Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

Dopson, Mark; Somee, Maryam Rezaei; González-Rosales, Carolina; Lui, Lauren M.; Turner, Stephanie; Buck, Moritz; Nilsson, Emelie; Westmeijer, George; Ashoor, Kamal; Nielsen, Torben N.; Mehrshad, Maliheh; Bertilsson, Stefan

doi:10.1093/ismeco/ycae113

Title: Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

Journal Article · 23 September 2024 · ISME Communications

DOI: https://doi.org/10.1093/ismeco/ycae113 · OSTI ID:2472469

Dopson, Mark ^[1]; Somee, Maryam Rezaei ^[1]; González-Rosales, Carolina ^[1]; Lui, Lauren M. ^[2]; Turner, Stephanie ^[3]; Buck, Moritz ^[4]; Nilsson, Emelie ^[1]; Westmeijer, George ^[1]; Ashoor, Kamal ^[1]; Nielsen, Torben N. ^[2]; Mehrshad, Maliheh ^[4]; Bertilsson, Stefan ^[4]

Linnaeus University, Kalmar (Sweden)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Linnaeus University, Kalmar (Sweden); Swedish University of Agricultural Sciences, Uppsala (Sweden)
Swedish University of Agricultural Sciences, Uppsala (Sweden)

The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood–Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community’s capacity, with up to 9.9% of fermentation, 6.4% of the Wood–Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2472469

Journal Information:: ISME Communications, Journal Name: ISME Communications Journal Issue: 1 Vol. 4; ISSN 2730-6151

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters

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