Leng G, Hall J. Crop yield sensitivity of global major agricultural countries to droughts and the projected changes in the future. Sci Total Environ. 2019;654:811–21.
Google Scholar
Hueso S, García C, Hernández T. Severe drought conditions modify the microbial community structure, size and activity in amended and unamended soils. Soil Biol Biochem. 2012;50:167–73.
Google Scholar
Alster CJ, German DP, Lu Y, Allison SD. Microbial enzymatic responses to drought and to nitrogen addition in a southern California grassland. Soil Biol Biochem. 2013;64:68–79.
Google Scholar
Bouskill NJ, Lim HC, Borglin S, Salve R, Wood TE, Silver WL, et al. Pre-exposure to drought increases the resistance of tropical forest soil bacterial communities to extended drought. ISME J. 2013;7:384–94.
Google Scholar
Acosta-Martinez V, Cotton J, Gardner T, Moore-Kucera J, Zak J, Wester D, et al. Predominant bacterial and fungal assemblages in agricultural soils during a record drought/heat wave and linkages to enzyme activities of biogeochemical cycling. Appl Soil Ecol. 2014;84:69–82.
Google Scholar
O’Connell CS, Ruan L, Silver WL. Drought drives rapid shifts in tropical rainforest soil biogeochemistry and greenhouse gas emissions. Nat Commun. 2018;9:1348.
Google Scholar
Schimel JP. Life in dry soils: Effects of drought on soil microbial communities and processes. Annu Rev Ecol Evol Syst. 2018;49:409–32.
Google Scholar
Naylor D, Colemann-Derr D. Drought stress and root-associated bacterial communities. Front Plant Sci. 2018;8:2223.
Google Scholar
de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science. 2020;368:270–4.
Google Scholar
Smith SE, Read D. Mycorrhizal symbiosis. 3rd ed. London: Academic Press; 2008. p. 145–90.
Kakouridis A, Hagen JA, Kan MP, Mambelli S, Feldman LJ, Herman DJ, et al. Routes to roots: direct evidence of water transport by arbuscular mycorrhizal fungi to host plants. New Phytol. 2022; https://doi.org/10.1111/nph.18281.
Rillig MC, Mummey DL. Mycorrhizas and soil structure. N Phytol. 2006;171:41–53.
Google Scholar
Gong M, You X, Zhang Q. Effects of Glomus intraradices on the growth and reactive oxygen metabolism of foxtail millet under drought. Ann Microbiol. 2015;65:595–602.
Google Scholar
Ruiz-Lozano JM. Arbuscular mycorrhizal symbiosis and alleviation of osmotic stress. N Perspect Mol Stud Mycorrhiza. 2003;13:309–17.
Google Scholar
Morte A, Lovisolo C, Schubert A. Effect of drought stress on growth and water relations of the mycorrhizal association Helianthemum almeriense–Terfezia claveryi. Mycorrhiza. 2000;10:115–9.
Google Scholar
Birhane E, Sterck F, Fetene M, Bongers F, Kuyper T. Arbuscular mycorrhizal fungi enhance photosynthesis, water use efficiency, and growth of frankincense seedlings under pulsed water availability conditions. Oecologia. 2012;169:895–904.
Google Scholar
Duan X, Neuman DS, Reiber JM, Green CD, Saxton AM, Augé RM. Mycorrhizal influence on hydraulic and hormonal factors implicated in the control of stomatal conductance during drought. J Exp Bot. 1996;47:1541–50.
Google Scholar
Emmett BD, Levesque-Tremblay V, Harrison MJ. Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi. ISME J. 2021;15:2276–88.
Google Scholar
Toljander JF, Artursson V, Paul LR, Jansson JK, Finlay RD. Attachment of different soil bacteria to arbuscular mycorrhizal fungal extraradical hyphae is determined by hyphal vitality and fungal species. FEMS Microbiol Lett. 2006;254:34–40.
Google Scholar
Svenningsen NB, Watts-Williams SJ, Joner EJ, Battini F, Efthymiou A, Cruz-Paredes C, et al. Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota. ISME J. 2018;12:1296–307.
Google Scholar
Cruz-Paredes C, Svenningsen NB, Nybroe O, Kjøller R, Frøslev TG, Jakobsen I. Suppression of arbuscular mycorrhizal fungal activity in a diverse collection of non-cultivated soils. FEMS Microbiol Ecol. 2019;95:fiz020.
Google Scholar
Nuccio EE, Hodge A, Pett-Ridge J, Herman DJ, Weber PK, Firestone MK. An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition. Environ Microbiol. 2013;15:1870–81.
