-
Microorganisms Jan 2023Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we...
Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic . Our polyphasic taxonomic investigations revealed its identity as . The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on , as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of and , and the consequent blast suppressive activity. Strikingly, induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing mediated bioformulation for sustainably managing rice blast disease.
PubMed: 36838327
DOI: 10.3390/microorganisms11020362 -
Microbiology Spectrum Jun 2022Mixing plant litters of multiple species can alter litter decomposition, a key driver of carbon and nutrient cycling in terrestrial ecosystems. Changes in microbial...
Mixing plant litters of multiple species can alter litter decomposition, a key driver of carbon and nutrient cycling in terrestrial ecosystems. Changes in microbial decomposer communities is proposed as one of the mechanisms explaining this litter-mixture effect, but the underlying mechanism is unclear. In a microcosm litterbag experiment, we found that, at the early stage of decomposition, litter mixing promoted tomato root litter decomposition, thus generating a synergistic nonadditive litter-mixture effect. The transplanting decomposer community experiment showed that changes in microbial decomposer communities contributed to the nonadditive litter-mixture effect on tomato root litter decomposition. Moreover, litter mixing altered the abundance and diversity of bacterial and fungal communities on tomato root litter. Litter mixing also stimulated several putative keystone operational taxonomic units (OTUs) in the microbial correlation network, such as Fusarium sp. fOTU761 and Microbacterium sp. bOTU6632. Then, we isolated and cultured representative isolates of these two taxa, named Fusarium sp. F13 and Microbacterium sp. B26. Subsequent tests found that F13, but not B26, had strong decomposing ability; moreover, these two isolates developed synergistic interaction, thus promoted litter decomposition in coculture. Addition of F13 or B26 both promoted the decomposing activity of the resident decomposer community on tomato root litter, confirming their importance for litter decomposition. Overall, litter mixing promoted tomato root litter decomposition through altering microbial decomposers, especially through stimulating certain putative keystone taxa. Microbial decomposer community plays a key role in litter decomposition, which is an important regulator of soil carbon and nutrient cycling. Though changes in decomposer communities has been proposed as one of the potential underlying mechanisms driving the litter-mixture effects, direct evidence is still lacking. Here, we demonstrated that litter mixing stimulated litter decomposition through altering microbial decomposers at the early stage of decomposition. Moreover, certain putative keystone taxa stimulated by litter mixing contributed to the nonadditive litter-mixture effect. culturing validated the role of these taxa in litter decomposition. This study also highlights the possibility of regulating litter decomposition through manipulating certain microbial taxa.
Topics: Carbon; Ecosystem; Solanum lycopersicum; Microbiota; Soil; Soil Microbiology
PubMed: 35604181
DOI: 10.1128/spectrum.00186-22 -
Microbiology Resource Announcements Oct 2022Eula is a lytic microbacteriophage extracted from a soil sample collected in Statesville, NC, and isolated on Microbacterium foliorum NRRL B-24224. The Eula...
Eula is a lytic microbacteriophage extracted from a soil sample collected in Statesville, NC, and isolated on Microbacterium foliorum NRRL B-24224. The Eula double-stranded DNA genome is 41,379 bp, with 69 predicted protein-coding genes and 1 tRNA. Based on gene content similarity, Eula was assigned to bacteriophage cluster EB.
PubMed: 36154145
DOI: 10.1128/mra.00728-22 -
Indian Journal of Microbiology Jun 2008A rod-shaped, Gram-positive bacterial strain, designated C57-33, was isolated from the liver of the laboratory mouse strain C57Bl/6J and characterised by a polyphasic...
Identification of a bacterial strain isolated from the liver of a laboratory mouse as Microbacterium paraoxydans and emended description of the species Microbacterium paraoxydans Laffineur et al 2003.
