Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome Sequences of Novel Azospirillum sp. Strains B21 and Sh1, Isolated from Raised Sphagnum Bogs, and Type Strains Azospirillum lipoferum 59b and Azospirillum oryzae COC8.

ABSTRACT: Here, we report the genomic sequences of the novel Azospirillum sp. strains B21 and Sh1, isolated from raised bogs, along with the genome sequences of Azospirillum lipoferum 59bT, the type species of the genus, and Azospirillum oryzae COC8T, which were analyzed to get more knowledge about the genus Azospirillum.

SUBMITTER: Grouzdev DS

PROVIDER: S-EPMC6813400 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Genome Sequences of Novel Azospirillum sp. Strains B21 and Sh1, Isolated from Raised Sphagnum Bogs, and Type Strains Azospirillum lipoferum 59b and Azospirillum oryzae COC8.

Grouzdev Denis S DS Tikhonova Ekaterina N EN Kravchenko Irina K IK

Microbiology resource announcements 20191024 43

Here, we report the genomic sequences of the novel Azospirillum sp. strains B21 and Sh1, isolated from raised bogs, along with the genome sequences of Azospirillum lipoferum 59bT, the type species of the genus, and Azospirillum oryzae COC8T, which were analyzed to get more knowledge about the genus Azospirillum. ...[more]

PMID: 31649088

Similar Datasets

Acidophilic methanotrophic communities from Sphagnum peat bogs.

Project description:Highly enriched methanotrophic communities (> 25 serial transfers) were obtained from acidic ombrotrophic peat bogs from four boreal forest sites. The enrichment strategy involved using media conditions that were associated with the highest rates of methane uptake by the original peat samples, namely, the use of diluted mineral medium of low buffering capacity, moderate incubation temperature (20 degrees C), and pH values of 3 to 6. Enriched communities contained a mixture of rod-shaped bacteria arranged in aggregates with a minor contribution of Hyphomicrobium-like cells. The growth stoichiometry of isolates was characteristic of methanotrophic bacteria (CH4/O2/CO2 = 1:1.1:0.59), with an average apparent yield of 0.41 +/- 0.03 g of biomass C/g of CH4-C. DNA from each enrichment yielded a PCR product of the expected size with primers for both mmoX and mmoY genes of soluble methane monooxygenase. Two types of sequences were obtained for PCR-amplified fragments of mmoX. One of them exhibited high identity to the mmoX protein of the Methylocystis-Methylosinus group, whereas the other showed an equal level of divergence from both the Methylosinus-Methylocystis group and Methylococcus capsulatus (Bath) and formed a distinct branch. The pH optimum for growth and for CH4 uptake was 4.5 to 5.5, which is very similar to that for the optimum CH4 uptake observed in the original peat samples. These methanotrophs are moderate acidophiles rather than acidotolerant organisms, since their growth rate and methane uptake were much lower at neutral pH. The growth of the methanotrophic community was enhanced by using media with a very low salt content (20 to 200 mg/liter), more typical of their natural environment. All four enriched communities grew on N-free medium.

| S-EPMC106347 | biostudies-literature

Azospirillum sp. Sh1

Project description:Azospirillum sp. Sh1 Genome sequencing and assembly

| PRJNA562938 | ENA

Azospirillum sp. B21

Project description:Azospirillum sp. B21 Genome sequencing and assembly

| PRJNA563053 | ENA

Genome Sequences of Two Azospirillum sp. Strains, TSA2S and TSH100, Plant Growth-Promoting Rhizobacteria with N2O Mitigation Abilities.

Project description:Azospirillum sp. strains TSA2S and TSH100 are plant growth-promoting rhizobacteria with the capacity to mitigate N2O from agricultural soil. They were isolated from the rhizosphere of paddy soil in Tokyo, Japan. Here, we present the genome sequences of these two strains.

| S-EPMC6687917 | biostudies-literature

Metalaxyl Degradation by Mucorales Strains Gongronella sp. and Rhizopus oryzae.

Project description:In this study, the degradation of metalaxyl was investigated in the presence of two Mucorales strains, previously isolated from soil subjected to repeated treatments with this fungicide and selected after enrichment technique. Fungal strains were characterised by a polyphasic approach using phylogenetic analysis of the Internal Transcribed Spacer (ITS) gene region, phenotypic characterisation by Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) spectral analysis, and growth kinetics experiments. The strains were identified as Gongronella sp. and Rhizopus oryzae. The fungal growth kinetics in liquid cultures containing metalaxyl fits with Haldane model. Under laboratory conditions, the ability of Gongronella sp. and R. oryzae cultures to degrade metalaxyl was evaluated in liquid cultures and soil experiments. Both species were able to: (a) use metalaxyl as the main carbon and energy source; and (b) degrade metalaxyl in polluted soils, with rates around 1.0 mg kg-¹ d-¹. This suggests these strains could degrade metalaxyl in soils contaminated with this fungicide.

| S-EPMC6149714 | biostudies-literature

Predicting the dynamic distribution of Sphagnum bogs in China under climate change since the last interglacial period.

