Establishment of a model multi-species biofilm and metatranscriptome analysis of biofilm and planktonic cell communities.. biofilm metagenome

We collected several biofilm samples from Japanese rivers and established a model multi-species biofilm that is reproducible and analyzable in laboratories. Bacterial abundance at the generic level was very similar between the planktonic and biofilm communities, whereas comparative metatranscriptomic analysis revealed many up- and down- regulated genes in the biofilm. Many genes involved in cysteine biosynthesis, iron-sulfur metabolism, stress response, and cell envelope function were upregulated; biofilm formation is cued by an iron-dependent signaling mechanism and the cued signal is relayed to stress responsive and cell envelope function genes. Interestingly, the opposite function of two sulfur-containing amino acids, cysteine and methionine, on biofilm formation was suggested. Expression of flagellar-related genes was regulated depending upon the growth phase, indicating different roles of flagellar during the adherence, maturation, and dispersal steps of biofilm formation. Downregulation of the 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 new genetic characteristics. Although the significance remains unclear, expression from the genes for rRNA methyltransferase, chromosome partitioning, aminoacyl-tRNA synthase, and leucine, thiamine, nucleotide, and fatty acid metabolism were found to be 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.