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Pendimethalin biodegradation by soil strains of Burkholderia sp. and Methylobacterium radiotolerans.Anais Da Academia Brasileira de Ciencias 2021Pendimethalin herbicide is widely used and persists in the environment as a contaminant causing negative impacts, including for human health. Microorganisms have the...
Pendimethalin herbicide is widely used and persists in the environment as a contaminant causing negative impacts, including for human health. Microorganisms have the capacity to remove many contaminants from the environment. Thus, the aim of this work was to evaluate the efficiency of soil bacterial species prospected by molecular modelling of cytochrome P450 in to degrade pendimethalin. Strains of Burkholderia sp. and Methylobacterium radiotolerans were cultivated in a mineral saline medium enriched with 281 mg/L pendimethalin (MSPEN) and another containing glucose 1.0 g/L as extra carbon source (MSPENGLI). Both strains were able to degrade pendimethalin under the two conditions experienced. Burkholderia sp. F7G4PR33-4 was more efficient in degrading 65% of the herbicide in MSPEN medium, with 49.3% in MSPENGLI; while Methylobacterium radiotolerans A6A1PR46-4 degraded 55.4% in MSPEN and 29.8% in MSPENGLI mediums. These findings contribute to the expansion of knowledge on the competence of isolates of these two bacterial genera in degrading herbicidal xenobiotics and biotechnological potential for pendimethalin degradation and bioremediation.
Topics: Aniline Compounds; Biodegradation, Environmental; Burkholderia; Humans; Methylobacterium; Soil; Soil Microbiology
PubMed: 34909833
DOI: 10.1590/0001-3765202120210924 -
Clinical Microbiology and Infection :... Aug 2016Roseomonas spp. are increasingly involved in human infectious diseases. The environmental source for infection is generally admitted in published cases owing to the...
Roseomonas spp. are increasingly involved in human infectious diseases. The environmental source for infection is generally admitted in published cases owing to the origin of most Roseomonas species and to their affiliation to the family Acetobacteraceae in Rhodospirillales, which mainly groups environmental bacteria. For a better delineation of Roseomonas habitat and infectious reservoir, we related phenotype, phylotype (16S rRNA gene), genomotype (pulsed-field gel electrophoresis) and origin of 33 strains isolated from humans, hospital environment and natural environment. Genetic and metagenomic databases were also surveyed. The population structure of the genus showed clades associated with humans, whereas others grouped environmental strains only. Roseomonas mucosa is the main human-associated species and the study supported the idea that opportunistic infections due to this species are related to the patient skin microbiota rather than to the environment. In contrast, some strains belonging to other species isolated from patients with cystic fibrosis were related to environmental clades, suggesting an exogenous source for patient colonization. Accurate knowledge about the reservoirs of opportunistic pathogens that have long been considered of environmental origin is still needed and would be helpful to improve infection control and epidemiological survey of emerging human pathogens.
Topics: Anti-Bacterial Agents; Cross Infection; Drug Resistance, Bacterial; Environmental Microbiology; Genome, Bacterial; Gram-Negative Bacterial Infections; Humans; Metagenome; Metagenomics; Methylobacteriaceae; Microbial Sensitivity Tests; Microbiota; Opportunistic Infections; Phylogeny; RNA, Ribosomal, 16S; Skin
PubMed: 27269884
DOI: 10.1016/j.cmi.2016.05.024 -
Bioresource Technology May 2022In the context of algal wastewater bioremediation, this study has identified a novel consortium formed by the bacterium Methylobacterium oryzae and the microalga...
In the context of algal wastewater bioremediation, this study has identified a novel consortium formed by the bacterium Methylobacterium oryzae and the microalga Chlamydomonas reinhardtii that greatly increase biomass generation (1.22 g L·d), inorganic nitrogen removal (>99%), and hydrogen production (33 mL·L) when incubated in media containing ethanol and methanol. The key metabolic aspect of this relationship relied on the bacterial oxidation of ethanol to acetate, which supported heterotrophic algal growth. However, in the bacterial monocultures the acetate accumulation inhibited bacterial growth. Moreover, in the absence of methanol, ethanol was an unsuitable carbon source and its incomplete oxidation to acetaldehyde had a toxic effect on both the alga and the bacterium. In cocultures, both alcohols were used as carbon sources by the bacteria, the inhibitory effects were overcome and both microorganisms mutually benefited. Potential biotechnological applications in wastewater treatment, biomass generation and hydrogen production are discussed.
Topics: Acetates; Biomass; Carbon; Chlamydomonas; Denitrification; Ethanol; Hydrogen; Methanol; Methylobacterium; Nitrogen
PubMed: 35364237
DOI: 10.1016/j.biortech.2022.127088 -
ACS Synthetic Biology Nov 2019Genetic tools are a prerequisite to engineer cellular factories for synthetic biology and biotechnology. AM1 is an important platform organism of a future C-bioeconomy....
