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872100.9959Chromium metabolism characteristics of coexpression of ChrA and ChrT gene. OBJECTIVE: Serratia sp. S2 is a wild strain with chromium resistance and reduction ability. Chromium(VI) metabolic-protein-coding gene ChrA and ChrT were cloned from Serratia sp. S2, and ligated with prokaryotic expression vectors pET-28a (+) and transformed into E. coli BL21 to construct ChrA, ChrT and ChrAT engineered bacteria. By studying the characteristics of Cr(VI) metabolism in engineered bacteria, the function and mechanism of the sole expression and coexpression of ChrA and ChrT genes were studied. METHODS: Using Serratia sp. S2 genome as template, ChrA and ChrT genes were amplified by PCR, and prokaryotic expression vectors was ligated to form the recombinant plasmid pET-28a (+)-ChrA, pET-28a (+)-ChrT and pET-28a (+)-ChrAT, and transformed into E. coli BL21 to construct ChrA, ChrT, ChrAT engineered bacteria. The growth curve, tolerance, and reduction of Cr(VI), the distribution of intracellular and extracellular Cr, activity of chromium reductase and intracellular oxidative stress in engineered bacteria were measured to explore the metabolic characteristics of Cr(VI) in ChrA, ChrT, ChrAT engineered bacteria. RESULTS: ChrA, ChrT and ChrAT engineered bacteria were successfully constructed by gene recombination technology. The tolerance to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrA > ChrT > Control (P < 0.05), and the reduction ability to Cr(VI) was Serratia sp. S2 > ChrAT ≈ ChrT > ChrA (P < 0.05). The chromium distribution experiments confirmed that Cr(VI) and Cr(III) were the main valence states. Effect of electron donors on chromium reductase activity was NADPH > NADH > non-NAD(P)H (P < 0.05). The activity of chromium reductase increased significantly with NAD(P)H (P < 0.05). The Glutathione and NPSH (Non-protein Sulfhydryl) levels of ChrA, ChrAT engineered bacteria increased significantly (P < 0.05) under the condition of Cr(VI), but there was no significant difference in the indexes of ChrT engineered bacteria (P > 0.05). CONCLUSION: ChrAT engineered bacteria possesses resistance and reduction abilities of Cr(VI). ChrA protein endows the strain with the ability to resist Cr(VI). ChrT protein reduces Cr(VI) to Cr(III) by using NAD(P)H as electronic donor. The reduction process promotes the production of GSH, GSSG and NPSH to maintain the intracellular reduction state, which further improves the Cr(VI) tolerance and reduction ability of ChrAT engineered bacteria.202032768747
872010.9956Chromium resistance characteristics of Cr(VI) resistance genes ChrA and ChrB in Serratia sp. S2. OBJECTIVE: To find an efficient chromium (VI) resistance system, with a highly efficient, economical, safe, and environmentally friendly chromium-removing strain, ChrA, ChrB, and ChrAB fragments of the chromium (VI) resistance gene in Serratia sp. S2 were cloned, and their prokaryotic expression vectors were constructed and transformed into E. coli BL21. The anti-chromium (VI) capacity and characteristics of engineered bacteria, role of ChrA and ChrB genes in the anti-chromium (VI) processes, and the mechanism of chromium metabolism, were explored. METHODS: The PCR technique was used to amplify ChrA, ChrB, and ChrAB genes from the Serratia sp. S2 genome. ChrA, ChrB, and ChrAB genes were connected to the prokaryotic expression vector pET-28a and transferred into E. coli BL21 for prokaryotic expression. Cr-absorption and Cr-efflux ability of the engineered strains were determined. The effects of respiratory inhibitors and oxygenated anions on Cr-efflux of ChrA and ChrB engineered strains were explored. RESULTS: ChrA, ChrB, and ChrAB engineered strains were constructed successfully; there was no significant difference between the control strain and the ChrB engineered strain for Cr-metabolism (P > 0.05). Cr-absorption and Cr-efflux of ChrA and ChrAB engineered strains were significantly stronger than the control strain (P < 0.05). Oxyanions (sulfate and molybdate) and inhibitors (valinomycin and CN(-)) could significantly inhibit the Cr-efflux capacities of ChrA and ChrAB engineered strains (P < 0.05), while NADPH could significantly promote such capacities (P < 0.05). CONCLUSION: The Cr-transporter, encoded by ChrA gene, confer the ability to pump out intracellular Cr on ChrA and ChrAB engineered strains. The ChrB gene plays a positive regulatory role in ChrA gene regulation. The Cr-metabolism ability of the ChrAB engineered strain is stronger than the ChrA engineered strain. ChrA and ChrAB genes in the Cr-resistance system may involve a variety of mechanisms, such as sulfate ion channel and respiratory chain electron transfer.201829655157
