Habitat heterogeneity effects on microbial communities of the Gulf of Maine

Achbergerová, 2011, An ancient energy source and active metabolic regulator, Microb. Cell Factories, 10, 63, 10.1186/1475-2859-10-63 Albertelli, 1999, Differential responses of bacteria, meiofauna and macrofauna in a shelf area (Ligurian Sea, NW Mediterranean): role of food availability, J. Sea Res., 42, 11, 10.1016/S1385-1101(99)00012-X Anderson, 2006, Distance‐based tests for homogeneity of multivariate dispersions, Biometrics, 62, 245, 10.1111/j.1541-0420.2005.00440.x Anderson, 2013, PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing?, Ecol. Monogr., 83, 557, 10.1890/12-2010.1 Archer, 1992, Benthic oxygen fluxes on the Washington shelf and slope: a comparison of in situ microelectrode and chamber flux measurements, Limnol. Oceanogr., 37, 614, 10.4319/lo.1992.37.3.0614 Arndt, 2013, Quantifying the degradation of organic matter in marine sediments: a review and synthesis, Earth Sci. Rev., 123, 53, 10.1016/j.earscirev.2013.02.008 Bartsch, 1960, Isolation and properties of two soluble heme proteins in extracts of the photoanaerobe Chromatium, JBC, 235, 825, 10.1016/S0021-9258(19)67945-7 Belley, 2016, Relative contributions of biodiversity and environment to benthic ecosystem functioning, Front. Mar. Sci., 3 Belley, 2017, The role of infaunal functional groups in short-term response of contrasting benthic communities to an experimental food pulse, J. Exp. Mar. Biol. Ecol., 491, 38, 10.1016/j.jembe.2017.03.005 Bolyen, 2019, Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2, Nat. Biotechnol., 37, 852, 10.1038/s41587-019-0209-9 Borcard, 2018, 299 Bowman, 2003, Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment, Appl. Environ. Microbiol., 69, 2463, 10.1128/AEM.69.5.2463-2483.2003 Carriot, 2022, Impact of phosphate concentration on the metabolome of biofilms of the marine bacterium Pseudoalteromonas lipolytica, Metabolomics, 18, 1, 10.1007/s11306-022-01875-x Christensen, 1996, Water column nutrients and sedimentary denitrification in the Gulf of Maine, Continent. Shelf Res., 16, 489, 10.1016/0278-4343(95)00027-5 Clarke, 1993, Non-parametric multivariate analyses of changes in community structure, Aust. J. Ecol., 18, 117, 10.1111/j.1442-9993.1993.tb00438.x Comeau, 2017, Microbiome helper: a custom and streamlined workflow for microbiome research, mSystems, 2, 10.1128/mSystems.00127-16 Corinaldesi, 2019, High diversity of benthic bacterial and archaeal assemblages in deep-Mediterranean canyons and adjacent slopes, Prog. Oceanogr., 171, 154, 10.1016/j.pocean.2018.12.014 Corsaro, 2004, Influence of growth temperature on lipid and phosphate contents of surface polysaccharides from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC 125, J. Bacterial., 186, 29, 10.1128/JB.186.1.29-34.2004 Crump, 2004, Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time, Appl. Environ. Microbiol., 70, 1494, 10.1128/AEM.70.3.1494-1505.2004 Danovaro, 2009, 45 Dell'Anno, 2021, Highly contaminated marine sediments can host rare bacterial taxa potentially useful for bioremediation, Front. Microbiol., 12 D'Hondt, 2004, Distributions of microbial activities in deep subseafloor sediments, Science, 306, 2216, 10.1126/science.1101155 Diaz, 2008, Marine polyphosphate: a key player in geologic phosphorus sequestration, Science, 320, 652, 10.1126/science.1151751 Dyksma, 2016, Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments, ISME J., 10, 1939, 10.1038/ismej.2015.257 Fernandez-Arcaya, 2017, Ecological role of submarine canyons and need for canyon conservation: a review, Front. Mar. Sci., 5 Foshtomi, 2015, The link between microbial diversity and nitrogen cycling in marine sediments is modulated by macrofaunal bioturbation, PLoS One, 10 Fox, 2011 Fuerst, 2011, Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function, Nat. Rev. Microbiol., 9, 403, 10.1038/nrmicro2578 Gärtner, 2011, Isolation and