(1) Amir, A., Daniel, M., Navas-Molina, J., Kopylova, E., Morton, J., Xu, Z.Z., Eric, K.,
Thompson, L., Hyde, E., Gonzalez, A., Knight, R., 2017. Deblur rapidly resolves
single-nucleotide community sequence patterns. mSystems 2, e00191–16.
(2) Antwis, R.E., Griffiths, S.M., Harrison, X.A., Aranega-Bou, P., Arce, A., Bettridge,
A.S., Brailsford, F.L., de Menezes, A., Devaynes, A., Forbes, K.M., Fry, E.L.,
Goodhead, I., Haskell, E., Heys, C., James, C., Johnston, S.R., Lewis, G.R., Lewis, Z.,
Macey, M.C., McCarthy, A., McDonald, J.E., Mejia-Florez, N.L., O’Brien, D., Orland,
C., Pautasso, M., Reid, W.D.K., Robinson, H.A., Wilson, K., Sutherland, W.J., 2017.
Fifty important research questions in microbial ecology. FEMS Microbiol. Ecol. 93,
fiz044. https://doi.org/10.1093/femsec/fix044
(3) Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D.R.,
Fernandes, G.R., Tap, J., Bruls, T., Batto, J.-M., Bertalan, M., Borruel, N., Casellas, F.,
Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M.,
Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H.B., Nielsen, T.,
Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E.,
Zoetendal, E.G., Wang, J., Guarner, F., Pedersen, O., de Vos, W.M., Brunak, S., Doré,
J., Weissenbach, J., Ehrlich, S.D., Bork, P., 2011. Enterotypes of the human gut
microbiome. Nature 473, 174–180. https://doi.org/10.1038/nature09944
(4) Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y.,
Xia, Y., Xie, H., Zhong, H., Khan, M.T., Zhang, J., Li, J., Xiao, L., Al-Aama, J., Zhang,
D., Lee, Y.S., Kotowska, D., Colding, C., Tremaroli, V., Yin, Y., Bergman, S., Xu, X.,
Madsen, L., Kristiansen, K., Dahlgren, J., Jun, W., 2015. Dynamics and stabilization
of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690–
703. https://doi.org/10.1016/j.chom.2015.04.004
(5) Bálint, M., Bahram, M., Eren, A.M., Faust, K., Fuhrman, J.A., Lindahl, B., O’Hara,
R.B., öpik, M., Sogin, M.L., Unterseher, M., Tedersoo, L., 2016. Millions of reads,
thousands of taxa: Microbial community structure and associations analyzed via
marker
genesa.
FEMS
Microbiol.
Rev.
40,
686–700.
https://doi.org/10.1093/femsre/fuw017
(6) Barberán, A., Caceres Velazquez, H., Jones, S., Fierer, N., 2017. Hiding in plain sight:
Mining bacterial species records for phenotypic trait information. mSphere 2,
e00237–17. https://doi.org/10.1128/mSphere.00237-17
(7) Barberán, A., Ramirez, K.S., Leff, J.W., Bradford, M.A., Wall, D.H., Fierer, N., 2014.
Why are some microbes more ubiquitous than others? Predicting the habitat
breadth of soil bacteria. Ecol. Lett. 17, 794–802. https://doi.org/10.1111/ele.12282
(8) Bergkemper, F., Schöler, A., Engel, M., Lang, F., Krüger, J., Schloter, M., Schulz, S.,
2016. Phosphorus depletion in forest soils shapes bacterial communities towards
phosphorus
recycling
systems.
Environ.
Microbiol.
18,
1988–2000.
https://doi.org/10.1111/1462-2920.13442
(9) Caporaso, J.G., Lauber, C.L., Walters, W.A., Berg-Lyons, D., Lozupone, C.A.,
Turnbaugh, P.J., Fierer, N., Knight, R., 2011. Global patterns of 16S rRNA diversity
at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. 108, 4516–4522.
https://doi.org/10.1073/pnas.1000080107
57
(10) Carter, K.M., Lu, M., Luo, Q., Jiang, H., An, L., 2020. Microbial community
dissimilarity for source tracking with application in forensic studies. PLoS One 15,
e0236082. https://doi.org/10.1371/journal.pone.0236082
(11) Castle, S.C., Sullivan, B.W., Knelman, J., Hood, E., Nemergut, D.R., Schmidt, S.K.,
Cleveland, C.C., 2017. Nutrient limitation of soil microbial activity during the
earliest stages of ecosystem development. Oecologia 185, 513–524.
https://doi.org/10.1007/s00442-017-3965-6
(12) Choudoir, M.J., Barberán, A., Menninger, H.L., Dunn, R.R., Fierer, N., 2018.
