Groundwater metagenome
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ABSTRACT:
PROVIDER: PRJDB16264 | ENA |
REPOSITORIES: ENA
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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:Microcosm based exploration of contaminated groundwater microbial diversity
| PRJNA649362 | ENA
Project description:Groundwater-derived microorganisms are known to play an important role in biogeochemical C, S and N cycling. Thereby, the presence and majorly the activity of microorganisms in aquifers affect enormously the nutrient cycling. However, the diversity and their functional capability in natural aquifers are still rare and therefore a better knowledge of the core microbial communities is urgently needed. Metaproteome analysis was applied to characterize the repertoire of microbes in the depth and to identify the key drivers of major biogeochemical processes. Therefore, 1000 L water from the aquifer was sampled by filtration on 0.3 µm glass filters. After protein extraction, proteolytic cleavage and mass spectrometric analysis (Ultimate 3000 nanoRSLC coupled to Q Exactive HF instrument), 3808 protein groups (2371 proteins with ≥2 peptides) were identified from 13,204 peptides. The findings of our study have broad implications for the understanding of aquifer cycling’s which finally leads to a greatly improved understanding of the ecosystem services provided by the microbial communities present in aquifers. In the future, functional results would allow to monitor and to assess pollution effects which would beneficially assist groundwater resource management.
2016-12-23 | PXD004351 | Pride
Project description:Metagenome-assembled genomes (MAGs) have revealed the existence of novel bacterial and archaeal groups and provided insight into their genetic potential. However, metagenomics and even metatranscriptomics cannot resolve how the genetic potential translates into metabolic functions and physiological activity. Here, we present a novel approach for the quantitative and organism-specific assessment of the carbon flux through microbial communities with stable isotope probing-metaproteomics and integration of temporal dynamics in 13C incorporation by Stable Isotope Cluster Analysis (SIsCA). We used groundwater microcosms labeled with 13CO2 and D2O as model systems and stimulated them with reduced sulfur compounds to determine the ecosystem role of chemolithoautotrophic primary production. Raman microspectroscopy detected rapid deuterium incorporation in microbial cells from 12 days onwards, indicating activity of the groundwater organisms. SIsCA revealed that groundwater microorganisms fell into five distinct carbon assimilation strategies. Only one of these strategies, comprising less than 3.5% of the community, consisted of obligate autotrophs (Thiobacillus), with a 13C incorporation of approximately 95%. Instead, mixotrophic growth was the most successful strategy, and was represented by 12 of the 15 MAGs expressing pathways for autotrophic CO2 fixation, including Hydrogenophaga, Polaromonas and Dechloromonas, with varying 13C incorporation between 5% and 90%. Within 21 days, 43% of carbon in the community was replaced by 13C, increasing to 80% after 70 days. Of the 31 most abundant MAGs, 16 expressed pathways for sulfur oxidation, including strict heterotrophs. We concluded that chemolithoautotrophy drives the recycling of organic carbon and serves as a fill-up function in the groundwater. Mixotrophs preferred the uptake of organic carbon over the fixation of CO2, and heterotrophs oxidize inorganic compounds to preserve organic carbon. Our study showcases how next-generation physiology approach like SIsCA can move beyond metagenomics studies by providing information about expression of metabolic pathways and elucidating the role of MAGs in ecosystem functioning.
2022-05-20 | PXD024889 | Pride
Project description:Background. Bacteria of the Candidate Phyla Radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways suggesting symbiotic life styles. Gracilibacteria (BD1-5) are part of the CPR branch, they possess alternate coded genomes and have two cultivated members that were shown to be microbial predators. However, besides genomic sampling, little is known about the lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, and particularly groundwater where they have initially been genomically resolved. The current study was set out with the aim of investigating the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany, to estimate their activity in situ and discern expressed genes involved in their lifestyle. Results. We coupled genome-resolved metagenomics and metaproteomics to investigate a microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered onto 0.2-μm and 0.1-μm filters to fraction CPR and other bacteria. Based on 670 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Galionellales and Gracilibacteria along with keystone microbes, low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations in their central metabolism but no co-occurrence to potential hosts. Their genomes encoded for a high number of proteins related to a predatory lifestyle, whose expression was detected in the proteome and included subunits related to type IV and type II secretion systems, as well as features related to cell-cell interactions and cell motility. Conclusion. We present a highly resolved analysis coupling metagenomics to metaproteomics for elucidating microbial dynamics of Gracilibacteria in groundwater. We posit that Gracilibacteria are successful microbial predators in this ecosystem potentially aiding in population control of this highly disturbed microbial community from the deep biosphere.
2024-08-08 | PXD042980 | Pride
Project description:Gene expression microarrays were performed to investigate the molecular effects of exposure to environmental polluted groundwater. Zebrafish was treated with polluted waters collected from dumps located upstream and downstream a sanitary landfills. Gene expression profiling of zebrafish liver was analyzed after acute exposure to sampled waters.
2014-09-30 | E-MTAB-2906 | biostudies-arrayexpress
Project description:Gene expression microarrays were performed to investigate the molecular effects of exposure to environmental polluted groundwater. Mice were treated with polluted waters collected from dumps located upstream and downstream a sanitary landfills. Gene expression profiling of mouse liver was analyzed after acute and chronic exposure to sampled waters.
2014-09-30 | E-MTAB-2905 | biostudies-arrayexpress
Project description:HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 M-BM-5g of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 M-BM-5g of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed. A 3 chip study was realized. The first one is a negative control performed with a complex background material (labelled antisense mRNA from sheep rumen content). The second one is a positive control realized with labelled antisense RNA derived from in vitro transcription of three synthetic genes mixed the same complex background material. The third consists in the hybridization of antisense mRNA retrieved from a contaminated groundwater. Each probe (3392) was synthetized in triplicate, and a total of 8,863 random probes was used to determine the background noise.
2011-04-13 | E-GEOD-21492 | biostudies-arrayexpress
Project description:HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 µg of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 µg of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed.
2011-04-13 | GSE21492 | GEO
Project description:Groundwater microbial communities (OL-KR13), Olkiluoto, Finland
| PRJNA625450 | ENA