• No results found

University of Groningen Soil bacterial community assembly during succession Jia, Xiu

N/A
N/A
Protected

Academic year: 2021

Share "University of Groningen Soil bacterial community assembly during succession Jia, Xiu"

Copied!
21
0
0

Bezig met laden.... (Bekijk nu de volledige tekst)

Hele tekst

(1)

Soil bacterial community assembly during succession

Jia, Xiu

DOI:

10.33612/diss.156586683

IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from

it. Please check the document version below.

Document Version

Publisher's PDF, also known as Version of record

Publication date:

2021

Link to publication in University of Groningen/UMCG research database

Citation for published version (APA):

Jia, X. (2021). Soil bacterial community assembly during succession. University of Groningen.

https://doi.org/10.33612/diss.156586683

Copyright

Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).

Take-down policy

If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.

Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.

(2)

References

Aanderud, Z. T., S. E. Jones, N. Fierer, and J. T. Lennon. 2015. Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Front Microbiol 6:24.

Aanderud, Z. T., S. Saurey, B. A. Ball, D. H. Wall, J. E. Barrett, M. E. Muscarella, N. A. Griffin, R. A. Virginia, and B. J. Adams. 2018. Stoichiometric Shifts in Soil C:N:P Promote Bacterial Taxa Dominance, Maintain Biodiversity, and Deconstruct Community Assemblages. Front Microbiol 9:1401.

Adams, R. I., M. Miletto, J. W. Taylor, and T. D. Bruns. 2013. Dispersal in microbes: fungi in in-door air are dominated by outin-door air and show dispersal limitation at short distances. ISME J 7:1262-1273.

Adler, P. B., J. Hillerislambers, and J. M. Levine. 2007. A niche for neutrality. Ecol Lett 10:95-104. Ai, D., C. Chu, M. F. Ellwood, R. Hou, and G. Wang. 2013. Migration and niche partitioning

simul-taneously increase species richness and rarity. Ecological Modelling 258:33-39.

Albert Barberán, J. L., Jonathan W. Leff, Katherine S. Pollard, Holly L. Menninger, Robert R. Dunn, and Noah Fierer. 2015. Continental-scale distributions of dust-associated bacteria and fungi. PNAS 112:5756-5761.

Albertsen, M., P. Hugenholtz, A. Skarshewski, K. L. Nielsen, G. W. Tyson, and P. H. Nielsen. 2013. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533-538.

Albright, M. B. N., and J. B. H. Martiny. 2018. Dispersal alters bacterial diversity and composition in a natural community. ISME J 12:296-299.

Anderson, M. J., K. E. Ellingsen, and B. H. McArdle. 2006. Multivariate dispersion as a measure of beta diversity. Ecol Lett 9:683-693.

Anderson, R. E., M. L. Sogin, and J. A. Baross. 2015. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents. FEMS Microbiol Ecol 91:1-11. Arndt, N. T., and E. G. Nisbet. 2012. Processes on the Young Earth and the Habitats of Early Life.

Annual Review of Earth and Planetary Sciences 40:521-549.

Ashby, M. N., J. Rine, E. F. Mongodin, K. E. Nelson, and D. Dimster-Denk. 2007. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl Environ Microbiol 73:4532-4542.

Baker, B. J., C. S. Lazar, A. P. Teske, and G. J. Dick. 2015. Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria. Microbiome 3:14. Bannar-Martin, K. H., C. T. Kremer, S. K. M. Ernest, M. A. Leibold, H. Auge, J. Chase, S. A. J. De-clerck, N. Eisenhauer, S. Harpole, H. Hillebrand, F. Isbell, T. Koffel, S. Larsen, A. Narwani, J. S. Petermann, C. Roscher, J. S. Cabral, and S. R. Supp. 2018. Integrating community assem-bly and biodiversity to better understand ecosystem function: the Community Assemassem-bly and the Functioning of Ecosystems (CAFE) approach. Ecol Lett 21:167-180.

Bar-On, Y. M., R. Phillips, and R. Milo. 2018. The biomass distribution on Earth. Proc Natl Acad Sci U S A 115:6506-6511.

Bardgett, R. D., W. D. Bowman, R. Kaufmann, and S. K. Schmidt. 2005. A temporal approach to linking aboveground and belowground ecology. Trends Ecol Evol 20:634-641.

(3)

func-tioning. Nature 515:505-511.

Bastida, F., I. F. Torres, M. Andres-Abellan, P. Baldrian, R. Lopez-Mondejar, T. Vetrovsky, H. H. Richnow, R. Starke, S. Ondono, C. Garcia, F. R. Lopez-Serrano, and N. Jehmlich. 2017. Dif-ferential sensitivity of total and active soil microbial communities to drought and forest man-agement. Glob Chang Biol 23:4185-4203.

Bell, G. 2000. The Distribution of Abundance in Neutral Communities. Am Nat 155:606-617. Berg, G., D. Rybakova, D. Fischer, T. Cernava, M. C. Verges, T. Charles, X. Chen, L. Cocolin, K.

Eversole, G. H. Corral, M. Kazou, L. Kinkel, L. Lange, N. Lima, A. Loy, J. A. Macklin, E. Magu-in, T. Mauchline, R. McClure, B. Mitter, M. Ryan, I. Sarand, H. Smidt, B. Schelkle, H. Roume, G. S. Kiran, J. Selvin, R. S. C. Souza, L. van Overbeek, B. K. Singh, M. Wagner, A. Walsh, A. Sessitsch, and M. Schloter. 2020. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8:103.

Berg, G., and K. Smalla. 2009. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68:1-13. Blevins, S. M., and M. S. Bronze. 2010. Robert Koch and the ‘golden age’ of bacteriology. Int J

Infect Dis 14:e744-751.

Bolyen, E., J. R. Rideout, M. R. Dillon, N. A. Bokulich, C. C. Abnet, G. A. Al-Ghalith, H. Alexan-der, E. J. Alm, M. Arumugam, F. Asnicar, Y. Bai, J. E. Bisanz, K. Bittinger, A. Brejnrod, C. J. Brislawn, C. T. Brown, B. J. Callahan, A. M. Caraballo-Rodriguez, J. Chase, E. K. Cope, R. Da Silva, C. Diener, P. C. Dorrestein, G. M. Douglas, D. M. Durall, C. Duvallet, C. F. Edwardson, M. Ernst, M. Estaki, J. Fouquier, J. M. Gauglitz, S. M. Gibbons, D. L. Gibson, A. Gonzalez, K. Gorlick, J. Guo, B. Hillmann, S. Holmes, H. Holste, C. Huttenhower, G. A. Huttley, S. Jans-sen, A. K. Jarmusch, L. Jiang, B. D. Kaehler, K. B. Kang, C. R. Keefe, P. Keim, S. T. Kelley, D. Knights, I. Koester, T. Kosciolek, J. Kreps, M. G. I. Langille, J. Lee, R. Ley, Y. X. Liu, E. Loftfield, C. Lozupone, M. Maher, C. Marotz, B. D. Martin, D. McDonald, L. J. McIver, A. V. Melnik, J. L. Metcalf, S. C. Morgan, J. T. Morton, A. T. Naimey, J. A. Navas-Molina, L. F. Nothias, S. B. Orchanian, T. Pearson, S. L. Peoples, D. Petras, M. L. Preuss, E. Pruesse, L. B. Rasmussen, A. Rivers, M. S. Robeson, 2nd, P. Rosenthal, N. Segata, M. Shaffer, A. Shiffer, R. Sinha, S. J. Song, J. R. Spear, A. D. Swafford, L. R. Thompson, P. J. Torres, P. Trinh, A. Tripathi, P. J. Turnbaugh, S. Ul-Hasan, J. J. J. van der Hooft, F. Vargas, Y. Vazquez-Baeza, E. Vogtmann, M. von Hippel, W. Walters, Y. Wan, M. Wang, J. Warren, K. C. Weber, C. H. D. Williamson, A. D. Willis, Z. Z. Xu, J. R. Zaneveld, Y. Zhang, Q. Zhu, R. Knight, and J. G. Caporaso. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852-857.

Brown, S. P., and A. Jumpponen. 2014. Contrasting primary successional trajectories of fungi and bacteria in retreating glacier soils. Mol Ecol 23:481-497.

Browne, H. P., S. C. Forster, B. O. Anonye, N. Kumar, B. A. Neville, M. D. Stares, D. Goulding, and T. D. Lawley. 2016. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 533:543-546.

Bundy, J. G., M. P. Davey, and M. R. Viant. 2009. Environmental metabolomics: a critical review and future perspectives. Metabolomics 5:3-21.

Burcham, Z. M., J. L. Pechal, C. J. Schmidt, J. L. Bose, J. W. Rosch, M. E. Benbow, and H. R. Jordan. 2019. Bacterial Community Succession, Transmigration, and Differential Gene Tran-scription in a Controlled Vertebrate Decomposition Model. Front Microbiol 10:745. Callahan, B. J., P. J. McMurdie, and S. P. Holmes. 2017. Exact sequence variants should replace

(4)

Callahan, B. J., P. J. McMurdie, M. J. Rosen, A. W. Han, A. J. Johnson, and S. P. Holmes. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581-583.

