Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7

Brown, Steven D.; Podar, Mircea; Klingeman, Dawn M.; Johnson, C. M.; Yang, Zamin K.; Utturkar, Sagar M.; Land, Miriam; Mosher, Jennifer J.; Hurt, Richard A.; Phelps, Tommy J.; Palumbo, Anthony V.; Arkin, Adam P.; Hazen, Terry C.; Elias, Dwayne A.

doi:10.1128/jb.01174-12

Cited by 22 publications

(14 citation statements)

References 13 publications

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“…1): (i) the generation of hydrogen and acetate by lactate-fermenting DvH, providing Dhc195 with electron donor and carbon source; (ii) the production of acetate by lactate-fermenting PfR7, providing Dhc195 with a carbon source; (iii) hydrogen consumption by Dhc195, maintaining positive energetics for lactate fermentation of DvH; and (iv) the generation by PfR7 of corrinoids that could be salvaged and remodeled by Dhc195 for use as essential cofactors. Pelosinus is a recently described genus that is commonly found associated with subsurface microbial communities stimulated with lactate for in situ bioremediation of metals (22,27). This study is the first to identify PfR7 as a corrinoid producer with the capability of synthesizing phenolic cobamides (i.e., [p-Cre]Cba and [Phe]Cba) de novo.…”

Section: Discussionmentioning

confidence: 95%

Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia

Men

Seth

et al. 2014

Appl Environ Microbiol

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dCorrinoids are essential cofactors of reductive dehalogenases in Dehalococcoides mccartyi, an important bacterium in bioremediation, yet sequenced D. mccartyi strains do not possess the complete pathway for de novo corrinoid biosynthesis. Pelosinus sp. and Desulfovibrio sp. have been detected in dechlorinating communities enriched from contaminated groundwater without exogenous cobalamin corrinoid. To investigate the corrinoid-related interactions among key members of these communities, we constructed consortia by growing D. mccartyi strain 195 (Dhc195) in cobalamin-free, trichloroethene (TCE)-and lactateamended medium in cocultures with Desulfovibrio vulgaris Hildenborough (DvH) or Pelosinus fermentans R7 (PfR7) and with both in tricultures. Only the triculture exhibited sustainable dechlorination and cell growth when a physiological level of 5,6-dimethylbenzimidazole (DMB), the lower ligand of cobalamin, was provided. In the triculture, DvH provided hydrogen while PfR7 provided corrinoids to Dhc195, and the initiation of dechlorination and Dhc195 cell growth was highly dependent on the growth of PfR7. Corrinoid analysis indicated that Dhc195 imported and remodeled the phenolic corrinoids produced by PfR7 into cobalamin in the presence of DMB. Transcriptomic analyses of Dhc195 showed the induction of the CbiZ-dependent corrinoid-remodeling pathway and BtuFCD corrinoid ABC transporter genes during corrinoid salvaging and remodeling. In contrast, another operon annotated to encode a putative iron/cobalamin ABC transporter (DET1174-DET1176) was induced when cobalamin was exogenously provided. Interestingly, a global upregulation of phage-related genes was observed when PfR7 was present. These findings provide insights into both the gene regulation of corrinoid salvaging and remodeling in Dhc195 when it is grown without exogenous cobalamin and microbe-to-microbe interactions in dechlorinating microbial communities.C hlorinated solvents such as tetra-and trichloroethene (PCE/ TCE) have been among the most common subsurface contaminants in the United States for decades (1, 2). In situ bioremediation is an effective, economical, and environmentally friendly technology for treating chlorinated solvents (2, 3). Dehalococcoides mccartyi is the only known bacterium capable of carrying out respiratory reductive dechlorination of chloroethenes to nontoxic ethene and plays a key role in the bioremediation of contaminated groundwater (4, 5).As cofactors of reductive dehalogenases (RDases), the enzymes responsible for reductive dechlorination, corrinoids (e.g., cobalamin) are essential nutrients for supporting D. mccartyi growth and dechlorination. Genomic analyses of sequenced D. mccartyi strains reveal a lack of complete corrinoid biosynthesis pathways, rendering D. mccartyi incapable of synthesizing corrinoids de novo (6, 7). Exogenous cobalamin (a specific corrinoid also known as vitamin B 12 ) is generally added to grow D. mccartyi in isolation (8). Cobalamin, 5-methylbenzimidazolylcobamide ([5-MeBza]Cba), and 5-methoxyb...

