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Oxygen diffusion pathways in mutated forms of a LOV photoreceptor from : A molecular dynamics study.Biomolecular Concepts Mar 20224511 from is a photoreceptor of the light, oxygen voltage (LOV) family, binding flavin mononucleotide (FMN) as a chromophore. It exhibits the prototypical LOV...
4511 from is a photoreceptor of the light, oxygen voltage (LOV) family, binding flavin mononucleotide (FMN) as a chromophore. It exhibits the prototypical LOV photocycle, with the reversible formation of an FMN-Cys71 adduct via fast decay of the FMN triplet state. 4511 has high potential as a photosensitiser for singlet oxygen (SO) upon mutation of C71. 4511-C71S shows a triplet lifetime ( ) of several hundreds of microseconds, ensuring efficient energy transfer to dioxygen to form SO. In this work, we have explored the potential diffusion pathways for dioxygen within 4511 using molecular dynamics (MD) simulations. The structural model of wild-type (wt) 4511 showed a dimeric structure stabilised by a strong leucine zipper at the two C-terminal helical ends. We then introduced the C71S mutation and analysed transient and persistent oxygen channels. MD simulations indicate that the chromophore binding site is highly accessible to dioxygen. Mutations that might favour SO generation were designed based on their position with respect to FMN and the oxygen channels. In particular, the C71S-Y61T and C71S-Y61S variants showed an increased diffusion and persistence of oxygen molecules inside the binding cavity.
Topics: Flavin Mononucleotide; Methylobacterium; Molecular Dynamics Simulation; Oxygen
PubMed: 35334189
DOI: 10.1515/bmc-2022-0013 -
BMJ Case Reports Mar 2022Hepatic abscesses can rarely cause pericardial disease by erosion into the pericardial space and present with haemodynamic instability due cardiac tamponade. While rare,...
Hepatic abscesses can rarely cause pericardial disease by erosion into the pericardial space and present with haemodynamic instability due cardiac tamponade. While rare, these dramatic presentations are more often due to amoebic abscesses than bacterial abscesses. Importantly, a cause must be found for any cryptogenic hepatic abscess regardless of presentation, as there is a high association with underlying malignancy. We report a previously healthy man in his 30s who presented with cardiac tamponade from perforation of a pyogenic hepatic abscess into the pericardium in the absence of bacteremia and biliary disease. One year later, he was found to have diffusely metastatic hepatoid carcinoma.
Topics: Adenocarcinoma; Cardiac Tamponade; Humans; Liver Abscess, Pyogenic; Male; Methylobacteriaceae
PubMed: 35304358
DOI: 10.1136/bcr-2022-248947 -
Microorganisms Jan 2022Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These...
Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were , , , and , of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed (26.7%) (23.6%) and (10%), while the gene revealed (70.3%) and (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; (39%) and (24.4%) (all legumes), (7.9%), (4.6%) and (3%) (, , ) (4.2%; ), (4%; , ), (3.1%; ), and (2.7%; ) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of species was common in all rhizosphere soils considered. had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.
PubMed: 35208671
DOI: 10.3390/microorganisms10020216 -
BMC Microbiology Feb 2022Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting...
BACKGROUND
Symbiotic Methylobacterium strains comprise a significant part of plant microbiomes. Their presence enhances plant productivity and stress resistance, prompting classification of these strains as plant growth-promoting bacteria (PGPB). Methylobacteria can synthesize unusually high levels of plant hormones, called cytokinins (CKs), including the most active form, trans-Zeatin (tZ).
RESULTS
This study provides a comprehensive inventory of 46 representatives of Methylobacterium genus with respect to phytohormone production in vitro, including 16 CK forms, abscisic acid (ABA) and indole-3-acetic acid (IAA). High performance-liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analyses revealed varying abilities of Methylobacterium strains to secrete phytohormones that ranged from 5.09 to 191.47 pmol mL for total CKs, and 0.46 to 82.16 pmol mL for tZ. Results indicate that reduced methanol availability, the sole carbon source for bacteria in the medium, stimulates CK secretion by Methylobacterium. Additionally, select strains were able to transform L-tryptophan into IAA while no ABA production was detected.