characterisation of bacteria from the Eastern Mediterranean deep sea, Antonie Leeuwenhoek, 100, 421, 10.1007/s10482-011-9599-5 Grieshaber, 1998, Animal adaptations for tolerance and exploitation of poisonous sulfide, Annu. Rev. Physiol., 60, 33, 10.1146/annurev.physiol.60.1.33 Gooday, 1990, Responses by benthic organisms to inputs of organic material to the ocean floor: a review, Philos. Trans. Royal Soc. A, 331, 119 Goffredi, 2010, Bacterial community shifts in taxa and diversity in response to localized organic loading in the deep sea, Environ. Microbiol., 12, 344, 10.1111/j.1462-2920.2009.02072.x Guitton, 2015, Biogeochemical consequences of vertical and lateral transport of particulate organic matter in the southern North Sea: a multiproxy approach, Estuar. Coast Shelf Sci., 165, 117, 10.1016/j.ecss.2015.09.010 Hammond, 1985, Benthic fluxes in San Francisco Bay, Hydrobiologia, 129, 69, 10.1007/BF00048688 Hargrave, 2008, Towards a classification of organic enrichment in marine sediments based on biogeochemical indicators, Mar. Pollut. Bull., 56, 810, 10.1016/j.marpolbul.2008.02.006 Harrison, 2018, Abrupt burial imparts persistent changes to the bacterial diversity of turbidite‐associated sediment profiles, Geobiology, 16, 190, 10.1111/gbi.12271 Hedges, 2000, Organic matter in Bolivian tributaries of the Amazon River: a comparison to the lower mainstream, Limnol. Oceanogr., 45, 1449, 10.4319/lo.2000.45.7.1449 Hensen, 2006, 207 Henrichs, 1992, Early diagenesis of organic matter in marine sediments: progress and perplexity, Mar. Chem., 39, 119, 10.1016/0304-4203(92)90098-U Hinrichs, 2006, Biological formation of ethane and propane in the deep marine subsurface, Proc. Natl. Acad. Sci. U.S.A., 103, 14684, 10.1073/pnas.0606535103 Hoffmann, 2020, Diversity and metabolism of Woeseiales bacteria, global members of marine sediment communities, ISME J., 14, 1042, 10.1038/s41396-020-0588-4 Hunter, 2012, Macrobenthic assemblage structure and organismal stoichiometry control faunal processing of particulate organic carbon and nitrogen in oxygen minimum zone sediments, Biogeosciences, 9, 993, 10.5194/bg-9-993-2012 Huvenne, 2014, Towards a new and integrated approach to submarine canyon research. Introduction, Deep Sea Res. Part II Top. Stud. Oceanogr., 104, 1, 10.1016/j.dsr2.2013.09.012 Ingall, 1994, Evidence for enhanced phosphorus regeneration from marine sediments overlain by oxygen depleted waters, Geochem. Cosmochim. Acta, 58, 2571, 10.1016/0016-7037(94)90033-7 Ismail, 2018, Quantifying spatial heterogeneity in submarine canyons, Prog. Oceanogr., 169, 181, 10.1016/j.pocean.2018.03.006 Jacob, 2013, Biogeography of deep-sea benthic bacteria at regional scale (LTER HAUSGARTEN, Fram Strait, Arctic), PLoS One, 8, 10.1371/journal.pone.0072779 Jørgensen, 1982, Mineralization of organic matter in the sea bed—the role of sulphate reduction, Nature, 296, 643, 10.1038/296643a0 Jørgensen, 2007, Feast and famine—microbial life in the deep-sea bed, Nat. Rev. Microbiol., 5, 770, 10.1038/nrmicro1745 Kallmeyer, 2012, Global distribution of microbial abundance and biomass in subseafloor sediment, Proc. Natl. Acad. Sci. USA, 109, 16213, 10.1073/pnas.1203849109 Keil, 2011, Terrestrial influences on carbon burial at sea, Proc. Natl. Acad. Sci. U.S.A., 108, 9729, 10.1073/pnas.1106928108 Keuter, 2016, Spatial homogeneity of bacterial and archaeal communities in the deep eastern Mediterranean Sea surface sediments, Int. Microbiol., 19, 109 Kim, 2017, Deciphering diversity indices for a better understanding of microbial communities, J. Microbiol. Biotechnol., 27, 2089, 10.4014/jmb.1709.09027 Kristensen, 2005, 125 Kulaev, 1975, Biochemistry of inorganic polyphosphates, Rev. Physiol. Biochem. Pharmacol., 73, 131, 10.1007/BFb0034661 Levin, 2005, Ecology of cold seep sediments: interactions of fauna with flow, chemistry and microbes, Oceanogr. Mar. Biol., 11–56 Li, 2009, Bacterial diversity in surface