Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth’s biogeochemical cycles. Science (New York, N.Y.) 320, 1034–1039 (2008).
Google Scholar
Jørgensen, B. B. & Kasten, S. in Marine Geochemistry, edited by H. D. Schulz & M. Zabel (Springer, 2006), 271–309.
Broman, E., Sjöstedt, J., Pinhassi, J. & Dopson, M. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. Microbiome 5, 96 (2017).
Google Scholar
Billerbeck, M. et al. Surficial and deep pore water circulation governs spatial and temporal scales of nutrient recycling in intertidal sand flat sediment. Mar. Ecol. Prog. Ser. 326, 61–76 (2006).
Google Scholar
Booth, J. M., Fusi, M., Marasco, R., Mbobo, T. & Daffonchio, D. Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions. Sci. Rep. 9, 3749 (2019).
Google Scholar
Torti, A., Lever, M. A. & Jørgensen, B. B. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar. Genom. 24(Pt 3), 185–196 (2015).
Starke, R., Pylro, V. S. & Morais, D. K. 16S rRNA gene copy number normalization does not provide more reliable conclusions in metataxonomic surveys. Microb. Ecol. 81, 535–539 (2021).
Google Scholar
Blazewicz, S. J., Barnard, R. L., Daly, R. A. & Firestone, M. K. Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses. ISME J. 7, 2061–2068 (2013).
Google Scholar
de Vrieze, J., Pinto, A. J., Sloan, W. T. & Ijaz, U. Z. The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. Microbiome 6, 63 (2018).
Google Scholar
Zhang, Y., Zhao, Z., Dai, M., Jiao, N. & Herndl, G. J. Drivers shaping the diversity and biogeography of total and active bacterial communities in the South China Sea. Mol. Ecol. 23, 2260–2274 (2014).
Google Scholar
Meyer, K. M., Petersen, I. A. B., Tobi, E., Korte, L. & Bohannan, B. J. M. Use of RNA and DNA to identify mechanisms of bacterial community homogenization. Front. Microbiol. 10, 2066 (2019).
Google Scholar
Petro, C., Starnawski, P., Schramm, A. & Kjeldsen, K. U. Microbial community assembly in marine sediments. Aquat. Microb. Ecol. 79, 177–195 (2017).
Walsh, E. A. et al. Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment. Appl. Environ. Microbiol. 82, 4994–4999 (2016).
Google Scholar
Dinsdale, E. A. et al. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE 3, e1584 (2008).
Google Scholar
Schmitt, S. et al. Salinity, microbe and carbonate mineral relationships in brackish and hypersaline lake sediments: A case study from the tropical Pacific coral atoll of Kiritimati. Depositional Rec. 5, 212–229 (2019).
Schneider, D., Arp, G., Reimer, A., Reitner, J. & Daniel, R. Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific. PLoS ONE 8, e66662 (2013).
Google Scholar
Zhang, B. et al. Sediment microbial communities and their potential role as environmental pollution indicators in Xuande Atoll, South China Sea. Front. Microbiol. 11, 1011 (2020).
Google Scholar
Galand, P. E. et al. Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific). FEMS Microbiol. Ecol. 79, 203–217 (2012).
Google Scholar
Stoddart, D. R. The conservation of Aldabra. Geogr. J. 134, 471 (1968).
Farrow, G. E. & Brander, K. M. Tidal studies on Aldabra. Phil. Trans. R. Soc. Lond. B 260, 93–121 (1971).
Google Scholar
Gaillard, C., Bernier, P. & Gruet, Y. L. lagon d’Aldabra (Seychelles, Océan indien), un modèle pour le paléoenvironnement de Cerin (Kimméridgien supérieur, Jura méridional, France). Geobios 27, 331–348 (1994).
Hamylton, S., Spencer, T. & Hagan, A. B. Spatial modelling of benthic cover using remote sensing data in the Aldabra lagoon, western Indian Ocean. Mar. Ecol. Prog. Ser. 460, 35–47 (2012).
Google Scholar
Braithwaite, C. J. R. Last interglacial changes in sea level on Aldabra, western Indian Ocean. Sedimentology 67, 3236–3258 (2020).
