- Flavivirga spongiicola sp. nov. and Flavivirga abyssicola sp. nov., Isolated from Marine Environments
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Sung-Hyun Yang , Mi-Jeong Park , Hyun-Myung Oh , Yeong-Jun Park , Kae Kyoung Kwon
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J. Microbiol. 2024;62(1):11-19. Published online February 6, 2024
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DOI: https://doi.org/10.1007/s12275-023-00102-z
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 Abstract
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Two novel Gram-stain-negative, strictly-aerobic, rod-shaped (1.2 ± 3.4 μm × 0.3 ± 0.7 μm), and non-motile marine bacterial
species, designated MEBiC05379T
and MEBiC07777T,
were isolated from a marine sponge Pseudaxinella sp. in Gangneung
City and deep-sea sediments of the Ulleung basin in the East Sea of Korea, respectively. The 16S rRNA gene sequence
analysis revealed high levels of similarities between these strains and members of the genus Flavivirga (97.0–98.4% sequence
identities). Both novel strains revealed as mesophilic, neutrophilic in pH and slightly halophilic. Similar to those of other Flavivirga
members, the primary cellular fatty acids of both strains were iso-C15:0, iso-C15:1 G, iso-C15:03-OH, and iso-C17:0 3-OH,
with MEBiC05379T
and MEBiC07777T
containing relatively higher proportions of C12:
0 and summed feature 3 (
C16:1ω7c
and/or C16:
1ω6c). In both taxa, the major isoprenoid quinone was MK-6. The DNA G + C contents of MEBiC05379T
and
MEBiC07777T
genomes were 32.62 and 32.46 mol%, respectively. Compared to other members of Flavivirga, both strains
exhibited similar DNA G + C ratio and fatty acids pattern, yet enzyme expression and carbon sources utilization pattern were
different. Genomes of the genus Flavivirga showed enzyme preferences to fucoidan and sulfated galactans. Considering the
monophyly rule, AAI values delineate the genus Flavivirga from adjacent genera calculated to be 76.0–78.7%. Based on
the phenotypic, genomic and biochemical data, strains for MEBiC05379T
and MEBiC07777T
thus represent two novel species
in the genus Flavivirga, for which the names Flavivirga spongiicola sp. nov. (
MEBiC05379T [= KCTC 92527
T = JCM
16662
T]), and Flavivirga abyssicola sp. nov. (
MEBiC07777T [= KCTC 92563
T = JCM 36477
T]) are proposed.
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Citations
Citations to this article as recorded by  - Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef - Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - Optimization of Culture Medium for the Production of an Exopolysaccharide (p-CY02) with Cryoprotective Activity by Pseudoalteromonas sp. RosPo-2 from the Antarctic Sea
Pilsung Kang, Sung Jin Kim, Ha Ju Park, Il Chan Kim, Se Jong Han, Joung Han Yim
Journal of Microbiology and Biotechnology.2024; 34(5): 1135. CrossRef
- Crystal structure of the phage-encoded N-acetyltransferase in complex with acetyl-CoA, revealing a novel dimeric arrangement
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Nayeon Ki , Inseong Jo , Yongseong Hyun , Jinwook Lee , Nam-Chul Ha , Hyun-Myung Oh
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J. Microbiol. 2022;60(7):746-755. Published online July 4, 2022
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DOI: https://doi.org/10.1007/s12275-022-2030-2
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73
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Abstract
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Bacteriophages employ diverse mechanisms to facilitate the
proliferation of bacteriophages. The Salmonella-infecting
phage SPN3US contains a putative N-acetyltransferase, which
is widely found in bacteriophages. However, due to low sequence
similarity to the N-acetyltransferases from bacteria
and eukaryotic cells, the structure and function of phage-encoded
acetyltransferases are mainly unknown. This study
determines the crystal structure of the putative N-acetyltransferase
of SPN3US in complex with acetyl-CoA. The crystal
structure showed a novel homodimeric arrangement stabilized
by exchanging the C-terminal α-helix within the dimer.
