Graham EB, Knelman JE, Schindlbacher A, Siciliano S, Breulmann M, Yannarell A, et al. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Front Microbiol. 2016;7:214.
Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW. Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol. 2010;76:999–1007.
Drigo B, Nielsen UN, Jeffries TC, Curlevski NJA, Singh BK, Duursma RA, et al. Interactive effects of seasonal drought and elevated atmospheric carbon dioxide concentration on prokaryotic rhizosphere communities. Environ Microbiol. 2017;19:3175–85.
Carey CJ, Michael Beman J, Eviner VT, Malmstrom CM, Hart SC. Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands. Front Microbiol. 2015;6:466.
Zhang K, Shi Y, Jing X, He JS, Sun R, Yang Y, et al. Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau. Front Microbiol. 2016;7:1032.
Pérez Castro S, Cleland EE, Wagner R, Al Sawad R, Lipson DA. Soil microbial responses to drought and exotic plants shift carbon metabolism. ISME J. 2019;13:1776–87.
Sheik CS, Beasley WH, Elshahed MS, Zhou X, Luo Y, Krumholz LR. Effect of warming and drought on grassland microbial communities. ISME J. 2011;5:1692–1700.
Lange M, Habekost M, Eisenhauer N, Roscher C, Bessler H, Engels C, et al. Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland. PLoS ONE. 2014;9:e96182.
Zak DR, Holmes WE, White DC, Peacock AD, Tilman D. Plant diversity, soil microbial communities, and ecosystem function: Are there any links? Ecology. 2003;84:2042–50.
Roy-Bolduc A, Laliberté E, Boudreau S, Hijri M. Strong linkage between plant and soil fungal communities along a successional coastal dune system. FEMS Microbiol Ecol. 2016;92:fiw156.
Koyama A, Steinweg JM, Haddix ML, Dukes JS, Wallenstein MD. Soil bacterial community responses to altered precipitation and temperature regimes in an old field grassland are mediated by plants. FEMS Microbiol Ecol. 2018;94:fix156.
Bergelson J, Vivanco JM, Manter DK, Broz AK, Broeckling CD. Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol. 2007;74:738–44.
Eisenhauer N, Lanoue A, Strecker T, Scheu S, Steinauer K, Thakur MP, et al. Root biomass and exudates link plant diversity with soil bacterial and fungal biomass. Sci Rep. 2017;7:44641.
Karlowsky S, Augusti A, Ingrisch J, Akanda MKU, Bahn M, Gleixner G. Drought-induced accumulation of root exudates supports post-drought recovery of microbes in mountain grassland. Front Plant Sci. 2018;9:1593.
Zhang P, Li B, Wu J, Hu S. Invasive plants differentially affect soil biota through litter and rhizosphere pathways: a meta-analysis. Ecol Lett. 2019;22:200–10.
Burns JH, Anacker BL, Strauss SY, Burke DJ. Soil microbial community variation correlates most strongly with plant species identity, followed by soil chemistry, spatial location and plant genus. AoB Plants. 2015;7:plv030.
Roberts KJ, Anderson RC. Effect of garlic mustard [Alliaria petiolata (Beib. Cavara & Grande)] extracts on plants and arbuscular mycorrhizal (AM) fungi. Am Midl Nat. 2001;146:146–52.
Broz AK, Manter DK, Vivanco JM. Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa. ISME J. 2007;1:763–5.
Burke EJ, Brown SJ, Christidis N. Modeling the recent evolution of global drought and projections for the twenty-first century with the Hadley Centre Climate Model. J Hydrometeorol. 2006;7:1113–25.
Singh D, Tsiang M, Rajaratnam B, Diffenbaugh NS. Precipitation extremes over the continental United States in a transient, high-resolution, ensemble climate model experiment. J Geophys Res Atmos. 2013;118:7063–86.
