A frozen asset: the potential of flow cytometry in constraining the glacial biome

The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats

Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.

Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss

The rapid warming of the Arctic is threatening the demise of its glaciers and their associated ecosystems. Therefore, there is an urgent need to explore and understand the diversity of genomes resident within glacial ecosystems endangered by human-induced climate change. In this study we use genome-resolved metagenomics to explore the taxonomic and functional diversity of different habitats within glacier-occupied catchments. Comparing different habitats within such catchments offers a natural experiment for understanding the effects of changing habitat extent or even loss upon Arctic microbiota. Through binning and annotation of metagenome-assembled genomes (MAGs) we describe the spatial differences in taxon distribution and their implications for glacier-associated biogeochemical cycling. Multiple taxa associated with carbon cycling included organisms with the potential for carbon monoxide oxidation. Meanwhile, nitrogen fixation was mediated by a single taxon, although diverse taxa contribute to other nitrogen conversions. Genes for sulphur oxidation were prevalent within MAGs implying the potential capacity for sulphur cycling. Finally, we focused on cyanobacterial MAGs, and those within cryoconite, a biodiverse microbe-mineral granular aggregate responsible for darkening glacier surfaces. Although the metagenome-assembled genome of Phormidesmis priestleyi, the cyanobacterium responsible for forming Arctic cryoconite was represented with high coverage, evidence for the biosynthesis of multiple vitamins and co-factors was absent from its MAG. Our results indicate the potential for cross-feeding to sustain P. priestleyi within granular cryoconite. Taken together, genome-resolved metagenomics reveals the vulnerability of glacier-associated microbiota to the deletion of glacial habitats through the rapid warming of the Arctic.

High prevalence of parasitic chytrids infection of glacier algae in cryoconite holes in Alaska

Glacier algae, which are photosynthetic microbes growing on ice, considerably reduce the surface albedo of glaciers and accelerate their melting rate. Although the growth of glacier algae can be suppressed by parasitic chytrids, the impact of chytrids on algal populations is still largely unknown. In this study, we described the morphology of the chytrid infecting the glacier alga Ancylonema nordenskioeldii and quantified the prevalence of infection in different habitats on a mountain glacier in Alaska, USA. Microscopic observations revealed three different morphological types of chytrids with distinct rhizoid shapes. Variations in the size of the sporangia were probably because of their different growth stages, indicating that they actively propagated on the glacier. The prevalence of infection did not vary among sites with different elevations but was substantially higher in cryoconite holes (20%) than on ice surfaces (4%) at all sites. This indicates that cryoconite holes are hot spots for chytrid infections of glacier algae, and the dynamics of cryoconite holes might affect the host-parasite interactions between chytrids and the glacier algae, which may in turn alter surface albedo and ice melting.

Cryosphere Microbiome Biobanks for Mountain Glaciers in China

The glaciers in China have an important role as one of the most climate-sensitive constituents of the Tibetan Plateau which is known as the Asian Water Tower. Although the cryosphere is one of the most extreme environments for organisms, the soils of the glacier foreland harbor surprisingly rich microbiomes. A large amount of accelerated glacier retreat accompanied by global warming will not only raise the sea level, but it will also lead to the massive release of a considerable amount of carbon stored in these glaciers. The responses of glacier microbiomes could alter the biogeochemical cycle of carbon and have a complex impact on climate change. Thus, understanding present-day and future glacier microbiome changes is crucial to assess the feedback on climate change and the impacts on ecosystems. To this end, we discuss here the diversity and biogeochemical functions of the microbiomes in Chinese mountain glacier ecosystems.

