1.Kannenberg, S. A., Schwalm, C. R. & Anderegg, W. R. L. Ghosts of the past: how drought legacy effects shape forest functioning and carbon cycling. Ecol. Lett. 23, 891–901 (2020).PubMed
Article
PubMed Central
Google Scholar
2.Padisak, J. Seasonal succession of phytoplankton in a large shallow lake (Balaton, Hungary)—a dynamic approach to ecological memory, its possible role and mechanisms. J. Ecol. 80, 217–230 (1992).Article
Google Scholar
3.Power, D. A. et al. What can ecosystems learn? Expanding evolutionary ecology with learning theory. Biol. Direct 10, 69 (2015).PubMed
PubMed Central
Article
Google Scholar
4.Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth’s biogeochemical cycles. Science 320, 1034–1039 (2008).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
5.Reichstein, M. et al. Climate extremes and the carbon cycle. Nature 500, 287 (2013).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
6.Seneviratne, S. I. et al. Changes in climate extremes and their impacts on the natural physical environment. In Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation. A Special Report of Working Groups I and II of the Intergovernmental Panel on Climate Change (IPCC) (eds. Field, C.B. et al.) 109–230 (Cambridge University Press, 2017).7.Pappas, C., Mahecha, M. D., Frank, D. C., Babst, F. & Koutsoyiannis, D. Ecosystem functioning is enveloped by hydrometeorological variability. Nat. Ecol. Evol. 1, 1263–1270 (2017).PubMed
Article
PubMed Central
Google Scholar
8.Hawkes, C. V. & Keitt, T. H. Resilience vs. historical contingency in microbial responses to environmental change. Ecol. Lett. 18, 612–625 (2015).PubMed
Article
PubMed Central
Google Scholar
9.Johnstone, J. F. et al. Changing disturbance regimes, ecological memory, and forest resilience. Front. Ecol. Environ. 14, 369–378 (2016).Article
Google Scholar
10.Ochoa‐Hueso, R. et al. Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents. Glob. Chang. Biol. 24, 2818–2827 (2018).11.Bastida, F. et al. Differential sensitivity of total and active soil microbial communities to drought and forest management. Glob. Chang. Biol. 23, 4185–4203 (2017).PubMed
Article
PubMed Central
Google Scholar
12.Evans, S. E., Wallenstein, M. D. & Burke, I. C. Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought? Ecology 95, 110–122 (2014).PubMed
Article
PubMed Central
Google Scholar
13.de Vries, F. T. et al. Soil bacterial networks are less stable under drought than fungal networks. Nat. Commun. 9, 3033 (2018).ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
14.Rousk, J., Smith, A. R. & Jones, D. L. Investigating the long-term legacy of drought and warming on the soil microbial community across five European shrubland ecosystems. Glob. Chang. Biol. 19, 3872–3884 (2013).ADS
PubMed
Article
PubMed Central
Google Scholar
15.Kaisermann, A., de Vries, F. T., Griffiths, R. I. & Bardgett, R. D. Legacy effects of drought on plant–soil feedbacks and plant–plant interactions. New Phytol. 215, 1413–1424 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
16.Fuchslueger, L. et al. Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event. J. Ecol. 104, 1453–1465 (2016).CAS
PubMed
PubMed Central
Article
Google Scholar
17.Meisner, A., De Deyn, G. B., de Boer, W. & van der Putten, W. H. Soil biotic legacy effects of extreme weather events influence plant invasiveness. Proc. Natl Acad. Sci. USA 110, 9835–9838 (2013).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
18.de Nijs, E. A., Hicks, L. C., Leizeaga, A., Tietema, A. & Rousk, J. Soil microbial moisture dependences and responses to drying–rewetting: the legacy of 18 years drought. Glob. Chang. Biol. 25, 1005–1015 (2019).ADS
PubMed
Article
PubMed Central
Google Scholar
19.Fuchslueger, L., Bahn, M., Fritz, K., Hasibeder, R. & Richter, A. Experimental drought reduces the transfer of recently fixed plant carbon to soil microbes and alters the bacterial community composition in a mountain meadow. New Phytol. 201, 916–927 (2014).CAS
