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microbiomes reveals reproducible impacts on plant function. ISME J 9:980–989
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networks shape gut microbial composition in wild Verreaux’s sifaka. Proc Roy Soc B Biol
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response to depletion of microbial diversity. ISME J 5:351–361
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microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799
Qin J, MetaHIT Consortium (2010) A human gut microbial gene catalogue established by
metagenomic sequencing. Nature 464:59–65
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (2011) Toward molecular trait-based ecology
through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol
7:473
Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R (2004) Recognition of
commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell
118:229–241
Rakoff-Nahoum S, Coyne MJ, Comstock LE (2014) An ecological network of polysaccharide
utilization among human intestinal symbionts. Curr Biol 24:40–49
17 Diversity–Function Relationships and the Underlying Ecological Mechanisms in. . .
323
Formicidae). Behav Ecol 15:357–364
Munoz-Ucros J, Zwetsloot MJ, Cuellar-Gempeler C, Bauerle T (2020) Spatio-temporal patterns of
rhizosphere microbiome assembly: from ecological theory to agricultural application. J Appl
Ecol, in review
Nawroth JC, Guo H, Koch E, Heath-Heckman EAC, Hermanson JC, Ruby EG, Dabiri JO, Kanso E,
McFall-Ngai M (2017) Motile cilia create fluid-mechanical microhabitats for the active recruitment of the host microbiome. Proc Natl Acad Sci USA 114:9510–9516
Nelson MS, Sadowsky MJ (2015) Secretion systems and signal exchange between nitrogen-fixing
rhizobia and legumes. Front Plant Sci. https://doi.org/10.3389/fpls.2015.00491
Nelson MB, Martiny AC, Martiny JBH (2016) Global biogeography of microbial nitrogen-cycling
traits in soil. Proc Natl Acad Sci USA 113:8033–8040
Niu B, Paulson JN, Zheng X, Kolter R (2017) Simplified and representative bacterial community of
maize roots. Proc Natl Acad Sci USA 114:E2450–E2459
Nyholm SV, McFall-Ngai M (2004) The winnowing: establishing the squid–vibrio symbiosis. Nat
Rev Microbiol 2:632–642
Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao J, Abe F, Osawa R (2016)
Age-related changes in gut microbiota composition from newborn to centenarian: a crosssectional study. BMC Microbiol 16:90
Oh J, Byrd AL, Park M, Kong HH, Segre JA (2016) Temporal stability of the human skin
microbiome. Cell 165:854–866
Ooijevaar RE, Terveer EM, Verspaget HW, Kuijper EJ, Keller JJ (2019) Clinical application and
potential of fecal microbiota transplantation. Annu Rev Med 70:335–351
Oono R, Anderson CG, Denison RF (2011) Failure to fix nitrogen by non-reproductive symbiotic
rhizobia triggers host sanctions that reduce fitness of their reproductive clonemates. Proc Roy
Soc B Biol Sci 278:2698–2703
Ortiz N, Armada E, Duque E, Roldán A, Azcón R (2015) Contribution of arbuscular mycorrhizal
fungi and/or bacteria to enhancing plant drought tolerance under natural soil conditions:
effectiveness of autochthonous or allochthonous strains. J Plant Physiol 174:87–96
Ottman N, Smidt H, de Vos W, Belzer C (2012) The function of our microbiota: who is out there
and what do they do? Front Cell Infect Microbiol 2:1–11
Panke-Buisse K, Poole AC, Goodrich JK, Ley RE, Kao-Kniffin J (2015) Selection on soil
microbiomes reveals reproducible impacts on plant function. ISME J 9:980–989
Pérez-García A, Romero D, de Vicente A (2011) Plant protection and growth stimulation by
microorganisms: biotechnological applications of Bacilli in agriculture. Curr Opin Biotechnol
22:187–193
Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA (2017) Hierarchical social
networks shape gut microbial composition in wild Verreaux’s sifaka. Proc Roy Soc B Biol
Sci 284:20172274
Peter H, Beier S, Bertilsson S, Lindström ES, Langenheder S, Tranvik LJ (2011) Function-specific
response to depletion of microbial diversity. ISME J 5:351–361
Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH (2013) Going back to the roots: the
microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799
Qin J, MetaHIT Consortium (2010) A human gut microbial gene catalogue established by
metagenomic sequencing. Nature 464:59–65
Raes J, Letunic I, Yamada T, Jensen LJ, Bork P (2011) Toward molecular trait-based ecology
through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol
7:473
Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R (2004) Recognition of
commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell
118:229–241
Rakoff-Nahoum S, Coyne MJ, Comstock LE (2014) An ecological network of polysaccharide
utilization among human intestinal symbionts. Curr Biol 24:40–49
17 Diversity–Function Relationships and the Underlying Ecological Mechanisms in. . .
323