The dynamic bacterial communities of a melting High Arctic glacier snowpack

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.

Cryosphere: a frozen home of microbes and a potential source for drug discovery

The world is concerned about the emergence of pathogens and the occurrence and spread of antibiotic resistance among pathogens. Drug development requires time to combat these issues. Consequently, drug development from natural sources is unavoidable. Cryosphere represents a gigantic source of microbes that could be the bioprospecting source of natural products with unique scaffolds as molecules or drug templates. This review focuses on the novel source of drug discovery and cryospheric environments as a potential source for microbial metabolites having potential medicinal applications. Furthermore, the problems encountered in discovering metabolites from cold-adapted microbes and their resolutions are discussed. By adopting modern practical approaches, the discovery of bioactive compounds might fulfill the demand for new drug development.

Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait

The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.

Alcanivorax bacteria as important polypropylene degraders in mesopelagic environments

IMPORTANCE

PP biodegradation has not been clearly shown (it has been uncertain whether the PP structure is actually biodegraded or not). This is the first report on the obvious biodegradation of PP. At the same time, this study shows that Alcanivorax bacteria could be major degraders of PP in mesopelagic environments. Moreover, PP biodegradation has been investigated by using solid PP as the sole carbon source. However, this study shows that PP would not be used as a sole carbon and energy source. Our data thus provide very important and key knowledge for PP bioremediation.

Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard)

Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.

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.

Insights into Antarctic microbiomes: diversity patterns for terrestrial and marine habitats

Microorganisms in Antarctica are recognized for having crucial roles in ecosystems functioning and biogeochemical cycles. To explore the diversity and composition of microbial communities through different terrestrial and marine Antarctic habitats, we analyze 16S rRNA sequence datasets from fumarole and marine sediments, soil, snow and seawater environments. We obtained measures of alpha- and beta-diversities, as well as we have identified the core microbiome and the indicator microbial taxa of a particular habitat. Our results showed a unique microbial community structure according to each habitat, including specific taxa composing each microbiome. Marine sediments harbored the highest microbial diversity among the analyzed habitats. In the fumarole sediments, the core microbiome was composed mainly of thermophiles and hyperthermophilic Archaea, while in the majority of soil samples Archaea was absent. In the seawater samples, the core microbiome was mainly composed by cultured and uncultured orders usually identified on Antarctic pelagic ecosystems. Snow samples exhibited common taxa previously described for habitats of the Antarctic Peninsula, which suggests long-distance dispersal processes occurring from the Peninsula to the Continent. This study contributes as a baseline for further efforts on evaluating the microbial responses to environmental conditions and future changes.

RNA outperforms DNA-based metabarcoding in assessing the diversity and response of microeukaryotes to environmental variables in the Arctic Ocean

The Arctic Ocean (AO) has a harsh environment characterized by low temperatures, extensive ice coverage, and periodic freezing and melting of sea ice, which has provided diverse habitats for microorganisms. Prior studies primarily focused on microeukaryote communities in the upper water or sea ice based on environmental DNA, leaving the composition of active microeukaryotes in the diverse AO environments largely unknown. This study provided a vertical assessment of microeukaryote communities in the AO from snow and ice to sea water at a depth of 1670 m using high-throughput sequencing of co-extracted DNA and RNA. RNA extracts depicted microeukaryote community structure and intergroup correlations more accurately and responded more sensitively to environmental conditions than those derived from DNA. Using RNA:DNA ratios as a proxy for relative activity of major taxonomic groups, the metabolic activities of major microeukaryote groups were determined along depth. Analysis of co-occurrence networks showed that parasitism between Syndiniales and dinoflagellates/ciliates in the deep ocean may be significant. This study increased our knowledge of the diversity of active microeukaryote communities and highlighted the importance of using RNA-based sequencing over DNA-based sequencing to examine the relationship between microeukaryote assemblages and the responses of microeukaryotes to environmental variables in the AO.

Are intratumoral microbiota involved in the progression of intraductal papillary mucinous neoplasms of the pancreas?

BACKGROUND

Microbiota have been reported to influence the development of various gastrointestinal neoplasms through the mechanism of sustained inflammation; however, few data are available regarding their influence on intraductal papillary mucinous neoplasms. The aim of this study was to assess the association between specific microbiota and the clinicopathologic characteristics of intraductal papillary mucinous neoplasms of the pancreas.

