Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 2013;64:807–38.
Article
CAS
PubMed
Google Scholar
Innerebner G, Knief C, Vorholt JA. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl Environ Microbiol. 2011;77:3202–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haney CH, Samuel BS, Bush J, Ausubel FM. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nature Plants. 2015;1:1–9.
Article
CAS
Google Scholar
Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Métraux J-P, L’Haridon F. The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytol. 2016;210:1033–43.
Article
CAS
PubMed
Google Scholar
Santhanam R, Luu VT, Weinhold A, Goldberg J, Oh Y, Baldwin IT. Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proc Natl Acad Sci USA. 2015;112:E5013–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rodriguez H, Fraga R. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv. 1999;17:319–39.
Article
CAS
PubMed
Google Scholar
Richardson AE, Simpson RJ. Soil microorganisms mediating phosphorus availability update on microbial phosphorus. Plant Physiol. 2011;156:989–96.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ali B, Sabri AN, Ljung K, Hasnain S. Auxin production by plant associated bacteria: impact on endogenous IAA content and growth of Triticum aestivum L. Lett Appl Microbiol. 2009;48:542–7.
Article
CAS
PubMed
Google Scholar
Friesen ML, Porter SS, Stark SC, von Wettberg EJ, Sachs JL, Martinez-Romero E. Microbially mediated plant functional traits. Annu Rev Ecol Evol Syst. 2011;42:23–46.
Article
Google Scholar
Lau JA, Lennon JT. Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc Natl Acad Sci USA. 2012;109:14058–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang H, Kim M-S, Sun Y, Dowd SE, Shi H, Paré PW. Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1. Mol Plant-Microbe Interact. 2008;21:737–44.
Article
PubMed
CAS
Google Scholar
Panke-Buisse K, Poole AC, Goodrich JK, Ley RE, Kao-Kniffin J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J. 2015;9:980–9.
Article
CAS
PubMed
Google Scholar
Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett. 2014;17:717–26.
Article
PubMed
PubMed Central
Google Scholar
Berendsen RL, Pieterse CMJ, Bakker PAHM. The rhizosphere microbiome and plant health. Trends Plant Sci. 2012;17:478–86.
Article
CAS
PubMed
Google Scholar
Gehring CA, Sthultz CM, Flores-Rentería L, Whipple AV, Whitham TG. Tree genetics defines fungal partner communities that may confer drought tolerance. Proc Natl Acad Sci USA. 2017;114:11169–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: embracing complexity in host-microbe interactions. Plant J. 2019;97:164–81.
Article
CAS
PubMed
Google Scholar
Timmis K, de Vos WM, Ramos JL, Vlaeminck SE, Prieto A, Danchin A, et al. The contribution of microbial biotechnology to sustainable development goals. Microb Biotechnol. 2017;10:984–7.
Article
PubMed
PubMed Central
Google Scholar
Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 2017;15:e2001793.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zahn G, Amend AS. Foliar microbiome transplants confer disease resistance in a critically-endangered plant. PeerJ [Internet]. 2017 [cited 2020 Mar 10];5. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5683046/.
Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev. 2004;68:669–85.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bordenstein SR, Theis KR. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLOS Biology Public Library of Science. 2015;13:e1002226.
Google Scholar
Rosenberg E, Zilber-Rosenberg I. Microbes drive evolution of animals and plants: the hologenome concept. mBio [Internet]. 2016 [cited 2020 Mar 11];7. Available from: https://mbio.asm.org/content/7/2/e01395-15.
Bouffaud M-L, Poirier M-A, Muller D, Moënne-Loccoz Y. Root microbiome relates to plant host evolution in maize and other Poaceae. Environ Microbiol. 2014;16:2804–14.
Article
PubMed
Google Scholar
Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N. The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol. 2010;12:2885–93.
Article
PubMed
PubMed Central
Google Scholar
Schlaeppi K, Dombrowski N, Oter RG, Ver Loren van Themaat E, Schulze-Lefert P. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA. 2014;111:585–92.
Article
CAS
PubMed
Google Scholar
Weinert N, Piceno Y, Ding G-C, Meincke R, Heuer H, Berg G, et al. PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol. 2011;75:497–506.
