| The effect of structural complexity, prey density, and ‘predator-free space’ on prey survivorship at created oyster reef mesocosms.Crossref | GoogleScholarGoogle Scholar |
Kimball, ME, and Able, KW (2012). Tidal migrations of intertidal salt marsh creek nekton examined with underwater video. Northeastern Naturalist 19, 475–486.
| Tidal migrations of intertidal salt marsh creek nekton examined with underwater video.Crossref | GoogleScholarGoogle Scholar |
Kimball, ME, Rozas, LP, Boswell, KM, and Cowan, JH (2010). Evaluating the effect of slot size and environmental variables on the passage of estuarine nekton through a water control structure. Journal of Experimental Marine Biology and Ecology 395, 181–190.
| Evaluating the effect of slot size and environmental variables on the passage of estuarine nekton through a water control structure.Crossref | GoogleScholarGoogle Scholar |
Kimball, ME, Rozas, LP, Boswell, KM, and Cowan, JH (2015). Effects of slotted water control structures on nekton movement within salt marshes. Marine and Coastal Fisheries 7, 177–189.
| Effects of slotted water control structures on nekton movement within salt marshes.Crossref | GoogleScholarGoogle Scholar |
Kimball, ME, Connolly, RM, Alford, SB, Colombano, DD, James, WR, Kenworthy, MD, Norris, GS, Ollerhead, J, Ramsden, S, Rehage, JS, Sparks, EL, Waltham, NJ, Worthington, TA, and Taylor, MD (2021). Novel applications of technology for advancing tidal marsh ecology. Estuaries and Coasts 44, 1568–1578.
| Novel applications of technology for advancing tidal marsh ecology.Crossref | GoogleScholarGoogle Scholar |
Kingsley-Smith, PR, Joyce, RE, Arnott, SA, Roumillat, WA, McDonough, CJ, and Reichert, MJM (2012). Habitat use of intertidal eastern oyster (Crassostrea virginica) reefs by nekton in South Carolina estuaries. Journal of Shellfish Research 31, 1009–1021.
| Habitat use of intertidal eastern oyster (Crassostrea virginica) reefs by nekton in South Carolina estuaries.Crossref | GoogleScholarGoogle Scholar |
Lefcheck, JS, Hughes, BB, Johnson, AJ, Pfirrmann, BW, Rasher, DB, Smyth, AR, Williams, BL, Beck, MW, and Orth, RJ (2019). Are coastal habitats important nurseries? A meta-analysis. Conservation Letters 12, e12645.
| Are coastal habitats important nurseries? A meta-analysis.Crossref | GoogleScholarGoogle Scholar |
Lillis, A, Eggleston, DB, and Bohnenstiehl, DR (2014). Estuarine soundscapes: distinct acoustic characteristics of oyster reefs compared to soft-bottom habitats. Marine Ecology Progress Series 505, 1–17.
| Estuarine soundscapes: distinct acoustic characteristics of oyster reefs compared to soft-bottom habitats.Crossref | GoogleScholarGoogle Scholar |
Luckenbach, MW, Coen, LD, Ross, PG, and Stephen, JA (2005). Oyster reef habitat restoration: relationships between oyster abundance and community development based on two studies in Virginia and South Carolina. Journal of Coastal Research 40, 64–78.
Margiotta, AM, Shervette, VR, Hadley, NH, Plante, CJ, and Wilber, DH (2016). Species-specific responses of resident crabs to vertical habitat complexity on intertidal oyster reefs. Journal of Experimental Marine Biology and Ecology 477, 7–13.
| Species-specific responses of resident crabs to vertical habitat complexity on intertidal oyster reefs.Crossref | GoogleScholarGoogle Scholar |
Martignac, F, Daroux, A, Bagliniere, J-L, Ombredane, D, and Guillard, J (2015). The use of acoustic cameras in shallow waters: new hydroacoustic tools for monitoring migratory fish population. A review of DIDSON technology. Fish and Fisheries 16, 486–510.
| The use of acoustic cameras in shallow waters: new hydroacoustic tools for monitoring migratory fish population. A review of DIDSON technology.Crossref | GoogleScholarGoogle Scholar |
Miller, RJ, Lafferty, KD, Lamy, T, Kui, L, Rassweiler, A, and Reed, DC (2018). Giant kelp, Macrocystis pyrifera, increases faunal diversity through physical engineering. Proceedings of the Royal Society of London – B. Biological Sciences 285, 20172571.
| Giant kelp, Macrocystis pyrifera, increases faunal diversity through physical engineering.Crossref | GoogleScholarGoogle Scholar |
Moore, C, Drazen, JC, Radford, BT, Kelley, C, and Newman, SJ (2016). Improving essential fish habitat designation to support sustainable ecosystem-based fisheries management. Marine Policy 69, 32–41.