sediments from the Pacific Arctic Ocean, Extremophiles, 13, 233, 10.1007/s00792-009-0225-7 Loubere, 1991, Deep‐sea benthic foraminiferal assemblage response to a surface ocean productivity gradient: a test, Paleoceanography, 6, 193, 10.1029/90PA02612 Loubere, 1998, The impact of seasonality on the benthos as reflected in the assemblages of deep-sea foraminifera, Deep-Sea Res. Part I Oceanogr. Res. Pap., 45, 409, 10.1016/S0967-0637(97)00092-7 Lücker, 2014, The family Nitrospinaceae Mayer, 1994, Surface area control of organic carbon accumulation in continental shelf sediments, Geochem. Cosmochim. Acta, 58, 1271, 10.1016/0016-7037(94)90381-6 Mayer, 1995, Bioavailable amino acids in sediments: a biomimetic, kinetics-based approach, Limnol. Oceanogr., 40, 511, 10.4319/lo.1995.40.3.0511 McArdle, 2001, Fitting multivariate models to community data: a comment on distance‐based redundancy analysis, Ecol., 82 1, 290, 10.1890/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2 Meyers, 1994, Preservation of elemental and isotopic source identification of sedimentary organic matter, Chem. Geol., 114, 289, 10.1016/0009-2541(94)90059-0 Middelburg, 2011, Chemoautotrophy in the ocean, Geophys. Res. Lett., 38, 10.1029/2011GL049725 Moodley, 2002, Bacteria and foraminifera: key players in a short-term deep-sea benthic response to phytodetritus, Mar. Ecol. Prog. Ser., 236, 23, 10.3354/meps236023 Mosier, 2012, Genome sequence of “Candidatus Nitrosopumilus salaria” BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary, J. Bacteriol. Res., 2121, 10.1128/JB.00013-12 Moens, 1997, Observations on the feeding ecology of estuarine nematodes, J. Mar. Biol. Assoc. U. K., 77, 211, 10.1017/S0025315400033889 Moens, 2005, Dual stable isotope abundances unravel trophic position of estuarine nematodes, J. Mar. Biol. Assoc. U. K., 85, 1401, 10.1017/S0025315405012580 Namirimu, 2023, Microbial diversity of Deep-sea Sediments from three newly discovered hydrothermal vent Fields in the central Indian ridge, Ocean Sci. J., 58, 11, 10.1007/s12601-023-00106-1 Oksanen, 2005, 7 Orsi, 2018, Ecology and evolution of seafloor and subseafloor microbial communities, Nat. Rev. Microbiol., 16, 671, 10.1038/s41579-018-0046-8 Øvreås, 1997, Distribution of bacterioplankton in meromictic Lake Sælenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA, Appl. Environ. Microbiol., 63, 3367, 10.1128/aem.63.9.3367-3373.1997 Park, 2010, Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria, Appl. Environ. Microbiol., 76, 7575, 10.1128/AEM.01478-10 Parrish, 1987, Separation of aquatic lipid classes by chromarod thin-layer chromatography with measurement by iatroscan flame ionization detection, Can. J. Fish. Aquat. Sci Aquat. Sci, 44, 722, 10.1139/f87-087 Parrish, 1999, Determination of total lipid, lipid classes, and fatty acids in aquatic samples, 4 Paull, 2006, Discordant 14C-stratigraphies in upper Monterey Canyon: a signal of anthropogenic disturbance, Mar. Geol., 233, 21, 10.1016/j.margeo.2006.07.008 Pester, 2011, The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology, Curr. Opin. Microbiol., 14, 300, 10.1016/j.mib.2011.04.007 Petrie, 2000, Annual and interannual variability of nutrients and their estimated fluxes in the Scotian Shelf-Gulf of Maine region, Can. J. Fish. Aquat. Sci., 57, 2536, 10.1139/f00-235 Pinhassi, 2003, Differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from Lake Kinneret (Israel), the Eastern Mediterranean Sea, and the Gulf of Eilat, Appl. Environ. Microbiol., 69, 199, 10.1128/AEM.69.1.199-211.2003 Polinski, 2019, Metabarcoding assessment of prokaryotic and eukaryotic taxa in sediments from Stellwagen Bank National marine sanctuary, Sci. Rep., 9, 1, 10.1038/s41598-019-51341-3 Polymenakou, 2008, Exo-enzymatic activities and organic matter properties in deep-sea canyon and slope systems off the southern Cretan margin, Deep-Sea Res. Part I Oceanogr. Res. Pap., 55, 1318, 