Article
CAS
PubMed
Google Scholar
Zancarini A, Mougel C, Voisin A-S, Prudent M, Salon C, Munier-Jolain N. Soil nitrogen availability and plant genotype modify the nutrition strategies of M. truncatula and the associated rhizosphere microbial communities. PLoS One [Internet]. 2012 [cited 2020 Mar 10];7. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471967/.
Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, et al. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat Commun. 2014;5:5320.
Article
PubMed
Google Scholar
Wagner MR, Lundberg DS, Del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun. 2016;7:12151.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, et al. Large-scale replicated field study of maize rhizosphere identifies heritable microbes. Proc Natl Acad Sci USA. 2018;115:7368–73.
Article
PubMed
PubMed Central
Google Scholar
Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA. 2013;110:6548–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, et al. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PLoS One. 2013;8:e76382.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA. 2015;112:E911–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio. 2014;5:e01371–14.
Article
PubMed
PubMed Central
CAS
Google Scholar
Goss-Souza D, Mendes LW, Borges CD, Baretta D, Tsai SM, Rodrigues JLM. Soil microbial community dynamics and assembly under long-term land use change. FEMS Microbiol Ecol. 2017;93.
Rastogi G, Coaker GL, Leveau JHJ. New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett. 2013;348:1–10.
Article
CAS
PubMed
Google Scholar
Vorholt JA. Microbial life in the phyllosphere. Nat Rev Microbiol. 2012;10:828–40.
Article
CAS
PubMed
Google Scholar
Hacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P. Interplay between innate immunity and the plant microbiota. Annu Rev Phytopathol. 2017;55:565–89.
Article
CAS
PubMed
Google Scholar
Hersch-Green EI, Turley NE, Johnson MTJ. Community genetics: what have we accomplished and where should we be going? Philos Trans R Soc Lond Ser B Biol Sci. 2011;366:1453–60.
Article
Google Scholar
Tiffin P, Moeller DA. Molecular evolution of plant immune system genes. Trends Genet. 2006;22:662–70.
Article
CAS
PubMed
Google Scholar
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol. 2016;90:635–44.
Article
PubMed
CAS
Google Scholar
Bouffaud M-L, Kyselková M, Gouesnard B, Grundmann G, Muller D, Moënne-Loccoz Y. Is diversification history of maize influencing selection of soil bacteria by roots? Mol Ecol. 2012;21:195–206.
Article
PubMed
Google Scholar
Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe. 2015;17:392–403.
Article
CAS
PubMed
PubMed Central
Google Scholar
Graham PH, Vance CP. Legumes: importance and constraints to greater use. Plant Physiol. 2003;131:872–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oldroyd GED. Speak, friend, and enter: signalling systems that promote beneficial symbiotic associations in plants. Nat Rev Microbiol. 2013;11:252–63.
Article
CAS
PubMed
Google Scholar
Wang D, Yang S, Tang F, Zhu H. Symbiosis specificity in the legume: rhizobial mutualism. Cell Microbiol. 2012;14:334–42.
Article
PubMed
CAS
Google Scholar
Genre A, Russo G. Does a common pathway transduce symbiotic signals in plant–microbe interactions? Front Plant Sci [Internet]. 2016 [cited 2020 Mar 10];7. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754458/.
Rey T, Chatterjee A, Buttay M, Toulotte J, Schornack S. Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen. New Phytol. 2015;206:497–500.
Article
PubMed
Google Scholar
Rey T, Nars A, Bonhomme M, Bottin A, Huguet S, Balzergue S, et al. NFP, a LysM protein controlling Nod factor perception, also intervenes in Medicago truncatula resistance to pathogens. New Phytol. 2013;198:875–86.
Article
CAS
PubMed
Google Scholar
Lace B, Ott T. Commonalities and differences in controlling multipartite intracellular infections of legume roots by symbiotic microbes. Plant Cell Physiol. 2018;59:661–72.