Ochoa-Hueso R, Collins SL, Delgado-Baquerizo M, Hamonts K, Pockman WT, Sinsabaugh RL, et al. Drought consistently alters the composition of soil fungal and bacterial communities in grasslands from two continents. Glob Chang Biol. 2018;24:2818–27.
Manzoni S, Schimel JP, Porporato A. Responses of soil microbial communities to water stress: Results from a meta-analysis. Ecology. 2011;93:930–8.
Naylor D, Coleman-Derr D. Drought stress and root-associated bacterial communities. Front Plant Sci. 2018;8:2223.
Alba C, NeSmith JE, Fahey C, Angelini C, Flory SL. Methods to test the interactive effects of drought and plant invasion on ecosystem structure and function using complementary common garden and field experiments. Ecol Evol. 2017;7:1442–52.
Levine JM, Vilà M, D’Antonio CM, Dukes JS, Grigulis K, Lavorel S. Mechanisms underlying the impacts of exotic plant invasions. Proc R Soc B Biol Sci. 2003;270:775–81.
Suseela V, Tharayil N. Decoupling the direct and indirect effects of climate on plant litter decomposition: Accounting for stress-induced modifications in plant chemistry. Glob Chang Biol. 2018;24:1428–51.
Yang J, Kloepper JW, Ryu CM. Rhizosphere bacteria help plants tolerate abiotic stress. Trends Plant Sci. 2009;14:1–4.
Augé RM. Water relations, drought and vesicular-arbuscular mycorrhizal symbiosis. Mycorrhiza. 2001;11:3–42.
Frost C. History and future of the longleaf pine ecosystem. In: Jose S, Jokela EJ, Miller DL, editors. The longleaf pine ecosystem: ecology, silviculture, and restoration. New York, NY: Springer; 2007. p. 9–42.
Estrada JA, Flory SL. Cogongrass (Imperata cylindrica) invasions in the US: mechanisms, impacts, and threats to biodiversity. Glob Ecol Conserv. 2015;3:1–10.
Brewer S. Declines in plant species richness and endemic plant species in longleaf pine savannas invaded by Imperata cylindrica. Biol Invasions. 2008;10:1257–64.
Fahey C, Angelini C, Flory SL. Grass invasion and drought interact to alter the diversity and structure of native plant communities. Ecology. 2018;99:2692–702.
Bradley BA, Wilcove DS, Oppenheimer M. Climate change increases risk of plant invasion in the Eastern United States. Biol Invasions. 2010;12:1855–72.
Anthony MA, Frey SD, Stinson KA. Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion. Ecosphere. 2017;8:e01951.
Nguyen NH, Song Z, Bates ST, Branco S, Tedersoo L, Menke J, et al. FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecol. 2016;20:241–8.
Matulich KL, Weihe C, Allison SD, Amend AS, Berlemont R, Goulden ML, et al. Temporal variation overshadows the response of leaf litter microbial communities to simulated global change. ISME J. 2015;9:2477–89.
Cline LC, Schilling JS, Menke J, Groenhof E, Kennedy PG. Ecological and functional effects of fungal endophytes on wood decomposition. Funct Ecol. 2018;32:181–91.
Hagan DL, Jose S, Lin CH. Allelopathic exudates of cogongrass (Imperata cylindrica): implications for the performance of native pine savanna plant species in the Southeastern US. J Chem Ecol. 2013;39:312–22.
Lekberg Y, Gibbons SM, Rosendahl S, Ramsey PW. Severe plant invasions can increase mycorrhizal fungal abundance and diversity. ISME J. 2013;7:1424–33.
Melillo JM, Richmond TC, Yohe GW. Highlights of climate change impacts in the United States: the third national climate assessment. Washington DC, USA: Global Change Research Program; 2014.
Yahdjian L, Sala OE. A rainout shelter design for intercepting different amounts of rainfall. Oecologia. 2002;133:95–101.
