Pace, N. R. The small things can matter. PLoS Biol. 16(8), e3000009. https://doi.org/10.1371/journal.pbio.3000009 (2018).
Google Scholar
Hoshino, T. et al. Global diversity of microbial communities in marine sediment. PNAS 117, 27587–27597 (2020).
Google Scholar
Baker, B. J., Appler, K. E. & Gong, X. New microbial biodiversity in marine sediments. Ann. Rev. Mar. Sci. 13, 161–175. https://doi.org/10.1146/annurev-marine-032020-014552 (2021).
Google Scholar
Zinger, L. et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6, e24570. https://doi.org/10.1371/journal.pone.0024570 (2011).
Google Scholar
Jiao, N. et al. Microbial production of recalcitrant dissolved organic matter: Long-term carbon storage in the global ocean. Nat. Rev. Microbiol. 8, 593–599 (2010).
Google Scholar
Ward, N. D. et al. Representing the function and sensitivity of coastal interfaces in earth system models. Nat. Commun. 11, 2458 (2020).
Google Scholar
Cook, R., & Auster, P. J. Developing alternatives for optimal representation of seafloor habitats and associated communities in Stellwagen Bank National Marine Sanctuary. Marine Sanctuaries Conservation Series ONMS-06–02. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD (2006).
Wauchope, H. S. Evaluating impact using time-series data. Trends Ecol. Evol. 36, 3. https://doi.org/10.1016/j.tree.2020.11.001 (2021).
Google Scholar
Stellwagen Bank National Marine Sanctuary (SBNMS) Condition Report. Office of National Marine Sanctuaries National Oceanic and Atmospheric Administration. doi:https://doi.org/10.25923/48ZK-BB07. pp. 1–263. (2020).
Grieve, C., Brady, D. C. & Polet, H. Best practices for managing, measuring and mitigating the benthic impacts of fishing—Part 1. Mar. Stewardship Council Sci. Ser. 2, 18–88 (2014).
Watling, L. & Norse, E. A. Disturbance of the seafloor by mobile fishing gear: A comparison to forest clear cutting. Conserv. Biol. 12, 1180–1197 (1998).
Google Scholar
Snelgrove, P. V. R. et al. The importance of marine sediment biodiversity in ecosystem processes. Ambio 26, 578–583 (1997).
Grassle, J. F. & Maciolek, N. J. Deep-sea species richness: Regional and local diversity estimates from quantitative bottom samples. Am. Nat. 139, 313–341 (1992).
Google Scholar
Polinski, J. M., Bucci, J. P., Gasser, M. & Bodnar, A. G. Targeted metagenomic assessment of biodiversity across prokaryotic and eukaryotic taxa in sediments from the Stellwagen Bank National Marine Sanctuary. Sci. Rep. 9, 14820 (2019).
Google Scholar
Petro, C. et al. Microbial community assembly in marine sediments. Aquat. Microb. Ecol. 79, 177–195 (2017).
Google Scholar
Cook, R. et al. The substantial first impact of bottom fishing on rare biodiversity hotspots: A dilemma for evidence-based conservation. PLoS ONE 8, e69904 (2013).
Google Scholar
Grabowski, J. H. et al. Assessing the vulnerability of marine benthos to fishing gear impacts. Rev. Fisheries Sci. Aquacult. 22, 142–155 (2014).
Google Scholar
Silva, T. L. State of the science report: An addendum to the Stellwagen Bank National Marine Sanctuary 2020 Condition Report 1–20 (U.S. Department of Commerce, 2021).
Parks, D. H. et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat. Microbiol. 2, 1533–1542 (2017).
Google Scholar
Bech, P. K. et al. Marine sediments hold an untapped potential for novel taxonomic and bioactive bacterial diversity. MSystems 5, e00782-e820 (2020).
Google Scholar
Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod. 79, 629–661 (2016).
Google Scholar
Hou, Z. Geochemical and microbial community attributes in relation to hyporheic zone geological facies. Sci. Rep. 7, 12006 (2017).