The following biochemical analyses suggested that the phageencoded
acetyltransferase might have a very narrow substrate
specificity. Further studies are required to reveal the biochemical
activity, which would help elucidate the interaction
between the phage and host bacteria in controlling pathogenic
bacteria.
-
Citations
Citations to this article as recorded by - Characteristics of the smallest brucellaphage with strong lytic ability
Hongbaiyu Liu, Youhong Zhong, Zhihong Zhang, Kehong Xu, Chunpeng Mao, Qiuju Yang, Lihua Yang, Binbin Yu, Ying Long, Xinyu Qin, Liyuan Shi, Sheng Chang, Yuanying Shen, Peng Wang
Frontiers in Veterinary Science.2025;[Epub] CrossRef - Posttranslational modifications in bacteria during phage infection
Hannelore Longin, Nand Broeckaert, Vera van Noort, Rob Lavigne, Hanne Hendrix
Current Opinion in Microbiology.2024; 77: 102425. CrossRef
- Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea
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Sung-Hyun Yang , Hyun-Myung Oh , Mi-Jeong Park , Dongil Jang , Kae Kyoung Kwon
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J. Microbiol. 2022;60(1):11-17. Published online December 29, 2021
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DOI: https://doi.org/10.1007/s12275-022-1468-6
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85
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2
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Abstract
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A Gram-stain-negative, aerobic, rod-shaped (0.3–0.5 × 1.0–
1.9 μm), non-motile marine bacterium designated as ALE3EIT
was isolated from a saline volcanic rock aquifer (lava seawater)
on Jeju Island, Republic of Korea. The 16S rRNA gene
sequence analysis revealed that strain ALE3EIT showed high
similarity to ‘Altibacter lentus’ JLT2010T (97.2%), followed by
Marixanthomonas ophiurae KMM 3046T (94.5%). Growth
was observed at 10–41°C (optimum, 30°C), at pH 6.0–8.5
(optimum, pH 7.5) and at 0.5–8% (optimum, 4.0%) NaCl.
The predominant cellular fatty acids were iso-C15:0 (23.5%),
iso-C16:0 (10.2%), iso-C16:0 3OH (10.5%), and iso-C17:0 3OH
(16.8%). The DNA G + C contents was 40.4 mol%. The major
respiratory quinone was MK-6. The major polar lipids were
determined to be phosphatidylethanolamine, two unidentified
glycolipids, and two unidentified aminolipids. Several phenotypic
characteristics such as production of acetoin, activities
of arginine dihydrolase and acid phosphatase, and utilization
pattern of carbon sources differentiate strain ALE3EIT
from ‘A. lentus’ JLT2010T. Activities of the lipase, trypsin, α-
chymotrypsin and gelatinase and utilization pattern of carbon
sources differentiate strain ALE3EIT from M. ophiurae
KMM 3046T. The genome of strain ALE3EIT is 3.0 Mbp long
and its ANI and AAI values against ‘A. lentus’ JLT2010T were
76.58 and 72.76, respectively, however, AAI values against
members in other genera were lower than 72%. The phylogenomic
tree inferred by PhyloPhlAn clearly differentiated
the strain ALE3EIT together with strain JLT2010T from other
genera in the Falvobacteriaceae. This polyphasic taxonomic
data indicates that strain ALE3EIT should be identified as a
novel species in the genus ‘Altibacter’, however, the name
has not been validated. Therefore, the strain is classified as a
novel genus and is proposed as Constantimarinum furrinae
gen. nov., sp. nov. The type strain is ALE3EIT (= KCCM
43303T = JCM 33022T).