Project description:Sphagnum bogs possess irreplaceable ecological and economic value, and they are scarce in China, with a fragmented distribution. Based on 19 high-resolution bioclimatic environmental datasets and 71 bog center point locations, we employed a maximum entropy model (MaxEnt) to reconstruct and predict the spatial-temporal geographical distribution patterns of Sphagnum bogs from the last interglacial (LIG) period to two typical CO2 representative concentration pathway scenarios (RCP2.6, RCP8.5) in the future. We further computed the migratory paths of the distribution center points. Finally, a jackknife test was used to uncover the crucial environmental factors restricting the geographical distribution of the bogs. Our data indicated that the MaxEnt niche model had a high simulation precision with an area under the ROC curve value of 0.957. Spatially, the suitable bog habitats are currently centralized in northeastern China, including the Greater Khingan Mountains, the Lesser Khingan Mountains, and the Changbai Mountains, as well as peripheral areas of the Sichuan Basin. Temporally, the contours of Sphagnum bogs were similar to the present and rendered from the last glacial maximum (LMG) period, and had much more total area than the current. The total area in LIG was nearly the same as the current because of the similar climate. It was worth noting that there would be a reduction of the total area in the future. Loss of area occurred at the edges of bogs, especially under RCP8.5. The distribution center of bogs will shift to the northwest in the immediate future. The precipitation of driest month, the mean temperature of warmest quarter and the precipitation of warmest quarter were identified as crucial climatic factors affecting the distribution of Sphagnum bogs. Overall, our research provides scientific evidence for the long-term protection and effective management of these rare, precious natural resources and suggestions for in situ conservation.

| S-EPMC7135081 | biostudies-literature

Genome Sequences of 11 Conspecific Streptomyces sp. Strains.

Project description:The genomes of 11 conspecific Streptomyces strains, i.e., from the same species and inhabiting the same ecological niche, were sequenced and assembled. This data set offers an ideal framework to assess the genome evolution of Streptomyces species in their ecological context.

| S-EPMC6753273 | biostudies-literature

Closely Located but Totally Distinct: Highly Contrasting Prokaryotic Diversity Patterns in Raised Bogs and Eutrophic Fens.

Project description:Large areas in Northern Russia are covered by extensive mires, which represent a complex mosaic of ombrotrophic raised bogs, minerotrophic and eutrophic fens, all in a close proximity to each other. In this paper, we compared microbial diversity patterns in the surface peat layers of the neighbouring raised bogs and eutrophic fens that are located within two geographically remote mire sites in Vologda region using 16S rRNA gene sequencing. Regardless of location, the microbial communities in raised bogs were highly similar to each other but were clearly distinct from those in eutrophic fens. Bogs were dominated by the Acidobacteria (30%-40% of total 16S rRNA gene reads), which belong to the orders Acidobacteriales and Bryobacterales. Other bog-specific bacteria included the Phycisphaera-like group WD2101 and the families Isosphaeraceae and Gemmataceae of the Planctomycetes, orders Opitutales and Pedosphaerales of the Verrucomicrobia and a particular group of alphaproteobacteria within the Rhizobiales. In contrast, fens hosted Anaerolineae-affiliated Chloroflexi, Vicinamibacteria- and Blastocatellia-affiliated Acidobacteria, Rokubacteria, uncultivated group OM190 of the Planctomycetes and several groups of betaproteobacteria. The Patescibacteria were detected in both types of wetlands but their relative abundance was higher in fens. A number of key parameters that define the distribution of particular bacterial groups in mires were identified.

| S-EPMC7232223 | biostudies-literature

Azospirillum oryzae

Project description:Azospirillum oryzae overview

| PRJNA563105 | ENA

Sampling event dataset on five-year observations of macrofungi fruit bodies in raised bogs, Western Siberia, Russia.

Project description:BackgroundThe data paper includes the results of a long-term monitoring programme for macrofungi fruiting using permanent plots located in the raised bog ecosystem in central part of Western Siberia (nearby Khanty-Mansiysk), Russia. The goal of the project was to describe the quantitative and qualitative structure and spatial variation of the community of macromycetes, to follow its dynamics seasonally and inter-annually and also elucidate the relationship between the fruiting and climate variables. A total of 263 circular 5 m2 subplots (for a total area of 1,315 m2) were inspected weekly during vegetation seasons 2014-2018 and carpophores of different fungal taxa were counted. The resulting sampling-event dataset includes 16,569 of plot-based observations (= sampling events) with corresponding 6,011 occurrence records of macromycetes identified to species or genus level. In total, 69 species were revealed during the study. About 80% of plot-based observations contain zero records and mark absence of visible fruiting bodies in a certain plot and time.New informationThis is the first sampling-event dataset on plot-based observations of macrofungi published in GBIF and the first long-term series of macrofungi monitoring in a raised bog ecosystem accomplished in Western Siberia. The aim of the data paper publication was to provide the description and the link to the published data in the format of a peer-reviewed journal paper and to provide recognition for the effort by means of a scholarly article (based on Data paper definition published at https://www.gbif.org/en/data-papers).

| S-EPMC6684528 | 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