Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation
Tài liệu tham khảo
Ahmed, 2007, Overfishing in the Gulf of Thailand: policy challenges and bioeconomic analysis, Environ. Dev. Econ., 12, 145, 10.1017/S1355770X06003433
Alberdi, 2018, Scrutinizing key steps for reliable metabarcoding of environmental samples, Methods Ecol. Evol., 9, 134, 10.1111/2041-210X.12849
Alexander, 2019, Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding, Coral Reefs
Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2
Anderson, 2001, A new method for non-parametric multivariate analysis of variance: non-parametric MANOVA for ecology, Austral Ecol., 26, 32
Anderson, 2008
Andrews
Ardura, 2015, Environmental DNA evidence of transfer of North Sea molluscs across tropical waters through ballast water, J. Molluscan Stud., 81, 495, 10.1093/mollus/eyv022
Ardura, 2015, eDNA and specific primers for early detection of invasive species – a case study on the bivalve Rangia cuneata, currently spreading in Europe, Mar. Environ. Res., 112, 48, 10.1016/j.marenvres.2015.09.013
Berry, 2017, DNA metabarcoding for diet analysis and biodiversity: a casestudy using the endangered Australian sea lion (Neophoca cinerea), Ecol. Evol., 7, 5435, 10.1002/ece3.3123
Boyer, 2016, Obitools : a unix -inspired software package for DNA metabarcoding, Mol Ecol Resour, 16, 176, 10.1111/1755-0998.12428
Bull, 2019, Worldwide oil and gas platform decommissioning: a review of practices and reefing options, Ocean Coast Manag., 168, 274, 10.1016/j.ocecoaman.2018.10.024
Callahan, 2016, DADA2: high-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581, 10.1038/nmeth.3869
Cheevaporn, 2003, Water pollution and habitat degradation in the Gulf of Thailand, Mar. Pollut. Bull., 47, 43, 10.1016/S0025-326X(03)00101-2
Claisse, 2014, Oil platforms off California are among the most productive marine fish habitats globally, Proc. Natl. Acad. Sci. USA, 111, 15462, 10.1073/pnas.1411477111
Clarke, 2015
Cole, 2021, Estuarine fishes associated with intertidal oyster reefs characterized using environmental DNA and baited remote underwater video, Environmental DNA edn3, 190
Collins, 2018, Persistence of environmental DNA in marine systems, Commun Biol, 1, 185, 10.1038/s42003-018-0192-6
Consoli, 2013, Factors affecting fish assemblages associated with gas platforms in the Mediterranean Sea, J. Sea Res., 77, 45, 10.1016/j.seares.2012.10.001
Cordier, 2019, Multi-marker eDNA metabarcoding survey to assess the environmental impact of three offshore gas platforms in the North Adriatic Sea (Italy), Mar. Environ. Res., 146, 24, 10.1016/j.marenvres.2018.12.009
Core Team, 2020
Creed, 2017, The invasion of the azooxanthellate coral Tubastraea (Scleractinia: dendrophylliidae) throughout the world: history, pathways and vectors, Biol. Invasions, 19, 283, 10.1007/s10530-016-1279-y
Deagle, 2007, Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (eudyptes chrysolophus), PLoS One, 2, 10.1371/journal.pone.0000831
Di Muri, 2020, Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds, MBMG, 4, 10.3897/mbmg.4.56959
Emel’yanova, 2020, Some data on reproductive biology of spotted ghoul inimicus sinensis (Synanceiidae), J. Ichthyol., 60, 453, 10.1134/S0032945220030078
Fam, 2018, A review of offshore decommissioning regulations in five countries – strengths and weaknesses, Ocean Eng., 160, 244, 10.1016/j.oceaneng.2018.04.001
Fields, 2015, A novel mini-DNA barcoding assay to identify processed fins from internationally protected shark species, PLoS One, 10, 10.1371/journal.pone.0114844
Fonseca, 2018, Pitfalls in relative abundance estimation using eDNA metabarcoding, Mol Ecol Resour, 18, 923, 10.1111/1755-0998.12902
Friedlander, 2014, Communities on oil platforms in Gabon, west africa: high biodiversity oases in a low biodiversity environment, PLoS One, 9, 10.1371/journal.pone.0103709
