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The ISME Journal Jul 2024Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remains poorly understood....
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remains poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted the tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
PubMed: 38952008
DOI: 10.1093/ismejo/wrae120 -
BMC Veterinary Research Jun 2024The aim of this research was to estimate the immunopotentiation effect of brown algae Padina boergesenii water extract on Nile tilapia, Oreochromis niloticus through...
The aim of this research was to estimate the immunopotentiation effect of brown algae Padina boergesenii water extract on Nile tilapia, Oreochromis niloticus through resistance to Pseudomonas putida infection. Gas Chromatography Mass Spectrometry was utilized to characterize the seaweed phytoconstituents. One hundred and twenty-six fish were divided in triplicates into two equal groups corresponding to two diet variants that used to feed Nile tilapia for 20 successive days: a basal (control), and P. boergesenii water extract supplemented group. Fish samples were collected at 10-days intervals throughout the experiment. Serum biochemical constituents, total antioxidant capacity (TAC), and some immune related genes expression of the spleen and intestinal tissues of experimental fish were studied, as well as histological examination of fish immune tissues. Moreover, following 20 days of feeding, the susceptibility of Nile tilapia to P. putida infection was evaluated to assess the protective effect of the used extract. The findings indicated that the studied parameters were significantly increased, and the best immune response profiles were observed in fish fed P. boergesenii water extract for 20 successive days. A bacterial challenge experiment using P. putida resulted in higher survival within the supplemented fish group than the control. Thus, the lowered post-challenge mortality of the fish may be related to the protection provided by the stimulation of the innate immune system, reduced oxidative stress by higher activity of TAC, and elevated levels of expression of iterleukin-1beta (IL-1β), beta-defensin (β-defensin), and natural killer-lysin (NKl). Moreover, the constituents of the extract used showed potential protective activity for histological features of the supplemented fish group when compared to the control. Collectively, this study presents a great insight on the protective role of P. boergesenii water extract as an additive in Nile tilapia feed which suggests its potential for improving the immune response against P. putida infection.
Topics: Animals; Pseudomonas putida; Fish Diseases; Cichlids; Animal Feed; Pseudomonas Infections; Dietary Supplements; Phaeophyceae; Diet; Disease Resistance; Plant Extracts
PubMed: 38951863
DOI: 10.1186/s12917-024-04115-7 -
Journal of Hazardous Materials Jun 2024Faced with the escalating challenge of global plastic pollution, this study specifically addresses the research gap in the biodegradation of polystyrene (PS). A...
Faced with the escalating challenge of global plastic pollution, this study specifically addresses the research gap in the biodegradation of polystyrene (PS). A PS-degrading bacterial strain was isolated from the gut of Tenebrio molitor, and genomics, molecular docking, and proteomics were employed to thoroughly investigate the biodegradation mechanisms of Pseudomonas putida H-01 against PS. Using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (ATR-FTIR), and contact angle analysis, significant morphological and structural changes in the PS films under the influence of the H-01 strain were observed. The study revealed several potential degradation genes and ten enzymes that were specifically upregulated in the PS degradation environment. Additionally, a novel protein with laccase-like activity, LacQ1, was purified from this strain for the first time, and its crucial role in the PS degradation process was confirmed. Through molecular docking and molecular dynamics (MD) simulations, the interactions between the enzymes and PS were detailed, elucidating the binding and catalytic mechanisms of the degradative enzymes with the substrate. These findings have deepened our understanding of PS degradation.
PubMed: 38943889
DOI: 10.1016/j.jhazmat.2024.135031 -
International Journal of Systematic and... Jun 2024A Gram-negative, strictly aerobic bacterial strain was isolated from asymptomatic leaf tissue of a wild yam plant. Optimal growth was observed at 28 °C and pH 7, and...
A Gram-negative, strictly aerobic bacterial strain was isolated from asymptomatic leaf tissue of a wild yam plant. Optimal growth was observed at 28 °C and pH 7, and catalase and oxidase activities were detected. Polyphasic taxonomic and comparative genomics revealed that strain LMG 33091 represents a novel species of . The nearest phylogenetic neighbours of strain LMG 33091 were NBRC 14164 (with 99.79 % 16S rRNA sequence identity), KL28 (99.28 %) and (99.07 %) ATCC 23835. MALDI-TOF MS analysis yielded distinct profiles for strain LMG 33091 and the nearest phylogenetic neighbours. Average nucleotide identity analyses between the whole genome sequence of strain LMG 33091 and of the type strains of its nearest-neighbour taxa yielded values below the species delineation threshold and thus confirmed that the strain represented a novel species, for which we propose the name sp. nov., with strain LMG 33091 (=GMI12077= CFBP 9143) as the type strain.
