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Molecular Microbiology May 2019Recently, rare-earth elements lanthanides (Ln ) have emerged as enzyme cofactors of methanol dehydrogenases of the XoxF type. It is now understood that XoxF enzymes can...
Recently, rare-earth elements lanthanides (Ln ) have emerged as enzyme cofactors of methanol dehydrogenases of the XoxF type. It is now understood that XoxF enzymes can functionally replace the alternative, calcium-dependent, MxaFI-type methanol dehydrogenases, when Ln are available. These rare-earth metals are not only essential for XoxF activity, but they also regulate gene expression, in a reverse fashion, activating the expression of XoxF and repressing the expression of MxaFI. This type of regulation has created multiple conundrums, including the details of the solubility, transport, sensing and selection mechanisms for Ln by the bacterial cells, as well as the questions relevant to the evolution of the alternative enzymes and their potentially different redox properties. Overall, the newly discovered biological activity of Ln presents a big puzzle. Ochsner et al. add several pieces to this puzzle, utilizing a model phyllosphere colonizer Methylobacterium extorquens PA1. They determine that Ln sensing by this organism can take place via both XoxF-dependent and XoxF-independent mechanisms. They also identify genes for a TonB-dependent transporter and an ABC-type transporter and demonstrate that both are essential for Ln -dependent methanol metabolism. The puzzle still requires multiple additional pieces for completion, but great strides have been made toward the goal of solving it.
PubMed: 30673122
DOI: 10.1111/mmi.14210 -
Journal of Microorganism Control 2023Bedside dialysis monitoring equipment for hemodialysis are located in the bioburden section upstream of the endotoxin-retentive filter for dialysis fluid sterilization....
Bedside dialysis monitoring equipment for hemodialysis are located in the bioburden section upstream of the endotoxin-retentive filter for dialysis fluid sterilization. We observed 26 equipment at our institution for bacterial contamination at least once every 4 weeks for 5 years with another ultrafiltration membrane upstream to prevent bacterial contamination. Bacterial contamination levels were highest and most diverse at the time of the first flush. During subsequent initial cleanng, the contamination level decreased, and bacterial species converged almost exclusively to one genus, namely Methylobacterium spp. During clinical use, the equipment were cleaned and disinfected daily after dialysis, and daily operations and maintenance were performed using aseptic techniques. Although the frequency of bacterial detection decreased annually, the same bacterial genotypes observed at the first flush were isolated even after long time periods and were thought to persist in the equipment possibly by forming biofilm. Pseudomonas aeruginosa was newly detected after the replacement of parts during breakdown maintenance, indicating the need to sterilize replacement parts. Thus, the bioburden should be assessed regularly as part of the management of in-house-produced dialysis fluid.
Topics: Renal Dialysis; Bacteria; Dialysis Solutions; Ultrafiltration; Endotoxins
PubMed: 37866898
DOI: 10.4265/jmc.28.3_69 -
Sichuan Da Xue Xue Bao. Yi Xue Ban =... Mar 2022To observe the dynamic changes in the salivary microbiota of children with dental caries and those who were caries-free and to analyze the functional differences in the...
OBJECTIVE
To observe the dynamic changes in the salivary microbiota of children with dental caries and those who were caries-free and to analyze the functional differences in the oral microecology of the two groups during the course of sugar metabolism and the synthesis and transport of multiple amino acids.
METHODS
Ten children with dental caries and 10 caries-free children were enrolled. We employed Illumina metagenomics technology to analyze the composition and function of salivary microbiome in children with and without caries. Six months later, PacBio single-molecule long-read sequencing technology was used to analyze the changes over time in the oral microbial communities of the two groups. We studied the patterns of change in the oral microbial communities under diseased or healthy conditions and attempted to offer a comprehensive interpretation of children's oral microbiota in terms of its composition and functions.
RESULTS
The composition of the oral microbiota of children with or without dental caries changed significantly over time. At the phylum level, changing trends in the salivary microbial communities of children with dental caries were in line with those in caries-free children. In these microbial communities, increased proportions of and decreased proportions of and were found in the two groups. At the genus level, however, the two groups showed significantly different changes of the salivary microbial communities. Upward trends in the abundance of , , and were found in the caries group, while the abundance of these genera in the caries-free group showed downward trends. At the species level, , , , , and some other species belonging to the genus showed upward trends in the saliva of children with caries, while they consistently stayed at a relative low level of abundance in caries-free children. The abundance of and decreased to a certain extent in children with dental caries, but the abundance of and in caries-free children were always at a low level. Species such as and were positively correlated to the sum of decayed, missing and filled teeth (dmft), while was negatively correlated to dmft. , , and , the key genes related to tricarboxylic acid (TCA) cycle, , a glutamate synthesis-related gene, and //, arginine synthesis-related genes, were significantly increased in caries-free children. In addition, the abundance of the NADH dehydrogenase-related gene ///////// in the electron transport chain increased significantly in caries-free children.
