Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines

Abstract

Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.

Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

“…Due to the extreme temperature and salinity conditions of subzero brines, bacterial growth rates in these environments are expected to be slow, yet the concentrating effect of freezing saline water means that infection pressure from viruses within the resulting brines may be much higher than in their source waters ( Wells and Deming, 2006 ; Collins and Deming, 2011 ). In subzero cryopeg brines with high bacterial densities, cell–cell interactions are also expected to be high ( Rapp et al, 2021 ). Given the anticipated low rates of vertical inheritance associated with slow growth rates, we hypothesized that HGT plays an essential role in the evolution and adaptation of bacteria in the extreme subzero hypersaline environment.…”

“…Metagenomic sequencing was conducted using both Illumina short (2 × 150 bp) and ONT long reads. The Illumina sequencing library was prepared, sequenced, and analyzed at the DOE Joint Genome Institute as previously described ( Rapp et al, 2021 ), and the ONT sequencing library was prepared, sequenced, and quality-controlled following the VirION2 pipeline ( Zablocki et al, 2021 ). Long reads were first assembled using Flye v2.5 ( Kolmogorov et al, 2019 ), and short reads were subsequently used for error correction using Pilon v1.23 ( Walker et al, 2014 ).…”

“…Each metagenome was assembled from a single sample of cryopeg brine, allowing for recovery of MAGs from discrete samples. The raw Illumina metagenomic reads were produced previously and have been described in detail by Rapp et al (2021) ; they are available through IMG/M under accession numbers 3300031836 (CBIW17), 3300032129 (CBIW18), 3300032135 (CBIA), and 3300034171 (CB1). The long-read metagenomic reads used to generate the polished assemblies produced here are available in the Sequence Read Archive under accession numbers SRR17952620, SRR17952621, SRR17952622, and SRR17952623.…”

“…Across the climate-threatened cryosphere (below 0°C) where water can remain liquid due to increased concentrations of salt ions and other impurities ( Cox and Weeks, 1983 ), microbial life remains ubiquitous ( Boetius et al, 2015 ). Though extreme environments present unique challenges to life, microorganisms can be highly abundant in them (e.g., >10 8 ml −1 in subzero brines; Cooper et al, 2019 ), with niche competition continuing as an important selective pressure ( Rapp et al, 2021 ).…”

“…It has also been applied to Sulfurovum , a mesophilic chemolithoautotrophic genus ubiquitous in hydrothermal vent environments, to investigate the influences of biogeography and environmental conditions on genomic differentiation ( Moulana et al, 2020 ). Motivating this study was the successful acquisition of new genomes of Marinobacter from the Alaskan cryopeg brines we have been studying ( Cooper et al, 2019 ; Iwahana et al, 2021 ; Rapp et al, 2021 ) using both classical cultivation methods and sample recovery of metagenome-assembled genomes (MAGs), in the latter case using short-read (Illumina) and long-read (Nanopore) assembly approaches to maximize their quality. These genomes add novelty to the known diversity of this genus and allow a new focus on the cryosphere.…”