Variation in range size and dispersal capabilities of microbial taxa. Ecology 99, 322–
334. https://doi.org/10.1002/ecy.2094
(13) Chvatal, V., 1979. A Greedy Heuristic for the Set-Covering Problem. Math. Oper.
Res. 4, 233.
(14) Corlett, R.T., Westcott, D.A., 2013. Will plant movements keep up with climate
change? Trends Ecol. Evol. 28, 482–8. https://doi.org/10.1016/j.tree.2013.04.003
(15) Delgado-Baquerizo, M., Bardgett, R.D., Vitousek, P.M., Maestre, F.T., Williams,
M.A., Eldridge, D.J., Lambers, H., Neuhauser, S., Gallardo, A., García-Velázquez, L.,
Sala, O.E., Abades, S.R., Alfaro, F.D., Berhe, A.A., Bowker, M.A., Currier, C.M.,
Cutler, N.A., Hart, S.C., Hayes, P.E., Hseu, Z.-Y., Kirchmair, M., Peña-Ramírez, V.M.,
Pérez, C.A., Reed, S.C., Santos, F., Siebe, C., Sullivan, B.W., Weber-Grullon, L., Fierer,
N., 2019. Changes in belowground biodiversity during ecosystem development.
Proc. Natl. Acad. Sci. 116, 6891–6896. https://doi.org/10.1073/pnas.1818400116
(16) Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-gonzález, A.,
Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., Fierer, N., 2018. A global
atlas of the dominant bacteria found in soil. Science. 325, 320–325.
https://doi.org/10.1126/science.aap9516
(17) Delgado-Baquerizo, M., Reich, P.B., Khachane, A.N., Campbell, C.D., Thomas, N.,
Freitag, T.E., Abu Al-Soud, W., Sørensen, S., Bardgett, R.D., Singh, B.K., 2017. It is
elemental: soil nutrient stoichiometry drives bacterial diversity. Environ. Microbiol.
19, 1176–1188. https://doi.org/10.1111/1462-2920.13642
(18) DiMucci, D., Kon, M., Segrè, D., 2018. Machine learning reveals missing edges and
putative interaction mechanisms in microbial ecosystem networks. mSystems 3, 1–
13. https://doi.org/10.1128/mSystems.00181-18
(19) Edgar, R.C., 2010. Search and clustering orders of magnitude faster than BLAST.
Bioinformatics 26, 2460–2461. https://doi.org/10.1093/bioinformatics/btq461
(20) Evans, S., Martiny, J.B.H., Allison, S.D., 2017. Effects of dispersal and selection on
stochastic assembly in microbial communities. ISME J. 11, 176–185.
https://doi.org/10.1038/ismej.2016.96
(21) Ferrenberg, S., O ’neill, S.P., Knelman, J.E., Todd, B., Duggan, S., Bradley, D.,
Robinson, T., Schmidt, S.K., Townsend, A.R., Williams, M.W., Cleveland, C.C.,
Melbourne, B.A., Jiang, L., Nemergut, D.R., 2013. Changes in assembly processes in
soil bacterial communities following a wildfire disturbance. ISME J. 7, 1102–1111.
https://doi.org/10.1038/ismej.2013.11
(22) Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T.,
Thomson, N., Allen, M.J., Angiuoli, S. V, Ashburner, M., Axelrod, N., Baldauf, S.,
58
Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., De Vos, P., DePamphilis,
C., Edwards, R., Faruque, N., Feldman, R., Gilbert, J., Gilna, P., Glöckner, F.O.,
Goldstein, P., Guralnick, R., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C.,
Hugenholtz, P., Joint, I., Kagan, L., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann,
R., Kolker, E., Kravitz, S., Kyrpides, N., Leebens-Mack, J., Lewis, S.E., Li, K., Lister,
A.L., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Mizrachi, I., Moxon,
R., Nelson, K., Parkhill, J., Proctor, L., White, O., Sansone, S.-A., Spiers, A., Stevens,
R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward,
N., Whetzel, T., San Gil, I., Wilson, G., Wipat, A., 2008. The minimum information
about a genome sequence (MIGS) specification. Nat. Biotechnol. 26, 541–7.
https://doi.org/10.1038/nbt1360
(23) Fierer, N., 2017. Embracing the unknown: Disentangling the complexities of the soil
microbiome.
Nat.
Rev.
Microbiol.