A rod-shaped, Gram-positive bacterial strain, designated C57-33, was isolated from the liver of the laboratory mouse strain C57Bl/6J and characterised by a polyphasic approach. 16S rRNA gene sequence similarity placed strain C57-33 in the genus Microbacterium with Microbacterium paraoxydans CF36(T) as the next relative (99.9% sequence similarity). Major fatty acids ai-C(15:0), i-C(16:0) and ai-C(17:0) and peptidoglycan type B2β with ornithine as the diagnostic cell-wall diamino acid and glycolyl residues were in agreement with the description of Microbacterium paraoxydans. The quinone system of C57-33 (major menaquinones MK-12 and MK-11) and polar lipid profile (major polar lipids diphosphatidyl glycerol, phosphatidyl glycerol and two unknown glycolipids) were in accordance with those of Microbacterium paraoxydans strains CF36(T), CF7 and CF40 which were analysed in this study as well. The results of biochemical/physiological characterisation, DNA-DNA hybridization, MALDI-TOF mass spectrometry of cell extracts and comparison of protein patterns after SDS-PAGE demonstrated that our isolate C57-33 (= DSM 15461) is a strain of the species Microbacterium paraoxydans. Based on new characteristics such as quinone system, polar lipid profile and physiological traits analysed for strain C57-33, the type strain of Microbacterium paraoxydans and some additional strains an emended description of the species Microbacterium paraoxydans is provided.
PubMed: 23100717
DOI: 10.1007/s12088-008-0035-0 -
Microbes and Environments 2020Plant growth-promoting bacteria (PGPB) are beneficial microbes that increase plant growth and yield. However, limited information is currently available on PGPB in onion...
Plant growth-promoting bacteria (PGPB) are beneficial microbes that increase plant growth and yield. However, limited information is currently available on PGPB in onion (Allium cepa Linn.). The aims of the present study were to isolate and identify PGPB in onion and examine the effects of isolated PGPB on germination and growth during the vegetative stage in onion, pak choy (Brassica chinensis), and sweet pepper (Capsicum annuum). Twenty-three strains of PGPB were isolated from the roots, bulbs, and rhizosphere soil of onion. All isolated bacterial strains showed one or more PGP traits, including indole acetic acid production, phosphate solubilization ability, and 1-aminocyclopropane-1-carboxylate deaminase and nitrogenase activities; most of these traits were derived from Bacillus sp., Microbacterium sp., and Pseudomonas sp. Eight bacteria that exhibited strong abilities to produce indole acetic acid were selected for a Petri dish trial, soil pot test, and vermiculate pot test. The Petri dish trial showed that strains ORE8 and ORTB2 simultaneously increased radicle and hypocotyl lengths in onion, but inhibited growth in sweet pepper after 7 d. The soil pot experiment on onion revealed that strains ORE5, ORE8, and ORTB2 strongly promoted growth during the vegetative stage with only a half dose of chemical fertilizer. The present results indicate that ORE8 (Bacillus megaterium) and ORTB2 (Pantoea sp.) are the most promising biofertilizers of onion and may simultaneously inhibit the seedling growth of other plants.
Topics: Bacteria; Biomass; Brassica; Capsicum; Nitrogen Fixation; Onions; Plant Roots; Rhizosphere; Soil Microbiology
PubMed: 32147605
DOI: 10.1264/jsme2.ME19147 -
Frontiers in Nutrition 2023The bioreactor based on solid-state fermentation technology has been developed for vinegar production, standardization of fermentation process and stabilization of...
The bioreactor based on solid-state fermentation technology has been developed for vinegar production, standardization of fermentation process and stabilization of vinegar quality. The microbial community diversity, and volatile compounds of six cultivars of vinegar samples fermented in a self-designed solid-state fermentation bioreactors were investigated using Illumina MiSeq platform and gas chromatography mass spectrometry (GC-MS) technology. The correlations between the richness and diversity of microbiota and volatile profiles, organic acids, as well as physicochemical indicators were explored by R software with the coplot package. The findings indicated that , , and played key roles during fermentation process. , , , and had significant correlations with the physicochemical characteristics. The most common bacterial species were associated with a citric acid content, whereas the least number of bacterial species correlated with malic acid content. Findings could be helpful for the bioreactor optimization, and thus reaching the level of pilot scale and industrialization.
PubMed: 36908901
DOI: 10.3389/fnut.2023.1126562 -
Applied and Environmental Microbiology Mar 2023Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health...
