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Genome-wide association study of Arabidopsis thaliana leaf microbial community.

Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J - Nat Commun (2014)

Bottom Line: Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health.Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community.Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA [2] Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria.

ABSTRACT
Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

No MeSH data available.


Related in: MedlinePlus

Genetic variation within A. thaliana shapes the composition of the best-sequenced members of the microbial community(a) Using eigenvector techniques, inbred replicates of A. thaliana cluster together only when analyzing the most heavily sequenced bacteria. Nevertheless, the vast majority of the sequencing effort characterizes a small number (and %) of taxa in each community (b). Taken together, this implies that vagrant species and other poorly characterized/sequenced taxa (and occasionally, sequencing artifacts) obscure evidence that hosts shape their microbial communities. (c) Host-genetic variation within A. thaliana also affects the ability of fungi to colonize and proliferate on its leaves. All P values take into account technical confounders.
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Figure 1: Genetic variation within A. thaliana shapes the composition of the best-sequenced members of the microbial community(a) Using eigenvector techniques, inbred replicates of A. thaliana cluster together only when analyzing the most heavily sequenced bacteria. Nevertheless, the vast majority of the sequencing effort characterizes a small number (and %) of taxa in each community (b). Taken together, this implies that vagrant species and other poorly characterized/sequenced taxa (and occasionally, sequencing artifacts) obscure evidence that hosts shape their microbial communities. (c) Host-genetic variation within A. thaliana also affects the ability of fungi to colonize and proliferate on its leaves. All P values take into account technical confounders.

Mentions: We found that genetic variation within A. thaliana clearly shapes the leaf bacterial community, but only when we focused on the most heavily sequenced OTUs. As an example, PCA of the bacterial community distinguishes accessions of A. thaliana according to host-genotype, with inbred replicates of the same accession significantly clustered together (Fig. 1a; Methods) when analyzing, at most, the top 50% of the community (H2 ~ 40%; P = 0.044, 1000 permutations; for the top 1%, H2 ~ 42%; P = 0.004). However, these 2,528 bacterial OTUs correspond to more than 99% of the sequencing reads, which suggests that rare species or sequencing artifacts16,17 may obscure evidence that hosts structure their microbial communities (Fig. 1b).


Genome-wide association study of Arabidopsis thaliana leaf microbial community.

Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Vilhjálmsson BJ, Nordborg M, Gordon JI, Bergelson J - Nat Commun (2014)

Genetic variation within A. thaliana shapes the composition of the best-sequenced members of the microbial community(a) Using eigenvector techniques, inbred replicates of A. thaliana cluster together only when analyzing the most heavily sequenced bacteria. Nevertheless, the vast majority of the sequencing effort characterizes a small number (and %) of taxa in each community (b). Taken together, this implies that vagrant species and other poorly characterized/sequenced taxa (and occasionally, sequencing artifacts) obscure evidence that hosts shape their microbial communities. (c) Host-genetic variation within A. thaliana also affects the ability of fungi to colonize and proliferate on its leaves. All P values take into account technical confounders.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4232226&req=5

Figure 1: Genetic variation within A. thaliana shapes the composition of the best-sequenced members of the microbial community(a) Using eigenvector techniques, inbred replicates of A. thaliana cluster together only when analyzing the most heavily sequenced bacteria. Nevertheless, the vast majority of the sequencing effort characterizes a small number (and %) of taxa in each community (b). Taken together, this implies that vagrant species and other poorly characterized/sequenced taxa (and occasionally, sequencing artifacts) obscure evidence that hosts shape their microbial communities. (c) Host-genetic variation within A. thaliana also affects the ability of fungi to colonize and proliferate on its leaves. All P values take into account technical confounders.
Mentions: We found that genetic variation within A. thaliana clearly shapes the leaf bacterial community, but only when we focused on the most heavily sequenced OTUs. As an example, PCA of the bacterial community distinguishes accessions of A. thaliana according to host-genotype, with inbred replicates of the same accession significantly clustered together (Fig. 1a; Methods) when analyzing, at most, the top 50% of the community (H2 ~ 40%; P = 0.044, 1000 permutations; for the top 1%, H2 ~ 42%; P = 0.004). However, these 2,528 bacterial OTUs correspond to more than 99% of the sequencing reads, which suggests that rare species or sequencing artifacts16,17 may obscure evidence that hosts structure their microbial communities (Fig. 1b).

Bottom Line: Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health.Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community.Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

View Article: PubMed Central - PubMed

Affiliation: 1] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA [2] Gregor Mendel Institute, Austrian Academy of Sciences, Vienna 1030, Austria.

ABSTRACT
Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the fungi and bacteria that colonize its leaves and the host loci that influence the microbe numbers. The composition of this community differs among accessions of A. thaliana. Genome-wide association studies (GWAS) suggest that plant loci responsible for defense and cell wall integrity affect variation in this community. Furthermore, species richness in the bacterial community is shaped by host genetic variation, notably at loci that also influence the reproduction of viruses, trichome branching and morphogenesis.

No MeSH data available.


Related in: MedlinePlus