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Frontiers in Plant Science 2016The studies on the biocontrol potential of pink pigmented facultative methylotrophic (PPFM) bacteria other than the genus are scarce. In the present study, we report...
The studies on the biocontrol potential of pink pigmented facultative methylotrophic (PPFM) bacteria other than the genus are scarce. In the present study, we report three facultative methylotrophic isolates; PPO-1, PPT-1, and PPB-1, respectively, identified as , and by 16S rRNA gene sequence analysis. Hemolytic activity was tested to investigate the potential pathogenicity of isolates to plants and humans, the results indicates that the isolates PPO-1, PPT-1, and PPB-1 are not pathogenic strains. Under conditions, PPO-1, . PPT-1, and . PPB-1 showed direct antagonistic effect by inhibiting the mycelial growth of fungal pathogens; f. sp. (2.15, 2.05, and 1.95 cm), (2.14, 2.04, and 1.94 cm), (2.12, 2.02, and 1.92 cm), and (2.18, 2.08, and 1.98 cm) and also produced volatile inhibitory compounds. Under plant growth chamber condition methylotrophic bacterial isolates; . PPO-1, . PPT-1, and PPB-1 significantly reduced the disease incidence of tomato. Under greenhouse condition, . PPO-1, . PPT-1, and . PPB-1 inoculated tomato plants, when challenged with . f. sp. . . , and . , increased the pathogenesis related proteins (β-1,3-glucanase and chitinase) and defense enzymes (phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, and catalase) on day 5 after inoculation. In the current study, we first report the facultative methylotrophy in pink pigmented . , and . and their antagonistic potential against fungal pathogens. Direct antagonistic and ISR effects of these isolates against fungal pathogens of tomato evidenced their possible use as a biocontrol agent.
PubMed: 27872630
DOI: 10.3389/fpls.2016.01626 -
Veterinary Research Forum : An... Sep 2022To search endophytic bacteria diversity and evaluate their antibacterial activity, healthy medicinal plant of was chosen in this study. One hundred endophytic bacteria...
To search endophytic bacteria diversity and evaluate their antibacterial activity, healthy medicinal plant of was chosen in this study. One hundred endophytic bacteria were isolated from surface-sterilized tissues (root, stem and leaf) of . Using sequence analysis targeting 16S rRNA gene, eight genera, including , , , , , , and were identified. Antibacterial activity of endophytic bacteria was examined against some test bacteria, employing agar well diffusion method. Out of 31 endophytic bacterial isolates, 24(77.42%) isolates showed significant antimicrobial activity against , 17(54.84%) isolates exhibited maximum activity against , 14(45.16%) isolates against and 5(16.13%) isolates showed positive activity against .The results obtained in this study suggested that the medicinal plant, is is a potent source of endophytic bacteria with antibacterial activity and offers promise for discovery of more impressive biological compounds.
PubMed: 36320307
DOI: 10.30466/vrf.2021.529714.3174 -
Wound Repair and Regeneration :... Nov 2022Xenopus laevis tadpoles can regenerate functional tails, containing the spinal cord, notochord, muscle, fin, blood vessels and nerves, except for a brief refractory...
Xenopus laevis tadpoles can regenerate functional tails, containing the spinal cord, notochord, muscle, fin, blood vessels and nerves, except for a brief refractory period at around 1 week of age. At this stage, amputation of the tadpole's tail may either result in scarless wound healing or the activation of a regeneration programme, which replaces the lost tissues. We recently demonstrated a link between bacterial lipopolysaccharides and successful tail regeneration in refractory stage tadpoles and proposed that this could result from lipopolysaccharides binding to Toll-like receptor 4 (TLR4). Here, we have used 16S rRNA sequencing to show that the tadpole skin microbiome is highly variable between sibships and that the community can be altered by raising embryos in the antibiotic gentamicin. Six Gram-negative genera, including Delftia and Chryseobacterium, were over-represented in tadpoles that underwent tail regeneration. Lipopolysaccharides purified from a commensal Chryseobacterium spp. XDS4, an exogenous Delftia spp. or Escherichia coli, could significantly increase the number of antibiotic-raised tadpoles that attempted regeneration. Conversely, the quality of regeneration was impaired in native-raised tadpoles exposed to the antagonistic lipopolysaccharide of Rhodobacter sphaeroides. Editing TLR4 using CRISPR/Cas9 also reduced regeneration quality, but not quantity, at the level of the cohort. However, we found that the editing level of individual tadpoles was a poor predictor of regenerative outcome. In conclusion, our results suggest that variable regeneration in refractory stage tadpoles depends at least in part on the skin microbiome and lipopolysaccharide signalling, but that signalling via TLR4 cannot account for all of this effect.