513720.9951Genomic Islands Confer Heavy Metal Resistance in Mucilaginibacter kameinonensis and Mucilaginibacter rubeus Isolated from a Gold/Copper Mine. Heavy metals (HMs) are compounds that can be hazardous and impair growth of living organisms. Bacteria have evolved the capability not only to cope with heavy metals but also to detoxify polluted environments. Three heavy metal-resistant strains of Mucilaginibacer rubeus and one of Mucilaginibacter kameinonensis were isolated from the gold/copper Zijin mining site, Longyan, Fujian, China. These strains were shown to exhibit high resistance to heavy metals with minimal inhibitory concentration reaching up to 3.5 mM Cu((II)), 21 mM Zn((II)), 1.2 mM Cd((II)), and 10.0 mM As((III)). Genomes of the four strains were sequenced by Illumina. Sequence analyses revealed the presence of a high abundance of heavy metal resistance (HMR) determinants. One of the strain, M. rubeus P2, carried genes encoding 6 putative P(IB-1)-ATPase, 5 putative P(IB-3)-ATPase, 4 putative Zn((II))/Cd((II)) P(IB-4) type ATPase, and 16 putative resistance-nodulation-division (RND)-type metal transporter systems. Moreover, the four genomes contained a high abundance of genes coding for putative metal binding chaperones. Analysis of the close vicinity of these HMR determinants uncovered the presence of clusters of genes potentially associated with mobile genetic elements. These loci included genes coding for tyrosine recombinases (integrases) and subunits of mating pore (type 4 secretion system), respectively allowing integration/excision and conjugative transfer of numerous genomic islands. Further in silico analyses revealed that their genetic organization and gene products resemble the Bacteroides integrative and conjugative element CTnDOT. These results highlight the pivotal role of genomic islands in the acquisition and dissemination of adaptive traits, allowing for rapid adaption of bacteria and colonization of hostile environments.201830477188
871930.9950Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source. Here, we present the draft genome sequence of Pseudomonas sp. GC01, a cadmium-resistant Antarctic bacterium capable of biosynthesizing CdS fluorescent nanoparticles (quantum dots, QDs) employing a unique mechanism involving the production of methanethiol (MeSH) from methionine (Met). To explore the molecular/metabolic components involved in QDs biosynthesis, we conducted a comparative genomic analysis, searching for the genes related to cadmium resistance and sulfur metabolic pathways. The genome of Pseudomonas sp. GC01 has a 4,706,645 bp size with a 58.61% G+C content. Pseudomonas sp. GC01 possesses five genes related to cadmium transport/resistance, with three P-type ATPases (cadA, zntA, and pbrA) involved in Cd-secretion that could contribute to the extracellular biosynthesis of CdS QDs. Furthermore, it exhibits genes involved in sulfate assimilation, cysteine/methionine synthesis, and volatile sulfur compounds catabolic pathways. Regarding MeSH production from Met, Pseudomonas sp. GC01 lacks the genes E4.4.1.11 and megL for MeSH generation. Interestingly, despite the absence of these genes, Pseudomonas sp. GC01 produces high levels of MeSH. This is probably associated with the metC gene that also produces MeSH from Met in bacteria. This work is the first report of the potential genes involved in Cd resistance, sulfur metabolism, and the process of MeSH-dependent CdS QDs bioproduction in Pseudomonas spp. strains.202133514061
