Wisz MS, Pottier J, Kissling WD, Pellissier L, Lenoir J, Damgaard CF, et al. The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling. Biol Rev Camb Philos Soc. 2013;88:15–30.
Google Scholar
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457–63.
Google Scholar
Cho BC, Azam F. Major role of bacteria in biogeochemical fluxes in the oceans interior. Nature. 1988;332:441–3.
Google Scholar
Rousk J, Bengtson P. Microbial regulation of global biogeochemical cycles. Front Microbiol. 2014;5:103.
Google Scholar
Guilhon M, Montserrat F, Turra A. Recognition of ecosystem-based management principles in key documents of the seabed mining regime: implications and further recommendations. ICES J Marine Sci. 2020:fsaa229.
Sherman K, Sissenwine M, Christensen V, Duda A, Hempel G, Ibe C, et al. A global movement toward an ecosystem approach to management of marine resources. Mar Ecol Prog Ser. 2005;300:275–9.
Google Scholar
Passarelli C, Olivier F, Paterson DM, Hubas C. Impacts of biogenic structures on benthic assemblages: microbes, meiofauna, macrofauna and related ecosystem functions. Mar Ecol Prog Ser. 2012;465:85–97.
Google Scholar
Baldrighi E, Aliani S, Conversi A, Lavaleye M, Borghini M, Manini E. From microbes to macrofauna: an integrated study of deep benthic communities and their response to environmental variables along the Malta Escarpment (Ionian Sea). Sci Mar. 2013;77:625–39.
Google Scholar
Foshtomi MY, Braeckman U, Derycke S, Sapp M, Van Gansbeke D, Sabbe K, et al. The link between microbial diversity and nitrogen cycling in marine sediments is modulated by macrofaunal bioturbation. PLoS ONE. 2015;10:e0130116.
Hope JA, Paterson DM, Thrush SF. The role of microphytobenthos in soft-sediment ecological networks and their contribution to the delivery of multiple ecosystem services. J Ecology. 2020;108:815–30.
Google Scholar
Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, et al. Ocean plankton. Determinants of community structure in the global plankton interactome. Science. 2015;348:1262073.
Google Scholar
Blanchet FG, Cazelles K, Gravel D. Co-occurrence is not evidence of ecological interactions. Ecol Lett. 2020;23:1050–63.
Google Scholar
Pearson K. Mathematical contributions to the theory of evolution—on a form of spurious correlation which may arise when indices are used in the measurement of organs. Proc R Soc Lond. 1897;60:489–98.
Google Scholar
Jackson DA. Compositional data in community ecology: the paradigm or peril of proportions? Ecology. 1997;78:929–40.
Google Scholar
Gloor GB, Reid G. Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data. Can J Microbiol. 2016;62:692–703.
Google Scholar
Lovell D, Pawlowsky-Glahn V, Egozcue JJ, Marguerat S, Bahler J. Proportionality: a valid alternative to correlation for relative data. PLoS Comput Biol. 2015;11:e1004075.
Google Scholar
Sievert SM, Vetriani C. Chemoautotrophy at deep-sea vents: past, present, and future. Oceanography. 2012;25:218–33.
Google Scholar
Huber JA, Butterfield DA, Baross JA. Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat. Appl Environ Microbiol. 2002;68:1585–94.
Google Scholar
Karl DM, Wirsen CO, Jannasch HW. Deep-sea primary production at the Galapagos hydrothermal vents. Science. 1980;207:1345–7.
Google Scholar
Meyer JL, Akerman NH, Proskurowski G, Huber JA Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount Juan de Fuca Ridge. Front Microbiol. 2013;4:153.
Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev. 2011;75:361–422.
Google Scholar
Dubilier N, Bergin C, Lott C. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis. Nat Rev Microbiol. 2008;6:725–40.
Google Scholar
Yamanaka T et al. A Compilation of the Stable Isotopic Compositions of Carbon, Nitrogen, and Sulfur in Soft Body Parts of Animals Collected from Deep-Sea Hydrothermal Vent and Methane Seep Fields: Variations in Energy Source and Importance of Subsurface Microbial Processes in the Sediment-Hosted Systems. In: Ishibashi J, Okino K, Sunamura M, editors. Subseafloor Biosphere Linked to Hydrothermal Systems. Tokyo, Japan: Springer Open; 2015. p. 105–29.
Bergquist D, Eckner J, Urcuyo I, Cordes E, Hourdez S, Macko S, Fisher C. Using stable isotopes and quantitative community characteristics to determine a local hydrothermal vent food web. Mar Ecol Prog Ser. 2007;330:49–65.
