Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans

Abstract

BackgroundThe Delta-Proteobacterium Desulfotignum phosphitoxidans is a type strain of the genus Desulfotignum, which comprises to date only three species together with D. balticum and D. toluenicum. D. phosphitoxidans oxidizes phosphite to phosphate as its only source of electrons, with either sulfate or CO2 as electron acceptor to gain its metabolic energy, which is of exclusive interest. Sequencing of the genome of this bacterium was undertaken to elucidate the genomic basis of this so far unique type of energy metabolism.ResultsThe genome contains 4,998,761 base pairs and 4646 genes of which 3609 were assigned to a function, and 1037 are without function prediction. Metabolic reconstruction revealed that most biosynthetic pathways of Gram negative, autotrophic sulfate reducers were present. Autotrophic CO2 assimilation proceeds through the Wood-Ljungdahl pathway. Additionally, we have found and confirmed the ability of the strain to couple phosphite oxidation to dissimilatory nitrate reduction to ammonia, which in itself is a new type of energy metabolism. Surprisingly, only two pathways for uptake, assimilation and utilization of inorganic and organic phosphonates were found in the genome. The unique for D. phosphitoxidans Ptx-Ptd cluster is involved in inorganic phosphite oxidation and an atypical C-P lyase-coding cluster (Phn) is involved in utilization of organophosphonates.ConclusionsWe present the whole genome sequence of the first bacterium able to gain metabolic energy via phosphite oxidation. The data obtained provide initial information on the composition and architecture of the phosphite–utilizing and energy-transducing systems needed to live with phosphite as an unusual electron donor.

‘Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep‐branching clade of Deltaproteobacteria and a putative homoacetogen

“…Originally referred to as formate–hydrogen lyase, the HDCR complex comprises a hydrogen‐linked formate dehydrogenase H (FDH H ) and a hydrogenase (Axley et al ., ). An involvement of FDH H in the hydrogen‐dependent reduction of CO 2 had been proposed already for the homoacetogenic Treponema primitia , which possesses two homologs of fdhF encoding a selenium‐free and a selenium‐containing variant of FDH H (Matson et al ., ), and later also for A. woodii (Poehlein et al ., ). Like these organisms, the genome of strain Adiu1 contains two clusters of HDCR components (Schuchmann and Müller, ), which include two homologs ( fdhF1 and fdhF2 ), putatively encoding a selenium‐free and a selenium‐containing variant of FDH H (Supporting Information Fig.…”

Freshwater Bacteria Release Methane as a By-Product of Phosphorus Acquisition

“…2). Several glyphosate-and phosphite-utilizing microbes have phn gene clusters with two copies of phnE (51,52). In the gene cluster on Contig00117, these appear to be fused: no stop codon between the two phnE genes could be found, so we predict that they encode a single polypeptide.…”

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

“…The ABCtransporter proteins OpuA, B and C responsible for osmotic homeostasis in TCS1 were present only in Moorella thermoacetica ATCC39073 genome rather than the other acetogens in Table S1. Besides the TCS1 draft genome, Moorella thermoacetica ATCC39073 [40], Desulfotignum phosphitoxidans DSM13687 [41] and Treponema azotonutricium genomes [42] also possess a full set of the genes involved in Wood-Ljungdahl pathway for autotrophic acetate production.…”