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PLoS Genetics Mar 2024C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited...
C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
Topics: Animals; Humans; Caenorhabditis elegans; Caenorhabditis elegans Proteins; RNA, Small Interfering; RNA Interference; RNA, Bacterial; Pseudomonas aeruginosa; Bacteria
PubMed: 38547071
DOI: 10.1371/journal.pgen.1011178 -
MSystems Apr 2024Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N...
Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with , , , and . Furthermore, eight dominant taxa belonging to and were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to . Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
Topics: Microbiota; Agriculture; Soil; Nitrogen; Crops, Agricultural; Plant Development
PubMed: 38501864
DOI: 10.1128/msystems.01055-23 -
Microorganisms Nov 2023Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe) levels in surface...
Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe) levels in surface waters in the marine environment, microbes produce a variety of siderophores. In the current study, halophilic bacteria SMI_1, sp., AABM_9, and AMPPS_5 were isolated from marine surface water of Kalinga beach, Bay of Bengal (Visakhapatnam, Andhra Pradesh, India) and were investigated for siderophore production using the Chrome Azurol S (CAS) assay. The effect of various production parameters was also studied. The optimum production of siderophores for SMI_1 was 93.57% siderophore units (SU) (after 48 h of incubation at 30 °C, pH 8, sucrose as carbon source, sodium nitrate as nitrogen source, 0.4% succinic acid), and for AABM_9, it was 87.18 %SU (after 36 h of incubation period at 30 °C, pH 8, in the presence of sucrose, ammonium sulfate, 0.4% succinic acid). The maximum production of siderophores for AMPPS_5 was 91.17 %SU (after 36 h of incubation at 35 °C, pH 8.5, glucose, ammonium sulfate, 0.4% citric acid). The bacterial isolates SMI_1, AABM_9, and AMPPS_5 showed siderophore production at low Fe concentrations of 0.10 µM, 0.01 µM, and 0.01 µM, respectively. The SMI_1 (73.09 %SU) and AMPPS_5 (68.26 %SU) isolates showed siderophore production in the presence of Zn (10 µM), whereas AABM_9 (50.4 %SU) exhibited siderophore production in the presence of Cu (10 µM). Additionally, these bacterial isolates showed better heavy-metal chelation ability and rapid development in seed germination experiments. Based on these results, the isolates of marine-derived bacteria effectively produced the maximum amount of siderophores, which could be employed in a variety of industrial and environmental applications.
PubMed: 38138017
DOI: 10.3390/microorganisms11122873 -
Toxics Jul 2023Phytoremediation can help remediate potential toxic elements (PTE) in soil. Microorganisms and soil amendments are effective means to improve the efficiency of...
Phytoremediation can help remediate potential toxic elements (PTE) in soil. Microorganisms and soil amendments are effective means to improve the efficiency of phytoremediation. This study selected three microorganisms that may promote phytoremediation, including bacteria (), fungi (), and arbuscular-mycorrhizal fungi (AMF, ). The effects of single or mixed inoculation of three microorganisms on the phytoremediation efficiency of and were tested under three different degrees of cadmium-contaminated soil (low 10 mg/kg, medium 50 mg/kg, and high 100 mg/kg). The results showed that single inoculation of AMF or could significantly increase the biomass of two plants under three different degrees of cadmium-contaminated soil, and the growth-promoting effect of AMF was better than . However, simultaneous inoculation of these two microorganisms did not show a better effect than the inoculation of one. Inoculation of reduced the biomass of the two plants under high concentrations of cadmium-contaminated soil. Among all treatments, the remediation ability of the two plants was the strongest when inoculated with AMF alone. On this basis, this study explored the effect of AMF combined with corn-straw-biochar on the phytoremediation efficiency of and . The results showed that biochar could affect plant biomass and Cd concentration in plants by reducing Cd concentration in soil. The combined use of biochar and AMF increased the biomass of by 8.9-48.6% and the biomass of by 8.04-32.92%. Compared with the single use of AMF or biochar, the combination of the two is better, which greatly improves the efficiency of phytoremediation.
PubMed: 37505548
DOI: 10.3390/toxics11070582 -
BioRxiv : the Preprint Server For... Oct 2023Previously, we discovered that a small RNA from a clinical isolate of PA14, induces learned avoidance and its transgenerational inheritance in . is an important human...