513140.9949Conjugative Transfer of the pVA1-Type Plasmid Carrying the pirAB(vp) Genes Results in the Formation of New AHPND-Causing Vibrio. Acute hepatopancreatic necrosis disease (AHPND) has caused sharp declines in aquaculture industries of whiteleg shrimp Penaeus vannamei in Asia and the Americas since 2010. Vibrio parahaemolyticus, V. campbellii, V. owensii, and V. punensis have been proved to cause AHPND. However, the mechanisms underlying the burgeoning number of Vibrio species that cause AHPND is not known. All of AHPND-causing Vibrio bacteria (V(AHPND)) harbor a highly homologous plasmid (designated as pVA1-type) carrying pirAB(vp) toxin genes. In this study, we demonstrate conclusively that the pVA1-type plasmid can be transferred from V(AHPND) to non-pathogenic bacteria. We constructed a pVPGX1-Cm(r) plasmid (a pVA1-type plasmid) by adding a chloramphenicol resistance gene as a marker in a donor AHPND-causing V. parahaemolyticus 20130629002S01 (Vp2S01). Horizontal transfer of this plasmid was successfully performed from the AHPND-Vp2S01 to a non-pathogenic strain of V. campbellii at the transfer efficiency of 2.6×10(-8) transconjugant/recipient, and DNase I treatment did not eliminate the transfer. The recipient V. campbellii acquired the pVA1-type plasmid and was shown to produce pirAB(vp) RNA and proteins. Challenge studies using the transconjugant caused 100% mortality in exposed groups of P. vannamei. The challenged shrimp, infected with the transconjugant bacteria, showed typical gross signs and histological lesions of AHPND. These results demonstrated the conjugative transfer of an AHPND pVA1-type plasmid. It provides timely information for explaining the increased species of AHPND-causing Vibrio bacteria and will be useful in the development of management strategies leading to the prevention and control of AHPND.201931231618
635050.9949Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1. BACKGROUND: Chromium is a toxic heavy metal, which primarily exists in two inorganic forms, Cr(VI) and Cr(III). Chromate [Cr(VI)] is carcinogenic, mutational, and teratogenic due to its strong oxidizing nature. Biotransformation of Cr(VI) to less-toxic Cr(III) by chromate-resistant and reducing bacteria has offered an ecological and economical option for chromate detoxification and bioremediation. However, knowledge of the genetic determinants for chromate resistance and reduction has been limited so far. Our main aim was to investigate chromate resistance and reduction by Bacillus cereus SJ1, and to further study the underlying mechanisms at the molecular level using the obtained genome sequence. RESULTS: Bacillus cereus SJ1 isolated from chromium-contaminated wastewater of a metal electroplating factory displayed high Cr(VI) resistance with a minimal inhibitory concentration (MIC) of 30 mM when induced with Cr(VI). A complete bacterial reduction of 1 mM Cr(VI) was achieved within 57 h. By genome sequence analysis, a putative chromate transport operon, chrIA1, and two additional chrA genes encoding putative chromate transporters that likely confer chromate resistance were identified. Furthermore, we also found an azoreductase gene azoR and four nitroreductase genes nitR possibly involved in chromate reduction. Using reverse transcription PCR (RT-PCR) technology, it was shown that expression of adjacent genes chrA1 and chrI was induced in response to Cr(VI) but expression of the other two chromate transporter genes chrA2 and chrA3 was constitutive. In contrast, chromate reduction was constitutive in both phenotypic and gene expression analyses. The presence of a resolvase gene upstream of chrIA1, an arsenic resistance operon and a gene encoding Tn7-like transposition proteins ABBCCCD downstream of chrIA1 in B. cereus SJ1 implied the possibility of recent horizontal gene transfer. CONCLUSION: Our results indicate that expression of the chromate transporter gene chrA1 was inducible by Cr(VI) and most likely regulated by the putative transcriptional regulator ChrI. The bacterial Cr(VI)-resistant level was also inducible. The presence of an adjacent arsenic resistance gene cluster nearby the chrIA1 suggested that strong selective pressure by chromium and arsenic could cause bacterial horizontal gene transfer. Such events may favor the survival and increase the resistance level of B. cereus SJ1.201020723231
