Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities

Abstract

We collected several biofilm samples from Japanese rivers and established a reproducible multi-species biofilm model that can be analyzed in laboratories. Bacterial abundance at the generic level was highly similar between the planktonic and biofilm communities, whereas comparative metatranscriptomic analysis revealed many upregulated and downregulated genes in the biofilm. Many genes involved in iron-sulfur metabolism, stress response, and cell envelope function were upregulated; biofilm formation is mediated by an iron-dependent signaling mechanism and the signal is relayed to stress-responsive and cell envelope function genes. Flagella-related gene expression was regulated depending upon the growth phase, indicating different roles of flagella during the adherence, maturation, and dispersal steps of biofilm formation. Downregulation of DNA repair genes was observed, indicating that spontaneous mutation frequency would be elevated within the biofilm and that the biofilm is a cradle for generating novel genetic traits. Although the significance remains unclear, genes for rRNA methyltransferase, chromosome partitioning, aminoacyl-tRNA synthase, and cysteine, methionine, leucine, thiamine, nucleotide, and fatty acid metabolism were found to be differentially regulated. These results indicate that planktonic and biofilm communities are in different dynamic states. Studies on biofilm and sessile cells, which have received less attention, are important for understanding microbial ecology and for designing tailor-made anti-biofilm drugs.

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels

“…Studies that link structure and function of phototrophic biofilms on a molecular level are rare, yet the few existing studies report a composition of organisms and gene expression under stable conditions that is a broadly similar to our results (Krohn‐Molt et al., ; Nakamura et al., ; Schneider, Reimer, Hahlbrock, Arp, & Daniel, ). In a recent study, Lindemann and colleagues investigated protein expression patterns during succession in cyanobacterial biofilms (Lindemann et al., ).…”

Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer

“…BCAAs, which include valine, leucine, and isoleucine, may also contribute to fatty acid synthesis, which is also a feature of cancer metabolism (57). Valine and/or leucine secretion were previously associated with E. coli (58) and polymicrobial environmental biofilms (59). Polyamines were previously shown through metabolomics to be increased in CRC patients, with a rare polyamine, N1, N12-diacetylspermine detected in biofilm-positive CRCs (60), and we found that multiple microbial polyamine-related genes were increased in BFϩT mice (61).…”

Biofilms in the Spotlight: Detection, Quantification, and Removal Methods

“…As mentioned above, the initial step for biofilm formation is the attachment of the planktonic cells to the surface to become sessile cells and trigger the development of the biofilm. Cells that form biofilms and planktonic cells have differences in gene expression, such as those involved in lipid metabolism, metabolite production, carbohydrate and amino acid transport, stress response, and iron‐sulfur metabolism (Nakamura et al., ). Regarding iron metabolism, the expression of certain adhesion factors that are crucial for initial cell attachment to the surface are induced by a high concentration of iron in the environment (Berlanga & Guerrero, ).…”