Froese, 2020
Froese, 2021
Furlan, 2020, Identifying error and accurately interpreting environmental DNA metabarcoding results: a case study to detect vertebrates at arid zone waterholes, Mol Ecol Resour, 20, 1259, 10.1111/1755-0998.13170
Golani, 1985, The biology of the indo-pacific squirrelfish, sargocentron rubrum (forsskal), a suez canal migrant to the eastern mediterranean, J. Fish. Biol., 27, 249, 10.1111/j.1095-8649.1985.tb04025.x
Harvey, 2010, Influence of range, angle of view, image resolution and image compression on underwater stereo-video measurements: high-definition and broadcast-resolution video cameras compared, Mar. Technol. Soc. J., 44, 75, 10.4031/MTSJ.44.1.3
Harvey, 2012, Comparison of the relative efficiencies of stereo-BRUVs and traps for sampling tropical continental shelf demersal fishes, Fish. Res., 125, 108, 10.1016/j.fishres.2012.01.026
Harvey, 2021, Fish assemblages associated with oil and gas platforms in the Gulf of Thailand, Front. Mar. Sci., 10.3389/fmars.2021.664014
Heidmann, 2021, Home range characteristics and diel patterns in space use of mutton snapper, Lutjanus analis, vol. 9, 15
Hinz, 2022, Evaluating eDNA for use within marine environmental impact assessments, JMSE, 10, 375, 10.3390/jmse10030375
Holmes, 2013, A comparison of visual- and stereo-video based fish community assessment methods in tropical and temperate marine waters of Western Australia: comparison of fish community assessment methods, Limnol Oceanogr. Methods, 11, 337, 10.4319/lom.2013.11.337
Jagerroos, 2016, Rigs-to-reef; impact or enhancement on marine biodiversity, J. Ecosyst. Ecography, 6, 10.4172/2157-7625.1000187
Jalal, 2020, Fish detection and species classification in underwater environments using deep learning with temporal information, Ecol. Inf., 57, 10.1016/j.ecoinf.2020.101088
Jeunen, 2019, Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement, Mol Ecol Resour, 19, 426, 10.1111/1755-0998.12982
Jo, 2019, Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution, Ecol. Evol., 9, 1135, 10.1002/ece3.4802
Kolian, 2017, Abundance of corals on offshore oil and gas platforms in the gulf of Mexico, Environ. Manag., 60, 357, 10.1007/s00267-017-0862-z
Koziol, 2018, Environmental DNA metabarcoding studies are critically affected by substrate selection, Molecular Ecology Resources
Kulanujaree, 2020, The transition from unregulated to regulated fishing in Thailand, Sustainability, 12, 5841, 10.3390/su12145841
Lacoursière-Roussel, 2016, Quantifying relative fish abundance with eDNA: a promising tool for fisheries management, J. Appl. Ecol., 53, 1148, 10.1111/1365-2664.12598
Lacoursière-Roussel, 2016, Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions, Mol Ecol Resour, 16, 1401, 10.1111/1755-0998.12522
Langlois, 2020, A field and video annotation guide for baited remote underwater stereo‐video surveys of demersal fish assemblages, Methods Ecol. Evol., 11, 1401, 10.1111/2041-210X.13470
Laroche, 2017, Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities, PeerJ, 5, e3347, 10.7717/peerj.3347
Lindeque, 2013, Next generation sequencing reveals the hidden diversity of zooplankton assemblages, PLoS One, 8, 10.1371/journal.pone.0081327
Lindfield, 2014, Silent fish surveys: bubble-free diving highlights inaccuracies associated with SCUBA-based surveys in heavily fished areas, Methods Ecol. Evol., 5, 1061, 10.1111/2041-210X.12262
Love, 2006, The relationships between fish assemblages and the amount of bottom horizontal beam exposed at California oil platforms: fish habitat preferences at man-made platforms and (by inference) at natural reefs, Fish. Bull., 104
Love, 2019, An analysis of the fish assemblages around 23 oil and gas platforms off California with comparisons with natural habitats, bms, 95, 477, 10.5343/bms.2018.0061