PubMed
Article
PubMed Central
Google Scholar
20.Mooshammer, M., Wanek, W., Zechmeister-Boltenstern, S. & Richter, A. Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources. Front. Microbiol. 5, 22 (2014).PubMed
PubMed Central
Article
Google Scholar
21.Waring, B. G., Weintraub, S. R. & Sinsabaugh, R. L. Ecoenzymatic stoichiometry of microbial nutrient acquisition in tropical soils. Biogeochemistry 117, 101–113 (2014).CAS
Article
Google Scholar
22.Sinsabaugh, R. L. et al. Stoichiometry of soil enzyme activity at global scale. Ecol. Lett. 11, 1252–1264 (2008).PubMed
Article
PubMed Central
Google Scholar
23.Douglas, G. M. et al. PICRUSt2 for prediction of metagenome functions. Nat. Biotechnol. 38, 685–688, (2020).CAS
PubMed
PubMed Central
Article
Google Scholar
24.Csonka, L. N. Physiological and genetic responses of bacteria to osmotic stress. Microbiol. Mol. Biol. Rev. 53, 121–147 (1989).CAS
Google Scholar
25.Whitfield, G. B., Marmont, L. S. & Howell, P. L. Enzymatic modifications of exopolysaccharides enhance bacterial persistence. Front. Microbiol. 6, 471 (2015).26.Byrd, M. S. et al. Genetic and biochemical analyses of the Pseudomonas aeruginosa Psl exopolysaccharide reveal overlapping roles for polysaccharide synthesis enzymes in Psl and LPS production. Mol. Microbiol. 73, 622–638 (2009).CAS
PubMed
PubMed Central
Article
Google Scholar
27.El Zoeiby, A., Sanschagrin, F. & Levesque, R. C. Structure and function of the Mur enzymes: development of novel inhibitors. Mol. Microbiol. 47, 1–12 (2003).CAS
PubMed
Article
PubMed Central
Google Scholar
28.Lebre, P. H., De Maayer, P. & Cowan, D. A. Xerotolerant bacteria: surviving through a dry spell. Nat. Rev. Microbiol. 15, 285–296 (2017).CAS
PubMed
Article
PubMed Central
Google Scholar
29.Delgado-Baquerizo, M. et al. Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat. Commun. 7, 10541 (2016).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
30.Hughes, T. P. et al. Ecological memory modifies the cumulative impact of recurrent climate extremes. Nat. Clim. Chang. 9, 40–43 (2019).31.Seidl, R., Donato, D. C., Raffa, K. F. & Turner, M. G. Spatial variability in tree regeneration after wildfire delays and dampens future bark beetle outbreaks. Proc. Natl Acad. Sci. USA 113, 13075–13080 (2016).CAS
PubMed
PubMed Central
Article
Google Scholar
32.Hillebrand, H. & Kunze, C. Meta-analysis on pulse disturbances reveals differences in functional and compositional recovery across ecosystems. Ecol. Lett. 23, 575–585 (2020).33.Meisner, A., Jacquiod, S., Snoek, B. L., ten Hooven, F. C. & van der Putten, W. H. Drought legacy effects on the composition of soil fungal and prokaryote communities. Front. Microbiol. 9, 294 (2018).34.Bardgett, R. D. & Caruso, T. Soil microbial community responses to climate extremes: resistance, resilience and transitions to alternative states. Philos. Trans. R. Soc. B Biol. Sci. 375, 20190112 (2020).CAS
Article
Google Scholar
35.Isobe, K., Bouskill, N. J., Brodie, E. L., Sudderth, E. A. & Martiny, J. B. H. Phylogenetic conservation of soil bacterial responses to simulated global changes. Philos. Trans. R. Soc. B Biol. Sci. 375, 20190242 (2020).CAS
Article
Google Scholar
36.Barberán, A., Caceres Velazquez, H., Jones, S. & Fierer, N. Hiding in plain sight: mining bacterial species records for phenotypic trait information. mSphere 2, e00237–17 (2017).PubMed
PubMed Central
Article
Google Scholar
37.Bouskill, N. J. et al. Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. ISME J. 7, 384 (2012).PubMed
PubMed Central
Article
CAS
Google Scholar
38.Taketani, R. G. et al. Dry season constrains bacterial phylogenetic diversity in a semi-arid rhizosphere system. Microb. Ecol. 73, 153–161 (2017).PubMed
Article
PubMed Central
Google Scholar