Campbell, B. J., L. Yu, J. F. Heidelberg, and D. L. Kirchman. 2011. Activity of abundant and rare bacteria in a coastal ocean. Proc Natl Acad Sci U S A 108:12776-12781.

Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S. M. Owens, J. Betley, L. Fraser, M. Bauer, N. Gormley, J. A. Gilbert, G. Smith, and R. Knight. 2012. Ul-tra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq plat-forms. ISME J 6:1621-1624.

Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, C. A. Lozupone, P. J. Turnbaugh, N. Fierer, and R. Knight. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108 Suppl 1:4516-4522.

Carini, P., M. Delgado-Baquerizo, E. S. Hinckley, H. Holland-Moritz, T. E. Brewer, G. Rue, C. Van-derburgh, D. McKnight, and N. Fierer. 2020. Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities. MBio 11:e02776-02719.

Carini, P., P. J. Marsden, J. W. Leff, E. E. Morgan, M. S. Strickland, and N. Fierer. 2016. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nature microbiology 2:16242.

Castle, S. C., D. R. Nemergut, A. S. Grandy, J. W. Leff, E. B. Graham, E. Hood, S. K. Schmidt, K. Wickings, and C. C. Cleveland. 2016. Biogeochemical drivers of microbial community conver-gence across actively retreating glaciers. Soil Biology and Biochemistry 101:74-84.

Chaparro, J. M., D. V. Badri, and J. M. Vivanco. 2014. Rhizosphere microbiome assemblage is affected by plant development. ISME J 8:790-803.

Chase, J. M., A. Jeliazkov, E. Ladouceur, and D. S. Viana. 2020. Biodiversity conservation through the lens of metacommunity ecology. Ann N Y Acad Sci 1469:86-104.

Chase, J. M., N. J. B. Kraft, K. G. Smith, M. Vellend, and B. D. Inouye. 2011. Using null models to disentangle variation in community dissimilarity from variation in α-diversity. Ecosphere 2:art24.

Chase, J. M., and M. A. Leibold. 2003. Ecological niches: linking classical and contemporary ap-proaches. University of Chicago Press.

Chen, H., and P. C. Boutros. 2011. VennDiagram: a package for the generation of highly-customiz-able Venn and Euler diagrams in R. BMC bioinformatics 12:35.

Chesson, P. 2000. Mechanisms of Maintenance of Species Diversity. Annual Review of Ecology and Systematics 31:343-366.

Church, J., P. Clark, A. Cazenave, J. Gregory, S. Jevrejeva, A. Levermann, M. Merrifield, G. Milne, R. Nerem, and P. Nunn. 2013. Climate change 2013: the physical science basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Cli-mate Change. Sea level change:1137.

Clegg, C. D. 2006. Impact of cattle grazing and inorganic fertiliser additions to managed grass-lands on the microbial community composition of soils. Applied Soil Ecology 31:73-82. Clements, F. E. 1916. Plant succession: an analysis of the development of vegetation. Carnegie

(5)

Cline, L. C., and D. R. Zak. 2015. Soil microbial communities are shaped by plant-driven changes in resource availability during secondary succession. Ecology 96:3374-3385.

Cook, K. L., J. L. Garland, A. C. Layton, H. M. Dionisi, L. H. Levine, and G. S. Sayler. 2006. Effect of microbial species richness on community stability and community function in a model plant-based wastewater processing system. Microb Ecol 52:725-737.

Dam, H. T., J. Vollmers, M. S. Sobol, A. Cabezas, and A. K. Kaster. 2020. Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics. Front Microbiol 11:1377.

Datta, M. S., E. Sliwerska, J. Gore, M. F. Polz, and O. X. Cordero. 2016. Microbial interactions lead to rapid micro-scale successions on model marine particles. Nat Commun 7:11965.

Dawson, W., J. Hor, M. Egert, M. van Kleunen, and M. Pester. 2017. A Small Number of Low-abun-dance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization. Front Microbiol 8:975.

de Wit, R., and T. Bouvier. 2006. ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environ Microbiol 8:755-758.

Debroas, D., M. Hugoni, and I. Domaizon. 2015. Evidence for an active rare biosphere within freshwater protists community. Mol Ecol 24:1236-1247.

Deiglmayr, K., L. Philippot, D. Tscherko, and E. Kandeler. 2006. Microbial succession of nitrate-re-ducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Environ Microbiol 8:1600-1612.

Del Moral, R., and C. Jones. 2002. Vegetation development on pumice at Mount St. Helens, USA. Plant Ecology 162:9-22.

Denef, V. J., M. Fujimoto, M. A. Berry, and M. L. Schmidt. 2016. Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria. Front Microbiol 7:606.

Dini Andreote, F. 2016. Microbial community assembly in an evolving ecosystem: Ecological suc-cession and functional properties of soil microbes. University of Groningen, Groningen. Dini-Andreote, F., M. J. Brossi, J. D. van Elsas, and J. F. Salles. 2016a. Reconstructing the Genetic

Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem. Front Mi-crobiol 7:902.

Dini-Andreote, F., M. de Cassia Pereira e Silva, X. Triado-Margarit, E. O. Casamayor, J. D. van Elsas, and J. F. Salles. 2014. Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning. ISME J 8:1989-2001.

Dini-Andreote, F., V. S. Pylro, P. Baldrian, J. D. van Elsas, and J. F. Salles. 2016b. Ecological suc-cession reveals potential signatures of marine-terrestrial transition in salt marsh fungal com-munities. ISME J 10:1984-1997.

Dini-Andreote, F., J. C. Stegen, J. D. van Elsas, and J. F. Salles. 2015. Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succes-sion. Proc Natl Acad Sci U S A 112:E1326-1332.

Dini-Andreote, F., J. D. van Elsas, H. Olff, and J. F. Salles. 2018. Dispersal-competition tradeoff in microbiomes in the quest for land colonization. Sci Rep 8:9451.

Dixon, P. 2003. VEGAN, a package of R functions for community ecology. Journal of Vegetation Science 14:927-930.

(6)

Doud, D. F. R., R. M. Bowers, F. Schulz, M. De Raad, K. Deng, A. Tarver, E. Glasgow, K. Vander Meulen, B. Fox, S. Deutsch, Y. Yoshikuni, T. Northen, B. P. Hedlund, S. W. Singer, N. Ivano-va, and T. Woyke. 2020. Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. ISME J 14:659-675.

Elhottova, D., T. Szili-Kovacs, and J. Triska. 2002. Soil microbial community of abandoned sand fields. Folia Microbiol (Praha) 47:435-440.

Emerson, J. B., R. I. Adams, C. M. B. Roman, B. Brooks, D. A. Coil, K. Dahlhausen, H. H. Ganz, E. M. Hartmann, T. Hsu, N. B. Justice, I. G. Paulino-Lima, J. C. Luongo, D. S. Lymperopoulou, C. Gomez-Silvan, B. Rothschild-Mancinelli, M. Balk, C. Huttenhower, A. Nocker, P. Vaisham-payan, and L. J. Rothschild. 2017. Schrodinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5:86.

Evans, S., J. B. Martiny, and S. D. Allison. 2017. Effects of dispersal and selection on stochastic assembly in microbial communities. ISME J 11:176-185.

Falkowski, P. G., T. Fenchel, and E. F. Delong. 2008. The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034-1039.

Faust, K., and J. Raes. 2012. Microbial interactions: from networks to models. Nat Rev Microbiol 10:538-550.

Ferrenberg, S., S. P. O’Neill, J. E. Knelman, B. Todd, S. Duggan, D. Bradley, T. Robinson, S. K. Schmidt, A. R. Townsend, M. W. Williams, C. C. Cleveland, B. A. Melbourne, L. Jiang, and D. R. Nemergut. 2013. Changes in assembly processes in soil bacterial communities following a wildfire disturbance. ISME J 7:1102-1111.

Fierer, N., M. A. Bradford, and R. B. Jackson. 2007. Toward an ecological classification of soil bacteria. Ecology 88:1354-1364.

Fierer, N., and R. B. Jackson. 2006. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626-631.

Fierer, N., C. L. Lauber, K. S. Ramirez, J. Zaneveld, M. A. Bradford, and R. Knight. 2012. Compar-ative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007-1017.

Fierer, N., D. Nemergut, R. Knight, and J. M. Craine. 2010. Changes through time: integrating microorganisms into the study of succession. Research in microbiology 161:635-642. Fierer, N., M. S. Strickland, D. Liptzin, M. A. Bradford, and C. C. Cleveland. 2009. Global patterns

in belowground communities. Ecol Lett 12:1238-1249.

Fillinger, L., K. Hug, and C. Griebler. 2019. Selection imposed by local environmental condi-tions drives differences in microbial community composition across geographically distinct groundwater aquifers. FEMS Microbiol Ecol 95.