Google Scholar
Hugenholtz, P., Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765–4774 (1998).
Google Scholar
Durazzi, F. et al. Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota. Sci. Rep. 11, 3030 (2021).
Google Scholar
Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun. 11, 2500 (2020).
Google Scholar
Dance, A. The search for microbial dark matter. Nature 582, 301–303. https://doi.org/10.1038/d41586-020-01684-z (2020).
Google Scholar
Fishing Restrictions. Magnuson Fishery Conservation and Management Act (MFCMA) (16 U.S.C. Part 1801 et seq.) (1990).
Begon, M., Harper, J. L. & Townsend, C. R. Ecology: Individuals, Populations, and Communities 3rd edn. (Blackwell Science Ltd., 1996).
Google Scholar
Uritskiy, G. V., DiRuggiero, J. & Taylor, J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome 6, 158 (2018).
Google Scholar
Andrews, S. Babraham bioinformatics-FastQC a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Next Gen. Sequencing Data Anal. 17, 1 (2011).
Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Google Scholar
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
Google Scholar
Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 2, e104 (2017).
Google Scholar
Wickham, H. ggplot2. WIREs Comput. Stat. 3, 180–185 (2011).
Google Scholar
Breitwieser, F. P. & Salzberg, S. L. Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics 36, 1303–1304 (2020).
Google Scholar
Wu, Y. W. et al. MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016).
Google Scholar
Alneberg, J. et al. CONCOCT: Clustering cONtigs on COverage and ComposiTion. ArXiv 1312, 4038 (2013).
Google Scholar
Kang, D. et al. MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Google Scholar
Parks, D. H. et al. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Google Scholar
Ondov, B. D., Bergman, N. H. & Phillippy, A. M. Interactive metagenomic visualization in a web browser. BMC Bioinform. 12, 385 (2011).
Google Scholar
Seemann, T. Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).
Google Scholar
Blin, K. et al. antiSMASH 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29–W35 (2021).
Google Scholar
Wickham, H. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978–3–319–24277–4. (2016).
Moon, K. W. Interactive Plot. In Learn ggplot2 Using Shiny App (ed. Moon, K.-W.) 295–347 (Springer International Publishing, 2016).
Google Scholar
Oksanen, J., et al. Package ‘vegan’. Community ecology package, version 2, 1-295 (2013).
Wilkinson, L. SYSTAT. In Wiley Interdisciplinary Reviews: Computational Statistics, Multidimensional Scaling (eds Wegman, E. & Said, Y. H.) (John Wiley & Sons, New York, 2010).
Dexter, E., Rollwagen-Bollens, G. & Bollens, M. The trouble with stress: A flexible method for the evaluation of nonmetric multidimensional scaling. Limnol. Oceanogr. Methods 16, 434–443 (2018).
Google Scholar
Longford, N. T. Longitudinal and time-series analysis. In Studying Human Populations. Springer Texts in Statistics (Springer, 2008). https://doi.org/10.1007/978-0-387-73251-0_11.
Google Scholar
NOAA Office of Law Enforcement. Speed-filtered vessel monitoring system (VMS) data from Greater. Atlantic VMS Program (2019).
Palmer, M. C., & Wigley, S. E. Validating the stock apportionment of commercial fisheries landings using positional data from vessel monitoring systems (VMS). Northeast Fisheries Science Center Reference Document 07–22. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northeast Fisheries Science Center, Woods Hole, MA. (2007).
Northeastern Regional Association of Coastal Ocean Observing Systems Buoy (NERACOOS) Monitoring Program. Portsmouth, NH. www.neracoos.org (2021).
Stroup, W. Generalized Linear Mixed Models: Modern Concepts (Methods and Applications. Taylor & Francis Group, 2013).
Google Scholar
Ridout, M. S., Hinde, J. P., & Demétrio, C. G. B. “Models for Count Data with Many Zeros,” in Proceedings of the 19th International Biometric Conference, 179–192, Cape Town. (1998).