Google Scholar
Verbruggen E, Jansa J, Hammer EC, Rillig MC. Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil? J Ecol. 2016;104:261–9.
Google Scholar
Kaiser C, Kilburn MR, Clode PL, Fuchslueger L, Koranda M, Cliff JP, et al. Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation. N Phytol. 2015;205:1537–51.
Google Scholar
Zhang L, Shi N, Fan J, Wang F, George TS, Feng G. Arbuscular mycorrhizal fungi stimulate organic phosphate mobilization associated with changing bacterial community structure under field conditions. Environ Microbiol. 2018a;20:2639–51.
Google Scholar
Hodge A, Campbell CD, Fitter AH. An arbuscular mycorrhizal fungus accelerates decomposition and acquires nitrogen directly from organic matter. Nature. 2001;413:297–9.
Google Scholar
Hestrin R, Hammer EC, Mueller CW, Lehmann J. Synergies between mycorrhizal fungi and soil microbial communities increase plant nitrogen acquisition. Commun Biol. 2019;2:233.
Google Scholar
Medina A, Probanza A, Gutierrez Mañero FJ, Azcón R. Interactions of arbuscular-mycorrhizal fungi and Bacillus strains and their effects on plant growth, microbial rhizosphere activity (thymidine and leucine incorporation) and fungal biomass (ergosterol and chitin). Appl Soil Ecol. 2003;22:15–28.
Google Scholar
Drigo B, Pijl AS, Duyts H, Kielak AM, Gamper HA, Houtekamer MJ, et al. Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2. Proc Natl Acad Sci USA. 2010;107:10938–42.
Google Scholar
Jakobsen I, Rosenthal L. Carbon flow into soil and external hyphae from roots of mycorrhizal cucumber plants. N Phytol. 1990;115:77–83.
Google Scholar
Zhou J, Chai X, Zhang L, George TS, Wang F, Feng G. Different arbuscular mycorrhizal fungi cocolonizing on a single plant root system recruit distinct microbiomes. mSystems. 2020;5:e00929–0.
Google Scholar
See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. Glob Change Biol. 2022;28:2527–40.
Google Scholar
Carini P, Marsden P, Leff J, Morgan E, Strickland M, Fierer N. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol. 2017;2:16242.
Google Scholar
Lennon JT, Muscarella ME, Placella MA, Lehmkuhl BK. How, when, and where relic DNA affects microbial diversity. mBio. 2018;9:e00637–18.
Google Scholar
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.
Google Scholar
Neufeld JD, Vohra J, Dumont MG, Lueders T, Manefield M, Friedrich MW, et al. DNA stable-isotope probing. Nat Protoc. 2007;2:860–6.
Google Scholar
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.
Google Scholar
Blazewicz SJ, Hungate BA, Koch BJ, Nuccio EE, Morrissey E, Brodie EL, et al. Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J. 2020;14:1520–32.
Google Scholar
Kilronomos JN. Host-specificity and functional diversity among arbuscular mycorrhizal fungi. In: Proceedings of the 8th International Symposium on Microbial Ecology. Bell CR, Brylinski M, Johnson-Green P, editors. Halifax: Atlantic Canada Society from Microbial Ecology; 2000. p. 845–51.
Ray P, Guo Y, Chi MH, Krom N, Saha MC, Craven KD. Serendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvation. Environ Microbiol. 2021;23:1876–88.
Google Scholar
Lee MR, Hawkes CV. Widespread co-occurrence of Sebacinales and arbuscular mycorrhizal fungi in switchgrass roots and soils has limited dependence on soil carbon or nutrients. Plants People Planet. 2021;3:614–26.
Google Scholar
Ruiz-Lozano JM, Azcon R, Gomez M. Effects of arbuscular-mycorrhizal glomus species on drought tolerance: physiological and nutritional plant responses. Appl Environ Microbiol. 1995;61:456–60.
Google Scholar
He F, Sheng M, Tang M. Effects of Rhizophagus irregularis on photosynthesis and antioxidative enzymatic system in Robinia pseudoacacia L. under drought stress. Front Plant Sci. 2017;8:183.
Google Scholar
Ghimire SR, Craven KD. Enhancement of switchgrass (Panicum virgatum L.) biomass production under drought conditions by the ectomycorrhizal fungus Sebacina vermifera. Appl Environ Microbiol. 2011;77:7063–7.
Google Scholar
Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, et al. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci USA. 2013;110:20117–22.
Google Scholar
Kamel L, Keller-Pearson M, Roux C, Ané JM. Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics. N Phytol. 2017;213:531–6.
