Kieft T, Soroker E, Firestone M. Microbial biomass response to a rapid increase in water potential when dry soil is wetted. Soil Biol Biochem. 1987;19:119–26.
Placella SA, Brodie EL, Firestone MK. Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups. Proc Natl Acad Sci USA. 2012;109:10931–6.
Birch H. The effect of soil drying on humus decomposition and nitrogen availability. Plant Soil. 1958;10:9–31.
Unger S, Máguas C, Pereira JS, David TS, Werner C. The influence of precipitation pulses on soil respiration—Assessing the “Birch effect” by stable carbon isotopes. Soil Biol Biochem. 2010;42:1800–10.
Fierer N, Schimel J. Effects of drying–rewetting frequency on soil carbon and nitrogen transformations. Soil Biol Biochem. 2002;34:777–87.
Schimel J, Jackson L, Firestone M. Spatial and temporal effects on plant-microbial competition for inorganic nitrogen in a California annual grassland. Soil Biol Biochem. 1989;21:1059–66.
Davidson EA. Sources of nitric oxide and nitrous oxide following wetting of dry soil. Soil Sci Soc Am J. 1992;56:95–102.
Barnard RL, Osborne CA, Firestone MK. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. ISME J. 2013;7:2229–41.
Hungate BA, Lund CP, Pearson HL, Chapin III FS. Elevated CO2 and nutrient addition after soil N cycling and N trace gas fluxes with early season wet-up in a California annual grassland. Biogeochemistry. 1997;37:89–109.
Schimel JP. Life in dry soils: effects of drought on soil microbial communities and processes. Annu Rev Ecol Evol Syst. 2018;49:409–32.
Xu L, Baldocchi DD, Tang J. How soil moisture, rain pulses, and growth alter the response of ecosystem respiration to temperature. Glob Biogeochem Cycles. 2004;18:GB4002.
Fierer N, Schimel JP, Holden PA. Influence of drying-rewetting frequency on soil bacterial community structure. Micro Ecol. 2003;45:63–71.
Barnard RL, Osborne CA, Firestone MK. Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate. ISME J. 2015;9:946–57.
Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 2015;349:1101–6.
Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotechnol. 2016;34:1256–63.
Koch BJ, McHugh TA, Hayer M, Schwartz E, Blazewicz SJ, Dijkstra P, et al. Estimating taxon-specific population dynamics in diverse microbial communities. Ecosphere. 2018;9:e02090–15.
Hungate BA, Mau RL, Schwartz E, Caporaso JG, Dijkstra P, van Gestel N, et al. Quantitative microbial ecology through stable isotope probing. Appl Environ Microbiol. 2015;81:7570–81.
Pritchard JR, Schluter D. Declining interspecific competition during character displacement: summoning the ghost of competition past. Evol Ecol Res. 2001;3:209–20.
Reich PB, Walters MB, Ellsworth DS. From tropics to tundra: global convergence in plant functioning. Proc Natl Acad Sci USA. 1997;94:13730–4.
Schimel D. Terrestrial ecosystems and the carbon cycle. Glob Change Biol. 1995;1:77–91.
Tilman D. Resource competition between plankton algae: an experimental and theoretical approach. Ecology. 1977;58:338–48.
Morris WF, Doak DF. Quantitative conservation biology: theory and practice of population viability analysis. Sunderland, MA: Sinauer Associates; 2002.
Chapin III FS, Walker LR, Fastie CL, Sharman LC. Mechanisms of primary succession following deglaciation at Glacier Bay, Alaska. Ecol Monogr. 1994;64:149–75.
Nicholson AJ. The balance of animal populations. J Anim Ecol. 1933;2:132–78.
Andrewartha HG, Birch LC. The distribution and abundance of animals. Chicago: University of Chicago Press; 1954.
Egerton FN. Changing concepts of the balance of nature. Quart Rev Biol. 1973;48:322–50.
Rousk J, Bååth E. Growth of saprotrophic fungi and bacteria in soil. FEMS Microbiol Ecol. 2011;78:17–30.
Newell SY, Fallon RD. Toward a method for measuring instantaneous fungal growth rates in field samples. Ecology. 1991;72:1547–59.
Poulsen L, Ballard G, Stahl D. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl Environ Microbiol. 1993;59:1354.
Muttray AF, Yu Z, Mohn WW. Population dynamics and metabolic activity of Pseudomonas abietaniphila BKME-9 within pulp mill wastewater microbial communities assayed by competitive PCR and RT-PCR. FEMS Microbiol Ecol. 2001;38:21–31.
