Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

Beckers, Bram; Beeck, Michiel Op De; Weyens, Nele; Boerjan, Wout; Vangronsveld, Jaco

doi:10.1186/s40168-017-0241-2

Cited by 406 publications

(370 citation statements)

References 116 publications

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“…Mexican Dioon species, similar to that detected in the root endosphere from angiosperm plants as Arabidopsis [27], sugarcane [46], poplar trees [47], and inside the specialized root nodules of legumes [48]. We found that Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes and Planctomycetes were the dominant bacterial phyla in the Dioon coralloid root microbiome.…”

Section: A Taxonomically Diverse Bacterial Community Inside Dioon Corsupporting

confidence: 77%

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

Suárez-Moo

Vovides

Griffith

et al. 2018

Preprint

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Cycads are among the few plants that have developed specialized roots to host nitrogenfixing bacteria. We describe the bacterial diversity of the coralloid roots from seven Dioon species and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species of Dioon that we evaluated, suggesting a recent divergence of Dioon populations and/or similar plantdriven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched with Nostoc spp and Calothrix spp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

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Section: A Taxonomically Diverse Bacterial Community Inside Dioon Corsupporting

confidence: 77%

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

Suárez-Moo

Vovides

Griffith

et al. 2018

Preprint

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“…In addition to the higher alpha diversity (richness and evenness) found in the olive rhizosphere microbial communities compared to that observed for the microbiota inhabiting the root endosphere, and the finding that quite different communities were found in each compartment, a common scenario described in several studies 25,26 , the following major results must be highlighted from our work. Concerning the endosphere, cultivars originating from Syria showed the highest diversity level in contrast to the Turkish cultivars that showed the lowest one.…”

Section: Discussionsupporting

confidence: 60%

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection

Fernández-González¹,

Villadas²,

Cabanás

et al. 2019

Preprint

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Up to date, the bacterial and fungal microbial communities from the olive (Olea europaea L.) root systems have not been simultaneously studied. In this work, we show that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore, Actinophytocola, Streptomyces and Pseudonocardia are the most abundant bacterial genera in the olive root endosphere, Actinophytocola being the most prevalent genus by far. In contrast, Gp6, Gp4, Rhizobium and Sphingomonas are the main genera in the olive rhizosphere. Canalisporium, Aspergillus, Minimelanolocus and Macrophomina are the main fungal genera present in the olive root system. Interestingly enough, a high proportion of so far unclassified fungal sequences at class level were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genus Actinophytocola may play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity suggests that there are still some fungi with important ecological and biotechnological implications that have yet to be discovered.

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“…Unidentifiable sequences or sequences classified as Eukaryota , chloroplasts, mitochondria, or Wolbachia (endosymbiont) were removed. Low abundance sequences (singletons, doubletons, and tripletons) could potentially reflect the rare biosphere of a microbial community (D Ainsworth et al., ), but to avoid inflating the actual microbial diversity in the cricket gut due to PCR or sequencing errors (Dickie, ; Kunin, Engelbrektson, Ochman, & Hugenholtz, ), singletons were excluded from downstream analyses (Beckers, Op De Beeck, Weyens, Boerjan, & Vangronsveld, ; Tedersoo et al., ) (quality control step 7). Finally, a total of nineteen OTUs, with a maximum of three sequence reads for any individual OTU, were obtained from all the negative controls.…”

Section: Methodsmentioning

confidence: 99%

The influence of diet and environment on the gut microbial community of field crickets

Stat

Bunce

et al. 2018

Ecology and Evolution

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The extent to which diet and environment influence gut community membership (presence or absence of taxa) and structure (individual taxon abundance) is the subject of growing interest in microbiome research. Here, we examined the gut bacterial communities of three cricket groups: (1) wild caught field crickets, (2) laboratory‐reared crickets fed cat chow, and (3) laboratory‐reared crickets fed chemically defined diets. We found that both environment and diet greatly altered the structure of the gut bacterial community. Wild crickets had greater gut microbial diversity and higher Firmicutes to Bacteroidetes ratios, in contrast to laboratory‐reared crickets. Predictive metagenomes revealed that laboratory‐reared crickets were significantly enriched in amino acid degradation pathways, while wild crickets had a higher relative abundance of peptidases that would aid in amino acid release. Although wild and laboratory animals differ greatly in their bacterial communities, we show that the community proportional membership remains stable from Phylum to Family taxonomic levels regardless of differences in environment and diet, suggesting that endogenous factors, such as host genetics, have greater control in shaping gut community membership.

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Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

Cited by 406 publications

References 116 publications

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection

The influence of diet and environment on the gut microbial community of field crickets

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