Barnhardt, W. A., Kelley, J. T., Dickson, S. M. & Belknap, D. F. Mapping the Gulf of maine with side-scan sonar: A new bottom-type classification for complex seafloors. J. Coast. Res. 14, 646–659 (1998).
Carrier-Belleau, C. et al. Environmental stressors, complex interactions and marine benthic communities’ responses. Sci. Rep. 11, 4194. https://doi.org/10.1038/s41598-021-83533-1 (2021).
Google Scholar
Auster, P., Joy, K. & Valentine, P. C. Fish species and community distributions as proxies for seafloor habitat distributions: the Stellwagen Bank National Marine Sanctuary example (Northwest Atlantic, Gulf of Maine). Environ. Biol. Fishes 60, 331–346 (2001).
Google Scholar
Solan, M., Raffaelli, D. G., Paterson, D. M., White, P. C. L. & Pierce, G. J. Marine biodiversity and ecosystem function: Empirical approaches and future research needs. Mar. Ecol. Prog. Ser. 311, 175–178 (2006).
Google Scholar
Worm, B. et al. Impacts of biodiversity loss on ocean ecosystem services. Science 314, 787–790 (2006).
Google Scholar
Dyksma, S. et al. Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME J. 10, 1939–1953 (2016).
Google Scholar
Tuttle, R. N. et al. Detection of natural products and their producers in ocean sediments. Appl. Environ. Microbiol. 85, e02830-e2918 (2019).
Google Scholar
Heinrichs, L., Aytur, S. A. & Bucci, J. P. Whole metagenomic sequencing to characterize the sediment microbial community within the Stellwagen Bank National Marine Sanctuary and preliminary biosynthetic gene cluster screening of Streptomyces scabrisporus. Mar. Genom. 50, 100718 (2020).
Google Scholar
Belknap, K. C. et al. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria. Sci. Rep. 10, 2003. https://doi.org/10.1038/s41598-020-58904-9 (2020).
Google Scholar
Sánchez-Soto Jiménez, M. F., Cerqueda-García, D., Montero-Muñoz, J. L., Aguirre-Macedo, M. L. & García-Maldonado, J. Q. Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. PeerJ 6, e5583. https://doi.org/10.7717/peerj (2018).
Google Scholar
Pershing, A. J. et al. Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery. Science 62, 809–812 (2015).
Google Scholar
Pittman, S. J. Relevance of the Northeast Integrated Ecosystem Assessment for the Stellwagen Bank National Marine Sanctuary Condition Report (2007–2018) Marine Sanctuaries Conservation Science Series ONMS-19–08. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD. (2019).
Bucci, J. P., Szempruch, A. J., Caldwell, J. M., Ellis, C. & Levine, J. F. Seasonal changes in microbial community structure in freshwater stream sediment in a North Carolina River Basin. Diversity 6, 18–32 (2014).
Google Scholar
Won, N. I., Kim, K. H., Kang, J. H., Park, S. R. & Lee, H. J. Exploring the impacts of anthropogenic disturbance on seawater and sediment microbial communities in korean coastal waters using metagenomics analysis. Int. J. Environ. Res. Public Health 14, 130 (2017).
Google Scholar
Zinger, L. et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6(9), e24570 (2011).
Google Scholar
Auster, P., Lindholm, J., Cramer, A., Nenandovic, M., Prindle, C., & Tamsett, A. The seafloor habitat recovery monitoring project (SHRMP) at Stellwagen Bank National Marine Sanctuary. Final Project Report. (2013b).
UN General Assembly, Transforming our world: The 2030 Agenda for Sustainable Development, 21 October, A/RES/70/1, available at: https://www.refworld.org/docid/57b6e3e44.html. (2015).
Malve, H. Exploring the ocean for new drug developments: Marine pharmacology. J. Pharm. Bioall. Sci. 8, 83–91. https://doi.org/10.4103/0975-7406.171700 (2016).
Google Scholar
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