CONCLUSION
Dynamic changes were found in the oral microbiota of children with or without caries. The trends of microbial shifts over time were associated with the oral health status. Oxidative phosphorylation and the synthesis and transport of amino acids such as glutamate and arginine in the oral microecology were more active in caries-free children.
Topics: Child; Dental Caries; Dental Caries Susceptibility; Humans; Microbiota; Saliva; Sequence Analysis, DNA
PubMed: 35332724
DOI: 10.12182/20220360103 -
Frontiers in Microbiology 2020Soybean () is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United...
Soybean () is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by and while belowground samples were dominated by and Aboveground fungal communities were dominated by across all management systems, while belowground samples were dominated by and . Specific taxa including potential plant beneficials such as were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.
PubMed: 32582080
DOI: 10.3389/fmicb.2020.01116 -
Rice (New York, N.Y.) May 2023Rice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant-microbe interactions. As modulators of the rice...
BACKGROUND
Rice is colonized by plant growth promoting bacteria such as Methylobacterium leading to mutually beneficial plant-microbe interactions. As modulators of the rice developmental process, Methylobacterium influences seed germination, growth, health, and development. However, little is known about the complex molecular responsive mechanisms modulating microbe-driven rice development. The application of proteomics to rice-microbe interactions helps us elucidate dynamic proteomic responses mediating this association.
RESULTS
In this study, a total of 3908 proteins were detected across all treatments of which the non-inoculated IR29 and FL478 share up to 88% similar proteins. However, intrinsic differences appear in IR29 and FL478 as evident in the differentially abundant proteins (DAPs) and their associated gene ontology terms (GO). Successful colonization of M. oryzae CBMB20 in rice resulted to dynamic shifts in proteomes of both IR29 and FL478. The GO terms of DAPs for biological process in IR29 shifts in abundance from response to stimulus, cellular amino acid metabolic process, regulation of biological process and translation to cofactor metabolic process (6.31%), translation (5.41%) and photosynthesis (5.41%). FL478 showed a different shift from translation-related to response to stimulus (9%) and organic acid metabolic acid (8%). Both rice genotypes also showed a diversification of GO terms due to the inoculation of M. oryzae CBMB20. Specific proteins such as peptidyl-prolyl cis-trans isomerase (A2WJU9), thiamine thiazole synthase (A2YM28), and alanine-tRNA ligase (B8B4H5) upregulated in IR29 and FL478 indicate key mechanisms of M. oryzae CBMB20 mediated plant growth promotion in rice.
CONCLUSIONS
Interaction of Methylobacterium oryzae CBMB20 to rice results in a dynamic, similar, and plant genotype-specific proteomic changes supporting associated growth and development. The multifaceted CBMB20 expands the gene ontology terms and increases the abundance of proteins associated with photosynthesis, diverse metabolic processes, protein synthesis and cell differentiation and fate potentially attributed to the growth and development of the host plant. The specific proteins and their functional relevance help us understand how CBMB20 mediate growth and development in their host under normal conditions and potentially link subsequent responses when the host plants are exposed to biotic and abiotic stresses.
PubMed: 37145322
DOI: 10.1186/s12284-023-00639-y -
Microbes and Environments 2020The Vietnamese Mekong delta is one of the largest rice-producing areas globally. Methylobacterium spp. are persistent colonizers of the rice plant and exert beneficial...
The Vietnamese Mekong delta is one of the largest rice-producing areas globally. Methylobacterium spp. are persistent colonizers of the rice plant and exert beneficial effects on plant growth and health. Sixty-one Methylobacterium strains belonging to seven species were predominantly isolated from the phyllosphere of rice cultivated in six Mekong delta provinces. Inoculation tests revealed that some strains exhibited plant growth-promoting activity. Moreover, three strains possessed the novel characteristics of inducing leaf bleaching and killing rice seedlings. These results revealed the complex diversity of Methylobacterium in Mekong delta rice and that healthy and productive rice cultivation requires a proper balance of Methylobacterium.