Google Scholar
Bukovská P, Bonkowski M, Konvalinková T, Beskid O, Hujslová M, Püschel D, et al. Utilization of organic nitrogen by arbuscular mycorrhizal fungi-is there a specific role for protists and ammonia oxidizers? Mycorrhiza. 2018;28:269–83.
Google Scholar
Zhang L, Feng G, Declerck S. Signal beyond nutrient, fructose, exuded by an arbuscular mycorrhizal fungus triggers phytate mineralization by a phosphate solubilizing bacterium. ISME J. 2018;12:2339.
Google Scholar
Zuccaro A, Lahrmann U, Güldener U, Langen G, Pfiffi S, Biedenkopf D, et al. Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog. 2011;7:e1002290.
Google Scholar
Ray P, Chi MH, Guo Y, Chen C, Adam C, Kuo A, et al. Genome sequence of the plant growth promoting fungus Serendipita vermifera subsp. bescii: The first native strain from North America. Phytobiomes J. 2018;2:62–3.
Google Scholar
Dias T, Pimentel V, Cogo AJD, Costa R, Bertolazi AA, Miranda C, et al. The free-living stage growth conditions of the endophytic fungus Serendipita indica may regulate its potential as plant growth promoting microbe. Front Microbiol. 2020;11:562238.
Google Scholar
Moffatt HH. Soil Survey of Caddo County, Oklahoma. Washington, D.C.: United States Department of 836 Agriculture Soil Conservation Service; 1973.
Sher Y, Baker NR, Herman NR, Fossum C, Hale L, Zhang XX, et al. Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential. Soil Biol Biochem. 2020;143:107742.
Google Scholar
Seki K. SWRC fit—a nonlinear fitting program with a water retention curve for soils having unimodal and bimodal pore structure. Hydrol Earth Syst Sci Discuss. 2007;4:407–37.
Ray P, Ishiga T, Decker SR, Turner GB, Craven KD. A novel delivery system for the root symbiotic fungus, Sebacina vermifera, and consequent biomass enhancement of low lignin COMT switchgrass lines. BioEnerg Res. 2015;8:922–33.
Google Scholar
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.
Google Scholar
Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, et al. HT-SIP: a semi-automated Stable Isotope Probing pipeline identifies interactions in the hyphosphere of arbuscular mycorrhizal fungi. bioRxiv. 2022; https://biorxiv.org/cgi/content/short/2022.07.01.498377v1.
Buckley DH, Huangyutitham V, Hsu SF, 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.
Google Scholar
Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ Microbiol. 2016;18:1403–14.
Google Scholar
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 Micro Ecol. 2015;75:129–37.
Google Scholar
Badri A, Stefani FOP, Lachance G, Roy-Arcand L, Beaudet D, Vialle A, et al. Molecular diagnostic toolkit for Rhizophagus irregularis isolate DAOM-197198 using quantitative PCR assay targeting the mitochondrial genome. Mycorrhiza. 2016;26:721–33.
Google Scholar
Gamper HA, Young JP, Jones DL, Hodge A. Real-time PCR and microscopy: are the two methods measuring the same unit of arbuscular mycorrhizal fungal abundance? Fungal Genet Biol. 2008;45:581–96.
Google Scholar
Tellenbach C, Grünig CR, Sieber TN. Suitability of quantitative real-time PCR to estimate the biomass of fungal root endophytes. Appl Environ Microbiol. 2010;76:5764–72.
Google Scholar
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.
Google Scholar
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;67:2354–9.
Google Scholar
Louca S, Doebeli M, Parfrey LW. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome. 2018;6:41.
Google Scholar
Kanagawa T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J Biosci Bioeng. 2003;96:317–23.
Google Scholar
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.
Google Scholar
Manzoni S, Taylor P, Richter A, Porporato A, Ågren GI. Environmental and stoichiometric controls on microbial carbon-use efficiency in soils. N Phytol. 2012;196:79–91.
Google Scholar
Geyer KM, Dijkstra P, Sinsabaugh R, Frey SD. Clarifying the interpretation of carbon use efficiency in soil through methods comparison. Soil Biol Biochem. 2019;128:79–88.
Google Scholar
R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2019.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, OHara RB, et al. vegan: Community Ecology Package R package version 2.3-0. 2015. http://CRAN.R-project.org/package=vegan.
Lozupone C, Lladser ME, Knights D, Stombaugh J, Knight R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 2011;5:169–72.
Google Scholar
Harris RF. Effect of water potential on microbial growth and activity. In: Water Potential Relations in Soil Microbiology. Parr JF, Gardner WR, Elliott LF, editors. Madison, WI: Am Soc Agron; 1981. p. 23–95.