Haverkamp, P. J. et al. Giant tortoise habitats under increasing drought conditions on Aldabra Atoll—Ecological indicators to monitor rainfall anomalies and related vegetation activity. Ecol. Ind. 80, 354–362 (2017).
Hughes, R. N. & Gamble, J. C. A quantitative survey of the biota of intertidal soft substrata on Aldabra Atoll, Indian Ocean. Phil. Trans. R. Soc. Lond. B 279, 327–355 (1977).
Google Scholar
Braithwaite, C., Casanova, J., Frevert, T. & Whitton, B. A. Recent stromatolites in landlocked pools on Aldabra, Western Indian Ocean. Palaeogeogr. Palaeoclimatol. Palaeoecol. 69, 145–165 (1989).
Potts, M. & Whitton, B. A. Nitrogen fixation by blue-green algal communities in the intertidal zone of the lagoon of Aldabra Atoll. Oecologia 27, 275–283 (1977).
Google Scholar
Potts, M. & Whitton, B. A. Vegetation of the intertidal zone of the lagoon of Aldabra, with particular reference to the photosynthetic prokaryotic communities. Proc. R. Soc. Lond. B. 208, 13–55 (1980).
Google Scholar
Meyers, P. A. Preservation of elemental and isotopic source identification of sedimentary organic matter. Chem. Geol. 114, 289–302 (1994).
Google Scholar
Choi, A., Lee, K., Oh, H.-M., Feng, J. & Cho, J.-C. Litoricola marina sp. nov.. Int. J. Syst. Evolut. Microbiol. 60, 1303–1306 (2010).
Google Scholar
Durham, B. P. et al. Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome. Stand Genom. Sci. 9, 632–645 (2014).
Boehm, A. B., Yamahara, K. M. & Sassoubre, L. M. Diversity and transport of microorganisms in intertidal sands of the California coast. Appl. Environ. Microbiol. 80, 3943–3951 (2014).
Google Scholar
Probandt, D., Eickhorst, T., Ellrott, A., Amann, R. & Knittel, K. Microbial life on a sand grain: From bulk sediment to single grains. ISME J. 12, 623–633 (2018).
Google Scholar
Wong, H. L., Smith, D.-L., Visscher, P. T. & Burns, B. P. Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats. Sci. Rep. 5, 15607 (2015).
Google Scholar
Dupraz, C., Visscher, P. T., Baumgartner, L. K. & Reid, R. P. Microbe-mineral interactions: Early carbonate precipitation in a hypersaline lake (Eleuthera Island, Bahamas). Sedimentology 51, 745–765 (2004).
Google Scholar
Diaz, M. R., Piggot, A. M., Eberli, G. P. & Klaus, J. S. Bacterial community of oolitic carbonate sediments of the Bahamas Archipelago. Mar. Ecol. Prog. Ser. 485, 9–24 (2013).
Google Scholar
Cui, H., Yang, K., Pagaling, E. & Yan, T. Spatial and temporal variation in enterococcal abundance and its relationship to the microbial community in Hawaii beach sand and water. Appl. Environ. Microbiol. 79, 3601–3609 (2013).
Google Scholar
Petriglieri, F., Nierychlo, M., Nielsen, P. H. & McIlroy, S. J. In situ visualisation of the abundant Chloroflexi populations in full-scale anaerobic digesters and the fate of immigrating species. PLoS ONE 13, e0206255 (2018).
Google Scholar
Wietz, M., Gram, L., Jørgensen, B. & Schramm, A. Latitudinal patterns in the abundance of major marine bacterioplankton groups. Aquat. Microb. Ecol. 61, 179–189 (2010).
Wemheuer, B. et al. Impact of a phytoplankton bloom on the diversity of the active bacterial community in the southern North Sea as revealed by metatranscriptomic approaches. FEMS Microbiol. Ecol. 87, 378–389 (2014).
Google Scholar
Heywood, K. J., Stevens, D. P. & Bigg, G. R. Eddy formation behind the tropical island of Aldabra. Deep Sea Res. Part I 43, 555–578 (1996).
