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

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.

Protistan community patterns within the brine and halocline of deep hypersaline anoxic basins in the eastern Mediterranean Sea

“…150-200 protistan clones (Fig. 1 A general overview of all sequences ( largely agrees with observed diversity and total diversity estimates of other molecular protistan diversity surveys in (anoxic) deep-sea environments (Edgcomb et al 2002;Stoeck and Epstein 2003;Stoeck et al 2006;Takishita et al 2007). This further supports the notion that our interface and brine libraries are not primarily reflections of detritus from the water column but at least to a large extent reflects indigenous protistan assemblages.…”

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

“…For example, MAST-9 was only abundant in anoxic samples (Supplementary Figure S5). Previous studies found MAST-9 associated to hydrothermal vents (Massana et al, 2004) as well as anoxic sea sediments (Takishita et al, 2005, Takishita et al, 2007. MAST-12 was also recovered from the anoxic layers of the Black Sea (Supplementary Figure S5), but it was also recovered from the oxic water column in the same as well as in other locations (for example, Oslo, Roscoff and others; Supplementary Figure S5).…”

“…Most MASTs branch near Bicosoecida, Blastocystis and Labyrinthulida (Figure 1), the earliest diverging stramenopile lineages (Riisberg et al, 2009;Tsui et al, 2009). After the initial description of MASTs, they have been regularly detected in diverse marine environmental surveys in different marine geographical areas around the world (for example, Richards and Bass, 2005;Takishita et al, 2005;Takishita et al, 2007;Not et al, 2008Not et al, , 2009Orsi et al, 2011). MAST groups are mostly composed of free-living bacterivorous flagellates, with some groups displaying algivorous preferences (MAST-6; Piwosz and Pernthaler, 2010) and other lineages being parasites (Gomez et al, 2011).…”

“…Different morphotypes of MAST-6 appear to have a large variability in their seasonal abundances (Piwosz and Pernthaler, 2010). Although most MAST groups seem to be planktonic (Massana et al, 2004), the groups MAST-9 and -12 appear to be associated to sediments, anoxic waters and/or deep-sea sediments (Massana et al, 2004;Takishita et al, 2005;Takishita et al, 2007).…”

Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor

“…Environmental molecular surveys have revolutionized our understanding of microbial systems (6). Phylogenetic surveys also have been applied successfully to study the community composition of eukaryotic microbes at several deep-sea sites (7)(8)(9)(10)(11)(12)(13)(14)(15)(16); however, to date, no study has addressed the phylogenetic diversity of eukaryotic microbial life of one of the largest habitats, covering over half of the Earth's surface: the abyssal plains.…”