Plant compartment and genetic variation drive microbiome composition in switchgrass roots

Abstract

SummarySwitchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth‐promoting bacteria and fungi, however, plant‐associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non‐native soil. We show that differences in bacterial, archaeal and fungal community composition and diversity are strongly driven by plant compartment and switchgrass genotypes and ecotypes. Plant‐associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared with the surrounding soil. Root associated compartments display low‐complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot of host‐specific bacterial and fungal associations of switchgrass in the field and confirms that host‐selected microbiomes persist after transfer to non‐native soil.

Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species

“…Similarly, we found fewer reads on average in BFL vs. PKL RS and RE samples (Supplementary Figure S2). Alpha diversity analysis across samples from different Panicum species, ecotypes, and planting sites showed that RS microbial communities are generally more complex than RE communities (Figures 2A,B), which matched our expectations based on previous findings in switchgrass (Singer et al, 2018) and other host plants (Caporaso et al, 2010; Coleman-Derr et al, 2016; Wagner et al, 2016b). As microorganisms have to overcome plant immune defense mechanisms to inhabit the endosphere compartment, this generally leads to reduced complexity in the microbial community compared to respective surface communities, such as found in rhizosphere and phyllosphere (Schulz et al, 2006).…”

Cooperation between Broussonetia papyrifera and Its Symbiotic Fungal Community To Improve Local Adaptation of the Host

“…In addition, our observations showed that the compartment had a limited effect on the response of fungal OTUs to B. papyrifera genotypes. These results are different from those of previous studies in switchgrass (41) and Populus (40). This difference could be attributed to two factors.…”

Prioritizing host phenotype to understand microbiome heritability in plants

“…Strikingly different communities inhabit aboveground vs. belowground organs, the interior vs. exterior of an organ, and fine-scale spatial niches within organsdespite originating largely from the same pool of environmental microbes (Figure 1) (Zarraonaindia et al, 2015). Sample type or "compartment" consistently explains more microbiome variation than genotype or environment (Hamonts et al, 2018;Singer et al, 2019;Guo et al, 2021). Because a given pair of host genotypes might exhibit more phenotypic variation in one compartment than another, patterns of microbiome heritability can differ among plant parts.…”