Topics: Genetic Variation; Lactuca; Methylobacterium; Oryza; Plant Components, Aerial; Plant Growth Regulators; Vietnam
PubMed: 31969531
DOI: 10.1264/jsme2.ME19111 -
Microbiome Jan 2021Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats;...
BACKGROUND
Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets.
RESULTS
The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 10 16S rRNA gene copies ng DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential.
CONCLUSIONS
Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.
Topics: Anti-Infective Agents; Ascomycota; Colistin; Drug Resistance, Microbial; Glycine; Microbiota; Pyrazines; RNA, Ribosomal, 16S; Tetracycline; Glyphosate
PubMed: 33504360
DOI: 10.1186/s40168-020-00982-y -
Data in Brief Jun 2022Plants harbor varied communities of bacterial endophytes which play a crucial role in plant health and growth. is a medicinal plant that is known for its excellent...
Plants harbor varied communities of bacterial endophytes which play a crucial role in plant health and growth. is a medicinal plant that is known for its excellent ethnomedicinal uses which include treatment of coughs, fever, ulcers, and dysentery. This data in Brief article provides information on the diversity of bacterial endophytes associated with a medicinal plant, targeting the 16S rRNA gene using Illumina sequencing technology during three different seasons. Plant samples were collected in Eisleben, Limpopo province, South Africa, in the months of April, June, August and October 2018. The dataset revealed that the leaf samples collected in August had the highest species diversity as indicated by the Shannon index (4.25), Chao1 (1456.01), abundance-based coverage estimator (ACE) (1492.07) and the Simpson indices of diversity (0.05) irrespective of the species. The order of the bacterial endophyte's richness in was April> October> June> August, from lowest to highest. The taxonomic composition analysis showed that most endophytic bacteria were composed of and Some endophytic bacteria were found to be tissue specific. Sequences of and were prevalent in the leaves, whereas and were the dominant genera in the root samples.
PubMed: 35434223
DOI: 10.1016/j.dib.2022.108112 -
Folia Microbiologica Feb 2024The effectiveness of Methylobacterium symbioticum in maize and strawberry plants was measured under different doses of nitrogen fertilisation. The biostimulant effect of...
The effectiveness of Methylobacterium symbioticum in maize and strawberry plants was measured under different doses of nitrogen fertilisation. The biostimulant effect of the bacteria was observed in maize and strawberry plants treated with the biological inoculant under different doses of nitrogen fertiliser compared to untreated plants (control). It was found that bacteria allowed a 50 and 25% decrease in the amount of nitrogen applied in maize and strawberry crops, respectively, and the photosynthetic capacity increased compared with the control plant under all nutritional conditions. A decrease in nitrate reductase activity in inoculated maize plants indicated that the bacteria affects the metabolism of the plant. In addition, inoculated strawberry plants grown with a 25% reduction in nitrogen had a higher concentration of nitrogen in leaves than control plants under optimal nutritional conditions. Again, this indicates that Methylobacterium symbioticum provide an additional supply of nitrogen.
Topics: Zea mays; Fragaria; Methylobacterium; Nitrogen; Photosynthesis; Crops, Agricultural
PubMed: 37526803
DOI: 10.1007/s12223-023-01078-4 -
IScience Apr 2022Upon exposure to the prevailing environment, leaves become increasingly colonized by fungi and bacteria located on the surface (epiphytic) or within (endophytic) the...
Upon exposure to the prevailing environment, leaves become increasingly colonized by fungi and bacteria located on the surface (epiphytic) or within (endophytic) the leaves. Many cool season grasses, including , host a seed-borne, intercellular, mutualistic fungal endophyte, the growth of which is synchronized with the host grass. A study utilizing illumina sequencing was used to examine the epiphytic and endophytic microbial communities in endophyte-infected and endophyte-free plants growing under hot dry field conditions. The presence of endophyte increased the Shannon and decreased Simpson diversity of bacterial and fungal communities. and bacteria and and fungi were growing largely epiphytically, whereas and the fungus were mostly found within leaves with the location of colonization influenced by the endophyte. In addition, leaf metabolites in -infected and -free leaves were examined using LC/MS. was significantly correlated with 132 metabolites.
PubMed: 35402863
DOI: 10.1016/j.isci.2022.104144