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Bioresources and Bioprocessing Jun 2024Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum...
Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum SIT101 through genome mining and phylogenetic analysis. EstSIT01 demonstrated remarkable efficiency in asymmetrically hydrolyzing meso-dimethyl ester [Dimethyl cis-1,3-Dibenzyl-2-imidazolidine-4,5-dicarboxyate], producing over 99% yield and 99% enantiomeric excess (e.e.) for (4S, 5R)-monomethyl ester, a crucial chiral intermediate during the synthesis of d-biotin. Notably, the recombinant E. coli expressing EstSIT01 exhibited over 40-fold higher activity than that of the wild strain. EstSIT01 displays a preference for short-chain p-NP esters. The optimal temperature and pH were 45 °C and 10.0, with K and k values of 0.147 mmol/L and 5.808 s, respectively. Molecular docking and MD simulations suggest that the high stereoselectivity for meso-diester may attribute to the narrow entrance tunnel and unique binding pocket structure. Collectively, EstSIT01 holds great potential for preparing chiral carboxylic acids and esters.
PubMed: 38879848
DOI: 10.1186/s40643-024-00776-2 -
Microbiology Resource Announcements Jun 2024We purified a lytic bacteriophage from soil collected in Guasave, Sinaloa: phiExGM16. This bacteriophage was isolated using the host, . Its 17.6 kb genome contains 33...
We purified a lytic bacteriophage from soil collected in Guasave, Sinaloa: phiExGM16. This bacteriophage was isolated using the host, . Its 17.6 kb genome contains 33 putative genes and shows a cover of 64% with 76.37% of nucleotide identity to Noelani.
PubMed: 38860812
DOI: 10.1128/mra.00342-24 -
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 -
Frontiers in Microbiology 2024Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the familiy, leading to... (Review)
Review
Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that and are the most prevalent genera of nodule endophytic bacteria, succeeded by , , , , and . To date, the bibliographic data available show that followed by and are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of and as the most abundant nodule endophytic bacteria, alongside , , and . Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.
PubMed: 38812696
DOI: 10.3389/fmicb.2024.1386742 -
Scientific Reports May 2024In the present study, ten (10) selected bacteria isolated from chasmophytic wild Chenopodium were evaluated for alleviation of drought stress in chickpea. All the...
In the present study, ten (10) selected bacteria isolated from chasmophytic wild Chenopodium were evaluated for alleviation of drought stress in chickpea. All the bacterial cultures were potential P, K and Zn solubilizer. About 50% of the bacteria could produce Indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The bacteria showed wide range of tolerance towards pH, salinity, temperature and osmotic stress. Bacillus paralicheniformis L38, Pseudomonas sp. LN75, Enterobacter hormachei subsp. xiangfengensis LJ89, B. paramycoides L17 and Micrococcus luteus LA9 significantly improved growth and nutrient (N, P, K, Fe and Zn) content in chickpea under water stress during a green house experiment conducted following a completely randomized design (CRD). Application of Microbacterium imperiale LJ10, B. stercoris LN74, Pseudomonas sp. LN75, B. paralicheniformis L38 and E. hormachei subsp. xiangfengensis LJ89 reduced the antioxidant enzymes under water stress. During field experiments conducted following randomized block design (RBD), all the bacterial inoculations improved chickpea yield under water stress. Highest yield (1363 kg ha) was obtained in plants inoculated with Pseudomonas sp. LN75. Pseudomonas sp. LN75, B. paralicheniformis L38 and E. hormachei subsp. xiangfengensis LJ89 have potential as microbial stimulants to alleviate the water stress in chickpea. To the best of our knowledge this is the first report of using chasmophyte associated bacteria for alleviation of water stress in a crop plant.
Topics: Cicer; Droughts; Stress, Physiological; Bacteria; Indoleacetic Acids; Nutrients; Carbon-Carbon Lyases; Enterobacter; Pseudomonas; Antioxidants
PubMed: 38806526
DOI: 10.1038/s41598-024-58695-3 -
Molecules (Basel, Switzerland) May 2024Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic...