Franzosa, E. A., T. Hsu, A. Sirota-Madi, A. Shafquat, G. Abu-Ali, X. C. Morgan, and C. Huttenhow-er. 2015a. Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 13:360-372.

Franzosa, E. A., T. Hsu, A. Sirota-Madi, A. Shafquat, G. Abu-Ali, X. C. Morgan, and C. Huttenhow-er. 2015b. Sequencing and beyond: integrating molecular’omics’ for microbial community profiling. Nature Reviews Microbiology 13:360-372.

Fukami, T. 2015. Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects. Annual Review of Ecology, Evolution, and Systematics 46:1-23.

(7)

Galand, P. E., E. O. Casamayor, D. L. Kirchman, and C. Lovejoy. 2009. Ecology of the rare microbi-al biosphere of the Arctic Ocean. Proc Natl Acad Sci U S A 106:22427-22432.

Gans, J., M. Wolinsky, and J. Dunbar. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309:1387-1390.

Gao, Z., I. Karlsson, S. Geisen, G. Kowalchuk, and A. Jousset. 2019. Protists: Puppet Masters of the Rhizosphere Microbiome. Trends Plant Sci 24:165-176.

Gause, G. F. 1934. Experimental Analysis of Vito Volterra’s Mathematical Theory of the Struggle for Existence. Science 79:16-17.

Gilbert, B., and M. J. Lechowicz. 2004. Neutrality, niches, and dispersal in a temperate forest un-derstory. Proc Natl Acad Sci U S A 101:7651-7656.

Gilbert, J. A., J. K. Jansson, and R. Knight. 2014. The Earth Microbiome project: successes and aspirations. BMC Biol 12:69.

Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.

Girvan, M. S., C. D. Campbell, K. Killham, J. I. Prosser, and L. A. Glover. 2005. Bacterial diversity promotes community stability and functional resilience after perturbation. Environ Microbi-ol 7:301-313.

Goberna, M., J. A. Navarro-Cano, A. Valiente-Banuet, C. Garcia, and M. Verdu. 2014. Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities. Ecol Lett 17:1191-1201.

Gobet, A., S. I. Boer, S. M. Huse, J. E. van Beusekom, C. Quince, M. L. Sogin, A. Boetius, and A. Ramette. 2012. Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6:542-553.

Gobet, A., C. Quince, and A. Ramette. 2010. Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic Acids Res 38:e155.

Godwin, H. 1929. The sub-climax and deflected succession. Journal of Ecology 17:144-147. Goldfarb, K. C., U. Karaoz, C. A. Hanson, C. A. Santee, M. A. Bradford, K. K. Treseder, M. D.

Wal-lenstein, and E. L. Brodie. 2011. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2:94.

Graham, E. B., and J. C. Stegen. 2017. Stochastic microbial community assembly decreases biogeo-chemical function. bioRxiv:doi: https://doi.org/10.1101/183897.

Gravel, D., C. D. Canham, M. Beaudet, and C. Messier. 2006. Reconciling niche and neutrality: the continuum hypothesis. Ecol Lett 9:399-409.

Griffiths, B., K. Ritz, R. Wheatley, H. Kuan, B. Boag, S. Christensen, F. Ekelund, S. J. Sørensen, S. Muller, and J. Bloem. 2001. An examination of the biodiversity–ecosystem function rela-tionship in arable soil microbial communities. Soil Biology and Biochemistry 33:1713-1722.

Griffiths, R. I., A. S. Whiteley, A. G. O’Donnell, and M. J. Bailey. 2000. Rapid method for coex-traction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488-5491. Grossart, H. P., C. Dziallas, F. Leunert, and K. W. Tang. 2010. Bacteria dispersal by hitchhiking on

zooplankton. Proc Natl Acad Sci U S A 107:11959-11964.

(8)

Haegeman, B., J. Hamelin, J. Moriarty, P. Neal, J. Dushoff, and J. S. Weitz. 2013. Robust estima-tion of microbial diversity in theory and in practice. ISME J 7:1092-1101.

Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Mi-crobiol Mol Biol Rev 68:669-685.

Hannula, S. E., E. Morrien, M. de Hollander, W. H. van der Putten, J. A. van Veen, and W. de Boer. 2017. Shifts in rhizosphere fungal community during secondary succession following aban-donment from agriculture. ISME J 11:2294-2304.

Hanson, C. A., J. A. Fuhrman, M. C. Horner-Devine, and J. B. Martiny. 2012. Beyond biogeograph-ic patterns: processes shaping the mbiogeograph-icrobial landscape. Nat Rev Mbiogeograph-icrobiol 10:497-506. Harantová, L., O. Mudrák, P. Kohout, D. Elhottová, J. Frouz, and P. Baldrian. 2017. Development

of microbial community during primary succession in areas degraded by mining activities. Land Degradation & Development 28:2574-2584.

Hausmann, B., C. Pelikan, T. Rattei, A. Loy, and M. Pester. 2019. Long-Term Transcriptional Ac-tivity at Zero Growth of a Cosmopolitan Rare Biosphere Member. MBio 10:e02189-02118. Hawkes, C. V., and T. H. Keitt. 2015. Resilience vs. historical contingency in microbial responses to

environmental change. Ecology Letters 18:612-625.

Hell, K., A. Edwards, J. Zarsky, S. M. Podmirseg, S. Girdwood, J. A. Pachebat, H. Insam, and B. Sattler. 2013. The dynamic bacterial communities of a melting High Arctic glacier snowpack. ISME J 7:1814-1826.

Hirsch, J. E. 2005. An index to quantify an individual’s scientific research output. Proc Natl Acad Sci U S A 102:16569-16572.

Hodkinson, I. D., S. J. Coulson, and N. R. Webb. 2003. Community assembly along proglacial chronosequences in the high Arctic: vegetation and soil development in north‐west Svalbard. Journal of Ecology 91:651-663.

Holland, H. D. 2006. The oxygenation of the atmosphere and oceans. Philos Trans R Soc Lond B Biol Sci 361:903-915.

Holt, R. D. 2009. Bringing the Hutchinsonian niche into the 21st century: ecological and evolution-ary perspectives. Proc Natl Acad Sci U S A 106 Suppl 2:19659-19665.

Hooper, D. U., F. Chapin, J. Ewel, A. Hector, P. Inchausti, S. Lavorel, J. Lawton, D. Lodge, M. Loreau, and S. Naeem. 2005. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecological Monographs 75:3-35.

Horn, H. S. 1974. The ecology of secondary succession. Annual Review of Ecology and Systematics 5:25-37.

Horner-Devine, M. C., M. Lage, J. B. Hughes, and B. J. Bohannan. 2004. A taxa-area relationship for bacteria. Nature 432:750-753.

Hubbell, S. P. 2001. The Unified Neutral Theory of Biodiversity and Biogeography: MacArthur and Wilson’s Radical Theory. Princeton University Press, Princeton, NJ.

Hultman, J., M. P. Waldrop, R. Mackelprang, M. M. David, J. McFarland, S. J. Blazewicz, J. Hard-en, M. R. Turetsky, A. D. McGuire, M. B. Shah, N. C. VerBerkmoes, L. H. Lee, K. Mavromma-tis, and J. K. Jansson. 2015. Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521:208-212.

Huston, M., and T. Smith. 1987. Plant succession: life history and competition. The American Nat-uralist 130:168-198.

(9)

Huttl, R. F., and E. Weber. 2001. Forest ecosystem development in post-mining landscapes: a case study of the Lusatian lignite district. Naturwissenschaften 88:322-329.

Inceoglu, O., M. Lliros, S. A. Crowe, T. Garcia-Armisen, C. Morana, F. Darchambeau, A. V. Borges, J. P. Descy, and P. Servais. 2015. Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu. Microb Ecol 70:596-611.

Ivanov, II, and K. Honda. 2012. Intestinal commensal microbes as immune modulators. Cell Host Microbe 12:496-508.

Jansson, J. K., and J. I. Prosser. 2013. Microbiology: The life beneath our feet. Nature 494:40-41. Jessup, C. M., R. Kassen, S. E. Forde, B. Kerr, A. Buckling, P. B. Rainey, and B. J. Bohannan. 2004.

Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19:189-197.

Jia, X., F. Dini-Andreote, and J. Falcao Salles. 2018. Community Assembly Processes of the Micro-bial Rare Biosphere. Trends Microbiol 26:738-747.

Jia, X., F. Dini-Andreote, and J. Falcao Salles. 2020. Comparing the Influence of Assembly Pro-cesses Governing Bacterial Community Succession Based on DNA and RNA Data. Microor-ganisms 8.

Jiao, S., and Y. Lu. 2020. Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems. Environ Microbiol 22:1052-1065.

