Search

Bromate, a possible human carcinogen, can be reduced to innocuous bromide by microorganisms. To characterize bromate reducers, microbes were enriched anaerobically from activated sludge by using bromate as the sole electron acceptor and different carbon sources as the electron donor. Bacteria that showed significant bromate-reducing activity but not coupled to cell growth were isolated. Two whole genomes of the isolates, namely, Raoultella electrica Lac1 and Klebsiella variicola Glu3, were reconstructed by Illumina and Nanopore sequencing. Transcriptomic analysis suggested that neither the respiratory nitrate reductase, the selenate reductase, nor the dimethylsulfoxide reductase was involved in the bromate reduction process, and strain K. variicola Glu3 reduced bromate via a yet undiscovered enzymatic mechanism. The results provide novel phylogenetic insights into bromate-reducing microorganisms and clues in putative genes encoding enzymes related to bromate reduction. [ABSTRACT FROM AUTHOR]

Bioremediation has been considered as a promising method for recovering chemical polluted environments. Here Shewanella decolorationis strain Ni1-3 showed versatile abilities in bioremediation. To improve the bioremediation activity, RNA polymerase (RNAP) mutations of strain Ni1-3 were screened. Eleven mutants were obtained, of which mutant #40 showed enhanced Amaranth (AMR) degradation capacity, while mutant #21 showed defected capacity in AMR degradation but greatly enhanced capacity in cathodic metal leaching which is three to four times faster than that of the wild-type (WT) strain Ni1-3, suggesting that different pathways were involved in these two processes. Transcriptional profiling and gene co-expression networks between the mutants (i.e., #40 and #22) and the WT strain disclosed that the non-CymA-Mtr but cytochrome b - and flavin-oxidoreductase-dominated azo dye degradation pathways existed in S. decolorationis , which involved key proteins TorC, TorA, YceJ, YceI, Sye4, etc. Furthermore, the involvement of TorA was verified by trimethylamine N-oxide reduction and molybdenum enzyme inhibitory experiments. This study clearly demonstrates that RNAP mutations are effective to screen active microbial candidates in bioremediation. Meanwhile, by clarifying the novel gene co-expression network of extracellular electron transfer pathways, this study provides new insights in azo dye degradation and broadens the application of Shewanella spp. in bioremediation as well. [ABSTRACT FROM AUTHOR]

Heavy metal pollution is one of the most widespread and complex environmental issues globally, posing a great threat to the ecosystem as well as human health. Bioremediation through heavy metal-resistant bacteria (HMRB) is currently the most promising technology to address this issue. To obtain HMRB to remediate heavy metal pollution potentially, 15 culturable HMRB strains were isolated from the sludge samples of an electroplating wastewater treatment plant (EWWTP), which belonged to the Bacillus , Shewanella , Lysinibacillus , and Acinetobacter genera. Their maximum tolerance concentrations to Cu2+, Ni2+, Mn2+, Co2+, and Cr 2 O 7 2− were 40 mM, 10 mM, 200 mM, 40 mM, and 10 mM, respectively, and strain Mn1-4 showed much higher Mn2+ tolerance and removal effectiveness (3.355 g/L) than previously published reports. Moreover, multiple heavy metal-resistant genotypes and phenotypes were identified among these strains, of which strain Co1-1 carried the most of resistant gene sequences (10) and exhibited resistance to 7 categories of heavy metals, and the co-occurrence of heavy metal and antibiotic resistance were clearly observed in strain Ni1-3. In addition, flanked insert sequence (IS) elements on the heavy metal resistant genes (HMRGs) suggested that horizontal gene transfer (HGT) events may have resulted in multiple heavy metal resistance phenotypes and genotypes in these strains, and IS982 family transposase was presumed to result in the high Ni2+ tolerance in strain Ni1-3. This study expands our understanding of bacterial heavy metal resistance and provides promising candidates for heavy metal bioremediation. Image 1 • Fifteen bacterial strains with multiple heavy metal resistance were isolated. • The most frequently isolated Ni2+ resistant strains implied environmental selection. • A strain with high Mn2+ tolerance and removal capability were isolated. • Co-occurrence of heavy metal and antibiotic resistance were observed ubiquitously. • Horizontal gene transfer events result in the high Ni2+ tolerance in strain Ni1-3. [ABSTRACT FROM AUTHOR]

