The organohalide-respiring bacterium Sulfurospirillum multivorans: a natural source for unusual cobamides

Understanding the sources, function, and irreplaceable role of cobamides in organohalide-respiring bacteria

Halogenated organic compounds are persistent pollutants that pose a serious threat to human health and the safety of ecosystems. Cobamides are essential cofactors for reductive dehalogenases (RDase) in organohalide-respiring bacteria (OHRB), which catalyze the dehalogenation process. This review systematically summarizes the impact of cobamides on organohalide respiration. The catalytic processes of cobamide in dehalogenation processes are also discussed. Additionally, we examine OHRB, which cannot synthesize cobamide and must obtain it from the environment through a salvage pathway; the co-culture with cobamide producer is more beneficial and possible. This review aims to help readers better understand the importance and function of cobamides in reductive dehalogenation. The presented information can aid in the development of bioremediation strategies.

Sulfurospirillum oryzae sp. nov., A Novel Nitrogen-Fixing Bacterium Isolated from Paddy Soil

An anaerobic, Gram-staining-negative, rod shaped, nitrogen-fixing strain designed SG202^T, was isolated from paddy soil collected from Fujian Province in China. Strain SG202^T showed the highest 16S rRNA gene sequence similarity with the type strain Sulfurospirillum multivorans DSM 12446^T (98.5%). Phylogenetic trees based on 16S rRNA gene sequences and conserved core genes from genomes indicated that strain SG202^T branched with members of the genus Sulfurospirillum. Growth was observed at 25-37 °C (optimum 30 °C), pH 6.0-10.5 (optimum 7.5), and 0-0.6% (w/v) NaCl (optimum 0.2%). Strain SG202^T contained MK-6 as the menaquinone and C_16:1ω7c (40.6%), C_16:0 (33.3%), C_18:1ω7c (13.6%) and C_14:0 (9.0%) as the major fatty acids. The genomic DNA G+C content was 39.0%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG202^T and its closely related species S. multivorans DSM 12446^T, Sulfurospirillum halorespirans DSM 13726^T, Sulfurospirillum arsenophilum DSM 10659^T and Sulfurospirillum diekertiae ACS_DCE^T were 81.3, 81.5, 84.4, 82.2% and 24.5, 24.5, 27.9, 25.2%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG202^T possessed core genes (nifHDK) of nitrogen fixation, and nitrogenase activities (3470.45 μmol C₂H₄ g^-1 protein h^-1) was examined using the acetylene reduction assay. Based on the observed physiological properties, chemotaxonomic characteristics and genome analysis, strain SG202^T is recognized as a novel species of the genus Sulfurospirillum, for which the name Sulfurospirillum oryzae sp. nov. is proposed. The type strain is SG202^T (= GDMCC 1.3379^T= JCM 35596^T).

Comparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains

Sulfurospirillum species strains are frequently detected in various pristine and contaminated environments and participate in carbon, sulfur, nitrogen, and halogen elements cycling. Recently we obtained the complete genome sequences of two newly isolated Sulfurospirillum strains, ACS_DCE and ACS_TCE, capable of dechlorinating tetrachloroethene to cis-1,2-dichloroethene and trichloroethene under low-pH conditions, but a detailed analysis of these two genomes in reference to other Sulfurospirillum genomes for an improved understanding of Sulfurospirillum evolution and ecophysiology has not been accomplished. Here, we performed phylogenetic and pangenome analyses with 12 completed Sulfurospirillum genomes, including those of strain ACS_TCE and strain ACS_DCE, to unravel the evolutionary and metabolic potentials in the genus Sulfurospirillum. Based on 16S rRNA gene and whole-genome phylogenies, strains ACS_TCE, ACS_DCE, and JPD-1 could be clustered into a single species, proposed as “Candidatus Sulfurospirillum acididehalogenans.” TimeTree analysis suggested that the organohalide-respiring (OHR) Sulfurospirillum might acquire the ability to use chlorinated electron acceptors later than other energy conservation processes. Nevertheless, the ambiguity of the phylogenetic relations among Sulfurospirillum strains complicated the interpretation of acquisition and loss of metabolic traits. Interestingly, all OHR Sulfurospirillum genomes except the ones of Sulfurospirillum multivorans strains harbor a well-aligned and conserved region comprising the genetic components required for the organohalide respiration chain. Pangenome results further revealed that a total of 34,620 gene products, annotated from the 12 Sulfurospirillum genomes, can be classified into 4,118 homolog families and 2,075 singleton families. Various Sulfurospirillum species strains have conserved metabolisms as well as individual enzymes and biosynthesis capabilities. For instance, only the OHR Sulfurospirillum species strains possess the quinone-dependent pyruvate dehydrogenase (PoxB) gene, and only “Ca. Sulfurospirillum acididehalogenans” strains harbor urea transporter and urease genes. The plasmids found in strain ACS_TCE and strain ACS_DCE feature genes coding for type II toxin-antitoxin systems and transposases and are promising tools for the development of robust gene editing tools for Sulfurospirillum.

