Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species

Abstract

Panicum represents a large genus of many North American prairie grass species. These include switchgrass (Panicum virgatum), a biofuel crop candidate with wide geographic range, as well as Panicum hallii, a close relative to switchgrass, which serves as a model system for the study of Panicum genetics due to its diploid genome and short growth cycles. For the advancement of switchgrass as a biofuel crop, it is essential to understand host microbiome interactions, which can be impacted by plant genetics and environmental factors inducing ecotype-specific phenotypic traits. We here compared rhizosphere and root endosphere bacterial communities of upland and lowland P. virgatum and P. hallii genotypes planted at two sites in Texas. Our analysis shows that sampling site predominantly contributed to bacterial community variance in the rhizosphere, however, impacted root endosphere bacterial communities much less. Instead we observed a relatively large core endophytic microbiome dominated by ubiquitously root-colonizing bacterial genera Streptomyces, Pseudomonas, and Bradyrhizobium. Endosphere communities displayed comparable diversity and conserved community structures across genotypes of both Panicum species. Functional insights into interactions between P. hallii and its root endophyte microbiome could hence inform testable hypotheses that are relevant for the improvement of switchgrass as a biofuel crop.

Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis

“…Leymus chinensis is an ecologically and economically important herbage that is widely distributed in the grasslands of Inner Mongolia and is a native perennial rhizome grass with prominent forage value and great palatability (Zhang et al , 2018). However, knowledge regarding the root microorganisms associated with L. chinensis remains limited, although root‐associated microbiomes have been extensively studied in other related plants (Yamamoto et al , 2018; Poudel et al , 2019; Singer et al , 2019). In addition, the microbial community structure of root‐associated microbiomes is different between bacterial and fungal communities, and this difference depends on the chemical and physical properties of the soil.…”

“…The OTUs, richness and diversity of bacterial and fungal communities in the rhizosphere from L. chinensis were higher than those observed in the root endosphere (Table S1). Root‐associated microbiomes have to overcome the immune defence mechanisms of plants to inhabit the endosphere compartment, which generally leads to reduced density and diversity in the microbial communities compared with that observed in rhizosphere soil communities (Singer et al , 2019). Previous reports have also shown that microbial richness and diversity gradually increase from the root endosphere to the rhizosphere soil and that microbial density is generally lower in the root endosphere than in the rhizosphere (Hacquard et al , 2015; Edwards et al , 2015; Yamamoto et al , 2018).…”

Host genomic influence on bacterial composition in the switchgrass rhizosphere

“…For example, Singer et al (2019) observed a large core endophytic switchgrass microbiome dominated by root-colonizing bacterial genera such as Streptomyces , Pseudomonas , and Bradyrhizobium , while rhizosphere diversity was more variable between their two sampling sites. Likewise, Singer et al (2019b) observed different core bacterial classes associated with upland and lowland switchgrass ecotypes, with each ecotype preferentially enriched for Alphaproteobacteria and Actinobacteria, respectively. For our study, out of 268 families, only two associated with the majority (>=90%) of our rhizosphere samples (Xanthobacteraceae and Sphingomonadaceae) and less than half (n = 110) associated with more than 10% of our samples.…”

Possible role of arbuscular mycorrhizal fungi and associated bacteria in the recruitment of endophytic bacterial communities by plant roots

“…Culture-independent techniques, PCR-denaturing gradient gel electrophoresis (DGGE) and Illumina MiSeq sequencing of the 16S rDNA of root endophytic bacterial communities confirmed the selectivity of genotypes in durum wheat, as different cultivars hosted significantly different bacterial communities in their root tissues (Agnolucci et al 2019b). However, Singer et al (2019) found conserved community structures across different genotypes of Panicum virgatum and Panicum hallii.…”