Environmental pollution stands as one of the significant global challenges we face today. Polycyclic aromatic hydrocarbons (PAHs), a class of stubborn organic pollutants, have long been a focal point of bioremediation research. This study aims to explore the impact and mechanisms of graphene oxide (GO) on the phytoremediation effectiveness of PAHs. The results underscore the significant efficacy of GO in accelerating the degradation of PAHs. Additionally, the introduction of GO altered the diversity and community structure of endophytic bacteria within the roots, particularly those genera with potential for PAH degradation. Through LEfSe analysis and correlation studies, we identified specific symbiotic bacteria, such as , , , , , , and , which coexist and interact under the influence of GO, synergistically degrading PAHs. These bacteria may serve as key biological markers in the PAH degradation process. These findings provide new theoretical and practical foundations for the application of nanomaterials in plant-based remediation of polluted soils and showcase the immense potential of plant-microbe interactions in environmental restoration.
Topics: Graphite; Polycyclic Aromatic Hydrocarbons; Soil Pollutants; Biodegradation, Environmental; Soil Microbiology; Bacteria; Endophytes; Plant Roots; Sphingomonas; Plants; Mycobacterium; Flavobacterium; Streptomyces; Microbacterium
PubMed: 38792204
DOI: 10.3390/molecules29102342 -
Microbiology Resource Announcements May 2024We report the whole genome sequence of KACC 19337. The genome consists of a 4.05-Mb circular chromosome, with a G + C content of 69.7 %, and 3,627 total coding genes...
We report the whole genome sequence of KACC 19337. The genome consists of a 4.05-Mb circular chromosome, with a G + C content of 69.7 %, and 3,627 total coding genes predicted.
PubMed: 38785431
DOI: 10.1128/mra.00345-24 -
PeerJ 2024Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative...
BACKGROUND
Antibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, .
METHODS
Ampicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL, and in combination at 50 µg mL each, to assess their impact on . First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones.
RESULTS
Under most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as and . The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments.
DISCUSSION
Antibiotics resulted in a significant increase to settlement time of larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals.
Topics: Animals; Anti-Bacterial Agents; Sea Anemones; Larva; Ampicillin; Neomycin; Streptomycin; Rifampin; Gene Expression
PubMed: 38784394
DOI: 10.7717/peerj.17349 -
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 -
Scientific Reports May 2024Spider silk is a promising material with great potential in biomedical applications due to its incredible mechanical properties and resistance to degradation of...
Spider silk is a promising material with great potential in biomedical applications due to its incredible mechanical properties and resistance to degradation of commercially available bacterial strains. However, little is known about the bacterial communities that may inhabit spider webs and how these microorganisms interact with spider silk. In this study, we exposed two exopolysaccharide-secreting bacteria, isolated from webs of an orb spider, to major ampullate (MA) silk from host spiders. The naturally occurring lipid and glycoprotein surface layers of MA silk were experimentally removed to further probe the interaction between bacteria and silk. Extensibility of major ampullate silk produced by Triconephila clavata that was exposed to either Microbacterium sp. or Novosphigobium sp. was significantly higher than that of silk that was not exposed to bacteria (differed by 58.7%). This strain-enhancing effect was not observed when the lipid and glycoprotein surface layers of MA silks were removed. The presence of exopolysaccharides was detected through NMR from MA silks exposed to these two bacteria but not from those without exposure. Here we report for the first time that exopolysaccharide-secreting bacteria inhabiting spider webs can enhance extensibility of host MA silks and silk surface layers play a vital role in mediating such effects.
Topics: Animals; Spiders; Silk; Bacteria; Polysaccharides, Bacterial
PubMed: 38744937
DOI: 10.1038/s41598-024-61723-x