15,
579–590.
https://doi.org/10.1038/nrmicro.2017.87
(24) Fierer, N., Grandy, A.S., Six, J., Paul, E.A., 2009. Searching for unifying principles in
soil
ecology.
Soil
Biol.
Biochem.
41,
2249–2256.
https://doi.org/10.1016/j.soilbio.2009.06.009
(25) Fierer, N., Nemergut, D., Knight, R., Craine, J.M., 2010. Changes through time:
Integrating microorganisms into the study of succession. Res. Microbiol. 161, 635–
642. https://doi.org/10.1016/j.resmic.2010.06.002
(26) Freedman, Z., Zak, D.R., 2015. Soil bacterial communities are shaped by temporal
and environmental filtering: evidence from a long-term chronosequence. Environ.
Microbiol. 17, 3208–3218. https://doi.org/10.1111/1462-2920.12762
(27) Friedman, J., Higgins, L.M., Gore, J., 2017. Community structure follows simple
assembly rules in microbial microcosms. Nat. Ecol. Evol. 1, 0109.
https://doi.org/10.1038/s41559-017-0109
(28) Garnier, E., Navas, M.-L., 2012. A trait-based approach to comparative functional
plant ecology: concepts, methods and applications for agroecology. A review.
Agron. Sustain. Dev. 32, 365–399. https://doi.org/10.1007/s13593-011-0036-y
(29) Giagnoni, L., Arenella, M., Galardi, E., Nannipieri, P., Renella, G., 2018. Bacterial
culturability and the viable but non-culturable (VBNC) state studied by a proteomic
approach using an artificial soil. Soil Biol. Biochem. 118, 51–58.
https://doi.org/10.1016/j.soilbio.2017.12.004
(30) Gilbert, J.A., Jansson, J.K., Knight, R., 2018. Earth Microbiome Project and Global
Systems
Biology.
mSystems
3,
e00217–17.
https://doi.org/10.1128/mSystems.00217-17
(31) Girvan, M.S., Campbell, C.D., Killham, K., Prosser, J.I., Glover, L.A., 2005. Bacterial
diversity promotes community stability and functional resilience after perturbation.
Environ. Microbiol. 7, 301–313. https://doi.org/10.1111/j.1462-2920.2005.00695.x
(32) Glöckner, F.O., Yilmaz, P., Quast, C., Gerken, J., Beccati, A., Ciuprina, A., Bruns, G.,
Yarza, P., Peplies, J., Westram, R., Ludwig, W., 2017. 25 years of serving the
community with ribosomal RNA gene reference databases and tools. J. Biotechnol.
261, 169‒176. https://doi.org/10.1016/j.jbiotec.2017.06.1198
(33) Goto, D.K., Yan, T., 2011. Effects of land uses on fecal indicator bacteria in the water
59
and soil of a tropical watershed.
https://doi.org/10.1264/jsme2.me11115
Microbes
Environ.
26,
254–260.
(34) Graham, E.B., Knelman, J.E., Schindlbacher, A., Siciliano, S., Breulmann, M.,
Yannarell, A., Beman, J.M., Abell, G., Philippot, L., Prosser, J., Foulquier, A., Yuste,
J.C., Glanville, H.C., Jones, D.L., Angel, R., Salminen, J., Newton, R.J., Bürgmann,
H., Ingram, L.J., Hamer, U., Siljanen, H.M.P., Peltoniemi, K., Potthast, K., Bañeras,
L., Hartmann, M., Banerjee, S., Yu, R.Q., Nogaro, G., Richter, A., Koranda, M., Castle,
S.C., Goberna, M., Song, B., Chatterjee, A., Nunes, O.C., Lopes, A.R., Cao, Y.,
Kaisermann, A., Hallin, S., Strickland, M.S., Garcia-Pausas, J., Barba, J., Kang, H.,
Isobe, K., Papaspyrou, S., Pastorelli, R., Lagomarsino, A., Lindström, E.S., Basiliko,
N., Nemergut, D.R., 2016. Microbes as engines of ecosystem function: When does
community structure enhance predictions of ecosystem processes? Front. Microbiol.
7, 214. https://doi.org/10.3389/fmicb.2016.00214
(35) Graham, E.B., Wieder, W.R., Leff, J.W., Weintraub, S.R., Townsend, A.R., Cleveland,
C.C., Philippot, L., Nemergut, D.R., 2014. Do we need to understand microbial
communities to predict ecosystem function? A comparison of statistical models of
nitrogen
cycling
processes.
Soil
Biol.
Biochem.
68,
279–282.
https://doi.org/10.1016/j.soilbio.2013.08.023
(36) Griffiths, B.S., Philippot, L., 2013. Insights into the resistance and resilience of the
soil
microbial
community.