Pérez-Cataluña, A. et al. Revisiting the taxonomy of the genus Arcobacter: Getting order from the chaos. Front. Microbiol. 9, 2077 (2018).
Google Scholar
Revsbech, N. P. & Jørgensen, B. B. Microelectrodes: Their Use in Microbial Ecology. In Advances in Microbial Ecology (ed. Marshall, K. C.) 293–352 (Springer, 1989).
Watson, J. et al. Reductively debrominating strains of Propionigenium maris from burrows of bromophenol-producing marine infauna. Int. J. Syst. Evol. Microbiol. 50(Pt 3), 1035–1042 (2000).
Google Scholar
Sasi, J. T. S., Rahul, K., Ramaprasad, E. V. V., Sasikala, C. & Ramana, C. V. Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter. Int. J. Syst. Evolut. Microbiol. 63, 4619–4625 (2013).
Rinke, C. et al. High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont ‘Candidatus Thiobios zoothamnicoli’. FEMS Microbiol. Ecol. 67, 229–241 (2009).
Google Scholar
Vartoukian, S. R., Palmer, R. M. & Wade, W. G. The division “Synergistes”. Anaerobe 13, 99–106 (2007).
Google Scholar
Janssen, P. H. & Liesack, W. Succinate decarboxylation by Propionigenium maris sp. nov., a new anaerobic bacterium from an estuarine sediment. Arch. Microbiol. 164, 29–35 (1995).
Google Scholar
Shiozaki, T. et al. Nitrification and its influence on biogeochemical cycles from the equatorial Pacific to the Arctic Ocean. ISME J. 10, 2184–2197 (2016).
Google Scholar
González-Domenech, C. M., Martínez-Checa, F., Béjar, V. & Quesada, E. Denitrification as an important taxonomic marker within the genus Halomonas. Syst. Appl. Microbiol. 33, 85–93 (2010).
Google Scholar
Farmer, J. J., Michael, J. J., Brenner, F. W., Cameron, D. N. & Birkhead, K. M. The Book. In Bergey’s Manual of Systematics of Archaea and Bacteria (eds Whitman, W. B. et al.) 1–79 (Wiley, 2016).
Ventosa, A. & Haba, R. R. in Bergey’s Manual of Systematics of Archaea and Bacteria, edited by W. B. Whitman, et al. (Wiley, 2015), 1–16.
Lloyd, K. G. Time as a microbial resource. Environ. Microbiol. Rep. 13, 18–21 (2021).
Google Scholar
Holguin, G., Vazquez, P. & Bashan, Y. The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: An overview. Biol. Fertil. Soils 33, 265–278 (2001).
Google Scholar
Nanca, C. L., Neri, K. D., Ngo, A. C. R., Bennett, R. M. & Dedeles, G. R. Degradation of polycyclic aromatic hydrocarbons by moderately halophilic bacteria from Luzon salt beds. J. Health Pollut. 8, 180915 (2018).
Google Scholar
Bird, J. T. et al. Uncultured microbial phyla suggest mechanisms for multi-thousand-year subsistence in Baltic Sea sediments. MBio 10, 1002 (2019).
Moulton, O. M. et al. Microbial associations with macrobiota in coastal ecosystems: Patterns and implications for nitrogen cycling. Front. Ecol. Environ. 14, 200–208 (2016).
Park, S., Park, J.-M., Kang, C.-H. & Yoon, J.-H. Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat. Int. J. Syst. Evol. Microbiol. 64, 1841–1846 (2014).
Google Scholar
Evans, M. V. et al. Members of Marinobacter and Arcobacter influence system biogeochemistry during early production of hydraulically fractured natural gas wells in the Appalachian Basin. Front. Microbiol. 9, 2646 (2018).
Google Scholar
Wilhelm, R. C. Following the terrestrial tracks of Caulobacter – redefining the ecology of a reputed aquatic oligotroph. ISME J. 12, 3025–3037 (2018).
Google Scholar
Suzuki, D., Ueki, A., Amaishi, A. & Ueki, K. Desulfopila aestuarii gen. nov., sp. nov., a Gram-negative, rod-like, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. Int. J. Syst. Evol. Microbiol. 57, 520–526 (2007).
