Borer ET, Seabloom EW, Mitchell CE, Cronin JP. Multiple nutrients and herbivores interact to govern diversity, productivity, composition, and infection in a successional grassland. Oikos. 2014;123:214–24.
Google Scholar
Isbell F, Reich PB, Tilman D, Hobbie SE, Polasky S, Binder S. Nutrient enrichment, biodiversity loss, and consequent declines in ecosystem productivity. Proc Natl Acad Sci. 2013;110:11911–6.
Google Scholar
Robinson RJ, Fraaije BA, Clark IM, Jackson RW, Hirsch PR, Mauchline TH. Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type developmental stage and soil nutrient availability. Plant Soil. 2016;405:381–96.
Google Scholar
Ratzke C, Barrere J, Gore J. Strength of species interactions determines biodiversity and stability in microbial communities. Nat Ecol Evol. 2020;4:376–83.
Google Scholar
Lambers JHR, Harpole WS, Tilman D, Knops J, Reich PB. Mechanisms responsible for the positive diversity–productivity relationship in minnesota grasslands. Ecol Lett. 2004;7:661–8.
Google Scholar
Essarioui A, LeBlanc N, Kistler HC, Kinkel LL. Plant community richness mediates inhibitory interactions and resource competition between Streptomyces and fusarium populations in the rhizosphere. Micro Ecol. 2017;74:157–67.
Google Scholar
Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RH, et al. Impact of long-term n, p, k, and npk fertilization on the composition and potential functions of the bacterial community in grassland soil. FEMS Microbiol Ecol. 2014;90:195–205.
Google Scholar
Schlatter DC, DavelosBaines AL, Xiao K, Kinkel LL. Resource use of soilborne Streptomyces varies with location phylogeny, and nitrogen amendment. Micro Ecol. 2013;66:961–71.
Google Scholar
Firn J, McGree JM, Harvey E, Flores-Moreno H, Schütz M, Buckley YM, et al. Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs. Nat Ecol Evol. 2019;3:400–6.
Google Scholar
Anderson TM, Griffith DM, Grace JB, Lind EM, Adler PB, Biederman LA, et al. Herbivory and eutrophication mediate grassland plant nutrient responses across a global climatic gradient. Ecol. 2018;99:822–31.
Google Scholar
Bernstein N, Gorelick J, Zerahia R, Koch S. Impact of n, p, k, and humic acid supplementation on the chemical profile of medical cannabis (Cannabis sativa L.). Front Plant Sci. 2019;10:736.
Google Scholar
Tangolar S, Tangolar S, Torun AA, Ada M, Göçmez S. Influence of supplementation of vineyard soil with organic substances on nutritional status, yield and quality of ‘black magic’ grape (Vitis vinifera L.) and soil microbiological and biochemical characteristics. OENO One. 2020;54:1143–57.
Google Scholar
De Long JR, Sundqvist MK, Gundale MJ, Giesler R, Wardle DA. Effects of elevation and nitrogen and phosphorus fertilization on plant defence compounds in subarctic tundra heath vegetation. Funct Ecol. 2016;30:314–25.
Google Scholar
Dietrich R, Ploss K, Heil M. Constitutive and induced resistance to pathogens in Arabidopsis thaliana depends on nitrogen supply. Plant Cell Environ. 2004;27:896–906.
Google Scholar
Bryant JP, Chapin III FS, Klein DR. Carbon/nutrient balance of boreal plants in relation to vertebrate herbivory. Oikos. 1983;40:357–68.
Kinkel LL, Otto-Hanson LK, Otto-Hansen Z, Johnson M, Spawn S, Song Z, et al. Foliar endophytic microbiome composition and functional capacities vary with soil nutrient inputs. Phytopathol. 2018;108:77.
Seabloom EW, Condon B, Kinkel L, Komatsu KJ, Lumibao CY, May G, et al. Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity. Ecol. 2019;100:e02758.
Google Scholar
Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. N. Phytol. 2015;206:1196–206.
Google Scholar
Stulberg E, Fravel D, Proctor LM, Murray DM, LoTempio J, Chrisey L, et al. An assessment of US microbiome research. Nat Microbiol. 2016;1:15015.
Google Scholar
Hanson BM, Weinstock GM. The importance of the microbiome in epidemiologic research. Ann Epidemiol. 2016;26:301–5.
Google Scholar
Bell TH, Hockett KL, Alcalá-Briseño RI, Barbercheck M, Beattie GA, Bruns MA, et al. Manipulating wild and tamed phytobiomes: Challenges and opportunities. Phytobiomes J 2019;3:3–21.
Google Scholar
Henning JA, Kinkel L, May G, Lumibao CY, Seabloom EW, Borer ET. Plant diversity and litter accumulation mediate the loss of foliar endophyte fungal richness following nutrient addition. Ecol. 2021;102:e03210.
Google Scholar
Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE. The phyllosphere: microbial jungle at the plant–climate interface. Annu Rev Ecol Evol Syst. 2016;47:1–24.