FEMS
Microbiol.
Rev.
37,
112–129.
https://doi.org/10.1111/j.1574-6976.2012.00343.x
(37) Grime, J.P., 1974. Vegetation classification by reference to strategies. Nature 250, 26–
31. https://doi.org/10.1038/250026a0
(38) Grossart, H.-P., Dziallas, C., Leunert, F., Tang, K.W., 2010. Bacteria dispersal by
hitchhiking on zooplankton. Proc. Natl. Acad. Sci. 107, 11959–11964.
https://doi.org/10.1073/pnas.1000668107
(39) Guieysse, B., Wuertz, S., 2012. Metabolically versatile large-genome prokaryotes.
Curr. Opin. Biotechnol. 23, 467–473. https://doi.org/10.1016/j.copbio.2011.12.022
(40) Guittar, J., Shade, A., Litchman, E., 2019. Trait-based community assembly and
succession of the infant gut microbiome. Nat. Commun. 10, 512.
(41) Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J., Goodman, R.M., 1998.
Molecular biological access to the chemistry of unknown soil microbes: a new
frontier for natural products. Chem. Biol. 5, R245-9. https://doi.org/10.1016/s10745521(98)90108-9
(42) Higashi, K., Suzuki, S., Kurosawa, S., Mori, H., Kurokawa, K., 2018. Latent
environment allocation of microbial community data. PLOS Comput. Biol. 14,
e1006143. https://doi.org/10.1371/journal.pcbi.1006143
(43) Hiraoka, S., Yang, C.C., Iwasaki, W., 2016. Metagenomics and Bioinformatics in
Microbial Ecology: Current Status and Beyond. Microbes Environ. 31, 204–212.
https://doi.org/10.1264/jsme2.ME16024
(44) Hitchens, A.P., Leikind, M.C., 1939. The introduction of agar into bacteriology. J.
Bacteriol. 37, 485–93.
(45) Isobe, K., Ikutani, J., Fang, Y., Yoh, M., Mo, J., Suwa, Y., Yoshida, M., Senoo, K.,
Otsuka, S., Koba, K., 2018. Highly abundant acidophilic ammonia-oxidizing archaea
60
causes high rates of nitrification and nitrate leaching in nitrogen-saturated forest
soils. Soil Biol. Biochem. in press. https://doi.org/10.1016/j.soilbio.2018.04.021
(46) Isobe, K., Ise, Y., Kato, H., Oda, T., Vincenot, C.E., Koba, K., Tateno, R., Senoo, K.,
Ohte, N., 2019. Consequences of microbial diversity in forest nitrogen cycling:
diverse ammonifiers and specialized ammonia oxidizers. ISME J.
https://doi.org/10.1038/s41396-019-0500-2
(47) Ji, M., Kong, W., Yue, L., Wang, J., Deng, Y., Zhu, L., 2019. Salinity reduces bacterial
diversity, but increases network complexity in Tibetan Plateau lakes. FEMS
Microbiol. Ecol. 95, fiz190. https://doi.org/10.1093/femsec/fiz190
(48) Jiang, Y., Lei, Y., Yang, Y., Korpelainen, H., Niinemets, Ü., Li, C., 2018. Divergent
assemblage patterns and driving forces for bacterial and fungal communities along
a glacier forefield chronosequence. Soil Biol. Biochem. 118, 207–216.
https://doi.org/10.1016/j.soilbio.2017.12.019
(49) Karsch-Mizrachi, I., Takagi, T., Cochrane, G., 2018. The international nucleotide
sequence database collaboration. Nucleic Acids Res. 46, D48–D51.
https://doi.org/10.1093/nar/gkx1097
(50) Kearns, P.J., Shade, A., 2017. Trait-based patterns of microbial succession in
dormancy potential and heterotrophic strategy: case studies of resource-based and
post-press succession. ISME J. 12, 2575–2581. https://doi.org/10.1038/s41396-0180194-x
(51) Kirs, M., Kisand, V., Wong, M., Caffaro-Filho, R.A., Moravcik, P., Harwood, V.J.,
Yoneyama, B., Fujioka, R.S., 2017. Multiple lines of evidence to identify sewage as
the cause of water quality impairment in an urbanized tropical watershed. Water
Res. 116, 23–33. https://doi.org/10.1016/j.watres.2017.03.024
(52) Klindworth, A., Peplies, J., Pruesse, E., Schweer, T., Glöckner, F.O., Quast, C., Horn,
M., 2012. Evaluation of general 16S ribosomal RNA gene PCR primers for classical
and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41, e1.
