Romuvaara deep biosphere
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB25908 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2504050.fastq.gz | Fastqsanger.gz | |||
| ERR2504051.fastq.gz | Fastqsanger.gz | |||
| ERR2504042.fastq.gz | Fastqsanger.gz | |||
| ERR2504052.fastq.gz | Fastqsanger.gz | |||
| ERR2504043.fastq.gz | Fastqsanger.gz |
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Project description:Microbial metabolite profiles in anaerobic enrichment cultures from deep anoxic groundwater
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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:CO2 and carbonate as substrate for the activation of the microbial community in 180 m deep bedrock fracture fluid of Outokumpu Deep Drill Hole, Finland
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Project description:This project aims to investigate the metabolic pathways expressed by the active microbial community occurring at the deep continental subsurface. Subsurface chemoLithoautotrophic Microbial Ecosystems (SLiMEs) under oligotrophic conditions are supported by H2; however, the overall ecological trophic structures of these communities are poorly understood. Some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa appear to support inverted trophic pyramids wherein methanogens contributing <5% of the total DNA apparently produce CH4 that supports the rest of the community. Here we show the active metabolic relationships of one such trophic structure by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Four autotrophic β-proteobacteria genera that are capable of oxidizing sulfur by denitrification dominate. They co-occur with sulfate reducers, anaerobic methane oxidizers and methanogens, which each comprises <5% of the total community. Defining trophic levels of microbial chemolithoautotrophs by the number of transfers from the initial abiotic H2-driven CO2 fixation, we propose a top-down cascade influence of the metabolic consumers that enhances the fitness of the metabolic producers to explain the inverted biomass pyramid of a multitrophic SLiME. Symbiotic partnerships are pivotal in the deep biosphere on and potentially beyond the Earth.
2018-10-27 | PXD004634 | Pride
Project description:Organotrophic diversity of bacteria in deep continental bedrock fracture fluid assessed with acetate-amended microcosms
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Project description:Chemical communication is crucial in ecosystems with complex microbial assemblages. However, due to archaeal cultivation challenges, our understanding of the structure diversity and function of secondary metabolites (SMs) within archaeal communities is limited compared to the extensively studied and well-documented bacterial counterparts. Our comprehensive investigation into the biosynthetic potential of archaea, combined with metabolic analyses and the first report of heterologous expression in archaea, has unveiled the previously unexplored biosynthetic capabilities and chemical diversity of archaeal ribosomally synthesized and post-translationally modified peptide (RiPP). We have identified twenty-four new lanthipeptides of RiPPs exhibiting unique chemical characteristics, including a novel subfamily featuring an unexplored type with diamino-dicarboxylic (DADC) termini, largely expanding the chemical landscape of archaeal SMs. This sheds light on the chemical novelty of archaeal metabolites and emphasizes their potential as an untapped resource for natural product discovery. Additionally, archaeal lanthipeptides demonstrate specific antagonistic activity against haloarchaea, mediating the unique biotic interaction in the halophilic niche. Furthermore, they showcased a unique ecological role in enhancing the host's motility by inducing the rod-shaped cell morphology and upregulating the archaellum gene flgA1, facilitating the archaeal interaction with abiotic environments. These discoveries broaden our understanding of archaeal chemical language and provide promising prospects for future exploration of SM-mediated interaction.
2024-11-09 | GSE281021 | GEO
Project description:Background: Idiopathic Chronic Diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions including corticosteroid, antiparasitic and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. Results: Fecal samples were collected from twelve ICD-diagnosed macaques and twelve age and sex-matched controls. RNA was extracted for metatranscriptomic analysis of species and activity within the gut microbiome. Using SAMSA2, these samples were contrasted to identify shifts both in overall organism activity and functional activity. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased activity of known bacterial pathogens and by decreased activity of archaeal methanogens. Interestingly, known fungal opportunists were not increased in ICD, nor were the usual enteric protozoans, although Trichomonas activity is up-regualted. Known mucin degrading organisms and mucin-degrading enzymes were up-regulated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry confirmed differential mucin composition between healthy control and ICD animals. Finally, assessment of host-derived transcripts confirms colonic inflammation and suggests that the lumen is infiltrated by granulocytes. Conclusions: The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples suggests that ICD of rhesus macaques is associated with increased pathogen activity and altered mucin degradation.
2019-03-09 | GSE108572 | GEO