Identification of Bacteria Potentially Responsible for Oxic and Anoxic Sulfide Oxidation in Biofilters of a Recirculating Mariculture System

Abstract

Bacteria presumably involved in oxygen-or nitrate-dependent sulfide oxidation in the biofilters of a recirculating marine aquaculture system were identified using a new application of reverse transcription-PCR denaturing gradient gel electrophoresis (DGGE) analysis termed differential-transcription (DT)-DGGE. Biofilter samples were incubated in various concentrations of sulfide or thiosulfate (0 to 5 mM) with either oxygen or nitrate as the sole electron acceptor. Before and after short-term incubations (10 to 20 h), total DNA and RNA were extracted, and a 550-bp fragment of the 16S rRNA genes was PCR amplified either directly or after reverse transcription. DGGE analysis of DNA showed no significant change of the original microbial consortia upon incubation. In contrast, DGGE of cDNA revealed several phylotypes whose relative band intensities markedly increased or decreased in response to certain incubation conditions, indicating enhanced or suppressed rRNA transcription and thus implying metabolic activity under these conditions. Specifically, species of the gammaproteobacterial genus Thiomicrospira and phylotypes related to symbiotic sulfide oxidizers could be linked to oxygen-dependent sulfide oxidation, while members of the Rhodobacteraceae (genera Roseobacter, Rhodobacter, and Rhodobium) were putatively active in anoxic, nitrate-dependent sulfide oxidation. For all these organisms, the physiology of their closest cultured relatives matches their DT-DGGE-inferred function. In addition, higher band intensities following exposure to 5 mM sulfide and nitrate were observed for Thauera-, Hydrogenophaga-, and Dethiosulfovibrio-like phylotypes. For these genera, nitrate-dependent sulfide oxidation has not been documented previously and therefore DT-DGGE might indicate a higher relative tolerance to high sulfide concentrations than that of other community members. We anticipate that DT-DGGE will be of general use in tracing functionally equivalent yet phylogenetically diverse microbial populations in nature.Zero-discharge marine aquaculture (mariculture) systems provide a solution for the environmentally detrimental effects of conventional mariculture (16). These closed systems utilize biofilters to convert the main contaminants from the process water to harmless gases. Treatment encompasses oxidation of ammonia to nitrate in an aerobic trickling filter and anaerobic removal of organic matter and nitrate by denitrification in a parallel purification loop comprising a digestion/sedimentation basin (DB) and a fluidized-bed reactor (FBR) (16).The high organic load entering the DB creates sharp redox potential gradients with extensive sulfate reduction within settled sludge. In these nitrate-depleted zones, sulfide concentrations can reach values exceeding 5,000 M (11). Due to extensive sulfide oxidation, sulfide concentrations in the overlying water of the basin are generally more than 1 order of magnitude below these values (11). Remaining sulfide from the DB effluent is oxidized in the organic carbon-limited FBR (12...

Denitrification by sulfur-oxidizing bacteria in a eutrophic lake

“…Evidence for sulfurdriven denitrification has been reported in marine ecosystems, including oceanic redoxclines (Brettar et al 2006, Grote et al 2008, near-coastal upwelling zones (Fossing et al 1995, Schulz et al 1999, and engineered mariculture systems (Cytryn et al 2005a, Sher et al 2008. The patterns of biogeochemical activity that we observed over depth are very similar to those documented in the Baltic Sea (Brettar & Rheinheimer 1991, Brettar et al 2006, albeit over a much smaller spatial scale (1 m vs. 10s of meters).…”

Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic

“…Samples taken in 2005 and in 2007 for this spring, however, had ␦ 13 C values of Ϫ6.1‰ and Ϫ12.4‰, respectively. Such pronounced isotopic enrichments are typical of methanotrophy, which enriches the residual methane pool in 13 C (resulting in a less negative ␦ 13 C value) due to preferential enzymatic breakage of 12 C-H bonds versus that of 13 C-H bonds (52). Similarly, GH-4 showed very enriched ␦ DIC ␦ 13 C values were Ϫ5.6‰ and Ϫ6.5‰ for GH-2 and GH-4, respectively.…”

Molecular analysis of the diversity of the sulfide : quinone reductase (sqr) gene in sediment environments

“…Besides chemical oxidation, microorganisms are involved in the oxidation of sulfide at oxicanoxic interfaces; this reaction initiates the first step of the sulfur oxidation process (Cytryn et al, 2005;Jorgensen, 1982) and produces sulfate or sulfur as the major oxidation product (Friedrich, 1998;Ruepp et al, 2000;She et al, 2001;Theissen et al, 2003).…”