Jiao, S., Y. Yang, Y. Xu, J. Zhang, and Y. Lu. 2020. Balance between community assembly process-es mediatJiao, S., Y. Yang, Y. Xu, J. Zhang, and Y. Lu. 2020. Balance between community assembly process-es speciJiao, S., Y. Yang, Y. Xu, J. Zhang, and Y. Lu. 2020. Balance between community assembly process-es coexistence in agricultural soil microbiomJiao, S., Y. Yang, Y. Xu, J. Zhang, and Y. Lu. 2020. Balance between community assembly process-es across eastern China. ISME J 14:202-216.

Johnson, E. A., and K. Miyanishi. 2008. Testing the assumptions of chronosequences in succes-sion. Ecol Lett 11:419-431.

Jones, D. L., C. Nguyen, and R. D. Finlay. 2009. Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant and Soil 321:5-33.

Jones, S. E., and J. T. Lennon. 2010. Dormancy contributes to the maintenance of microbial diver-sity. Proc Natl Acad Sci U S A 107:5881-5886.

Jousset, A., C. Bienhold, A. Chatzinotas, L. Gallien, A. Gobet, V. Kurm, K. Kusel, M. C. Rillig, D. W. Rivett, J. F. Salles, M. G. van der Heijden, N. H. Youssef, X. Zhang, Z. Wei, and W. H. Hol. 2017. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J 11:853-862.

Jurburg, S. D., T. Natal-da-Luz, J. Raimundo, P. V. Morais, J. P. Sousa, J. D. van Elsas, and J. F. Salles. 2018. Bacterial communities in soil become sensitive to drought under intensive graz-ing. Science of The Total Environment 618:1638-1646.

Jurburg, S. D., I. Nunes, A. Brejnrod, S. Jacquiod, A. Prieme, S. J. Sorensen, J. D. Van Elsas, and J. F. Salles. 2017a. Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation. Front Microbiol 8:1832.

Jurburg, S. D., I. Nunes, J. C. Stegen, X. Le Roux, A. Prieme, S. J. Sorensen, and J. F. Salles. 2017b. Autogenic succession and deterministic recovery following disturbance in soil bacterial com-munities. Sci Rep 7:45691.

Kandeler, E., K. Deiglmayr, D. Tscherko, D. Bru, and L. Philippot. 2006. Abundance of narG, nirS, nirK, and nosZ genes of denitrifying bacteria during primary successions of a glacier foreland. Applied and environmental microbiology 72:5957-5962.

(10)

Kassambara, A. 2017. ggpubr:’ggplot2’ based publication ready plots. R package version 0.1 6. Kembel, S. W., P. D. Cowan, M. R. Helmus, W. K. Cornwell, H. Morlon, D. D. Ackerly, S. P.

Blomberg, and C. O. Webb. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463-1464.

Kirwan, M. L., and A. B. Murray. 2007. A coupled geomorphic and ecological model of tidal marsh evolution. Proc Natl Acad Sci U S A 104:6118-6122.

Kitzinger, K., C. C. Padilla, H. K. Marchant, P. F. Hach, C. W. Herbold, A. T. Kidane, M. Konneke, S. Littmann, M. Mooshammer, J. Niggemann, S. Petrov, A. Richter, F. J. Stewart, M. Wagner, M. M. M. Kuypers, and L. A. Bristow. 2019. Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment. Nat Microbiol 4:234-243.

Klappenbach, J. A., J. M. Dunbar, and T. M. Schmidt. 2000. rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66:1328-1333.

Knelman, J. E., T. M. Legg, S. P. O’Neill, C. L. Washenberger, A. González, C. C. Cleveland, and D. R. Nemergut. 2012. Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield. Soil Biology and Bio-chemistry 46:172-180.

Knight, R., A. Vrbanac, B. C. Taylor, A. Aksenov, C. Callewaert, J. Debelius, A. Gonzalez, T. Kos-ciolek, L. I. McCall, D. McDonald, A. V. Melnik, J. T. Morton, J. Navas, R. A. Quinn, J. G. Sanders, A. D. Swafford, L. R. Thompson, A. Tripathi, Z. Z. Xu, J. R. Zaneveld, Q. Zhu, J. G. Caporaso, and P. C. Dorrestein. 2018. Best practices for analysing microbiomes. Nat Rev Microbiol 16:410-422.

Knoll, A. H., K. D. Bergmann, and J. V. Strauss. 2016. Life: the first two billion years. Philos Trans R Soc Lond B Biol Sci 371.

Koeppel, A. F., and M. Wu. 2014. Species matter: the role of competition in the assembly of conge-neric bacteria. ISME J 8:531-540.

Konopka, A. 2009. What is microbial community ecology? ISME J 3:1223.

Kozdrój, J., and J. D. van Elsas. 2001. Structural diversity of microbial communities in arable soils of a heavily industrialised area determined by PCR-DGGE fingerprinting and FAME profil-ing. Applied Soil Ecology 17:31-42.

Kuramae, E. E., H. A. Gamper, E. Yergeau, Y. M. Piceno, E. L. Brodie, T. Z. Desantis, G. L. Ander-sen, J. A. van Veen, and G. A. Kowalchuk. 2010. Microbial secondary succession in a chrono-sequence of chalk grasslands. ISME J 4:711-715.

Kurm, V., S. Geisen, and W. H. Gera Hol. 2019a. A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa. Environ Microbiol 21:750-758.

Kurm, V., W. H. van der Putten, W. de Boer, S. Naus-Wiezer, and W. H. Hol. 2017. Low abundant soil bacteria can be metabolically versatile and fast growing. Ecology 98:555-564.

Kurm, V., W. H. van der Putten, S. Weidner, S. Geisen, B. L. Snoek, T. Bakx, and W. H. G. Hol. 2019b. Competition and predation as possible causes of bacterial rarity. Environ Microbiol 21:1356-1368.

Kuzyakov, Y., and W. Cheng. 2001. Photosynthesis controls of rhizosphere respiration and organic matter decomposition. Soil Biology and Biochemistry 33:1915-1925.

Lamendella, R., N. VerBerkmoes, and J. K. Jansson. 2012. ‘Omics’ of the mammalian gut–new insights into function. Current opinion in biotechnology 23:491-500.

(11)

Langenheder, S., M. T. Bulling, M. Solan, and J. I. Prosser. 2010. Bacterial biodiversity-ecosystem functioning relations are modified by environmental complexity. PLoS One 5:e10834. Langille, M. G., J. Zaneveld, J. G. Caporaso, D. McDonald, D. Knights, J. A. Reyes, J. C. Clemente, D.

E. Burkepile, R. L. V. Thurber, and R. Knight. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature biotechnology 31:814-821. Lankiewicz, T. S., M. T. Cottrell, and D. L. Kirchman. 2016. Growth rates and rRNA content of four

marine bacteria in pure cultures and in the Delaware estuary. ISME J 10:823-832.

Lauber, C. L., M. Hamady, R. Knight, and N. Fierer. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75:5111-5120.

Legendre, P., D. Borcard, and P. R. Peres-Neto. 2005. Analyzing Beta Diversity: Partitioning the Spatial Variation of Community Composition Data. Ecological Monographs 75:435-450. Leibold, M. A., J. M. Chase, and S. K. Ernest. 2017. Community assembly and the functioning of

ecosystems: how metacommunity processes alter ecosystems attributes. Ecology 98:909-919. Leibold, M. A., M. Holyoak, N. Mouquet, P. Amarasekare, J. M. Chase, M. F. Hoopes, R. D. Holt,

J. B. Shurin, R. Law, D. Tilman, M. Loreau, and A. Gonzalez. 2004. The metacommunity con-cept: a framework for multi-scale community ecology. Ecology Letters 7:601-613.

Leibold, M. A., and M. A. McPeek. 2006. Coexistence of the niche and neutral perspectives in com-munity ecology. Ecology 87:1399-1410.

Lennon, J. T., and S. E. Jones. 2011. Microbial seed banks: the ecological and evolutionary impli-cations of dormancy. Nat Rev Microbiol 9:119-130.

Lennon, J. T., M. E. Muscarella, S. A. Placella, and B. K. Lehmkuhl. 2018. How, When, and Where Relic DNA Affects Microbial Diversity. MBio 9:e00637-00618.

Lenski, R. E. 2017. Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations. ISME J 11:2181-2194.

Lewis, W. H., G. Tahon, P. Geesink, D. Z. Sousa, and T. J. G. Ettema. 2020. Innovations to cultur-ing the uncultured microbial majority. Nature Reviews Microbiology.

Liang, Y., X. Xiao, E. E. Nuccio, M. Yuan, N. Zhang, K. Xue, F. M. Cohan, J. Zhou, and B. Sun. 2020. Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes. Environ Microbiol 22:1327-1340.

Locey, K. J., and J. T. Lennon. 2016. Scaling laws predict global microbial diversity. Proc Natl Acad Sci U S A 113:5970-5975.