Recycling of spent lithium-ion batteries (LIBs) has become a global issue because of the potential environment risks raised by spent LIBs as well as high valuable metal content remaining in them. Although bioleaching is an environmentally friendly method to recover metals from spent LIBs, the commonly utilized bioleaching bacterial consortia or strains enriched/isolated from acidic environments cannot be applied at large scales owing to their long leaching cycle and poor tolerance to organic compounds. Here, two bioleaching consortia were enriched in 60 days from neutral activated sludge and were identified phylogenetically divergent from the documented bioleaching bacteria. The results showed that the novel consortia shortened the leaching cycle almost by half when compared to the previous reported consortia or strains, of which one consortium dominated by Acidithiobacillus ferrooxidans displayed high bioleaching efficiency on LiMn 2 O 4 , as 69.46% lithium (Li) and 67.60% manganese (Mn) were leached out in seven days. This consortium was further domesticated using cathodic materials for 100 days and proved consisted of three mixotrophs and two chemoautotrophs, three of which were novel species from the genera Sulfobacillus and Leptospirillum. More genes coding for proteins that utilize organic compounds were annotated in the metagenomic assembled genomes (MAGs) than previously reported. A mutualistic relationship between mixotrophs and chemoautotrophs was suggested to help the consortium surviving under either organic- rich or shortage environments. The results discovered that novel bioleaching bacteria with shorter leaching cycle and higher tolerance to organics could be enriched from non-acidic environments, which showed high potential for the metal recovering from spent LIBs or other organic-rich environments. [Display omitted] • Novel bioleaching consortia were enriched from non-acidic AS samples. • Three novel species in the genera of Sulfobacillus and Leptospirillum were enriched. • The consortia carried more genes for stress adaptation and energy production. • The consortia showed shorter bioleaching cycle and high capacity to tolerate organics. • Bioleaching consortia enriched from non-acidic environments showed high diversity. [ABSTRACT FROM AUTHOR]

Bromate is a weakly carcinogenic disinfection by-product generated from naturally existing bromide during ozonation. In order to uncover the phylogenetic diversity of bromate-reducing aquatic bacteria, the microbial mixed cultures were enriched anaerobically from various activated sludge samples with a high concentration of 3.6 mmol/L bromate which served as the electron acceptor in batch-fed reactors. Then the phylogenetic diversity was characterized by employing 16S rRNA gene-based clone libraries and high-throughput sequencing. Results showed that as highest as 48.65 mg/L [BrO 3 −-Br] (0.61 mmol/L) could be reduced to Br− within an operational cycle of 48 h, indicating the presence of bromate-reducing bacteria. The microbial analysis based on 16S rRNA gene clone libraries indicated that the dominant bacteria in the enriched consortium were affiliated to the genera of Aeromonas , which had been reported and implied its functional application to reduce bromate. In addition, some other subdivisions of bromate-reducing bacteria were enriched at different operational cycles. The abundance of the genus Rivibacter belonging to Comamonadaceae were increased after 10 cycles enrichment, which might represent another type of novel bromate bio-reducers. The study provided new insights for the phylogenetic diversity of the bromate-reducing microorganisms while further researches are required to verify the bromate bio-reduction mechanism. • Bromate reduction was observed by activated sludges under high bromate stress. • High throughput sequencing uncovered phylogeny of bromate-reducing bacteria. • Aeromonas and Rivibacter spp. dominated the enriched bromate-reducing bacteria. • Rivibacter spp. might be the potentially novel bromate-reducing bacteria. [ABSTRACT FROM AUTHOR]