Taylor DL, Walters WA, Lennon NJ, Bochicchio J, Krohn A, Caporaso JG, et al. Accurate estimation of fungal diversity and abundance through improved lineage-specific primers optimized for Illumina amplicon sequencing. Appl Environ Microbiol. 2016;82:7217–26.
Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME J. 2011;5:908–17.
Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, et al. Strong succession in arbuscular mycorrhizal fungal communities. ISME J. 2018;13:214–26.
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.
McDonald D, Price MN, Goodrich J, Nawrocki EP, Desantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994;44:846–9.
Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4:914–9.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Kõljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, et al. Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol. 2013;22:5271–7.
Koyama A, Maherali H, Antunes PM. Plant geographic origin and phylogeny as potential drivers of community structure in root-inhabiting fungi. J Ecol. 2019;107:1720–36.
Price MN, Dehal PS, Arkin AP. Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26:1641–50.
Louca S, Parfrey LW, Doebeli M. Decoupling function and taxonomy in the global ocean microbiome. Science. 2016;353:1272–7.
R Development Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria 2016; 3.3.1. https://www.r-project.org/.
Pinheiro J, Bates D, DebRoy S, Sarkar D, The R Development Core Team. nlme: linear and nonlinear mixed effects models. R Package version 31-113. 2016. R package: 1–86.
Chao A. Nonparametric estimation of the numbers of classes in a population. Scand J Stat. 1984;11:265–70.
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, et al. vegan: community ecology package. R Packag version 24-1. 2016.
Anderson MJ, Walsh DCI. PERMANOVA, ANOSIM, and the mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing? Ecol Monogr. 2013;83:557–74.
Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Micro Ecol Health Dis. 2015;26:27663.
Lefcheck JS. piecewiseSEM: Piecewise structural equation modelling in R for ecology, evolution, and systematics. Methods Ecol Evol. 2016;7:573–9.
Alba C, Fahey C, Flory SL. Global change stressors alter resources and shift plant interactions from facilitation to competition over time. Ecology. 2019;100:e02859.
Folt CL, Chen CY, Moore MV, Burnaford J. Synergism and antagonism among multiple stressors. Limnol Oceanogr. 1999;44:864–77.
Piggott JJ, Townsend CR, Matthaei CD. Reconceptualizing synergism and antagonism among multiple stressors. Ecol Evol. 2015;5:1538–47.
Hawkes CV, Kivlin SN, Rocca JD, Huguet V, Thomsen MA, Suttle KB. Fungal community responses to precipitation. Glob Chang Biol. 2011;17:1637–45.
Horner-Devine MC, Leibold MA, Smith VH, Bohannan BJM. Bacterial diversity patterns along a gradient of primary productivity. Ecol Lett. 2003;6:613–22.
Evans SE, Wallenstein MD, Burke IC. Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought. Ecology. 2014;95:110–22.
Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B, et al. Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci USA. 2015;112:15684–9.
Zhou Z, Wang C, Luo Y. Response of soil microbial communities to altered precipitation: a global synthesis. Glob Ecol Biogeogr. 2018;27:1121–36.
Weiß M, Sýkorová Z, Garnica S, Riess K, Martos F, Krause C, et al. Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes. PLoS ONE. 2011;6:e16793.
Weiß M, Waller F, Zuccaro A, Selosse M-A. Sebacinales—one thousand and one interactions with land plants. N Phytol. 2016;211:20–40.
Chagnon P-L, Bradley RL, Maherali H, Klironomos JN. A trait-based framework to understand life history of mycorrhizal fungi. Trends Plant Sci. 2013;18:484–91.
Staddon PL, Thompson K, Jakobsen I, Grime JP, Askew AP, Fitter AH. Mycorrhizal fungal abundance is affected by long-term climatic manipulations in the field. Glob Chang Biol. 2003;9:186–94.
Mummey DL, Rillig MC. The invasive plant species Centaurea maculosa alters arbuscular mycorrhizal fungal communities in the field. Plant Soil. 2006;288:81–90.