Logares, R., S. Audic, D. Bass, L. Bittner, C. Boutte, R. Christen, J. M. Claverie, J. Decelle, J. R. Dolan, M. Dunthorn, B. Edvardsen, A. Gobet, W. H. Kooistra, F. Mahe, F. Not, H. Ogata, J. Pawlowski, M. C. Pernice, S. Romac, K. Shalchian-Tabrizi, N. Simon, T. Stoeck, S. Santini, R. Siano, P. Wincker, A. Zingone, T. A. Richards, C. de Vargas, and R. Massana. 2014. Patterns of rare and abundant marine microbial eukaryotes. Curr Biol 24:813-821.

Logares, R., T. H. Haverkamp, S. Kumar, A. Lanzen, A. J. Nederbragt, C. Quince, and H. Kauserud. 2012. Environmental microbiology through the lens of high-throughput DNA sequencing: syn-opsis of current platforms and bioinformatics approaches. J Microbiol Methods 91:106-113. Logares, R., E. S. Lindstrom, S. Langenheder, J. B. Logue, H. Paterson, J. Laybourn-Parry, K.

Rengefors, L. Tranvik, and S. Bertilsson. 2013. Biogeography of bacterial communities ex-posed to progressive long-term environmental change. ISME J 7:937-948.

(12)

Lorenz, M. G., and W. Wackernagel. 1987. Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl Environ Microbiol 53:2948-2952.

Losos, J. B. 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship be-tween phylogenetic relatedness and ecological similarity among species. Ecol Lett 11:995-1003.

Louca, S., S. M. S. Jacques, A. P. F. Pires, J. S. Leal, D. S. Srivastava, L. W. Parfrey, V. F. Farjalla, and M. Doebeli. 2016. High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 1:15.

Lozano, Y. M., S. Hortal, C. Armas, and F. I. Pugnaire. 2014. Interactions among soil, plants, and microorganisms drive secondary succession in a dry environment. Soil Biology and Biochem-istry 78:298-306.

Lozupone, C. A., and R. Knight. 2007. Global patterns in bacterial diversity. Proc Natl Acad Sci U S A 104:11436-11440.

Lv, X., K. Zhao, R. Xue, Y. Liu, J. Xu, and B. Ma. 2019. Strengthening Insights in Microbial Ecolog-ical Networks from Theory to Applications. mSystems 4.

Lynch, M. D., and J. D. Neufeld. 2015. Ecology and exploration of the rare biosphere. Nat Rev Microbiol 13:217-229.

Lyons, T. W., C. T. Reinhard, and N. J. Planavsky. 2014. The rise of oxygen in Earth’s early ocean and atmosphere. Nature 506:307-315.

Magurran, A. E., and P. A. Henderson. 2003. Explaining the excess of rare species in natural spe-cies abundance distributions. Nature 422:714-716.

Magurran, A. E., and P. A. Henderson. 2011. Commonness and rarity. Pages 97-104 Biological Diversity: Frontiers in Measurement and Assessment. Oxford University Press: Oxford. Mallon, C. A., X. Le Roux, G. S. van Doorn, F. Dini-Andreote, F. Poly, and J. F. Salles. 2018. The

impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche. ISME J 12:728-741.

Mallon, C. A., F. Poly, X. Le Roux, I. Marring, J. D. van Elsas, and J. F. Salles. 2015. Resource puls-es can alleviate the biodiversity-invasion relationship in soil microbial communitipuls-es. Ecology 96:915-926.

Marteinsson, V., A. Klonowski, E. Reynisson, P. Vannier, B. D. Sigurdsson, and M. Ólafsson. 2015. Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota. Biogeosciences 12:1191-1203.

Martiny, J. B., B. J. Bohannan, J. H. Brown, R. K. Colwell, J. A. Fuhrman, J. L. Green, M. C. Horner-Devine, M. Kane, J. A. Krumins, C. R. Kuske, P. J. Morin, S. Naeem, L. Ovreas, A. L. Reysenbach, V. H. Smith, and J. T. Staley. 2006. Microbial biogeography: putting microor-ganisms on the map. Nat Rev Microbiol 4:102-112.

Matthiessen, B., E. Mielke, and U. Sommer. 2010. Dispersal decreases diversity in heterogeneous metacommunities by enhancing regional competition. Ecology 91:2022-2033.

Mayr, E. 1997. This is biology: The science of the living world. Universities Press.

McGill, B. J., J. M. Chase, J. Hortal, I. Overcast, A. J. Rominger, J. Rosindell, P. A. V. Borges, B. C. Emerson, R. S. Etienne, M. J. Hickerson, D. L. Mahler, F. Massol, A. McGaughran, P. Neves, C. Parent, J. Patiño, M. Ruffley, C. E. Wagner, R. Gillespie, and A. Algar. 2019. Unifying mac-roecology and macroevolution to answer fundamental questions about biodiversity. Global

(13)

Ecology and Biogeography 28:1925-1936.

Melbourne, B. A., and A. Hastings. 2008. Extinction risk depends strongly on factors contributing to stochasticity. Nature 454:100-103.

Meyer, K. M., H. Memiaghe, L. Korte, D. Kenfack, A. Alonso, and B. J. M. Bohannan. 2018. Why do microbes exhibit weak biogeographic patterns? ISME J 12:1404-1413.

Meyer, K. M., I. A. B. Petersen, E. Tobi, L. Korte, and B. J. M. Bohannan. 2019. Use of RNA and DNA to Identify Mechanisms of Bacterial Community Homogenization. Front Microbiol 10:2066.

Mitsch, W. J., and J. G. Gosselink. 2000. Wetlands, 5th Edition. New York, USA.

Mo, Y., W. Zhang, J. Yang, Y. Lin, Z. Yu, and S. Lin. 2018. Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral process-es. ISME J 12:2198-2210.

Moeller, A. H., T. A. Suzuki, D. Lin, E. A. Lacey, S. K. Wasser, and M. W. Nachman. 2017. Dispersal limitation promotes the diversification of the mammalian gut microbiota. Proc Natl Acad Sci U S A 114:13768-13773.

Mori, A. S., F. Isbell, and R. Seidl. 2018. beta-Diversity, Community Assembly, and Ecosystem Functioning. Trends Ecol Evol 33:549-564.

Mueller, R. C., L. Gallegos-Graves, D. R. Zak, and C. R. Kuske. 2016. Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient. Microb Ecol 71:57-67. Nawaz, A., W. Purahong, M. Herrmann, K. Kusel, F. Buscot, and T. Wubet. 2019. DNA- and RNA-

Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors. Microorganisms 7.

Nayfach, S., Z. J. Shi, R. Seshadri, K. S. Pollard, and N. C. Kyrpides. 2019. New insights from uncul-tivated genomes of the global human gut microbiome. Nature 568:505-510.

Nemergut, D. R., S. P. Anderson, C. C. Cleveland, A. P. Martin, A. E. Miller, A. Seimon, and S. K. Schmidt. 2007. Microbial community succession in an unvegetated, recently deglaciated soil. Microb Ecol 53:110-122.

Nemergut, D. R., E. K. Costello, M. Hamady, C. Lozupone, L. Jiang, S. K. Schmidt, N. Fierer, A. R. Townsend, C. C. Cleveland, L. Stanish, and R. Knight. 2011. Global patterns in the biogeogra-phy of bacterial taxa. Environ Microbiol 13:135-144.

Nemergut, D. R., J. E. Knelman, S. Ferrenberg, T. Bilinski, B. Melbourne, L. Jiang, C. Violle, J. L. Darcy, T. Prest, S. K. Schmidt, and A. R. Townsend. 2016. Decreases in average bacterial community rRNA operon copy number during succession. ISME J 10:1147-1156.

Nemergut, D. R., S. K. Schmidt, T. Fukami, S. P. O’Neill, T. M. Bilinski, L. F. Stanish, J. E. Kn-elman, J. L. Darcy, R. C. Lynch, P. Wickey, and S. Ferrenberg. 2013. Patterns and processes of microbial community assembly. Microbiol Mol Biol Rev 77:342-356.

Nocker, A., M. Burr, and A. K. Camper. 2007. Genotypic microbial community profiling: a critical technical review. Microb Ecol 54:276-289.

Nuccio, E. E., J. Anderson-Furgeson, K. Y. Estera, J. Pett-Ridge, P. De Valpine, E. L. Brodie, and M. K. Firestone. 2016. Climate and edaphic controllers influence rhizosphere community as-sembly for a wild annual grass. Ecology 97:1307-1318.

O’Malley, M. A. 2007. The nineteenth century roots of ‘everything is everywhere’. Nature Reviews Microbiology 5:647-651.

(14)

Oades, J. M. 1984. Soil organic matter and structural stability: mechanisms and implications for management. Plant and Soil 76:319-337.

Ochman, H., J. G. Lawrence, and E. A. Groisman. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304.

Olff, H., J. D. Leeuw, J. P. Bakker, R. J. Platerink, and H. J. van Wijnen. 1997. Vegetation Succes-sion and Herbivory in a Salt Marsh: Changes Induced by Sea Level Rise and Silt Deposition Along an Elevational Gradient. The Journal of Ecology 85:799-814.

