Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes

Abstract

A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of several Desulfotomaculum species (low G+C gram-positive division) and two members of the genus Thermodesulfobacterium (a separate bacterial division) were monophyletic with delta-proteobacterial DsrAB sequences. The most parsimonious interpretation of these data is that dsrAB genes from ancestors of as-yet-unrecognized sulfate reducers within the delta-Proteobacteria were laterally transferred across divisions. A number of insertions and deletions in the DsrAB alignment independently support these inferred lateral acquisitions of dsrAB genes. Evidence for a dsrAB lateral gene transfer event also was found within the delta-Proteobacteria, affecting Desulfobacula toluolica. The root of the dsr tree was inferred to be within the Thermodesulfovibrio lineage by paralogous rooting of the alpha and beta subunits. This rooting suggests that the dsrAB genes in Archaeoglobus species also are the result of an ancient lateral transfer from a bacterial donor. Although these findings complicate the use of dsrAB genes to infer phylogenetic relationships among sulfate reducers in molecular diversity studies, they establish a framework to resolve the origins and diversification of this ancient respiratory lifestyle among organisms mediating a key step in the biogeochemical cycling of sulfur.

FIG. 1

Comparison of 16S rRNA (ML) and DsrAB (ED) trees for the sulfate- and sulfite-reducing prokaryotes investigated. Branch points supported by phylogenetic analysis (bootstrap support values of >90% in all ED and MP methods) are indicated by filled circles. Open circles at branch points indicate >75% bootstrap support in most or all analyses, while branch points without circles were not resolved (bootstrap values of <75%) as specific groups in the different analyses. Both trees are collapsed back at the division level. Thermophilic prokaryotes are in boldface. Consistent monophyletic groups between both trees are shaded gray. Microorganisms affected by putative LGT events of the dsrAB genes are color coded. dsrAB recipient or donor lineages are indicated by circled letters (a to c) located above or below the branch, respectively. The bars represent 0.1 changes per nucleotide or amino acid, respectively.

FIG. 2

Unrooted amino acid tree (ED) based on an alignment of DsrA to DsrB. The dissimilatory sulfite reductases of Allochromatium vinosum and Pyrobaculum islandicum were excluded from the analysis since they likely are members of different enzyme families (9, 22). The bar represents 0.1 changes per amino acid. Bootstrap analyses were performed using the PHYLIP parsimony method with 100 resamplings (Felsenstein, University of Washington). Branch points with parsimony bootstrap support of >85% are indicated by filled circles. Open circles at branch points indicate >50% bootstrap support, while branch points without circles either have parsimony bootstrap values of <50% (authentic gram-positive sulfate-reducing bacteria [SRB] DsrB; δ-SRB + xenologous SRB DsrB) or are not obtained with the parsimony method (Archaeoglobus and authentic gram-positive sulfate-reducing bacteria DsrA sequences form a monophyletic cluster in the parsimony method).

FIG. 3

Amino acid alignment of DsrA and DsrB showing insertions supporting the δ-proteobacterial origin of the putative laterally transferred sulfite reductases (labeled with an asterisk). It should be noted that the presumably xenologous DsrA and DsrB of Archaeoglobus do not show the typical δ-proteobacterial insertions.