Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fungal communities colonizing decomposing fungal necromass in wood and soil at Itasca Biological Station & Laboratories

ABSTRACT: Fungal communities colonizing decomposing fungal necromass in wood and soil at Itasca Biological Station & Laboratories Targeted loci environmental

PROVIDER: PRJNA560400 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9987910_1.fastq.gz	Fastqsanger.gz
	SRR9987910_2.fastq.gz	Fastqsanger.gz
	SRR9987920_1.fastq.gz	Fastqsanger.gz
	SRR9987920_2.fastq.gz	Fastqsanger.gz
	SRR9987930_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 156

Similar Datasets

Melanization of fungal necromass drives the upregulation of multiple chitinase, protease, and laccase genes when being degraded by Trichoderma reesei

Project description:Fungal necromass in soil represents the stable carbon pools. While fungi are known to decompose fungal necromass, how fungi decomopose melanin, remains poorly understood. Recently, Trichoderma species was found to be one of the most commonly associated fungi in soil, we have used a relevant fungal species, Trichoderma reesei, to characterized Genes involved in the decomposition of melanized and non-melanized necromass from Hyaloscypha bicolor.

2024-05-01 | GSE263516 | GEO

Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation

Project description:Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are under characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. To address this gap, we conducted a multi-timepoint transcriptomic analysis using three Gram-negative, bacterial species grown on low or high melanin necromass of Hyaloscypha bicolor. The bacterial species, Cellvibrio japonicus, Chitinophaga pinensis, and Serratia marcescens, belong to genera known to degrade necromass in situ. We found that while bacterial growth was consistently higher on low than high melanin necromass, the CAZyme-encoding gene expression response of the three species was similar between the two necromass types. Interestingly, this trend was not shared for genes encoding nitrogen utilization, which varied in C. pinensis and S. marcescens during growth on high versus low melanin necromass. Additionally, this study tested the metabolic capabilities of these bacterial species to grow on a diversity of C and N sources and found that the three bacteria have substantially different abilities to utilize carbon and nitrogen compounds. Collectively, our data suggests that as necromass changes chemically over the course of degradation, certain bacterial species are favored based on their differential metabolic capacities.

2024-05-29 | GSE268149 | GEO

Comparative transcriptomic analysis of a wood decomposing fungus in various atmospheres

Project description:AIM: By adopting comparative transcriptomic approach, we investigated the gene expression of wood decomposing Basidiomycota fungus Phlebia radiata. Our aim was to reveal how hypoxia and lignocellulose structure affect primary metabolism and the expression of wood decomposition related genes. RESULTS: Hypoxia was a major regulator for intracellular metabolism and extracellular enzymatic degradation of wood polysaccharides by the fungus. Our results manifest how oxygen depletion affects not only over 200 genes of fungal primary metabolism but also plays central role in regulation of secreted CAZyme (carbohydrate-active enzyme) encoding genes. Based on these findings, we present a hypoxia-response mechanism in wood-decaying fungi divergent from the regulation described for Ascomycota fermenting yeasts and animal-pathogenic species of Basidiomycota.

2020-02-01 | GSE141153 | GEO

Necromass Interactions 16S

Project description:Necromass Interactions 16S Metagenome

| PRJNA1231136 | ENA

Puerto Rican fungal communities associated with decomposing wood following Hurricane Maria

Project description:Puerto Rican fungal communities associated with decomposing wood following Hurricane Maria Targeted loci environmental

| PRJNA560937 | ENA

Ailaoshan Station fungal community

Project description:Ailaoshan Station fungal community

| PRJNA482782 | ENA

ITS2 amplicons of soil and necromass-associated fungal communities in Minnesota Savannahs, USA

Project description:ITS2 amplicons of soil and necromass-associated fungal communities in Minnesota Savannahs, USA Targeted loci environmental

| PRJNA607030 | ENA

Bacterial necromass is rapidly metabolized by heterotrophic bacteria and supports multiple trophic levels of the groundwater microbiome

Project description:Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce excess particulate organic matter including surface-derived microbes into the groundwater, hereby creating a disturbance to the groundwater microbiome. Some of the translocated bacteria are not able to thrive in groundwater and will form necromass. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time by employing a combined protein and DNA stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within four days, accompanied by a strong decrease of Shannon diversity and an increase of bacterial 16S rRNA gene copy numbers by one order of magnitude. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax and Undibacterium dominated the microbial community within two days and were identified as key players in necromass degradation, based on a 13C incorporation of > 90% in their peptides. Their proteomes showed various uptake and transport related proteins, and many proteins involved in metabolizing amino acids. After four and eight days of incubation, autotrophic and mixotrophic groundwater species of Nitrosomonas, Limnohabitans, Paucibacter and Acidovorax increased in abundance, with a 13C incorporation between 0.5 and 23%. Our data point towards a very fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.

2022-05-31 | PXD031173 | Pride

Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation

Project description:Transcriptomic analyses of bacterial growth on fungal necromass reveals different microbial community niches during degradation

| PRJNA1114768 | ENA

Ebola virus sequencing Dutch Mobile Laboratories

Project description:Ebola virus sequencing Dutch Mobile Laboratories

| PRJEB10265 | ENA