Google Scholar
Colaço A, Dehairs F, Desbruyères D. Nutritional relations of deep-sea hydrothermal fields at the Mid-Atlantic Ridge: a stable isotope approach. Deep-Sea Res Part I-Oceanogr Res Pap. 2002;49:395–412.
Google Scholar
Van Dover C, Fry B. Stable isotopic compositions of hydrothermal vent organisms. Mar Biol. 1989;102:257–63.
Google Scholar
Colaço A, Desbruyères D, Guezennec J. Polar lipid fatty acids as indicators of trophic associations in a deep-sea vent system community. Marine Ecology-an Evolut Perspect. 2007;28:15–24.
Google Scholar
Limen H, Stevens CJ, Bourass Z, Juniper SK. Trophic ecology of siphonostomatoid copepods at deep-sea hydrothermal vents in the northeast Pacific. Mar Ecol Prog Ser. 2008;359:161–70.
Google Scholar
Van Dover CL. Trophic relationships among invertebrates at the Kairei hydrothermal vent field (Central Indian Ridge). Mar Biol. 2002;141:761–72.
Google Scholar
Lamy T, Koenigs C, Holbrook SJ, Miller RJ, Stier AC, Reed DC. Foundation species promote community stability by increasing diversity in a giant kelp forest. Ecology. 2020;101:e02987.
Google Scholar
Bruno JF, Bertness MD Habitat modification and facilitation in benthic marine communities. In: Bertness MD, Gaines SD, Hay ME, editors. Marine Community Ecology. Sunderland, MA: Sinauer Associates; 2001. p. 201–18.
Dayton PK Toward an Understanding of Community Resilience and the Potential Effects of Enrichments to the Benthos at McMurdo Sound, Antarctica. Pages 81-95. In: Parker BC, editor. Proceedings of the Colloquium on Conservation Problems. Lawrence, Kansas, USA.: Allen Press; 1972.
Tunnicliffe V, Cordes EE The tubeworm forests of hydrothermal vents and cold seeps. In: Rossi S, Bramanti L, editors. Perspectives on the Marine Animal Forests of the World Springer; 2020. p. 147–92.
López-García P, Gaill F, Moreira D. Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila. Environ Microbiol. 2002;4:204–15.
Google Scholar
Rincon-Tomas B, Francisco Javier González, Luis Somoza, Kathrin Sauter, Pedro Madureira, Teresa Medialdea et al. Siboglinidae Tubes as an Additional Niche for Microbial Communities in the Gulf of Cadiz-A Microscopical Appraisal. Microorganisms. 2020;8:367.
Page A, Juniper SK, Olagnon M, Alain K, Desrosiers G, Querellou J, et al. Microbial diversity associated with a Paralvinella sulfincola tube and the adjacent substratum on an active deep-sea vent chimney. Geobiology. 2004;2:225–38.
Google Scholar
Govenar B Shaping Vent and Seep Communities: Habitat Provision and Modification by Foundation Species. In: Kiel S, editor. The vent and seep biota: aspects from microbes to ecosystems. Dordrecht: Springer; 2010. p. 403–32.
Tunnicliffe V, Germain CS, Hilario A Phenotypic Variation and Fitness in a Metapopulation of Tubeworms (Ridgeia piscesae Jones) at Hydrothermal Vents. PLoS ONE. 2014;9:e110578.
Sarrazin J, Juniper SK. Biological characteristics of a hydrothermal edifice mosaic community. Mar Ecol Prog Ser. 1999;185:1–19.
Google Scholar
Sarrazin J, Juniper SK, Massoth G, Legendre P. Physical and chemical factors influencing species distributions on hydrothermal sulfide edifices of the Juan de Fuca Ridge, northeast Pacific. Mar Ecol Prog Ser. 1999;190:89–112.
Google Scholar
Govenar BW, Bergquist DC, Urcuyo IA, Eckner JT, Fisher CR. Three Ridgeia piscesae assemblages from a single Juan de Fuca Ridge sulphide edifice: structurally different and functionally similar. Cah Biol Mar. 2002;43:247–52.
Forget NL, Juniper SK. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge. MicrobiologyOpen. 2013;2:259–75.
Google Scholar
Danovaro R, Gambi C, Dell’Anno A, Corinaldesi C, Fraschetti S, Vanreusel A, et al. Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss. Curr Biol. 2008;18:1–8.