39.Naylor, D., DeGraaf, S., Purdom, E. & Coleman-Derr, D. Drought and host selection influence bacterial community dynamics in the grass root microbiome. ISME J. 11, 2691 (2017).PubMed
PubMed Central
Article
Google Scholar
40.Xu, L. et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl Acad. Sci. USA 115, E4284–E4293 (2018).CAS
PubMed
PubMed Central
Article
Google Scholar
41.Taniguchi, T., Kitajima, K., Douhan, G. W., Yamanaka, N. & Allen, M. F. A pulse of summer precipitation after the dry season triggers changes in ectomycorrhizal formation, diversity, and community composition in a Mediterranean forest in California, USA. Mycorrhiza 28, 665–677 (2018).CAS
PubMed
PubMed Central
Article
Google Scholar
42.Ren, C. et al. Responses of soil total microbial biomass and community compositions to rainfall reductions. Soil Biol. Biochem. 116, 4–10 (2018).CAS
Article
Google Scholar
43.Furze, J. R. et al. Resistance and resilience of root fungal communities to water limitation in a temperate agroecosystem. Ecol. Evol. 7, 3443–3454 (2017).PubMed
PubMed Central
Article
Google Scholar
44.Deveautour, C., Donn, S., Power, S. A., Bennett, A. E. & Powell, J. R. Experimentally altered rainfall regimes and host root traits affect grassland arbuscular mycorrhizal fungal communities. Mol. Ecol. 27, 2152–2163 (2018).PubMed
Article
PubMed Central
Google Scholar
45.Averill, C., Turner, B. L. & Finzi, A. C. Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature 505, 543–545 (2014).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
46.Dijkstra, F. A., He, M., Johansen, M. P., Harrison, J. J. & Keitel, C. Plant and microbial uptake of nitrogen and phosphorus affected by drought using 15N and 32P tracers. Soil Biol. Biochem. 82, 135–142 (2015).CAS
Article
Google Scholar
47.Kakumanu, M. L., Ma, L. & Williams, M. A. Drought-induced soil microbial amino acid and polysaccharide change and their implications for C–N cycles in a climate change world. Sci. Rep. 9, 10968 (2019).ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
48.Sleator, R. D. & Hill, C. Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence. FEMS Microbiol. Rev. 26, 49–71 (2002).CAS
PubMed
Article
PubMed Central
Google Scholar
49.Warren, C. R. Response of osmolytes in soil to drying and rewetting. Soil Biol. Biochem. 70, 22–32 (2014).ADS
CAS
Article
Google Scholar
50.Bouskill, N. J. et al. Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism. Front. Microbiol. 7, 525 (2016).PubMed
PubMed Central
Google Scholar
51.Flemming, H.-C. et al. Biofilms: an emergent form of bacterial life. Nat. Rev. Microbiol. 14, 563 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
52.Malik, A. A. et al. Drought and plant litter chemistry alter microbial gene expression and metabolite production. ISME J. 14, 2236–2247 (2020).CAS
PubMed
PubMed Central
Article
Google Scholar
53.Nunan, N., Raynaud, X. & Schmidt, H. The ecology of heterogeneity: soil bacterial communities and C dynamics. Philos. Trans. R. Soc. B Biol. Sci. 375, 20190249 (2020).54.Li, J. et al. Predictive genomic traits for bacterial growth in culture versus actual growth in soil. ISME J. 13, 2162–2172 (2019).PubMed
PubMed Central
Article
Google Scholar
55.Maestre, F. T. et al. Plant species richness and ecosystem multifunctionality in global drylands. Science 335, 214–218 (2012).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
56.Grigulis, K. et al. Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services. J. Ecol. 101, 47–57 (2013).Article
Google Scholar
57.Lau, J. A. & Lennon, J. T. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl Acad. Sci. USA 109, 14058–14062 (2012).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
58.Fitzpatrick, C. R. et al. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl Acad. Sci. USA 115, E1157–E1165 (2018).CAS
PubMed
PubMed Central
Article
Google Scholar
59.Huang, S. et al. Autotrophic and heterotrophic soil respiration responds asymmetrically to drought in a subtropical forest in the Southeast China. Soil Biol. Biochem. 123, 242–249 (2018).CAS