Storage and export of microbial biomass across the western Greenland Ice Sheet

The Greenland Ice Sheet harbours a wealth of microbial life, yet the total biomass stored or exported from its surface to downstream environments is unconstrained. Here, we quantify microbial abundance and cellular biomass flux within the near-surface weathering crust photic zone of the western sector of the ice sheet. Using groundwater techniques, we demonstrate that interstitial water flow is slow (~10⁻² m d⁻¹), while flow cytometry enumeration reveals this pathway delivers 5 × 10⁸ cells m⁻² d⁻¹ to supraglacial streams, equivalent to a carbon flux up to 250 g km⁻² d⁻¹. We infer that cellular carbon accumulation in the weathering crust exceeds fluvial export, promoting biomass sequestration, enhanced carbon cycling, and biological albedo reduction. We estimate that up to 37 kg km⁻² of cellular carbon is flushed from the weathering crust environment of the western Greenland Ice Sheet each summer, providing an appreciable flux to support heterotrophs and methanogenesis at the bed.

Microbes that colonise ice sheet surfaces are important to the carbon cycle, but their biomass and transport remains unquantified. Here, the authors reveal substantial microbial carbon fluxes across Greenland’s ice surface, in quantities that may sustain subglacial heterotrophs and fuel methanogenesis.

Bacterial community characterization of Batura Glacier in the Karakoram Range of Pakistan

High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4-35 °C), pH (5-12), and salinity (1-6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.

Microbial genomics amidst the Arctic crisis

The Arctic is warming - fast. Microbes in the Arctic play pivotal roles in feedbacks that magnify the impacts of Arctic change. Understanding the genome evolution, diversity and dynamics of Arctic microbes can provide insights relevant for both fundamental microbiology and interdisciplinary Arctic science. Within this synthesis, we highlight four key areas where genomic insights to the microbial dimensions of Arctic change are urgently required: the changing Arctic Ocean, greenhouse gas release from the thawing permafrost, 'biological darkening' of glacial surfaces, and human activities within the Arctic. Furthermore, we identify four principal challenges that provide opportunities for timely innovation in Arctic microbial genomics. These range from insufficient genomic data to develop unifying concepts or model organisms for Arctic microbiology to challenges in gaining authentic insights to the structure and function of low-biomass microbiota and integration of data on the causes and consequences of microbial feedbacks across scales. We contend that our insights to date on the genomics of Arctic microbes are limited in these key areas, and we identify priorities and new ways of working to help ensure microbial genomics is in the vanguard of the scientific response to the Arctic crisis.

The microbiome of glaciers and ice sheets

Glaciers and ice sheets, like other biomes, occupy a significant area of the planet and harbour biological communities with distinct interactions and feedbacks with their physical and chemical environment. In the case of the glacial biome, the biological processes are dominated almost exclusively by microbial communities. Habitats on glaciers and ice sheets with enough liquid water to sustain microbial activity include snow, surface ice, cryoconite holes, englacial systems and the interface between ice and overridden rock/soil. There is a remarkable similarity between the different specific glacial habitats across glaciers and ice sheets worldwide, particularly regarding their main primary producers and ecosystem engineers. At the surface, cyanobacteria dominate the carbon production in aquatic/sediment systems such as cryoconite holes, while eukaryotic Zygnematales and Chlamydomonadales dominate ice surfaces and snow dynamics, respectively. Microbially driven chemolithotrophic processes associated with sulphur and iron cycle and C transformations in subglacial ecosystems provide the basis for chemical transformations at the rock interface under the ice that underpin an important mechanism for the delivery of nutrients to downstream ecosystems. In this review, we focus on the main ecosystem engineers of glaciers and ice sheets and how they interact with their chemical and physical environment. We then discuss the implications of this microbial activity on the icy microbiome to the biogeochemistry of downstream ecosystems.

Polar Marine Microorganisms and Climate Change

The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors.

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap

Microbial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe-mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance-decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co-occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps.

Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control?

