Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur‐oxidizing prokaryotes

Abstract

Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.

Nested PCR and New Primers for Analysis of Sulfate-Reducing Bacteria in Low-Cell-Biomass Environments

“…Applying these primers to techniques other than DGGE should result in sequences that are too short. We also took into account that dsrAB genes are not restricted to sulfate-reducing bacteria, and some specialized sulfur-oxidizing bacteria employ a reversely operating dissimilatory sulfite reductase (rDSR) (32). This enzyme is homologous to, but phylogenetically clearly distinguishable from, the DSR present in anaerobic SRP.…”

Metatranscriptomic Analysis of Diminutive Thiomargarita-Like Bacteria (“Candidatus Thiopilula” spp.) from Abyssal Cold Seeps of the Barbados Accretionary Prism

“…5A). Reverse DsrA phylogenies are generally congruent with 16S rRNA gene trees (50), so the pattern shown in Fig. 5A is unlikely to result from horizontal gene transfer.…”

“…Bootstrapping was performed with 1,000 replicates by using the RAxML rapid bootstrap algorithm. Hydroxylamine oxidoreductase (HAO)-like sequences were aligned with the Expresso algorithm in T-Coffee (49), and dissimilatory sulfite reductase (DsrA) sequences were aligned in ARB by using a database described previously (50). Alignments were trimmed with the automated1 option in TrimAL (51), for final lengths of 293 and 308 amino acids for the DsrA and HAO alignments, respectively.…”

Comprehensive Detection of Phototrophic Sulfur Bacteria Using PCR Primers That Target Reverse Dissimilatory Sulfite Reductase Gene

“…Thus, dsrAB coding for the reverse-operating DsrAB is a potential marker gene for phototrophic sulfur bacteria unlike primers and probes targeted to the 16S rRNA gene (7). Recently, PCR assays have been developed for the amplification of dsrAB from cultures and natural environments (18). However, these researchers still used multiple sets of primers to amplify the dsrAB from the phototrophic sulfur bacteria.…”

“…Their polyphyletic nature restricts the concomitant detection of all recognized members using a single 16S rRNA genetargeting probe or primer set in environmental analyses (1,3,8,28,34). Alternative approaches have been developed to detect phototrophic sulfur bacteria using PCR primers that target functional genes coding for key enzymes of sulfur oxidation pathways; ATP sulfurylase, the iron-sulfur flavoprotein adenosine-5'-phosphosulfate (APS) reductase and siroheme sulfite reductase (18,20,21).Dissimilatory sulfite reductase (DsrAB) is a key enzyme in dissimilatory sulfate reduction in sulfate-reducing prokaryotes. The presence of DsrAB with a proposed function in sulfide oxidation has been demonstrated for colorless and purple sulfur bacteria (29,30).…”