Genetic tools are a prerequisite to engineer cellular factories for synthetic biology and biotechnology. AM1 is an important platform organism of a future C-bioeconomy. However, its application is currently limited by the availability of genetic tools. Here we systematically tested regions to maintain extrachromosomal DNA in . We used three elements to construct mini-chromosomes that are stably inherited at single copy number and can be shuttled between and . These mini-chromosomes are compatible among each other and with high-copy number plasmids of . We also developed a set of inducible promoters of wide expression range, reaching levels exceeding those currently available, notably the -promoter. In summary, we provide a set of tools to control the dynamic expression and copy number of genetic elements in , which opens new ways to unleash the metabolic and biotechnological potential of this organism for future applications.
Topics: Bacterial Proteins; Biotechnology; DNA Helicases; DNA Replication; Escherichia coli; Extrachromosomal Inheritance; Gene Expression Regulation, Bacterial; Genome, Bacterial; Metabolic Engineering; Methylobacterium extorquens; Plasmids; Promoter Regions, Genetic; Replicon; Synthetic Biology; Trans-Activators
PubMed: 31584803
DOI: 10.1021/acssynbio.9b00220 -
Microbiome Sep 2021Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria-their microbiome. However, the nature of the...
BACKGROUND
Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria-their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies-including cyanobacteria and associated bacterial genomes-isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil.
RESULTS
We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.
CONCLUSIONS
We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations. Video Abstract.
Topics: Cyanobacteria; Lakes; Microbiota; Microcystis; Phylogeny
PubMed: 34579777
DOI: 10.1186/s40168-021-01140-8 -
Journal of the American Chemical Society Feb 2018Methane-oxidizing bacteria, aerobes that utilize methane as their sole carbon and energy source, are being increasingly studied for their environmentally significant...
Methane-oxidizing bacteria, aerobes that utilize methane as their sole carbon and energy source, are being increasingly studied for their environmentally significant ability to remove methane from the atmosphere. Their genomes indicate that they also have a robust and unusual secondary metabolism. Bioinformatic analysis of the Methylobacter tundripaludum genome identified biosynthetic gene clusters for several intriguing metabolites, and this report discloses the structural and genetic characterization of tundrenone, one of these metabolites. Tundrenone is a highly oxidized metabolite that incorporates both a modified bicyclic chorismate-derived fragment and a modified lipid tail bearing a β,γ-unsaturated α-hydroxy ketone. Tundrenone has been genetically linked to its biosynthetic gene cluster, and quorum sensing activates its production. M. tundripaludum's genome and tundrenone's discovery support the idea that additional studies of methane-oxidizing bacteria will reveal new naturally occurring molecular scaffolds and the biosynthetic pathways that produce them.
Topics: Biosynthetic Pathways; Computational Biology; Genome, Bacterial; Hydroxy Acids; Indenes; Methane; Methylobacteriaceae; Multigene Family; Secondary Metabolism
PubMed: 29361220
DOI: 10.1021/jacs.7b12240 -
Skin Health and Disease Sep 2021While patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the...
BACKGROUND
While patients and families struggling with atopic dermatitis (AD) have documented concerns for a contributory role of skin care products in AD pathology, nearly all the skin microbiome studies to date have asked participants to avoid topical products (such as soaps or select medications) for the preceding days to weeks prior to sample collection. Thus, given the established role of the microbiome in AD, the interactions between topical exposures, dysbiosis and AD remains underrepresented in the academic literature.
OBJECTIVES
To address this knowledge gap, we expanded our previous evaluations to test the toxicological effects of a broader range of common chemicals, AD treatment lotions, creams and ointments using both health- and AD-associated strains of and spp.
METHODS
Use of in vitro culture techniques and mouse models were deployed to identify chemicals with dysbiotic or pre-biotic potential. A proof-of-concept study was subsequently performed in healthy volunteers to assess global microbiome shifts after exposure to select chemicals using dermatologic patch testing.
RESULTS
Numerous chemicals possessed antibiotic properties, including many not marketed as anti-microbials. Through targeted combination of potentially beneficial chemicals, we identified combinations which promoted the growth of health-associated isolates over disease-associated strains in bacterial culture and enhanced microbe-specific outcomes in an established mouse model of AD; the most promising of which was the combination of citral and colophonium (often sold as lemon myrtle oil and pine tar). Additional studies would likely further optimize the combination of ingredients use. Similar results were seen in the proof-of-concept human studies.
CONCLUSIONS
Our results could offer a systematic, multiplex approach to identify which products carry dysbiotic potential and thus may guide formulation of new topicals to benefit patients with AD.
PubMed: 34723253
DOI: 10.1002/ski2.41 -
The Journal of Biological Chemistry Oct 2017G-proteins regulate various processes ranging from DNA replication and protein synthesis to cytoskeletal dynamics and cofactor assimilation and serve as models for...