904060.9948Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BACKGROUND: Bacteria from the Burkholderia cepacia complex (Bcc) are the only group of cystic fibrosis (CF) respiratory pathogens that may cause death by an invasive infection known as cepacia syndrome. Their large genome (> 7000 genes) and multiple pathways encoding the same putative functions make virulence factor identification difficult in these bacteria. METHODS: A novel microarray was designed to the genome of Burkholderia cenocepacia J2315 and transcriptomics used to identify genes that were differentially regulated when the pathogen was grown in a CF sputum-based infection model. Sputum samples from CF individuals infected with the same B. cenocepacia strain as genome isolate were used, hence, other than a dilution into a minimal growth medium (used as the control condition), no further treatment of the sputum was carried out. RESULTS: A total of 723 coding sequences were significantly altered, with 287 upregulated and 436 downregulated; the microarray-observed expression was validated by quantitative PCR on five selected genes. B. cenocepacia genes with putative functions in antimicrobial resistance, iron uptake, protection against reactive oxygen and nitrogen species, secretion and motility were among the most altered in sputum. Novel upregulated genes included: a transmembrane ferric reductase (BCAL0270) implicated in iron metabolism, a novel protease (BCAL0849) that may play a role in host tissue destruction, an organic hydroperoxide resistance gene (BCAM2753), an oxidoreductase (BCAL1107) and a nitrite/sulfite reductase (BCAM1676) that may play roles in resistance to the host defenses. The assumptions of growth under iron-depletion and oxidative stress formulated from the microarray data were tested and confirmed by independent growth of B. cenocepacia under each respective environmental condition. CONCLUSION: Overall, our first full transcriptomic analysis of B. cenocepacia demonstrated the pathogen alters expression of over 10% of the 7176 genes within its genome when it grows in CF sputum. Novel genetic pathways involved in responses to antimicrobial resistance, oxidative stress, and iron metabolism were revealed by the microarray analysis. Virulence factors such as the cable pilus and Cenocepacia Pathogenicity Island were unaltered in expression. However, B. cenocepacia sustained or increased expression of motility-associated genes in sputum, maintaining a potentially invasive phenotype associated with cepacia syndrome.200818801206
870470.9947Unraveling nitrogen metabolism, cold and stress adaptation in polar Bosea sp. PAMC26642 through comparative genome analysis. Nitrogen metabolism, related genes, and other stress-resistance genes are poorly understood in Bosea strain. To date, most of the research work in Bosea strains has been focused on thiosulfate oxidation and arsenic reduction. This work aimed to better understand and identify genomic features that enable thiosulfate-oxidizing lichen-associated Bosea sp. PAMC26642 from the Arctic region of Svalbard, Norway, to withstand harsh environments. Comparative genomic analysis was performed using various bioinformatics tools to compare Bosea sp. PAMC26642 with other strains of the same genus, emphasizing nitrogen metabolism and stress adaptability. During genomic analysis of Bosea sp. PAMC26642, assimilatory nitrogen metabolic pathway and its associated enzymes such as nitrate reductase, NAD(P)H-nitrite reductase, ferredoxin-nitrite reductase, glutamine synthetase, glutamine synthase, and glutamate dehydrogenase were identified. In addition, carbonic anhydrase, cyanate lyase, and nitronate monooxygenase were also identified. Furthermore, the strain demonstrated nitrate reduction at two different temperatures (15°C and 25°C). Enzymes associated with various stress adaptation pathways, including oxidative stress (superoxide dismutase, catalase, and thiol peroxidase), osmotic stress (OmpR), temperature stress (Csp and Hsp), and heavy metal resistance, were also identified. The average Nucleotide Identity (ANI) value is found to be below the threshold of 94-95%, indicating this bacterium might be a potential new species. This study is very helpful in determining the diversity of thiosulfate-oxidizing nitrate-reducing bacteria, as well as their ability to adapt to extreme environments. These bacteria can be used in the future for environmental, biotechnological, and agricultural purposes, particularly in processes involving sulfur and nitrogen transformation.202439925882