Google Scholar
Dawson, K. S., Scheller, S., Dillon, J. G. & Orphan, V. J. Stable isotope phenotyping via cluster analysis of nanoSIMS data as a method for characterizing distinct microbial ecophysiologies and sulfur-cycling in the environment. Front. Microbiol. 7, 774 (2016).
Google Scholar
Fadhlaoui, K. et al. Fusibacter fontis sp. nov., a sulfur-reducing, anaerobic bacterium isolated from a mesothermic Tunisian spring. Int. J. Syst. Evol. Microbiol. 65, 3501–3506 (2015).
Google Scholar
Kjeldsen, K. U. et al. Diversity of sulfate-reducing bacteria from an extreme hypersaline sediment, Great Salt Lake (Utah). FEMS Microbiol. Ecol. 60, 287–298 (2007).
Google Scholar
Schneider, D., Wemheuer, F., Pfeiffer, B. & Wemheuer, B. Extraction of total DNA and RNA from marine filter samples and generation of a cDNA as universal template for marker gene studies. Methods Mol. Biol. Clifton N J 1539, 13–22 (2017).
Google Scholar
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1 (2013).
Google Scholar
Berkelmann, D., Schneider, D., Hennings, N., Meryandini, A. & Daniel, R. Soil bacterial community structures in relation to different oil palm management practices. Sci. Data 7, 421 (2020).
Google Scholar
von Hoyningen-Huene, A. J. E. et al. Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria. Sci. data 6, 163 (2019).
Tange, O. Gnu parallel-the command-line power tool. login: The USENIX Mag. 36, 42–47 (2011).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England) 34, i884–i890 (2018).
Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: A fast and accurate Illumina paired-end read merger. Bioinformatics (Oxford, England) 30, 614–620 (2014).
Google Scholar
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet j. 17, 10 (2011).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Edgar, R. C. UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing (2016).
Quast, C. et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
Google Scholar
SILVAngs. SILVAngs – rDNA-based microbial community analysis using next-generation sequencing (NGS) data – user guide. Available at https://www.arb-silva.de/fileadmin/silva_databases/sngs/SILVAngs_User_Guide.pdf (2017).
McDonald, D. et al. The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome. GigaScience 1, 7 (2012).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
Google Scholar
Rambaut, A. FigTree – tree figure drawing tool (2018).
R Core Team. R: A language and environment for statistical computing. (R Foundation for Statistical Computing, 2020).
RStudio Team. RStudio: integrated development for R (RStudio Inc., 2021).
Chen, L. et al. GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ 6, e4600 (2018).
Google Scholar
Pereira, M. B., Wallroth, M., Jonsson, V. & Kristiansson, E. Comparison of normalization methods for the analysis of metagenomic gene abundance data. BMC Genom. 19, 274 (2018).
Andersen, K. S., Kirkegaard, R. H., Karst, S. M. & Albertsen, M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data (2018).
Oksanen, J. et al. vegan: Community ecology package (2018).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Kembel, S. W. et al. Picante: R tools for integrating phylogenies and ecology. Bioinformatics (Oxford, England) 26, 1463–1464 (2010).
Google Scholar
Harrel Jr, F. E., with contributions from Charles Dupont and many others. Hmisc: Harrell Miscellaneous (2021).
Wei, T. & Simko, V. R package “corrplot”: Visualization of a Correlation (2021).
de Cáceres, M. & Legendre, P. Associations between species and groups of sites: Indices and statistical inference. Ecology 90, 3566–3574 (2009).
Google Scholar
Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Google Scholar
Esri Inc. ArcGIS Desktop (Esri Inc., 2019).
Inkscape Developers. Inkscape (2020).
Fussmann, D. et al. Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria. Biogeosciences 17, 2085–2106 (2020).
Google Scholar
Parkhurst, D. L. & Appelo, C. A. in U.S. Geological Survey Techniques and Methods (2013), Vol. 6, pp. 2328–7055.
Source: Ecology - nature.com