Article
Google Scholar
60.López-Ballesteros, A. et al. Enhancement of the net CO2 release of a semiarid grassland in SE Spain by rain pulses. J. Geophys. Res. Biogeosci. 121, 52–66 (2016).Article
CAS
Google Scholar
61.Schimel, J. P. Life in dry soils: effects of drought on soil microbial communities and processes. Annu. Rev. Ecol. Evol. Syst. 49, 409–432 (2018).Article
Google Scholar
62.Canarini, A., Kaiser, C., Merchant, A., Richter, A. & Wanek, W. Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli. Front. Plant Sci. 10, 157 (2019).63.de Vries, F. T. et al. Changes in root-exudate-induced respiration reveal a novel mechanism through which drought affects ecosystem carbon cycling. New Phytol. 224, 132–145 (2019).PubMed
PubMed Central
Article
CAS
Google Scholar
64.Teste, F. P. et al. Plant-soil feedback and the maintenance of diversity in Mediterranean-climate shrublands. Science 355, 173–176 (2017).ADS
CAS
PubMed
Article
PubMed Central
Google Scholar
65.Hu, L. et al. Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat. Commun. 9, 2738 (2018).ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
66.Canarini, A., Merchant, A. & Dijkstra, F. A. Drought effects on Helianthus annuus and Glycine max metabolites: from phloem to root exudates. Rhizosphere 2, 85–97 (2016).67.Canarini, A. & Dijkstra, F. A. Dry-rewetting cycles regulate wheat carbon rhizodeposition, stabilization and nitrogen cycling. Soil Biol. Biochem. 81, 195–203 (2015).68.Morecroft, M. D. et al. Changing precipitation patterns alter plant community dynamics and succession in an ex-arable grassland. Funct. Ecol. 18, 648–655 (2004).Article
Google Scholar
69.Strickland, M. S., Osburn, E., Lauber, C., Fierer, N. & Bradford, M. A. Litter quality is in the eye of the beholder: initial decomposition rates as a function of inoculum characteristics. Funct. Ecol. 23, 627–636 (2009).Article
Google Scholar
70.Allison, S. D. et al. Microbial abundance and composition influence litter decomposition response to environmental change. Ecology 94, 714–725 (2013).PubMed
Article
PubMed Central
Google Scholar
71.Walker, T. W. N. et al. A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem. Nat. Ecol. Evol. 4, 101–108 (2020).PubMed
Article
PubMed Central
Google Scholar
72.Ogle, K. et al. Quantifying ecological memory in plant and ecosystem processes. Ecol. Lett. 18, 221–235 (2015).PubMed
Article
PubMed Central
Google Scholar
73.Bahn, M., Knapp, M., Garajova, Z., Pfahringer, N. & Cernusca, A. Root respiration in temperate mountain grasslands differing in land use. Glob. Chang. Biol. 12, 995–1006 (2006).ADS
Article
Google Scholar
74.Bahn, M. et al. Soil respiration at mean annual temperature predicts annual total across vegetation types and biomes. Biogeosciences 7, 2147 (2010).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
75.Schmitt, M., Bahn, M., Wohlfahrt, G., Tappeiner, U. & Cernusca, A. Land use affects the net ecosystem CO2 exchange and its components in mountain grasslands. Biogeosciences 7, 2297 (2010).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
76.Estiarte, M. et al. Few multiyear precipitation–reduction experiments find a shift in the productivity–precipitation relationship. Glob. Chang. Biol. 22, 2570–2581 (2016).ADS
PubMed
Article
PubMed Central
Google Scholar
77.Spohn, M., Klaus, K., Wanek, W. & Richter, A. Microbial carbon use efficiency and biomass turnover times depending on soil depth—Implications for carbon cycling. Soil Biol. Biochem. 96, 74–81 (2016).CAS
Article
Google Scholar
78.Manzoni, S., Taylor, P., Richter, A., Porporato, A. & Ågren, G. I. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. New Phytol. 196, 79–91 (2012).CAS
PubMed
Article
PubMed Central
Google Scholar
79.Schinner, F., Öhlinger, R., Kandeler, E., Margesin, R. & Kaiser, P. Methods in soil biology. Bull. Inst. Pasteur 4, 311–312 (1996).