Topics: Pseudomonas; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Plant Leaves; Sequence Analysis, DNA; Bacterial Typing Techniques; Dioscorea; Whole Genome Sequencing; Base Composition; Fatty Acids; Genome, Bacterial
PubMed: 38940814
DOI: 10.1099/ijsem.0.006395 -
Metabolic Engineering Jun 2024Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from...
Biological conversion of lignin from biomass offers a promising strategy for sustainable production of fuels and chemicals. However, aromatic compounds derived from lignin commonly contain methoxy groups, and O-demethylation of these substrates is often a rate-limiting reaction that influences catabolic efficiency. Several enzyme families catalyze aromatic O-demethylation, but they are rarely compared in vivo to determine an optimal biocatalytic strategy. Here, two pathways for aromatic O-demethylation were compared in Pseudomonas putida KT2440. The native Rieske non-heme iron monooxygenase (VanAB) and, separately, a heterologous tetrahydrofolate-dependent demethylase (LigM) were constitutively expressed in P. putida, and the strains were optimized via adaptive laboratory evolution (ALE) with vanillate as a model substrate. All evolved strains displayed improved growth phenotypes, with the evolved strains harboring the native VanAB pathway exhibiting growth rates ∼1.8x faster than those harboring the heterologous LigM pathway. Enzyme kinetics and transcriptomics studies investigated the contribution of selected mutations toward enhanced utilization of vanillate. The VanAB-overexpressing strains contained the most impactful mutations, including those in VanB, the reductase for vanillate O-demethylase, PP_3494, a global regulator of vanillate catabolism, and fghA, involved in formaldehyde detoxification. These three mutations were combined into a single strain, which exhibited approximately 5x faster vanillate consumption than the wild-type strain in the first 8 h of cultivation. Overall, this study illuminates the details of vanillate catabolism in the context of two distinct enzymatic mechanisms, yielding a platform strain for efficient O-demethylation of lignin-related aromatic compounds to value-added products.
PubMed: 38936762
DOI: 10.1016/j.ymben.2024.06.009 -
Journal of Hazardous Materials Jun 2024Cd is highly mobile, non-essential trace element, that has become serious environmental issue due to its elevated concentration in soil. The present study was taken up...
Integrated transcriptomic and physio-molecular studies unveil the melatonin and PGPR induced protection to photosynthetic attributes in Brassica juncea L. under cadmium toxicity.
Cd is highly mobile, non-essential trace element, that has become serious environmental issue due to its elevated concentration in soil. The present study was taken up to work out salutary effect of melatonin (Mlt) and PGPR ((Pseudomonas putida (Pp), Pseudomonas fluorescens (Pf) in 10 days old Cd stressed (0.3 mM) Brassica juncea L. seedlings. The present work investigated growth characteristics, photosynthetic pigments, secondary metabolites in melatonin-PGPR inoculated B. juncea seedlings. It was backed by molecular studies entailing RT-PCR and transcriptomic analyses. Our results revealed, substantial increase in photosynthetic pigments and secondary metabolites, after treatment with melatonin, P.putida, P. fluorescens in Cd stressed B. juncea seedlings, further validated with transcriptome analysis. Comparative transcriptome analyses identified 455, 5953, 3368, 2238 upregulated and 4921, 430, 137, 27 down regulated DEGs, Cn-vs-Cd, Cd-vs-Mlt, Cd-vs-Mlt-Pp-Pf, Cd-vs-Mlt-Pp-Pf-Cd comparative groups respectively. In depth exploration of genome analyses (Gene ontology, Kyoto encyclopaedia of genes), revealed that Cd modifies the expression patterns of most DEGs mainly associated to photosystem and chlorophyll synthesis. Also, gene expression studies for key photosynthetic genes (psb A, psb B, CHS, PAL, and PSY) suggested enhanced expression in melatonin-rhizobacteria treated Cd stressed B. juncea seedlings. Overall, results provide new insights into probable mechanism of Mlt-PGPR induced protection to photosynthesis in Cd stressed B. juncea plants.
PubMed: 38936187
DOI: 10.1016/j.jhazmat.2024.134875 -
The Journal of Physical Chemistry. B Jun 2024Antimicrobial resistance in bacteria often arises from their ability to actively identify and expel toxic compounds. The bacterium strain DOT-T1E utilizes its TtgABC...