Macreadie, 2011, Rigs-to-reefs: will the deep sea benefit from artificial habitat?, Front. Ecol. Environ., 9, 455, 10.1890/100112
Martel, 2021, Using environmental DNA and occupancy modelling to estimate rangewide metapopulation dynamics, Mol. Ecol., 30, 3340, 10.1111/mec.15693
Mauffrey, 2020, Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding, Mol Ecol mec
McKnight, 2019, microDecon: a highly accurate read‐subtraction tool for the post‐sequencing removal of contamination in metabarcoding studies, Environmental DNA, 1, 14, 10.1002/edn3.11
McLean, 2017, Using industry ROV videos to assess fish associations with subsea pipelines, Continent. Shelf Res., 141, 76, 10.1016/j.csr.2017.05.006
Mousavi‐Derazmahalleh, 2021, eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA (eDNA) sequences exploiting Nextflow and Singularity, Molecular Ecology Resources, 10.1111/1755-0998.13356
Mueller, 1994, Size-specific social interactions and foraging styles in a shallow water population of mutton snapper, Lutjanus analis (Pisces: Lutjanidae), in the central Bahamas, Environ. Biol. Fish., 40, 175, 10.1007/BF00002544
Murakami, 2019, Dispersion and degradation of environmental DNA from caged fish in a marine environment, Fish. Sci., 85, 327, 10.1007/s12562-018-1282-6
Murray, 2015, From benchtop to desktop: important considerations when designing amplicon sequencing workflows, PLoS One, 10, 10.1371/journal.pone.0124671
Nester, 2020, Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: syngnathidae), Environmental DNA edn3, 93
O'Donnell, 2017, Spatial distribution of environmental DNA in a nearshore marine habitat, PeerJ, 5
Page, 2006, Exotic invertebrate species on offshore oil platforms, Mar. Ecol. Prog. Ser., 325, 101, 10.3354/meps325101
Pajuelo, 2016, Introduction of non-native marine fish species to the Canary Islands waters through oil platforms as vectors, J. Mar. Syst., 163, 23, 10.1016/j.jmarsys.2016.06.008
Parente, 2006, Offshore decommissioning issues: deductibility and transferability, Energy Pol., 34, 1992, 10.1016/j.enpol.2005.02.008
Pearman, 2016, Please mind the gap – visual census and cryptic biodiversity assessment at central Red Sea coral reefs, Mar. Environ. Res., 118, 20, 10.1016/j.marenvres.2016.04.011
Piggott, 2021, Comparison of traditional and environmental DNA survey methods for detecting rare and abundant freshwater fish, Aquat. Conserv. Mar. Freshw. Ecosyst., 31, 173, 10.1002/aqc.3474
Pompanon, 2012, Who is eating what: diet assessment using next generation sequencing, Mol. Ecol., 21, 1931, 10.1111/j.1365-294X.2011.05403.x
Robertson, 2008, Rotenone: an essential but demonized tool for assessing marine fish diversity, Bioscience, 58, 165, 10.1641/B580211
Robinson, 2013, Whale sharks, rhincodon typus, aggregate around offshore platforms in Qatari waters of the arabian gulf to feed on fish spawn, PLoS One, 8, 10.1371/journal.pone.0058255
Rooker, 1997, Fish assemblages on artiþcial and natural reefs in the flower garden banks national marine sanctuary, USA, Coral Reefs, 16, 83, 10.1007/s003380050062
Rourke, 2021, Environmental DNA (eDNA) as a tool for assessing fish biomass: a review of approaches and future considerations for resource surveys, Environmental DNA edn3., 185
2020
Ryer, 2009, Effects of simulated underwater vehicle lighting on fish behavior, Mar. Ecol. Prog. Ser., 391, 97, 10.3354/meps08168
Sammarco, 2014, Coral communities on artificial reefs in the Gulf of Mexico: standing vs. toppled oil platforms, ICES (Int. Counc. Explor. Sea) J. Mar. Sci., 71, 417, 10.1093/icesjms/fst140
Satapoomin, 2000, A preliminary checklist of coral reef fishes of the Gulf of Thailand, South China Sea, The Raffles Bullettin of Zoology, 48, 31
Scaps, 2006, Eight new records of coral reef fishes from the Gulf of Thailand, South China Sea, Phuket Mar. Biol. Cent. Res. Bull., 67, 53