-
Citations
Citations to this article as recorded by - Comparison of the anti-inflammatory effects of carotenoids-rich product from microalgal mass-cultured between natural seawater and magma seawater
Jayeon Cheon, Eun-A Kim, Nalae Kang, Taeho Kim, Lei Wang, Soo-Jin Heo, Seon-Heui Cha
Biocatalysis and Agricultural Biotechnology.2024; 62: 103420. CrossRef - Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef
- Isolation, cultivation, and genome analysis of proteorhodopsincontaining SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322
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Junhak Lee , Kae Kyoung Kwon , Seung-Il Lim , Jaeho Song , Ah Reum Choi , Sung-Hyun Yang , Kwang-Hwan Jung , Jung-Hyun Lee , Sung Gyun Kang , Hyun-Myung Oh , Jang-Cheon Cho
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J. Microbiol. 2019;57(8):676-687. Published online June 14, 2019
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DOI: https://doi.org/10.1007/s12275-019-9001-2
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82
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11
Crossref
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Abstract
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Strain IMCC1322 was isolated from a surface water sample
from the East Sea of Korea. Based on 16S rRNA analysis,
IMCC1322 was found to belong to the OCS28 sub-clade of
SAR116. The cells appeared as short vibrioids in logarithmicphase
culture, and elongated spirals during incubation with
mitomycin or in aged culture. Growth characteristics of strain
IMCC1322 were further evaluated based on genomic information;
proteorhodopsin (PR), carbon monoxide dehydrogenase,
and dimethylsulfoniopropionate (DMSP)-utilizing
enzymes. IMCC1322 PR was characterized as a functional
retinylidene protein that acts as a light-driven proton pump
in the cytoplasmic membrane. However, the PR-dependent
phototrophic potential of strain IMCC1322 was only observed
under CO-inhibited and nutrient-limited culture conditions.
A DMSP-enhanced growth response was observed in addition
to cultures grown on C1 compounds like methanol, formate,
and methane sulfonate. Strain IMCC1322 cultivation
analysis revealed biogeochemical processes characteristic of
the SAR116 group, a dominant member of the microbial community
in euphotic regions of the ocean. The polyphasic taxonomy
of strain IMCC1322 is given as Candidatus Puniceispirillum
marinum, and was confirmed by chemotaxonomic
tests, in addition to 16S rRNA phylogeny and cultivation
analyses.
-
Citations
Citations to this article as recorded by - Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322
Ji Hyen Lee, Hyun-Myung Oh
Journal of Microbiology.2024; 62(4): 297. CrossRef - Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses
Stephen C. Hardies, Byung Cheol Cho, Gwang Il Jang, Zhiqing Wang, Chung Yeon Hwang
Viruses.2023; 15(7): 1475. CrossRef - Seasonal niche differentiation among closely related marine bacteria
Adrià Auladell, Albert Barberán, Ramiro Logares, Esther Garcés, Josep M Gasol, Isabel Ferrera
The ISME Journal.2022; 16(1): 178. CrossRef - Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef - Towards culturing the microbe of your choice
J. Cameron Thrash
Environmental Microbiology Reports.2021; 13(1): 36. CrossRef - Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics
Atsushi Kobiyama, Jonaira Rashid, Md. Shaheed Reza, Yuri Ikeda, Yuichiro Yamada, Toshiaki Kudo, Nanami Mizusawa, Saki Yanagisawa, Daisuke Ikeda, Shigeru Sato, Takehiko Ogata, Kazuho Ikeo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Sat
Scientific Reports.2021;[Epub] CrossRef - Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater
Shan-Hui Li, Jaeho Song, Ilnam Kang, Juchan Hwang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(6): 463. CrossRef - Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea
Paul A. Steiner, Javier Geijo, Eduard Fadeev, Aleix Obiol, Eva Sintes, Thomas Rattei, Gerhard J. Herndl
Frontiers in Microbiology.2020;[Epub] CrossRef - High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(11): 893. CrossRef - Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy
Konstantinos T. Konstantinidis, Ramon Rosselló‐Móra, Rudolf Amann
Environmental Microbiology.2020; 22(3): 819. CrossRef - Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation
