Viral Ecogenomics of Arctic Cryopeg Brine and Sea Ice

Abstract

Arctic regions, which are changing rapidly as they warm 2 to 3 times faster than the global average, still retain microbial habitats that serve as natural laboratories for understanding mechanisms of microbial adaptation to extreme conditions. Seawater-derived brines within both sea ice (sea-ice brine) and ancient layers of permafrost (cryopeg brine) support diverse microbes adapted to subzero temperatures and high salinities, yet little is known about viruses in these extreme environments, which, if analogous to other systems, could play important evolutionary and ecosystem roles. Here, we characterized viral communities and their functions in samples of cryopeg brine, sea-ice brine, and melted sea ice. Viral abundance was high in cryopeg brine (1.2 × 108 ml−1) and much lower in sea-ice brine (1.3 × 105 to 2.1 × 105 ml−1), which roughly paralleled the differences in cell concentrations in these samples. Five low-input, quantitative viral metagenomes were sequenced to yield 476 viral populations (i.e., species level; ≥10 kb), only 12% of which could be assigned taxonomy by traditional database approaches, indicating a high degree of novelty. Additional analyses revealed that these viruses: (i) formed communities that differed between sample type and vertically with sea-ice depth; (ii) infected hosts that dominated these extreme ecosystems, including Marinobacter, Glaciecola, and Colwellia; and (iii) encoded fatty acid desaturase (FAD) genes that likely helped their hosts overcome cold and salt stress during infection, as well as mediated horizontal gene transfer of FAD genes between microbes. Together, these findings contribute to understanding viral abundances and communities and how viruses impact their microbial hosts in subzero brines and sea ice. IMPORTANCE This study explores viral community structure and function in remote and extreme Arctic environments, including subzero brines within marine layers of permafrost and sea ice, using a modern viral ecogenomics toolkit for the first time. In addition to providing foundational data sets for these climate-threatened habitats, we found evidence that the viruses had habitat specificity, infected dominant microbial hosts, encoded host-derived metabolic genes, and mediated horizontal gene transfer among hosts. These results advance our understanding of the virosphere and how viruses influence extreme ecosystems. More broadly, the evidence that virally mediated gene transfers may be limited by host range in these extreme habitats contributes to a mechanistic understanding of genetic exchange among microbes under stressful conditions in other systems.

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

“…Beyond the oceans, viromics is also providing novel biological insights in e.g., humans (Lim et al, 2015;Norman et al, 2015;Reyes et al, 2015;Aiemjoy et al, 2019;Clooney et al, 2019;Fernandes et al, 2019;Gregory et al, 2020b), soils (Zablocki, Adriaenssens & Cowan, 2015;Trubl et al, 2018;Jin et al, 2019;Li et al, 2019;Santos-Medellin et al, 2020), and extreme environments (Adriaenssens et al, 2015;Scola et al, 2017;Bäckström et al, 2019;Zhong et al, 2020). Together these studies provide a baseline ecological understanding of viral diversity and functions across diverse ecosystems.…”

Glacier ice archives nearly 15,000-year-old microbes and phages

“…For example, in marine systems, viruses are abundant (10 6 to 10 9 particles ml −1 of seawater [33]), with virulent viruses altering microbial communities through lysis, horizontal gene transfer, and metabolic reprogramming (e.g., [34][35][36][37][38]), and temperate viruses modulating host gene regulation and providing novel niche-defining features [39]. In the cryosphere, viruses are much less known, but some data are starting to emerge, such as the studies of viral ecology and evolution in Arctic cryoconite holes [40,41] and a recent work in Arctic sea ice and ancient cryopegs which revealed viruses are abundant, predicted to infect dominant microbial community members, and encoded auxiliary metabolic genes that enabled host adaptations to extreme cold and salt conditions [42]. Thus, even in these extreme conditions, it appears viruses can play key roles in the ecosystem when they and their hosts are active.…”

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

“…Because most viruses are uncultivated, advances have mainly arisen through metagenomic approaches, which have rapidly improved with new sequencing technologies ( Brum & Sullivan, 2015 ). The importance of viruses in community composition and nutrient cycling is also increasingly being recognized across diverse ecosystems, including soils ( Emerson et al., 2018 ; Trubl et al., 2018 ), the human microbiome ( Shkoporov et al., 2019 ), glacial ice ( Zhong et al., 2020 ), and invertebrates ( Shi et al., 2016 ; Wolf et al., 2020 ). For example, viruses have the potential to aid in soil carbon flux by encoding plant polysaccharide-degrading enzymes ( Emerson et al., 2018 ), or can be involved in human gut dysbiosis that leads to various health issues ( Mirzaei & Maurice, 2017 ).…”