Topics: Animals; Anti-Bacterial Agents; Larva; Lipopolysaccharides; Microbiota; RNA, Ribosomal, 16S; Toll-Like Receptor 4; Wound Healing; Xenopus laevis
PubMed: 35212086
DOI: 10.1111/wrr.13003 -
Frontiers in Microbiology 2022Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism....
Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism. In this work, the changes of BA content were analyzed during mustard fermentation, and microbes and gene abundance responsible for producing BAs were revealed by metagenomic analyses. The results showed that cadaverine, putrescine, tyramine, and histamine were generated during mustard fermentation, which mainly accumulate in the first 6 days of fermentation. According to the metagenome sequencing, the predominant genus was (64.78%), followed by (11.67%), (8.88%), and (1.71%) in the initial fermentation stage (second day), while (76.03%) became the most dominant genus in the late stage. In addition, the gene abundance of BA production enzymes was the highest in the second day and decreased continuously as fermentation progressed. By tracking the source of the enzyme in the KEGG database, both and closely correlated to the generation of putrescine. Besides, also correlated to the generation of tyramine and spermidine, and also correlated to the generation of cadaverine and spermine. In the processes of fermentation, the pH of fermented mustard showed slower decrease compared with other similar fermented vegetables, which may allow to grow at high levels before the pH <4. This study reveals the change of BA content and microbes involved in BA formation during mustard fermentation.
PubMed: 35572710
DOI: 10.3389/fmicb.2022.824644 -
Food Research International (Ottawa,... Jun 2020Bacterial communities and Volatile Organic Compounds (VOCs) profile of deepwater rose shrimp (Parapenaeus longirostris) stored at 0 °C (ice) and 4 °C were...
Bacterial communities and Volatile Organic Compounds (VOCs) profile of deepwater rose shrimp (Parapenaeus longirostris) stored at 0 °C (ice) and 4 °C were investigated using 16S amplicon based sequencing and Solid phase micro-extraction (SPME) - Gas chromatography/mass spectrometry (GC/MS), respectively. The shelf-life of shrimps determined by sensory assessment was 5 and 2 days at 0 °C and 4 °C, respectively. Based on 16S analysis (culture-independed), the initial microbiota of shrimps mainly consists of Photobacterium, Candidatus Hepatoplasma, Psychrobacter, Acinetobacter and Delftia. Psychrobacter and Carnobacterium dominated during storage at both temperatures. Psychrobacter was the most dominant taxon at the end of shelf-life of chill-stored shrimps. A minor microbial population composed by Brevundimonas, Stenotrophomonas, Staphylococcus, Legionella, Acinetobacter, Bacillus, Escherichia-Shigella, Enterococcus, Enterobacter, Klebsiella was also detected. Those taxa may be originated from the environment due to an inadequate hygienic practice during fishing, handling and icing. VOCs such as ethanol, 3-methyl-1-butanol, 2-ethyl-1-hexanol, 3-hydroxy-2-butanone, indole etc., were found to be associated with shrimps at 4 °C, while acetone and dimethyl sulfide with shrimps in ice. Some VOCs, from microbial or chemical origin, increased in shrimps either at 0 °C (i.e. 1-octen-3-ol, trans-2-octenal) or at 4 °C (i.e. 3-methyl-1-butanol, indole), while 2-methylbutanal and 3-methylbutanal increased in both temperatures. A positive correlation between Psychrobacter with 2-ethyl-1-hexanol and Carnobacterium with 3-methyl-1-butanol was also observed. Concluding, we suggest the reinforcement of Good Hygiene Practices on fishing boats during fishing/handling, the rapid onboard icing and keeping shrimps iced avoiding even small increase of storage temperature that affects quality parameters (e.g. microbial population level, synthesis of microbiota, VOCs profile) in order to provide a product of the highest quality and safety in the market.