Paraclostridium bifermentans (P.b) is an emerging human pathogen that is phylogenomically close to Paeniclostridium sordellii (P.s), while their populational genomic features and virulence capacity remain understudied. Here, we performed comparative genomic analyses of P.b and compared their pan-genomic features and virulence coding profiles to those of P.s. Our results revealed that P.b has a more plastic pangenome, a larger genome size, and a higher GC content than P.s. Interestingly, the P.b and P.s share similar core-genomic functions, but P.b encodes more functions in nutrient metabolism and energy conversion and fewer functions in host defense in their accessory-genomes. The P.b may initiate extracellular infection processes similar to those of P.s and Clostridium perfringens by encoding three toxin homologs (i.e., microbial collagenase, thiol-activated cytolysin, phospholipase C, which are involved in extracellular matrices degradation and membrane damaging) in their core-genomes. However, P.b is less toxic than the P.s by encoding fewer secretion toxins in the core-genome and fewer lethal toxins in the accessory-genome. Notably, P.b carries more toxins genes in their accessory-genomes, particularly those of plasmid origin. Moreover, three within-species and highly conserved plasmid groups, encoding virulence, gene acquisition, and adaptation, were carried by 25-33% of P.b strains and clustered by isolation source rather than geography. This study characterized the pan-genomic virulence features of P.b for the first time, and revealed that P. bifermentans is an emerging pathogen that can threaten human health in many aspects, emphasizing the importance of phenotypic and genomic characterizations of in situ clinical isolates., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Cai, Peng, Yang, Feng, Tian, Huang, Mao and Xu.)

With the development of endoscopic technology, an increasing number of patients with esophageal disease are being diagnosed, although the underlying pathogenesis of many esophageal diseases remains unclear. In recent years, a large number of studies have demonstrated that the occurrence and development of various intestinal diseases were related to intestinal flora. As a result, researchers have shifted their focus towards investigating esophageal flora to better understand the pathogenesis, early diagnosis, and treatment of esophageal diseases. This paper reviewed the normal esophageal flora and the changes of esophageal flora under different esophageal disease states. It was observed that there are distinct differences in the composition of esophageal microflora among Gastroesophageal Reflux, Barrett's esophagus, eosinophilic esophagitis and normal esophagus. The normal esophageal flora was dominated by gram-positive bacteria, particularly Streptococcus , while the esophageal flora under esophagitis was dominated by gram-negative bacteria. Furthermore, the diversity of esophageal flora is significantly decreased in patients with esophageal cancer. Several potential microbial biomarkers for esophageal cancer have been identified, among which Fusobacterium nucleatum showed a close association with esophageal squamous cell carcinoma's pathological stage and clinical stage., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zou, Feng, Cai, Qian and Xu.)

Background: Winkia neuii , previously known as Actinomyces neuii , is increasingly recognized as a causative agent of various human infections, while its taxonomy and genomic insights are still understudied., Methods: A Winkia strain NY0527 was isolated from the hip abscess of a patient, and its antibiotic susceptibility was assessed. The genome was hybrid assembled from long-reads and short-reads sequencing. Whole-genome-based analyses on taxa assignment, strain diversity, and pathogenesis were conducted., Results: The strain was found to be highly susceptible to beta-lactam antibiotics, but resistant to erythromycin, clindamycin, and amikacin. The complete genome sequences of this strain were assembled and found to consist of a circular chromosome and a circular plasmid. Sequence alignment to the NCBI-nt database revealed that the plasmid had high sequence identity (>90%) to four Corynebacterium plasmids, with 40-50% query sequence coverage. Furthermore, the plasmid was discovered to possibly originate from the sequence recombination events of two Corynebacterium plasmid families. Phylogenomic tree and genomic average nucleotide identity analyses indicated that many Winkia sp. strains were still erroneously assigned as Actinomyces sp. strains, and the documented subspecies within W. neuii should be reclassified as two separate species (i.e., W. neuii and W. anitratus ). The core genome of each species carried a chromosome-coded beta-lactamase expression repressor gene, which may account for their broadly observed susceptibility to beta-lactam antibiotics in clinical settings. Additionally, an ermX gene that expresses fluoroquinolone resistance was shared by some W. neuii and W. anitratus strains, possibly acquired by IS6 transposase-directed gene transfer events. In contrast, tetracycline resistance genes were exclusively carried by W. neuii strains. In particular, W. neuii was found to be more pathogenic than W. anitratus by encoding more virulence factors (i.e., 35-38 in W. neuii vs 27-31 in W. anitratus ). Moreover, both species encoded two core pathogenic virulence factors, namely hemolysin and sialidase, which may facilitate their infections by expressing poreformation, adhesion, and immunoglobulin deglycosylation activities., Conclusion: This study highlights the underappreciated taxonomic diversity of Winkia spp. and provides populational genomic insights into their antibiotic susceptibility and pathogenesis for the first time, which could be helpful in the clinical diagnosis and treatment of Winkia spp. infections., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Cai, Peng, Li, Qiu, Wang, Xu and Hou.)