Article
PubMed
CAS
Google Scholar
Zgadzaj R, Garrido-Oter R, Jensen DB, Koprivova A, Schulze-Lefert P, Radutoiu S. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proc Natl Acad Sci USA. 2016;113:E7996–8005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tjepkema JD, Yocum CS. Measurement of oxygen partial pressure within soybean nodules by oxygen microelectrodes. Planta. 1974;119:351–60.
Article
CAS
PubMed
Google Scholar
Avenhaus U, Cabeza RA, Liese R, Lingner A, Dittert K, Salinas-Riester G, et al. Short-term molecular acclimation processes of legume nodules to increased external oxygen concentration. Front Plant Sci [Internet]. 2016 [cited 2020 Mar 11];6. Available from: https://www.frontiersin.org/articles/10.3389/fpls.2015.01133/full.
Libault M. The carbon-nitrogen balance of the nodule and its regulation under elevated carbon dioxide concentration. Biomed Res Int [Internet]. 2014 [cited 2020 Mar 10]; 2014. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058508/.
Scheublin TR, Ridgway KP, Young JPW, van der Heijden MGA. Nonlegumes, legumes, and root nodules harbor different arbuscular mycorrhizal fungal communities. Appl Environ Microbiol. 2004;70:6240–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Martínez-Hidalgo P, Hirsch AM. The nodule microbiome: N2-fixing rhizobia do not live alone. Phytobiomes Journal. 2017;1:70–82.
Article
Google Scholar
Santos MS, Nogueira MA, Hungria M. Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture. AMB Express. 2019;9:205.
Article
PubMed
PubMed Central
Google Scholar
Lesins KA, Lesins I. Genus Medicago (Leguminosae): a taxogenetic study [Internet]. Springer Netherlands; 1979 [cited 2020 Mar 25]. Available from: https://www.springer.com/gp/book/9789400996366.
Barker DG, Bianchi S, Blondon F, Dattée Y, Duc G, Essad S, et al. Medicago truncatula, a model plant for studying the molecular genetics of theRhizobium-legume symbiosis. Plant Mol Biol Report. 1990;8:40–9.
Article
CAS
Google Scholar
Cook DR. Medicago truncatula--a model in the making! Curr Opin Plant Biol. 1999;2:301–4.
Article
CAS
PubMed
Google Scholar
Young ND, Debellé F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480:520–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bonito G, Benucci GMN, Hameed K, Weighill D, Jones P, Chen K-H, et al. Fungal-bacterial networks in the Populus rhizobiome are impacted by soil properties and host genotype. Front Microbiol [Internet]. Frontiers; 2019 [cited 2020 Mar 25];10. Available from: https://www.frontiersin.org/articles/10.3389/fmicb.2019.00481/full.
Liu F, Hewezi T, Lebeis SL, Pantalone V, Grewal PS, Staton ME. Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly. BMC Microbiol. 2019;19:201.
Article
PubMed
PubMed Central
CAS
Google Scholar
Veach AM, Morris R, Yip DZ, Yang ZK, Engle NL, Cregger MA, et al. Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin. Microbiome. 2019;7:76.
Article
PubMed
PubMed Central
Google Scholar
Bruijn FJ de. The model legume Medicago truncatula, 2 Volume Set. John Wiley & Sons; 2020.
Fierer N, Strickland MS, Liptzin D, Bradford MA, Cleveland CC. Global patterns in belowground communities. Ecol Lett. 2009;12:1238–49.
Article
PubMed
Google Scholar
Yeoh YK, Dennis PG, Paungfoo-Lonhienne C, Weber L, Brackin R, Ragan MA, et al. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nat Commun Nature Publishing Group. 2017;8:1–9.
CAS
Google Scholar
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.
Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev. 2013;37:634–63.
Article
CAS
PubMed
Google Scholar
Rolfe SA, Griffiths J, Ton J. Crying out for help with root exudates: adaptive mechanisms by which stressed plants assemble health-promoting soil microbiomes. Curr Opin Microbiol. 2019;49:73–82.