868680.9947Improving Cadmium Resistance in Escherichia coli Through Continuous Genome Evolution. Cadmium (Cd) is a heavy metal that is extremely toxic to many organisms; however, microbes are highly adaptable to extreme conditions, including heavy metal contamination. Bacteria can evolve in the natural environment, generating resistant strains that can be studied to understand heavy-metal resistance mechanisms, but obtaining such adaptive strains usually takes a long time. In this study, the genome replication engineering assisted continuous evolution (GREACE) method was used to accelerate the evolutionary rate of the Escherichia coli genome to screen for E. coli mutants with high resistance to cadmium. As a result, a mutant (8mM-CRAA) with a minimum inhibitory concentration (MIC) of 8 mM cadmium was generated; this MIC value was approximately eightfold higher than that of the E. coli BL21(DE3) wild-type strain. Sequencing revealed 329 single nucleotide polymorphisms (SNPs) in the genome of the E. coli mutant 8mM-CRAA. These SNPs as well as RNA-Seq data on gene expression induced by cadmium were used to analyze the genes related to cadmium resistance. Overexpression, knockout and mutation of the htpX (which encodes an integral membrane heat shock protein) and gor (which encodes glutathione reductase) genes revealed that these two genes contribute positively to cadmium resistance in E. coli. Therefore, in addition to the previously identified cadmium resistance genes zntA and capB, many other genes are also involved in bacterial cadmium resistance. This study assists us in understanding the mechanism of microbial cadmium resistance and facilitating the application of heavy-metal remediation.201930842762
608390.9946Bioactivity and genome analysis of Bacillus amyloliquefaciens GL18 isolated from the rhizosphere of Kobresia myosuroides in an alpine meadow. The unique eco-environment of the Qinghai-Tibet Plateau breeds abundant microbial resources. In this research, Bacillus amyloliquefaciens GL18, isolated from the rhizosphere of Kobresia myosuroides from an alpine meadow, and the antagonistic activity, bacteriostatic hydrolase activity, and low temperature, salt, and drought resistance of it were determined and analysed. The seedlings of Avena sativa were root-irrigated using bacteria suspensions (cell concentration 1 × 10(7) cfu/mL) of GL18, and the growth-promoting effect of GL18 on it was determined under cold, salt and drought stress, respectively. The whole genome of GL18 was sequenced, and its functional genes were analysed. GL18 presented significant antagonistic activity to Fusarium graminearum, Fusarium acuminatum, Fusarium oxysporum and Aspergillus niger (inhibition zone diameter > 17 mm). Transparent zones formed on four hydrolase detection media, indicating that GL18 secreted cellulase, protease, pectinase and β-1,3-glucanase. GL18 tolerated conditions of 10 °C, 11% NaCl and 15% PEG-6000, presenting cold, salt and drought resistance. GL18 improved the cold, salt and drought tolerance of A. sativa and it showed significant growth effects under different stress. The total length of the GL18 genome was 3,915,550 bp, and the number of coding DNA sequence was 3726. Compared with the clusters of orthologous groups of proteins, gene ontology and kyoto encyclopedia of genes and genomes databases, 3088, 2869 and 2357 functional genes were annotated, respectively. GL18 contained gene clusters related to antibacterial substances, functional genes related to the synthesis of plant growth-promoting substances, and encoding genes related to stress resistance. This study identified an excellent Bacillus strain and provided a theoretical basis for improving stress resistance and promoting the growth of herbages under abiotic stress.202438189906
5130100.9946Genomic mining of Vibrio parahaemolyticus highlights prevalence of antimicrobial resistance genes and new genetic markers associated with AHPND and tdh + /trh + genotypes. BACKGROUND: Acute Hepatopancreatic Necrosis Disease (AHPND) causes significant mortality in shrimp aquaculture. The infection is primarily instigated by Vibrio parahaemolyticus (Vp) strains carrying a plasmid encoding the binary toxin PirAB. Yet, comprehension of supplementary virulence factors associated with this relatively recent disease remains limited. Furthermore, the same holds for gastroenteritis in humans caused by other Vp genotypes. Additionally, given the prevalent use of antibiotics to combat bacterial infections, it becomes imperative to illuminate the presence of antimicrobial resistance genes within these bacteria. RESULTS: A subsampled number of 1,036 Vp genomes was screened for the presence of antimicrobial resistance genes, revealing an average prevalence of 5 ± 2 (SD) genes. Additional phenotypic antimicrobial susceptibility testing of three Vp strains (M0904, TW01, and PV1) sequenced in this study demonstrated resistance to ampicillin by all