https://doi.org/10.1093/nar/gks808
(53) Knights, D., Kuczynski, J., Charlson, E.S., Zaneveld, J., Mozer, M.C., Collman, R.G.,
Bushman, F.D., Knight, R., Kelley, S.T., 2011. Bayesian community-wide cultureindependent microbial source tracking. Nat. Methods 8, 761–765.
https://doi.org/10.1038/nmeth.1650
(54) Kopylova, E., Noé, L., Touzet, H., 2012. SortMeRNA: Fast and accurate filtering of
ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211–3217.
https://doi.org/10.1093/bioinformatics/bts611
(55) Krause, S., Le Roux, X., Niklaus, P.A., van Bodegom, P.M., Lennon T., J.T., Bertilsson,
S., Grossart, H.P., Philippot, L., Bodelier, P.L.E., 2014. Trait-based approaches for
understanding microbial biodiversity and ecosystem functioning. Front. Microbiol.
5, 251. https://doi.org/10.3389/fmicb.2014.00251
(56) Lauber, C.L., Hamady, M., Knight, R., Fierer, N., 2009. Pyrosequencing-based
assessment of soil pH as a predictor of soil bacterial community structure at the
continental
scale.
Appl.
Environ.
Microbiol.
75,
5111–20.
https://doi.org/10.1128/AEM.00335-09
(57) Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., Zhang, Y., Shen,
61
J., Pang, X., Zhang, M., Wei, H., Chen, Y., Lu, H., Zuo, J., Su, M., Qiu, Y., Jia, W.,
Xiao, C., Smith, L.M., Yang, S., Holmes, E., Tang, H., Zhao, G., Nicholson, J.K., Li,
L., Zhao, L., 2008. Symbiotic gut microbes modulate human metabolic phenotypes.
Proc. Natl. Acad. Sci. 105, 2117–2122. https://doi.org/10.1073/pnas.0712038105
(58) Liu, W.T., Marsh, T.L., Cheng, H., Forney, L.J., 1997. Characterization of microbial
diversity by determining terminal restriction fragment length polymorphisms of
genes encoding 16S rRNA. Appl. Environ. Microbiol. 63, 4516–22.
(59) Louca, Stilianos, Jacques, S.M.S., Pires, A.P.F., Leal, J.S., Srivastava, D.S., Parfrey,
L.W., Farjalla, V.F., Doebeli, M., 2016a. High taxonomic variability despite stable
functional structure across microbial communities. Nat. Ecol. Evol. 1, 0015.
https://doi.org/10.1038/s41559-016-0015
(60) Louca, S., Parfrey, L.W., Doebeli, M., 2016b. Decoupling function and taxonomy in
the
global
ocean
microbiome.
Science.
353,
1272–1277.
https://doi.org/10.1126/science.aaf4507
(61) Lozupone, C.A., Knight, R., 2007. Global patterns in bacterial diversity. Proc. Natl.
Acad. Sci. U. S. A. 104, 11436–11440. https://doi.org/10.1073/pnas.0611525104
(62) Lynch, M.D.J., Neufeld, J.D., 2015. Ecology and exploration of the rare biosphere.
Nat. Rev. Microbiol. 13, 217–229. https://doi.org/10.1038/nrmicro3400
(63) Mapelli, F., Marasco, R., Fusi, M., Scaglia, B., Tsiamis, G., Rolli, E., Fodelianakis, S.,
Bourtzis, K., Ventura, S., Tambone, F., Adani, F., Borin, S., Daffonchio, D., 2018. The
stage of soil development modulates rhizosphere effect along a High Arctic desert
chronosequence. ISME J. 12, 1188–1198. https://doi.org/10.1038/s41396-017-00264
(64) Markowitz, V.M., Ivanova, N.N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D.,
Chen, I.-M.A., Grechkin, Y., Dubchak, I., Anderson, I., Lykidis, A., Mavromatis, K.,
Hugenholtz, P., Kyrpides, N.C., 2007. IMG/M: a data management and analysis
system
for
metagenomes.
Nucleic
Acids
Res.
36,
D534–D538.
https://doi.org/10.1093/nar/gkm869
(65) Martiny, J.B.H., Jones, S.E., Lennon, J.T., Martiny, A.C., 2015. Microbiomes in light
of
traits:
phylogenetic
perspective.
Science.