Google Scholar
80.Kuo, S. Phosphorus. In Methods of Soil Analysis, Part 3 (eds. Sparks, D. L. et al.) Ch. 32, 869–919 (SSSA, 1996).81.Vance, E. D., Brookes, P. C. & Jenkinson, D. S. An extraction method for measuring soil microbial biomass C. Soil Biol. Biochem. 19, 703–707 (1987).CAS
Article
Google Scholar
82.Brookes, P. C., Landman, A., Pruden, G. & Jenkinson, D. S. Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol. Biochem. 17, 837–842 (1985).CAS
Article
Google Scholar
83.Doyle, A., Weintraub, M. N. & Schimel, J. P. Persulfate digestion and simultaneous colorimetric analysis of carbon and nitrogen in soil extracts. Soil Sci. Soc. Am. J. 68, 669–676 (2004).ADS
CAS
Article
Google Scholar
84.Kandeler, E. & Gerber, H. Short-term assay of soil urease activity using colorimetric determination of ammonium. Biol. Fertil. Soils 6, 68–72 (1988).CAS
Article
Google Scholar
85.Hood-Nowotny, R., Umana, N. H.-N., Inselbacher, E., Oswald- Lachouani, P. & Wanek, W. Alternative methods for measuring inorganic, organic, and total dissolved nitrogen in soil. Soil Sci. Soc. Am. J. 74, 1018–1027 (2010).ADS
CAS
Article
Google Scholar
86.Jones, D. L., Owen, A. G. & Farrar, J. F. Simple method to enable the high resolution determination of total free amino acids in soil solutions and soil extracts. Soil Biol. Biochem. 34, 1893–1902 (2002).CAS
Article
Google Scholar
87.Prommer, J. et al. Biochar decelerates soil organic nitrogen cycling but stimulates soil nitrification in a temperate arable field trial. PLoS ONE 9, e86388 (2014).ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
88.Kaiser, C., Frank, A., Wild, B., Koranda, M. & Richter, A. Negligible contribution from roots to soil-borne phospholipid fatty acid fungal biomarkers 18:2ω6,9 and 18:1ω9. Soil Biol. Biochem. 42, 1650–1652 (2010).CAS
PubMed
PubMed Central
Article
Google Scholar
89.Kaiser, C. et al. Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil. New Phytol. 187, 843–858 (2010).CAS
PubMed
PubMed Central
Article
Google Scholar
90.Olsson, P. A. Signature fatty acids provide tools for determination of the distribution and interactions of mycorrhizal fungi in soil. FEMS Microbiol. Ecol. 29, 303–310 (1999).CAS
Article
Google Scholar
91.Ngosong, C., Gabriel, E. & Ruess, L. Use of the signature fatty acid 16:1ω5 as a tool to determine the distribution of arbuscular mycorrhizal fungi in soil. J. Lipids 2012, 236807 (2012).PubMed
PubMed Central
Article
CAS
Google Scholar
92.Quideau, S. A. et al. Extraction and analysis of microbial phospholipid fatty acids in soils. J. Vis. Exp. 2016, 54360 (2016).93.García-Orenes, F., Morugán-Coronado, A., Zornoza, R., Cerdà, A. & Scow, K. Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem. PLoS ONE 8, e80522–e80522 (2013).ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
94.Herbold, C. et al. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes. Front. Microbiol. 6, 731 (2015).95.Apprill, A., McNally, S., Parsons, R. & Weber, L. Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquat. Microb. Ecol. 75, 129–137 (2015).Article
Google Scholar
96.Parada, A. E., Needham, D. M. & Fuhrman, J. A. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 18, 1403–1414 (2016).CAS
PubMed
Article
PubMed Central
Google Scholar