| Improving essential fish habitat designation to support sustainable ecosystem-based fisheries management.Crossref | GoogleScholarGoogle Scholar |
Moulton, DL, Dance, MA, Williams, JA, Sluis, MZ, Stunz, GW, and Rooker, JR (2017). Habitat partitioning and seasonal movement of red drum and spotted seatrout. Estuaries and Coasts 40, 905–916.
| Habitat partitioning and seasonal movement of red drum and spotted seatrout.Crossref | GoogleScholarGoogle Scholar |
Pierson, KJ, and Eggleston, DB (2014). Response of estuarine fish to large-scale oyster reef restoration. Transactions of the American Fisheries Society 143, 273–288.
| Response of estuarine fish to large-scale oyster reef restoration.Crossref | GoogleScholarGoogle Scholar |
Rieucau, G, Boswell, KM, Kimball, ME, Diaz, G, and Allen, DM (2015). Tidal and diel variations in abundance and schooling behavior of estuarine fish within an intertidal salt marsh pool. Hydrobiologia 753, 149–162.
| Tidal and diel variations in abundance and schooling behavior of estuarine fish within an intertidal salt marsh pool.Crossref | GoogleScholarGoogle Scholar |
Risk, MJ (1972). Fish diversity on a coral reef in the Virgin Islands. Atoll Research Bulletin 153, 1–4.
| Fish diversity on a coral reef in the Virgin Islands.Crossref | GoogleScholarGoogle Scholar |
Rodriguez-Pinto, II, Rieucau, G, Handegard, NO, Kimball, ME, and Boswell, KM (2022). Anthropogenic marsh impoundments alter collective tendency in schooling fish. Estuaries and Coasts 45, 856–865.
| Anthropogenic marsh impoundments alter collective tendency in schooling fish.Crossref | GoogleScholarGoogle Scholar |
Rountree, RA, and Able, KW (1993). Diel variation in decapod crustacean and fish assemblages in New Jersey polyhaline marsh creeks. Estuarine, Coastal and Shelf Science 37, 181–201.
| Diel variation in decapod crustacean and fish assemblages in New Jersey polyhaline marsh creeks.Crossref | GoogleScholarGoogle Scholar |
Rountree, RA, and Able, KW (2007). Spatial and temporal habitat use patterns for salt marsh nekton: implications for ecological functions. Aquatic Ecology 41, 25–45.
| Spatial and temporal habitat use patterns for salt marsh nekton: implications for ecological functions.Crossref | GoogleScholarGoogle Scholar |
Schneider, CA, Rasband, WS, and Eliceiri, KW (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods 9, 671–675.
| NIH Image to ImageJ: 25 years of image analysis.Crossref | GoogleScholarGoogle Scholar |
Seitz, KM, Atlas, WI, Millard-Martin, B, Reid, J, Heavyside, J, Hunt, BPV, and Moore, JW (2020). Size-spectra analysis in the estuary: assessing fish nursery function across a habitat mosaic. Ecosphere 11, e03291.
| Size-spectra analysis in the estuary: assessing fish nursery function across a habitat mosaic.Crossref | GoogleScholarGoogle Scholar |
Smith, CS, Paxton, AB, Donaher, SE, Kochan, DP, Neylan, IP, Pfeifer, T, Van Hoeck, RV, and Taylor, JC (2021). Acoustic camera and net surveys reveal that nursery enhancement at living shorelines may be restricted to the marsh platform. Ecological Engineering 166, 106232.
| Acoustic camera and net surveys reveal that nursery enhancement at living shorelines may be restricted to the marsh platform.Crossref | GoogleScholarGoogle Scholar |
TinHan, TC, Mohan, JA, Dumesnil, M, DeAngelis, BM, and Wells, RJD (2018). Linking habitat use and trophic ecology of spotted seatrout (Cynoscion nebulosus) on a restored oyster reef in a subtropical estuary. Estuaries and Coasts 41, 1793–1805.
| Linking habitat use and trophic ecology of spotted seatrout (Cynoscion nebulosus) on a restored oyster reef in a subtropical estuary.Crossref | GoogleScholarGoogle Scholar |
Tolley, SG, and Volety, AK (2005). The role of oysters in habitat use of oyster reefs by resident fishes and decapod crustaceans. Journal of Shellfish Research 24, 1007–1012.
| The role of oysters in habitat use of oyster reefs by resident fishes and decapod crustaceans.Crossref | GoogleScholarGoogle Scholar |
Wenner, E, Beatty, HR, and Coen, LD (1996). A method for quantitatively sampling nekton on intertidal oyster reefs. Journal of Shellfish Research 15, 769–775.
Yeoh, DE, Valesini, FJ, Hallett, CS, Abdo, DA, and Williams, J (2017). Diel shifts in the structure and function of nearshore estuarine fish communities. Journal of Fish Biology 90, 1214–1243.
| Diel shifts in the structure and function of nearshore estuarine fish communities.Crossref | GoogleScholarGoogle Scholar |
