Ontology highlight
ABSTRACT:
PROVIDER: PRJNA993426 | ENA |
REPOSITORIES: ENA
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Project description:Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies focused on how fire affects both the taxonomic and functional diversity of soil microbial communities, along with plant diversity and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects for a grassland ecosystem 9-months after an experimental fire at the Jasper Ridge Global Change Experiment (JRGCE) site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis indicating that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa were able to withstand the disturbance. In addition, fire decreased the relative abundances of most genes associated with C degradation and N cycling, implicating a slow-down of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated plant growth, likely enhancing plant-microbe competition for soil inorganic N. To synthesize our findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for the significantly higher soil respiration rates in burned sites. In conclusion, fire is well-documented to considerable alter the taxonomic and functional composition of soil microorganisms, along with the ecosystem functioning, thus arousing feedback of ecosystem responses to affect global climate.
2022-02-19 | GSE126737 | GEO
Project description:Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems
| PRJEB41211 | ENA
Project description:To characterize the taxonomic and functional diversity of biofilms on plastics in marine environments, plastic pellets (PE and PS, ø 3mm) and wooden pellets (as organic control) were incubated at three stations: at the Baltic Sea coast in Heiligendamm (coast), in a dead branch of the river Warnow in Warnemünde (inlet), and in the Warnow estuary (estuary). After two weeks of incubation, all pellets were frozen for subsequent metagenome sequencing and metaproteomic analysis. Biofilm communities in the samples were compared on multiple levels: a) between the two plastic materials, b) between the individual incubation sites, and c) between the plastic materials and the wooden control. Using a semiquantitative approach, we established metaproteome profiles, which reflect the dominant taxonomic groups as well as abundant metabolic functions in the respective samples.
2021-11-01 | PXD012062 | Pride
Project description:Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. Sixteen samples analyzed.
2015-07-09 | E-GEOD-70539 | biostudies-arrayexpress
Project description:Functional profiles predicted based on taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacity based on plant location. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems.
2015-07-09 | GSE70539 | GEO
Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to investigate spring microbial functional genes in mesocosm-simulated shallow lake ecosystems having been undergoing nutrient enrichment and warming for nine years.
2020-12-30 | GSE155582 | GEO
Project description:This study began with 72 male 4-week-old BALB/c mice. The mice were split evenly into one of four cohorts: Control, River, Pine, and Road. The control mice were raised with standard corn cob bedding whereas the remaining mice were raised with clean bedding amended with 300 mL of one of three different types of soil. The soil exposure continued throughout the experiment, with 300 mL of new soil added with bi-weekly cage changes. The soils used to amend the cage bedding were previously characterized as having high (Pine), medium (River), and low (Road) diversity. The River and Pine soil were collected from Duke Forest and the Road soil was collected adjacent to Highway 15-501 in Chapel Hill, North Carolina. All mice were given a standard diet and the cages were distributed reverse osmosis treated water through a centralized Lixit® system that was fed to each cage in parallel. After 32 days of standard rearing with amended soils, the mice were exposed via oropharyngeal aspiration to either live influenza A (PR8) virus or heat inactivated (HI) virus.
2022-10-17 | GSE215292 | GEO
Project description:Because of severe abiotic limitations, Antarctic soils represent simplified ecosystems, where microorganisms are the principle drivers of nutrient cycling. This relative simplicity makes these ecosystems particularly vulnerable to perturbations, like global warming, and the Antarctic Peninsula is among the most rapidly warming regions on the planet. However, the consequences of the ongoing warming of Antarctica on microorganisms and the processes they mediate are unknown. Here, using 16S rRNA gene pyrosequencing and qPCR, we report a number of highly consistent changes in microbial community structure and abundance across very disparate sub-Antarctic and Antarctic environments following three years of experimental field warming (+ 0.5-2°C). Specifically, we found significant increases in the abundance of fungi and bacteria and in the Alphaproteobacteria-to-Acidobacteria ratio. These alterations were linked to a significant increase in soil respiration. Furthermore, the shifts toward generalist or opportunistic bacterial communities following warming weakened the linkage between bacterial diversity and functional diversity. Warming also increased the abundance of some organisms related to the N-cycle, detected as an increase in the relative abundance of nitrogenase genes via GeoChip microarray analyses. Our results demonstrate that soil microorganisms across a range of sub-Antarctic and Antarctic environments can respond consistently and rapidly to increasing temperatures, thereby potentially disrupting soil functioning. We conducted in situ warming experiments for three years using open-top chambers (OTCs) at one sub-Antarctic (Falkland Islands, 52ºS) and two Antarctic locations (Signy and Anchorage Islands, 60ºS and 67ºS respectively) (see Supplementary Fig. 1 for a map). OTCs increased annual soil temperature by an average of 0.8°C (at a depth of 5 cm), resulting in 8-43% increase in positive-degree days annually and a decrease in freeze-thaw cycle frequency by an average of 15 cycles per year (8). At each location, we included densely vegetated and bare fell-field soils in the experimental design for a total of six environments. Densely vegetated and bare environments represent two contrasting environments for Antarctic soil microorganisms, with large differences in terms of C and N inputs to soils. Massively parallel pyrosequencing (Roche 454 GS FLX Titanium) of 16S rRNA gene amplicons was used to follow bacterial diversity and community composition [GenBank Accession Numbers: HM641909-HM744649], and functional gene microarrays (GeoChip 2.0)(11) were used to assess changes in functional gene distribution. Bacterial and fungal communities were also quantified using real-time PCR.
2010-12-30 | E-GEOD-22825 | biostudies-arrayexpress