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

GND
1211605353
ORCID
0000-0002-2132-2709
LSF
59692
Affiliation
Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
Rahlff, Janina;
GND
1312066881
ORCID
0000-0003-4151-3307
Affiliation
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
Turzynski, Victoria;
GND
1333209940
ORCID
0000-0001-6772-8635
Affiliation
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
Esser, Sarah P.;
GND
1309073538
LSF
58198
Affiliation
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
Monsees, Indra;
GND
1155729366
ORCID
0000-0003-3182-6596
LSF
63672
Affiliation
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
Bornemann, Till L. V.;
GND
1264585373
Affiliation
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
Figueroa-Gonzalez, Perla Abigail;
ORCID
0000-0002-4932-4677
Affiliation
DOE Joint Genome Institute, Berkeley, USA
Schulz, Frederik;
GND
128525304
ORCID
0000-0002-9485-5637
Affiliation
DOE Joint Genome Institute, Berkeley, USA
Woyke, Tanja;
GND
1014989949
ORCID
0000-0001-8414-8317
Affiliation
Plant Development & Electron Microscopy, Biocenter LMU Munich, Planegg-Martinsried, Germany
Klingl, Andreas;
GND
143321323
ORCID
0000-0002-5375-5437
LSF
63673
Affiliation
Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Oldenburg, Germany
Moraru, Cristina;
GND
1259833097
ORCID
0000-0002-9392-6544
LSF
59319
Affiliation
Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology, University of Duisburg-Essen, Essen, Germany
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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