Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft genome sequence of Bacillus velezensis 2A-2B strain: a rhizospheric inhabitant of Sporobolus airoides (Torr.) Torr., with antifungal activity against root rot causing phytopathogens.

ABSTRACT: A Bacillus velezensis strain from the rhizosphere of Sporobolus airoides (Torr.) Torr., a grass in central-north México, was isolated during a biocontrol of phytopathogens scrutiny study. The 2A-2B strain exhibited at least 60% of growth inhibition of virulent isolates of phytopathogens causing root rot. These phytopathogens include Phytophthora capsici, Fusarium solani, Fusarium oxysporum and Rhizoctonia solani. Furthermore, the 2A-2B strain is an indolacetic acid producer, and a plant inducer of PR1, which is an induced systemic resistance related gene in chili pepper plantlets. Whole genome sequencing was performed to generate a draft genome assembly of 3.953 MB with 46.36% of GC content, and a N50 of 294,737. The genome contains 3713 protein coding genes and 89 RNA genes. Moreover, comparative genome analysis revealed that the 2A-2B strain had the greatest identity (98.4%) with Bacillus velezensis.

SUBMITTER: Martinez-Raudales I

PROVIDER: S-EPMC5717847 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Rhizospheric fungi of Panax notoginseng: diversity and antagonism to host phytopathogens.

Project description:BackgroundRhizospheric fungi play an essential role in the plant-soil ecosystem, affecting plant growth and health. In this study, we evaluated the fungal diversity in the rhizosphere soil of 2-yr-old healthy Panax notoginseng cultivated in Wenshan, China.MethodsCulture-independent Illumina MiSeq and culture-dependent techniques, combining molecular and morphological characteristics, were used to analyze the rhizospheric fungal diversity. A diffusion test was used to challenge the phytopathogens of P. notoginseng.ResultsA total of 16,130 paired-end reads of the nuclear ribosomal internal transcribed spacer 2 were generated and clustered into 860 operational taxonomic units at 97% sequence similarity. All the operational taxonomic units were assigned to five phyla and 79 genera. Zygomycota (46.2%) and Ascomycota (37.8%) were the dominant taxa; Mortierella and unclassified Mortierellales accounted for a large proportion (44.9%) at genus level. The relative abundance of Fusarium and Phoma sequences was high, accounting for 12.9% and 5.5%, respectively. In total, 113 fungal isolates were isolated from rhizosphere soil. They were assigned to five classes, eight orders (except for an Incertae sedis), 26 genera, and 43 species based on morphological characteristics and phylogenetic analysis of the internal transcribed spacer. Fusarium was the most isolated genus with six species (24 isolates, 21.2%). The abundance of Phoma was also relatively high (8.0%). Thirteen isolates displayed antimicrobial activity against at least one test fungus.ConclusionOur results suggest that diverse fungi including potential pathogenic ones exist in the rhizosphere soil of 2-yr-old P. notoginseng and that antagonistic isolates may be useful for biological control of pathogens.

| S-EPMC4845048 | biostudies-literature

Antifungal Potential of Canarian Plant Extracts against High-Risk Phytopathogens.

Project description:Phytopathogens are responsible for great losses in agriculture. In particular, Fusarium, Alternaria and Botrytis are fungal diseases that affect crops worldwide. In the search for eco-friendly solutions to pest control, plants and their chemo-biodiversity are promising sources of biopesticides for integrated pest management. The aim of the present study is to report the evaluation of sixteen plant species from the Canary Islands Archipelago against the phytopathogenic fungi Botrytis cinerea, Fusarium oxysporum, and Alternaria alternata. The plants were selected on the basis of their traditional uses in medicine and/or pest control, as well as on scientific studies reporting their uses in crop protection. Their growth inhibition (% I), in an in vitro test-assay on mycelium, was used to identify six ethanolic plant extracts displaying activity (% I > 30% at 1 mg/mL) against at least one of the assayed fungi. The most effective plant extracts were further fractionated by liquid-liquid partition, using solvents of increasing polarity. This procedure led to an improvement of the bioactivity against the phytopathogens, even affecting the hexane fraction from S. canariensis and achieving an 83.93% of growth inhibition at 0.5 mg/mL on B. cinerea. These findings identified five plant-derived extracts as potential candidates for the future development of new biofungicides, which could be applied in integrated pest management.

| S-EPMC9656886 | biostudies-literature

Depiction of secondary metabolites and antifungal activity of Bacillus velezensis DTU001.