Google Scholar
Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nature Rev Microbiol. 2019;17:271–83.
Google Scholar
Lee W-K, Juniper SK, Perez M, Ju S-J, Kim S-J Diversity and characterization of bacterial communities of five co-occurring species at a hydrothermal vent on the Tonga Arc. Ecol Evol. 2021;11:4481–93.
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA. 2006;103:12115–20.
Google Scholar
Eren AM, Vineis JH, Morrison HG, Sogin ML. A filtering method to generate high quality short reads using illumina paired-end technology. PLoS One. 2013;8:e66643.
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
Google Scholar
Caron DA, Countway PD, Savai P, Gast RJ, Schnetzer A, Moorthi SD, et al. Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol. 2009;75:5797–808.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–6.
Google Scholar
Guillou L, Bachar D, Audic S, Bass D, Berney C, Bittner L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2013;41:D597–604.
Google Scholar
Quinn TP, Ionas Erb, Greg Gloor, Cedric Notredame, Mark F Richardson, Tamsyn M Crowley et al. A field guide for the compositional analysis of any-omics data. Gigascience. 2019;8:giz107.
Martín-Fernández JA, Palarea-Albaladejo J, Olea RA Dealing with Zeros. In: Pawlowsky‐Glahn V, Buccianti A, editors. Compositional Data Analysis2011. p. 43-58.
Palarea-Albaladejo J, Martin-Fernandez JA. zCompositions – R Package for multivariate imputation of left-censored data under a compositional approach. Chemometr Intell Lab. 2015;143:85–96.
Google Scholar
Aitchison J The statistical analysis of compositional data. London: Chapman & Hall; 1986. p. 416.
Aitchison J, Barcelo-Vidal C, Martin-Fernandez JA, Pawlowsky-Glahn V. Logratio analysis and compositional distance. Math Geol. 2000;32:271–5.
Google Scholar
Comas-Cufí M coda.base: A Basic Set of Functions for Compositional Data Analysis. R package version 0.2.1 2019 [Available from: https://CRAN.R-project.org/package=coda.base.
Oksanen J et al. vegan: Community Ecology Package. R package version 2.2-1. 2015 [Available from: http://CRAN.R-project.org/package=vegan.
Fernandes AD, Macklaim JM, Linn TG, Reid G, Gloor GB. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS One. 2013;8:e67019.
Google Scholar
Quinn TP, Richardson MF, Lovell D, Crowley TM. propr: an R-package for identifying proportionally abundant features using compositional data analysis. Sci Rep. 2017;7:16252.
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research. 2003;13:2498–504.
Google Scholar
Huber JA, Butterfield DA, Baross JA. Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. FEMS Microbiol Ecol. 2003;43:393–409.
Google Scholar
Akerman NH, Butterfield DA, Huber JA Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids. Front Microbiol. 2013;4:185.
Tsurumi M, Tunnicliffe V. Tubeworm-associated communities at hydrothermal vents on the Juan de Fuca Ridge, northeast Pacific. Deep-Sea Res Part I-Oceanogr Res Pap. 2003;50:611–29.
Google Scholar
Butterfield DA, Massoth GJ, McDuff RE, Lupton JE, Lilley MD. Geochemistry of hydrothermal fluids from Axial Seamount Hydrothermal Emissions Study vent field, Juan de Fuca Ridge: subseafloor boiling and subsequent fluid-rock interaction. J Geophys Res. 1990;95:12895–921.
Google Scholar
Johnson KS, Beehler CL, Sakamotoarnold CM, Childress JJ. insitu measurements of chemical-distributions in a deep-sea hydrothermal vent field. Science. 1986;231:1139–41.
Google Scholar
Du Preez C, Fisher CP Long-Term Stability of back-Arc basin hydrothermal vents. Front Mar Sci. 2018;5:54.
Urcuyo IA, Bergquist DC, MacDonald IR, VanHorn M, Fisher CR. Growth and longevity of the tubeworm Ridgeia piscesae in the variable diffuse flow habitats of the Juan de Fuca Ridge. Mar Ecol Prog Ser. 2007;344:143–57.
Google Scholar
Perner M, Bach W, Hentscher M, Koschinsky A, Garbe-Schönberg D, Streit WR, et al. Short-term microbial and physico-chemical variability in low-temperature hydrothermal fluids near 5 degrees S on the Mid-Atlantic Ridge. Environ Microbiol. 2009;11:2526–41.
