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Microbiology Resource Announcements Dec 2023We report here the draft genome sequences of ( = 1), ( = 1), ( =1), spp. ( = 5), ( = 3), and isolated from high-touch surfaces in washrooms at a post-secondary...
We report here the draft genome sequences of ( = 1), ( = 1), ( =1), spp. ( = 5), ( = 3), and isolated from high-touch surfaces in washrooms at a post-secondary institution.
PubMed: 37971276
DOI: 10.1128/MRA.00910-23 -
Current Research in Microbial Sciences 2023Rhizobacteria associated with cultivated crops are known to stimulate plant growth through various indirect or direct mechanisms. In recent years, the host list of plant...
Rhizobacteria associated with cultivated crops are known to stimulate plant growth through various indirect or direct mechanisms. In recent years, the host list of plant growth promotion/promoting rhizobacteria has expanded to include bean, barley, cotton, maize, rice, vegetables, peanut, rice, wheat, and several plantation crops. However, interaction of rhizobacteria with tea plants of organic and conventional tea gardens is poorly understood. In the present study, rhizobacterial species associated with tea rhizosphere were isolated from 14 tea gardens located in North Bengal, India. In total, 16 rhizobacterial isolates isolated from collected soil samples were assessed for antagonistic and plant growth promotion/promoting activity under laboratory conditions. Molecular characterization based on sequencing of 16S rRNA gene revealed dominance of with five species followed by with two species. Interestingly, only one isolate was affiliated with actinobacteria, i.e., . Out of 16 isolates, isolates OKAKP01, BNLG01, BOK01, BPATH02, and BSEY01 showed highest growth inhibition against (68.2 to 72.8%), (71.1 to 85.6%), and (67.4 to 78.3%) causing respective Fusarium dieback, gray blight, and blister blight diseases in tea crop. Further, these five isolates also possessed significantly greater antifungal (siderophore producer, protease, chitinase, and cellulase activity) and plant growth promotion/promoting (indole-3-acetic acid production, ACC deaminase, ammonia, and phosphate solubilization) traits over other eleven rhizobacterial isolates. Therefore, these five isolates of rhizobacteria were chosen for their plant growth promotion/promoting activity on tea plants in nursery conditions. Results from nursery experiments revealed that these five rhizobacteria significantly improved growth rates of tea plants compared with the control. Therefore, this study suggests that these rhizobacteria could be used to formulate biopesticides and biofertilizers, which could be applied to sustainable tea cultivation to improve crop health and reduce disease attack.
PubMed: 37706093
DOI: 10.1016/j.crmicr.2023.100200 -
Frontiers in Microbiology 2023This research aims to elucidate the physiological mechanisms behind the accidental acquisition of high-concentration cesium ions (Cs) tolerance of and apply this...
This research aims to elucidate the physiological mechanisms behind the accidental acquisition of high-concentration cesium ions (Cs) tolerance of and apply this understanding to develop bioremediation technologies. Bacterial Cs resistance has attracted attention, but its physiological mechanism remains largely unknown and poorly understood. In a prior study, we identified the Cs/H antiporter TS_CshA in sp. TS-1, resistant to high Cs concentrations, exhibits a low Cs affinity with a value of 370 mM at pH 8.5. To enhance bioremediation efficacy, we conducted random mutagenesis of using Error-Prone PCR, aiming for higher-affinity mutants. The mutations were inserted downstream of the P promoter in the pBAD24 vector, creating a mutant library. This was then transformed into -competent cells. As a result, we obtained a Cs-resistant strain, ZX-1, capable of thriving in 400 mM CsCl-a concentration too high for ordinary . Unlike the parent strain Mach1, which struggled in 300 mM CsCl, ZX-1 showed robust growth even in 700 mM CsCl. After 700 mM CsCl treatment, the 70S ribosome of Mach1 collapsed, whereas ZX-1 and its derivative ΔZX-1/pBR322ΔAp remained stable. This means that the ribosomes of ZX-1 are more stable to high Cs. The inverted membrane vesicles from strain ZX-1 showed an apparent value of 28.7 mM (pH 8.5) for Cs/H antiport activity, indicating an approximately 12.9-fold increase in Cs affinity. Remarkably, the entire plasmid isolated from ZX-1, including the region, was mutation-free. Subsequent whole-genome analysis of ZX-1 identified multiple SNPs on the chromosome that differed from those in the parent strain. No mutations in transporter-related genes were identified in ZX-1. However, three mutations emerged as significant: genes encoding the ribosomal bS6 modification enzyme RimK, the phage lysis regulatory protein LysB, and the flagellar base component protein FlgG. These mutations are hypothesized to affect post-translational modifications, influencing the value of TS_CshA and accessory protein expression. This study unveils a novel Cs resistance mechanism in ZX-1, enhancing our understanding of Cs resistance and paving the way for developing technology to recover radioactive Cs from water using TS_CshA-expressing inverted membrane vesicles.
