Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

Abstract

Maintaining integrity of the plant cell walls is critical for plant health, however, our previous study showed that Cellvibrio, which is recognized by its robust ability to degrade plant cell walls, was enriched from the citrus rhizosphere to the rhizoplane (i.e., the root surface). Here we investigated the mechanisms underlying the rhizosphere-to-rhizoplane enrichment of Cellvibrio through genome-centric metagenomics and metatranscriptomics analyses. We recovered a near-complete metagenome-assembled genome representing a potentially novel species of Cellvibrio, herein designated Bin79, with genome size of 5.71 Mb across 11 scaffolds. Differential gene expression analysis demonstrated that plant cell wall degradation genes were repressed, whereas genes encoding chitin-degrading enzymes were induced in the rhizoplane compared with the rhizosphere. Enhanced expression of multi-drug efflux genes and iron acquisition- and storage-associated genes in the rhizoplane indicated mechanisms by which Bin79 competes with other microbes. In addition, genes involved in repelling plant immune responses were significantly activated in the rhizoplane. Comparative genomics analyses with five related Cellvibrio strains showed the importance of gene gain events for the rhizoplane adaptation of Bin79. Overall, this study characterizes a novel Cellvibrio strain and indicates the mechanisms involved in its adaptation to the rhizoplane from meta-omics data without cultivation.

Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full‐length 16S rDNA amplicon and metatranscriptomic analyses

“…through a bacterial taxon adapts to a given niche native microbiomes, as revealed by previous studies (Hao et al, 2020;Zhang et al, 2020). Thus, genomecentric comparative metatranscriptomic analyses were performed to identify differentially expressed genes between the rhizosphere and rhizoplane during the colonization process of strain B23.…”

Critical analysis of polycyclic tetramate macrolactam biosynthetic cluster phylogeny and functional diversity

“…In terms of producer phylogeny, these efforts immediately expanded the catalog of putative PTM producers into the actinobacterial genera Actinophytocola , Amycolatopsis, Thermomonospora, and Streptosporangium. Several new proteobacterial producers were also identified including Chitinimonas , plus several metagenome assembled genomes (MAG) including Cellvibrio from citrus rhizosphere (43) , Thiohalocapsa from a ‘pink berry’ sulfur cycling consortium (44–46), and a putative Myxococcales bacterium found in wastewater sludge (47) (Fig S2).…”

Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth

“…These associations provide hypotheses for laboratory and field studies on whether and how these rhizobacteria promote plant growth and associate with other members of rhizosphere communities. Because many rhizobacteria remain uncultured or resistant to cultivation, culture-independent approaches such as genome-resolved metagenomics and metatranscriptomics can be used to identify adaptation strategies of recalcitrant populations in plant-associated systems ( 59 ). Further investigations should include comparative genomic investigations to characterize variability in growth association patterns among members of influential rhizosphere genera and link changes in rhizosphere communities with plant gene expression and root exudation patterns.…”