Functional overlap of the Arabidopsis leaf and root microbiota

Abstract

Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiota. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf- and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiota on their cognate host organs, but are also capable of ectopic leaf or root colonization. While this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.

Snowball: strain aware gene assembly of metagenomes

“…We evaluated Snowball using 21 simulated datasets, each containing 3-9 closely related E. coli strains and one simulated dataset containing ten novel recently published Rhizobia strains (Bai et al, 2015) (Section 3.4). We recall that good performance on different strains implies good performance on different species, which is why we put the emphasis on distinguishing between closely related strains in our experiments.…”

“…Nonetheless, it does not require closely related reference genomes of the studied species to be available. We have assessed the performance of Snowball using 21 simulated datasets, each containing 3-9 closely related E. coli strains and one simulated dataset containing ten recently published Rhizobia strains (Bai et al, 2015), which demonstrates the capability of the Snowball assembler to assemble novel strains. We have compared our Snowball assembler to the SAT assembler, which, to our knowledge, establishes the current state of the art in gene assembly.…”

“…Since two different species are substantially more divergent in terms of sequence than two different strains from the same species, good results on strains from one species also imply good or even better performance on datasets that contain several species-distinguishing species is the much easier task. We assessed the performance of Snowball using 21 simulated datasets, each containing 3-9 closely related Escherichia coli strains and on one simulated dataset containing ten recently published strains of a novel Rhizobia species (Bai et al, 2015). The results for the latter demonstrate the capability of the Snowball assembler to assemble genes of novel strains.…”

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

“…The bacterial community can be influencing the endophytic colonization of this strain or the host plant favored the colonization of other strains. The design of simplified microbial communities has been recently considered as a priority for harnessing the plant microbiome in sustainable agriculture [36] and this approach has been addressed in Arabidopsis [88] and in maize [67]. In this work we initiated PGP and colonization studies of a simplified community of 10 bacterial strains and initial results encourage further studies of synergistic, signaling and cooperative behavior of a multispecies consortium as well as the role of the plant genotype.…”

The Swiss Society of Microbiology: Small Bugs, Big Questions and Cool Answers

“…Such an approach has shown that there was not only an extensive taxonomic overlap between the Arabidopsis leaf and root microbiota but also a large overlap of genome-encoded functional capabilities. [13] Finally, nucleic acid-based techniques also enable the investigation of bacterial pure cultures introduced into an environmental compartment. Sphingomonas wittichii strain RW1 for example was inoculated into soil to achieve increased pollutant degradation.…”