Large-scale replicated field study of maize rhizosphere identifies heritable microbes

Walters, William A.; Jin, Zhao; Youngblut, Nicholas D.; Wallace, Jason G.; Sutter, Jessica L.; Zhang, Wei; González-Peña, Antonio; Peiffer, Jason A.; Koren, Omry; Shi, Qiaojuan; Knight, Rob; Rio, Tijana Glavina del; Tringe, Susannah G.; Buckler, Edward S.; Dangl, Jeffery L.; Ley, Ruth E.

doi:10.1073/pnas.1800918115

Cited by 444 publications

(375 citation statements)

References 35 publications

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“…Interestingly, another nitrifier taxa affiliated to the bacterial genus Nitrospira (Nitrospira phylum, 67% of all samples) was also identified as core taxon which suggests that microorganisms involved in nitrification could play an important role for nitrogen availability on roots. Nitrososphaera taxa were described as hubs in the wheat rhizosphere [30] and as highly prevalent in the rhizosphere and rhizoplane of Arabidopsis thaliana and maize [36,37], indicating that root surfaces represent a common habitat for these archaea.…”

Section: Evidences For a Wheat Core Microbiome And Identification Ofmentioning

confidence: 99%

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

Simonin

Dasilva²,

Terzi

et al. 2019

Preprint

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AbstractHere, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea, bacteria) and eukaryotic (fungi, protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 179 taxa (2 archaea, 104 bacteria, 41 fungi, 32 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our dataset. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.Graphical Abstract

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Section: Evidences For a Wheat Core Microbiome And Identification Ofmentioning

confidence: 99%

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

Simonin

Dasilva²,

Terzi

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…; Walters et al. ) and evolution of microbial populations (Toft and Andersson ; Guidot et al. ; Laine et al.…”

mentioning

confidence: 99%

Legacy of prior host and soil selection on rhizobial fitness in planta

2019

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Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil‐ and host‐dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant‐associated microbes.

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“…In subterranean environments, host plants establish root microbiomes with incredibly diverse microbial communities (Bulgarelli et al., ), and a recent research focus has been to detect the influence of host genotypes on the compositions of microbial communities. There is a small but significant influence of A. thaliana host genotypes on the microbes inhabiting the endophyte compartment of its roots (Bulgarelli et al., ; Lundberg et al., ), and a similar pattern was also observed in maize rhizosphere microbial communities (Peiffer et al., ; Walters et al., ). Phylogenetic distance between hosts and root microbiome dissimilarity appeared to be correlated in Brassicaceae and Poaceae (Bouffaud, Poirier, Muller, & Moenne‐Loccoz, ; Schlaeppi et al., ), further supporting the effects of host genetics on the root microbiome.…”

Section: Adaptation To Biotic Environmentsmentioning

confidence: 88%

Plant adaptation and speciation studied by population genomic approaches

2018

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Ever since Darwin, one of the major challenges in evolutionary biology is to unravel the process and mechanisms of adaptation and speciation. Population genomics—the analysis of whole‐genome polymorphism data from large population samples—is a critical approach to study adaptation and speciation, as population genomics datasets enable us to: (1) perform genome‐wide association studies (GWAS) to find genes underlying adaptive phenotypic variations; (2) scan the footprints of selection across the genome to pinpoint loci under selection; and (3) infer the structure and demographic history of populations. Here, we review recent studies of plants using population genomics, covering those focusing on interactions with other organisms, adaptations to local climatic conditions, and the genomic causes and consequences of reproductive isolation. Integrative studies involving GWAS, selection scans, functional studies, and fitness measurements in the field have successfully identified loci for adaptation, revealed the molecular basis of genetic trade‐offs, and shown that fitness can be predicted by polygenic effects of a number of loci associated with local climate. We highlight the importance of the measurement of fitness and phenotypes in the field, which can be powerful tools when combined with population genomic analyses.

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Large-scale replicated field study of maize rhizosphere identifies heritable microbes

Cited by 444 publications

References 35 publications

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

Legacy of prior host and soil selection on rhizobial fitness in planta

Plant adaptation and speciation studied by population genomic approaches

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