Madsen, E. L. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nat. Rev. Micro. 3, 439 (2005).
Google Scholar
Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L. & Lilley, A. K. The contribution of species richness and composition to bacterial services. Nature 436, 1157–1160 (2005).
Google Scholar
Delgado-Baquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).
Google Scholar
Galand, P. E., Pereira, O., Hochart, C., Auguet, J. C. & Debroas, D. A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME J. 12, 2470 (2018).
Google Scholar
Galand, P. E., Salter, I. & Kalenitchenko, D. Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters. Mol. Ecol. 24, 5785–5795 (2015).
Google Scholar
Chase, J. M. Community assembly: When should history matter?. Oecologia 136, 489–498 (2003).
Google Scholar
Lozupone, C. A. & Knight, R. Global patterns in bacterial diversity. Proc. Natl. Acad. Sci. USA 104, 11436–11440 (2007).
Google Scholar
Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457 (2017).
Google Scholar
Hanson, C. A., Fuhrman, J. A., Horner-Devine, M. C. & Martiny, J. B. Beyond biogeographic patterns: Processes shaping the microbial landscape. Nat. Rev. Micro. 10, 497 (2012).
Google Scholar
Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).
Google Scholar
Fukami, T. Historical contingency in community assembly: Integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1–23 (2015).
Google Scholar
Martiny, J. B. H. et al. Microbial biogeography: Putting microorganisms on the map. Nat. Rev. Micro. 4, 102 (2006).
Google Scholar
Hawkes, C. V. & Keitt, T. H. Resilience vs. historical contingency in microbial responses to environmental change. Ecol. Lett. 18, 612–625 (2015).
Google Scholar
Bouskill, N. J. et al. Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. ISME J. 7, 384 (2013).
Google Scholar
Ge, Y. et al. Differences in soil bacterial diversity: Driven by contemporary disturbances or historical contingencies?. ISME J. 2, 254 (2008).
Google Scholar
Rousk, J., Smith, A. R. & Jones, D. L. Investigating the long-term legacy of drought and warming on the soil microbial community across five European shrubland ecosystems. Glob. Change Biol. 19, 3872–3884 (2013).
Google Scholar
Langenheder, S., Lindström, E. S. & Tranvik, L. J. Structure and function of bacterial communities emerging from different sources under identical conditions. Appl. Environ. Microbiol. 72, 212–220 (2006).
Google Scholar
Langenheder, S., Lindström, E. S. & Tranvik, L. J. Weak coupling between community composition and functioning of aquatic bacteria. Limnol. Oceanogr. 50, 957–967 (2005).
Google Scholar
Vass, M. & Langenheder, S. The legacy of the past: Effects of historical processes on microbial metacommunities. Aquat. Microb. Ecol. 79, 13–19 (2017).
Google Scholar
Svoboda, P., Lindström, E. S., Osman, O. A. & Langenheder, S. Dispersal timing determines the importance of priority effects in bacterial communities. ISME J. 12, 644 (2018).
Google Scholar
Rummens, K., De Meester, L. & Souffreau, C. Inoculation history affects community composition in experimental freshwater bacterioplankton communities. Environ. Microbiol. 20, 1120–1133 (2018).
Google Scholar
Andersson, M. G., Berga, M., Lindström, E. S. & Langenheder, S. The spatial structure of bacterial communities is influenced by historical environmental conditions. Ecology 95, 1134–1140 (2014).
Google Scholar
Vyverman, W. et al. Historical processes constrain patterns in global diatom diversity. Ecology 88, 1924–1931 (2007).
Google Scholar
Sefbom, J., Sassenhagen, I., Rengefors, K. & Godhe, A. Priority effects in a planktonic bloom-forming marine diatom. Biol. Lett. 11, 20150184 (2015).
Google Scholar
Kalenitchenko, D. et al. Ecological succession leads to chemosynthesis in mats colonizing wood in sea water. ISME J. 10, 2246–2258 (2016).
Google Scholar
Kalenitchenko, D., Le Bris, N., Peru, E. & Galand, P. E. Ultrarare marine microbes contribute to key sulphur-related ecosystem functions. Mol. Ecol. 27, 1494–1504 (2018).
Google Scholar
Ghiglione, J. F. et al. Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea. Biogeosciences 5, 1751–1764 (2008).
Google Scholar
Ghiglione, J.-F. et al. Pole-to-pole biogeography of surface and deep marine bacterial communities. Proc. Natl. Acad. Sci. USA 109, 17633–17638 (2012).
Google Scholar
Salazar, G. et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell 179, 1068-1083.e1021 (2019).
Google Scholar
Kalenitchenko, D. et al. The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring. Sci. Rep. 8, 907. https://doi.org/10.1038/s41598-017-17463-2 (2018).