PubMed: 38304862
DOI: 10.3389/fmicb.2023.1340033 -
Microbial Ecology Jan 2024Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions...
Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.
Topics: Ecosystem; Lakes; Metagenome; Bacteria; Potamogetonaceae; Nitrogen
PubMed: 38286834
DOI: 10.1007/s00248-024-02346-7 -
Heliyon Mar 2024In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a...
Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture.
In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, , , KB913035, , and , known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included , , , , , , , , , and Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.
PubMed: 38533070
DOI: 10.1016/j.heliyon.2024.e27985 -
Environmental Science & Technology Jun 2024The presence of organic micropollutants in water and sediments motivates investigation of their biotransformation at environmentally low concentrations, usually in the...
The presence of organic micropollutants in water and sediments motivates investigation of their biotransformation at environmentally low concentrations, usually in the range of μg L. Many are biotransformed by cometabolic mechanisms; however, there is scarce information concerning their direct metabolization in this concentration range. Threshold concentrations for microbial assimilation have been reported in both pure and mixed cultures from different origins. The literature suggests a range value for bacterial growth of 1-100 μg L for isolated aerobic heterotrophs in the presence of a single substrate. We aimed to investigate, as a model case, the threshold level for sulfamethoxazole (SMX) metabolization in pure cultures of strain BR1. Previous research with this strain has covered the milligram L range. In this study, acclimated cultures were exposed to concentrations from 0.1 to 25 μg L of C-labeled SMX, and the C-CO produced was trapped and quantified over 24 h. Interestingly, SMX removal was rapid, with 98% removed within 2 h. In contrast, mineralization was slower, with a consistent percentage of 60.0 ± 0.7% found at all concentrations. Mineralization rates increased with rising concentrations. Therefore, this study shows that bacteria are capable of the direct metabolization of organic micropollutants at extremely low concentrations (sub μg L).
Topics: Sulfamethoxazole; Water Pollutants, Chemical
PubMed: 38761139
DOI: 10.1021/acs.est.4c02191 -
Biology Nov 2023The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial...
The efficiency of plant-growth-promoting rhizobacteria (PGPR) may not be consistently maintained under field conditions due to the influence of soil microbial communities. The present study aims to investigate their impact on three PGPR-based biofertilizers in wheat. We used the PGPR sp. strain B2 (PB2), PB2 in co-inoculation with 4042 (Mix 2), or with sp. SSM-004 and sp. SSM-001 (Mix 3). Inoculation of PB2, Mix 2, and Mix 3 into non-sterile field soil had a positive effect on root and aboveground dry biomass, depending on the wheat cultivar. The efficiency of the PGPR was further confirmed by the protection they provided against , the causal agent of Septoria leaf blotch disease. PB2 exhibited protection of ≥37.8%, while Mix 2 showed ≥47.9% protection in the four cultivars tested. These results suggest that the interactions between PGPR and native soil microbial communities are crucial for promoting wheat growth and protection. Additionally, high-throughput sequencing of microbial communities conducted 7 days after PGPR inoculations revealed no negative effects of PB2, Mix 2, and Mix 3 on the soil microbial community structure. Interestingly, the presence of spp. appeared to mitigate the potential negative effect of PB2 on bacterial community and foster root colonization by other beneficial bacterial strains.
PubMed: 37998015
DOI: 10.3390/biology12111416 -
Frontiers in Cellular and Infection... 2024Gallstones are crystalline deposits in the gallbladder that are traditionally classified as cholesterol, pigment, or mixed stones based on their composition. Microbiota...
