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Chapter 13 : Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments

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Abstract:

This chapter focuses on studies of the microbial diversity in deep-sea methane-impacted sediments using culture-independent procedures. It discusses sulfur and carbon cycling ecosystems in chemosynthetic pathways which are independent of solar-power-dependent energy-generating systems. Microbial diversity studies in deep-sea sediments have been performed at depths ranging from ~1,000 m, in Sagami Bay, to ~11,000 m, in the Mariana Trench Challenger Deep. To study the different cold-seep microbial ecosystems present between the Japan Trench land slope and the Nankai Trough, the microbial diversity of Nankai Trough cold-seep sites at different depths was investigated and correlations were sought between the microbial communities and their geological settings. Methylotrophs are a group of bacteria which can utilize methane (methanotrophs) and/or a variety of other one-carbon (C) compounds more reduced than formic acid, such as methanol and methylated amines, as sole carbon and energy sources. The levels of methylotrophs in the sediments of the tropical West Pacific Warm Pool (WP) were semiquantified by quantitative competitive PCR. It was found that the WP contained around 3 * 10 to 3 * 10 molecules of gene copy per gram of sediment. Using this method, the distribution and abundance of methylotrophs in deep-sea sediments from the West Pacific WP were compared with those in east and middle Pacific deep-sea sediments, seashore sediments, and flower garden and rice field soils.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13

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Microbial Ecology
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Bacteria and Archaea
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Restriction Fragment Length Polymorphism
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Figures

Image of Figure 1.
Figure 1.

Comparison of the microbial abundance of the Japan Trench cold-seep sediments at different depths (JT58, 5,791 m; JT64, 6,367 m; and JT75, 7,434 m) calculated from the numbers of 16S rRNA gene clones. (A) Bacterial diversity; (B) archaeal diversity.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 2.
Figure 2.

t-RFLP profiles of bacterial (A) and archaeal (B) community structures of the NT06, NT20, and NT33 sites. γ,δ, and ε indicate the corresponding proteobacterial groups. SYM, symbiotic bacteria related to SOx; Met, methanogenic archaea; Uk, unknown. The lengths of fragments ( axis) and relative fluorescence intensities of peaks ( axis) are also displayed.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 3.
Figure 3.

t-RFLP profiles of bacterial (A) and archaeal (B) community structures of the SBC and SBM. Abbreviations are the same as in Fig. 2 .

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 4.
Figure 4.

Comparison of t-RFLP profiles of bacterial (A) and archaeal (B) communities between the microbial mats at the M1 and M2 sites. Abbreviations are the same as in Fig. 2 .

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 5.
Figure 5.

Sulfur and carbon cycling ecosystems within the microbial community in the cold-seep environment.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 6.
Figure 6.

Phylogenetic tree constructed based on deduced partial MxaF amino acid sequences. The MxaF sequences retrieved from the sediment of tropical West Pacific WP and from the cultured representative methylotrophs, including type I and type II methanotrophs, are involved in the tree construction. Only bootstrap values above 90 from 1,000 replicates are shown. The scale bar represents 0.05 substitution per amino acid site. The environmental clones from the Pacific WP sediment are designated by “wp”; the numbers in parentheses are the numbers of clones with identical sequences in the 90 sequenced clones.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 7.
Figure 7.

Phylogenetic tree constructed based on 16S rRNA gene sequences of archaea. Archaeal 16S rRNA gene clones retrieved from the Pacific WP sediments were named AW. Nine A clones together with relative clones in the data bank were used for phylogenetic tree construction. The phylogenetic tree was constructed from a matrix by least-squares distance matrix analysis and the neighbor-joining method using the DNAMAN program. One thousand trials of bootstrap analysis were used to provide confident estimates for phylogenetic tree topologies. Only bootstrap values above 50 are shown. The scale bar represents 0.05 substitution per nucleic acid site.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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Image of Figure 8.
Figure 8.

Phylogenetic tree showing the relationship of WPA and related clones and strains. Archaeal 16S rRNA gene clones retrieved by PCR using primers ANMEF and 907R from the Pacific WP sediment were named WPA. Fifteen sequences representing 15 different RFLP types of WPA and 16S rRNA gene sequences of reference clones or strains in the data bank were used for dendrogram construction. The phylogenetic tree was constructed from a matrix by least-squares distance matrix analysis and the neighbor-joining method using the DNAMAN program, and 1,000 trials of bootstrap analysis were used to provide confident estimates for phylogenetic tree topologies. Only bootstrap values above 50 are shown. The scale bar represents 0.05 substitution per nucleic acid site.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13
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