Ortiz-Alvarez, R., N. Fierer, A. de Los Rios, E. O. Casamayor, and A. Barberan. 2018. Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession. ISME J 12:1658-1667.

Ovaskainen, O., G. Tikhonov, A. Norberg, F. Guillaume Blanchet, L. Duan, D. Dunson, T. Roslin, and N. Abrego. 2017. How to make more out of community data? A conceptual framework and its implementation as models and software. Ecol Lett 20:561-576.

Pachiadaki, M. G., J. M. Brown, J. Brown, O. Bezuidt, P. M. Berube, S. J. Biller, N. J. Poulton, M. D. Burkart, J. J. La Clair, S. W. Chisholm, and R. Stepanauskas. 2019. Charting the Complexity of the Marine Microbiome through Single-Cell Genomics. Cell 179:1623-1635 e1611. Paradis, E., J. Claude, and K. Strimmer. 2004. APE: Analyses of Phylogenetics and Evolution in R

language. Bioinformatics 20:289-290.

Parks, D. H., M. Chuvochina, D. W. Waite, C. Rinke, A. Skarshewski, P. A. Chaumeil, and P. Hugenholtz. 2018. A standardized bacterial taxonomy based on genome phylogeny substan-tially revises the tree of life. Nat Biotechnol 36:996-1004.

Parks, D. H., C. Rinke, M. Chuvochina, P. A. Chaumeil, B. J. Woodcroft, P. N. Evans, P. Hugen-holtz, and G. W. Tyson. 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2:1533-1542.

Pascoal, F., C. Magalhães, and R. Costa. 2020. The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential. Frontiers in Microbiology 11:231. Pedros-Alio, C. 2006. Marine microbial diversity: can it be determined? Trends Microbiol

14:257-263.

Pedros-Alio, C. 2012. The rare bacterial biosphere. Ann Rev Mar Sci 4:449-466.

Pereira, E. S. M. C., B. Schloter-Hai, M. Schloter, J. D. van Elsas, and J. F. Salles. 2013. Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils. PLoS One 8:e74500.

Pester, M., N. Bittner, P. Deevong, M. Wagner, and A. Loy. 2010. A ‘rare biosphere’microorganism contributes to sulfate reduction in a peatland. ISME J 4:1591-1602.

Pester, M., T. Rattei, S. Flechl, A. Grongroft, A. Richter, J. Overmann, B. Reinhold-Hurek, A. Loy, and M. Wagner. 2012. amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions. Environ Mi-crobiol 14:525-539.

Pickett, S. T. A. 1989. Space-for-Time Substitution as an Alternative to Long-Term Studies. Pages 110-135 in G. E. Likens, editor. Long-Term Studies in Ecology: Approaches and Alternatives. Springer New York, New York, NY.

Price, M. N., P. S. Dehal, and A. P. Arkin. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641-1650.

(15)

Props, R., F. M. Kerckhof, P. Rubbens, J. De Vrieze, E. Hernandez Sanabria, W. Waegeman, P. Monsieurs, F. Hammes, and N. Boon. 2017. Absolute quantification of microbial taxon abun-dances. ISME J 11:584-587.

Prosser, J. I. 2015. Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology. Nature Reviews Microbiology 13:439-446.

Prosser, J. I., B. J. Bohannan, T. P. Curtis, R. J. Ellis, M. K. Firestone, R. P. Freckleton, J. L. Green, L. E. Green, K. Killham, J. J. Lennon, A. M. Osborn, M. Solan, C. J. van der Gast, and J. P. Young. 2007. The role of ecological theory in microbial ecology. Nat Rev Microbiol 5:384-392. R Core Team. 2017. R: A language and environment for statistical computing. R Foundation for

Statistical Computing, Vienna, Austria.

Rabinowitz, D., S. Cairns, and T. Dillon. 1986. Seven forms of rarity and their frequency in the flora of the British Isles. Pages 182-204 Conservation Biology: The Science of Scarcity and Diversity. Sinauer Associates Inc., Sunderland, Massachusetts.

Rabinowitz, D., J. K. Rapp, and P. M. Dixon. 1984. Competitive Abilities of Sparse Grass Species: Means of Persistence or Cause of Abundance. Ecology 65:1144-1154.

Rainey, P. B., and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72.

Ramos, C., L. Molbak, and S. Molin. 2000. Bacterial activity in the rhizosphere analyzed at the sin-gle-cell level by monitoring ribosome contents and synthesis rates. Appl Environ Microbiol 66:801-809.

Ratzke, C., J. Barrere, and J. Gore. 2020. Strength of species interactions determines biodiversity and stability in microbial communities. Nat Ecol Evol 4:376-383.

Reinhardt, K., G. Köhler, S. Maas, and P. Detzel. 2005. Low dispersal ability and habitat specificity promote extinctions in rare but not in widespread species: the Orthoptera of Germany. Ecog-raphy 28:593-602.

Reiss, J., J. R. Bridle, J. M. Montoya, and G. Woodward. 2009. Emerging horizons in biodiversity and ecosystem functioning research. Trends Ecol Evol 24:505-514.

Reveillaud, J., L. Maignien, A. Murat Eren, J. A. Huber, A. Apprill, M. L. Sogin, and A. Vanreu-sel. 2014. Host-specificity among abundant and rare taxa in the sponge microbiome. ISME J 8:1198-1209.

Rivett, D. W., and T. Bell. 2018. Abundance determines the functional role of bacterial phylotypes in complex communities. Nat Microbiol 3:767-772.

Rodriguez-Valera, F., A. B. Martin-Cuadrado, B. Rodriguez-Brito, L. Pasic, T. F. Thingstad, F. Rohwer, and A. Mira. 2009. Explaining microbial population genomics through phage pre-dation. Nat Rev Microbiol 7:828-836.

Rothschild, L. J., and R. L. Mancinelli. 2001. Life in extreme environments. Nature 409:1092-1101.

RStudio Team. 2015. RStudio: integrated development for R. RStudio, Inc., Boston, MA.

Salles, J. F., M. C. Pereira e Silva, F. Dini-Andreote, A. C. F. Dias, N. Guillaumaud, F. Poly, and J. D. van Elsas. 2017. Successional patterns of key genes and processes involved in the microbial nitrogen cycle in a salt marsh chronosequence. Biogeochemistry 132:185-201.

Scheuerl, T., M. Hopkins, R. W. Nowell, D. W. Rivett, T. G. Barraclough, and T. Bell. 2020. Bacte-rial adaptation is constrained in complex communities. Nat Commun 11:754.

(16)

Schimel, J. P., J. M. Gulledge, J. S. Clein-Curley, J. E. Lindstrom, and J. F. Braddock. 1999. Mois-ture effects on microbial activity and community structure in decomposing birch litter in the Alaskan taiga. Soil Biology and Biochemistry 31:831-838.

Schipper, L., B. Degens, G. Sparling, and L. Duncan. 2001. Changes in microbial heterotrophic di-versity along five plant successional sequences. Soil Biology and Biochemistry 33:2093-2103. Schippers, A., L. N. Neretin, J. Kallmeyer, T. G. Ferdelman, B. A. Cragg, R. J. Parkes, and B. B.

Jorgensen. 2005. Prokaryotic cells of the deep sub-seafloor biosphere identified as living bac-teria. Nature 433:861-864.

Schmidt, S. K., D. R. Nemergut, J. L. Darcy, and R. Lynch. 2014. Do bacterial and fungal commu-nities assemble differently during primary succession? Mol Ecol 23:254-258.

Schmidt, S. K., S. C. Reed, D. R. Nemergut, A. S. Grandy, C. C. Cleveland, M. N. Weintraub, A. W. Hill, E. K. Costello, A. F. Meyer, J. C. Neff, and A. M. Martin. 2008. The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils. Proc Biol Sci 275:2793-2802.

Schrama, M., M. P. Berg, and H. Olff. 2012. Ecosystem assembly rules: the interplay of green and brown webs during salt marsh succession. Ecology 93:2353-2364.

Schrama, M., J. Jouta, M. P. Berg, and H. Olff. 2013. Food Web Assembly at the Landscape Scale: Using Stable Isotopes to Reveal Changes in Trophic Structure During Succession. Ecosystems 16:627-638.

Sexton, J. P., J. Montiel, J. E. Shay, M. R. Stephens, and R. A. Slatyer. 2017. Evolution of Ecological Niche Breadth. Annual Review of Ecology, Evolution, and Systematics 48:183-206.

Shade, A., J. G. Caporaso, J. Handelsman, R. Knight, and N. Fierer. 2013. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J 7:1493-1506.

Shade, A., R. R. Dunn, S. A. Blowes, P. Keil, B. J. M. Bohannan, M. Herrmann, K. Kusel, J. T. Len-non, N. J. Sanders, D. Storch, and J. Chase. 2018. Macroecology to Unite All Life, Large and Small. Trends Ecol Evol 33:731-744.

