Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Soil bacteria in forest

PROVIDER: PRJNA1250177 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33127800_1.fastq.gz	Fastqsanger.gz
	SRR33127800_2.fastq.gz	Fastqsanger.gz
	SRR33127801_1.fastq.gz	Fastqsanger.gz
	SRR33127801_2.fastq.gz	Fastqsanger.gz
	SRR33127802_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

Project description:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, -glucosidases, endoxylanases, -xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.

2016-05-02 | PXD003844 | Pride

Metaproteome analysis of different soil types

Project description:Metaproteome analysis of a forest soil and a potting soil. Different protein extraction methods were compared to investigate protein extraction efficiency and compatibility with sample downstream processing.

2015-03-26 | PRD000542 | Pride

Transcription profiling of mycorrhized European beech (Fagus sylvatica L.) roots in response to fertilization with different forms of inorganic nitrogen

Project description:Young Fagus sylvatica trees (approximately 7 to 8 years) were collected from a natural regeneration beech forest. The trees were excavated with intact soil cores, roots and top organic layer. The trees were then kept outdoors at the Department of Forest Botany, Georg-August-Universität Göttingen. Plants were protected from rain, and light conditions were matched to those of the natural stand using a shading net; otherwise, plants were exposed to natural climatic conditions. The soil moisture was regularly measured; plants were watered with deionized water as needed to keep soil moisture close to the original conditions. Trees was randomly relocated on a weekly basis throughout the experiment to avoid biasses caused by location or light effects. After 21 weeks, a treatment was applied to understand the physiological mechanisms of inorganic nitrogen uptake and assimilation under conditions of an inorganic nitrogen saturated forest simulation: Plants were fertilized with either a 20 mM solution of KNO3, a 20 mM solution of NH4Cl, or demineralized water (control) for 2 days. On the third day, the trees were harvested. Root tips were immediately shock-frozen in liquid nitrogen and used for RNA extraction.

2020-12-14 | E-MTAB-8931 | biostudies-arrayexpress

Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer

Project description:ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.

2022-10-19 | GSE191259 | GEO

Project description:EST China forest soil bacteria

| PRJNA511359 | ENA

uncultured bacterium

Project description:Uncultured bacteria from forest soil

| PRJNA32159 | ENA

soil metagenome

Project description:Forest soil for bacteria study

| PRJNA262010 | ENA

Proteome data on soil microbial community

Project description:Soil microbial community is a complex blackbox that requires a multi-conceptual approach (Hultman et al., 2015; Bastida et al., 2016). Most methods focus on evaluating total microbial community and fail to determine its active fraction (Blagodatskaya & Kuzyakov 2013). This issue has ecological consequences since the behavior of the active community is more important (or even essential) and can be different to that of the total community. The sensitivity of the active microbial community can be considered as a biological mechanism that regulates the functional responses of soil against direct (i.e. forest management) and indirect (i.e. climate change) human-induced alterations. Indeed, it has been highglihted that the diversity of the active community (analyzed by metaproteomics) is more connected to soil functionality than the that of the total community (analyzed by 16S rRNA gene and ITS sequencing) (Bastida et al., 2016). Recently, the increasing application of soil metaproteomics is providing unprecedented, in-depth characterisation of the composition and functionality of active microbial communities and overall, allowing deeper insights into terrestrial microbial ecology (Chourey et al., 2012; Bastida et al., 2015, 2016; Keiblinger et al., 2016). Here, we predict the responsiveness of the soil microbial community to forest management in a climate change scenario. Particularly, we aim: i) to evaluate the impacts of 6-years of induced drought on the diversity, biomass and activity of the microbial community in a semiarid forest ecocosystem; and ii) to discriminate if forest management (thinning) influences the resistance of the microbial community against induced drought. Furthermore, we aim to ascertain if the functional diversity of each phylum is a trait that can be used to predict changes in microbial abundance and ecosystem functioning.

2021-02-02 | PXD005447 | Pride

Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Psychotria genus (Rubiacaeae) from Cuba

Project description:The leaf transcriptome of the nickel hyperaccumulator species Psychotria grandis and Psychotria costivenia (Rubiaceae) from Cuba were compared to the closely related non-accumulator Psychotria revoluta, living on Gallery forest on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

2019-06-05 | GSE116050 | GEO

Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Leucocroton and Lasiocroton genus (Euphorbiaceae) from Cuba

Project description:The leaf transcriptome of the nickel hyperaccumulator Leucocroton havanensis (Euphorbiaceae) living on serpentine Cuabal, from Cuba, was compared to the closely related non-accumulator Lasiocroton microphyllus living on Gallery forest on limestone soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

2019-06-05 | GSE116049 | GEO

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