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The ISME Journal Jan 2021Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease...
Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.
Topics: Actinobacteria; Bacillus; Bacteria; Firmicutes; Incidence; Solanum lycopersicum; Planococcaceae; Plant Diseases; Ralstonia solanacearum; Rhizosphere; Soil Microbiology
PubMed: 33028974
DOI: 10.1038/s41396-020-00785-x -
Frontiers in Veterinary Science 2022The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer...
The horse gut is colonized by a rich and complex microbial community that has important roles in horse physiology, metabolism, nutrition, and immune functions. Fewer across-breed variations in horse gut microbial diversity have been illustrated. In this article, the gut microbiota of Thoroughbred, Mongolian, and Hybrid horses [first filial generation (F1) of Mongolian (maternal) and Thoroughbred (paternal)] were studied by second-generation high-throughput sequencing technology. Differences in gut microbiota composition and function between breeds were determined using diversity and functional prediction analysis. The alpha diversity analysis showed that Thoroughbred horses had a more abundant and diverse gut microbiota, while the diversity of gut microbiota in Hybrid horses was intermediate between Thoroughbred and Mongolian horses. Subsequent cluster analysis showed that Hybrid horses have a microbiota composition more similar to Mongolian horses. LEfSe analysis revealed that the bacterial biomarkers for Thoroughbred horses at the family level were Prevotellaceae, Rikenellaceae, Fibrobacteraceae, p_251_o5, Lactobacillaceae, and uncultured_bacterium_o_WCHB1_41; the bacterial biomarker for Mongolian horses was Planococcaceae; and the bacterial biomarkers for Hybrid horses were Moraxellaceae, Enterobacteriaceae, and Ruminococcaceae. The functional prediction results indicated that the metabolic pathways differ significantly between the breeds. Regarding metabolism, the Hybrid horses had the lowest proportion of the carbohydrate metabolic pathways, while the energy metabolic pathway had the highest proportion. The abundance ratios of the remaining eight metabolic pathways in Hybrid horses were between Thoroughbred and Mongolian horses. In conclusion, the results of this study showed an association between horse breeds and gut microbiota.
PubMed: 35968025
DOI: 10.3389/fvets.2022.920080 -
Journal of Biotechnology Jun 2017The type strain Planococcus donghaensis JH1 is a psychrotolerant and halotolerant bacterium with starch-degrading ability. Here, we determine the carbon utilization...
The type strain Planococcus donghaensis JH1 is a psychrotolerant and halotolerant bacterium with starch-degrading ability. Here, we determine the carbon utilization profile of P. donghaensis JH1 and report the first complete genome of the strain. This study revealed the strain's ability to utilize pectin and d-galacturonic acid, and identified genes responsible for degradation of the polysaccharides. The genomic information provided may serve as a fundamental resource for full exploration of the biotechnological potential of P. donghaensis JH1.
Topics: DNA, Bacterial; Genome, Bacterial; Hexuronic Acids; Pectins; Planococcus Bacteria; Sequence Analysis, DNA
PubMed: 28483443
DOI: 10.1016/j.jbiotec.2017.05.005 -
Environmental Pollution (Barking, Essex... Jul 2022The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the...
The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.
Topics: Bacteria; Carbon; Microbiota; Pyrenes; Soil; Soil Microbiology
PubMed: 35429592
DOI: 10.1016/j.envpol.2022.119301 -
Applied and Environmental Microbiology Jun 2017A stable NADP-dependent d-amino acid dehydrogenase (DAADH) was recently created from -diaminopimelate dehydrogenase through site-directed mutagenesis. To produce a novel...