Blazewicz SJ, Barnard RL, Daly RA, Firestone MK. Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J. 2013;7:2061–8.
DeAngelis KM, Wu CH, Beller HR, Brodie EL, Chakraborty R, DeSantis TZ, et al. PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl Environ Microbiol. 2011;77:6313–22.
Gaidos E, Rusch A, Ilardo M. Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds. Environ Microbiol. 2011;13:1138–52.
Baldrian P, Kolarík M, Štursová M, Kopecky J, Valášková V, Vētrovsky T, et al. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J. 2012;6:248–58.
Schwartz E. Characterization of growing microorganisms in soil by stable isotope probing with H218O. Appl Environ Microbiol. 2007;73:2541–6.
Aanderud ZT, Lennon JT. Validation of heavy-water stable isotope probing for the characterization of rapidly responding soil bacteria. Appl Environ Microbiol. 2011;77:4589–96.
Blazewicz SJ, Schwartz E. Dynamics of 18O incorporation from H218O into soil microbial DNA. Micro Ecol. 2011;61:911–6.
Blazewicz SJ, Schwartz E, Firestone MK. Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil. Ecology. 2014;95:1162–72.
Sambrook J, Russell DW Molecular cloning. A laboratory Manual. 3rd ed. New York: Cold Spring Harbor Laboratory Press; 2001.
Buckley DH, Huangyutitham V, Hsu S-F, Nelson TA. Stable isotope probing with 15N achieved by disentangling the effects of genome G+C content and isotope enrichment on DNA density. Appl Environ Microbiol. 2007;73:3189–95.
Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, et al. DNA stable-isotope probing. Nat Protoc. 2007;2:860–6.
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 2012;40:W622–W7.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Desantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069–72.
Caporaso JG, Bittinger K, Bushman FD, Desantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2010;26:266–7.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–200.
Schildkraut CL, Marmur J, Doty P. Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol. 1962;4:430–43.
Martin-Laurent F, Phillipot L, Hallet S, Chaussod R, Germon JC, Soulas G, et al. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol. 2001;67:2354–59.
Kanagawa T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng. 2003;96:317–23.
Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods. 2009;6:291–5.
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Australia 2016. http://www.R-project.org/.
Hashimoto T, Frieben WR, Conti SF. Germination of single bacterial spores. J Bacteriol. 1969;98:1011–20.
Levinson HS, Hyatt MT. Correlation of respiratory activity with phases of spore germination and growth in bacillus megaterium as influenced by manganese and L-alanine. J Bacteriol. 1956;72:176–83.
Morrissey EM, Mau RL, Hayer M, Liu XJ, Schwartz E, Dijkstra P, et al. Evolutionary history constrains microbial traits across environmental variation. Nat Ecol Evol. 2019;3:1064–9.
Karaoz U, Couradeau E, da Rocha UN, Lim HC, Northen T, Garcia-Pichel F, et al. Large blooms of bacillales (Firmicutes) underlie the response to wetting of cyanobacterial biocrusts at various stages of maturity. MBio. 2018;9:e01366–16-17.
Engelhardt IC, Welty A, Blazewicz SJ, Bru D, Rouard N, Breuil MC, et al. Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system. ISME J. 2018;12:1061–71.
Ortiz-Álvarez R, Fierer N, de los Ríos A, Casamayor EO, Barberan A. Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession. ISME J. 2018;12:1658–67.
Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI. Optimization of lag phase shapes the evolution of a bacterial enzyme. Nat Ecol Evol. 2017;1:8396–18.
Gans J, Wolinsky M, Dunbar J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science. 2005;309:1387–90.
Curtis TP, Sloan WT. Exploring microbial diversity-a vast below. Science. 2005;309:1331–3.
Philippot L, Andersson GE, Battin TJ, Prosser JI, Schimel JP, Whitman WB, et al. The ecological coherence of high bacterial taxonomic ranks. Nat Rev Micro. 2010;8:523–9.
Philippot L, Bru D, Saby NPA, Čuhel J, Arrouays D, Šimek M, et al. Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree. Environ Microbiol. 2009;11:3096–104.
Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.
Morrissey EM, McHugh TA, Preteska L, Hayer M, Dijkstra P, Hungate BA, et al. Dynamics of extracellular DNA decomposition and bacterial community composition in soil. Soil Biol Biochem. 2015;86:42–9.
USDA Office of Communications. New aerial survey identifies more than 100 million dead trees in California. 2016. https://www.usda.gov/media/press-releases/2016/11/18/new-aerial-survey-identifies-more-100-million-dead-trees-california.
Source: Ecology - nature.com