Google Scholar
Orcutt BN, Bradley JA, Brazelton WJ, Estes ER, Goordial JM, Huber JA, et al. Impacts of deep-sea mining on microbial ecosystem services. Limnology Oceanogr. 2020;65:1489–510.
Google Scholar
Gollner S, Ivanenko VN, Arbizu PM, Bright M. Advances in taxonomy, ecology, and biogeography of Dirivultidae (copepoda) associated with chemosynthetic environments in the deep sea. PLoS One. 2010;5:e9801.
Google Scholar
Kalanetra KM, Nelson DC. Vacuolate-attached filaments: highly productive Ridgeia piscesae epibionts at the Juan de Fuca hydrothermal vents. Mar Biol. 2010;157:791–800.
Google Scholar
Girguis PR, Lee RW. Thermal preference and tolerance of alvinellids. Science. 2006;312:231.
Google Scholar
Burgaud G, Le Calvez T, Arzur D, Vandenkoornhuyse P, Barbier G. Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environ Microbiol. 2009;11:1588–600.
Google Scholar
Murdock SA, Juniper SK. Hydrothermal vent protistan distribution along the Mariana arc suggests vent endemics may be rare and novel. Environ Microbiol. 2019;21:3796–815.
Google Scholar
Meier DV, Bach W, Girguis PR, Gruber-Vodicka HR, Reeves EP, Richter M, et al. Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting. Environ Microbiol. 2016;18:4348–68.
Google Scholar
Stokke R, Dahle H, Roalkvam I, Wissuwa J, Daae FL, Tooming-Klunderud A, et al. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environ Microbiol. 2015;17:4063–77.
Google Scholar
Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, et al. Revisions to the classification, nomenclature, and diversity of eukaryotes. J Eukaryot Microbiol. 2019;66:4–119.
Google Scholar
Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AG, et al. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc Biol Sci. 2013;280:20131755.
Google Scholar
Hamann E, Gruber-Vodicka H, Kleiner M, Tegetmeyer HE, Riedel D, Littmann S, et al. Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature. 2016;534:254–8.
Google Scholar
Gollner S, Riemer B, Arbizu PM, Le Bris N, Bright M. Diversity of meiofauna from the 9 degrees 50’ N East Pacific rise across a gradient of hydrothermal fluid emissions. PLoS ONE. 2010;5:e12321.
Sarrazin J, Legendre P, de Busserolles F, Fabri MC, Guilini K, Ivanenko VN, et al. Biodiversity patterns, environmental drivers and indicator species on a high-temperature hydrothermal edifice, Mid-Atlantic Ridge. Deep-Sea Res Part Ii-Topical Stud Oceanogr. 2015;121:177–92.
Google Scholar
Bates AE, Harmer TL, Roeselers G, Cavanaugh CM. Phylogenetic characterization of episymbiotic bacteria hosted by a hydrothermal vent limpet (lepetodrilidae, vetigastropoda). Biol Bull-US. 2011;220:118–27.
Google Scholar
Schratzberger M, Ingels J. Meiofauna matters: the roles of meiofauna in benthic ecosystems. J Exp Mar Biol Ecol. 2018;502:12–25.
Google Scholar
Cronin-O’Reilly S, Joe D Taylor, Ian Jermyn, A Louise Allcock, Michael Cunliffe, Mark P Johnson et al. Limited congruence exhibited across microbial, meiofaunal and macrofaunal benthic assemblages in a heterogeneous coastal environment. Sci Rep-UK. 2018;8:15500.
Reimann F, Schrage M. The mucus-trap hypothesis on feeding of aquatic nematodes and implications for biodegradation and sediment texture. Oecologia. 1978;34:75–88.
Google Scholar
Léveillé RJ, Levesque C, Juniper SK Biotic interactions and feedback processes in deep-sea hydrothermal vent ecosystems. In: Kristensen E, Haese RR, Kostka JE, editors. Interactions between macro- and microorganisms in marine sediments. Washington, DC: American Geophysical Union; 2005. p. 299–321.
Ingels J, Ann Vanreusel, Ellen Pape, Francesca Pasotti, Lara Macheriotou, Pedro Martínez Arbizu et al. Ecological variables for deep-ocean monitoring must include microbiota and meiofauna for effective conservation. Nat Ecology Evolut. 2020: https://doi.org/10.1038/s41559-020-01335-6.
Thompson KF, Miller KA, Currie D, Johnston P, Santillo D. Seabed mining and approaches to governance of the deep seabed. Front Mar Sci. 2018;5:480.
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