A stable NADP-dependent d-amino acid dehydrogenase (DAADH) was recently created from -diaminopimelate dehydrogenase through site-directed mutagenesis. To produce a novel DAADH mutant with different substrate specificity, the crystal structure of apo-DAADH was determined at a resolution of 1.78 Å, and the amino acid residues responsible for the substrate specificity were evaluated using additional site-directed mutagenesis. By introducing a single D94A mutation, the enzyme's substrate specificity was dramatically altered; the mutant utilized d-phenylalanine as the most preferable substrate for oxidative deamination and had a specific activity of 5.33 μmol/min/mg at 50°C, which was 54-fold higher than that of the parent DAADH. In addition, the specific activities of the mutant toward d-leucine, d-norleucine, d-methionine, d-isoleucine, and d-tryptophan were much higher (6 to 25 times) than those of the parent enzyme. For reductive amination, the D94A mutant exhibited extremely high specific activity with phenylpyruvate (16.1 μmol/min/mg at 50°C). The structures of the D94A-Y224F double mutant in complex with NADP and in complex with both NADPH and 2-keto-6-aminocapronic acid (lysine oxo-analogue) were then determined at resolutions of 1.59 Å and 1.74 Å, respectively. The phenylpyruvate-binding model suggests that the D94A mutation prevents the substrate phenyl group from sterically clashing with the side chain of Asp94. A structural comparison suggests that both the enlarged substrate-binding pocket and enhanced hydrophobicity of the pocket are mainly responsible for the high reactivity of the D94A mutant toward the hydrophobic d-amino acids with bulky side chains. In recent years, the potential uses for d-amino acids as source materials for the industrial production of medicines, seasonings, and agrochemicals have been growing. To date, several methods have been used for the production of d-amino acids, but all include tedious steps. The use of NAD(P)-dependent d-amino acid dehydrogenase (DAADH) makes single-step production of d-amino acids from oxo-acid analogs and ammonia possible. We recently succeeded in creating a stable DAADH and demonstrated that it is applicable for one-step synthesis of d-amino acids, such as d-leucine and d-isoleucine. As the next step, the creation of an enzyme exhibiting different substrate specificity and higher catalytic efficiency is a key to the further development of d-amino acid production. In this study, we succeeded in creating a novel mutant exhibiting extremely high catalytic activity for phenylpyruvate amination. Structural insight into the mutant will be useful for further improvement of DAADHs.
Topics: Amino Acid Motifs; Amino Acid Oxidoreductases; Amino Acid Sequence; Bacterial Proteins; Binding Sites; Kinetics; Models, Molecular; Mutagenesis, Site-Directed; NADP; Planococcaceae; Protein Engineering; Substrate Specificity
PubMed: 28363957
DOI: 10.1128/AEM.00491-17 -
Nucleic Acids Research Apr 2024RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in...
RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
Topics: RNA Ligase (ATP); Substrate Specificity; Archaeal Proteins; Planococcaceae; Protein Engineering; Mutation; Models, Molecular; Adenosine Triphosphate; Oligonucleotides
PubMed: 38421610
DOI: 10.1093/nar/gkae149 -
Synthesis and urease inhibitory potential of benzophenone sulfonamide hybrid in vitro and in silico.Bioorganic & Medicinal Chemistry Mar 2019This study deals with the synthesis of benzophenone sulfonamides hybrids (1-31) and screening against urease enzyme in vitro. Studies showed that several synthetic...
This study deals with the synthesis of benzophenone sulfonamides hybrids (1-31) and screening against urease enzyme in vitro. Studies showed that several synthetic compounds were found to have good urease enzyme inhibitory activity. Compounds 1 (N'-((4'-hydroxyphenyl)(phenyl)methylene)-4''-nitrobenzenesulfonohydrazide), 2 (N'-((4'-hydroxyphenyl)(phenyl)methylene)-3''-nitrobenzenesulfonohydrazide), 3 (N'-((4'-hydroxyphenyl)(phenyl)methylene)-4''-methoxybenzenesulfonohydrazide), 4 (3'',5''-dichloro-2''-hydroxy-N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 6 (2'',4''-dichloro-N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 8 (5-(dimethylamino)-N'-((4-hydroxyphenyl)(phenyl)methylene)naphthalene-1-sulfono hydrazide), 10 (2''-chloro-N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide), 12 (N'-((4'-hydroxyphenyl)(phenyl)methylene)benzenesulfonohydrazide) have found to be potently active having an IC value in the range of 3.90-17.99 µM. These compounds showed superior activity than standard acetohydroxamic acid (IC = 29.20 ± 1.01 µM). Moreover, in silico studies on most active compounds were also performed to understand the binding interaction of most active compounds with active sites of urease enzyme. Structures of all the synthetic compounds were elucidated by H NMR, C NMR, EI-MS and FAB-MS spectroscopic techniques.