Article
CAS
PubMed
Google Scholar
Lareen A, Burton F, Schäfer P. Plant root-microbe communication in shaping root microbiomes. Plant Mol Biol. 2016;90:575–87.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bonnin I, Huguet T, Gherardi M, Prosperi JM, Olivieri I. High level of polymorphism and spatial structure in a selfing plant species, Medicago truncatula (Leguminosae), Shown Using RAPD Markers. American Journal of Botany Botanical Society of America. 1996;83:843–55.
Article
Google Scholar
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature Nature Publishing Group. 2012;488:86–90.
CAS
Google Scholar
Bulgarelli D, Rott M, Schlaeppi K, van Themaat EVL, Ahmadinejad N, Assenza F, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature Nature Publishing Group. 2012;488:91–5.
CAS
Google Scholar
Ehinger M, Mohr TJ, Starcevich JB, Sachs JL, Porter SS, Simms EL. Specialization-generalization trade-off in a Bradyrhizobium symbiosis with wild legume hosts. BMC Ecol. 2014;14:8.
Article
PubMed
PubMed Central
Google Scholar
Batstone RT, Carscadden KA, Afkhami ME, Frederickson ME. Using niche breadth theory to explain generalization in mutualisms. Ecology. 2018;99:1039–50.
Article
PubMed
Google Scholar
Simonsen AK, Dinnage R, Barrett LG, Prober SM, Thrall PH. Symbiosis limits establishment of legumes outside their native range at a global scale. Nat Commun Nature Publishing Group. 2017;8:1–9.
Google Scholar
Harrison TL, Wood CW, Heath KD, Stinchcombe JR. Geographically structured genetic variation in the Medicago lupulina–Ensifer mutualism. Evolution. 2017;71:1787–801.
Article
PubMed
Google Scholar
Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Assembly and ecological function of the root microbiome across angiosperm plant species. PNAS National Academy of Sciences. 2018;115:E1157–65.
CAS
Google Scholar
Tkacz A, Bestion E, Bo Z, Hortala M, Poole PS. Influence of plant fraction, soil, and plant species on microbiota: a multikingdom comparison. mBio [Internet]. American Society for Microbiology; 2020 [cited 2020 Mar 25];11. Available from: https://mbio.asm.org/content/11/1/e02785-19.
Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S-T, Weigel D, et al. Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol. 2016;14:e1002352.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, et al. PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015;349:860–4.
Article
CAS
PubMed
Google Scholar
Bergelson J, Mittelstrass J, Horton MW. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Sci Rep [Internet]. 2019 [cited 2020 Mar 25];9. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328596/.
Wagner MR, Busby PE, Balint-Kurti P. Analysis of leaf microbiome composition of near-isogenic maize lines differing in broad-spectrum disease resistance. New Phytol. 2020;225:2152–65.
Article
CAS
PubMed
Google Scholar
Parker MA. Local population differentiation for compatibility in an annual legume and its host-specific fungal pathogen. Evolution. 1985;39:713–23.
Article
PubMed
Google Scholar
Burdon JJ, Gibson AH, Searle SD, Woods MJ, Brockwell J. Variation in the effectiveness of symbiotic associations between native rhizobia and temperate Australian acacia: within-species interactions. J Appl Ecol. [British Ecological Society, Wiley]; 1999;36:398–408.
Heath KD. Intergenomic epistasis and coevolutionary constraint in plants and rhizobia. Evolution. 2010;64:1446–58.
CAS
PubMed
Google Scholar
Burghardt LT, Epstein B, Guhlin J, Nelson MS, Taylor MR, Young ND, et al. Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments. PNAS National Academy of Sciences. 2018;115:2425–30.
Article
CAS
Google Scholar
Dangl JL, Horvath DM, Staskawicz BJ. Pivoting the plant immune system from dissection to deployment. Science. 2013;341:746–51.
Article
CAS
PubMed
Google Scholar
Morella NM, Weng FC-H, Joubert PM, Metcalf CJE, Lindow SE, Koskella B. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. 2019.
Bendall ML, Stevens SL, Chan L-K, Malfatti S, Schwientek P, Tremblay J, et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J Nature Publishing Group. 2016;10:1589–601.
Google Scholar
Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLOS Biology Public Library of Science. 2019;17:e3000102.
