Dror, B. | bioRxiv Science

bioRxiv2020

Plant cell wall polysaccharides induce colony expansion of soil-derived Flavobacterium spp.

The genus Flavobacterium is characterized by the capacity to metabolize complex organic compounds and a unique gliding motility mechanism. They are often abundant in root microbiomes of various plants, but the factors contributing to this high abundance are currently unknown. In this study, we evaluated the effect of various plant-associated poly- and mono-saccharides on colony expansion of two Flavobacterium strains. Both strains were able to spread on pectin and other polysaccharides such as microcrystalline cellulose. However, only pectin (but not pectin monomers), a component of plant cell walls, enhanced colony expansion on solid surfaces in a dose- and substrate-dependent manner. On pectin, flavobacteria exhibited bi-phasic motility, with an initial phase of rapid expansion, followed by growth within the colonized area. Proteomic and gene expression analyses revealed significant induction of carbohydrate metabolism related proteins when flavobacteria were grown on pectin, including selected SusC/D, TonB-dependent glycan transport operons. Our results show a positive correlation between colony expansion and the upregulation of proteins involved in sugar uptake, suggesting an unknown linkage between specific operons encoding for glycan uptake and metabolism and flavobacterial expansion. Furthermore, within the context of flavobacterial-plant interactions, they suggest that pectin may facilitate flavobacterial expansion on plant surfaces in addition to serving as an essential carbon source. Contribution to the field statementMembers of the Flavobacterium genus are frequently rhizosphere competent, i.e. abundant and generally enriched on root surfaces relative to surrounding bulk soil, and previous studies suggest that they may play a role in plant health and ecosystem functioning. However, little is known about genetic and physiological factors that facilitate flavobacterial colonization and proliferation in this highly competitive environment. In this study we found that pectin stimulates flavobacterial colonies in a bi-phasic manner, initially characterized by rapid expansion on agar followed by increased biomass production. This appears to be linked to pectin-stimulated induction of specific TonB-associated proteins evidentially involved in the binding and uptake of complex sugars. Given the fact that pectin and other glycans are a primary component of plant cell walls, we hypothesize that these mechanisms are at least partially responsible for the rhizosphere competence of flavobacteria.

microbiology↗

bioRxiv2020

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome

Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores and others. Despite their involvement in bacteria-bacteria and bacteria-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with Actinobacteria, while the remaining were not associated with known bacteria. One Streptomyces-derived BGC was predicted to encode for a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic datasets revealed a higher abundance of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs. ImportanceWe identified distinct secondary metabolite (polyketide and nonribosomal peptide) encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems, yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding for antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode for novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary metabolite encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in inter-bacterial and bacterial-plant interactions.

microbiology↗