METHODS

DNA was extracted from formalin-fixed, paraffin-embedded samples of 30 patients who underwent pancreatectomy for intraductal papillary mucinous neoplasm, and polymerase chain reaction was used to create sequence libraries using the primer set for the V3 and V4 region of 16S recombinant DNA. Filtered sequence reads were then processed into operational taxonomic units with a 97% identity threshold and the relative abundance of bacteria compared between the 2 groups using operational taxonomic units.

RESULTS

There was a trend toward fewer Firmicutes and more Proteobacteria and Fusobacteria in the relative abundance of main duct operational taxonomic units than in branch duct operational taxonomic units. The relative abundances of Bacteroidetes (P < .01) and Fusobacteria (P = .04) were significantly higher in invasive intraductal papillary mucinous neoplasms than in noninvasive intraductal papillary mucinous neoplasms. The relative abundance of the intestinal type was significantly lower in Firmicutes than the relative abundance of the nonintestinal type (P = .04). Notably, main duct operational taxonomic units with the intestinal subtype were affected by increased proportions of Proteobacteria and Fusobacteria, and Fusobacteria were abundant in the intestinal type of invasive main duct operational taxonomic units.

CONCLUSION

Intratumoral microbiota may be involved in the progression of operational taxonomic units.

Gut microbiota diversity and specific composition during immunotherapy in responders with non-small cell lung cancer

Cancer immunotherapy including immune checkpoint inhibitors (ICI) has revolutionized non-small cell lung cancer (NSCLC) therapy. Recently, the microbiota status “before” initiation of ICI therapy has been emphasized as a predictive biomarker in patients undergoing ICI therapy. However, the microbiota diversity and composition “during” ICI therapy is unknown. This multicenter, prospective observational study analyzed both saliva and feces from 28 patients with NSCLC. We performed 16S ribosomal RNA gene sequencing, then analyzed associations of oral and gut microbiota diversity or composition with ICI response. At the genus level, the alpha diversity of the gut microbiota was significantly greater in responders (n = 17) than in non-responders (n = 11) (Chao 1, p = 0.0174; PD whole tree, p = 0.0219; observed species, p = 0.0238; Shannon, p = 0.0362), while the beta diversity of the gut microbiota was significantly different (principal coordinates analysis, p = 0.035). Compositional differences in the gut microbiota were observed between the two groups; in particular, g_Blautia was enriched in responders, whereas o_RF32 order unclassified was enriched in non-responders. The progression-free survival (PFS) of patients enriched gut microbiota of g_Blautia was significantly longer [median survival time (MST): not reached vs. 549 days, p = 0.0480] and the PFS of patients with gut microbiota of o_RF32 unclassified was significantly shorter (MST: 49 vs. 757 days, p = 0.0205). There were no significant differences between groups in the oral microbiota. This study revealed a strong association between gut microbiota diversity and ICI response in NSCLC patients. Moreover, specific gut microbiota compositions may influence the ICI response. These findings might be useful in identifying biomarkers to predict ICI response.

Chronological analysis of the gut microbiome for efficacy of atezolizumab-based immunotherapy in non-small cell lung cancer: Protocol for a multicenter prospective observational study

Background

Cancer immunotherapy with immune checkpoint inhibitors (ICIs) is an innovative treatment for non‐small cell lung cancer (NSCLC). Recently, the specific composition of the gut microbiome before initiation of cancer immunotherapy has been highlighted as a predictive biomarker in patients undergoing cancer immunotherapy, mainly in the US or Europe. However, the fact gut microbiome status is completely different in races or countries has been revealed. In addition, how the microbiome composition and diversity chronologically change during cancer immunotherapy is still unclear.

Methods

This multicenter, prospective observational study will analyze the association between the gut microbiome and therapeutic response in NSCLC patients who received atezolizumab‐based immunotherapy. The aim of the present study is to clarify not only how the specific composition of the gut microbiome influences clinical response in NSCLC patients but the chronological changes of gut microbiota during atezolizumab‐based immunotherapy. The gut microbiota will be analyzed using 16S rRNA gene sequencing. The main inclusion criteria are as follows: (1) Pathologically‐ or cytologically‐confirmed stage IV or postoperative recurrent NSCLC. (2) Patients ≥20 years old at the time of informed consent. (3) Planned to treat with atezolizumab‐based immunotherapy combined with platinum‐based chemotherapy (cohort 1) and monotherapy (cohort 2) as a first immunotherapy. (4) Patients to provide fecal samples. A total of 60 patients will be enrolled prospectively. Enrollment will begin in 2020 and the final analyses will be completed by 2024.