Shade, A., S. E. Jones, J. G. Caporaso, J. Handelsman, R. Knight, N. Fierer, and J. A. Gilbert. 2014. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diver-sity. MBio 5:e01371-01314.

Shade, A., H. Peter, S. D. Allison, D. L. Baho, M. Berga, H. Burgmann, D. H. Huber, S. Langen-heder, J. T. Lennon, J. B. Martiny, K. L. Matulich, T. M. Schmidt, and J. Handelsman. 2012. Fundamentals of microbial community resistance and resilience. Front Microbiol 3:417. Shi, Y., G. W. Tyson, and E. F. DeLong. 2009. Metatranscriptomics reveals unique microbial small

RNAs in the ocean’s water column. Nature 459:266-269.

Sigler, W. V., S. Crivii, and J. Zeyer. 2002. Bacterial succession in glacial forefield soils charac-terized by community structure, activity and opportunistic growth dynamics. Microb Ecol 44:306-316.

Sigler, W. V., and J. Zeyer. 2002. Microbial diversity and activity along the forefields of two reced-ing glaciers. Microb Ecol 43:397-407.

Singh, B. K., C. D. Campbell, S. J. Sorenson, and J. Zhou. 2009. Soil genomics. Nat Rev Microbiol 7:756; author reply 756-757.

Smith, T. W., and J. T. Lundholm. 2010. Variation partitioning as a tool to distinguish between niche and neutral processes. Ecography 33:648-655.

(17)

Snell Taylor, S. J., B. S. Evans, E. P. White, and A. H. Hurlbert. 2018. The prevalence and impact of transient species in ecological communities. Ecology 99:1825-1835.

Sogin, M. L., H. G. Morrison, J. A. Huber, D. Mark Welch, S. M. Huse, P. R. Neal, J. M. Arrieta, and G. J. Herndl. 2006. Microbial diversity in the deep sea and the underexplored ‘rare bio-sphere’. Proc Natl Acad Sci U S A 103:12115-12120.

Sprockett, D., T. Fukami, and D. A. Relman. 2018. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastroenterol Hepatol 15:197-205.

Staley, J. T., and A. Konopka. 1985. Measurement of in situ activities of nonphotosynthetic micro-organisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39:321-346.

Stegen, J. C., A. H. Hurlbert, B. Bond-Lamberty, X. Chen, C. G. Anderson, R. K. Chu, F. Dini-An-dreote, S. J. Fansler, N. J. Hess, and M. Tfaily. 2016. Aligning the Measurement of Microbial Diversity with Macroecological Theory. Front Microbiol 7:1487.

Stegen, J. C., X. Lin, J. K. Fredrickson, X. Chen, D. W. Kennedy, C. J. Murray, M. L. Rockhold, and A. Konopka. 2013. Quantifying community assembly processes and identifying features that impose them. ISME J 7:2069-2079.

Stegen, J. C., X. Lin, J. K. Fredrickson, and A. E. Konopka. 2015. Estimating and mapping ecologi-cal processes influencing microbial community assembly. Front Microbiol 6:370.

Stegen, J. C., X. Lin, A. E. Konopka, and J. K. Fredrickson. 2012. Stochastic and deterministic as-sembly processes in subsurface microbial communities. ISME J 6:1653-1664.

Stevenson, B. S., and T. M. Schmidt. 2004. Life history implications of rRNA gene copy number in Escherichia coli. Appl Environ Microbiol 70:6670-6677.

Stewart, E. J. 2012. Growing unculturable bacteria. J Bacteriol 194:4151-4160.

Strous, M., J. J. Heijnen, J. G. Kuenen, and M. S. M. Jetten. 1998. The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorgan-isms. Applied Microbiology and Biotechnology 50:589-596.

Sukenik, A., R. N. Kaplan-Levy, J. M. Welch, and A. F. Post. 2012. Massive multiplication of ge-nome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobac-teria). ISME J 6:670-679.

Sul, W. J., T. A. Oliver, H. W. Ducklow, L. A. Amaral-Zettler, and M. L. Sogin. 2013. Marine bacte-ria exhibit a bipolar distribution. Proc Natl Acad Sci U S A 110:2342-2347.

Sunagawa, S., S. G. Acinas, P. Bork, C. Bowler, C. Tara Oceans, D. Eveillard, G. Gorsky, L. Guidi, D. Iudicone, E. Karsenti, F. Lombard, H. Ogata, S. Pesant, M. B. Sullivan, P. Wincker, and C. de Vargas. 2020. Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 18:428-445.

Sutherland, W. J., R. P. Freckleton, H. C. J. Godfray, S. R. Beissinger, T. Benton, D. D. Cameron, Y. Carmel, D. A. Coomes, T. Coulson, and M. C. Emmerson. 2013. Identification of 100 funda-mental ecological questions. Journal of Ecology 101:58-67.

Svoboda, P., E. S. Lindstrom, O. Ahmed Osman, and S. Langenheder. 2018. Dispersal timing de-termines the importance of priority effects in bacterial communities. ISME J 12:644-646. Szekely, A. J., and S. Langenheder. 2014. The importance of species sorting differs between habitat

generalists and specialists in bacterial communities. FEMS Microbiol Ecol 87:102-112. Telford, R. J., V. Vandvik, and H. J. Birks. 2006. Dispersal limitations matter for microbial

(18)

Thompson, L. R., J. G. Sanders, D. McDonald, A. Amir, J. Ladau, K. J. Locey, R. J. Prill, A. Tripathi, S. M. Gibbons, G. Ackermann, J. A. Navas-Molina, S. Janssen, E. Kopylova, Y. Vazquez-Bae-za, A. Gonzalez, J. T. Morton, S. Mirarab, Z. Zech Xu, L. Jiang, M. F. Haroon, J. Kanbar, Q. Zhu, S. Jin Song, T. Kosciolek, N. A. Bokulich, J. Lefler, C. J. Brislawn, G. Humphrey, S. M. Owens, J. Hampton-Marcell, D. Berg-Lyons, V. McKenzie, N. Fierer, J. A. Fuhrman, A. Clauset, R. L. Stevens, A. Shade, K. S. Pollard, K. D. Goodwin, J. K. Jansson, J. A. Gilbert, R. Knight, and C. Earth Microbiome Project. 2017. A communal catalogue reveals Earth’s multi-scale microbial diversity. Nature 551:457-463.

Tilman, D. 2004. Niche tradeoffs, neutrality, and community structure: a stochastic theory of re-source competition, invasion, and community assembly. Proc Natl Acad Sci U S A 101:10854-10861.

Torsvik, V., L. Ovreas, and T. F. Thingstad. 2002. Prokaryotic diversity--magnitude, dynamics, and controlling factors. Science 296:1064-1066.

Tringe, S. G., C. von Mering, A. Kobayashi, A. A. Salamov, K. Chen, H. W. Chang, M. Podar, J. M. Short, E. J. Mathur, J. C. Detter, P. Bork, P. Hugenholtz, and E. M. Rubin. 2005. Comparative metagenomics of microbial communities. Science 308:554-557.

Tscherko, D., J. Rustemeier, A. Richter, W. Wanek, and E. Kandeler. 2003. Functional diversity of the soil microflora in primary succession across two glacier forelands in the Central Alps. European Journal of Soil Science 54:685-696.

Tucker, C. M., and T. Fukami. 2014. Environmental variability counteracts priority effects to facili-tate species coexistence: evidence from nectar microbes. Proc Biol Sci 281:20132637. Turnbaugh, P. J., R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight, and J. I. Gordon. 2007.

The human microbiome project. Nature 449:804-810.

van Elsas, J. D., M. Chiurazzi, C. A. Mallon, D. Elhottova, V. Kristufek, and J. F. Salles. 2012. Mi-crobial diversity determines the invasion of soil by a bacterial pathogen. Proc Natl Acad Sci U S A 109:1159-1164.

van Elsas, J. D., J. T. Trevors, J. K. Jansson, and P. Nannipieri. 2006. Modern soil microbiology. CRC Press.

van Veelen, H. P. J., J. Falcao Salles, and B. I. Tieleman. 2017. Multi-level comparisons of cloa-cal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. Microbiome 5:156.

Vass, M., and S. Langenheder. 2017. The legacy of the past: effects of historical processes on micro-bial metacommunities. Aquatic MicroVass, M., and S. Langenheder. 2017. The legacy of the past: effects of historical processes on micro-bial Ecology 79:13-19.

Vass, M., A. J. Székely, E. S. Lindström, O. A. Osman, and S. Langenheder. 2020. Warming-en-hanced priority effects at population and community levels in aquatic bacteria. bioRx-iv:2020.2001.2027.921726.

Vellend, M. 2010. Conceptual synthesis in community ecology. Q Rev Biol 85:183-206. Vellend, M. 2016. The Theory of Ecological Communities. Princeton University Pres:61-67. Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I.

Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Sci-ence 304:66-74.

