Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities.
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.
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Yuya
Y
Nakamura
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Nao
N
Yamamoto
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Yuta
Y
Kino
Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Nozomi
N
Yamamoto
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Shota
S
Kamei
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Hiroshi
H
Mori
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.|Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
Ken
K
Kurokawa
Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1-M6-5 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. n-nakashima@aist.go.jp.
Nobutaka
N
Nakashima
D001419:Bacteria / Q000145:classification / Q000235:genetics*; D018441:Biofilms / Q000254:growth & development*; D005407:Flagella / Q000235:genetics; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D007501:Iron / Q000378:metabolism; D007564:Japan; D064307:Microbiota / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010933:Plankton / Q000235:genetics / Q000254:growth & development*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D045483:Rivers / Q000382:microbiology*; D013455:Sulfur / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics
D012336:RNA, Ribosomal, 16S; D013455:Sulfur; D007501:Iron
Biofilm; DNA repair; Iron metabolism; Metatranscriptome; Planktonic cell; RNA-seq; Stress response; Sulfur metabolism