tested strains. Additionally, Vp M0904 showed multidrug resistance (against ampicillin, tetracycline, and trimethoprim-sulfamethoxazole). With a focus on AHPND, a screening of all Vibrio spp. for the presence of pirA and/or pirB indicates an estimated prevalence of 0.6%, including four V. campbellii, four V. owensii, and a Vibrio sp. next to Vp. Their pirAB-encoding plasmids exhibited a highly conserved backbone, with variations primarily in the region of the Tn3 family transposase. Furthermore, an assessment of the subsampled Vp genomes for the presence of known virulence factors showed a correlation between the presence of the Type 3 Secretion System 2 and tdh, while the presence of the Type 6 Secretion System 1 was clade dependent. Furthermore, a genome-wide association study (GWAS) unveiled (new) genes associated with pirA, pirB, tdh, and trh genotypes. Notable associations with the pirAB genotype included outer membrane proteins, immunoglobulin-like domain containing proteins, and toxin-antitoxin systems. For the tdh + /trh + genotypes (containing tdh, trh, or both genes), associations were found with T3SS2 genes, urease-related genes and nickel-transport system genes, and genes involved in a 'minimal' type I-F CRISPR mechanism. CONCLUSIONS: This study highlights the prevalence of antimicrobial resistance and virulence genes in Vp, identifying novel genetic markers associated with AHPND and tdh + /trh + genotypes. These findings contribute valuable insights into the genomic basis of these genotypes, with implications for shrimp aquaculture and food safety.202438355437
6086110.9946Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain. Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na(2)HAsO(4)·7H(2)O was identified using the 16S rRNA gene and whole genome analysis as Enterobacter cloacae FACU. The arsenic E. cloacae FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of E. cloacae FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the E. cloacae FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five arsRDABC genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of E. cloacae FACU at the genetic level.202439320439
8818120.9946Metatranscriptomic analysis of adaptive response of anammox bacteria Candidatus 'Kuenenia stuttgartiensis' to Zn(II) exposure. Zn(II) is frequently detected in biological nitrogen removal systems treating high-strength wastewater (e.g., landfill leachate), yet the cellular defense strategies of anammox bacteria against Zn(II) cytotoxicity is largely unknown. To uncover survival mechanisms under Zn(II) stress, responses of enriched anammox bacteria Candidatus 'Kuenenia stuttgartiensis' under exposure of various levels of Zn (II) were investigated through metatranscriptomic sequencing. Although increasing Zn(II) levels (50, 100 and 150 mg/L) resulted in decreasing anammox activities (86.1 ± 0.8%, 66.1 ± 1.4% and 43.9 ± 1.5% of the control, respectively), the viable cells in anammox sludge remained stable. Candidatus 'K. stuttgartiensis' possesses a complex network of regulatory systems to confer cells with the ability against Zn(II) toxicity, including functions related to substrate degradation, Zn(II) efflux, chelation, DNA repair, protein degradation, protein synthesis and signal transduction processes. Particularly, in order to maintain Zn(II) homeostasis, Candidatus 'K. stuttgartiensis' upregulated genes encoding RND efflux family (czcA, czcB, czcC, kustd1923 and kuste2279) for exporting Zn(II) actively. These heavy metal exporting genes could act as "sentinel genes" to detect the initial stage of Zn(II) inhibition on anammox bacteria, which might be beneficial to develop a diagnostic approach to predict the risk of operational failure when Zn(II) shock occurs.202031901527
