Lytic archaeal viruses infect abundant primary producers in Earth’s crust

Rahlff, Janina; Turzynski, Victoria; Esser, Sarah P.; Monsees, Indra; Bornemann, Till L. V.; Figueroa-Gonzalez, Perla Abigail; Schulz, Frederik; Woyke, Tanja; Klingl, Andreas; Moraru, Cristina; Probst, Alexander J.

doi:10.1038/s41467-021-24803-4

Article / Chapter Fri Jul 30 2021 CC BY 4.0

published

Lytic archaeal viruses infect abundant primary producers in Earth’s crust

Rahlff, Janina ; Turzynski, Victoria ; Esser, Sarah P.; Monsees, Indra ; Bornemann, Till L. V.; Figueroa-Gonzalez, Perla Abigail ; Schulz, Frederik ; Woyke, Tanja ; Klingl, Andreas ; Moraru, Cristina ; Probst, Alexander J.

The continental subsurface houses a major portion of life’s abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca . Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca . Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems.

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Date Issued:

30.07.2021

URN:

urn:nbn:de:hbz:465-20240904-134720-3

DOI:

10.1038/s41467-021-24803-4

Language:

English

Type of Resource:

Text

Keywords:

Biofilms; Microbial ecology; Virology

Collection:

E-Publications

Subject categories of the Deutsche Nationalbibliografie:

540 Chemistry & allied sciences

Subject categories of the Deutsche Nationalbibliografie:

570 Life science

Hosting institution:

Faculty of Chemistry, Environmental Microbiology and Biotechnology

funding:

The publication of this article was supported by the Publication Fund of the University of Duisburg-Essen.

This work received funding by the Alfred P. Sloan foundation (grant number G-2017-9955), the Ministry of Culture and Science of North Rhine-Westphalia (Nachwuchsgruppe “Dr. Alexander Probst”), and the NOVAC project of the German Science Foundation (grant number DFG PR1603/2-1). The authors acknowledge sampling logistics provided by the University of Regensburg, i.e., by Harald Huber and Sebastien Ferreira-Cerca, and sequencing of MSI metagenomes within the Census of Deep Life Sequencing call 2018, phase 14 project “Development of novel archaeal viruses and the corresponding CRISPR arrays of a highly abundant carbon fixer in Earth’s crust”. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.

Open Access funding enabled and organized by Projekt DEAL.

Info on primary publication:

Rahlff, J., Turzynski, V., Esser, S.P. et al. Lytic archaeal viruses infect abundant primary producers in Earth’s crust. Nat Commun 12, 4642 (2021). https://doi.org/10.1038/s41467-021-24803-4

Published 30 July 2021

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