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Section: Discussionmentioning

confidence: 95%

Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia

Men

Seth

et al. 2014

Appl Environ Microbiol

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“…Some of these genomes have been described (Bowen De León et al ., ; Brown et al ., ; Chang et al ., ; Gronow et al ., ; Marx et al ., ).…”

Section: Sporulation and Phylogeny Of The Negativicutesmentioning

confidence: 98%

“…c. Exact or rounded numbers for complete genomes, approximate numbers for draft genomes. d. Some of these genomes have been described (Bowen De León et al, 2012;Brown et al, 2012;Chang et al, 2010;Gronow et al, 2010;Marx et al, 2011). The maximum-likelihood tree was built from a concatenated alignment of 50 ribosomal proteins from 70 organisms with a total of 6164 unambiguously aligned positions, essentially as described in Yutin et al (2012) , which would also help in resolving the weak affiliation of the latter two organisms with the Sporomusa group.…”

Section: Sporulation and Phylogeny Of The Negativicutesmentioning

confidence: 99%

A genomic update on clostridial phylogeny: Gram‐negative spore formers and other misplaced clostridia

Yutin

Galperin

2013

Environmental Microbiology

708

427

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Summary The class Clostridia in the phylum Firmicutes (formerly low-G+C Gram-positive bacteria) includes diverse bacteria of medical, environmental, and biotechnological importance. The Selenomonas-Megasphaera-Sporomusa branch, which unifies members of the Firmicutes with Gram-negative-type cell envelopes, was recently moved from Clostridia to a separate class Negativicutes. However, draft genome sequences of the spore-forming members of the Negativicutes revealed typically clostridial sets of sporulation genes. To address this and other questions in clostridial phylogeny, we have compared a phylogenetic tree for a concatenated set of 50 widespread ribosomal proteins with the trees for beta subunits of the RNA polymerase (RpoB) and DNA gyrase (GyrB) and with the 16S rRNA-based phylogeny. The results obtained by these methods showed remarkable consistency, suggesting that they reflect the true evolutionary history of these bacteria. These data put the Selenomonas-Megasphaera-Sporomusa group back within the Clostridia. They also support placement of Clostridium difficile and its close relatives within the family Peptostreptococcaceae; we suggest resolving the long-standing naming conundrum by renaming it Peptoclostridium difficile. These data also indicate the existence of a group of cellulolytic clostridia that belong to the family Ruminococcaceae. As a tentative solution to resolve the current taxonomical problems, we propose assigning 78 validly described Clostridium species that clearly fall outside the family Clostridiaceae to six new genera: Peptoclostridium, Lachnoclostridium, Ruminiclostridium, Erysipelatoclostridium, Gottschalkia, and Tyzzerella. This work reaffirms that 16S rRNA and ribosomal protein sequences are better indicators of evolutionary proximity than phenotypic traits, even such key ones as the structure of the cell envelope and Gram-staining pattern.

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“…Among Selenomonadales, complete genomes are currently available for several non-spore-forming representatives, such as Acidaminococcus intestini, Acidaminococcus fermentans Megasphaera elsdenii, Selenomonas ruminantium, and Veillonella parvula and just one spore-former, Sporomusa ovata (133). However, draft genomes of six metal-reducing strains of the spore-former Pelosinus fermentans have been sequenced and assembled into 65,76,98,134,844, and 887 contigs, respectively (57,58). In addition, a genome sequencing project of another spore-former, Acetonema longum, has been brought to the level of 296 contigs.…”

Section: Phylogenetic Diversitymentioning

confidence: 99%

Genome Diversity of Spore-Forming Firmicutes

Galperin

2016

The Bacterial Spore

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Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes: Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in nutrient-rich environment. It argues that systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.

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Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7

Cited by 22 publications

References 13 publications

Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia

Sustainable Growth of Dehalococcoides mccartyi 195 by Corrinoid Salvaging and Remodeling in Defined Lactate-Fermenting Consortia

A genomic update on clostridial phylogeny: Gram‐negative spore formers and other misplaced clostridia

Genome Diversity of Spore-Forming Firmicutes

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