Temporal and spatial dynamics of microbial communities and greenhouse gas flux responses to experimental flooding in riparian forest soils
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB86668 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14709400_1.fastq.gz | Fastqsanger.gz | |||
| ERR14709400_2.fastq.gz | Fastqsanger.gz | |||
| ERR14709500.fastq.gz | Fastqsanger.gz | |||
| ERR14709401_1.fastq.gz | Fastqsanger.gz | |||
| ERR14709401_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 420 |
Similar Datasets
Project description:Climate change will lead to more extreme precipitation and associated increase of flooding events of soils. This can turn these soils from a sink into a source of atmospheric methane. The latter will depend on the balance of microbial methane production and oxidation. In the present study, the structural and functional response of methane oxidizing microbial communities was investigated in a riparian flooding gradient. Four sites differing in flooding frequency were sampled and soil-physico-chemistry as well as methane oxidizing activities, numbers and community composition were assessed. Next to this, the active community members were determined by stable isotope probing of lipids. Methane consumption as well as population size distinctly increased with flooding frequency. All methane consumption parameters (activity, numbers, lipids) correlated with soil moisture, organic matter content, and conductivity. Methane oxidizing bacteria were present and activated quickly even in seldom flooded soils. However, the active species comprised only a few representatives belonging to the genera Methylobacter, Methylosarcina, and Methylocystis, the latter being active only in permanently or regularly flooded soils.This study demonstrates that soils exposed to irregular flooding harbor a very responsive methane oxidizing community that has the potential to mitigate methane produced in these soils. The number of active species is limited and dominated by one methane oxidizing lineage. Knowledge on the characteristics of these microbes is necessary to assess the effects of flooding of soils and subsequent methane cycling therein.
| S-EPMC3297182 | biostudies-literature
Project description:Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulating greenhouse gas emissions and prokaryotic communities. The results showed that the addition of viruses has a strong impact on methane (CH4) and nitrous oxide (N2O) emissions and, to a minor extent, carbon dioxide (CO2) emissions, along with dissolved carbon and nitrogen pools, depending on soil fertilization history. The addition of a high viral load resulted in a decrease in microbial biomass carbon (MBC) by 31.4%, with changes in the relative abundance of 16.6% of dominant amplicon sequence variants (ASVs) in comparison to control treatments. More specifically, large effects of viral pressure are observed on some specific microbial communities with decreased relative abundance of prokaryotes that dissimilate sulfur compounds and increased relative abundance of Nanoarchaea. Structural equation modeling further highlighted the differential direct and indirect effects of viruses on CO2, N2O, and CH4 emissions. These findings underpin the understanding of the complex microbe-virus interactions and advance current knowledge on soil virus ecology.
| S-EPMC11672255 | biostudies-literature
Project description:Organic fertilizers have been shown to stimulate CH4 uptake from agricultural soils. Managing fertilizer application to maximize this effect and to minimize emission of other greenhouse gasses offers possibilities to increase sustainability of agriculture. To tackle this challenge, we incubated an agricultural soil with different organic amendments (compost, sewage sludge, digestate, cover crop residues mixture), either as single application or in a mixture and subjected it to different soil moisture concentrations using different amounts of organic amendments. GHG fluxes and in vitro CH4 oxidation rates were measured repeatedly, while changes in organic matter and abundance of GHG relevant microbial groups (nitrifiers, denitrifiers, methanotrophs, methanogens) were measured at the end of the incubation. Overall the dynamics of the analyzed GHGs differed significantly. While CO2 and N2O differed considerably between the treatments, CH4 fluxes remained stable. In contrast, in vitro CH4 oxidation showed a clear increase for all amendments over time. CO2 fluxes were mostly dependent on the amount of organic residue that was used, while N2O fluxes were affected more by soil moisture. Several combinations of amendments led to reductions of CO2, CH4, and/or N2O emissions compared to un-amended soil. Most optimal GHG balance was obtained by compost amendments, which resulted in a similar overall GHG balance as compared to the un-amended soil. However, compost is not very nutrient rich potentially leading to lower crop yield when applied as single fertilizer. Hence, the combination of compost with one of the more nutrient rich organic amendments (sewage sludge, digestate) provides a trade-off between maintaining crop yield and minimizing GHG emissions. Additionally, we could observe a strong increase in microbial communities involved in GHG consumption in all amendments, with the strongest increase associated with cover crop residue mixtures. Future research should focus on the interrelation of plants, soil, and microbes and their impact on the global warming potential in relation to applied organic amendments.
| S-EPMC6292959 | biostudies-literature
Project description:Salt marshes are highly effective carbon (C) sinks and bury more C per square meter annually than any other ecosystem. Reclamation and anthropogenic impacts, however, have resulted in extensive losses of salt marshes. Carbon credits can be generated and sold by restoring marshes, but only if C sequestration and net reductions in greenhouse gases (GHG) are reliably quantified. Restored marshes, however, may exhibit different patterns of GHG emissions than natural marshes and it is possible that they could temporarily become sources of N2O even in the usually N-limited estuarine environment. Research on short-term GHG flux following salt marsh restoration is limited to studies of two restored marshes which examined GHG flux more than six months after the return of tidal flooding. Here we report on a laboratory experiment in which soil cores collected from a drained agricultural marsh on the St. Lawrence Estuary were flooded with estuary water. Gas flux measurements immediately after flooding revealed small increases in N2O and CH4, but a large decline in CO2 yielding, from a climatic perspective, a net cooling effect over the observation period. In addition to restoring the land's capacity to sequester C once a marsh develops, returning tidal flooding thus appears to have the added benefit of stemming large ongoing C losses. With more than 400 km2 of undeveloped dykeland, Eastern Canada is well positioned to restore large sections of marsh and contribute to reducing atmospheric CO2 concentrations.