CONCLUSIONS
To better understand features of CKs in plants, this study uncovers CK profiles of Methylobacterium that are instrumental in microbe selection for effective biofertilizer formulations.
Topics: Chromatography, High Pressure Liquid; Cytokinins; Methylobacterium; Tandem Mass Spectrometry
PubMed: 35135483
DOI: 10.1186/s12866-022-02454-9 -
MBio Feb 2022is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like...
is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we uncovered a considerable diversity of in the phyllosphere. We cultured different subsets of lineages depending upon the temperature of isolation and growth (20°C or 30°C), suggesting long-term adaptation to temperature. To a lesser extent than temperature adaptation, diversity was also structured across large (>100 km; between forests) and small (<1.2 km; within forests) geographical scales, among host tree species, and was dynamic over seasons. By measuring the growth of 79 isolates during different temperature treatments, we observed contrasting growth performances, with strong lineage- and season-dependent variations in growth strategies. Finally, we documented a progressive replacement of lineages with a high-yield growth strategy typical of cooperative, structured communities in favor of those characterized by rapid growth, resulting in convergence and homogenization of community structure at the end of the growing season. Together, our results show how is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This work paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus. is a bacterial group tied to plants. Despite the ubiquity of methylobacteria and the importance to their hosts, little is known about the processes driving community dynamics. By combining traditional culture-dependent and -independent (metabarcoding) approaches, we monitored diversity in two temperate forests over a growing season. On the surface of tree leaves, we discovered remarkably diverse and dynamic communities over short temporal (from June to October) and spatial (within 1.2 km) scales. Because we cultured different subsets of diversity depending on the temperature of incubation, we suspected that these dynamics partly reflected climatic adaptation. By culturing strains under laboratory conditions mimicking seasonal variations, we found that diversity and environmental variations were indeed good predictors of growth performances. Our findings suggest that community dynamics at the surface of tree leaves results from the succession of strains with contrasting growth strategies in response to environmental variations.
Topics: Methylobacterium; Phylogeny; Forests; Plants; Host Specificity; Plant Leaves
PubMed: 35073752
DOI: 10.1128/mbio.03175-21 -
Animals : An Open Access Journal From... Nov 2021As one of the pioneer bacterial sources of intestinal microbiota, the information of bacterial composition in colostrum might provide a reference for developing specific...
As one of the pioneer bacterial sources of intestinal microbiota, the information of bacterial composition in colostrum might provide a reference for developing specific probiotics for newborn calves, especially calves fed with pasteurized milk. The present study aimed to detect the core bacteria at different taxonomic levels and the common beneficial ones in colostrum by analyzing the bacterial composition in 34 colostrum samples of healthy cows selected from two dairy farms. The results of the further analysis showed that the bacterial composition in the colostrum of the two dairy farms was different, but their four most dominant phyla were the same including , , , and The microbiome of all colostrum samples shared ten core operational taxonomic units (OTUs), 21 core genera, and 34 core families, and most of them had no difference in relative abundance between the two farms. The ten core OTUs did not belong to the identified commensal bacteria and have not been detected by previous study. However, several core genera found in our study were also identified as core genus in a previous study. Some well-known beneficial and pathogenic bacteria including , , , and were present in the colostrum of healthy cows. However, none had a correlation with the number of somatic cell count (SCC), but the core genera and and the core families and positively correlated with the number of SCC. The genus , , and in colostrum had a positive correlation with each other, while the probiotics ---- had a negative correlation with and . In addition, more than 50% bacterial OTUs in colostrum were detected in the rectal content including some strictly anaerobic bacteria that are generally present in the intestine and rumen. However, of the top 30 commonly shared bacterial genera in the colostrum and rectal feces, no genus in colostrum was positively correlated with that same genus in rectal feces. In conclusion, the bacterial composition of colostrum microbiota is greatly influenced by external factors and individuals. There were several core OTUs, and some core genus and families in the colostrum samples. Colostrum from healthy cows contained both beneficial and pathogenic bacteria and shared many common bacteria with rectal content including some gastrointestinal anaerobes.