Project description:For a safe and sustainable environment, effective microbes as biocontrol agents are in high demand. We have isolated a new Bacillus velezensis strain DTU001, investigated its antifungal spectrum, sequenced its genome, and uncovered the production of lipopeptides in HPLC-HRMS analysis. To test the antifungal efficacy, extracts of B. velezensis DTU001 was tested against a range of twenty human or plant pathogenic fungi. We demonstrate that inhibitory potential of B. velezensis DTU001 against selected fungi is superior in comparison to single lipopeptide, either iturin or fengycin. The isolate showed analogous biofilm formation to other closely related Bacilli. To further support the biocontrol properties of the isolate, coculture with Candida albicans demonstrated that B. velezensis DTU001 exhibited excellent antiproliferation effect against C. albicans. In summary, the described isolate is a potential antifungal agent with a broad antifungal spectrum that might assist our aims to avoid hazardous pathogenic fungi and provide alternative to toxicity caused by chemicals.

| S-EPMC6719288 | biostudies-literature

Rhizospheric Actinomycetes Revealed Antifungal and Plant-Growth-Promoting Activities under Controlled Environment

Project description:Actinomycetes has large habitats and can be isolated from terrestrial soil, rhizospheres of plant roots, and marine sediments. Actinomycetes produce several bioactive secondary metabolites with antibacterial, antifungal, and antiviral properties. In this study, some Actinomycetes strains were isolated from the rhizosphere zone of four different plant species: rosemary, acacia, strawberry, and olive. The antagonistic activity of all isolates was screened in vitro against Escherichia coli and Bacillus megaterium. Isolates with the strongest bioactivity potential were selected and molecularly identified as Streptomyces sp., Streptomyces atratus, and Arthrobacter humicola. The growth-promoting activity of the selected Actinomycetes isolates was in vivo evaluated on tomato plants and for disease control against Sclerotinia sclerotiorum. The results demonstrated that all bacterized plants with the studied Actinomycetes isolates were able to promote the tomato seedlings’ growth, showing high values of ecophysiological parameters. In particular, the bacterized seedlings with Streptomyces sp. and A. humicola showed low disease incidence of S. sclerotiorum infection (0.3% and 0.2%, respectively), whereas those bacterized with S. atratus showed a moderate disease incidence (7.6%) compared with the positive control (36.8%). In addition, the ability of the studied Actinomycetes to produce extracellular hydrolytic enzymes was verified. The results showed that A. humicola was able to produce chitinase, glucanase, and protease, whereas Streptomyces sp. and S. atratus produced amylase and pectinase at high and moderate levels, respectively. This study highlights the value of the studied isolates in providing bioactive metabolites and extracellular hydrolytic enzymes, indicating their potential application as fungal-biocontrol agents.

| S-EPMC9317816 | biostudies-literature

Draft Genome Sequence of Paenibacillus polymyxa 3A-25AI, a Strain Antagonist to Root Rot Causal Phytopathogens.

Project description:Here, we report the draft genome sequence of the Paenibacillus polymyxa 3A-25AI strain, isolated from the rhizosphere of wild grass. This strain inhibits Phytophthora capsici and Rhizoctonia solani phytopathogens. The genome size is 5.6 Mb, with a G+C content of 45.59%, and contains 5,079 genes, 4,968 coding DNA sequences (CDSs), 35 tRNAs, 3 rRNAs, and 72 unexpected miscellaneous RNA (miscRNA) features.

| S-EPMC7019065 | biostudies-literature

Bacillus velezensis UTB96 Is an Antifungal Soil Isolate with a Reduced Genome Size Compared to That of Bacillus velezensis FZB42.

Project description:Bacillus velezensis UTB96 was isolated from soil based on its antifungal activity. Whole-genome sequencing of strain UTB96 provided further information about its secondary metabolite gene clusters. Compared to the well-known strain FZB42, UTB96 lacks an IS3 element and a type I restriction endonuclease.

| S-EPMC6753265 | biostudies-literature

Evaluation of the Antifungal Activity of Endophytic and Rhizospheric Bacteria against Grapevine Trunk Pathogens.