Previously, we discovered that a small RNA from a clinical isolate of PA14, induces learned avoidance and its transgenerational inheritance in . is an important human pathogen, and there are other in natural habitat, but it is unclear whether ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we found that a pathogenic strain isolated from the microbiota, GRb0427, like PA14, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure to GRb0427, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. Using bacterial small RNA sequencing, we identified Pv1, a small RNA from GRb0427, that matches the sequence of . We find that Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, ; this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance are functional in natural environment, and that different bacterial small RNA-mediated regulation systems evolved independently but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
PubMed: 37503135
DOI: 10.1101/2023.07.20.549962 -
Microbiology Spectrum Jun 2023Several variants of the plasmid-carried tigecycline resistance gene cluster, , have been identified. This study characterized another novel variant, , located on the...
Several variants of the plasmid-carried tigecycline resistance gene cluster, , have been identified. This study characterized another novel variant, , located on the chromosome of environmental-origin Pseudomonas mendocina. TMexC6D6-TOprJ1 mediates resistance to multiple drugs, including tigecycline. The promoter activity of and negative transcriptional repression by the upstream regulator tnfxB6 are crucial for the expression of . was found in the plasmids or chromosomes of different Pseudomonas species from six countries. Two genetic backgrounds, class 1 integrons and -carrying integrase units, were found adjacent to the gene cluster and might mediate the transfer of this novel efflux pump gene cluster in Pseudomonas. Further phylogenetic analysis revealed Pseudomonas as the major reservoir of variants, warranting closer monitoring in the future. Tigecycline is one of the treatment options for serious infections caused by multidrug-resistant bacteria, and tigecycline resistance has gained extensive attention. The emergence of a transferable tigecycline resistance efflux pump gene cluster, , severely challenged the efficiency of tigecycline. In this study, we identified another novel variant, , which could confer resistance to multiple classes of antibiotics, including tigecycline. Although was found only in Pseudomonas species, might spread to hosts via mobile genetic elements resembling those of other variants, compromising the therapeutic strategies. Meanwhile, novel transferable variants are constantly emerging and mostly exist in Pseudomonas spp., indicating Pseudomonas as the important hidden reservoir and origin of variants. Continuous monitoring and investigations of are urgent to control its spread.
Topics: Tigecycline; Pseudomonas; Phylogeny; Anti-Bacterial Agents; Plasmids; Microbial Sensitivity Tests
PubMed: 37067462
DOI: 10.1128/spectrum.00767-23 -
Foods (Basel, Switzerland) Mar 2023Previous research has shown that freshwater edible fish imported into Australia are not compliant with Australian importation guidelines and as a result may be high risk...
Previous research has shown that freshwater edible fish imported into Australia are not compliant with Australian importation guidelines and as a result may be high risk for bacterial contamination. In the present study, the outer surface of imported freshwater fish were swabbed, cultured, confirmatory tests performed and antimicrobial patterns investigated. Channidae fish (Sp. A/n = 66) were contaminated with zoonotic sp./ (n = 1/66) and other bacteria implicated in cases of opportunistic human infection, these being sp. (including . and (n = 34/66)); sp. (n = 32/66); (n = 27/66) and (n = 3/66). Pangasiidae fish (Species B/n = 47) were contaminated with zoonotic (n = 10/47); sp. (n = 6/47) and environmental bacteria sp. (n = 3/47). One sample was resistant to all antimicrobials tested and is considered to be Methicillin Resistant . Mud, natural diet, or vegetation identified in Sp. A fish/or packaging were significantly associated with the presence of spp. The study also showed that visibly clean fish (Sp. B) may harbour zoonotic bacteria and that certain types of bacteria are common to fish groups, preparations, and contaminants. Further investigations are required to support the development of appropriate food safety recommendations in Australia.
PubMed: 36981215
DOI: 10.3390/foods12061288 -
Chemistry (Weinheim An Der Bergstrasse,... Apr 2023Monooxygenases, an important class of enzymes, have been the subject of enzyme engineering due to their high activity and versatile substrate scope. Reactions performed...