| S-EPMC6240435 | biostudies-literature
Project description:The soil microorganisms of the riparian forest zone
| PRJNA1094880 | ENA
Project description:The formation of the potent neurotoxic methylmercury (MeHg) is a microbially mediated process that has raised much concern because MeHg poses threats to wildlife and human health. Since boreal forest soils can be a source of MeHg in aquatic networks, it is crucial to understand the biogeochemical processes involved in the formation of this pollutant. High-throughput sequencing of 16S rRNA and the mercury methyltransferase, hgcA, combined with geochemical characterisation of soils, were used to determine the microbial populations contributing to MeHg formation in forest soils across Sweden. The hgcA sequences obtained were distributed among diverse clades, including Proteobacteria, Firmicutes, and Methanomicrobia, with Deltaproteobacteria, particularly Geobacteraceae, dominating the libraries across all soils examined. Our results also suggest that MeHg formation is also linked to the composition of non-mercury methylating bacterial communities, likely providing growth substrate (e.g. acetate) for the hgcA-carrying microorganisms responsible for the actual methylation process. While previous research focused on mercury methylating microbial communities of wetlands, this study provides some first insights into the diversity of mercury methylating microorganisms in boreal forest soils.
| S-EPMC6345997 | biostudies-literature
Project description:Concerns about rising greenhouse gas (GHG) concentrations have spurred the promotion of no-tillage practices as a means to stimulate carbon storage and reduce CO2 emissions in agro-ecosystems. Recent research has ignited debate about the effect of earthworms on the GHG balance of soil. It is unclear how earthworms interact with soil management practices, making long-term predictions on their effect in agro-ecosystems problematic. Here we show, in a unique two-year experiment, that earthworm presence increases the combined cumulative emissions of CO2 and N2O from a simulated no-tillage (NT) system to the same level as a simulated conventional tillage (CT) system. We found no evidence for increased soil C storage in the presence of earthworms. Because NT agriculture stimulates earthworm presence, our results identify a possible biological pathway for the limited potential of no-tillage soils with respect to GHG mitigation.
| S-EPMC4642549 | biostudies-literature
Project description:Though citizen science programs have been broadly successful in diverse scientific fields, their adoption has lagged in some disciplines, including soil science and ecosystem ecology. Collaborations with citizen scientists may be viewed as a conundrum in these disciplines, which often require substantial labor and technical experience; citizen scientists could improve sampling capacity but may reduce sample quality or require training and oversight prior to and while performing specialized tasks. To demonstrate the feasibility of incorporating citizen scientists into soil biogeochemistry research, we conducted a proof-of-concept study in high-elevation meadows of the Sierra Nevada in California. A collaboration between university researchers and citizen scientists allowed us to assess spatial and diel patterns of soil greenhouse gas (GHG) fluxes with an intensity and frequency that would otherwise be beyond the capacity of a typical research laboratory. This collaboration with citizen scientists increased our sampling intensity by over 700% while only doubling the sampling error relative to that of full-time researchers. With training and support from project scientists, citizen scientists collected data that demonstrate spatial independence of carbon dioxide, methane, and nitrous oxide at scales between 1 m and 175 m. Additionally, we found a lack of temporal variation over a 24-h period for all three GHGs. Citizen scientists participating in this one-day event reported levels of satisfaction commensurate with longer-term, immersive campaigns. The place-based event also proved an effective tool for teaching intangible concepts of soil biogeochemistry and promoting local conservation. Despite perceived barriers to entry, this study demonstrates the mutual benefits of citizen science collaborations in soil science and ecosystem ecology, encouraging adoption by disciplines that have been slow to take advantage of such collaborations. Short-term, local citizen science events can provide meaningful experiences for area residents and teach global biogeochemical cycles in a place-based context.
| S-EPMC6033390 | biostudies-literature
Project description:Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
| S-EPMC4327730 | biostudies-literature
Project description:BackgroundA huge reservoir was formed by the Three Gorges Dam in China, which also formed a riparian zone along the bank of the reservoir. In the period of low water-level, the riparian zone in tributary bays of the Three Gorges Reservoir (TGR) was always unordered cultivated, owing to its gentle slope and high soil fertility. This land-use practice creates high potential of generating greenhouse gas (GHG) emissions with periodic water level fluctuation.MethodsTo evaluate potential GHG emissions from the soil-air interface, the static opaque chamber method was adopted to evaluate the effect of elevations (180 m, 175 m, 170 m and 165 m) and land use types (dry lands, paddy fields and grass fields) from April to September in 2015 and 2016.ResultsThe results showed that carbon dioxide (CO2) was the main contributor of GHG emission in riparian zone most likely because of high organic carbon from residues. Furthermore, high soil water content in paddy fields resulted in significantly higher methane (CH4) flux than that in dry lands and grass fields. Compared to grass fields, anthropogenic activities in croplands were attributed with a decrease of soil total carbon and GHG emissions. However, inundation duration of different elevations was found to have no significant effect on CH4 and CO2 emissions in the riparian zone, and the mean nitrous oxide (N2O) flux from dry lands at an elevation of 165 m was significantly higher than that of other elevations likely because of tillage and manure application. The high N2O fluxes produced from tillage and fertilizer suggested that, in order to potentially mitigate GHG emissions from the riparian zone, more attention must be paid to the farming practices in dry lands at low elevations (below 165 m) in the riparian zone. Understanding factors that contribute to GHG emissions will help guide ecological restoration of riparian zones in the TGR.
| S-EPMC7034375 | biostudies-literature