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

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 (C1) 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 * 104 to 3 * 105 molecules of mxaF 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.