Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures |
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Authors: | Kiyotaka Takishita Naoji Yubuki Natsuki Kakizoe Yuji Inagaki Tadashi Maruyama |
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Institution: | (1) Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka Kanagawa, 237-0061, Japan;(2) Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba Ibaraki, 305-8572, Japan;(3) College of Bioresource Sciences, Nihon University, Fujisawa Kanagawa, 252-8510, Japan;(4) Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba Ibaraki, 305-8577, Japan |
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Abstract: | Recent culture-independent surveys of eukaryotic small-subunit ribosomal DNA (SSU rDNA) from many environments have unveiled
unexpectedly high diversity of microbial eukaryotes (microeukaryotes) at various taxonomic levels. However, such surveys were
most probably biased by various technical difficulties, resulting in underestimation of microeukaryotic diversity. In the
present study on oxygen-depleted sediment from a deep-sea methane cold seep of Sagami Bay, Japan, we surveyed the diversity
of eukaryotic rDNA in raw sediment samples and in two enrichment cultures. More than half of all clones recovered from the
raw sediment samples were of the basidiomycetous fungus Cryptococcus curvatus. Among other clones, phylotypes of eukaryotic parasites, such as Apicomplexa, Ichthyosporea, and Phytomyxea, were identified.
On the other hand, we observed a marked difference in phylotype composition in the enrichment samples. Several phylotypes
belonging to heterotrophic stramenopiles were frequently found in one enrichment culture, while a phylotype of Excavata previously
detected at a deep-sea hydrothermal vent dominated the other. We successfully established a clonal culture of this excavate
flagellate. Since these phylotypes were not identified in the raw sediment samples, the approach incorporating a cultivation
step successfully found at least a fraction of the “hidden” microeukaryotic diversity in the environment examined.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Cultivation Diversity Methane seep Microbial eukaryotes SSU rDNA |
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