Topics: Aldehydes; Animals; Bacteria; Decapoda; Food Microbiology; Gas Chromatography-Mass Spectrometry; Hexanols; Microbiota; RNA, Ribosomal, 16S; Seafood; Volatile Organic Compounds
PubMed: 32331667
DOI: 10.1016/j.foodres.2020.109057 -
International Journal of Environmental... Feb 2022Chloropicrin (CP) can effectively combat soil-borne diseases but has significant side effects on nontarget microorganisms. The rhizosphere microflora play a crucial role...
Chloropicrin (CP) can effectively combat soil-borne diseases but has significant side effects on nontarget microorganisms. The rhizosphere microflora play a crucial role in promoting plant growth and protecting plants from infection by soil-borne pathogens. We conducted a laboratory pot experiment to evaluate the effect of CP on the rhizosphere soil bacterial flora and the effect of biochar amendments on the reconstruction of microbial communities. Our results show that CP fumigation and biochar additions promoted the growth of cucumber plants in the later stage of the pot experiment. CP significantly inhibited the rhizobacterial diversity and changed the community composition. Biochar amendments after CP fumigation shortened the time for the rhizobacterial diversity to recover to unfumigated levels. Biochar amendments promoted the transplantation of new populations to empty microbiome niches that were caused by CP and, in particular, stimulated many beneficial microorganisms to become the predominant flora. The relative abundances of many functional taxa related to plant-disease suppressiveness and pollutant bioremediation increased, including , , , , , , , Cytophagaceae, and . These changes stimulated by biochar amendments would promote multifunctionality in the soil rhizosphere and benefit plant growth and disease resistance.
Topics: Charcoal; Fumigation; Hydrocarbons, Chlorinated; Rhizosphere; Soil; Soil Microbiology
PubMed: 35206314
DOI: 10.3390/ijerph19042126 -
Frontiers in Microbiology 2022The current symbiotic view of the organisms also calls for new approaches in the way we perceive and manage our pest species. The olive fruit fly, the most important...
The current symbiotic view of the organisms also calls for new approaches in the way we perceive and manage our pest species. The olive fruit fly, the most important olive tree pest, is dependent on an obligate bacterial symbiont to its larvae development in the immature fruit. This symbiont, (.) Erwinia dacicola, is prevalent throughout the host life stages, and we have shown significant changes in its numbers due to olive fruit fly metamorphosis. The olive fruit fly microbiota was analyzed through 16S metabarcoding, at three development stages: last instar larvae, pupae, and adult. Besides . E. dacicola, the olive fruit flies harbor a diverse bacterial flora of which 13 operational taxonomic units (grouped in 9 genera/species) were now determined to persist excluding at metamorphosis ( sp., sp., sp., sp., sp., sp., sp., sp., and sp.). These findings open a new window of opportunities in symbiosis-based pest management.
PubMed: 35509306
DOI: 10.3389/fmicb.2022.868458 -
Frontiers in Plant Science 2023The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. is an aquatic...
INTRODUCTION
The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).
METHODS
In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the plant beneficial potential of isolated bacterial endophytes of .
RESULTS AND DISCUSSION
Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as were mainly associated with leaf tissue, whereas the genera and from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from showed plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of to various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.
PubMed: 37404529
DOI: 10.3389/fpls.2023.1176648 -
Scientific Reports Aug 2017Aspartate family amino acids (AFAAs) have important commercial values due to their wide spectrum of applications. Most if not all AFAAs are produced under aerobic...