Gallstones are crystalline deposits in the gallbladder that are traditionally classified as cholesterol, pigment, or mixed stones based on their composition. Microbiota and host metabolism variances among the different types of gallstones remain largely unclear. Here, the bile and gallstone microbial species spectra of 29 subjects with gallstone disease (GSD, 24 cholesterol and 5 pigment) were revealed by type IIB restriction site-associated DNA microbiome sequencing (2bRAD-M). Among them (21 subjects: 18 cholesterol and 3 pigment), plasma samples were subjected to liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics. The microbiome yielded 896 species comprising 882 bacteria, 13 fungi, and 1 archaeon. Microbial profiling revealed significant enrichment of and sp005774735 in gallstone and and sp013044135 in the bile of cholesterol GSD subjects. The metabolome revealed 2296 metabolites, in which malvidin 3-(6''-malonylglucoside), 2-Methylpropyl glucosinolate, and ergothioneine were markedly enriched in cholesterol GSD subjects. Metabolite set enrichment analysis (MSEA) demonstrated enriched bile acids biosynthesis in individuals with cholesterol GSD. Overall, the multi-omics analysis revealed that microbiota and host metabolism interaction perturbations differ depending on the disease type. Perturbed gallstone type-related microbiota may contribute to unbalanced bile acids metabolism in the gallbladder and host, representing a potential early diagnostic marker and therapeutic target for GSD.
Topics: Humans; Gallstones; Bile Acids and Salts; Bile; Cholesterol
PubMed: 38529471
DOI: 10.3389/fcimb.2024.1283737 -
Food Chemistry: X Dec 2023Pyrroloquinoline quinone disodium (PQQ·Na) has been considered a human food supplement for human health promotion with its antioxidant properties. To determine whether...
Pyrroloquinoline quinone disodium (PQQ·Na) has been considered a human food supplement for human health promotion with its antioxidant properties. To determine whether PQQ·Na had similar functions to improve the antioxidant ability of layers and eggs, 180 laying hens were fed with 0 or 0.4 mg/kg PQQ·Na diets. Supplementation with PQQ·Na increased the albumen height, Haugh unit of the eggs. PQQ·Na also led to a higher glutathione peroxidase (GSH-Px) concentration in plasma and a lower malondialdehyde (MDA) content in the liver and egg yolk. Similarly, liver gene and protein expression of nuclear factor erythroid 2-related 2 (Nrf2) and heme oxygenase 1 (HO-1) were up-regulated by PQQ·Na Moreover, PQQ·Na increased the abundance of , and in gut. Overall, these results suggested PQQ·Na increased the antioxidant ability of layers and eggs which might be in connection with the activation of the Nrf2/HO-1 pathway and optimized gut microflora.
PubMed: 38144785
DOI: 10.1016/j.fochx.2023.101021 -
Frontiers in Microbiology 2024, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African...
, a wild plant in southern Africa, is utilized in traditional medicine for various ailments, leading to its endangerment and listing on the Red List of South African Plants. To date, there have been no reports on bacterial endophytes from this plant, their classes of secondary metabolites, and potential medicinal properties. This study presents (i) taxonomic characterization of bacterial endophytes in leaf and root tissues using 16S rRNA, (ii) bacterial isolation, morphological, and phylogenetic characterization, (iii) bacterial growth, metabolite extraction, and LC-MS-based metabolite fingerprinting, and (iv) antimicrobial testing of bacterial crude extracts. Next-generation sequencing yielded 693 and 2,459 DNA read counts for the rhizomes and leaves, respectively, detecting phyla including Proteobacteria, Bacteroidota, Gemmatimonadota, Actinobacteriota, Verrucomicrobiota, Dependentiae, Firmicutes, and Armatimonodata. At the genus level, , , , and Ralstonia were the most dominant in both leaves and rhizomes. From root tissues, four bacterial isolates were selected, and 16S rRNA-based phylogenetic characterization identified two closely related sp. (strain BNWU4 and 5), BNWU2, and BNWU1. The ethyl acetate:chloroform (1:1 v/v) organic extract from each isolate exhibited antimicrobial activity against all selected bacterial pathogens. Strain BNWU5 displayed the highest activity, with minimum inhibitory concentrations ranging from 62.5 μg/mL to 250 μg/mL against diarrhoeagenic , , , antibiotic-resistant , , , and . LC-MS analysis of the crude extract revealed common antimicrobial metabolites produced by all isolates, including Phenoxomethylpenicilloyl (penicilloyl V), cis-11-Eicosenamide, 3-Hydroxy-3-phenacyloxindole, and 9-Octadecenamide.
PubMed: 38855763
DOI: 10.3389/fmicb.2024.1383854