The microbial impact on the decomposition of Cambarellus diminutus
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51206 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR10035428_1.fastq.gz | Fastqsanger.gz | |||
| ERR10035428_2.fastq.gz | Fastqsanger.gz | |||
| ERR10035975_1.fastq.gz | Fastqsanger.gz | |||
| ERR10035975_2.fastq.gz | Fastqsanger.gz | |||
| ERR10035976_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 100 |
Similar Datasets
Project description:Anthropogenic nitrogen (N) deposition may affect soil organic carbon (SOC) decomposition, thus affecting the global terrestrial carbon (C) cycle. However, it remains unclear how the level of N deposition affects SOC decomposition by regulating microbial community composition and function, especially C-cycling functional genes structure. We investigated the effects of short-term N addition on soil microbial C-cycling functional gene composition, SOC-degrading enzyme activities, and CO2 emission in a 5-year field experiment established in an artificial Pinus tabulaeformis forest on the Loess Plateau, China.
2022-03-01 | GSE147041 | GEO
Project description:decomposition metagenome Metagenomic assembly
| PRJNA923095 | ENA
Project description:decomposition metagenome Raw sequence reads
| PRJNA918781 | ENA
Project description:Accelerating the design of synthetic biological circuits for biosensing requires expanding the currently available genetic toolkit. Although whole-cell biosensors have been successfully engineered and deployed, particularly in applications such as environmental and medical diagnostics, novel sensing applications necessitate the discovery and optimization of novel biosensors. Here we develop a data-driven approach that combines dynamic mode decomposition and observability analysis to extract salient, endogenous genetic sensors for analytes of interest from dynamic gene expression profiles. We show that relatively few dynamic modes are required to capture the transcriptome dynamics. The concept of system observability is then used to rank genes based on their ability to reconstruct the cell state. Genes which contribute to the system's observability are dubbed encoder genes. As a demonstration of our method, we extract, construct, and characterize 15 genetic reporters for the organophosphate malathion in the host bacterium \textit{Pseudomonas fluorescens} SBW25. Furthermore, we demonstrate how the distinct responses of each genetic reporter can be used to construct a single-input, single-output virtual sensor network, approximating a pair of reference trajectories. This library of living malathion sensors can be optimized for use in environmental diagnostics while the developed machine learning tool can be applied to discover genetic reporters in the compendium of host organisms and environmental conditions.
2022-04-21 | GSE200822 | GEO
Project description:Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems.
2020-05-01 | GSE148618 | GEO
Project description:<p>Microbial life in soil is fueled by dissolved organic matter (DOM) that leaches from the litter layer. It is well known that decomposer communities adapt to the available litter source, but it remains unclear if they functionally compete or synergistically address different litter types. Therefore, we decomposed beech, oak, pine and grass litter from two geologically distinct sites in a lab-scale decomposition experiment. We performed a correlative network analysis on the results of direct infusion HR-MS DOM analysis and cross-validated functional predictions from 16S rRNA gene amplicon sequencing and with DOM and metaproteomic analyses. Here we show that many functions are redundantly distributed within decomposer communities and that their relative expression is rapidly optimized to address litter-specific properties. However, community changes are likely forced by antagonistic mechanisms as we identified several natural antibiotics in DOM. As a consequence, the decomposer community is specializing towards the litter source and the state of decomposition (community divergence) but showing similar litter metabolomes (metabolome convergence). Our multi-omics-based results highlight that DOM not only fuels microbial life, but it additionally holds meta-metabolomic information on the functioning of ecosystems.</p>
2024-02-14 | MTBLS1885 | MetaboLights
Project description:We established simple synthetic microbial communities in a microcosm model system to determine the mechanisms that underlay cross-feeding in microbial methane-consuming communities. Co-occurring strains from Lake Washington sediment were used that are involved in methane consumption, a methanotroph and two non-methanotrophic methylotrophs.
2016-12-26 | GSE85736 | GEO
Project description:Abstract: A large part of the nitrogen in forest soils is found in recalcitrant organic matter-protein complexes. Ectomycorrhizal fungi are thought to have a key role in the decomposition and mobilization of nitrogen from such complexes. The knowledge on the functional mechanisms of these processes, and how they are regulated by carbon from the host plant and the availability of more easily available forms of nitrogen sources are limited. We used spectroscopic analyses and transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus. Amendments of glucose triggered the assimilation of nitrogen and the decomposition of the litter material. Concomitantly, the expression of genes encoding enzymes involved in oxidative (i.e. Fenton chemistry) degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism were upregulated in concert. Addition of ammonium had minute effects on both the expression of transcripts and decomposition of litter material, and only when glucose was present. Based on the spectroscopic analyses, three major types of chemical modifications of the litter material were observed. Each of them was correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggests that the expression of the decomposition and nitrogen assimilation machinery of ectomycorrhizal fungi can be firmly regulated by the host carbon supply, i.e. priming, and that the availability of inorganic nitrogen as such has limited effects on the saprotrophic activities. Rineau F, Shah F., Smits M.M., Persson P., Johansson T., Carleer R., Troein C., Tunlid A. (2013) Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus (submitted) A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 467991) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) after amendments of various soil-derived substrates. Transcriptome profiling to examine how the presence/absence of glucose and ammonium regulates the decomposition and mobilization of nitrogen from litter material by the ectomycorrhizal fungus Paxillus involutus.
2013-04-30 | E-GEOD-45303 | biostudies-arrayexpress
Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial. Samples were analyzed for physicochemical variables and microbial community structure and composition. Functional gene abundance was determined using GeoChip.
2014-12-22 | E-GEOD-64286 | biostudies-arrayexpress
Project description:The increased urban pressures are often associated with specialization of microbial communities. Microbial communities being a critical player in the geochemical processes, makes it important to identify key environmental parameters that influence the community structure and its function.In this proect we study the influence of land use type and environmental parameters on the structure and function of microbial communities. The present study was conducted in an urban catchment, where the metal and pollutants levels are under allowable limits. The overall goal of this study is to understand the role of engineered physicochemical environment on the structure and function of microbial communities in urban storm-water canals. Microbial community structure was determined using PhyoChio (G3) Water and sediment samples were collected after a rain event from Sungei Ulu Pandan watershed of >25km2, which has two major land use types: Residential and industrial. Samples were analyzed for physicochemical variables and microbial community structure and composition. Microbial community structure was determined using PhyoChio (G3)
2014-12-22 | E-GEOD-64368 | biostudies-arrayexpress