Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa trough - PubMed (original) (raw)

. 2010 Feb;76(4):1198-211.

doi: 10.1128/AEM.00924-09. Epub 2009 Dec 18.

Hanako Oida, Miwako Nakaseama, Ayako Kosaka, Satoru B Ohkubo, Toru Kikuchi, Hiromi Kazama, Shoko Hosoi-Tanabe, Ko-Ichi Nakamura, Masataka Kinoshita, Hisako Hirayama, Fumio Inagaki, Urumu Tsunogai, Jun-Ichiro Ishibashi, Ken Takai

Affiliations

Archaeal diversity and distribution along thermal and geochemical gradients in hydrothermal sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa trough

Takuro Nunoura et al. Appl Environ Microbiol. 2010 Feb.

Abstract

A variety of archaeal lineages have been identified using culture-independent molecular phylogenetic surveys of microbial habitats occurring in deep-sea hydrothermal environments such as chimney structures, sediments, vent emissions, and chemosynthetic macrofauna. With the exception of a few taxa, most of these archaea have not yet been cultivated, and their physiological and metabolic traits remain unclear. In this study, phylogenetic diversity and distribution profiles of the archaeal genes encoding small subunit (SSU) rRNA, methyl coenzyme A (CoA) reductase subunit A, and the ammonia monooxygenase large subunit were characterized in hydrothermally influenced sediments at the Yonaguni Knoll IV hydrothermal field in the Southern Okinawa Trough. Sediment cores were collected at distances of 0.5, 2, or 5 m from a vent emission (90 degrees C). A moderate temperature gradient extends both horizontally and vertically (5 to 69 degrees C), indicating the existence of moderate mixing between the hydrothermal fluid and the ambient sediment pore water. The mixing of reductive hot hydrothermal fluid and cold ambient sediment pore water establishes a wide spectrum of physical and chemical conditions in the microbial habitats that were investigated. Under these different physico-chemical conditions, variability in archaeal phylotype composition was observed. The relationship between the physical and chemical parameters and the archaeal phylotype composition provides important insight into the ecophysiological requirements of uncultivated archaeal lineages in deep-sea hydrothermal vent environments, giving clues for approximating culture conditions to be used in future culturing efforts.

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Figures

FIG. 1.

FIG. 1.

Physical and chemical characterization of sediment cores 816M1, 760M3, and 763MW. Temperatures and concentrations of silica (A), concentrations of sulfate and methane (B), concentrations of ammonium and carbon dioxide (C), and carbon stable isotopic ratio of methane and carbon dioxide (D) in interstitial waters from three cores are shown. Concentrations of these gases and ions in the vent emission (90°C) from the abyss vent were as follows: CH4, 5,600 μmol kg−1; SO42−, 24.1 mmol liter−1; SiO2, 2.63 mmol liter−1; NH4+, 1.05 mmol liter−1; CO2, 93.4 mmol kg−1; δ13CCH4, −24.2 ‰; δ13CCO2, −9.1 ‰.

FIG. 2.

FIG. 2.

Relationship between distance from the vent emission and the SiO2, CO2, and CH4 concentrations in water samples from sediment cores. Dotted lines indicate the potential dilution rate presumed from SiO2 concentrations.

FIG. 3.

FIG. 3.

Copy numbers of total prokaryotic and archaeal SSU rRNA genes, mcrA from ANME group c-d, and archaeal amoA determined by quantitative PCR.

FIG. 4.

FIG. 4.

Distributions of Bacteria shown by SSU rRNA gene clone analysis in hydrothermal sediments, ISCS, vent emission, and deep-seawater from the Yonaguni Knoll IV hydrothermal field. Numbers of sequenced clones in each clone library are shown in parentheses. Black dots indicate in situ temperatures of sediments. Abbreviations: V, N, and R in Epsilonproteobacteria indicate families Thiovulgaceae, Nautiliaceae, and Thioreductoraceae, respectively.

FIG. 5.

FIG. 5.

Distributions of Archaea shown by SSU rRNA gene clone analysis in hydrothermal sediments, ISCS, vent emission, and deep-seawater in the Yonaguni Knoll IV hydrothermal field. Black dots indicate in situ temperatures of sediments. Numbers of sequenced clones in each clone library are shown in parentheses. MGI subgroups are shown using acronyms (see Fig. 6E).

FIG. 6.

FIG. 6.

SSU rRNA gene phylogenetic analysis of Archaea detected in hydrothermal sediments, ISCS, vent emission, and deep seawater from the Yonaguni Knoll IV hydrothermal field. Phylogenetic trees of Euryarchaeota (A), Crenarchaeota and deeply branching Archaea (B), Thermoprotei (C), MCG (D), and MG I (E) are based on the neighbor-joining method with 434, 424, 661, 737, and 757 homologous positions, respectively. Numbers indicate bootstrap values from 100 trials. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Bar, two substitutions per 100 nucleotides.

FIG. 6.

FIG. 6.

SSU rRNA gene phylogenetic analysis of Archaea detected in hydrothermal sediments, ISCS, vent emission, and deep seawater from the Yonaguni Knoll IV hydrothermal field. Phylogenetic trees of Euryarchaeota (A), Crenarchaeota and deeply branching Archaea (B), Thermoprotei (C), MCG (D), and MG I (E) are based on the neighbor-joining method with 434, 424, 661, 737, and 757 homologous positions, respectively. Numbers indicate bootstrap values from 100 trials. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Bar, two substitutions per 100 nucleotides.

FIG. 6.

FIG. 6.

SSU rRNA gene phylogenetic analysis of Archaea detected in hydrothermal sediments, ISCS, vent emission, and deep seawater from the Yonaguni Knoll IV hydrothermal field. Phylogenetic trees of Euryarchaeota (A), Crenarchaeota and deeply branching Archaea (B), Thermoprotei (C), MCG (D), and MG I (E) are based on the neighbor-joining method with 434, 424, 661, 737, and 757 homologous positions, respectively. Numbers indicate bootstrap values from 100 trials. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Bar, two substitutions per 100 nucleotides.

FIG. 7.

FIG. 7.

(A) Phylogenetic analysis of archaeal amoA gene detected in deep seawater and sediments in the Yonaguni Knoll IV hydrothermal field using the neighbor-joining method with 485 homologous positions of nucleotides. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Bar, two substitutions per 100 nucleotides. (B) Distribution of archaeal amoA gene in deep seawater and sediments from the Yonaguni Knoll IV hydrothermal field. Numbers of sequenced clones in each clone library are shown in parentheses.

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