ODS VOC
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ABSTRACT:
PROVIDER: PRJEB70921 | 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:In this study a gene expression (i.e., RNAseq) analysis was performed in HEK293T-ACE2 cellular model upon infection with viral particle belonging to VOC Delta (MOI: 0.026) for 24 hours in order to have a global picture of the transcriptome landscape in response to early phase of infection of SARS-CoV-2 ( VOC Delta infection and to evaluate the role of Ca2+ in HEK293-ACE2 cellular model and transfer to homeostasis in SARS-COV-2 patients (by Pasqualino de Antonellis1-2* and Veronica Ferrucci 1-2* (first authors) et al. and Massimo Zollo1-2# (corresponding author). Manuscript in preparation 2022 July 15th 2022. Short title "ATP2B1 (PMCA1), regulated by FOXO3, influences susceptibility to severe COVID19".
2022-12-01 | E-MTAB-11973 | biostudies-arrayexpress
Project description:Rhodococcus opacus VOC-14 - Genome sequencing and assembly
| PRJNA999064 | ENA
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:Diversity and functionality of archaeal, bacterial and fungal communities in deep Archaean bedrock groundwater
| PRJEB25908 | ENA
Project description:Microbial community structure in six deep crystalline bedrock fracture zones
| PRJEB10822 | ENA
Project description:Microbial communities in deep crystalline bedrock aquifers of Olkiluoto, Finkand
| PRJEB6874 | ENA
Project description:Groundwater microbial diversity from a VOC impacted site injected with nZVI/CMC
| PRJNA308958 | ENA