Wagg C, Dudenhöffer JH, Widmer F, van der Heijden MGA. Linking diversity, synchrony and stability in soil microbial communities. Funct Ecol. 2018;32:1280–92.
Google Scholar
Malik AA, Martiny JBH, Brodie EL, Martiny AC, Treseder KK, Allison SD. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J. 2020;14:1–9.
Google Scholar
Tiemann LK, Billings SA. Changes in variability of soil moisture alter microbial community C and N resource use. Soil Biol Biochem. 2011;43:1837–47.
Google Scholar
Domeignoz-Horta LA, Pold G, Liu XJA, Frey SD, Melillo JM, DeAngelis KM. Microbial diversity drives carbon use efficiency in a model soil. Nat Commun. 2020;11:3684.
Google Scholar
Gefen O, Balaban NQ. The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. FEMS Microbiol Rev. 2009;33:704–17.
Google Scholar
Fridman O, Goldberg O, Ronin I, Shoresh N, Balaban NQ. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature. 2014;513:418–21.
Google Scholar
Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, et al. Belowground response to drought in a tropical forest soil. II. Change in microbial function impacts carbon composition. Front Microbiol. 2016;7:323.
Google Scholar
Sutcliffe IC. A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol. 2010;18:464–70.
Google Scholar
Tocheva EI, Ortega DR, Jensen GJ. Sporulation, bacterial cell envelopes and the origin of life. Nat Rev Microbiol. 2016;14:535–42.
Google Scholar
Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc Natl Acad Sci USA. 2018;115:E4284–93.
Google Scholar
Santos-Medellín C, Liechty Z, Edwards J, Nguyen B, Huang B, Weimer BC, et al. Prolonged drought imparts lasting compositional changes to the rice root microbiome. Nat Plants. 2021;7:1065–77.
Google Scholar
Otoguro M, Yamamura H, Quintana ET The Family Streptosporangiaceae. In: The Prokaryotes. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F, editors. Berlin, Heidelberg: Springer; 2104. p. 1011–45.
Barnard RL, Osborne CA, Firestone MK. Responses of soil bacterial and fungal communities to extreme desiccation and rewetting. ISME J. 2013;7:2229–41.
Google Scholar
Cruz AF, Ishii T. Arbuscular mycorrhizal fungal spores host bacteria that affect nutrient biodynamics and biocontrol of soil-borne plant pathogens. Biol Open. 2012;1:52–7.
Google Scholar
Rillig MC, Lutgen ER, Ramsey PW, Klironomos JN, Gannon JE. Microbiota accompanying different arbuscular mycorrhizal fungal isolates influence soil aggregation. Pedobiologia. 2005;49:251–9.
Google Scholar
Jiang F, Zhang L, Zhou J, George TS, Feng G. Arbuscular mycorrhizal fungi enhance mineralisation of organic phosphorus by carrying bacteria along their extraradical hyphae. N Phytol. 2021;230:304–15.
Google Scholar
Hernandez DJ, David AS, Menges ES, Searcy CA, Afkhami ME. Environmental stress destabilizes microbial networks. ISME J. 2021;15:1722–34.
Google Scholar
Leigh J, Fitter AH, Hodge A. Growth and symbiotic effectiveness of an arbuscular mycorrhizal fungus in organic matter in competition with soil bacteria. FEMS Microbiol Ecol. 2011;76:428–38.
Google Scholar
Leifheit EF, Verbruggen E, Rillig MC. Arbuscular mycorrhizal fungi reduce decomposition of woody plant litter while increasing soil aggregation. Soil Biol Biochem. 2015;81:323–8.
Google Scholar
Bronstein JL. Conditional outcomes in mutualistic interactions. Trends Ecol Evol. 1994;9:214–7.
Google Scholar
Toljander JF, Lindahl BD, Paul LR, Elfstrand M, Finlay RD. Influence of arbuscular mycorrhizal mycelial exudates on soil bacterial growth and community structure. FEMS Microbiol Ecol. 2007;61:295–304.
Google Scholar
Zhang L, Zhou J, George TS, Limpens E, Feng G. Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra. Trends Plant Sci. 2022;27:402–11.
Google Scholar
Zhalnina K, Louie KB, Hao Z, Mansoori N, Nunes da Rocha U, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470–80.
Google Scholar
Chaparro JM, Badri DV, Bakker MG, Sugiyama A, Manter DK, Vivanco JM. Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS ONE. 2013;8:e55731.
Google Scholar
Shi S, Richardson AE, O’Callaghan M, DeAngelis KM, Jones EE, Stewart A, et al. Effects of selected root exudate components on soil bacterial communities. FEMS Microbiol Ecol. 2011;77:600–10.
Google Scholar
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