Antimicrobial resistance in bacteria often arises from their ability to actively identify and expel toxic compounds. The bacterium strain DOT-T1E utilizes its TtgABC efflux pump to confer robust resistance against antibiotics, flavonoids, and organic solvents. This resistance mechanism is intricately regulated at the transcriptional level by the TtgR protein. Through molecular dynamics and alchemical free energy simulations, we systematically examine the binding of seven flavonoids and their derivatives with the TtgR transcriptional regulator. Our simulations reveal distinct binding geometries and free energies for the flavonoids in the active site of the protein, which are driven by a range of noncovalent forces encompassing van der Waals, electrostatic, and hydrogen bonding interactions. The interplay of molecular structures, substituent patterns, and intermolecular interactions effectively stabilizes the bound flavonoids, confining their movements within the TtgR binding pocket. These findings yield valuable insights into the molecular determinants that govern ligand recognition in TtgR and shed light on the mechanism of antimicrobial resistance in DOT-T1E.
PubMed: 38935925
DOI: 10.1021/acs.jpcb.4c02303 -
Microbial Ecology Jun 2024Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since...
Antimicrobial resistance (AMR) is a major public health threat, exacerbated by the ability of bacteria to rapidly disseminate antimicrobial resistance genes (ARG). Since conjugative plasmids of the incompatibility group P (IncP) are ubiquitous mobile genetic elements that often carry ARG and are broad-host-range, they are important targets to prevent the dissemination of AMR. Plasmid-dependent phages infect plasmid-carrying bacteria by recognizing components of the conjugative secretion system as receptors. We sought to isolate plasmid-dependent phages from wastewater using an avirulent strain of Salmonella enterica carrying the conjugative IncP plasmid pKJK5. Irrespective of the site, we only obtained bacteriophages belonging to the genus Alphatectivirus. Eleven isolates were sequenced, their genomes analyzed, and their host range established using S. enterica, Escherichia coli, and Pseudomonas putida carrying diverse conjugative plasmids. We confirmed that Alphatectivirus are abundant in domestic and hospital wastewater using culture-dependent and culture-independent approaches. However, these results are not consistent with their low or undetectable occurrence in metagenomes. Therefore, overall, our results emphasize the importance of performing phage isolation to uncover diversity, especially considering the potential of plasmid-dependent phages to reduce the spread of ARG carried by conjugative plasmids, and to help combat the AMR crisis.
Topics: Plasmids; Wastewater; Bacteriophages; Genome, Viral; Escherichia coli; Host Specificity; Pseudomonas putida; Salmonella enterica; Phylogeny
PubMed: 38935220
DOI: 10.1007/s00248-024-02401-3 -
Life (Basel, Switzerland) Jun 2024"Lauren N [...].
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PubMed: 38929766
DOI: 10.3390/life14060767 -
Biology Jun 2024KT2440 is a popular platform for bioremediation due to its robust tolerance to environmental stress and strong biodegradation capacity. Limited research on the salt...
KT2440 is a popular platform for bioremediation due to its robust tolerance to environmental stress and strong biodegradation capacity. Limited research on the salt tolerance of KT2440 has hindered its application. In this study, the strain KT2440 was tested to tolerate a maximum of 4% / NaCl cultured with minimal salts medium. Transcriptomic data in a high-salinity environment showed significant expression changes in genes in membrane components, redox processes, chemotaxis, and cellular catabolic processes. -encoding betaine-aldehyde dehydrogenase was identified from the transcriptome data to overexpress and enhance growth profile of the strain KT2440 in minimal salts medium containing 4% / NaCl. Meanwhile, screening for exogenous salt-tolerant genes revealed that the Na/H antiporter from significantly increased the growth of the strain KT2440 in 4% / NaCl. Then, co-expression of and (KT2440-) increased the maximum salt tolerance of strain KT2440 to 5% / NaCl. Further addition of betaine and proline improved the salt tolerance of the engineered strain to 6% / NaCl. Finally, the engineered strain KT2440- was able to degrade 56.70% of benzoic acid and 95.64% of protocatechuic acid in minimal salt medium containing 4% / NaCl in 48 h, while no biodegradation was observed in the normal strain KT2440 in the same conditions. However, the strain KT2440- failed to degrade catechol in minimal salt medium containing 3% / NaCl. This study illustrated the improvement in the salt tolerance performance of KT2440 and the feasibility of engineered strain KT2440 as a potential salt-tolerant bioremediation platform.
PubMed: 38927284
DOI: 10.3390/biology13060404