The wild side of plant microbiomes

Pérez‐Jaramillo, Juan E.; Carrión, Víctor J.; Hollander, Mattias de; Raaijmakers, Jos M.

doi:10.1186/s40168-018-0519-z

Cited by 199 publications

(156 citation statements)

References 37 publications

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“…At first glance, the ‘direction’ of this bacterial enrichment is difficult to reconcile with the eco-geographic adaptation of wild barleys and, in particular, the fact that Actinobacteria are more tolerant to arid conditions 34 and, consequently, more abundant in desert vs. non-desert soils 35 . However, the enrichment of Actinobacteria in modern crops compared to ancestral relatives has recently emerged as a distinctive feature of the microbiota of multiple plant species 36 . Although the ecological significance of this trait of the domesticated microbiota remains to be fully elucidated, studies conducted in rice 37 and other grasses, including barley 38 , indicate a relationship between drought stress and Actinobacteria enrichments.…”

Section: Discussionmentioning

confidence: 99%

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

Terrazas

Balbirnie-Cumming

Morris

et al. 2020

Preprint

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The microbiota thriving in the rhizosphere, the thin layer of soil surrounding plant roots, plays a critical role in plant’s adaptation to the environment. Domestication and breeding selection have progressively differentiated the microbiota of modern crops from the ones of their wild ancestors. However, the impact of eco-geographical constraints faced by domesticated plants and crop wild relatives on recruitment and maintenance of the rhizosphere microbiota remains to be fully elucidated. Here we performed a comparative 16S rRNA gene survey of the rhizosphere of 4 domesticated and 20 wild barley (Hordeum vulgare) genotypes grown in an agricultural soil under controlled environmental conditions. We demonstrated the enrichment of individual bacteria mirrored the distinct eco-geographical constraints faced by their host plants. Unexpectedly, Elite varieties exerted a stronger genotype effect on the rhizosphere microbiota when compared with wild barley genotypes adapted to desert environments with a preferential enrichment for members of Actinobacteria. Finally, in wild barley genotypes, we discovered a limited, but significant, correlation between microbiota diversity and host genomic diversity. Our results revealed a footprint of the host’s adaptation to the environment on the assembly of the bacteria thriving at the root-soil interface. In the tested conditions, this recruitment cue layered atop of the distinct evolutionary trajectories of wild and domesticated plants and, at least in part, is encoded by the barley genome. This knowledge will be critical to design experimental approaches aimed at elucidating the recruitment cues of the barley microbiota across a range of soil types.

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Section: Discussionmentioning

confidence: 99%

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

Terrazas

Balbirnie-Cumming

Morris

et al. 2020

Preprint

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“…By comparing wild and modern crop genotypes, few studies have addressed the effect of domestication in altering the composition and structure of the plant-associated bacterial and fungal microbiota, (recently reviewed in Hassani et al 2019; Escudero-Martinez et al 2019; Cordovez et al 2019). Depending on the crop species, plant domestication has resulted in microbial diversity reduction (Zachow et al 2014), reduced symbiotic interactions (Kiers et al 2007) or depletion of a microbial phylogroup (Pérez-Jaramillo et al 2018). While genetic diversity of crop species is reduced at a population level, we still lack insight why individual crop plants assemble less diverse microbial communities compared to their wild relatives.…”

Section: Figurementioning

confidence: 99%

Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species

Hassani

Özkurt

Franzenburg³

et al. 2020

Preprint

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Plant domestication has led to substantial changes in the host physiology. How this anthropogenic intervention has contributed in altering the wheat microbiota is not well understood. Here, we investigated the role of ecological selection, drift and dispersal in shaping the bacterial and fungal communities associated with domesticated wheat Triticum aestivum and two wild relatives, Triticum boeoticum and Triticum urartu. Our study shows that the bacterial and fungal microbiota of wild and domesticated wheat species follow distinct community assembly patterns. Further, we revealed a more prominent role of neutral processes in the assembly of the microbiota of domesticated wheat and propose that domestication has relaxed selective processes in the assembly of the wheat microbiota.

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“…We conclude by considering how this study links to the call for greater research effort on microbiomes in natural populations of animals and plants (Hird, 2017;Perez-Jaramillo, Carrion, Hollander, & Raaijmakers, 2018). The tight environmental controls and simplifying conditions of laboratory studies facilitate the study of fundamental mechanisms, but there is increasing evidence that some important processes and interactions are not displayed under laboratory conditions Ericsson et al, 2017).…”

Section: Insights Into Microbiomes Of Wild Animalsmentioning

confidence: 84%

Correlation and causation between the microbiome, Wolbachia and host functional traits in natural populations of drosophilid flies

2019

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Resident microorganisms are known to influence the fitness and traits of animals under controlled laboratory conditions, but the relevance of these findings to wild animals is uncertain. This study investigated the host functional correlates of microbiota composition in a wild community of three sympatric species of mycophagous drosophilid flies, Drosophila falleni, Drosophila neotestacea and Drosophila putrida. Specifically, we quantified bacterial communities and host transcriptomes by parallel 16S rRNA gene amplicon sequencing and RNA‐Seq of individual flies. Among‐fly variation in microbiota composition did not partition strongly by sex or species, and included multiple modules, that is, sets of bacterial taxa whose abundance varied in concert across different flies. The abundance of bacteria in several modules varied significantly with multiple host transcripts, especially in females, but the identity of the correlated host transcriptional functions differed with host species, including epithelial barrier function in D. falleni, muscle function in D. putrida, and insect growth and development in D. neotestacea. In D. neotestacea, which harbours the endosymbionts Wolbachia and Spiroplasma, Wolbachia promotes the abundance of Spiroplasma, and is positively correlated with abundance of Lactobacillales and Bacteroidales. Furthermore, most correlations between host gene expression and relative abundance of bacterial modules were co‐correlated with abundance of Wolbachia (but not Spiroplasma), indicative of an interdependence between host functional traits, microbiota composition and Wolbachia abundance in this species. These data suggest that, in these natural populations of drosophilid flies, different host species interact with microbial communities in functionally different ways that can vary with the abundance of endosymbionts.

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The wild side of plant microbiomes

Cited by 199 publications

References 37 publications

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

Ecological assembly processes of the bacterial and fungal microbiota of wild and domesticated wheat species

Correlation and causation between the microbiome, Wolbachia and host functional traits in natural populations of drosophilid flies

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