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Photochemical & Photobiological... Dec 2023Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented...
Methylotrophs are a diverse group of bacteria that abundantly colonize the phyllosphere and have great potential to withstand UV irradiation because of their pigmented nature and ability to promote plant growth through various mechanisms. The present study investigated the effects of UVB radiation on plant growth-promoting (PGP) properties of methylotrophic bacteria and the growth of Vigna radiata L. A total of 55 methylotrophic bacteria were isolated from desert plants, and 15 methylotrophs were resistant to UVB radiation for 4 h. All UVB-resistant methylotrophs possess a methyldehydrogenase gene. Identification based on 16S rRNA gene sequencing revealed that all 15 UVB-resistant methylotrophs belonged to the genera Methylorubrum (07), Methylobacterium (07), and Rhodococcus (01). Screening of methylotrophs for PGP activity in the presence and absence of UVB radiation revealed that all isolates showed ACC deaminase activity and growth on a nitrogen-free medium. Furthermore, the production of IAA-like substances ranged from 8.62 to 85.76 µg/mL, siderophore production increased from 3.47 to 65.75% compared to the control. Seed germination assay with V. radiata L. (mung bean) exposed to UVB radiation revealed that methylotrophs improved seed germination, root length, and shoot length compared to the control. The present findings revealed that the isolates SD3, SD2, KD1, KD5, UK1, and UK3 reduced the deleterious effects of UVB radiation on mung bean plants and can be used to protect seedlings from UVB radiation for sustainable agriculture.
Topics: Vigna; RNA, Ribosomal, 16S; Methylobacterium; Seedlings
PubMed: 37838625
DOI: 10.1007/s43630-023-00490-6 -
World Journal of Microbiology &... Feb 2021Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH) emission. We...
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, K of 1.92 ± 0.092 mg CH L. Besides the ability to utilize CH, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
Topics: Bacteria; Biodiversity; Ecosystem; Enterobacteriaceae; India; Indoleacetic Acids; Kinetics; Methane; Methylobacterium; Nitrogen Fixation; Oryza; Paenibacillus polymyxa; Phylogeny; Plant Development; Rhizosphere; Soil; Soil Microbiology
PubMed: 33619649
DOI: 10.1007/s11274-021-03018-1 -
Current Microbiology Dec 2022The dynamic microflora associated within, and in the surrounding aquatic environment, has been found to be responsible for the functional properties of many aquatic...
The dynamic microflora associated within, and in the surrounding aquatic environment, has been found to be responsible for the functional properties of many aquatic plants. The aim of the current work was to evaluate the effectiveness of Lemnaceae-based wastewater treatment system under tropical conditions and investigate the changes in the aquatic microflora upon plant growth. A biological wastewater treatment system was designed and investigated using mixed Lemnaceae culture comprising Lemna minor and Spirodela polyrhiza in a batch mode. A significant reduction in total solids (31.8%), biochemical oxygen demand (93.5%), and chemical oxygen demand (73.2%) was observed after seven days of duckweed growth using a low inoculum. A preliminary study on the change in the microbial population diversity and functionality, in the wastewater before and after treatment, revealed an increase in the denitrifying microflora in wastewater post-Lemnaceae treatment. Dominance of 10 bacterial phyla, contributing for 98.3% of the total bacterial communities, was recorded, and ~ 50.6% loss of diversity post-treatment of wastewater was revealed by the Shannon Index. Among 16 bacterial families showing relative abundance of ≥ 1% in untreated wastewater, Methylobacteriaceae, Pseudomonadaceae, Brucellaceae, Rhodobacteraceae, and Acetobacteraceae prevailed in the water post-treatment by duckweeds. This is a novel work done on the dynamics of aquatic microflora associated with Lemnaceae under tropical Indian conditions. It confirms the application of Lemnaceae-based wastewater treatment system as effective biofilter and calls for further studies on the active involvement of the endophytic and aquatic microflora in the functions of these plant.
