Investigation of compatible solutes synthesis and transport of Virgibacillus halodenitrificans PDB-F2 with complete genome analysis

Zhou, Yang; Sun, Zhiyuan; Li, Hui; Qian, Chan-Juan; Wu, Xiao; Tang, Hongzhi; Ali, Fawad; Liu, Yongdi

doi:10.1016/j.ibiod.2017.05.005

Cited by 13 publications

(8 citation statements)

References 22 publications

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“…Further experiments are needed to verify and elucidate ectoine production by strain 21D in response to osmotic stress. The strain V. halodenitrificans PDB-F2 also showed the ability to synthesize or uptake ectoine, hydroxyectoine, trehalose, glutamic acid and betaine in presence of 12% (w/v) NaCl (Zhou et al, 2017). Although no reports are available on compatible solutes produced or acquired by strains belonging to V. dokdonensis species and considering our results and the available literature, we can hypothesize that this is a shared feature of V. dokdonensis – V. pantothenticus related species.…”

Section: Discussionmentioning

confidence: 99%

Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery

et al. 2019

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The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl 2 -saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl 2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis . The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.

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Section: Discussionmentioning

confidence: 99%

Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery

et al. 2019

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“…Microorganisms live in high‐salinity environments by accumulating intracellular organic solutes called “compatible solutes” (CSs) (Vyrides & Stuckey, 2017). CSs are low molecular weight organic compounds that can interact with macromolecules in harmless ways to maintain the balance of osmotic pressure between inner and outer cells (Zhou et al, 2017). Microorganisms can cope with osmotic stress under saline conditions through the use of CS that can be synthesized by the cells or provided externally (Wang et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

The application of glycine betaine to alleviate the inhibitory effect of salinity on one‐stage partial nitritation/anammox process

Zuo

Yao

Chen

et al. 2020

Water Environment Research

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One-stage partial nitritation/anammox (PN/A) has been proposed as a sustainable method for removing nitrogen from various wastewater. However, the activities of ammonium-oxidizing bacteria (AOB) and anammox bacteria are often inhibited by the exposure to salinity, thereby hindering their wide application in treating industrial wastewater with high salinity. This study reports that the addition of glycine betaine (GB), which is a compatible solute, could alleviate the inhibitory effects of salinity on both AOB and anammox, thereby improving nitrogen removal performance in a onestage PN/A system. Short-term tests showed that with an addition of GB higher than 1 mM, the activity of AOB and anammox under salinity of 30 g/L could be increased by at least 45% and 51%, respectively. The half-inhibitory concentration of AOB and anammox rose with increasing GB concentration, with 1 mM GB being the optimal cost-effective dosage. Long-term experiments also demonstrated that 1 mM GB addition could enhance nitrogen removal performance and shorten recovery time by 42.9% under a salinity stress of 30 g/L. Collectively, GB addition was found to be a feasible and effective strategy to the counteract adverse effects of salinity on PN/A process.

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“…halodenitrificans , and V . pantothenticus have been shown to produce ectoine, proline, glycine betaine, or glutamic acid in response to high salinity [ 5 – 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…Currently, complete genomic sequences are available for 6 Virgibacillus species (NCBI database, 2017). For instance, the complete genome of Virgibacillus halodenitrificans PDB-F2, which is used for phenol degradation in wastewater treatment, has been analyzed [ 9 ]. Compatible solute synthesis and transport were further investigated by whole-genome sequencing [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…For instance, the complete genome of Virgibacillus halodenitrificans PDB-F2, which is used for phenol degradation in wastewater treatment, has been analyzed [ 9 ]. Compatible solute synthesis and transport were further investigated by whole-genome sequencing [ 9 ]. Moreover, the production of an NaCl-activated extracellular proteinase was studied in Virgibacillus sp.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of candidate genes involved in halotolerance using high-throughput omics in the halotolerant bacterium Virgibacillus chiguensis

2018

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We previously used whole-genome sequencing and Tn5 transposon mutagenesis to identify 16 critical genes involved in the halotolerance of Halomonas beimenensis, a species in the phylum Proteobacteria. In this present study, we sought to determine if orthologous genes in another phylum are also critical for halotolerance. Virgibacillus spp. are halotolerant species that can survive in high-saline environments. Some Virgibacillus species are used in different aspects of food processing, compatible solute synthesis, proteinase production, and wastewater treatment. However, genomic information on Virgibacillus chiguensis is incomplete. We assembled a draft V. chiguensis strain NTU-102 genome based on high-throughput next-generation sequencing (NGS) and used transcriptomic profiling to examine the high-saline response in V. chiguensis. The V. chiguensis draft genome is approximately 4.09 Mbp long and contains 4,166 genes. The expression profiles of bacteria grown in 5% and 20% NaCl conditions and the corresponding Gene Ontology (GO) and clusters of orthologous groups (COG) categories were also analyzed in this study. We compared the expression levels of these 16 orthologs of halotolerance-related genes in V. chiguensis and H. beimenensis. Interestingly, the expression of 7 of the 16 genes, including trkA2, smpB, nadA, mtnN2, rfbP, lon, and atpC, was consistent with that in H. beimenensis, suggesting that these genes have conserved functions in different phyla. The omics data were helpful in exploring the mechanism of saline adaptation in V. chiguensis, and our results indicate that these 7 orthologs may serve as biomarkers for future screening of halotolerant species in the future.

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Investigation of compatible solutes synthesis and transport of Virgibacillus halodenitrificans PDB-F2 with complete genome analysis

Cited by 13 publications

References 22 publications

Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery

Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery

The application of glycine betaine to alleviate the inhibitory effect of salinity on one‐stage partial nitritation/anammox process

Characterization of candidate genes involved in halotolerance using high-throughput omics in the halotolerant bacterium Virgibacillus chiguensis

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