Bacteria and eukaryotes in groundwater
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33253 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3404240_1.fastq.gz | Fastqsanger.gz | |||
| ERR3404240_2.fastq.gz | Fastqsanger.gz | |||
| ERR3404250_1.fastq.gz | Fastqsanger.gz | |||
| ERR3404250_2.fastq.gz | Fastqsanger.gz | |||
| ERR3404260_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 276 |
Similar Datasets
Project description:Composition of bacterial and eukaryotic communities in oligotrophic groundwater of the Hainich Critical Zone Exploratory
| PRJEB33254 | ENA
Project description:Differential contributions of nitrifying microorganisms to nitrification in oligotrophic groundwater from the Hainich Critical Zone Exploratory
| PRJEB63087 | ENA
Project description:Differential contributions of nitrifying microorganisms to nitrification in oligotrophic groundwater from the Hainich Critical Zone Exploratory
| PRJEB57321 | ENA
Project description:Bacterial community structure in soils, seepage water and groundwater of the Hainich Critical Zone Exploratory
| PRJEB25133 | ENA
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
Project description:Bacterial diversity in carbonate rock aquifers of the Hainich Critical Zone Exploratory
| PRJEB20223 | ENA
Project description:<p>Understanding biogeochemical conversions of dissolved organic matter (DOM) in aquifers is paramount for the effective management of groundwater supplies. On its passage through the critical zone, DOM is subject to biogeochemical conversions and therefore carries cross-habitat information useful for monitoring and predicting the stability of groundwater ecosystem services. Groundwater metabolomics assesses this information. However, challenges arise from insufficient knowledge on groundwater metabolite composition and dynamics, and the necessity to maintain analytical conditions for long-term monitoring. We explored fractured sedimentary bedrock by 5-year untargeted metabolomics monitoring for oxic perched and anoxic phreatic sites along a hillslope recharge area, to evaluate DOM as groundwater tracer. Dimension reduction by principal component analysis revealed that metabolome dissimilarities between distant wells coincide with transient cross-stratal flow indicated by groundwater levels and environmental tracers. The metabolome was highly variable lacking seasonal patterns, and did not segregate by geographic location of sampling wells thus ruling out surface vegetation or (agricultura) land use as driving factor. The metabolome time series provide detailed insights into subsurface responses to recharge dynamics. Metabolomics monitoring provides information on groundwater flows, and allows concluding about below ground ecology and water quality evolution, required to understand the impact of interannual wet-dry cycles.</p>
2022-03-21 | MTBLS3450 | MetaboLights
Project description:The ecophysiology of complete ammonia oxidizing Nitrospira (CMX) and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the relevance of their activity from the ecosystem-level process perspective has remained unclear. We investigated oligotrophic carbonate rock aquifers as a model system to assess the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen. CMX accounted for up to 95% of the ammonia oxidizer communities. Nitrification rates were positively correlated to CMX clade A-associated phylotypes and AOB affiliated with Nitrosomonas ureae. Surprisingly, short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed more than 90% to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOA and AOB was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater is primarily governed by AOB. Higher growth yields at lower NH4+ turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations. Activity measurements combined with differential inhibition allowed a refined understanding of ammonia oxidizer coexistence, competition and cooperation beyond the insights from molecular data alone.
2023-10-24 | PXD039573 | Pride
Project description:<p>Anthropogenic activities cause the release of vast amounts of contaminants into the environment and thus also into surface- and groundwaters. Regulatory monitoring determines whether critical threshold concentrations are surpassed, by mostly occasional probing. This irregular testing, however, does not capture the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants in response to water flows. We report the detection and tracing of five contaminants in the 'Hainich Critical Zone Exploratory' (CZE) in central Germany, a monitoring site established for regular sampling of groundwater from different depths and locations along a hill-slope recharge area. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids), the latter being volatilised from wood burning in ovens, show phases of seasonal dynamics in line with their release mode. Further, and alongside legacy herbicides (simazine and the triazine transformation product hydroxypropazine) and the concurrent flame retardant and plasticiser TPP (triphenyl phosphate), mobilisation events emerge from periods of high precipitation and water flows. This investigation highlights the persistence and mobilization of anthropogenic contaminants even in pristine environments. It illustrates the importance of long-term research for understanding ecosystem processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time.</p><p><br></p><p><strong>MS2 data</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS3533' rel='noopener noreferrer' target='_blank'><strong>MTBLS3533</strong></a>.</p><p><strong>MS1 data</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS8433' rel='noopener noreferrer' target='_blank'><strong>MTBLS8433</strong></a>.</p>
2024-06-04 | MTBLS3533 | MetaboLights