Project description:Grapevine trunk diseases (GTDs) are caused by multiple unrelated fungal pathogens, and their management remains difficult worldwide. Biocontrol is an attractive and sustainable strategy given the current need for a cleaner viticulture. In this study, twenty commercial vineyards were sampled across California to isolate endophytic and rhizospheric bacteria from different grapevine cultivars with the presence and absence of GTD symptoms. A collection of 1344 bacterial isolates were challenged in vitro against Neofusicoccum parvum and Diplodia seriata, from which a subset of 172 isolates exerted inhibition levels of mycelial growth over 40%. Bacterial isolates were identified as Bacillus velezensis (n = 154), Pseudomonas spp. (n = 12), Serratia plymuthica (n = 2) and others that were later excluded (n = 4). Representative isolates of B. velezensis, P. chlororaphis, and S. plymuthica were challenged against six other fungal pathogens responsible for GTDs. Mycelial inhibition levels were consistent across bacterial species, being slightly higher against slow-growing fungi than against Botryosphaeriaceae. Moreover, agar-diffusible metabolites of B. velezensis strongly inhibited the growth of N. parvum and Eutypa lata, at 1, 15, and 30% v/v. The agar-diffusible metabolites of P. chlororaphis and S. plymuthica, however, caused lower inhibition levels against both pathogens, but their volatile organic compounds showed antifungal activity against both pathogens. These results suggest that B. velezensis, P. chlororaphis and S. plymuthica constitute potential biocontrol agents (BCAs) against GTDs and their application in field conditions should be further evaluated.

| S-EPMC9611468 | biostudies-literature

Methionine adenosyltransferase 2A/2B and methylation: gene sequence variation and functional genomics.

Project description:Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine, the major biological methyl donor. MAT1A and MAT2A encode two distinct MAT isoforms in mammals. MAT2A is expressed in nonhepatic tissues, whereas MAT1A is expressed in the liver. A third gene, MAT2B, encodes a MAT2A regulatory protein. We resequenced MAT2A and MAT2B exons, splice junctions, and flanking regions using 288 DNA samples from three ethnic groups and also imputed additional single nucleotide polymorphisms (SNPs) across both genes using data from the 1000 Genomes Project. For MAT2A, resequencing identified 74 polymorphisms, including two nonsynonymous (ns) SNPs. Functional genomic studies of wild type and the two MAT2A variant allozymes (Val11 and Val205) showed that the Val11 allozyme had approximately 40% decreases in levels of enzyme activity and immunoreactive protein after COS-1 cell transfection. For MAT2B, 44 polymorphisms, 2 nonsynonymous, were identified during resequencing. Neither of the two MAT2B nsSNPs displayed alterations in levels of protein. Imputation using 1000 Genomes Project data resulted in 1730 additional MAT2A and 1997 MAT2B polymorphisms within ± 200 kilobases of each gene, respectively. Coexpression of MAT2A and MAT2B in COS-1 cells resulted in significantly increased MAT enzyme activity that correlated with increased MAT2A and MAT2B immunoreactive protein, apparently as a result of decreased degradation. Finally, studies of mRNA expression in lymphoblastoid cells showed that 7 SNPs in MAT2A and 16 SNPs in MAT2B were significantly associated with mRNA expression with p < 0.01. These observations provide a foundation for future mechanistic and clinical translational pharmacogenomic studies of MAT2A/2B.

| S-EPMC3198898 | biostudies-literature

Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus.

Project description:Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.

| S-EPMC6213509 | biostudies-literature

Probiotic Consortia: Reshaping the Rhizospheric Microbiome and Its Role in Suppressing Root-Rot Disease of Panax notoginseng.

Project description:Root-rot disease caused by Fusarium oxysporum is a growing problem in agriculture for commercial cultivation of Panax notoginseng. Diverse microbes colonize plant roots, and numerous earlier studies have characterized the rhizospheric microbiome of P. notoginseng; nevertheless, the function of probiotic consortia on the rhizospheric microbiome against the root-rot disease remain elusive. We have compared and described the rhizospheric microbiome of lightly and severely diseased P. notoginseng as well as the interactions of the probiotic consortia and rhizospheric microbiome, and their function to alleviate the plant diseases were explored by inoculating probiotic consortia in bulk soil. From the perspective of microbial diversity, the rhizospheric dominant bacterial and fungal genera were utterly different between lightly and severely diseased plants. Through inoculating assembled probiotic consortia to diseased plant roots, we found that the application of probiotic consortia reshaped the rhizosphere microbiome, increasing the relative abundance of bacteria and fungi, while the relative abundance of potential pathogens was decreased significantly. We developed a microcosm system that provides a preliminary ecological framework for constructing an active probiotic community to reshape soil microbiota and restrain the disease. Microbial community structure differs between lightly and seriously diseased plants. The application of probiotic consortia changes the imbalance of micro-ecology to a state of relative health, reducing plant mortality. Plant disease suppression may be achieved by seeking and applying antagonistic microbes based on their direct inhibitory capability or by restructuring the soil microbiome structure and function.

| S-EPMC7203884 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data