10.1016/j.dsr.2008.05.010 Polymenakou, 2009, Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea, Syst. Appl. Microbiol., 32, 17, 10.1016/j.syapm.2008.09.006 Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Opens external link in new window Nucl. Acids Res., 41, D590 Qin, 2011, Comparative genomics reveals a deep-sea sediment-adapted lifestyle of Pseudoalteromonas sp. SM9913, ISME J., 5, 274, 10.1038/ismej.2010.103 Ransom, 1998, Organic matter preservation on continental slopes: importance of mineralogy and surface area, Geochem. Cosmochim. Acta, 62, 1329, 10.1016/S0016-7037(98)00050-7 Roman, 2019, Microbial community structure and functionality in the deep-sea floor: evaluating the causes of spatial heterogeneity in a submarine canyon system (NW Mediterranean, Spain), Front. Mar. Sci., 6, 108, 10.3389/fmars.2019.00108 Sánchez-Soto, 2023, Spatiotemporal dynamics of benthic bacterial communities in the Perdido fold Belt, Northwestern Gulf of Mexico, Front. Mar. Sci., 10, 10.3389/fmars.2023.1070548 Schauer, 2010, Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean, ISME J., 4, 159, 10.1038/ismej.2009.106 Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 75, 7537, 10.1128/AEM.01541-09 Schippers, 2005, Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria, Nature, 433, 861, 10.1038/nature03302 Schippers, 2012, Quantification of microbial communities in subsurface marine sediments of the Black Sea and off Namibia, Front. Microbiol., 3, 16, 10.3389/fmicb.2012.00016 Schwalbach, 2004, Viral effects on bacterial community composition in marine plankton microcosms, Aquat. Microb. Ecol., 34, 117, 10.3354/ame034117 Sevastou, 2013, Benthic communities in the deep Mediterranean Sea: exploring microbial and meiofaunal patterns in slope and basin ecosystems, Biogeosciences, 10, 4861, 10.5194/bg-10-4861-2013 Sogin, 2006, Microbial diversity in the deep sea and the underexplored “rare biosphere” Proc, Natl. Acad. Sci. U.S.A., 103, 12115, 10.1073/pnas.0605127103 Solan, 2005, 105 Soudry, 2000, Microbial phosphate sediment Teske, 2008, Uncultured archaea in deep marine subsurface sediments: have we caught them all?, ISME J., 2, 18 Townsend, 2005, On the nature of Alexandrium fundyense blooms in the Gulf of Maine, Deep. Res. Part II Top. Stud. Oceanogr., 52, 2603, 10.1016/j.dsr2.2005.06.028 Townsend, 2006, Oceanography of the Northwest Atlantic continental shelf, 119 Townsend, 2010, A changing nutrient regime in the Gulf of Maine, Continent. Shelf Res., 30, 820, 10.1016/j.csr.2010.01.019 Vairavamurthy, 1992, Occurrence of particle‐bound polysulfides and significance of their reaction with organic matters in marine sediments, Geophys. Res. Lett., 19, 2043, 10.1029/92GL01995 Varliero, 2019, Microbial diversity and connectivity in deep-sea sediments of the South Atlantic polar front, Front. Microbiol., 10, 665, 10.3389/fmicb.2019.00665 Walker, 2023, Benthic bacteria and archaea in the North American Arctic reflect food supply regimes and impacts of coastal and riverine inputs, Deep Sea Res. Part II Top. Stud. Oceanogr., 207, 10.1016/j.dsr2.2022.105224 Weiler, 2018, Bacterial communities in tissues and surficial mucus of the cold-water coral Paragorgia arborea, Front. Mar. Sci., 5, 378, 10.3389/fmars.2018.00378 Wilkins, 2013, Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects, Nat. Commun., 4, 1, 10.1038/ncomms3457 Witte, 2003, Rapid response of a deep-sea benthic community to POM enrichment: an in situ experimental study, Mar. Ecol. Prog. Ser., 251, 27, 10.3354/meps251027 Witte, 2003, In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor, Nature, 424, 763, 10.1038/nature01799 Woulds, 2007, Oxygen as a control on seafloor biological communities and their roles in sedimentary carbon cycling, Limnol. Oceanogr., 52, 1698, 10.4319/lo.2007.52.4.1698 Zhang, 2021, Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments, Mol. Ecol., 30, 2800, 10.1111/mec.15937 Zuur, 2009, 574