Glacial ice surfaces represent a seasonally evolving three-dimensional photic zone which accumulates microbial biomass and potentiates positive feedbacks in ice melt. Since viruses are abundant in glacial systems and may exert controls on supraglacial bacterial production, we examined whether changes in resource availability would promote changes in the bacterial community and the dynamics between viruses and bacteria of meltwater from the photic zone of a Svalbard glacier. Our results indicated that, under ambient nutrient conditions, low estimated viral decay rates account for a strong viral control of bacterial productivity, incurring a potent viral shunt of a third of bacterial carbon in the supraglacial microbial loop. Moreover, it appears that virus particles are very stable in supraglacial meltwater, raising the prospect that viruses liberated in melt are viable downstream. However, manipulating resource availability as dissolved organic carbon, nitrogen, and phosphorous in experimental microcosms demonstrates that the photic zone bacterial communities can escape viral control. This is evidenced by a marked decline in virus-to-bacterium ratio (VBR) concomitant with increased bacterial productivity and number. Pyrosequencing shows a few bacterial taxa, principally Janthinobacterium sp., dominate both the source meltwater and microcosm communities. Combined, our results suggest that viruses maintain high VBR to promote contact with low-density hosts, by the manufacture of robust particles, but that this necessitates a trade-off which limits viral production. Consequently, dominant bacterial taxa appear to access resources to evade viral control. We propose that a delicate interplay of bacterial and viral strategies affects biogeochemical cycling upon glaciers and, ultimately, downstream ecosystems.

Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord

Jorge Montt glacier, located in the Patagonian Ice Fields, has undergone an unprecedented retreat during the past century. To study the impact of the meltwater discharge on the microbial community of the downstream fjord, we targeted Bacteria, Archaea and Fungi communities during austral autumn and winter. Our results showed a singular microbial community present in cold and low salinity surface waters during autumn, when a thicker meltwater layer was observed. Meltwater bacterial sequences were related to Cyanobacteria, Proteobacteria, Actinobacteria and Bacteriodetes previously identified in freshwater and cold ecosystems, suggesting the occurrence of microorganisms adapted to live in the extreme conditions of meltwater. For Fungi, representative sequences related to terrestrial and airborne fungal taxa indicated transport of allochthonous Fungi by the meltwater discharge. In contrast, bottom fjord waters from autumn and winter showed representative Operational Taxonomic Units (OTUs) related to sequences of marine microorganisms, which is consistent with current models of fjord circulation. We conclude that meltwater can significantly modify the structure of microbial communities and support the development of a major fraction of microorganisms in surface waters of Patagonian fjords.

Microbial abundance in surface ice on the Greenland Ice Sheet

Measuring microbial abundance in glacier ice and identifying its controls is essential for a better understanding and quantification of biogeochemical processes in glacial ecosystems. However, cell enumeration of glacier ice samples is challenging due to typically low cell numbers and the presence of interfering mineral particles. We quantified for the first time the abundance of microbial cells in surface ice from geographically distinct sites on the Greenland Ice Sheet (GrIS), using three enumeration methods: epifluorescence microscopy (EFM), flow cytometry (FCM), and quantitative polymerase chain reaction (qPCR). In addition, we reviewed published data on microbial abundance in glacier ice and tested the three methods on artificial ice samples of realistic cell (10²–10⁷ cells ml⁻¹) and mineral particle (0.1–100 mg ml⁻¹) concentrations, simulating a range of glacial ice types, from clean subsurface ice to surface ice to sediment-laden basal ice. We then used multivariate statistical analysis to identify factors responsible for the variation in microbial abundance on the ice sheet. EFM gave the most accurate and reproducible results of the tested methodologies, and was therefore selected as the most suitable technique for cell enumeration of ice containing dust. Cell numbers in surface ice samples, determined by EFM, ranged from ~ 2 × 10³ to ~ 2 × 10⁶ cells ml⁻¹ while dust concentrations ranged from 0.01 to 2 mg ml⁻¹. The lowest abundances were found in ice sampled from the accumulation area of the ice sheet and in samples affected by fresh snow; these samples may be considered as a reference point of the cell abundance of precipitants that are deposited on the ice sheet surface. Dust content was the most significant variable to explain the variation in the abundance data, which suggests a direct association between deposited dust particles and cells and/or by their provision of limited nutrients to microbial communities on the GrIS.