Discussion

This trial will provide more evidence of how gut microbiota composition and diversity chronologically change during cancer immunotherapy and contribute to the development of biomarkers to predict ICI response as well as biotic therapies which enhance the ICI response.

Artificial intelligence-derived gut microbiome as a predictive biomarker for therapeutic response to immunotherapy in lung cancer: protocol for a multicentre, prospective, observational study

INTRODUCTION

Immunotherapy is the fourth leading therapy for lung cancer following surgery, chemotherapy and radiotherapy. Recently, several studies have reported about the potential association between the gut microbiome and therapeutic response to immunotherapy. Nevertheless, the specific composition of the gut microbiome or combination of gut microbes that truly predict the efficacy of immunotherapy is not definitive.

METHODS AND ANALYSIS

The present multicentre, prospective, observational study aims to discover the specific composition of the gut microbiome or combination of gut microbes predicting the therapeutic response to immunotherapy in lung cancer using artificial intelligence. The main inclusion criteria are as follows: (1) pathologically or cytologically confirmed metastatic or postoperative recurrent lung cancer including non-small cell lung cancer and small cell lung cancer; (2) age≥20 years at the time of informed consent; (3) planned treatment with immunotherapy including combination therapy and monotherapy, as the first-line immunotherapy; and (4) ability to provide faecal samples. In total, 400 patients will be enrolled prospectively. Enrolment will begin in 2021, and the final analyses will be completed by 2024.

ETHICS AND DISSEMINATION

The study protocol was approved by the institutional review board of each participating centre in 2021 (Kyushu Cancer Center, IRB approved No. 2021-13, 8 June 2021 and Kyushu Medical Center, IRB approved No. 21-076, 31 August 2021). Study results will be disseminated through peer-reviewed journals and national and international conferences.

TRIAL REGISTRATION NUMBER

UMIN000046428.

Seasonality of Glacial Snow and Ice Microbial Communities

Blooms of microalgae on glaciers and ice sheets are amplifying surface ice melting rates, which are already affected by climate change. Most studies on glacial microorganisms (including snow and glacier ice algae) have so far focused on the spring and summer melt season, leading to a temporal bias, and a knowledge gap in our understanding of the variations in microbial diversity, productivity, and physiology on glacier surfaces year-round. Here, we investigated the microbial communities from Icelandic glacier surface snow and bare ice habitats, with sampling spanning two consecutive years and carried out in both winter and two summer seasons. We evaluated the seasonal differences in microbial community composition using Illumina sequencing of the 16S rRNA, 18S rRNA, and ITS marker genes and correlating them with geochemical signals in the snow and ice. During summer, Chloromonas, Chlainomonas, Raphidonema, and Hydrurus dominated surface snow algal communities, while Ancylonema and Mesotaenium dominated the surface bare ice habitats. In winter, algae could not be detected, and the community composition was dominated by bacteria and fungi. The dominant bacterial taxa found in both winter and summer samples were Bacteriodetes, Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria. The winter bacterial communities showed high similarities to airborne and fresh snow bacteria reported in other studies. This points toward the importance of dry and wet deposition as a wintertime source of microorganisms to the glacier surface. Winter samples were also richer in nutrients than summer samples, except for dissolved organic carbon-which was highest in summer snow and ice samples with blooming microalgae, suggesting that nutrients are accumulated during winter but primarily used by the microbial communities in the summer. Overall, our study shows that glacial snow and ice microbial communities are highly variable on a seasonal basis.

Functional filtering and random processes affect the assembly of microbial communities of snow algae blooms at Maritime Antarctic

The increasing temperatures at the West Antarctic Peninsula (Maritime Antarctic) could lead to a higher occurrence of snow algal blooms which are ubiquitous events that change the snow coloration, reducing albedo and in turn exacerbating melting. However, there is a limited understanding of snow algae blooms biodiversity, composition, and their functional profiles, especially in one of the world's areas most affected by climate change. In this study we used 16S rRNA and 18S rRNA metabarcoding, and shotgun metagenomics to assess the diversity, composition, and functional potential of the snow algae blooms bacterial and eukaryotic communities at three different sites of Maritime Antarctic, between different colors of the algae blooms and between seasonal and semi-permanent snowfields. We tested the hypothesis that the functional potential of snow algae blooms is conserved despite a changing taxonomic composition. Furthermore, we determined taxonomic co-occurrence patterns of bacteria and eukaryotes and assessed the potential for the exchange of metabolites among bacterial taxa. Here, we tested the prediction that there are co-occurring taxa within snow algae whose biotic interactions are marked by the exchange of metabolites. Our results show that the composition of snow algae blooms vary significantly among sites. For instance, a higher abundance of fungi and protists were detected in Fildes Peninsula compared with Doumer Island and O'Higgins. Likewise, the composition varied between snow colors and snow types. However, the functional potential varied only among sampling sites with a higher abundance of genes involved in tolerance to environmental stress at O'Higgins. Co-occurrence patterns of dominant bacterial genera such as Pedobacter, Polaromonas, Flavobacterium and Hymenobacter were recorded, contrasting the absence of co-occurring patterns displayed by Chlamydomonadales algae with other eukaryotes. Finally, genome-scale metabolic models revealed that bacteria within snow algae blooms likely compete for resources instead of forming cooperative communities.