IMPORTANCE Organohalide-respiring bacteria (OHRB) play critical roles in the detoxification of chlorinated pollutants and bioremediation of subsurface environments (e.g., groundwater and sediment) impacted by anthropogenic chlorinated solvents. The majority of known OHRB cannot perform reductive dechlorination below neutral pH, hampering the applications of OHRB for remediating acidified groundwater due to fermentation and reductive dechlorination. Previously we isolated two Sulfurospirillum strains, ACS_TCE and ACS_DCE, capable of dechlorinating tetrachloroethene under acidic conditions (e.g., pH 5.5), and obtained the complete genomes of both strains. Notably, two plasmid sequences were identified in the genomes of strain ACS_TCE and strain ACS_DCE that may be conducive to unraveling the genetic modification mechanisms in the genus Sulfurospirillum. Our findings improve the current understanding of Sulfurospirillum species strains regarding their biogeographic evolution, genome dynamics, and functional diversity. This study has applied values for the bioremediation of toxic and persistent organohalide pollutants in low-pH environments.

Microbial sulfur metabolism and environmental implications

Sulfur as a macroelement plays an important role in biochemistry in both natural environments and engineering biosystems, which can be further linked to other important element cycles, e.g. carbon, nitrogen and iron. Consequently, the sulfur cycling primarily mediated by sulfur compounds oxidizing microorganisms and sulfur compounds reducing microorganisms has enormous environmental implications, particularly in wastewater treatment and pollution bioremediation. In this review, to connect the knowledge in microbial sulfur metabolism to environmental applications, we first comprehensively review recent advances in understanding microbial sulfur metabolisms at molecular-, cellular- and ecosystem-levels, together with their energetics. We then discuss the environmental implications to fight against soil and water pollution, with four foci: (1) acid mine drainage, (2) water blackening and odorization in urban rivers, (3) SANI® and DS-EBPR processes for sewage treatment, and (4) bioremediation of persistent organic pollutants. In addition, major challenges and further developments toward elucidation of microbial sulfur metabolisms and their environmental applications are identified and discussed.

Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene

Microbial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In co-cultures, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase-mandatory for D. mccartyi-was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B₁₂ produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.

Specificity of cobamide remodeling, uptake and utilization in Vibrio cholerae

Cobamides are a group of compounds including vitamin B₁₂ that can vary at the lower base position of the nucleotide loop. They are synthesized de novo by only a subset of prokaryotes, but some organisms encode partial biosynthesis pathways for converting one variant to another (remodeling) or completing biosynthesis from an intermediate (corrinoid salvaging). Here, we explore the cobamide specificity in Vibrio cholerae through examination of three natural variants representing major cobamide groups: commercially available cobalamin, and isolated pseudocobalamin and p-cresolylcobamide. We show that BtuB, the outer membrane corrinoid transporter, mediates the uptake of all three variants and the intermediate cobinamide. Our previous work suggested that V. cholerae could convert pseudocobalamin produced by cyanobacteria into cobalamin. In this work, cobamide specificity in V. cholerae is demonstrated by remodeling of pseudocobalamin and salvaging of cobinamide to produce cobalamin. Cobamide remodeling in V. cholerae is distinct from the canonical pathway requiring amidohydrolase CbiZ, and heterologous expression of V. cholerae CobS was sufficient for remodeling. Furthermore, function of V. cholerae cobamide-dependent methionine synthase MetH was robustly supported by cobalamin and p-cresolylcobamide, but not pseudocobalamin. Notably, the inability of V. cholerae to produce and utilize pseudocobalamin contrasts with enteric bacteria like Salmonella.