PubMed: 34944139
DOI: 10.3390/ani11123363 -
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 -
Journal of Microbiology (Seoul, Korea) Feb 2022Four novel Gram-negative, mesophilic, aerobic, motile, and cocci-shaped strains were isolated from tick samples (strains 546 and 573) and respiratory tracts of marmots...
Four novel Gram-negative, mesophilic, aerobic, motile, and cocci-shaped strains were isolated from tick samples (strains 546 and 573) and respiratory tracts of marmots (strains 1318 and 1311). The 16S rRNA gene sequencing revealed that strains 546 and 573 were 97.8% identical to Roseomonas wenyumeiae Z23, whereas strains 1311 and 1318 were 98.3% identical to Roseomonas ludipueritiae DSM 14915. In addition, a 98.0% identity was observed between strains 546 and 1318. Phylogenetic and phylogenomic analyses revealed that strains 546 and 573 clustered with R. wenyumeiae Z23, whereas strains 1311 and 1318 grouped with R. ludipueritiae DSM 14915. The average nucleotide identity between our isolates and members of the genus Roseomonas was below 95%. The genomic G+C content of strains 546 and 1318 was 70.9% and 69.3%, respectively. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the major polar lipids, with Q-10 as the predominant respiratory quinone. According to all genotypic, phenotypic, phylogenetic, and phylogenomic analyses, the four strains represent two novel species of the genus Roseomonas, for which the names Roseomonas haemaphysalidis sp. nov. and Roseomonas marmotae sp. nov. are proposed, with 546 (= GDMCC 1.1780 = JCM 34187) and 1318 (= GDMCC 1.1781 = JCM 34188) as type strains, respectively.
Topics: Animals; Bacterial Typing Techniques; Base Composition; Cardiolipins; DNA, Bacterial; Marmota; Methylobacteriaceae; Phosphatidylethanolamines; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ticks
PubMed: 34826100
DOI: 10.1007/s12275-022-1428-1 -
Frontiers in Microbiology 2021The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: and They have been separated into...
The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: and They have been separated into three major clades: A, B (), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other . The species in clade A, including the type species , were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to species; this finding led us to reunite the two genera into a single genus . Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the HMPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.
PubMed: 34737731
DOI: 10.3389/fmicb.2021.740610 -
Microbes and Environments 2021A new disease in rice that is characterized by leaf bleaching was recently identified in some fields in the Mekong Delta region of Vietnam. The present study was the...
A new disease in rice that is characterized by leaf bleaching was recently identified in some fields in the Mekong Delta region of Vietnam. The present study was the first to isolate and identify the pathogen of this disease. We confirmed that leaf bleaching symptoms were due to infection with Methylobacterium indicum bacteria using molecular biology approaches. A full-length genome analysis of pathogenic Methylobacterium strain VL1 revealed that it comprises a single chromosome and six plasmids, with a total size of 7.05 Mbp and GC content of 70.5%. The genomic features of VL1 were similar to those of the non-pathogenic M. indicum strain SE2.11; however, VL1 possessed additional unique genes, including those related to homoserine lactone biosynthesis. We established a loop-mediated isothermal amplification (LAMP) assay using the unique sequences of VL1 as target sequences for the rapid and simple detection of pathogenic M. indicum strains. Our initial evaluation demonstrated that the LAMP assay successfully distinguished between pathogenic and non-pathogenic strains infecting rice plants in a rapid and sensitive manner. The present results provide insights into the pathogenesis and development of control measures for novel rice diseases.
Topics: Genomics; Methylobacterium; Molecular Diagnostic Techniques; Nucleic Acid Amplification Techniques; Oryza; Plant Diseases; Plant Leaves; Vietnam
PubMed: 34732597
DOI: 10.1264/jsme2.ME21035