AME 54:135-152 (2009)  -  DOI: https://doi.org/10.3354/ame01258

Longitudinal changes in bacterial community composition in river epilithic biofilms: influence of nutrients and organic matter

Yuki Kobayashi1, Chulgoo Kim1,3, Chikage Yoshimizu1,2, Ayato Kohzu1,2,4, Ichiro Tayasu1, Toshi Nagata1,5,*

1Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
2Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
3Present address: Center for Aquatic Ecosystem Restoration, Kangwon National University, Chun-Cheon, Kangwon 200-701, Korea
4Present address: National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-8506, Japan
5Present address: Ocean Research Institute, The University of Tokyo, 1-15-1 Minamidai, Nakano, Tokyo 164-8639, Japan
*Corresponding author. Email:

ABSTRACT: Epilithic bacterial communities play a major role in biogeochemical cycles of rivers; however, distributional patterns and controls of epilithic communities remain unclear. The objective of the present study was to examine possible environmental factors that affect longitudinal distributional patterns of epilithic bacterial communities in 2 rivers (Yasu and Ado Rivers) draining the Lake Biwa basin, Japan. Phylogenetic analyses were conducted using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes and fluorescence in situ hybridization (FISH) with oligonucleotide probes targeted to small subunit rRNA. Non-metric multidimensional scaling and canonical correspondence analysis of the DGGE profile indicated that a clear shift in community composition occurred at the middle reach of the Yasu River. This shift was most closely related to variation in the nitrogen stable isotope ratio (δ15N) of epilithic materials (BIOENV analysis, ρw = 0.512), which is an indicator of the extent of anthropogenic nitrogen loading. The concentration of dissolved organic carbon (DOC) also affected community composition (ρw = 0.510 for the combination of δ15N and DOC). The longitudinal pattern of the DGGE profile was less evident in the Ado River. In both rivers, FISH results indicated that Alphaproteobacteria and Betaproteobacteria generally accounted for a large fraction (37 to 71%) of total bacterial abundance, indicating that species and clones affiliated with a limited number of the major phylogenetic groups occupy diverse epilithic habitats. Our results are consistent with the hypothesis that nutrients and organic matter of anthropogenic origin are major determinants of epilithic bacterial community structure in rivers.


KEY WORDS: Bacterial community · Epilithic biofilm · River · Stable isotopes · Nutrients · Dissolved organic carbon · Denaturing gradient gel electrophoresis · Fluorescence in situ hybridization


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Cite this article as: Kobayashi Y, Kim C, Yoshimizu C, Kohzu A, Tayasu I, Nagata T (2009) Longitudinal changes in bacterial community composition in river epilithic biofilms: influence of nutrients and organic matter. Aquat Microb Ecol 54:135-152. https://doi.org/10.3354/ame01258

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