8681130.9946The regulatory mechanism of Chryseobacterium sp. resistance mediated by montmorillonite upon cadmium stress. Cadmium (Cd) is a toxic heavy metal and its uptake by living organisms causes adverse effect, further resulting in cycle pollution of the biosphere. The specific regulatory mechanism between clays and microbes under Cd stress remains unclear. In this study, interface interactions among clays, microbes and Cd were confirmed. Comparative transcriptome was conducted to investigate how it regulated gene expression patterns of microbes (Chryseobacterium sp. WAL2), which exposed to a series of gradient concentrations of Cd (16, 32, 64 and 128 μg mL(-1)) for 12 d in the presence and absence of clay montmorillonite (Mt) (16 g L(-1)). Cd was highly enriched by the unique interface interactions between Mt and bacteria (67.6-82.1%), leading to a more hostile environment for bacterial cells. However, Mt ultimately enhanced bacterial resistance to Cd stress by stimulating the mechanism of bacterial resistance; namely: (i) Mt increased genes expression connected with ion transport, enhancing the uptake of Cd; (ii) Mt stimulated genes expression related to efflux pump and positively regulated cellular oxidative stress (e.g., glutathione) and Cd accumulation (e.g., cysteine) processes. Further, genes expression related to intracellular metabolic processes was enforced, which supplied a driving force and accelerated electron transfer; (iii) Mt improved genes expression involved in DNA replication and other biological processes (e.g., terpenoid backbone biosynthesis) to maintain bacterial vitality. Therefore, the study not only optimized a unique Cd resistance mechanism of Mt on Chryseobacterium sp., but also provided a novel insight for environmental mitigation of heavy metals from the perspective of molecular biology.202031546187
5139140.9946Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15. Chromosomal co-existence of metal and antibiotic resistance genes in bacteria offers a new perspective to the bacterial resistance proliferation in contaminated environment. In this study, an arsenotrophic bacterium Achromobacter xylosoxidans BHW-15, isolated from Arsenic (As) contaminated tubewell water in the Bogra district of Bangladesh, was analyzed using high throughput Ion Torrent Personal Genome Machine (PGM) complete genome sequencing scheme to reveal its adaptive potentiality. The assembled draft genome of A. xylosoxidans BHW-15 was 6.3 Mbp containing 5,782 functional genes, 1,845 pseudo genes, and three incomplete phage signature regions. Comparative genome study suggested the bacterium to be a novel strain of A. xylosoxidans showing significant dissimilarity with other relevant strains in metal resistance gene islands. A total of 35 metal resistance genes along with arsenite-oxidizing aioSXBA, arsenate reducing arsRCDAB, and mercury resistance merRTPADE operonic gene cluster and 20 broad range antibiotic resistance genes including β-lactams, aminoglycosides, and multiple multidrug resistance (MDR) efflux gene complex with a tripartite system OM-IM-MFP were found co-existed within the genome. Genomic synteny analysis with reported arsenotrophic bacteria revealed the characteristic genetic organization of ars and mer operonic genes, rarely described in β-Proteobacteria. A transposon Tn21 and mobile element protein genes were also detected to the end of mer (mercury) operonic genes, possibly a carrier for the gene transposition. In vitro antibiotic susceptibility assay showed a broad range of resistance against antibiotics belonging to β-lactams, aminoglycosides, cephalosporins (1st, 2nd, and 3rd generations), monobactams and even macrolides, some of the resistome determinants were predicted during in silico analysis. KEGG functional orthology analysis revealed the potential of the bacterium to utilize multiple carbon sources including one carbon pool by folate, innate defense mechanism against multiple stress conditions, motility, a proper developed cell signaling and processing unit and secondary metabolism-combination of all exhibiting a robust feature of the cell in multiple stressed conditions. The complete genome of the strain BHW-15 stands as a genetic basis for the evolutionary adaptation of metal and the antibiotic coexistence phenomenon in an aquatic environment.201930886770
6118150.9945Integrated genomics and transcriptomics reveal the extreme heavy metal tolerance and adsorption potentiality of Staphylococcus equorum. In this study, we successfully isolated 11 species of cadmium-tolerant bacterium from Pu-erh rhizosphere soil, of which Staphylococcus equorum PU1 showed the highest cadmium tolerance, with a minimum inhibitory concentration (MIC) value of 500 mg/L. The cadmium removal efficiency of PU1 in 400 mg/L cadmium medium reached 58.7 %. Based on the Nanopore PromethION and Illumina NovaSeq platforms, we successfully obtained the complete PU1 genome with a size of 2,705,540 bp, which encoded 2729 genes. We further detected 82 and 44 indel mutations in the PU1 genome compared with the