Aspartate family amino acids (AFAAs) have important commercial values due to their wide spectrum of applications. Most if not all AFAAs are produced under aerobic conditions which is energy-intensive. To establish a cost-effective anaerobic process for production of AFAAs, it holds great promise to develop a new pathway enabling the conversion of oxoloacetate into aspartate through direct amination which is catalyzed by aspartate dehydrogenase (AspDH). Compared with the well studied aspartate aminotransferase and aspartate ammonia-lyase, only a few AspDHs are characterized till date, and failure to reproduce the high activity of AspDH from Rastonia eutropha documented in the literature encouraged us to screen and characterize novel AspDHs from different origins. Interestingly, the AspDHs from Klebsiella pneumoniae 34618 (KpnAspDH) and Delftia sp. Cs1-4 (DelAspDH) showed successful soluble expression. KpnAspDH and DelAspDH containing C-terminal hexa-histidine tags were purified and characterized for their catalytic properties. Notably, in addition to its high reductive amination activity, DelAspDH exhibited considerable stability as compared to the other source of AspDHs. This work thus provides novel enzyme resource for engineering strains capable of producing AFAAs under anaerobic conditions.
Topics: Amination; Amino Acid Oxidoreductases; Anaerobiosis; Aspartic Acid; Bacterial Proteins; Delftia; Enzyme Stability; Industrial Microbiology; Kinetics; Klebsiella pneumoniae; Recombinant Proteins; Substrate Specificity
PubMed: 28801651
DOI: 10.1038/s41598-017-05522-7 -
Applied Microbiology and Biotechnology Sep 2014A highly active amide hydrolase (DamH) was purified from Delftia sp. T3-6 using ammonium sulfate precipitation, diethylaminoethyl anion exchange, hydrophobic interaction...
A highly active amide hydrolase (DamH) was purified from Delftia sp. T3-6 using ammonium sulfate precipitation, diethylaminoethyl anion exchange, hydrophobic interaction chromatography, and Sephadex G-200 gel filtration. The molecular mass of the purified enzyme was estimated to be 32 kDa by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. The sequence of the N-terminal 15 amino acid residues was determined to be Gly-Thr-Ser-Pro-Gln-Ser-Asp-Phe-Leu-Arg-Ala-Leu-Phe-Gln-Ser. Based on the N-terminal sequence and results of peptide mass fingerprints, the gene (damH) was cloned by PCR amplification and expressed in Escherichia coli BL21(DE3). DamH was a bifunctional hydrolase showing activity to amide and ester bonds. The specific activities of recombinant DamH were 5,036 U/mg for 2'-methyl-6'-ethyl-2- chloroacetanilide (CMEPA) (amide hydrolase function) and 612 U/mg for 4-nitrophenyl acetate (esterase function). The optimum substrate of DamH was CMEPA, with K m and k cat values of 0.197 mM and 2,804.32 s(-1), respectively. DamH could also hydrolyze esters such as 4-nitrophenyl acetate, glycerol tributyrate, and caprolactone. The optimal pH and temperature for recombinant DamH were 6.5 and 35 °C, respectively; the enzyme was activated by Mn(2+) and inhibited by Cu(2+), Zn(2+), Ni(2+), and Fe(2+). DamH was inhibited strongly by phenylmethylsulfonyl and SDS and weakly by ethylenediaminetetraacetic acid and dimethyl sulfoxide.
Topics: Amidohydrolases; Cations, Divalent; Chemical Precipitation; Chromatography, Gel; Chromatography, Ion Exchange; Cloning, Molecular; DNA, Bacterial; Delftia; Enzyme Activators; Enzyme Inhibitors; Enzyme Stability; Escherichia coli; Gene Expression; Hydrogen-Ion Concentration; Kinetics; Mass Spectrometry; Molecular Sequence Data; Molecular Weight; Recombinant Proteins; Sequence Analysis, DNA; Sequence Analysis, Protein; Substrate Specificity; Temperature
PubMed: 24723294
DOI: 10.1007/s00253-014-5710-y