Abstract
We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E > 1 × 10 -2) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.
| Original language | English |
|---|---|
| Pages (from-to) | 900-908 |
| Number of pages | 9 |
| Journal | Marine Biotechnology |
| Volume | 13 |
| Issue number | 5 |
| DOIs | |
| Publication status | Published - 2011 Oct |
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Keywords
- Comparative genomics
- Deep sea
- Environmental DNA
- Metagenomics
- Ultra-micro-sized organisms
ASJC Scopus subject areas
- Aquatic Science
- Biotechnology
Cite this
Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid. / Nakai, Ryosuke; Abe, Takashi; Takeyama, Haruko; Naganuma, Takeshi.
In: Marine Biotechnology, Vol. 13, No. 5, 10.2011, p. 900-908.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Metagenomic Analysis of 0.2-μm-Passable Microorganisms in Deep-Sea Hydrothermal Fluid
AU - Nakai, Ryosuke
AU - Abe, Takashi
AU - Takeyama, Haruko
AU - Naganuma, Takeshi
PY - 2011/10
Y1 - 2011/10
N2 - We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E > 1 × 10 -2) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.
AB - We pyrosequenced the bulk DNA extracted from microorganisms that passed through 0.2-μm-pore-size filters and trapped by 0.1-μm-pore-size filters in the hydrothermal fluid of the Mariana Trough. Using the 454-FLX sequencer, we generated 202,648 sequences with an average length of 173.8 bases. Functional profiles were assigned by the SEED Annotation Engine. In the metagenome of the 0.2-μm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as membrane transport, and multidrug-resistance efflux pumps classified as virulence, were dominant. There was a higher proportion of genes pertinent to the subsystem of membrane transport in our metagenomic library than in other oceanic and hydrothermal vent metagenomes. Genes associated with a RND-type efflux transporter for exogenous substances were specifically identified in the present study. After a comparative analysis with the genome of the known ultramicrobacterium Sphingopyxis alaskensis RB2256, we discovered 1,542 cases of significant hits (E > 1 × 10 -2) in our metagenome, and 1,172 of those were related to the DNA repair protein RadA. In this way, the microbial functional profile of 0.2-μm-passable fraction in the present study differs from oceanic metagenomes in the 0.2-μm-trapped fractions and hydrothermal vent metagenomes reported in previous research.
KW - Comparative genomics
KW - Deep sea
KW - Environmental DNA
KW - Metagenomics
KW - Ultra-micro-sized organisms
UR - http://www.scopus.com/inward/record.url?scp=80051666628&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=80051666628&partnerID=8YFLogxK
U2 - 10.1007/s10126-010-9351-6
DO - 10.1007/s10126-010-9351-6
M3 - Article
C2 - 21279410
AN - SCOPUS:80051666628
VL - 13
SP - 900
EP - 908
JO - Marine Biotechnology
JF - Marine Biotechnology
SN - 1436-2228
IS - 5
ER -