Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Abstract

Microbial communities in plant roots provide critical links between above- and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap-plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

“…In previous studies, the fungal community composition in roots was essentially analyzed either by cloning of PCR products (e.g., Vandenkoornhuyse et al, 2002a; Vandenkoornhuyse et al, 2002b) or more recently, by mass sequencing of amplicons using targeted DNA (e.g., Opik et al, 2013; Shakya et al, 2013a; Bonito et al, 2014). Others studies based on RNA and DNA extractions have used the RNA/DNA ratio as a proxy to investigate microbial dormancy and to estimate the metabolically active community (Aanderud et al, 2016; Jones & Lennon, 2010).…”

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach

“…Some studies have also shown that phosphorus [9,12] and soil texture [13] can shape soil bacterial communities. The effects of abiotic parameters have been less often demonstrated in fungal communities [10,14]. Regarding biotic factors, several studies have clearly shown that aboveground plant cover influences the fungal community structure and the functional diversity of forest soils [15–17].…”

“…Regarding biotic factors, several studies have clearly shown that aboveground plant cover influences the fungal community structure and the functional diversity of forest soils [15–17]. However, plant community composition has little to no effect on bacterial communities [14,18]. Furthermore, soil bacteria and fungi have also been known to interact with each other.…”

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

“…(2 SAGs), Armatimonadetes sp., Acidobacteria sp., and Verrucomicrobia sp. that had previously been observed in microbiome studies of Populus endospheres (16–18) but that were not present in our culture collections from these systems.…”

“…These two compartments represent distinct environments for the growth of microbes. Both culture-independent and culture-dependent assessments of microbial communities from Populus have been undertaken, which includes community profiling using phylogenetic marker genes (16–18) and large culture collections of endosphere and rhizosphere isolates (19–21). The microbiome in these root-associated environments is comprised primarily of bacteria and fungi and, to a lesser extent, archaea which are virtually absent from the endosphere (18).…”