Transcriptome profiling of Variovorax paradoxus EPS under different growth conditions reveals regulatory and structural novelty in biofilm formation

Abstract

<jats:p>We used transcriptome analysis by paired-end strand-specific RNA-seq to evaluate the specific changes in gene expression associated with the transition to static biofilm growth in the rhizosphere plant growth-promoting bacterium <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1833" xlink:type="simple">Variovorax paradoxus</jats:ext-link> </jats:named-content> </jats:italic> EPS. Triplicate biological samples of exponential growth, stationary phase and static biofilm samples were examined. DESeq2 and Rockhopper were used to identify robust and widespread shifts in gene expression specific to each growth phase. We identified 1711 protein-coding genes (28%) using DESeq2 that had altered expression greater than twofold specifically in biofilms compared to exponential growth. Fewer genes were specifically differentially expressed in stationary-phase culture (757, 12%). A small set of genes (103/6020) were differentially expressed in opposing fashions in biofilm and stationary phase, indicating potentially substantial shifts in phenotype. Gene-ontology analysis showed that the only class of genes specifically upregulated in biofilms was associated with nutrient transport, highlighting the importance of nutrient uptake in the biofilm. The biofilm-specific genes did not overlap substantially with the loci identified by mutagenesis studies, although some were present in both sets. The most highly upregulated biofilm-specific gene is predicted to be a part of the RNA degradosome, which indicates that RNA stability is used to regulate the biofilm phenotype. Two small putative proteins, Varpa_0407 and Varpa_3832, are highly expressed specifically in biofilms and are predicted to be secreted DNA-binding proteins, which may stabilize extracellular DNA as a component of the biofilm matrix. An flp/tad type-IV pilus locus (Varpa_5148–60) is strongly downregulated specifically in biofilms, in contrast with results from other systems for these pili. Mutagenesis confirms that this locus is important in surface motility rather than biofilm formation. These experimental results suggest that <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.1833" xlink:type="simple">V. paradoxus</jats:ext-link> </jats:named-content> </jats:italic> EPS biofilms have substantial regulatory and structural novelty.</jats:p>

Heat Stress Weakens the Skin Barrier Function in Sturgeon by Decreasing Mucus Secretion and Disrupting the Mucosal Microbiota

“…Methanobacterium and Asinibacterium are considered to produce poly-β-hydroxybutyrates that inhibit the growth of pathogens in the host bacterial community ( Defoirdt et al, 2007 ; Halet et al, 2007 ; Magalhes et al, 2020 ). And, Variovorax paradoxus is associated with biofilm formation ( Fredendall et al, 2020 ). In summary, the abundance changes in the potential pathogens and the probiotics indicate that heat stress derives adverse influences, which associate to break the balance between pathogens and probiotics in bacterial community of Siberian sturgeon.…”

Micro-fractionation shows microbial community changes in soil particles below 20 μm

“…Supernatant: Almost all bacterial taxa detected in the this fraction were previously reported to be involved in EPS production and biofilm formation (Pankratov et al, 2007;Pantanella et al, 2007;Urai et al, 2008;Andrews et al, 2010;Fish and Boxall, 2018;Sevinç Şengör, 2019;Fredendall et al, 2020;Pandit et al, 2020) and dominated by the phyla Proteobacteria (Pseudomonas, Massilia, Variovorax, Burkholderia, Duganella, and Janthinobacterium) and Bacteroidota (Mucilaginibacter and Edaphobaculum) which were present in the PSFs only at low abundances (Figure 3 and Supplementary Figure 2). Adding centrifugation steps to soil fractionation protocols could therefore be of use in studies focusing on biofilm forming microorganisms.…”

Micro-aggregation of a pristine grassland soil selects for bacterial and fungal communities and changes in nitrogen cycling potentials

“…Also, the observed changes in taxonomical composition of bacteria and fungi in this fraction indicates unique niches potentially created by biofilm like community assembly/dependency. Supernatant: Almost all of the taxa separated by centrifugation of the < 2 µm fraction were previously reported to be involved in EPS production and biofilm formation (22,61,(77)(78)(79)(80)(81)(82) and dominated by the phyla Proteobacteria (Pseudomonas, Massilia, Variovorax, Burkholderia, Duganella and Janthinobacterium) and Bacteroidota (Mucilaginibacter and Edaphobaculum) which were present in the PSFs only at low abundances (Fig. 3 and S2).…”