Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15:579–90.
Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA. 1998;95:6578–83.
Bardgett RD, van der Putten WH. Belowground biodiversity and ecosystem functioning. Nature. 2014;515:505–11.
Green JL, Bohannan BJM, Whitaker RJ. Microbial biogeography: from taxonomy to traits. Science. 2008;320:1039–43.
Martiny JBH, Jones SE, Lennon JT, Martiny AC. Microbiomes in light of traits: a phylogenetic perspective. Science. 2015;350:aac9323.
Koch AL. Oligotrophs versus copiotrophs. BioEssays. 2001;23:657–61.
Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.
Ho A, Di Lonardo DP, Bodelier PLE. Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol Ecol. 2017;93:fix006.
Klappenbach JA, Dunbar JM, Schmidt TM. rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol. 2000;66:1328–33.
Roller BRK, Stoddard SF, Schmidt TM. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat Microbiol. 2016;1:1–7.
Botzman M, Margalit H. Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biol. 2011;12:R109.
Vieira-Silva S, Rocha EPC. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 2010;6:e1000808.
Pereira-Flores E, Glöckner FO, Fernandez-Guerra A. Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data. BMC Bioinforma. 2019;20:453.
Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, et al. The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci USA. 2009;106:15527–33.
Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. A most wanted list of conserved microbial protein families with no known domains. PLoS ONE. 2018;13:e0205749.
Galand PE, Pereira O, Hochart C, Auguet JC, Debroas D. A strong link between marine microbial community composition and function challenges the idea of functional redundancy. ISME J. 2018;12:2470–8.
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44:D457–62.
Steen AD, Crits-Christoph A, Carini P, DeAngelis KM, Fierer N, Lloyd KG, et al. High proportions of bacteria and archaea across most biomes remain uncultured. ISME J. 2019;13:3126–30.
Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, et al. A global atlas of the dominant bacteria found in soil. Science. 2018;359:320–5.
Jaroszewski L, Li Z, Krishna SS, Bakolitsa C, Wooley J, Deacon AM, et al. Exploration of uncharted regions of the protein universe. PLoS Biol. 2009;7:e1000205.
Giovannoni S, Stingl U. The importance of culturing bacterioplankton in the ‘omics’ age. Nat Rev Microbiol. 2007;5:820–6.
Barberán A, Caceres Velazquez H, Jones S, Fierer N. Hiding in plain sight: Mining bacterial species records for phenotypic trait information. mSphere. 2017;2:e00237–17.
Aguiar MR, Sala OE. Patch structure, dynamics and implications for the functioning of arid ecosystems. Trends Ecol Evol. 1999;14:273–7.
Schlesinger WH, Raikes JA, Hartley AE, Cross AF. On the spatial pattern of soil nutrients in desert ecosystems. Ecology. 1996;77:364–74.
Maestre FT, Bautista S, Cortina J, Bellot J. Potential for using facilitation by grasses to establish shrubs on a semiarid degraded steppe. Ecol Appl. 2001;11:1641–55.
Butterfield BJ, Betancourt JL, Turner RM, Briggs JM. Facilitation drives 65 years of vegetation change in the Sonoran Desert. Ecology. 2010;91:1132–9.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–2.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.
Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017;35:1026–8.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754–60.
Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726–31.
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34:2115–22.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–14.
Novembre JA. Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol. 2002;19:1390–4.
Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Yunta RG, Okuda S, et al. Species–function relationships shape ecological properties of the human gut microbiome. Nat Microbiol. 2016;1:1–8.
Barberán A, Fenández-Guerra A, Bohannan BJ, Casamayor EO. Exploration of community traits as ecological markers in microbial metagenomes. Mol Ecol. 2012;21:1909–17.
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2018. https://www.R-project.org/.
Nakagawa S, Schielzeth H. A general and simple method for obtaining R2 from generalized linear mixed-effects models. Methods Ecol Evol. 2013;4:133–42.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995;57:289–300.
Goberna M, Navarro‐Cano JA, Valiente‐Banuet A, García C, Verdú M. Abiotic stress tolerance and competition‐related traits underlie phylogenetic clustering in soil bacterial communities. Ecol Lett. 2014;17:1191–201.
Rodríguez-Echeverría S, Lozano YM, Bardgett RD. Influence of soil microbiota in nurse plant systems. Funct Ecol. 2016;30:30–40.
Yahdjian L, Gherardi L, Sala OE. Nitrogen limitation in arid-subhumid ecosystems: a meta-analysis of fertilization studies. J Arid Environ. 2011;75:675–80.
Giovannoni SJ, Thrash JC, Temperton B. Implications of streamlining theory for microbial ecology. ISME J. 2014;8:1553–65.
Leff JW, Jones SE, Prober SM, Barberán A, Borer ET, Firn JL, et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci USA. 2015;112:10967–72.
Musto H, Naya H, Zavala A, Romero H, Alvarez-Valı́n F, Bernardi G. Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Lett. 2004;573:73–7.
Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 2006;34:564–74.
Neilson JW, Quade J, Ortiz M, Nelson WM, Legatzki A, Tian F, et al. Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile. Extremophiles. 2012;16:553–66.
Lajoie G, Kembel SW. Making the most of trait-based approaches for microbial ecology. Trends Microbiol. 2019;27:814–23.
Reich PB. The world-wide ‘fast-slow’ plant economics spectrum: a traits manifesto. J Ecol. 2014;102:275–301.
Nemergut DR, Knelman JE, Ferrenberg S, Bilinski T, Melbourne B, Jiang L, et al. Decreases in average bacterial community rRNA operon copy number during succession. ISME J. 2016;10:1147–56.
Ortiz-Álvarez R, Fierer N, de Los Ríos A, Casamayor EO, Barberán A. Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession. ISME J. 2018;12:1658–67.
Song H-K, Song W, Kim M, Tripathi BM, Kim H, Jablonski P, et al. Bacterial strategies along nutrient and time gradients, revealed by metagenomic analysis of laboratory microcosms. FEMS Microbiol Ecol. 2017;93:fix114.
Ferenci T. Trade-off mechanisms shaping the diversity of bacteria. Trends Microbiol. 2016;24:209–23.
Gray DA, Dugar G, Gamba P, Strahl H, Jonker MJ, Hamoen LW. Extreme slow growth as alternative strategy to survive deep starvation in bacteria. Nat Commun. 2019;10:890.
Trivedi P, Anderson IC, Singh BK. Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. Trends Microbiol. 2013;21:641–51.
Müller DB, Vogel C, Bai Y, Vorholt JA. The plant microbiota: systems-level insights and perspectives. Annu Rev Genet. 2016;50:211–34.
Brewer TE, Aronson EL, Arogyaswamy K, Billings SA, Botthoff JK, Campbell AN, et al. Ecological and genomic attributes of novel bacterial taxa that thrive in subsurface soil horizons. MBio. 2019;10:e01318–19.
Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, et al. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature. 2018;557:503–9.
Stewart EJ. Growing unculturable bacteria. J Bacteriol. 2012;194:4151–60.
Pascual-García A, Bell T. Community-level signatures of ecological succession in natural bacterial communities. Nat Commun. 2020;11:1–1.
Source: Ecology - nature.com