Microbial bromate reduction plays an important role in remediating bromate-contaminated waters as well as biogeochemical cycling of bromine. However, little is known about the molecular mechanism of microbial bromate reduction so far. Since the model strain Shewanella oneidensis MR-1 is capable of reducing a variety of oxyanions such as iodate, which has a high similarity to bromate, we hypothesize that S. oneidensis MR-1 can reduce bromate. Here, we conducted an experiment to investigate whether S. oneidensis MR-1 can reduce bromate, and report bromate reduction mediated by a dimethylsulfoxide reductase encoded with dmsA . S. oneidensis MR-1 is not a bromate-respiring bacterium but can reduce bromate to bromide under microaerobic conditions. When exposed to 0.15, 0.2, 0.25, 0.5, and 1 mM bromate, S. oneidensis MR-1 reduced bromate by around 100, 75, 64, 48, and 23%, respectively, within 12 h. In vivo evidence from gene deletion mutants and complemented strains of S. oneidensis MR-1 indicates that MtrB, MtrC, CymA, GspD, and DmsA are involved in bromate reduction, but not NapA, FccA, or SYE4. Based on our results as well as previous findings, a proposed molecular mechanism for bromate reduction is presented in this study. Moreover, a genomic survey indicates that 9 of the other 56 reported Shewanella species encode proteins highly homologous to CymA, GspD, and DmsA of S. oneidensis MR-1 by sequence alignment. The results of this study contribute to understanding a pathway for microbial bromate reduction., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wang, Fan, Shen, Ye, Feng, Yang, Wang, Cai and Mao.)

Background: Paraclostridium bifermentans is the most diverse distributed species of Paraclostridium and can cause fatal human infections under rare conditions. However, its pathogenic mechanisms and adaptation ability behind infections remain unclear. Herein, we reported the complete genome sequence of P. bifermentans HD0315_2 isolated from the feces of a patient with Crohn's disease. Then, we performed genomic analyses to understand its pathogenic mechanisms and adaptation ability., Results: The de novo assembly revealed that the HD0315_2 strain carried a circular chromosome of 3.27 Mb and six circular plasmids (19.41 to 139.50 kb). The phylogenomic analysis assigned the HD0315_2 strain as P. bifermentans and reclassified some previously non- P. bifermentans strains into this clade. The general genomic features showed that this species harbored a flexible genomic pool characterized by variable genome length and multiple plasmids. Then, the HD0315_2 strain was predicted as a human pathogen with high probability, and Listeria LIPI-1 virulence proteins were identified on its genome. Besides, abundant antibiotics/metal/stress resistant genes, such as asrABCH, cat, mccF, macB, entS, albA, bcrA , and tetB , were carried by either the genome or the plasmids. Furthermore, we proposed that transposase-directed horizontal gene transfer was responsible for the distribution of multiple copies of the hin gene in the plasmids., Conclusion: The flexible genomic pool of P. bifermentans encodes abundant functions for antimicrobial or oxidative stress resistance, helping it successfully inhabit and adapt to diverse environments. Moreover, P. bifermentans HD0315_2 might infect hosts via a Listeria LIPI-1-like cycle, with the help of a plasmid expressing the Hin DNA invertase to evade host immune responses., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhao, Wang, Peng, Cai, Liu, Huang, Huang and Nie.)