Michael W. Henson, V. Celeste Lanclos, David M. Pitre, Jessica Lee Weckhorst, Anna M. Lucchesi, Chuankai Cheng, Ben Temperton, J. Cameron Thrash, Robert M. Kelly
Applied and Environmental Microbiology.2020;[Epub] CrossRef
- Comparative genome analysis of the Flavobacteriales bacterium strain UJ101, isolated from the gut of Atergatis reticulatus
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Jhung-Ahn Yang , Sung-Hyun Yang , Junghee Kim , Kae Kyoung Kwon , Hyun-Myung Oh
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J. Microbiol. 2017;55(7):583-591. Published online June 30, 2017
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DOI: https://doi.org/10.1007/s12275-017-7172-2
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63
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Abstract
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Here we report the comparative genomic analysis of strain
UJ101 with 15 strains from the family Flavobacteriaceae,
using the CGExplorer program. Flavobacteriales bacterium
strain UJ101 was isolated from a xanthid crab, Atergatis reticulatus,
from the East Sea near Korea. The complete genome
of strain UJ101 is a 3,074,209 bp, single, circular chromosome
with 30.74% GC content. While the UJ101 genome
contains a number of annotated genes for many metabolic
pathways, such as the Embden–Meyerhof pathway, the pentose
phosphate pathway, the tricarboxylic acid (TCA) cycle,
and the glyoxylate cycle, genes for the Entner-Douddoroff
pathway are not found in the UJ101 genome. Overall, carbon
fixation processes were absent but nitrate reduction and
denitrification pathways were conserved. The UJ101 genome
was compared to genomes from other marine animals (three
invertebrate strains and 5 fish strains) and other marine animal-
derived genera. Notable results by genome comparisons
showed that UJ101 is capable of denitrification and nitrate
reduction, and that biotin-thiamine pathway participation
varies among marine bacteria; fish-dwelling bacteria, freeliving
bacteria, invertebrate-dwelling bacteria, and strain
UJ101. Pan-genome analysis of the 16 strains in this study
included 7,220 non-redundant genes that covered 62% of
the pan-genome. A core-genome of 994 genes was present
and consisted of 8% of the genes from the pan-genome. Strain
UJ101 is a symbiotic hetero-organotroph isolated from xanthid
crab, and is a metabolic generalist with nitrate-reducing
abilities but without the ability to synthesize biotin. There
is a general tendency of UJ101 and some fish pathogens to
prefer thiamine-dependent glycolysis to gluconeogenesis. Biotin
and thiamine auxotrophy or prototrophy may be used
as important markers in microbial community studies.
-
Citations
Citations to this article as recorded by - The hepatopancreas microbiome of velvet crab, Necora puber
Signe Martin, Cindy Smith, Kelly Stewart, William Barr, Deborah Cheslett, Ian O'Connor, Fiona Swords, Umer Zeeshan Ijaz, Katie O'Dwyer
Environmental Microbiology Reports.2024;[Epub] CrossRef - Advanced Treatment of Digested Restaurant Wastewater Using a Combination of Anaerobic/OxicUnit, Fenton, and a Biological Aerated Filter in Pilot-Scale Treatment
Jiang Yin, Jianhong Jiang, Qingchang Tang
Water, Air, & Soil Pollution.2023;[Epub] CrossRef - Climate warming, but not Spartina alterniflora invasion, enhances wetland soil HONO and NOx emissions
Dianming Wu, Lingling Deng, Yihua Sun, Ruhai Wang, Li Zhang, Rui Wang, Yaqi Song, Zhiwei Gao, Haroon Haider, Yue Wang, Lijun Hou, Min Liu
Science of The Total Environment.2022; 823: 153710. CrossRef - Climate Warming Enhances Wetland Soil Hono and Nox Emissions, Induces Shifts in Soil Fungal Community, and Decreases Soil Abundance of Nitrogen Cycling Genes
Dianming Wu, Lingling Deng, Yihua Sun, Ruhai Wang, Li Zhang, Rui Wang, Yaqi Song, Zhiwei Gao, Haroon Haider, Yue Wang, Lijun Hou, Min Liu
SSRN Electronic Journal .2021;[Epub] CrossRef -
Changes of the intestinal microbiota along the gut of Japanese Eel (
Anguilla japonica
)
P. Zhu, M.K.‐S. Wong, X. Lin, T.F. Chan, C.K.C. Wong, K.P. Lai, W.K.F. Tse
Letters in Applied Microbiology.2021; 73(4): 529. CrossRef - Out From the Shadows – Resolution of the Taxonomy of the Family Cryomorphaceae
John P. Bowman
Frontiers in Microbiology.2020;[Epub] CrossRef
- Antarcticimonas flava gen. nov., sp. nov., Isolated from Antarctic Coastal Seawater
