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

We characterized microbial communities from Japanese coastal sediments by u sing 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 (Sl: 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 automa ted DNA sequencer. The average fragment numbers (mean SD) estimated from th e 3 separate restriction analyses (Hhal, 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 hom ologs were found from S1. Major differences in the quinone profiles among s ampling sites were primarily related to the relative abundance of quinone h omologs, However, the difference in homolog number did not contribute to th e 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 rela ted to each other (13.9% divergence), but quinone profiling of Nankai Troug h 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 we re similar, but the relative abundance and physiological condition of the m icrobial populations was apparently different between Sagami Bay (S2 and S3 ) and Nankai Trough (S5), In this study, a combination of the methods T-RFL P and quinone profiling succeeded in characterizing the microbial community of marine sediments and it is likely that this approach will prove effecti ve in future analyses of microbial communities in marine sediments.