Shewanella decolorationis are Gram-negative γ-Proteobacteria with environmental bioremediation potential because they can perform anaerobic respiration using various types of pollutants as terminal electron acceptors. So far, three isolated and cultured strains of S. decolorationis have been reported. However, no complete S. decolorationis genome has been published yet, which limited exploring their metabolism and feasibility in application. Here, S. decolorationis Ni1-3 isolated from an electroplating wastewater treatment plant showed strong reduction capabilities on azo dyes and oxidized metals. In order to construct the complete genome, high-quality whole-genome sequencing of strain Ni1-3 were performed by using both Nanopore MinION and Illumina NovaSeq platforms, from which the first complete genome of S. decolorationis was obtained by hybrid assembly. The genome of strain Ni1-3 contains a megaplasmid and a circular chromosome which encodes more proteins than that of the strains LDS1 and S12 belonging to the same species. In addition, more Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are identified in strain Ni1-3 genome. Importantly, 32 cytochrome-c and AzoR azoreductase coding genes are identified in the genome, which make strain Ni1-3 competent to degrade the azo dyes and versatile to bioremediate some other environmental pollution. The complete genome sequence of strain Ni1-3 can expand our knowledge toward its metabolic capabilities and potential, meanwhile, provide a reference to reassemble genomes of other S. decolorationis strains., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Tritrophic interactions involving a biocontrol agent, a pathogen, and a plant have been analyzed predominantly from the perspective of the biocontrol agent. To explore the adaptive strategies of wheat in response to beneficial, pathogenic, and combined microorganisms, we performed the first comprehensive transcriptomic, proteomic, and biochemical analysis in wheat roots after exposure to Bacillus velezensis CC09, Gaeumannomyces graminis var. tritici , and their combined colonization, respectively. The transcriptional or translational programming of wheat roots inoculated with beneficial B. velezensis showed mild alterations compared with that of pathogenic G. graminis var. tritici . However, the combination of B. velezensis and G. graminis var. tritici activated a larger transcriptional or translational program than for each single microorganism, although the gene expression pattern was similar to that of individual infection by G. graminis var. tritici , suggesting a prioritization of defense against G. graminis var. tritici infection. Surprisingly, pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity made wheat pretreated with B. velezensis more sensitive to subsequent G. graminis var. tritici infection. Additionally, B. velezensis triggered a salicylic acid (SA)-dependent mode of induced systemic resistance that resembles pathogen-induced systemic acquired resistance. Wheat plants mainly depend on SA-mediated resistance, and not that mediated by jasmonic acid (JA), against the necrotrophic pathogen G. graminis var. tritici. Moreover, SA-JA interactions resulted in antagonistic effects regardless of the type of microorganisms in wheat. Further enhancement of SA-dependent defense responses such as lignification to the combined infection was shown to reduce the level of induced JA-dependent defense against subsequent infection with G. graminis var. tritici . Altogether, our results demonstrate how the hexaploid monocot wheat responds to beneficial or pathogenic microorganisms and prolongs the onset of take-all disease through modulation of cell reprogramming and signaling events.

Biocontrol bacteria that can act like a "vaccine", stimulating plant resistance to pathogenic diseases, are still not fully elucidated. In this study, an endophytic bacterium, Bacillus velezensis CC09, labeled with green fluorescent protein, was tested for its colonization, migration, and expression of genes encoding iturin A synthetase within wheat tissues and organs as well as for protective effects against wheat take-all and spot blotch diseases. The results showed that strain CC09 not only formed biofilm on the root surface but was also widely distributed in almost every tissue, including the epidermis, cortex, and xylem vessels, and even migrated to stems and leaves, resulting in 66.67% disease-control efficacy (DCE) of take-all and 21.64% DCE of spot blotch. Moreover, the gene cluster encoding iturin A synthase under the control of the p itu promoter is expressed in B. velezensis CC09 in wheat tissues, which indicates that iturin A might contribute to the in-vivo antifungal activity and leads to the disease control. All these data suggested that strain CC09 can act like a 'vaccine' in the control of wheat diseases, with a single treatment inoculated on roots through multiple mechanisms.

Bacillus velezensis is a heterotypic synonym of B. methylotrophicus, B. amyloliquefaciens subsp. plantarum, and Bacillus oryzicola, and has been used to control plant fungal diseases. In order to fully understand the genetic basis of antimicrobial capacities, we did a complete genome sequencing of the endophytic B. velezensis strain CC09. Genes tightly associated with biocontrol ability, including nonribosomal peptide synthetases, polyketide synthetases, iron acquisition, colonization, and volatile organic compound synthesis were identified in the genome., (Copyright © 2016 Cai et al.)