Structural and functional analysis of an l-serine O-phosphate decarboxylase involved in norcobamide biosynthesis

Structural diversity of natural cobamides (Cbas, B₁₂ vitamers) is limited to the nucleotide loop. The loop is connected to the cobalt-containing corrin ring via an (R)-1-aminopropan-2-ol O-2-phosphate (AP-P) linker moiety. AP-P is produced by the l-threonine O-3-phosphate (l-Thr-P) decarboxylase CobD. Here, the CobD homolog SMUL_1544 of the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans was characterized as a decarboxylase that produces ethanolamine O-phosphate (EA-P) from l-serine O-phosphate (l-Ser-P). EA-P is assumed to serve as precursor of the linker moiety of norcobamides that function as cofactors in the respiratory reductive dehalogenase. SMUL_1544 (SmCobD) is a pyridoxal-5'-phosphate (PLP)-containing enzyme. The structural analysis of the SmCobD apoprotein combined with the characterization of truncated mutant proteins uncovered a role of the SmCobD N-terminus in efficient l-Ser-P conversion.

An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research

Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.

Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans

The organohalide-respiring bacterium Sulfurospirillum multivorans produces a unique cobamide, namely, norpseudo-B₁₂, which serves as cofactor of the tetrachloroethene (PCE) reductive dehalogenase (PceA). As previously reported, a replacement of the adeninyl moiety, the lower base of the cofactor, by exogenously applied 5,6-dimethylbenzimidazole led to inactive PceA. To explore the general effect of benzimidazoles on the PCE metabolism, the susceptibility of the organism for guided biosynthesis of various singly substituted benzimidazolyl-norcobamides was investigated, and their use as cofactor by PceA was analyzed. Exogenously applied 5-methylbenzimidazole (5-MeBza), 5-hydroxybenzimidazole (5-OHBza), and 5-methoxybenzimidazole (5-OMeBza) were found to be efficiently incorporated as lower bases into norcobamides (NCbas). Structural analysis of the NCbas by nuclear magnetic resonance spectroscopy uncovered a regioselectivity in the utilization of these precursors for NCba biosynthesis. When 5-MeBza was added, a mixture of 5-MeBza-norcobamide and 6-MeBza-norcobamide was formed, and the PceA enzyme activity was affected. In the presence of 5-OHBza, almost exclusively 6-OHBza-norcobamide was produced, while in the presence of 5-OMeBza, predominantly 5-OMeBza-norcobamide was detected. Both NCbas were incorporated into PceA, and no negative effect on the PceA activity was observed. In crystal structures of PceA, both NCbas were bound in the base-off mode with the 6-OHBza and 5-OMeBza lower bases accommodated by the same solvent-exposed hydrophilic pocket that harbors the adenine as the lower base of authentic norpseudo-B₁₂ In this study, a selective production of different norcobamide isomers containing singly substituted benzimidazoles as lower bases is shown, and unique structural insights into their utilization as cofactors by a cobamide-containing enzyme are provided.IMPORTANCE Guided biosynthesis of norcobamides containing singly substituted benzimidazoles as lower bases by the organohalide-respiring epsilonproteobacterium Sulfurospirillum multivorans is reported. An unprecedented specificity in the formation of norcobamide isomers containing hydroxylated or methoxylated benzimidazoles was observed that implicated a strict regioselectivity of the norcobamide biosynthesis in the organism. In contrast to 5,6-dimethylbenzimidazolyl-norcobamide, the incorporation of singly substituted benzimidazolyl-norcobamides as a cofactor into the tetrachloroethene reductive dehalogenase was not impaired. The enzyme was found to be functional with different isomers and not limited to the use of adeninyl-norcobamide. Structural analysis of the enzyme equipped with either adeninyl- or benzimidazolyl-norcobamide cofactors visualized for the first time structurally different cobamides bound in base-off conformation to the cofactor-binding site of a cobamide-containing enzyme.