The Genome Sequence of the Obligately Chemolithoautotrophic, Facultatively Anaerobic Bacterium Thiobacillus denitrificans

Abstract

The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, ␤-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfurcompound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfurcompound oxidation by ␤-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.Thiobacillus denitrificans, first isolated by Beijerinck over a century ago (4), was one of the first nonfilamentous bacteria ever described to be capable of growth on inorganic sulfur compounds as sole energy sources (47, 49). Characterized by its ability to conserve energy from the oxidation of inorganic sulfur compounds under either aerobic or denitrifying conditions, T. denitrificans is the best studied of the very few obligate chemolithoautotrophic species known to couple denitrification to sulfur-compound oxidation (Thiomicrospira denitrificans and Thioalkalivibrio thiocyanodenitrificans also have this ability [76,85]). Despite many years of work on the biochemistry of inorganic sulfur-compound oxidation by Thiobacillus thioparus and T. denitrificans, the mechanisms of oxidation and how they are coupled to energy conservation are still not well understood in these ␤-proteobacteria, relative to the advances made with facultatively chemolithotrophic ␣-proteobacterial genera, such as Paracoccus and Starkeya (28,39,45,50). The availability of the complete genome sequence should enable elucidation of the sulfur-oxidation pathway(s) and lead to specifically focused biochemical investigations to resolve these knowledge gaps.Rec...

Performance and microbial community composition in a long-term sequential anaerobic-aerobic bioreactor operation treating coking wastewater

“…Hydrolytic fermentative acidogenic activity in anaerobic bioreactors is likely controlled by strict anaerobic bacteria like Longilinea, Clostridium, and Proteiniphilum (Yamada et al 2007;Kohda et al 1997;Letowski et al 2001;Chen and Dong 2005;Larsen et al 2009) and facultative aerobic bacteria such as Corynebacterium (Kampfer et al 2009). In the aerobic sludge, the high abundances of Thiobacillus, Comamonas, Diaphorobacter, Ottowia, and Weeksella (Table S8), which reportedly degrade several phenol and SCN − compounds (Felföldi et al 2010;Beller et al 2006;Klankeo et al 2009;Yuste et al 2000), were in accordance with the significant removal of pollutants in the final effluent. As referred in Table S8, the significant presence of PAHdegrading bacteria like Comamonas (Goyal and Zylstra 1996) and Diaphorobacter (Klankeo et al 2009) indicated the removal of corresponding pollutants in aerobic sludge leading to detoxification of CWW (Zhang et al 2013).…”

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

“…In addition to the group 3b hydrogenases previously reported from OD1 and OP11 genomes , we recovered group 3b sequences from two gammaproteobacterial genomes (ACD46 and ACD21) and a partial sequence from the ACD79 genomic bin of unknown taxonomic assignment (Supplementary Figure S8). Unlike the Archaeal sulf-hydrogenase homologs in the obligately fermentative Thermococcales, the physiological role for NADP group 3b hydrogenases in the Proteobacteria (for example, A. vinelandii and T. denitrificans) is not yet known (Beller et al, 2006). The ACD79 genome bin has a second hydrogenase, and along with sequences from the Chloroflexi (ACD34) and Deltaproteobacteria (ACD 62) genomes, is most closely related to group 3c sequences (Supplementary Figure S8).…”

Microbial interspecies electron transfer via electric currents through conductive minerals

“…1A). The anodic current [at +0.4 V vs. standard hydrogen electrode (SHE)] was initially stable at ∼7 μA cm −2 , although it increased afterward, probably owing to the formation of conductive biofilms (23 contrast, T. denitrificans is a chemolithoautotrophic bacterium and known to use solid iron minerals (e.g., pyrite) as electron donors (22). We confirmed that the metal-oxide electrode (at −0.4 V vs. SHE) served as an electron donor for T. denitrificans in the presence of nitrate (Fig.…”

“…IET mechanisms described so far are based on diffusion of redox chemical species (20) and/or direct contact in cell aggregates (21). To address the involvement of conductive minerals in IET, we constructed mixed cultures of two representative soil bacteria, G. sulfurreducens (2,5) and Thiobacillus denitrificans (22), in the presence and absence of iron-oxide minerals, and their IET-dependent cooperative catabolic reactions were investigated.…”