Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility

J, Ray; Keller, Kimberly L.; Catena, Michela; Juba, Thomas R.; Zemla, Marcin; Rajeev, Lara; Knierim, Bernhard; Zane, Grant M.; Robertson, Jarrod; Auer, Manfred; Wall, Judy D.; Mukhopadhyay, Aindrila

doi:10.3389/fmicb.2014.00077

Cited by 8 publications

(6 citation statements)

References 38 publications

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“…coli strain J-2561 containing a 5-kb (pBbS5c) plasmid was prepared using cells grown to an optical density (at 600 nm) of 1. Desulfovibrio was grown in LS4D supplemented with 0.1% (wt/vol) yeast extract (43) while E. coli was grown in LB medium.…”

Section: Methodsmentioning

confidence: 99%

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

Kothari

Chandonia

et al. 2019

mBio

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Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded on abundant circular plasmids, all of which could confer novel and advantageous traits to their hosts. This study confirms the ecological role of the plasmidome in maintaining the latent capacity of a microbiome, enabling rapid adaptation to environmental stresses. IMPORTANCE Plasmidomes have been typically studied in environments abundant in bacteria, and this is the first study to explore plasmids from an environment characterized by low cell density. We specifically target groundwater, a significant source of water for human/agriculture use. We used samples from a well-studied site and identified hundreds of circular plasmids, including one of the largest sizes reported in plasmidome studies. The striking similarity of the plasmid-borne ORFs in terms of taxonomical and functional classifications across several samples suggests a conserved plasmid pool, in contrast to the observed variability in the 16S rRNA-based microbiome distribution. Additionally, the stress response to environmental factors has stronger conservation via plasmid-borne genes as marked by abundance of metal resistance genes. Last, identification of novel and diverse plasmids enriches the existing plasmid database(s) and serves as a paradigm to increase the repertoire of biological parts that are available for modifying novel environmental strains.

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Section: Methodsmentioning

confidence: 99%

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

Kothari

Chandonia

et al. 2019

mBio

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“…2 & Table S6). Additionally, the che operon structure in ULRT4_3.bins.101 was the same as that of cheA3 in D. vulgaris ( Figure S7), suggesting it had the ability to sense electron acceptors like sulfate and lactate [60].…”

Section: Mcp System Of Srmsmentioning

confidence: 84%

Metagenomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

Li¹,

Jia²,

Wang³

et al. 2020

Preprint

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BackgroundThe widespread occurrence of sulfate-reducing microorganisms (SRMs, which are typically considered anaerobic organisms) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in continuously oxic/hypoxic terrestrial environments rich in sulfate. However, little attention has been paid to such a possibility, leading to an incomplete understanding of microorganisms driving terrestrial part of the global sulphur cycle.ResultsIn this study, genome-centric metagenomics was employed to explore SRMs in a revegetated acidic mine wasteland under continuously oxic/hypoxic conditions. We reconstructed 12 Acidobacteria and four Deltaproteobacteria genomes encoding reductive DsrAB, of which five represented three new SRM genera. Our results showed that Acidobacteria-related SRMs differed considerably from Deltaproteobacteria-related SRMs in metabolic potentials. Genomes of Acidobacteria-related SRMs harbored more glycoside hydrolase (GH) genes than those of previously known SRMs. They also tended to encode more oxygen-tolerant hydrogenases and cytochrome c oxidases, but less methyl-accepting chemotaxis proteins (MCPs) than genomes of Deltaproteobacteria-related SRMs. More importantly, we discovered that SRM-infecting viruses can contribute to glycoside hydrolysis, chemotaxis and antioxidation of their hosts. Remarkably, one GH encoded by a SRM-infecting virus is responsible for the liberation of rhamnose (a monosaccharide that is accessible directly to SRMs for dissimilatory sulfate reduction) from plant cell-wall-derived oligosaccharides.ConclusionsTaken together, our results do not only improve our understanding of microorganisms driving dissimilatory sulfate reduction in terrestrial environments under continuously oxic/hypoxic conditions but also provides the first evidence for putative roles of viruses in S biogeochemical cycle in terrestrial ecosystems.

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“…5). It was reported that Dv H forms motility halos on solid media that are mediated by flagella-related mechanisms via the CheA3 histidine kinase (37). This indicated that Dv H had increased motility or surface attachment in the anodic chamber.…”

Section: Discussionmentioning

confidence: 99%

“…A deletion mutant Dv H JWT716 was used in this study, which lacks the type 1 secretion system’s ABC transporter protein resulting in a deficiency in biofilm formation (36). The deletion mutant Dv H JW3422 strain, which is a deletion of the gene coding for the pilin protein (DVU2116), was constructed using the same marker replacement plasmid and method as strain JW9003 from a previous study (37). The plasmid for deleting DVU2116 and replacing with a kanamycin resistance gene was transformed into Dv H JWT700 and deletion was confirmed by Southern Blot.…”

Section: Methodsmentioning

confidence: 99%

Co-occurrence of Direct and Indirect Extracellular Electron Transfer Mechanisms during Electroactive Respiration in a Dissimilatory Sulfate Reducing Bacterium

Hou,

Cortez,

Hagerman

et al. 2024

Preprint

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Extracellular electron transfer (EET) propels microbial fuel cell (MFC) technology and contributes to the mobility of redox active minerals and microbial syntrophy in nature. Although extensive studies on Sulfate-reducing bacteria (SRB)-mediated metal electrode corrosion have been done, there remain knowledge gaps on SRB EET to electrodes. Our MFCs with Desulfovibrio vulgaris Hildenborough (DvH), a model SRB, indicated that DvH can harvest and send electrons to the carbon cloth electrode. Patterns in current production compared to variations of electron donor/acceptor ratios in the anode and cathode suggested that attachment of DvH to the electrode and biofilm density were critical for effective electricity generation. Analysis of DvH biofilms at different conditions by electron microscopy indicated DvH utilized filaments that resemble nano-pili to attach on electrodes and facilitate EET from cell-to-cell and to the electrode. Proteomics profiling of electroactive respiration proteins indicated DvH adapted to electroactive respiration by presenting more pili-, flagellar- related proteins and histidine kinases on electrodes. The mutant with a deletion of the major pilus-producing gene yielded less voltage and far less attachment to the electrode, suggesting the importance of pili in EET. The mutant with a deficiency in biofilm formation, however, did not eliminate current production indicating the existence of indirect EET. Untargeted metabolomics profiling showed flavin-based metabolites, potential electron shuttles, were dysregulated between respiration modes. This work revealed the metabolic flexibility of DvH to thrive in non-ideal conditions with solid surfaces as both an electron acceptor and donor by using a combination of direct and indirect EET mechanisms.

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Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility

Cited by 8 publications

References 38 publications

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

Metagenomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland

Co-occurrence of Direct and Indirect Extracellular Electron Transfer Mechanisms during Electroactive Respiration in a Dissimilatory Sulfate Reducing Bacterium

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