Topics: Humans; Wastewater; Araceae; Plants; Bacteria; Population Dynamics; Water Purification
PubMed: 36585971
DOI: 10.1007/s00284-022-03149-0 -
International Journal of Systematic and... Oct 2016A novel Gram-stain-negative, coccus to oval-shaped, non-motile bacterium, designated strain S5T, was isolated from lagoon sediments collected from North Carolina, USA....
A novel Gram-stain-negative, coccus to oval-shaped, non-motile bacterium, designated strain S5T, was isolated from lagoon sediments collected from North Carolina, USA. Strain S5T was able to grow at 12-45 °C (optima, 30-37 °C) and at pH 6.3-9.0 (optima, 6.5-7.5). No added NaCl was required for growth of strain S5T. Strain S5T was positive for catalase and oxidase activity. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c and C16 : 0 were predominant fatty acids with minor amounts of C8 : 0 3-OH, C14 : 0, C16 : 0 3-OH, C18 : 1 2-OH, C14 : 1ω5c, C16 : 1ω5c and C19 : 0 cyclo ω8c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were major polar lipids. Minor amounts of an unidentified amino lipid and three unidentified lipids were also detected. The G+C content of the genomic DNA was 73.5 mol%. 16S rRNA gene sequence comparisons indicated that strain S5T represents a member of the genus Roseomonas within the family Acetobacteraceae of the class Alphaproteobacteria. Strain S5T had a sequence similarity of 97.80 % with Roseomonas rhizosphaerae YW11T, 97.69 % with Roseomonas aestuarii JC17T and <97 % with other members of the genus Roseomonas. However, strain S5T showed only 45.2±2 and 17±2 % relatedness (based on DNA-DNA hybridization) with R. rhizosphaerae KACC 17225T (=YW11T) and R. aestuarii KCTC 22692T (=JC17T), respectively. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain S5T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas rubra sp. nov. is proposed. The type strain is S5T (=KEMB 563-468T=JCM 31177T).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Geologic Sediments; Methylobacteriaceae; North Carolina; Nucleic Acid Hybridization; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 27381046
DOI: 10.1099/ijsem.0.001271 -
Frontiers in Immunology 2022The cutaneous microbiome is increasingly recognized as a contributor to skin diseases like atopic dermatitis (AD) and psoriasis. Although traditionally AD and psoriasis...
The cutaneous microbiome is increasingly recognized as a contributor to skin diseases like atopic dermatitis (AD) and psoriasis. Although traditionally AD and psoriasis have been viewed as having opposing immunologic findings, recent evidence suggests an overlap in ceramide-family lipid production in the protection against symptoms. We recently identified that specific environmental pollutants may drive dysbiosis through direct suppression of ceramide-family lipids produced by health-associated skin bacteria in atopic dermatitis (AD). We further demonstrated that one such bacteria, , generated significant clinical improvement in AD lasting beyond active treatment lipid-mediated modulation of tumor necrosis factor (TNF) signaling. To assess the potential preclinical benefit of in psoriasis we assessed for direct effects on surface TNF signaling in cell cultures and identified direct effects on the TNF axis. We also identified preclinical efficacy of treatment in the imiquimod mouse model of psoriasis. Finally, we expanded our previous environmental assessment for psoriasis to include more traditional markers of air quality and found a strong association between disease rates and ambient carbon monoxide (CO), nitrogen dioxide (NO), and particulate matter (PM). At the current stage this work is speculative but does support consideration of further preclinical models and/or clinical assessments to evaluate any potential for therapeutic benefit through microbial manipulation and/or environmental mitigation.
Topics: Animals; Mice; Dermatitis, Atopic; Environmental Pollutants; Psoriasis; Ceramides; Lipids
PubMed: 36605199
DOI: 10.3389/fimmu.2022.1094376 -
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 -
Protein Expression and Purification Jun 2022A new glycoside hydrolase family 2 (GH2) β-galactosidase encoding gene galM was cloned from Microvirga sp. strain MC18 and overexpressed in Escherichia coli. The...