KS1039 and KM1031 genomes from the database. Transcriptional analysis showed that the expression of 11 genes in PU1 increased with increasing cadmium concentrations (from 0 to 200, then to 400 mg/L), which encoded cadmium resistance, cadmium transport, and mercury resistance genes. In addition, some genes showed differential expression patterns with changes in cadmium concentration, including quinone oxidoreductase-like protein, ferrous iron transport protein, and flavohemoprotein. Gene Ontology (GO) functions, including oxidation reduction process and oxidoreductase activity functions, and KEGG pathways, including glycolysis/gluconeogenesis and biosynthesis of secondary metals, were also considered closely related to the extreme cadmium tolerance of PU1. This study provides novel insight into the cadmium tolerance mechanism of bacteria.202336592848
6138160.9945Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.202032405446
6149170.9945Characterization and whole-genome sequencing of an extreme arsenic-tolerant Citrobacter freundii SRS1 strain isolated from Savar area in Bangladesh. Citrobacter freundii SRS1, gram-negative bacteria, were isolated from Savar, Bangladesh. The strain could tolerate up to 80 mmol L(-1) sodium arsenite, 400 mmol L(-1) sodium arsenate, 5 mmol L(-1) manganese sulfate, 3 mmol L(-1) lead nitrate, 2.5 mmol L(-1) cobalt chloride, 2.5  mmol L(-1) cadmium acetate, and 2.5 mmol L(-1) chromium chloride. The whole-genome sequencing revealed that the genome size of C. freundii SRS1 is estimated to be 5.4 Mb long, and the G + C content is 51.7%. The genome of C. freundii SRS1 contains arsA, arsB, arsC, arsD, arsH, arsR, and acr3 genes for arsenic resistance; czcA, czcD, cbiN, and cbiM genes for cobalt resistance; chrA and chrB genes for chromium resistance; mntH, sitA, sitB, sitC, and sitD genes for manganese resistance; and zntA gene for lead and cadmium resistance. This novel acr3 gene has never previously been reported in any C. freundii strain except SRS1. A set of 130 completely sequenced strains of C. freundii was selected for phylogenomic analysis. The phylogenetic tree showed that the SRS1 strain is closely related to the C. freundii 62 strain. Further analyses of the genes involved in metal and metalloid resistance might facilitate identifying the mechanisms and pathways involved in high metal resistance in the C. freundii SRS1 strain.202336332226
7832180.9945Reduction of antibiotics and antibiotic resistance genes in simulated-sunlight-supported counter-diffusion bacteria-Algae biofilms: Interface properties and functional gene responses. A novel bacteria-algae symbiotic counter-diffusion biofilm system integrated within simulated-sunlight (designated UV-MABAR) was engineered to simultaneously address antibiotic residuals and antibiotic resistance genes (ARGs) while maintaining functional microbial consortia under simulated solar irradiation. The non-algal control system (UV-MABR) demonstrated elevated repulsion energy barriers accompanied by significant suppression of ATP synthase (p < 0.01) and DNA repair-related gene clusters, leading to biofilm homeostasis disruption and subsequent sulfamethoxazole (SMX) effluent accumulation peaking at 138.11±2.34 μg/L. In contrast, the UV-MABAR configuration exhibited dynamic quenching of tyrosine-associated fluorescence moieties within extracellular polymeric substances, thereby diminishing complexation potential with SMX aromatic rings and achieving 70.75 %±3.21 % abiotic photodegradation efficiency, which substantially curtailed ARG proliferation pathways, promoting a significant downregulation of sul1 (-1.9 log(2) fold-change) and sul2 (-1.1 log(2) fold-change) expression compared to conventional MABR controls. Besides, algal in UV-MABAR attenuated the irradiation-induced α-helix/(β-sheet + random coil) conformational shift, moderating biofilm matrix compaction. Crucially, algal proliferation up-regulated bacterial recA expression (1.7-fold increase), thereby preserving catabolic gene integrity and preventing endogenous substances release. These protective measures kept effluent concentrations of SMX, NH(4)(+)-N, total nitrogen, and COD in UV-MABAR at 19.84 μg/L, 3.88 mg/L, 12.76 mg/L, and 34.97 mg/L, respectively, during 150 days of operation.202540738088
191190.9945Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO(2), carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.201121966516