(19)

Verberkmoes, N. C., A. L. Russell, M. Shah, A. Godzik, M. Rosenquist, J. Halfvarson, M. G. Lefs-rud, J. Apajalahti, C. Tysk, R. L. Hettich, and J. K. Jansson. 2009. Shotgun metaproteomics of the human distal gut microbiota. ISME J 3:179-189.

Vigneron, A., E. B. Alsop, B. P. Lomans, N. C. Kyrpides, I. M. Head, and N. Tsesmetzis. 2017. Succession in the petroleum reservoir microbiome through an oil field production lifecycle. ISME J 11:2141-2154.

Vogel, T. M., P. Simonet, J. K. Jansson, P. R. Hirsch, J. M. Tiedje, J. D. Van Elsas, M. J. Bailey, R. Nalin, and L. Philippot. 2009. TerraGenome: a consortium for the sequencing of a soil metag-enome. Nature Publishing Group.

Vos, M., A. B. Wolf, S. J. Jennings, and G. A. Kowalchuk. 2013. Micro-scale determinants of bacte-rial diversity in soil. FEMS Microbiol Rev 37:936-954.

Wagg, C., J. H. Dudenhöffer, F. Widmer, M. G. A. Heijden, and R. Gallery. 2018. Linking diversity, synchrony and stability in soil microbial communities. Functional Ecology 32:1280-1292. Walker, L. R., and R. Del Moral. 2003. Primary succession and ecosystem rehabilitation.

Cam-bridge University Press.

Walker, L. R., D. A. Wardle, R. D. Bardgett, and B. D. Clarkson. 2010. The use of chronosequences in studies of ecological succession and soil development. Journal of Ecology 98:725-736. Wang, H., Y. P. Hsieh, M. A. Harwell, and W. Huang. 2007. Modeling soil salinity distribution

along topographic gradients in tidal salt marshes in Atlantic and Gulf coastal regions. Ecolog-ical Modelling 201:429-439.

Wang, M., P. Yang, and J. Falcao Salles. 2015. Distribution of Root-Associated Bacterial Commu-nities Along a Salt-Marsh Primary Succession. Front Plant Sci 6:1188.

Wang, Y., J. K. Hatt, D. Tsementzi, R. L. Rodriguez, C. A. Ruiz-Perez, M. R. Weigand, H. Kizer, G. Maresca, R. Krishnan, R. Poretsky, J. C. Spain, and K. T. Konstantinidis. 2017. Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollut-ants in a Freshwater Ecosystem. Appl Environ Microbiol 83:e03321-03316.

Warmink, J. A., R. Nazir, B. Corten, and J. D. van Elsas. 2011. Hitchhikers on the fungal highway: The helper effect for bacterial migration via fungal hyphae. Soil Biology and Biochemistry 43:760-765.

Watterson, W. J., M. Tanyeri, A. R. Watson, C. M. Cham, Y. Shan, E. B. Chang, A. M. Eren, and S. Tay. 2020. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes. Elife 9.

Webb, C. O. 2000. Exploring the Phylogenetic Structure of Ecological Communities: An Example for Rain Forest Trees. Am Nat 156:145-155.

Webb, C. O., D. D. Ackerly, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenies and Communi-ty Ecology. Annual Review of Ecology and Systematics 33:475-505.

Weber, C., and G. King. 2010. Distribution and diversity of carbon monoxide‐oxidizing bacteria and bulk bacterial communities across a succession gradient on a Hawaiian volcanic deposit. Environmental Microbiology 12:1855-1867.

Weiss, M. C., F. L. Sousa, N. Mrnjavac, S. Neukirchen, M. Roettger, S. Nelson-Sathi, and W. F. Martin. 2016. The physiology and habitat of the last universal common ancestor. Nat Micro-biol 1:16116.

(20)

Vazquez-Baeza, A. Birmingham, and R. Knight. 2015. Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data. PeerJ PrePrints:3:e1157v1151.

Werner, C. M., K. L. Stuble, A. M. Groves, and T. P. Young. 2020. Year effects: Interannual varia-tion as a driver of community assembly dynamics. Ecology n/a:e03104.

Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998a. Prokaryotes: the unseen majority. Pro-ceedings of the National Academy of Sciences 95:6578-6583.

Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998b. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95:6578-6583.

Wickham, H. 2010. ggplot2: elegant graphics for data analysis. J Stat Softw 35:65-88.

Wilbanks, E. G., V. Salman-Carvalho, U. Jaekel, P. T. Humphrey, J. A. Eisen, D. H. Buckley, and S. H. Zinder. 2017. The Green Berry Consortia of the Sippewissett Salt Marsh: Millimeter-Sized Aggregates of Diazotrophic Unicellular Cyanobacteria. Front Microbiol 8:1623.

Wilhelm, L., K. Besemer, C. Fasching, T. Urich, G. A. Singer, C. Quince, and T. J. Battin. 2014. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environ Microbiol 16:2514-2524.

Wilkinson, D. M., S. Koumoutsaris, E. A. Mitchell, and I. Bey. 2012. Modelling the effect of size on the aerial dispersal of microorganisms. Journal of Biogeography 39:89-97.

Woese, C. R., and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088-5090.

Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: propos-al for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87:4576-4579. Woodcock, S., C. J. van der Gast, T. Bell, M. Lunn, T. P. Curtis, I. M. Head, and W. T. Sloan. 2007.

Neutral assembly of bacterial communities. FEMS Microbiol Ecol 62:171-180.

Woyke, T., D. F. R. Doud, and F. Schulz. 2017. The trajectory of microbial single-cell sequencing. Nat Methods 14:1045-1054.

Yamamoto, K., K. C. Hackley, W. R. Kelly, S. V. Panno, Y. Sekiguchi, R. A. Sanford, W. T. Liu, Y. Kamagata, and H. Tamaki. 2019. Diversity and geochemical community assembly processes of the living rare biosphere in a sand-and-gravel aquifer ecosystem in the Midwestern United States. Sci Rep 9:13484.

Yang, S., M. Winkel, D. Wagner, and S. Liebner. 2017. Community structure of rare methanogenic archaea: insight from a single functional group. FEMS Microbiol Ecol 93.

Yano, K., T. Wada, S. Suzuki, K. Tagami, T. Matsumoto, Y. Shiwa, T. Ishige, Y. Kawaguchi, K. Ma-suda, G. Akanuma, H. Nanamiya, H. Niki, H. Yoshikawa, and F. Kawamura. 2013. Multiple rRNA operons are essential for efficient cell growth and sporulation as well as outgrowth in Bacillus subtilis. Microbiology (Reading) 159:2225-2236.

Yenni, G., P. B. Adler, and S. K. Ernest. 2012. Strong self-limitation promotes the persistence of rare species. Ecology 93:456-461.

Yeoh, Y. K., P. G. Dennis, C. Paungfoo-Lonhienne, L. Weber, R. Brackin, M. A. Ragan, S. Schmidt, and P. Hugenholtz. 2017. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nat Commun 8:215.

Yilmaz, P., L. W. Parfrey, P. Yarza, J. Gerken, E. Pruesse, C. Quast, T. Schweer, J. Peplies, W. Ludwig, and F. O. Glockner. 2014. The SILVA and ‘All-species Living Tree Project (LTP)’ taxonomic frameworks. Nucleic Acids Res 42:D643-648.

(21)

Young, I. M., J. W. Crawford, N. Nunan, W. Otten, and A. Spiers. 2008. Microbial distribution in soils: physics and scaling. Advances in Agronomy 100:81-121.

Zhou, J., W. Liu, Y. Deng, Y. H. Jiang, K. Xue, Z. He, J. D. Van Nostrand, L. Wu, Y. Yang, and A. Wang. 2013. Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. MBio 4.

Zhou, J., and D. Ning. 2017. Stochastic Community Assembly: Does It Matter in Microbial Ecolo-gy? Microbiology and molecular biology reviews 81:e00002-00017.

Zhou, Z., C. Wang, L. Jiang, and Y. Luo. 2017. Trends in soil microbial communities during second-ary succession. Soil Biology and Biochemistry 115:92-99.

Referenties

GERELATEERDE DOCUMENTEN

This thesis focuses on disentangling the underlying mech- anisms governing the assembly and successional dynamics of distinct fractions of soil bacterial communities based

The diversity of rhizosphere-associated bacterial follows the successional patterns associated with plant biomass (Schrama et al. 2012; lowest at early stages and reaching a plateau

Our results revealed that variations in α -diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a

The work presented in this thesis studies ecological processes governing the turnover of soil bacterial communities during succession with particular attention to the dynamics of

Using a salt marsh chronosequence spanning over 100 years of primary succession as a model ecosystem (Schiermonnikoog, the Netherlands), I systematically examined the extent to which

In het kort, ik toon aan dat de assemblage van de zeldzame biosfeer grotendeels wordt aangedreven door homogene selectie, terwijl de algemene biosfeer - die bestaat uit

Lulu and Feifei, thank you for inviting me to your sweet home and letting me witness the important life moment of Chengcheng. My thanks also to other Chinese neigh- bours:

Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of