A new glycoside hydrolase family 2 (GH2) β-galactosidase encoding gene galM was cloned from Microvirga sp. strain MC18 and overexpressed in Escherichia coli. The recombinant β-galactosidase GalM showed optimal activity at pH 7.0 and 50 °C, with a stability at pH 6.0-9.0 and 20-40 °C, which are conditions suitable for the diary environment. The K and V values for o-nitrophenyl-β-d-galactopyranoside (oNPG) were 1.30 mmol/L and 15.974 μmol/(min·mg), respectively. GalM showed low product inhibition by galactose with a K of 73.18 mM and high tolerance for glucose that 86.5% activity retained in the presence of 500 mM glucose. It was also stable and active in 20% of methanol, ethanol and isopropanol. In addition, the enzyme activity of GalM was activated significantly over 0-2 mol/L NaCl (1.6-4.3 fold). These favorable properties make GalM a potential candidate for the industrial application.
Topics: Escherichia coli; Galactose; Glucose; Hydrogen-Ion Concentration; Kinetics; Methylobacteriaceae; beta-Galactosidase
PubMed: 35218889
DOI: 10.1016/j.pep.2022.106074 -
Current Issues in Molecular Biology 2019Experimental evolution has become an increasingly common approach for studying evolutionary phenomena, as well as uncovering physiological connections in a manner... (Review)
Review
Experimental evolution has become an increasingly common approach for studying evolutionary phenomena, as well as uncovering physiological connections in a manner complementary to traditional genetics. Here I describe the development of as a model system for using experimental evolution to study questions at the intersection of metabolism and evolution. Each experiment was initiated to address a particular question inspired by patterns in natural methylotrophs, such as tradeoffs between single-carbon and multi-carbon growth, or the challenges involved in incorporating novel metabolic pathways or genes with poor codon usage that are acquired via horizontal gene transfer. What I could not have appreciated initially, however, was just how many fortuitous surprise findings would emerge. These have ranged from the repeatability of evolution, complex dynamics within populations, epistasis between beneficial mutations, and even the ability to use simple mathematical models to generate testable, quantitative hypotheses about the fitness landscape.
Topics: Directed Molecular Evolution; Epistasis, Genetic; Evolution, Molecular; Gene Expression Regulation, Bacterial; Gene Transfer Techniques; Metabolic Engineering; Metabolic Networks and Pathways; Methylobacterium; Models, Biological; Organisms, Genetically Modified; Research
PubMed: 31166197
DOI: 10.21775/cimb.033.249 -
International Journal of Systematic and... Nov 2015A non-motile, cocobacilli-shaped and pink-pigmented bacterium, designated strain WW53T, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells...
A non-motile, cocobacilli-shaped and pink-pigmented bacterium, designated strain WW53T, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram-stain-negative, catalase- and oxidase-positive. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0.The predominant quinone and polyamine were ubiquinone 10 (Q-10) and spermidine, respectively. The DNA G+C content was 71 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WW53T belongs to the family Acetobacteraceae, and is related to the genus Roseomonas. Strain WW53T was most closely related to Roseomonas stagni HS-69T (95.3 % 16S rRNA gene sequence similarity). Results of a polyphasic taxonomy study suggested that the isolate represents a novel species in the genus Roseomonas, for which the name Roseomonas wooponensis sp. nov. is proposed. The type strain is WW53T ( = KCTC 32534T = JCM 19527T).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Fresh Water; Methylobacteriaceae; Phylogeny; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Spermidine; Ubiquinone; Wetlands
PubMed: 26289445
DOI: 10.1099/ijsem.0.000536 -
PeerJ 2019We investigated the effects of gastric infection on the daytime and overnight human oral microbiota.
BACKGROUND
We investigated the effects of gastric infection on the daytime and overnight human oral microbiota.
METHODS
Twenty four volunteers were recruited. Ten tested positive for infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of gene amplicons. The microbial abundance and composition were analysed in relation to infection status.
RESULTS
-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both and , while , , and were significantly decreased in the UBT-positive samples.
DISCUSSION
Our data demonstrated that infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to infection require more studies to examine their potential health effects on affected individuals.
PubMed: 30713820
DOI: 10.7717/peerj.6336