Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling

Abstract

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 220:47-57 (2001) - doi:10.3354/meps220047 Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling Hidetoshi Urakawa*, Tsutomu Yoshida, Masahiko Nishimura, Kouichi Ohwada** Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan *Present address: Civil and Environmental Engineering, University of Washington, 201 More Hall, Seattle, Washington 98195-2700, USA. **Present address: Faculty of Environmental and symbiotic Sciences, Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto 862-8502, Japan. E-mail: ohwada@pu-kumamoto.ac.jp ABSTRACT: We characterized microbial communities from Japanese coastal sediments by using terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling. Surface sediments (0 to 2 cm) were collected from 5 different locations, Tokyo Bay (S1: water depth 15 m), Sagami Bay (S2: 1520 m; S3: 1133 m), Suruga Bay (S4: 1290 m), and Nankai Trough (S5: 4023 m). The length of terminal-restriction fragments (T-RFs) was estimated by an automated DNA sequencer. The average fragment numbers (mean ± SD) estimated from the 3 separate restriction analyses (HhaI, RsaI and MspI) were S1 = 74 ± 6.2, S2 = 28 ± 4.6, S3 = 27 ± 6.2, S4 = 73 ± 4.0, and S5 = 35 ± 2.1. Sixteen quinone homologs were detected from S2, S3, S4 and S5, while 17 homologs were found from S1. Major differences in the quinone profiles among sampling sites were primarily related to the relative abundance of quinone homologs. However, the difference in homolog number did not contribute to the change of profile in each sampling site. The appearance and disappearance of quinone homologs were only seen in minor components. Community profiles from T-RFLP analysis revealed that the microbial population in Sagami Bay (S2 and S3) and Nankai Trough (S5) were similar (16.8 to 25.8% divergence). On the other hand, sediments from Sagami Bay (S2 and S3) were closely related to each other (13.9% divergence), but quinone profiling of Nankai Trough sediment (S5) was not similar to those of Sagami Bay. It was assumed that this difference derived from different characteristics of the 2 techniques used. Thus, we found that the phylogenetic structures in S2, S3, and S5 were similar, but the relative abundance and physiological condition of the microbial populations was apparently different between Sagami Bay (S2 and S3) and Nankai Trough (S5). In this study, a combination of the methods T-RFLP and quinone profiling succeeded in characterizing the microbial community of marine sediments and it is likely that this approach will prove effective in future analyses of microbial communities in marine sediments. KEY WORDS: Microbial community · Marine sediment · Terminal-restriction fragment length polymorphism (T-RFLP) analysis · Quinone profiling Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 220. Online publication date: September 27, 2001 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2001 Inter-Research.