Google Scholar
Martínez R, Espejo A, Sierra M, Ortiz-Bernad I, Correa-Galeote D, Bedmar E, et al. Co-inoculation of Halomonas maura and Ensifer meliloti to improve alfalfa yield in saline soils. Appl Soil Ecol. 2015;87:81–6.
Article
Google Scholar
Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, et al. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 2012;6:1378–90.
Article
CAS
PubMed
Google Scholar
Ottesen AR, González Peña A, White JR, Pettengill JB, Li C, Allard S, et al. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol. 2013;13:114.
Article
PubMed
PubMed Central
Google Scholar
Garrido-Oter R, Nakano RT, Dombrowski N, Ma K-W, AgBiome Team, McHardy AC, et al. Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia. Cell Host Microbe. 2018;24:155–167.e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Garcia-Fraile P, Seaman JC, Karunakaran R, Edwards A, Poole PS, Downie JA. Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. Plant Soil. 2015;390:251–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science. 2001;293:668–72.
Article
CAS
PubMed
Google Scholar
di Cenzo GC, Checcucci A, Bazzicalupo M, Mengoni A, Viti C, Dziewit L, et al. Metabolic modelling reveals the specialization of secondary replicons for niche adaptation in Sinorhizobium meliloti. Nat Commun. 2016;7:12219.
Article
CAS
Google Scholar
Bever JD, Dickie IA, Facelli E, Facelli JM, Klironomos J, Moora M, et al. Rooting theories of plant community ecology in microbial interactions. Trends Ecol Evol (Amst). 2010;25:468–78.
Article
Google Scholar
Béna G, Lyet A, Huguet T, Olivieri I. Medicago-Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago. J Evol Biol. 2005;18:1547–58.
Article
PubMed
Google Scholar
Martínez-Romero E. Coevolution in Rhizobium-Legume Symbiosis? DNA and Cell Biology. Mary Ann Liebert, Inc, publishers. 2009;28:361–70.
Google Scholar
Oldroyd GED, Murray JD, Poole PS, Downie JA. The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet. 2011;45:119–44.
Article
CAS
PubMed
Google Scholar
Weese DJ, Heath KD, Dentinger BTM, Lau JA. Long-term nitrogen addition causes the evolution of less-cooperative mutualists. Evolution. 2015;69:631–42.
Article
CAS
PubMed
Google Scholar
Sachs JL, Russell JE, Lii YE, Black KC, Lopez G, Patil AS. Host control over infection and proliferation of a cheater symbiont. J Evol Biol. 2010;23:1919–27.
Article
CAS
PubMed
Google Scholar
Batstone RT, Dutton EM, Wang D, Yang M, Frederickson ME. The evolution of symbiont preference traits in the model legume Medicago truncatula. New Phytol. 2017;213:1850–61.
Article
CAS
PubMed
Google Scholar
Thilakarathna MS, Raizada MN. A meta-analysis of the effectiveness of diverse rhizobia inoculants on soybean traits under field conditions. Soil Biol Biochem. 2017;105:177–96.
Article
CAS
Google Scholar
Heath KD, Stinchcombe JR. Explaining mutualism variation: a new evolutionary paradox? Evolution. 2014;68:309–17.
Article
PubMed
Google Scholar
Grillo MA, De Mita S, Burke PV, Solórzano-Lowell KLS, Heath KD. Intrapopulation genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula. Evolution. 2016;70:2704–17.
Article
CAS
PubMed
Google Scholar
De Mita S, Santoni S, Ronfort J, Bataillon T. Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago. BMC Evol Biol. 2007;7:210.
Article
PubMed
PubMed Central
CAS
Google Scholar
Trung BC, Yoshida S. Improvement of Leonard jar assembly for screening of effective rhizobium. Soil Sci Plant Nutr. 1983;29:97–100.
Article
Google Scholar
Brown SP, Leopold DR, Busby PE. Protocols for investigating the leaf mycobiome using high-throughput DNA sequencing. Methods Mol Biol. 1848;2018:39–51.
Google Scholar
Lawley RA, Campbell R, Newman EI. Composition of the bacterial flora of the rhizosphere of three grassland plants grown separately and in mixtures. Soil Biol Biochem. 1983;15:605–7.
