1887

Abstract

Our newly designed primers were evaluated for the molecular analysis of specific groups of the gene encoding sulfide : quinone reductase (SQR) in sediment environments. Based on the phylogenetic analysis, we classified the sequences into six groups. PCR primers specific for each group were developed. We successfully amplified -like gene sequences related to groups 1, 2 and 4 from diverse sediments including a marine sediment (SW), a tidal flat (TS), a river sediment (RS) and a lake sediment (FW). We recovered a total of 82 unique phylotypes (based on a 95 % amino acid sequence similarity cutoff) from 243 individual -like gene sequences. Phylotype richness varied widely among the groups of -like gene sequences (group 1>group 2>group 4) and sediments (SW>TS>RS>FW). Most of the -like gene sequences were affiliated with the clade and were distantly related to the reference gene sequences from cultivated strains (less than ∼80 % amino acid sequence similarity). Unique -like gene sequences were associated with individual sediment samples in groups 1 and 2. This molecular tool has also enabled us to detect -like genes in a sulfur-oxidizing enrichment from marine sediments. Collectively, our results support the presence of previously unrecognized gene-containing micro-organisms that play important roles in the global biogeochemical cycle of sulfur.

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2008-10-01
2019-10-14
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Estimations of sequence diversity and library coverage of SQR gene libraries in this study [ PDF] (11 kb) Conserved regions from the alignment of SQR sequences. FAD-binding domains, SQR-fingerprints, and other conserved regions are given. Conserved regions corresponding to Cys 159, the FAD-binding domain III (299), and Cys 353 following Griesbeck . (2002) are given. The residue number of the SQR sequence from (CAA66112) is used in the bottom of the alignment. Positions of similar or identical amino acid residues are marked by asterisks above the alignment. Gaps are indicated as dashes. Group designations refer to groups of sequence similarity as shown in Fig. 1 of the main paper. [ PDF] (25 kb) Mechanism of sulfide-quinone reductase investigated using site-directed mutagenesis and sulfur analysis. , 11552-11565.

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Estimations of sequence diversity and library coverage of SQR gene libraries in this study [ PDF] (11 kb) Conserved regions from the alignment of SQR sequences. FAD-binding domains, SQR-fingerprints, and other conserved regions are given. Conserved regions corresponding to Cys 159, the FAD-binding domain III (299), and Cys 353 following Griesbeck . (2002) are given. The residue number of the SQR sequence from (CAA66112) is used in the bottom of the alignment. Positions of similar or identical amino acid residues are marked by asterisks above the alignment. Gaps are indicated as dashes. Group designations refer to groups of sequence similarity as shown in Fig. 1 of the main paper. [ PDF] (25 kb) Mechanism of sulfide-quinone reductase investigated using site-directed mutagenesis and sulfur analysis. , 11552-11565.

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