350,
649.
https://doi.org/10.1126/science.aac9323
(66) McDonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., Desantis, T.Z., Probst, A.,
Andersen, G.L., Knight, R., Hugenholtz, P., 2012. An improved Greengenes
taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria
and archaea. ISME J. 6, 610–618. https://doi.org/10.1038/ismej.2011.139
(67) Mise, K., Maruyama, R., Miyabara, Y., Kunito, T., Senoo, K., Otsuka, S., 2019. Timeseries analysis of phosphorus-depleted microbial communities in carbon/nitrogenamended soils. Appl. Soil Ecol. https://doi.org/10.1016/j.apsoil.2019.08.008
(68) Moyer, C.L., Dobbs, F.C., Karl, D.M., 1994. Estimation of diversity and community
structure through restriction fragment length polymorphism distribution analysis
of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent
system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60, 871–9.
(69) Muyzer, G., de Waal, E.C., Uitterlinden, A.G., 1993. Profiling of complex microbial
populations by denaturing gradient gel electrophoresis analysis of polymerase
62
chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59,
695–700.
(70) Muyzer, G., Smalla, K., 1998. Application of denaturing gradient gel electrophoresis
(DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology.
Antonie Van Leeuwenhoek 73, 127–41. https://doi.org/10.1023/a:1000669317571
(71) Nemergut, D.R., Knelman, J.E., Ferrenberg, S., Bilinski, T., Melbourne, B., Jiang, L.,
Violle, C., Darcy, J.L., Prest, T., Schmidt, S.K., Townsend, A.R., 2016. Decreases in
average bacterial community rRNA operon copy number during succession. ISME
J. 10, 1147–1156. https://doi.org/10.1038/ismej.2015.191
(72) Nosho, K., Fukushima, H., Asai, T., Nishio, M., Takamaru, R., KobayashiKirschvink, K.J., Ogawa, T., Hidaka, M., Masaki, H., 2018. cAMP-CRP acts as a key
regulator for the viable but non-culturable state in escherichia coli. Microbiology
164, 410–419. https://doi.org/10.1099/mic.0.000618
(73) Oliverio, A.M., Bradford, M.A., Fierer, N., 2017. Identifying the microbial taxa that
consistently respond to soil warming across time and space. Glob. Chang. Biol. 23,
2117–2129. https://doi.org/10.1111/gcb.13557
(74) Ortiz-Álvarez, R., Fierer, N., De Los Ríos, A., Casamayor, E.O., Barberán, A., 2018.
Consistent changes in the taxonomic structure and functional attributes of bacterial
communities during primary succession. ISME J. 12, 1658–1667.
https://doi.org/10.1038/s41396-018-0076-2
(75) Pfeiffer, S., Pastar, M., Mitter, B., Lippert, K., Hackl, E., Lojan, P., Oswald, A.,
Sessitsch, A., 2014. Improved group-specific primers based on the full SILVA 16S
rRNA gene reference database. Environ. Microbiol. 16, 2389–2407.
https://doi.org/10.1111/1462-2920.12350
(76) Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J.,
Glöckner, F.O., 2013. The SILVA ribosomal RNA gene database project: Improved
data processing and web-based tools. Nucleic Acids Res. 41, 590–596.
https://doi.org/10.1093/nar/gks1219
(77) R Core Team, 2017. R: A language and environment for statistical computing. R
Foundation for Statistical Computing, Vienna, Austria. URL https://www.Rproject.org/.
(78) Ramirez, K.S., Knight, C.G., De Hollander, M., Brearley, F.Q., Constantinides, B.,
Cotton, A., Creer, S., Crowther, T.W., Davison, J., Delgado-Baquerizo, M., Dorrepaal,
E., Elliott, D.R., Fox, G., Griffiths, R.I., Hale, C., Hartman, K., Houlden, A., Jones,
D.L., Krab, E.J., Maestre, F.T., McGuire, K.L., Monteux, S., Orr, C.H., Van Der Putten,
W.H., Roberts, I.S., Robinson, D.A., Rocca, J.D., Rowntree, J., Schlaeppi, K.,
Shepherd, M., Singh, B.K., Straathof, A.L., Bhatnagar, J.M., Thion, C., Van Der
Heijden, M.G.A., De Vries, F.T., 2018. Detecting macroecological patterns in
bacterial communities across independent studies of global soils. Nat. Microbiol. 3,
189–196. https://doi.org/10.1038/s41564-017-0062-x
(79) Rath, K.M., Fierer, N., Murphy, D. V, Rousk, J., 2019. Linking bacterial community
composition to soil salinity along environmental gradients. ISME J. 13, 836–846.
