Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence

Abstract

It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae

“…Neither this effect increased in root compartments respect to the surrounding soil, where the influence of species-specific chemistry, defense responses, or microbial recognition, would expectably lead the processes of microbial enrichment and depletion described above. However, this finding is in line with previous reports of a limited host specificity of root-associated microbes (Bulgarelli et al, 2012;Colin et al, 2017;Dombrowski et al, 2016;Glynou et al, 2018b;Schlaeppi et al, 2014;Thiergart et al, 2019;Wagner et al, 2016;Zarraonaindia et al, 2015). This is at least true in related plant species, such as those investigated in our study, because phylogenetically distant hosts harbor clearly distinguishable microbial communities (U'Ren et al, 2019) likely due to major differences in cellular physiology and chemistry.…”

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion

“…The challenge in work-ing with complex and species-rich environments, such as soils, lies in the fact that the possible assembly configurations among species or sets of populations are almost limitless [12,21]. Those differences in microbial structure and composition in rhizosphere of several plants could be a result of selection process, modulated by the plant root system [9,[22][23][24].…”

Metatranscriptomics and nitrogen fixation from the rhizoplane of maize plantlets inoculated with a group of PGPRs

“…Nitrogen fixation is a key service in plant ecology but an energetically expensive process. Thus, diazotrophs are normally a minority among bacterial communities in plants (52, 53), and nitrogen fixation is a tightly regulated process which is turned off when fixed nitrogen is available. Therefore, we used a nitrogen free medium to grow maize plants to allow bacterial nitrogen fixing genes to be fully expressed.…”