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

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 (Hha I, Rsa I and Msp I) 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.

Bacterial diversity in deep Mediterranean sediments: relationship with the active bacterial fraction and substrate availability

“…(2001), which found from 27 to 73 TRFs. Both our study and the work by Urakawa et al . (2001) observed that the distribution of bacterial diversity was independent from water depth, thus suggesting that pressure does not represent a key driver controlling the overall ribotype abundance.…”

“…The top 1 cm of the sediment of all deep-sea stations revealed the dominance of the same ribotypes. This is consistent with results reported by Urakawa et al . (2001), who found few numerically important TRFs (such as 44, 60, 81 and 100 bp) to be present in all surface sediments investigated.…”

“…High values of deep‐sea benthic bacterial diversity, estimated using T‐RFLP technique, have been also reported in the Tokio Bay, at depths ranging from 1133 to 4023 m by Urakawa et al . (2001), which found from 27 to 73 TRFs.…”

Characterization of depth-related changes and site-specific differences of microbial communities in marine sediments using quinone profiles

“…Additionally, the relative abundance of K 1 was greater than that of PQ‐9 in some marine sediment samples, while PQ‐9 constantly predominated in the lake sediment samples 11 . The photosynthetic quinones detected in the deep‐sea sediments were considered to be vertically transported in the water column 31,32 . Boetius et al 33 .…”

Microbial diversity in a Pacific Ocean transect from the Arctic to Antarctic circles

“…Following digestion with restriction endonucleases, variably sized terminal fragments can be differentiated with high resolution (±1 base) through use of an automated DNA sequencer allowing researchers to generate 'fingerprints' of complex microbial communities (Liu et al 1997). This readily applied technique has been shown to be effective in the comparison of microbial assemblages in various marine and terrestrial environments (Urakawa et al 2001, Mummey & Stahl 2003, Gomez et al 2004). Both prokaryotic and eukaryotic diversity have been documented in specific oceanic regions, but not on global scales.…”