Topics: Benzophenones; Enzyme Inhibitors; Inhibitory Concentration 50; Molecular Docking Simulation; Sporosarcina; Structure-Activity Relationship; Sulfonamides; Urease
PubMed: 30738655
DOI: 10.1016/j.bmc.2019.01.043 -
Environmental Science & Technology Aug 2022Amorphous calcium carbonate (ACC) plays an important role in microbially induced calcium carbonate precipitation (MICP), which has great potential in broad applications...
Amorphous calcium carbonate (ACC) plays an important role in microbially induced calcium carbonate precipitation (MICP), which has great potential in broad applications such as building restoration, CO sequestration, and bioremediation of heavy metals, etc. However, our understanding of ACC is still limited. By combining microscopy of cell-laden microdroplets with confocal Raman microspectroscopy, we investigated the ACC dynamics during MICP. The results show that MICP inside droplets can be divided into three stages: liquid, gel-like ACC, and precipitated CaCO stages. In the liquid stage, the droplets are transparent. As the MICP process continues into the gel-like stage, the ACC structure appears and the droplets become opaque. Subsequently, dissolution of the gel-like structure is accompanied by growth of precipitated CaCO crystals. The size, morphology, and lifetime of the gel-like structures depend on the Ca concentration. Using polystyrene colloids as tracers, we find that the colloids exhibit diffusive behavior in both the liquid and precipitated CaCO stages, while their motion becomes arrested in the gel-like ACC stage. These results provide direct evidence for the formation-dissolution process of the ACC-formed structure and its gel-like mechanical properties. Our work provides a detailed view of the time evolution of ACC and its mechanical properties at the microscale level, which has been lacking in previous studies.
Topics: Calcium Carbonate; Chemical Precipitation; Sporosarcina
PubMed: 35858290
DOI: 10.1021/acs.est.1c08858 -
Marine Genomics Dec 2021A previously unreported tellurate reducing capacity was found in a marine bacteria Sporosarcina sp. Te-1, which was isolated from Bohai Sea, China. In this work, the...
A previously unreported tellurate reducing capacity was found in a marine bacteria Sporosarcina sp. Te-1, which was isolated from Bohai Sea, China. In this work, the complete genome of strain Te-1 was obtained using hybrid Nanopore/Illumina assemble method. A circular chromosome of 4,297,762 bp with a G + C content of 44.44 mol% was assembled. The genome harbors 4530 predicted protein-encoding genes, 71 tRNA genes, and 9 rRNA genes. Genes involved in tellurate metabolism, urea metabolism and salinity adaption were identified. These metabolic features reveal the genetic basis for the tellurate metabolism in the marine environment, which help us to further understand the marine tellurium biogeochemical cycle.
Topics: Bacteria; Base Composition; Sporosarcina; Tellurium
PubMed: 34627548
DOI: 10.1016/j.margen.2021.100888 -
Journal of Visualized Experiments : JoVE Apr 2016The particular bacterium under investigation here (S. pasteurii) is unique in its ability, under the right conditions, to induce the hydrolysis of urea (ureolysis) in...
The particular bacterium under investigation here (S. pasteurii) is unique in its ability, under the right conditions, to induce the hydrolysis of urea (ureolysis) in naturally occurring environments through secretion of an enzyme urease. This process of ureolysis, through a chain of chemical reactions, leads to the formation of calcium carbonate precipitates. This is known as Microbiologically Induced Calcite Precipitation (MICP). The proper culture protocols for MICP are detailed here. Finally, visualization experiments under different modes of microscopy were performed to understand various aspects of the precipitation process. Techniques like optical microscopy, Scanning Electron Microscopy (SEM) and X-Ray Photo-electron Spectroscopy (XPS) were employed to chemically characterize the end-product. Further, the ability of these precipitates to clog pores inside a natural porous medium was demonstrated through a qualitative experiment where sponge bars were used to mimic a pore-network with a range of length scales. A sponge bar dipped in the culture medium containing the bacterial cells hardens due to the clogging of its pores resulting from the continuous process of chemical precipitation. This hardened sponge bar exhibits superior strength when compared to a control sponge bar which becomes compressed and squeezed under the action of an applied external load, while the hardened bar is able to support the same weight with little deformation.
Topics: Calcium Carbonate; Chemical Precipitation; Sporosarcina; Urea; Urease
PubMed: 27167458
DOI: 10.3791/53253