Geological degassing enhances microbial metabolism in the continental subsurface

Abstract

23Mantle degassing provides a substantial amount of reduced and oxidized gases shaping microbial 24 metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life 25 under non-thermal conditions. Here, we characterized deep subsurface fluids from a cold-water 26 geyser driven by mantle degassing using genome-resolved metagenomics to investigate how the 27 gases impact the metabolism and activity of indigenous microbes compared to non-impacted sites. 28While species-specific analyses of Altiarchaeota suggest site-specific adaptations and a particular 29 biogeographic pattern, chemolithoautotrophic core features of the communities appeared to be 30 conserved across 17 groundwater ecosystems between 5 and 3200 m depth. We identified a 31 significant negative correlation between ecosystem depth and bacterial replication, except for 32 samples impacted by high amounts of subsurface gases, which exhibited near-surface activity. Our 33 results suggest that geological degassing leads to higher nutrient flows and microbial activity in 34 the deep subsurface than previously estimated.

uBin – a manual refining tool for metagenomic bins designed for educational purposes

“…The output of the four different binners was aggregated using DAS Tool [6]. Tomsk and SulCav binning has been described previously [30].…”

Genome-informed microscopy reveals infections of uncultivated carbon-fixing archaea by lytic viruses in Earth’s crust

“…We currently do not know if this statement can be transferred to other subsurface ecosystems that have low cell counts [2] as viruses might struggle with finding a new host. However, replication measures of bacteria in the ecosystem with the visualized virus suggest that microbial proliferation is similar to other oligotrophic systems [46]. Lytic infections in subsurface microbial hosts might thus launch heterotrophic carbon cycling similar to the viral shunt in the marine environment [95].…”

“…Therefore, metagenomic data from a microbial mat growing in the sulfidic groundwater-fed Alpena County Library Fountain (ACLF) (Alpena, MI, USA) were obtained from NCBI Sequence Read Archive (SRA) repository [45] as were metagenome samples from Horonobe Underground Research Laboratory at 140 and 250 m depth (HURL, Hokkaido, Japan) [21]. The analysis was complemented with three metagenomic datasets from CO2-enriched groundwater erupted from a cold-water Geyser (Andernach, Middle Rhine Valley, Germany) [46], and the metagenome of a sulfidic spring Mühlbacher Schwefelquelle Isling (MSI) in Regensburg, Germany [7]. All BioProject, BioSample accessions and information on sampling of MSI for various experiments are provided in Table S1 and S2, respectively.…”

“…Genes were predicted using prodigal [51] (meta mode) and functional annotations were determined by using DIAMOND [43] against UniRef100 [52]. Altiarchaeota genomes were retrieved from public datasets as described previously [46] and further cleaned or re-binned using GC, coverage and taxonomy information [53], which was necessary for all genomes except for Altiarchaeota from MSI_BF_2012 (Table S1). Viral scaffolds >3 kb were identified by applying a combination of tools as presented in Figure S1A.…”

“…Altiarchaeum (Table S1), previously also termed Alti-1 [20], ranging from 37 to 352 m below ground. These ecosystems included i) an anoxic aquifer accessible through an artesian well (Mühlbacher Schwefelquelle, Isling, MSI) [24] sampled in 2012 and 2018 and ii) a high-CO2 geyser (Geyser Andernach, GA) [46] both located in Germany, iii) a sulfidic spring in the US (Alpena County Library Fountain, ACLF) [45], and iv) a deep underground laboratory in Japan (Horonobe Underground Research Laboratory, HURL) at 140 and 250 m depth [21]. All eight genomes of Ca.…”