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Seung-Jo Yang , Hyun-Myung Oh , Sangyun Chung , Jang-Cheon Cho
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J. Microbiol. 2009;47(5):517-523. Published online October 24, 2009
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DOI: https://doi.org/10.1007/s12275-009-0225-4
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48
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Abstract
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A marine bacterium, designated IMCC3175T, was isolated from a seawater sample collected off the Antarctic coast. The strain was Gram-negative, obligately aerobic, carotenoid pigment-containing, and rod-shaped bacterium that divided by binary fission. As determined by 16S rRNA gene sequence comparisons, the most
closely related genera were Formosa (92.9~93.3%), Bizionia (91.6~93.2%), Gaetbulibacter (91.5~92.8%), Sediminibacter (92.7%), Yeosuana (92.6%), Subsaximicrobium (92.1~92.2%), and Gillisia (89.5~92.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a monophyletic clade together with the genera Sediminibacter and Subsaximicrobium but represented an independent phyletic line in this clade of the family Flavobacteriaceae. The DNA G+C content of the strain was 37.3 mol%. The
major respiratory quinone was MK-6 and the predominant cellular fatty acids were C16:1 ω7c and/or iso-C15:0 2-OH (12.8%), anteiso-C15:0 (9.4%), and iso-C16:1 (9.4%). Low 16S rRNA gene sequence similarity, formation of a distinct phylogenetic branch, and several phenotypic characteristics, including a narrow range of temperature and salinity for growth, differentiated strain IMCC3175T from other related genera in the family Flavobacteriaceae. Therefore the name Antarcticimonas flava gen. nov., sp. nov. is proposed, with strain IMCC3175T (=KCCM 42713T =NBRC 103398T) as the type strain.
- Identification and Characterization of Metagenomic Fragments from Tidal Flat Sediment
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Byung Kwon Kim , Yoon-Dong Park , Hyun-Myung Oh , Jongsik Chun
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J. Microbiol. 2009;47(4):402-410. Published online September 9, 2009
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DOI: https://doi.org/10.1007/s12275-009-0099-5
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52
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Abstract
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Phylogenetic surveys based on cultivation-independent methods have revealed that tidal flat sediments are environments with extensive microbial diversity. Since most of prokaryotes in nature cannot be easily cultivated under general laboratory conditions, our knowledge on prokaryotic dwellers in tidal flat sediment is mainly based on the analysis of metagenomes. Microbial community analysis based on the 16S rRNA gene and other phylogenetic markers has been widely used to provide important information on the role of microorganisms, but it is basically an indirect means, compared with direct sequencing of metagenomic DNAs. In this study, we applied a sequence-based metagenomic approach to characterize uncultivated prokaryotes from tidal flat sediment. Two large-insert genomic libraries based on fosmid were constructed from tidal flat metagenomic DNA. A survey based on end-sequencing of selected fosmid clones resulted in the identification of clones containing 274 bacterial and 16 archaeal homologs in which majority were of proteobacterial origins. Two fosmid clones containing large metagenomic DNAs were completely sequenced using the shot- gun method. Both DNA inserts contained more than 20 genes encoding putative proteins which implied their ecological roles in tidal flat sediment. Phylogenetic analyses of evolutionary conserved proteins indicate that these clones are not closely related to known prokaryotes whose genome sequence is known, and genes in tidal flat may be subjected to extensive lateral gene transfer, notably between domains Bacteria and Archaea. This is the first report demonstrating that direct sequencing of metagenomic gene library is useful in underpinning the genetic makeup and functional roles of prokaryotes in tidal flat sediments.
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