Article
Google Scholar
Jones JM, Heath KD, Ferrer A, Brown SP, Canam T, Dalling JW. Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes. FEMS Microbiol Ecol [Internet]. Oxford Academic; 2019 [cited 2020 Mar 29];95. Available from: https://academic.oup.com/femsec/article/95/1/fiy223/5184448.
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol American Society for Microbiology. 2009;75:7537–41.
Article
CAS
Google Scholar
Brown SP, Veach AM, Rigdon-Huss AR, Grond K, Lickteig SK, Lothamer K, et al. Scraping the bottom of the barrel: are rare high throughput sequences artifacts? Fungal Ecol. 2015;13:221–5.
Article
Google Scholar
Oliver AK, Brown SP, Callaham MA, Jumpponen A. Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %. Fungal Ecol. 2015;15:86–9.
Article
Google Scholar
Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecology. 2001;26:32–46.
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package [Internet]. 2019 [cited 2020 Mar 25]. Available from: https://CRAN.R-project.org/package=vegan.
Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, et al. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. BMC Genomics. 2008;9:285.
Article
PubMed
PubMed Central
CAS
Google Scholar
Heath KD, Burke PV, Stinchcombe JR. Coevolutionary genetic variation in the legume-rhizobium transcriptome. Mol Ecol. 2012;21:4735–47.
Article
PubMed
Google Scholar
Brown S, Veach A, Horton J, Ford E, Jumpponen A, Baird R. Context dependent fungal and bacterial soil community shifts in response to recent wildfires in the Southern Appalachian Mountains. For Ecol Manag. 2019;451.
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
Article
PubMed
PubMed Central
Google Scholar
Raup DM, Crick RE. Measurement of faunal similarity in paleontology. Journal of Paleontology Paleontological Society. 1979;53:1213–27.
Google Scholar
Chase JM, Kraft NJB, Smith KG, Vellend M, Inouye BD. Using null models to disentangle variation in community dissimilarity from variation in α-diversity. Ecosphere. 2011;2:art24.
Article
Google Scholar
Hammer O, Harper DAT, Ryan PD. PAST: Paleontological Statistics Software Package for Education and Data Analysis. 2001;9.
Gotelli NJ. Null model analysis of species co-occurrence patterns. Ecology. 2000;81:2606–21.
Article
Google Scholar
Pielou DP, Pielou EC. Association among species of infrequent occurrence: the insect and spider fauna of Polyporus betulinus (Bulliard) Fries. J Theor Biol. 1968;21:202–16.
Article
CAS
PubMed
Google Scholar
Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. PLOS Computational Biology Public Library of Science. 2012;8:e1002687.
Article
CAS
Google Scholar
Berry D, Widder S. Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Front Microbiol. 2014;5:219.
Article
PubMed
PubMed Central
Google Scholar
Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J. 2015;9:968–79.
Article
CAS
PubMed
Google Scholar
Bushnell B, Rood J, Singer E. BBMerge - accurate paired shotgun read merging via overlap. PLoS One. 2017;12:e0185056.
Article
PubMed
PubMed Central
CAS
Google Scholar
Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, et al. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics. 2014;15:312.
Article
PubMed
PubMed Central
CAS
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. Cold Spring Harbor: Cold Spring Harbor Lab Press. Publications Dept. 2017;27:824–34.
CAS
Google Scholar
O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733–45.
Article
PubMed
CAS
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421.
Article
PubMed
PubMed Central
CAS
Google Scholar
Coleman ML, Chisholm SW. Ecosystem-specific selection pressures revealed through comparative population genomics. Proc Natl Acad Sci USA. 2010;107:18634–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reeve W, Chain P, O’Hara G, Ardley J, Nandesena K, Bräu L, et al. Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419. Stand Genomic Sci. 2010;2:77–86.
Article
PubMed
PubMed Central
Google Scholar
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Article
CAS
PubMed
Google Scholar
Adékambi T, Drancourt M, Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol. 2009;17:37–45.
Article
PubMed
CAS
Google Scholar