G-proteins regulate various processes ranging from DNA replication and protein synthesis to cytoskeletal dynamics and cofactor assimilation and serve as models for uncovering strategies deployed for allosteric signal transduction. MeaB is a multifunctional G-protein chaperone, which gates loading of the active 5'-deoxyadenosylcobalamin cofactor onto methylmalonyl-CoA mutase (MCM) and precludes loading of inactive cofactor forms. MeaB also safeguards MCM, which uses radical chemistry, against inactivation and rescues MCM inactivated during catalytic turnover by using the GTP-binding energy to offload inactive cofactor. The conserved switch I and II signaling motifs used by G-proteins are predicted to mediate allosteric regulation in response to nucleotide binding and hydrolysis in MeaB. Herein, we targeted conserved residues in the MeaB switch I motif to interrogate the function of this loop. Unexpectedly, the switch I mutations had only modest effects on GTP binding and on GTPase activity and did not perturb stability of the MCM-MeaB complex. However, these mutations disrupted multiple MeaB chaperone functions, including cofactor editing, loading, and offloading. Hence, although residues in the switch I motif are not essential for catalysis, they are important for allosteric regulation. Furthermore, single-particle EM analysis revealed, for the first time, the overall architecture of the MCM-MeaB complex, which exhibits a 2:1 stoichiometry. These EM studies also demonstrate that the complex exhibits considerable conformational flexibility. In conclusion, the switch I element does not significantly stabilize the MCM-MeaB complex or influence the affinity of MeaB for GTP but is required for transducing signals between MeaB and MCM.
Topics: Amino Acid Motifs; Bacterial Proteins; Cobamides; Methylmalonyl-CoA Mutase; Methylobacterium extorquens; Molecular Chaperones; Multiprotein Complexes; Protein Stability; Signal Transduction; Transcription Factors
PubMed: 28882898
DOI: 10.1074/jbc.M117.786095 -
PloS One 2017Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and...
Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids-the other major isoprenoid product of this strain-and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can be mitigated by addition of cellulase to the medium, suggesting a link between the function of hopanoids and the secretion of cellulose in M. extorquens DM4. On solid media, colonies of the hopanoid-free mutant strain were smaller than wild-type, and were more sensitive to osmotic or pH stress, as well as to a variety of toxins. The results for M. extorquens DM4 are consistent with the hypothesis that hopanoids are important for membrane fluidity and lipid packing, but also indicate that the specific physiological processes that require hopanoids vary across bacterial lineages. Our work provides further support to emerging observations that the role of hopanoids in membrane robustness and barrier function may be important across lineages, possibly mediated through an interaction with lipid A in the outer membrane.
Topics: Carotenoids; Cell Membrane; Cellulase; Culture Media; Fatty Acids; Flocculation; Hydrogen-Ion Concentration; Membrane Fluidity; Membrane Lipids; Methylobacterium extorquens; Mutation; Osmolar Concentration; Stress, Physiological
PubMed: 28319163
DOI: 10.1371/journal.pone.0173323 -
MSystems Mar 2024Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for...
Skin microbiome can be altered in patients with atopic dermatitis (AD). An understanding of the changes from healthy to atopic skin can help develop new targets for treatment by identifying microbial and molecular biomarkers. This study investigates the skin microbiome and metabolome of healthy adult subjects and lesion (ADL) and non-lesion (ADNL) of AD patients by 16S rRNA gene sequencing and mass spectrometry, respectively. Samples from AD patients showed alterations in the diversity and composition of the skin microbiome, with ADL skin having the greatest divergence. species, especially , were significantly increased in AD patients. Metabolomic profiles were also different between the groups. Dipeptide derivatives are more abundant in ADL, which may be related to skin inflammation. Co-occurrence network analysis of the microbiome and metabolomics data revealed higher co-occurrence of metabolites and bacteria in healthy ADNL compared to ADL. co-occurred with dipeptide derivatives in ADL, while phytosphingosine-derived compounds showed co-occurrences with commensal bacteria, for example sp., sp., , , sp., sp., , , , and , in healthy and ADNL groups. Therefore, these findings provide valuable insights into how AD affects the human skin metabolome and microbiome.IMPORTANCEThis study provides valuable insight into changes in the skin microbiome and associated metabolomic profiles in an adult population with mild to moderate atopic dermatitis. It also identifies new therapeutic targets that may be useful for developing personalized treatments for individuals with atopic dermatitis based on their unique skin microbiome and metabolic profiles.
Topics: Adult; Humans; Dermatitis, Atopic; Staphylococcus aureus; RNA, Ribosomal, 16S; Microbiota; Metabolome; Bacteria; Dipeptides
PubMed: 38319107
DOI: 10.1128/msystems.01119-23