Google Scholar
Kalenitchenko, D. et al. Temporal and spatial constraints on community assembly during microbial colonization of wood in seawater. ISME J. 9, 2657–2670 (2015).
Google Scholar
Kalenitchenko, D. et al. Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. ISME J. 12, 367–379 (2018).
Google Scholar
Galand, P., Salter, I. & Kalenitchenko, D. Microbial productivity is associated with phylogenetic distance in surface marine waters. Mol. Ecol. 24, 5785–5795 (2015).
Google Scholar
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461. https://doi.org/10.1093/bioinformatics/btq461 (2010).
Google Scholar
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196. https://doi.org/10.1093/nar/gkm864 (2007).
Google Scholar
Cox, M. P., Peterson, D. A. & Biggs, P. J. SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform. 11, 485. https://doi.org/10.1186/1471-2105-11-485 (2010).
Google Scholar
Rho, M., Tang, H. & Ye, Y. FragGeneScan: Predicting genes in short and error-prone reads. Nucleic Acids Res. https://doi.org/10.1093/nar/gkq747 (2010).
Google Scholar
Wilke, A. et al. The M5nr: A novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinform. 13, 141. https://doi.org/10.1186/1471-2105-13-141 (2012).
Google Scholar
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44, D457–D462 (2016).
Google Scholar
Anders, S. & Huber, W. Differential expression analysis for sequence count data. Nat Précéd 1–1 https://doi.org/10.1038/npre.2010.4282.1 (2010).
Google Scholar
Meyer, F. et al. The metagenomics RAST server—A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 9, 386. https://doi.org/10.1186/1471-2105-9-386 (2008).
Google Scholar
Dixon, P. VEGAN, a package of R functions for community ecology. J Veg Sci 14, 927–930 (2003).
Google Scholar
Blanchette, R. A., Nilsson, T., Daniel, G. & Abad, A. Biological Degradation of Wood. in vol. 225, 141–174 (American Chemical Society, 1989).
Fagervold, S. K. et al. Microbial communities associated with the degradation of oak wood in the Blanes submarine canyon and its adjacent open slope (NW Mediterranean). Prog. Oceanogr. 118, 137–143. https://doi.org/10.1016/j.pocean.2013.07.012 (2013).
Google Scholar
Sommer, U. Convergent succession of phytoplankton in microcosms with different inoculum species composition. Oecologia 87, 171–179 (1991).
Google Scholar
Weiher, E. & Keddy, P. A. The assembly of experimental wetland plant communities. Oikos 73, 323–335 (1995).
Google Scholar
Wilson, J. B. et al. A test of community reassembly using the exotic communities of New Zealand roadsides in comparison to British roadsides. J. Ecol. 88, 757–764 (2000).
Google Scholar
Kodric-Brown, A. & Brown, J. H. Highly structured fish communities in Australian desert springs. Ecology 74, 1847–1855 (1993).
Google Scholar
Grover, J. P. & Lawton, J. H. Experimental studies on community convergence and alternative stable states: Comments on a paper by Drake et al. J. Anim. Ecol. 63, 484–487 (1994).
Google Scholar
Lawler, S. P. Direct and indirect effects in microcosm communities of protists. Oecologia 93, 184–190 (1993).
Google Scholar
Chase, J. M. Experimental evidence for alternative stable equilibria in a benthic pond food web. Ecol. Lett. 6, 733–741 (2003).
Google Scholar
Petraitis, P. S. & Latham, R. E. The importance of scale in testing the origins of alternative community states. Ecology 80, 429–442 (1999).
Google Scholar
Hiscox, J. et al. Priority effects during fungal community establishment in beech wood. ISME J. 9, 2246 (2015).
Google Scholar
Fukami, T. et al. Assembly history dictates ecosystem functioning: evidence from wood decomposer communities. Ecol. Lett. 13, 675–684 (2010).
Google Scholar
Dhami, M. K., Hartwig, T. & Fukami, T. Genetic basis of priority effects: Insights from nectar yeast. Proc. R. Soc. Lond. B. 283, 20161455 (2016).
Fukami, T. & Morin, P. J. Productivity–biodiversity relationships depend on the history of community assembly. Nature 424, 423 (2003).
Google Scholar
Khelaifia, S. et al. Desulfovibrio piezophilus sp. nov., a piezophilic, sulfate-reducing bacterium isolated from wood falls in the Mediterranean Sea. Int. J. Syst. Evol. Micr. 61, 2706–2711 (2011).
Google Scholar
Sievert, S. M., Wieringa, E. B., Wirsen, C. O. & Taylor, C. D. Growth and mechanism of filamentous-sulfur formation by Candidatus Arcobacter sulfidicus in opposing oxygen-sulfide gradients. Environ. Microbiol. 9, 271–276 (2007).
Google Scholar
Source: Ecology - nature.com