Microbial Diversity in Sediments Collected from the Deepest Cold-Seep Area, the Japan Trench

Abstract

: The Japan Trench land slope at a depth of 6,400 m is the deepest cold-seep environment with Calyptogena communities. Sediment samples from inside and beside the Calyptogena communities were collected, and the microbial diversity in the sediment samples was studied by molecular phylogenetic techniques. From DNA extracted directly from the sediment samples, 16S rDNAs were amplified by the polymerase chain reaction method. The sequences of the amplified 16S rDNAs selected by restriction fragment length polymorphism analysis were determined and compared with sequences in DNA databases. The results showed that 33 different bacterial 16S rDNA sequences from the two samples analyzed fell into similar phylogenetic categories, the alpha-, gamma-, delta-, and varepsilon-subdivisions of Proteobacteria, Cytophaga, and gram-positive bacteria; some of the 16S rDNA sequences were common to both samples. delta- and varepsilon-Proteobacteria-related sequences were abundant in both sediments. These sequences are mostly related to sulfate-reducing or sulfur-reducing bacteria and epibionts, respectively. Eight different archaeal 16S rDNA sequences were cloned from the sediments. The majority of the archaeal 16S rDNA sequences clustered in Crenarchaeota and showed high similarities to marine group I archaeal rDNA. A Methanococcoides burtonii-related sequence obtained from the sediment clustered in the Euryarchaeota indicating that M. burtonii-related strains in the area of Calyptogena communities may contribute to production of methane in this environment. From these results, we propose a possible model of sulfur circulation within the microbial community and that of Calyptogena clams in the cold-seep environment.

Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California

“…Specifically, archaeal assemblages in the reference core from the 2893 m whalefall primarily consisted of marine group I (MGI) and marine benthic group B (MBGB), representing up to 98% and 27% of the libraries from 'reference' sediment, respectively (Table 2 and Figure 4). The dominant Crenarchaeota MGI phylotypes in both depth horizons within reference sediments were related to an uncultured archaeon from a fish gut (R33_10d_G7; van der Maarel et al, 1998) as well as an uncultured Crenarchaeote from sediments in the Japan Trench (R33_0s_B10; Li et al, 1999). These MGI phylotypes fell within the MGI-a microcluster, which contains both surface and deep-water taxa (Massana et al, 2000).…”

“…The majority of phylotypes recovered from 'reference' sediments (T769_PC55) were related to uncultured marine Crenarchaeota, including phylotypes associated with groups previously recovered from deep-sea sediments (Li et al, 1999;Vetriani et al, 1999;Knittel et al, 2005;Inagaki et al, 2006). Specifically, archaeal assemblages in the reference core from the 2893 m whalefall primarily consisted of marine group I (MGI) and marine benthic group B (MBGB), representing up to 98% and 27% of the libraries from 'reference' sediment, respectively (Table 2 and Figure 4).…”

Psychroserpens mesophilus sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae isolated from a young biofilm

“…Psychroserpens burtonensis, isolated from the Antarctic ice at Lake Burton (Bowman et al, 1997), is the only currently recognized member of the genus. In the last decade, several bacterial isolates have been reported as putative members of the genus Psychroserpens (Brinkmeyer et al, 2003;DeLong et al, 1993;Li et al, 1999) but have yet to be formally taxonomically characterized. We have isolated several bacteria belonging to the family Flavobacteriaceae from a young marine biofilm and herein characterize one of these, designated strain KOPRI 13649 T , as representing a novel member of the genus Psychroserpens.…”

Generation of Acid Mine Lakes Associated with Abandoned Coal Mines in Northwest Turkey

“…Microbial diversity of the sediment samples was determined by the 16S rDNA UARR polymerase chain reaction (PCR) method (Li et al 1999;Menekse 2012;Balci et al 2015). A pair of universal primers namely, pA-F (5 0 -AGA GTTTGATCCTGGCTCAG-3 0 ) and pH-R (5 0 -AAGGAGG TGATCCAGCCGCA-3 0 ) were used for amplification (Li et al 1999).…”

“…A pair of universal primers namely, pA-F (5 0 -AGA GTTTGATCCTGGCTCAG-3 0 ) and pH-R (5 0 -AAGGAGG TGATCCAGCCGCA-3 0 ) were used for amplification (Li et al 1999). PCR products were visualized by agarose gel (1 %) electrophoresis and purified by ROCHE High Pure PCR Product Purification Kit (Catalogue No.…”