Google Scholar
Berendsen RL, Pieterse CM, Bakker PA. The rhizosphere microbiome and plant health. Trends Plant Sci. 2012;17:478–86.
Google Scholar
Turner TR, James EK, Poole PS. The plant microbiome. Genome Biol. 2013;14:1–10.
Google Scholar
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607–21.
Google Scholar
Sanchez-Gorostiaga A, Bajić D, Osborne ML, Poyatos JF, Sanchez A. High-order interactions distort the functional landscape of microbial consortia. PLOS Biol. 2019;17:e3000550.
Google Scholar
Gould AL, Zhang V, Lamberti L, Jones EW, Obadia B, Korasidis N, et al. Microbiome interactions shape host fitness. Proc Natl Acad Sci. 2018;115:E11951–E11960.
Google Scholar
O’Keeffe KR. Within-host Microbial Interactions and Plant Parasites: From Pairwise Interactions to the Microbiome. PhD thesis, The University of North Carolina at Chapel Hill, 2019.
Wemheuer F, Kaiser K, Karlovsky P, Daniel R, Vidal S, Wemheuer B. Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes. Sci Rep. 2017;7:1–13.
Google Scholar
Wemheuer B, Thomas T, Wemheuer F. Fungal endophyte communities of three agricultural important grass species differ in their response towards management regimes. Microorg. 2019;7:37.
Google Scholar
Layeghifard M, Hwang DM, Guttman DS. Disentangling interactions in the microbiome: a network perspective. Trends Microbiol. 2017;25:217–28.
Google Scholar
Barabási AL Network science. (Cambridge University Press, Cambridge, 2016).
Scott J. Social network analysis. Sociol. 1988;22:109–27.
Google Scholar
Borgatti SP, Mehra A, Brass DJ, Labianca G. Network analysis in the social sciences. Science. 2009;323:892–5.
Google Scholar
Nelson GD, Rae A. An economic geography of the United States: from commutes to megaregions. PLOS ONE. 2016;11:e0166083.
Google Scholar
Danon L, Ford AP, House T, Jewell CP, Keeling MJ, Roberts GO, et al. Networks and the epidemiology of infectious disease. Interdiscip Perspectives on Infect Dis. 2011.
Expert P, Evans TS, Blondel VD, Lambiotte R. Uncovering space-independent communities in spatial networks. Proc Natl Acad Sci. 2011;108:7663–8.
Google Scholar
Röttjers L, Faust K. From hairballs to hypotheses—biological insights from microbial networks. FEMS Microbiol Rev. 2018;42:761–80.
Google Scholar
Naqvi A, Rangwala H, Keshavarzian A, Gillevet P. Network-based modeling of the human gut microbiome. Chem Biodivers. 2010;7:1040–50.
Google Scholar
Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: networks, competition, and stability. Sci. 2015;350:663–6.
Google Scholar
Poudel R, Jumpponen A, Schlatter DC, Paulitz TC, McSpadden Gardener BB, Kinkel LL, et al. Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management. Phytopathol. 2016;106:1083–96.
Google Scholar
Bakker MG, Schlatter DC, Otto-Hanson L, Kinkel LL. Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome. Mol Ecol. 2014;23:1571–83.
Google Scholar
van der Heijden MG, Hartmann M. Networking in the plant microbiome. PLOS Biol. 2016;14:e1002378.
Google Scholar
Lau MK, Borrett SR, Baiser B, Gotelli NJ, Ellison AM. Ecological network metrics: opportunities for synthesis. Ecosphere. 2017;8:e01900.
Google Scholar
Billick I, Case TJ. Higher order interactions in ecological communities: what are they and how can they be detected? Ecol. 1994;75:1529–43.
Google Scholar
Carr A, Diener C, Baliga NS, Gibbons SM. Use and abuse of correlation analyses in microbial ecology. ISME J. 2019;13:2647–55.
Google Scholar
Vaz Jauri P, Bakker MG, Salomon CE, Kinkel LL. Subinhibitory antibiotic concentrations mediate nutrient use and competition among soil Streptomyces. PLOS ONE. 2013;8:e81064.
Google Scholar
Borer ET, Harpole WS, Adler PB, Lind EM, Orrock JL, Seabloom EW, et al. Finding generality in ecology: a model for globally distributed experiments. Methods Ecol Evol. 2014;5:65–73.
Google Scholar
Borer ET, Grace JB, Harpole WS, MacDougall AS, Seabloom EW. A decade of insights into grassland ecosystem responses to global environmental change. Nat Ecol Evol. 2017;1:1–7.
Google Scholar
Essarioui A, LeBlanc N, Kistler HC, Kinkel LL. Plant host and community diversity impact the dynamics of resource use by soil Streptomyces. Phytopathol. 2014;104:38.
LeBlanc N, Essarioui A, Kinkel LL, Kistler HC. Fusarium community structure and carbon metabolism phenotypes respond to grassland plant community richness and plant host. Phytopathol. 2014;104:67.