Monooxygenases, an important class of enzymes, have been the subject of enzyme engineering due to their high activity and versatile substrate scope. Reactions performed by these biocatalysts have long been monitored by a colorimetric method involving the coupling of a dye precursor to naphthalene hydroxylation products generated by the enzyme. Despite the popularity of this method, we found the dye product to be unstable, preventing quantitative readout. By incorporating an extraction step to solubilize the dye produced, we have improved this assay to the point where quantitation of enzyme activity is possible. Further, by incorporating spectral deconvolution, we have, for the first time, enabled independent quantification of the two possible regioisomeric products: 1-naphthol and 2-naphthol. Previously, such analysis was only possible with chromatographic separation, increasing the cost and complexity of analysis. The efficacy of our improved workflow was evaluated by monitoring the activity of a toluene-4-monooxygenase enzyme from Pseudomonas mendocina KR-1. Our colorimetric regioisomer quantification was found to be consistent with chromatographic analysis by HPLC. The development and validation of a quantitative colorimetric assay for monooxygenase activity that enables regioisomeric distinction and quantification represents a significant advance in analytical methods to monitor enzyme activity. By maintaining facile, low-cost, high-throughput readout while incorporating quantification, this assay represents an important alternative to more expensive chromatographic quantification techniques.
Topics: Oxygenases; Mixed Function Oxygenases
PubMed: 36593585
DOI: 10.1002/chem.202203322 -
Frontiers in Bioengineering and... 2022Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be...
Metformin is used globally to treat type II diabetes, has demonstrated anti-ageing and COVID mitigation effects and is a major anthropogenic pollutant to be bioremediated by wastewater treatment plants (WWTPs). Metformin is not adsorbed well by activated carbon and toxic N-chloro derivatives can form in chlorinated water. Most earlier studies on metformin biodegradation have used wastewater consortia and details of the genomes, relevant genes, metabolic products, and potential for horizontal gene transfer are lacking. Here, two metformin-biodegrading bacteria from a WWTP were isolated and their biodegradation characterized. sp. MET metabolized metformin stoichiometrically to guanylurea, an intermediate known to accumulate in some environments including WWTPs. MET completely metabolized metformin and utilized all the nitrogen atoms for growth. MET also metabolized metformin breakdown products sometimes observed in WWTPs: 1-N-methylbiguanide, biguanide, guanylurea, and guanidine. The genome of each bacterium was obtained. Genes involved in the transport of guanylurea in sp. MET were expressed heterologously and shown to serve as an antiporter to expel the toxic guanidinium compound. A novel guanylurea hydrolase enzyme was identified in MET, purified, and characterized. The and each contained one plasmid of 160 kb and 90 kb, respectively. In total, these studies are significant for the bioremediation of a major pollutant in WWTPs today.
PubMed: 36588930
DOI: 10.3389/fbioe.2022.1086261 -
Scientific Reports Dec 2022PmlR2, a class II LitR/CarH family transcriptional regulator, and PmSB-LOV, a "short" LOV-type blue light photoreceptor, are adjacently encoded in Pseudomonas mendocina...
PmlR2, a class II LitR/CarH family transcriptional regulator, and PmSB-LOV, a "short" LOV-type blue light photoreceptor, are adjacently encoded in Pseudomonas mendocina NBRC 14162. An effector protein for the "short" LOV-type photoreceptor in Pseudomonas has not yet been identified. Here, we show that PmlR2 is an effector protein of PmSB-LOV. Transcriptional analyses revealed that the expression of genes located near pmlR2 and its homolog gene, pmlR1, was induced in response to illumination. In vitro DNA-protein binding analyses showed that recombinant PmlR2 directly binds to the promoter region of light-inducible genes. Furthermore PmSB-LOV exhibited a typical LOV-type light-induced spectral change. Gel-filtration chromatography demonstrated that the illuminated PmSB-LOV was directly associated with PmlR2, whereas non-illuminated proteins did not interact. The inhibition of PmlR2 function following PmSB-LOV binding was verified by surface plasmon resonance: the DNA-binding ability of PmlR2 was specifically inhibited in the presence of blue light-illuminated-PmSB-LOV. An In vitro transcription assay showed a dose-dependent reduction in PmlR2 repressor activity in the presence of illuminated PmSB-LOV. Overall, evidence suggests that the DNA-binding activity of PmlR2 is inhibited by its direct association with blue light-activated PmSB-LOV, enabling transcription of light-inducible promoters by RNA polymerase.
Topics: Pseudomonas mendocina; Bacterial Proteins; Promoter Regions, Genetic; Protein Binding; DNA
PubMed: 36526696
DOI: 10.1038/s41598-022-26254-3