Comparative approach to capture bacterial diversity of coastal waters |
| |
Authors: | Hyunsoo Na Ok-Sun Kim Seok-Hwan Yoon Yunmin Kim Jongsik Chun |
| |
Institution: | 1.Center for Geomicrobiology,University of Aarhus,?rhus C,Denmark;2.School of Biological Sciences,Seoul National University,Seoul,Republic of Korea;3.Division of Life Sciences,Korea Polar Research Institute,Incheon,Republic of Korea |
| |
Abstract: | Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done
to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent
techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected
from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer
FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas
the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved,
92.1 % of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment,
and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed
a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By
directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of
the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison
of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage,
we suggest choosing the approach after carefully examining the scientific questions being asked. |
| |
Keywords: | |
本文献已被 PubMed SpringerLink 等数据库收录! |
|