Schramm, 2020, A comparison of stereo-BRUV, diver operated and remote stereo-video transects for assessing reef fish assemblages, J. Exp. Mar. Biol. Ecol., 524, 10.1016/j.jembe.2019.151273
Schramm, 2020, A comparison of stereo-BRUVs and stereo-ROV techniques for sampling shallow water fish communities on and off pipelines, Mar. Environ. Res., 162, 10.1016/j.marenvres.2020.105198
Seiler, 2012, Assessing size, abundance and habitat preferences of the Ocean Perch Helicolenus percoides using a AUV-borne stereo camera system, Fish. Res., 129, 64, 10.1016/j.fishres.2012.06.011
Shortis, 1998, Design and calibration of an underwater stereo-video system for the monitoring of marine fauna populations, Int Archives Photogrammetry Remote Sens, 32
Sickel, 2015, Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach, BMC Ecol., 15, 20, 10.1186/s12898-015-0051-y
Sommer, 2019, Decommissioning of offshore oil and gas structures – environmental opportunities and challenges, Sci. Total Environ., 658, 973, 10.1016/j.scitotenv.2018.12.193
Stanley, 1996, Abundance of fishes associated with a petroleum platform as measured with dual-beam hydroacoustics, ICES (Int. Counc. Explor. Sea) J. Mar. Sci., 53, 473, 10.1006/jmsc.1996.0067
Stat, 2017, Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment, Sci. Rep., 7, 10.1038/s41598-017-12501-5
Stat, 2019, Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity, Conserv. Biol., 33, 196, 10.1111/cobi.13183
Stoner, 2008, Evaluating the role of fish behavior in surveys conducted with underwater vehicles, Can. J. Fish. Aquat. Sci., 65, 1230, 10.1139/F08-032
Sutthacheep, 2013, Impacts of the 1998 and 2010 mass coral bleaching events on the Western Gulf of Thailand, Deep Sea Res. Part II Top. Stud. Oceanogr., 96, 25, 10.1016/j.dsr2.2013.04.018
Takahashi, 2020, Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding, Sci. Rep., 10, 4319, 10.1038/s41598-020-60779-9
Techera, 2015, Offshore installations, decommissioning and artificial reefs: do current legal frameworks best serve the marine environment?, Mar. Pol., 59, 53, 10.1016/j.marpol.2015.04.021
2021
Todd, 2020, Characterizing the first wave of fish and invertebrate colonization on a new offshore petroleum platform, ICES (Int. Counc. Explor. Sea) J. Mar. Sci., 77, 1127, 10.1093/icesjms/fsz077
Torquato, 2017, Vertical zonation and functional diversity of fish assemblages revealed by ROV videos at oil platforms in the Gulf: vertical zonation of fish at oil platforms, J. Fish. Biol., 91, 947, 10.1111/jfb.13394
Valdivia‐Carrillo, 2021, Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot, Mol Ecol Resour, 21, 1558, 10.1111/1755-0998.13375
van Elden, 2019, Offshore oil and gas platforms as novel ecosystems: a global perspective, Front. Mar. Sci., 6, 548, 10.3389/fmars.2019.00548
Watson, 2007, Behaviour of temperate and sub-tropical reef fishes towards a stationary SCUBA diver, Mar. Freshw. Behav. Physiol., 40, 85, 10.1080/10236240701393263
Wattayakorn, 2012, Petroleum pollution in the Gulf of Thailand: a historical review, Coastal Marine Science, 35, 234
West, 2020, eDNA metabarcoding survey reveals fine‐scale coral reef community variation across a remote, tropical island ecosystem, Mol. Ecol., 29, 1069, 10.1111/mec.15382
West, 2021, Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia, Divers Distrib ddi, 10.1111/ddi.13228
Yeemin, 2013, Long-term decline in Acropora species at Kut Island, Thailand, in relation to coral bleaching events, Mar. Biodivers., 43, 23, 10.1007/s12526-012-0138-z
Zintzen, 2012, Diversity and composition of demersal fishes along a depth gradient assessed by baited remote underwater stereo-video, PLoS One, 7, 10.1371/journal.pone.0048522
Zintzen, 2017, Effects of latitude and depth on the beta diversity of New Zealand fish communities, Sci. Rep., 7, 8081, 10.1038/s41598-017-08427-7