Global-scale estrone (E1) contamination of soil and aquatic environments results from the widespread use of animal manure as fertilizer, threatening both human health and environmental security. A detailed understanding of the degradation of E1 by microorganisms and the associated catabolic mechanism remains a key challenge for the bioremediation of E1-contaminated soil. Here, Microbacterium oxydans ML-6, isolated from estrogen-contaminated soil, was shown to efficiently degrade E1. A complete catabolic pathway for E1 was proposed via liquid chromatography-tandem mass spectrometry (LC-MS/MS), genome sequencing, transcriptomic analysis, and quantitative reverse transcription-PCR (qRT-PCR). In particular, a novel gene cluster () associated with E1 catabolism was predicted. The combination of heterologous expression, gene knockout, and complementation experiments demonstrated that the 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) encoded by the gene was responsible for the initial hydroxylation of E1. Furthermore, to demonstrate the detoxification of E1 by strain ML-6, phytotoxicity tests were performed. Overall, our findings provide new insight into the molecular mechanism underlying the diversity of E1 catabolism in microorganisms and suggest that ML-6 and its enzymes have potential applications in E1 bioremediation to reduce or eliminate E1-related environmental pollution. Steroidal estrogens (SEs) are mainly produced by animals, while bacteria are major consumers of SEs in the biosphere. However, the understanding of the gene clusters that participate in E1 degradation is still limited, and the enzymes involved in the biodegradation of E1 have not been well characterized. The present study reports that ML-6 has effective SE degradation capacity, which facilitates the development of strain ML-6 as a broad-spectrum biocatalyst for the production of certain desired compounds. A novel gene cluster () associated with E1 catabolism was predicted. The 3-hydroxybenzoate 4-monooxygenase (MocA; a single-component flavoprotein monooxygenase) identified in the cluster was found to be necessary and specific for the initial hydroxylation of E1 to generate 4-OHE1, providing new insight into the biological role of flavoprotein monooxygenase.
Topics: Animals; Humans; Estrone; Chromatography, Liquid; Tandem Mass Spectrometry; Mixed Function Oxygenases; Estrogens; Biodegradation, Environmental; Hydroxybenzoates; Multigene Family; Soil
PubMed: 36847539
DOI: 10.1128/aem.01489-22 -
BMC Microbiology May 2013Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of...
BACKGROUND
Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts.
RESULTS
The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 10(5) to 10(9) cfu g(-1) compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts.
CONCLUSION
The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost. These bacteria can be used as potential compost inoculants for accelerating composting process.
Topics: Bacteria; Bacterial Load; Bacterial Typing Techniques; Biodiversity; Cluster Analysis; DNA, Bacterial; DNA, Ribosomal; Molecular Sequence Data; Oryza; Phylogeny; Poaceae; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil; Soil Microbiology; Triticum
PubMed: 23651653
DOI: 10.1186/1471-2180-13-99 -
Environmental Microbiome May 2022With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere...
Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease.
BACKGROUND
With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future.
RESULTS
The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings.
CONCLUSIONS
PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.
PubMed: 35619157
DOI: 10.1186/s40793-022-00421-5 -
3 Biotech Jul 2021Arsenic (As) is an increasing threat across the globe, widely known as a non-threshold carcinogen, and it is reaching harmful values in several areas of the world. In...
Arsenic (As) is an increasing threat across the globe, widely known as a non-threshold carcinogen, and it is reaching harmful values in several areas of the world. In this study, the effect of plant growth promoting bacteria () on inorganic arsenic (Arsenate) phytoremediation by plants was investigated through histological analysis and proteome profiling of the plants. Two-dimensional gel electrophoresis and transmission electron microscopy were used to conduct the proteome and histological analysis. When arsenic-treated cells were compared to untreated cells, substantial changes were found (1) severely altered the morphology of the cells, intensely disturbed; (2) the cell wall was thicker; (3) drastically changed the cytoplasm, the cells were polygonal in shape, different in size (scattered), and relatively dense. Compared to the control group, the ultra-structure of the root cells of the control group revealed intact cytoplasm, vacuole, and cell wall under exposure to As + bacteria that had a minor effect on the cell form. To further understand As + bacteria interaction, proteome profiling of the root cell was analyzed. The As-induced oxidative stress enrichment was confirmed by the up-regulation of tubulin, nucleoside diphosphate kinase, and major allergen during As + bacteria exposure It was observed that the profusion of proteins involved in defence, protein biogenesis, signaling, photosynthesis, nucleoside and energy metabolism was greater in As + bacteria as compared to the rooting out of As only. Overall, it can be obviously seen that the current study demonstrates the effectiveness of phytoremediation by on proteins involved and responsive pathways in dealing with As toxicity in plant.
PubMed: 34221807
DOI: 10.1007/s13205-021-02864-y