Google Scholar
Essarioui A, Kistler HC, Kinkel LL. Nutrient use preferences among soil Streptomyces suggest greater resource competition in monoculture than polyculture plant communities. Plant Soil. 2016;409:329–43.
Google Scholar
Essarioui A, LeBlanc N, Otto-Hanson L, Schlatter DC, Kistler HC, Kinkel LL. Inhibitory and nutrient use phenotypes among coexisting fusarium and Streptomyces populations suggest local coevolutionary interactions in soil. Environ Microbiol. 2020;22:976–85.
Google Scholar
Schlatter D, Fubuh A, Xiao K, Hernandez D, Hobbie S, Kinkel L. Resource amendments influence density and competitive phenotypes of Streptomyces in soil. Micro Ecol. 2009;57:413–20.
Google Scholar
Kinkel LL, Schlatter DC, Xiao K, Baines AD. Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes. ISME J 2013;8:249–56.
Google Scholar
Reichardt J, Bornholdt S. Statistical mechanics of community detection. Phys Rev E 2006;74:016110.
Google Scholar
Watts DJ, Strogatz SH. Collective dynamics of ‘small-world’ networks. Nat. 1998;393:440–2.
Google Scholar
Allesina S, Levine JM. A competitive network theory of species diversity. Proc Natl Acad Sci. 2011;108:5638–42.
Google Scholar
Maynard DS, Bradford MA, Lindner DL, van Diepen LT, Frey SD, Glaeser JA, et al. Diversity begets diversity in competition for space. Nat Ecol Evol. 2017;1:1–8.
Google Scholar
Maynard DS, Crowther TW, Bradford MA. Competitive network determines the direction of the diversity–function relationship. Proc Natl Acad Sci. 2017;114:11464–9.
Google Scholar
Gallien L, Zimmermann NE, Levine JM, Adler PB. The effects of intransitive competition on coexistence. Ecol Lett. 2017;20:791–800.
Google Scholar
Schlatter DC, Song Z, Vaz-Jauri P, Kinkel LL. Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils. PLOS ONE. 2019;14:e0223779.
Google Scholar
Milo R. Network motifs: simple building blocks of complex networks. Sci. 2002;298:824–7.
Google Scholar
Case TJ, Bender EA. Testing for higher order interactions. Am Nat. 1981;118:920–9.
Google Scholar
Levine JM, Bascompte J, Adler PB, Allesina S. Beyond pairwise mechanisms of species coexistence in complex communities. Nat. 2017;546:56–64.
Google Scholar
Mayfield MM, Stouffer DB. Higher-order interactions capture unexplained complexity in diverse communities. Nat Ecol Evol. 2017;1:0062.
Google Scholar
Friedman J, Higgins LM, Gore J. Community structure follows simple assembly rules in microbial microcosms. Nat Ecol Evol. 2017;1:0109.
Google Scholar
Bender EA, Canfield E. The asymptotic number of labeled graphs with given degree sequences. J Comb Theory Ser A 1978;24:296–307.
Google Scholar
Newman ME. Modularity and community structure in networks. Proc Natl Acad Sci. 2006;103:8577–82.
Google Scholar
Guo X, Boedicker JQ. The contribution of high-order metabolic interactions to the global activity of a four-species microbial community. PLOS Comput Biol. 2016;12:e1005079.
Google Scholar
Borrelli JJ, Allesina S, Amarasekare P, Arditi R, Chase I, Damuth J, et al. Selection on stability across ecological scales. Trends Ecol Evol. 2015;30:417–25.
Google Scholar
Davis GH, Crofoot MC, Farine DR. Estimating the robustness and uncertainty of animal social networks using different observational methods. Anim Behav. 2018;141:29–44.
Google Scholar
Gilbertson ML, White LA, Craft ME. Trade-offs with telemetry-derived contact networks for infectious disease studies in wildlife. Methods Ecol Evol. 2020;12:76–87.
Google Scholar
Grilli J, Barabás G, Michalska-Smith MJ, Allesina S. Higher-order interactions stabilize dynamics in competitive network models. Nat. 2017;548:210–3.
Google Scholar
Letten AD, Stouffer DB. The mechanistic basis for higher-order interactions and non-additivity in competitive communities. Ecol Lett. 2019;22:423–36.
Google Scholar
Dormann CF, Roxburgh SH. Experimental evidence rejects pairwise modelling approach to coexistence in plant communities. Proc R Soc B Biol Sci. 2005;272:1279–85.
Google Scholar
Staniczenko PP, Kopp JC, Allesina S. The ghost of nestedness in ecological networks. Nat Commun. 2013;4:1–6.
Google Scholar
Großkopf T, Soyer OS. Synthetic microbial communities. Curr Opin Microbiol. 2014;18:72–77.
Google Scholar
Holm S. A simple sequentially rejective multiple test procedure. Scand J Stat. 1979;6:65–70.
Source: Ecology - nature.com