Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic

Microbial communities in the Hudson Strait amidst rapid environmental change

Climate change is rapidly altering Arctic marine environments, leading to warmer waters, increased river discharge, and accelerated sea ice melt. The Hudson Bay Marine System experiences the fastest rate of sea ice loss in the Canadian North resulting in a prolonged open water season during the summer months. We examined microbial communities in the Hudson Strait using high throughput 16s rRNA gene sequencing during the peak of summer, in which the bay was almost completely ice-free, and air temperatures were high. We found that salinity and temperature significantly affected the taxonomic composition among microbial communities across sites. We observed a higher relative abundance of specific Polaribacter sp. Amplicon sequence variants (ASVs) at more saline sites. Shannon diversity was not significantly impacted by salinity or temperature. These results contribute to our understanding of surface water microbial community composition in the Hudson Strait and shed light on how future salinity and temperature conditions may favour certain microbial populations.

Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.

Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum

Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.

IMPORTANCE

Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.

Spectroscopic Detection of Biosignatures in Natural Ice Samples as a Proxy for Icy Moons

Some of the icy moons of the solar system with a subsurface ocean, such as Europa and Enceladus, are the targets of future space missions that search for potential extraterrestrial life forms. While the ice shells that envelop these moons have been studied by several spacecrafts, the oceans beneath them remain unreachable. To better constrain the habitability conditions of these moons, we must understand the interactions between their frozen crusts, liquid layers, and silicate mantles. To that end, astrobiologists rely on planetary field analogues, for which the polar regions of Earth have proven to be great candidates. This review shows how spectroscopy is a powerful tool in space missions to detect potential biosignatures, in particular on the aforementioned moons, and how the polar regions of the Earth are being used as planetary field analogues for these extra-terrestrial environments.

Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.