Hawkes CV, Belnap J, D’Antonio C, Firestone MK. Arbuscular mycorrhizal assemblages in native plant roots change in the presence of invasive exotic grasses. Plant Soil. 2006;281:369–80.
Vogelsang KM, Bever JD. Mycorrhizal densities decline in association with normative plants and contribute to plant invasion. Ecology. 2009;90:399–407.
Cipollini D, Cipollini K. A review of garlic mustard (Alliaria petiolata, Brassicaceae) as an allelopathic plant. J Torre Bot Soc. 2016;143:339–48.
Talbot JM, Allison SD, Treseder KK. Decomposers in disguise: mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Funct Ecol. 2008;22:955–63.
Lindahl BD, Tunlid A. Ectomycorrhizal fungi—potential organic matter decomposers, yet not saprotrophs. N Phytol. 2015;205:1443–7.
Eppinga MB, Rietkerk M, Dekker SC, De Ruiter PC, Van Der Putten WH. Accumulation of local pathogens: a new hypothesis to explain exotic plant invasions. Oikos. 2006;114:168–76.
Stinson KA, Campbell SA, Powell JR, Wolfe BE, Callaway RM, Thelen GC, et al. Invasive plant suppresses the growth of native tree seedlings by disrupting belowground mutualisms. PLoS Biol. 2006;4:727–31.
Barto EK, Antunes PM, Stinson K, Koch AM, Klironomos JN, Cipollini D. Differences in arbuscular mycorrhizal fungal communities associated with sugar maple seedlings in and outside of invaded garlic mustard forest patches. Biol Invasions. 2011;13:2755–62.
Batten KM, Scow KM, Espeland EK. Soil microbial community associated with an invasive grass differentially impacts native plant performance. Micro Ecol. 2008;55:220–8.
Whipps JM. Prospects and limitations for mycorrhizas in biocontrol of root pathogens. Can J Bot. 2004;82:1198–227.
Cook RJ, Papendick RI. Influence of water potential of soils and plants on root disease. Annu Rev Phytopathol. 1972;10:349–74.
Krupa SV, Dommergues YR. Ecology of root pathogens. Amsterdam, The Netherlands: Elsevier Scientific Pub. Co.; 1979.
Reynolds HL, Packer A, Bever JD, Clay K. Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology. 2003;84:2281–91.
Armstrong A, Valverde A, Ramond JB, Makhalanyane TP, Jansson JK, Hopkins DW, et al. Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input. Sci Rep. 2016;6:34434.
Bachar A, Al-Ashhab A, Soares MIM, Sklarz MY, Angel R, Ungar ED, et al. Soil microbial abundance and diversity along a low precipitation gradient. Micro Ecol. 2010;69:453–61.
Clark JS, Campbell JH, Grizzle H, Acosta-Martìnez V, Zak JC. Soil microbial community response to drought and precipitation variability in the chihuahuan desert. Micro Ecol. 2009;57:248–60.
Fierer N, Schimel JP, Holden PA. Influence of drying-rewetting frequency on soil bacterial community structure. Micro Ecol. 2003;45:63–71.
Evans SE, Wallenstein MD. Soil microbial community response to drying and rewetting stress: does historical precipitation regime matter? Biogeochemistry. 2012;109:101–16.
Seitzinger S, Harrison JA, Böhlke JK, Bouwman AF, Lowrance R, Peterson B, et al. Denitrification across landscapes and waterscapes: a synthesis. Ecol Appl. 2006;16:2064–90.
Hawkes CV, Wren IF, Herman DJ, Firestone MK. Plant invasion alters nitrogen cycling by modifying the soil nitrifying community. Ecol Lett. 2005;8:976–85.
Lee MR, Flory SL, Phillips RP. Positive feedbacks to growth of an invasive grass through alteration of nitrogen cycling. Oecologia. 2012;170:457–65.
Source: Ecology - nature.com