Polar Cryoconite Associated Microbiota Is Dominated by Hemispheric Specialist Genera

Cryoconite holes, supraglacial depressions containing water and microbe-mineral aggregates, are known to be hotspots of microbial diversity on glacial surfaces. Cryoconite holes form in a variety of locations and conditions, which impacts both their structure and the community that inhabits them. Using high-throughput 16S and 18S rRNA gene sequencing, we have investigated the communities of a wide range of cryoconite holes from 15 locations across the Arctic and Antarctic. Around 24 bacterial and 11 eukaryotic first-rank phyla were observed in total. The various biotic niches (grazer, predator, photoautotroph, and chemotroph), are filled in every location. Significantly, there is a clear divide between the bacterial and microalgal communities of the Arctic and that of the Antarctic. We were able to determine the groups contributing to this difference and the family and genus level. Both polar regions contain a "core group" of bacteria that are present in the majority of cryoconite holes and each contribute >1% of total amplicon sequence variant (ASV) abundance. Whilst both groups contain Microbacteriaceae, the remaining members are specific to the core group of each polar region. Additionally, the microalgal communities of Arctic cryoconite holes are dominated by Chlamydomonas whereas the Antarctic cryoconite holes are dominated by Pleurastrum. Therefore cryoconite holes may be a global feature of glacier landscapes, but they are inhabited by regionally distinct microbial communities. Our results are consistent with the notion that cryoconite microbiomes are adapted to differing conditions within the cryosphere.

Spatial and Annual Variation in Microbial Abundance, Community Composition, and Diversity Associated With Alpine Surface Snow

Understanding microbial community dynamics in the alpine cryosphere is an important step toward assessing climate change impacts on these fragile ecosystems and meltwater-fed environments downstream. In this study, we analyzed microbial community composition, variation in community alpha and beta diversity, and the number of prokaryotic cells and virus-like particles (VLP) in seasonal snowpack from two consecutive years at three high altitude mountain summits along a longitudinal transect across the European Alps. Numbers of prokaryotic cells and VLP both ranged around 104 and 105 per mL of snow meltwater on average, with variation generally within one order of magnitude between sites and years. VLP-to-prokaryotic cell ratios spanned two orders of magnitude, with median values close to 1, and little variation between sites and years in the majority of cases. Estimates of microbial community alpha diversity inferred from Hill numbers revealed low contributions of common and abundant microbial taxa to the total taxon richness, and thus low community evenness. Similar to prokaryotic cell and VLP numbers, differences in alpha diversity between years and sites were generally relatively modest. In contrast, community composition displayed strong variation between sites and especially between years. Analyses of taxonomic and phylogenetic community composition showed that differences between sites within years were mainly characterized by changes in abundances of microbial taxa from similar phylogenetic clades, whereas shifts between years were due to significant phylogenetic turnover. Our findings on the spatiotemporal dynamics and magnitude of variation of microbial abundances, community diversity, and composition in surface snow may help define baseline levels to assess future impacts of climate change on the alpine cryosphere.