https://doi.org/10.1038/s41396-018-0313-8
(80) Reimer, L.C., Vetcininova, A., Carbasse, J.S., Söhngen, C., Gleim, D., Ebeling, C.,
63
Overmann, J., 2019. Bac Dive in 2019: bacterial phenotypic data for Highthroughput biodiversity analysis. Nucleic Acids Res. 47, D631–D636.
https://doi.org/10.1093/nar/gky879
(81) Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N.N., Anderson, I.J., Cheng, J.F.,
Darling, A., Malfatti, S., Swan, B.K., Gies, E.A., Dodsworth, J.A., Hedlund, B.P.,
Tsiamis, G., Sievert, S.M., Liu, W.T., Eisen, J.A., Hallam, S.J., Kyrpides, N.C.,
Stepanauskas, R., Rubin, E.M., Hugenholtz, P., Woyke, T., 2013. Insights into the
phylogeny and coding potential of microbial dark matter. Nature 499, 431–437.
https://doi.org/10.1038/nature12352
(82) Roller, B.R.K., Stoddard, S.F., Schmidt, T.M., 2016. Exploiting rRNA operon copy
number to investigate bacterial reproductive strategies. Nat. Microbiol. 1, 16160.
https://doi.org/10.1038/nmicrobiol.2016.160
(83) Schmieder, R., Edwards, R.A., 2011. Quality control and preprocessing of
metagenomic
datasets.
Bioinformatics
27,
863–864.
https://doi.org/10.1093/bioinformatics/btr026
(84) Schuster, S.C., 2008. Next-generation sequencing transforms today’s biology. Nat.
Methods 5, 16–18. https://doi.org/10.1038/nmeth1156
(85) Sinha, R., Stanley, G., Gulati, G.S., Ezran, C., Travaglini, K.J., Wei, E., Chan, C.K.F.,
Nabhan, A.N., Su, T., Morganti, R.M., Conley, S.D., Chaib, H., Red-Horse, K.,
Longaker, M.T., Snyder, M.P., Krasnow, M.A., Weissman, I.L., 2017. Index
switching causes “spreading-of-signal” among multiplexed samples in Illumina
HiSeq 4000 DNA sequencing. bioRxiv 125724. https://doi.org/10.1101/125724
(86) Sriswasdi, S., Yang, C.C., Iwasaki, W., 2017. Generalist species drive microbial
dispersion and evolution. Nat. Commun. 8, 1162. https://doi.org/10.1038/s41467017-01265-1
(87) Steen, A.D., Crits-Christoph, A., Carini, P., DeAngelis, K.M., Fierer, N., Lloyd, K.G.,
Cameron Thrash, J., 2019. High proportions of bacteria and archaea across most
biomes remain uncultured. ISME J. 13, 3126–3130. https://doi.org/10.1038/s41396019-0484-y
(88) Tanaka, R., Hino, A., Tsai, I.J., Palomares-Rius, J.E., Yoshida, A., Ogura, Y., Hayashi,
T., Maruyama, H., Kikuchi, T., Poulin, R., Morand, S., Sukhdeo, M., Bansemir, A.,
Korallo, N., Vinarski, M., Krasnov, B., Shenbrot, G., Mouillot, D., Combes, C.,
Waters, A., Higgins, D., McCutchan, T., Desai, N., Antonopoulos, D., Gilbert, J.,
Glass, E., Meyer, F., Weinstock, G., Yatsunenko, T., Rey, F., Manary, M., Trehan, I.,
Dominguez-Bello, M., Sogin, M., Morrison, H., Huber, J., Welch, D.M., Huse, S.,
Amir, A., Zeisel, A., Zuk, O., Elgart, M., Stern, S., Jumpponen, A., Jones, K.,
Porazinska, D., Giblin-Davis, R., Powers, T., Thomas, W., Porazinska, D., GiblinDavis, R., Faller, L., Farmerie, W., Kanzaki, N., Logares, R., Audic, S., Bass, D.,
Bittner, L., Boutte, C., Webster, J., Macdonald, D., Holterman, M., Wurff, A. van der,
Elsen, S. van den, Megen, H. van, Bongers, T., Waeschenbach, A., Webster, B., Bray,
R., Littlewood, D., Katoh, K., Misawa, K., Kuma, K., Miyata, T., Castresana, J.,
Stamatakis, A., Caporaso, J., Lauber, C., Walters, W., Berg-Lyons, D., Huntley, J.,
Amaral-Zettler, L., McCliment, E., Ducklow, H., Huse, S., Vestheim, H., Jarman, S.,
Caporaso, J., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F., Quast, C.,
Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Turnbaugh, P., Ley, R., Hamady, M.,
64
Fraser-Liggett, C., Knight, R., Bik, H., Fournier, D., Sung, W., Bergeron, R., Thomas,
W., Hugerth, L., Muller, E., Hu, Y., Lebrun, L., Roume, H., Hadziavdic, K., Lekang,
K., Lanzen, A., Jonassen, I., Thompson, E., Zhao, X., Duszynski, D., 2014.
