Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere

Abstract

A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Äspö Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.

Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins

“…So far, very little information is available on the specific eukaryotic metabolic activities in DHABs [31], even though existing methods have been proven to be reliable for the identification of eukaryotic-only transcripts (e.g., enrichment in eukaryotic transcripts in metatranscriptome data to capture a higher fraction of eukaryotic sequences). Recently, the metatranscriptomic approach has begun to blossom as a powerful method for the functional characterisation of complex microbial communities [46] and has been carried out in different ecosystems, including non-marine subsurface systems [47,48], marine deep-sea sediments [49,50]. The metatranscriptomic approach has several advantages over DNA-based amplicon sequencing: It is less susceptible to amplification biases, it captures only living organisms, and provides a larger set of genes, which can be exploited for taxonomic identification [51].…”

A Cryptic Alternative for the Evolution of Hyphae

“…[ 47 ] Thus most major and higher clades of fungi are represented in the deep fungal fossil record. Studies of modern fungal communities in deep settings are in agreement with this and show a surprisingly high diversity represented by all major fungal phyla [ 48,49 ] including several deep‐branching novel lineages [ 50 ] and adaptation to deep biosphere conditions. [ 51 ]…”

In‐depth prospection of Avène Thermal Spring Water reveals an uncommon and stable microbial community

“…Little is known about the way they impact upon groundwater chemistry, and bioprospecting from this environment may also lead to the discovery of novel bioactive compounds as therapeutic agents 6,7 . Several studies provide evidence of a microbial active life in the deep continental groundwaters 8,9 . Microorganisms inhabiting these ecosystems are very different from those usually encountered in surface waters, and their distribution is dependent on the geochemical and hydrological characteristics 10,11 .…”