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Novel adaptive immune systems in pristine Antarctic soils

Marc W. Van Goethem, Oliver K. I. Bezuidt, Rian Pierneef, Surendra Vikram, David W. Hopkins, Thomas Aspray, Grant Hall, Stephan Woodborne, Ian D. Hogg, Trent R. Northen, et al.
(2025) SCIENTIFIC REPORTS. 15(1).
Author
Organization
Abstract
Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.
Keywords
Adaptive immunity, Antarctica, Antiphage,, Bacteria, CRISPR-Cas, Evolutionary drivers, CRISPR-CAS SYSTEMS, ANTIBIOTIC-RESISTANCE, DIVERSITY, BACTERIA, VIRUSES, ECOLOGY, DEFENSE, BIOLOGY, GENES

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MLA
Van Goethem, Marc W., et al. “Novel Adaptive Immune Systems in Pristine Antarctic Soils.” SCIENTIFIC REPORTS, vol. 15, no. 1, 2025, doi:10.1038/s41598-024-83942-y.
APA
Van Goethem, M. W., Bezuidt, O. K. I., Pierneef, R., Vikram, S., Hopkins, D. W., Aspray, T., … Makhalanyane, T. P. (2025). Novel adaptive immune systems in pristine Antarctic soils. SCIENTIFIC REPORTS, 15(1). https://doi.org/10.1038/s41598-024-83942-y
Chicago author-date
Van Goethem, Marc W., Oliver K. I. Bezuidt, Rian Pierneef, Surendra Vikram, David W. Hopkins, Thomas Aspray, Grant Hall, et al. 2025. “Novel Adaptive Immune Systems in Pristine Antarctic Soils.” SCIENTIFIC REPORTS 15 (1). https://doi.org/10.1038/s41598-024-83942-y.
Chicago author-date (all authors)
Van Goethem, Marc W., Oliver K. I. Bezuidt, Rian Pierneef, Surendra Vikram, David W. Hopkins, Thomas Aspray, Grant Hall, Stephan Woodborne, Ian D. Hogg, Trent R. Northen, Weidong Kong, Daniele Daffonchio, Don A. Cowan, Yves Van de Peer, Manuel Delgado-Baquerizo, and Thulani P. Makhalanyane. 2025. “Novel Adaptive Immune Systems in Pristine Antarctic Soils.” SCIENTIFIC REPORTS 15 (1). doi:10.1038/s41598-024-83942-y.
Vancouver
1.
Van Goethem MW, Bezuidt OKI, Pierneef R, Vikram S, Hopkins DW, Aspray T, et al. Novel adaptive immune systems in pristine Antarctic soils. SCIENTIFIC REPORTS. 2025;15(1).
IEEE
[1]
M. W. Van Goethem et al., “Novel adaptive immune systems in pristine Antarctic soils,” SCIENTIFIC REPORTS, vol. 15, no. 1, 2025.
@article{01JJ3Y7WJAPKJ00CKVZY7X6ZQ1,
  abstract     = {{Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.}},
  articleno    = {{2368}},
  author       = {{Van Goethem, Marc W. and Bezuidt, Oliver K. I. and Pierneef, Rian and Vikram, Surendra and Hopkins, David W. and Aspray, Thomas and Hall, Grant and Woodborne, Stephan and Hogg, Ian D. and Northen, Trent R. and Kong, Weidong and Daffonchio, Daniele and Cowan, Don A. and Van de Peer, Yves and Delgado-Baquerizo, Manuel and Makhalanyane, Thulani P.}},
  issn         = {{2045-2322}},
  journal      = {{SCIENTIFIC REPORTS}},
  keywords     = {{Adaptive immunity,Antarctica,Antiphage,,Bacteria,CRISPR-Cas,Evolutionary drivers,CRISPR-CAS SYSTEMS,ANTIBIOTIC-RESISTANCE,DIVERSITY,BACTERIA,VIRUSES,ECOLOGY,DEFENSE,BIOLOGY,GENES}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{14}},
  title        = {{Novel adaptive immune systems in pristine Antarctic soils}},
  url          = {{http://doi.org/10.1038/s41598-024-83942-y}},
  volume       = {{15}},
  year         = {{2025}},
}
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