Assessment of helminth biodiversity in wild rats using 18S rDNA based
metagenomics.
PLoS
One
9,
e110769.
https://doi.org/10.1371/journal.pone.0110769
(89) Tanaka, T., Kawasaki, K., Daimon, S., Kitagawa, W., Yamamoto, K., Tamaki, H.,
Tanaka, M., Nakatsu, C.H., Kamagata, Y., 2014. A hidden pitfall in the preparation
of agar media undermines microorganism cultivability. Appl. Environ. Microbiol.
80, 7659–7666. https://doi.org/10.1128/AEM.02741-14
(90) Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., Prill,
R.J., Tripathi, A., Gibbons, S.M., Ackermann, G., Navas-Molina, J.A., Janssen, S.,
Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J.T., Mirarab, S., Zech Xu,
Z., Jiang, L., Haroon, M.F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich,
N.A., Lefler, J., Brislawn, C.J., Humphrey, G., Owens, S.M., Hampton-Marcell, J.,
Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J.A., Clauset, A., Stevens, R.L.,
Shade, A., Pollard, K.S., Goodwin, K.D., Jansson, J.K., Gilbert, J.A., Knight, R., 2017.
A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551,
457–463. https://doi.org/10.1038/nature24621
(91) Tkacz, A., Hortala, M., Poole, P.S., 2018. Absolute quantitation of microbiota
abundance
in
environmental
samples.
Microbiome
6,
110.
https://doi.org/10.1186/s40168-018-0491-7
(92) Torres, P.J., Edwards, R.A., McNair, K.A., 2017. PARTIE: A partition engine to
separate metagenomic and amplicon projects in the Sequence Read Archive.
Bioinformatics 33, 2389–2391. https://doi.org/10.1093/bioinformatics/btx184
(93) Unno, T., Staley, C., Brown, C.M., Han, D., Sadowsky, M.J., Hur, H.G., 2018. Fecal
pollution: new trends and challenges in microbial source tracking using nextgeneration
sequencing.
Environ.
Microbiol.
20,
3132–3140.
https://doi.org/10.1111/1462-2920.14281
(94) Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A.,
Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H.,
Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., BadenTillson, H., Pfannkoch, C., Rogers, Y.-H., Smith, H.O., 2004. Environmental genome
shotgun
sequencing
of
the
Sargasso
Sea.
Science.
304,
66–74.
https://doi.org/10.1126/science.1093857
(95) Violle, C., Navas, M.-L., Vile, D., Kazakou, E., Fortunel, C., Hummel, I., Garnier, E.,
2007. Let the concept of trait be functional! Oikos 116, 882–892.
https://doi.org/10.1111/j.2007.0030-1299.15559.x
(96) Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., 2007. Naive Bayesian classifier for
rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl.
Environ. Microbiol. 73, 5261–5267. https://doi.org/10.1128/AEM.00062-07
(97) Werner, G.D.A., Kiers, E.T., 2015. Order of arrival structures arbuscular mycorrhizal
colonization
of
plants.
New
Phytol.
205,
1515–1524.
https://doi.org/10.1111/nph.13092
(98) Wertz, S., Degrange, V., Prosser, J.I., Poly, F., Commeaux, C., Freitag, T.,
65
Guillaumaud, N., Roux, X. Le, 2006. Maintenance of soil functioning following
erosion of microbial diversity. Environ. Microbiol. 8, 2162–2169.
https://doi.org/10.1111/j.1462-2920.2006.01098.x
(99) Yang, C.C., Iwasaki, W., 2014. MetaMetaDB: A database and analytic system for
investigating
microbial
habitability.
PLoS
One
9,
e87126.
https://doi.org/10.1371/journal.pone.0087126
(100) Yao, Q., Li, Z., Song, Y., Wright, S.J., Guo, X., Tringe, S.G., Tfaily, M.M., Paša-Tolić,
L., Hazen, T.C., Turner, B.L., Mayes, M.A., Pan, C., 2018. Community
proteogenomics reveals the systemic impact of phosphorus availability on
microbial functions in tropical soil. Nat. Ecol. Evol. 2, 499–509.
https://doi.org/10.1038/s41559-017-0463-5
(101) Yassour, M., Vatanen, T., Siljander ...