97.White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications 315–322 (Academic Press, 1990).98.Paymaneh, Z., Sarcheshmehpour, M., Bukovská, P. & Jansa, J. Could indigenous arbuscular mycorrhizal communities be used to improve tolerance of pistachio to salinity and/or drought? Symbiosis 79, 269–283 (2019).99.Smith, D. P. & Peay, K. G. Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS ONE 9, e90234 (2014).ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
100.Tedersoo, L. & Lindahl, B. Fungal identification biases in microbiome projects. Environ. Microbiol. Rep. 8, 774–779 (2016).PubMed
Article
Google Scholar
101.Krüger, M., Stockinger, H., Krüger, C. & Schüßler, A. DNA‐based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi. New Phytol. 183, 212–223 (2009).PubMed
Article
CAS
Google Scholar
102.Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581 (2016).CAS
PubMed
PubMed Central
Article
Google Scholar
103.Bengtsson‐Palme, J. et al. Improved software detection and extraction of ITS1 and ITS 2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 4, 914–919 (2013).
Google Scholar
104.Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200 (2011).CAS
PubMed
PubMed Central
Article
Google Scholar
105.Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
106.Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537–7541 (2009).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
107.Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).PubMed
PubMed Central
Article
CAS
Google Scholar
108.Deshpande, V. et al. Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences. Mycologia 108, 1–5 (2016).PubMed
Article
Google Scholar
109.R Core Team. R: A Language and Environment for Statistical Computing (R Core Team, 2017).110.McMurdie, P. J. & Holmes, S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE 8, e61217 (2013).ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
111.Chen, L. et al. GMPR: a robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ 6, e4600–e4600 (2018).PubMed
PubMed Central
Article
CAS
Google Scholar
112.Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).PubMed
PubMed Central
Article
CAS
Google Scholar
113.Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).114.Kozak, M. & Piepho, H. What’s normal anyway? Residual plots are more telling than significance tests when checking ANOVA assumptions. J. Agron. Crop Sci. 204, 86–98 (2018).Article
Google Scholar
115.Ben-Shachar, M. S., Lüdecke, D. & Makowski, D. effectsize: Estimation of effect size indices and standardized parameters. J. Open Source Softw. 5, 2815 (2020).ADS
Article
Google Scholar
116.Oksanen, J. et al. Package ‘vegan’. Community Ecol. Packag. 2, 1–295 (2013).
Google Scholar
117.Hedges, L. V., Gurevitch, J. & Curtis, P. S. The meta‐analysis of response ratios in experimental ecology. Ecology 80, 1150–1156 (1999).Article
Google Scholar
118.Barbera, P. et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol. 68, 365–369 (2019).PubMed
Article
PubMed Central
Google Scholar
119.Czech, L. & Stamatakis, A. Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples. PLoS ONE 14, e0217050–e0217050 (2019).CAS
PubMed
PubMed Central
Article
Google Scholar
120.Louca, S. & Doebeli, M. Efficient comparative phylogenetics on large trees. Bioinformatics 34, 1053–1055 (2018).CAS
PubMed
Article
PubMed Central
Google Scholar
121.McMurdie, P. J. & Paulson, J. N. biomformat: An interface package for the BIOM file format. R/Bioconductor Package, version 1.0.0. (Bioconductor, 2015). More