Fate of glacier surface snow-originating bacteria in the glacier-fed hydrologic continuums

Glaciers represent important biomes of Earth and are recognized as key species pools for downstream aquatic environments. Worldwide, rapidly receding glaciers are driving shifts in hydrology, species distributions and threatening microbial diversity in glacier-fed aquatic ecosystems. However, the impact of glacier surface snow-originating taxa on the microbial diversity in downstream aquatic environments has been little explored. To elucidate the contribution of glacier surface snow-originating taxa to bacterial diversity in downstream aquatic environments, we collected samples from glacier surface snows, downstream streams and lakes along three glacier-fed hydrologic continuums on the Tibetan Plateau. Our results showed that glacier stream acts as recipients and vectors of bacteria originating from the glacier environments. The contributions of glacier surface snow-originating taxa to downstream bacterial communities decrease from the streams to lakes, which was consistently observed in three geographically separated glacier-fed ecosystems. Our results also revealed that some rare snow-originating bacteria can thrive along the hydrologic continuums and become dominant in downstream habitats. Finally, our results indicated that the dispersal patterns of bacterial communities are largely determined by mass effects and increasingly subjected to local sorting of species along the glacier-fed hydrologic continuums. Collectively, this study provides insights into the fate of bacterial assemblages in glacier surface snow following snow melt and how bacterial communities in aquatic environments are affected by the influx of glacier snow-originating bacteria.

Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia

Paradana is one of the biggest ice caves in Slovenia, with an estimated ice volume of 8,000 m³. Reflecting climatological conditions, the cave ice undergoes repeated freeze-thaw cycles and regular yearly deposition of fresh ice. Three distinct ice block samples, collected from the frozen lake in May 2016, were analysed to obtain data on ice physicochemical properties and the composition of associated microbiota. Isotopic composition of the ice samples (¹⁸O, ²H) and a local meteoric water line (LMWL) constructed for monthly precipitation at Postojna were used to estimate the isotopic composition of the water that formed the ice, which had high values of deuterium excess and low concentrations of chloride, sulphate and nitrate. The values of total organic carbon (1.93–3.95 mg/l) within the ice blocks fall within the range of those measured in karst streams. Total cell count in the ice was high and the proportion of cell viability increased along the depth gradient and ranged from 4.67 × 10⁴ to 1.52 × 10⁵ cells/ml and from 51.0 to 85.4%, respectively. Proteobacteria represented the core of the cave-ice microbiome (55.9–79.1%), and probably play an essential role in this ecosystem. Actinobacteria was the second most abundant phylum (12.0–31.4%), followed in abundance by Bacteroidetes (2.8–4.3%). Ice phylotypes recorded amounted to 442 genera, but only 43 genera had abundances greater than 0.5%. Most abundant were Pseudomonas, a well-known ice dweller, and Lysobacter, which previously was not reported in this context. Finally, two xanthophytes, Chloridella glacialis and Ellipsoidion perminimum, known from polar environments, were cultured from the ice. This indicates that the abundance and ecological role of phototrophs in such environments might be greater than previously deduced.

Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy

Purpose

Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).

Methods

Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.

Result

The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.

Conclusion

The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.

Exploration of Microbial Diversity of Himalayan Glacier Moraine Soil Using 16S Amplicon Sequencing and Phospholipid Fatty Acid Analysis Approaches

Changme Khangpu glacier is located in the northern district of Sikkim which comes under UNESCO heritage site Kanchenjunga Biosphere Reserve which is considered as one of the important biological hotspot regions in the Eastern Himalayas. This is the first report on microbial diversity analysis of moraine soil from one of the unexplored glaciers of Sikkim using high throughput sequencing platform and phospholipid fatty acids analysis (PLFA). It was found that the 16S amplicon sequence comprised 362,902 raw sequences with a sequence length of 150 bp and (G + C) content 52%. A total of 156,821 pre-processed reads were clustered into 378 OTUs (operational taxonomic units) comprising 6 bacterial phyla. The top four dominant phyla based on the 16S amplicon sequences were Proteobacteria (56%), Firmicutes (16%), Actinobacteria (12%), and Bacteroidetes (8%), respectively. PLFA analysis confirmed the dominance of Gram positive bacteria (72%) followed by Gram negative bacteria (32%) and the major fatty acids which are present in the moraine soil sample were PUFA (61%), and 18:2ω6,9c (29%). This is the primary study and first of its kind done on moraine soil from glaciers of Sikkim. Based on 16S amplicon sequencing and PLFA analysis of moraine soil samples from glaciers of Sikkim suggest that this glaciers harbours rich microbial diversity and thus can have wide industrial and biotechnological potential. Thus, there is an escalating scope to further study these extreme biomes with respect to their microbial diversity and their functional capabilities.

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard

We assessed the structure of microbial communities in the subglacial drainage system of the Werenskioldbreen glacier, Svalbard, which consists of three independent channels. Dome-shaped naled ice bodies that had been forming and releasing subglacial water in the glacial forefield during accumulations season were used to study glacial microbiome. We tested the hypothesis that the properties of the water transported by these channels are site-dependent and influence bacterial diversity. We therefore established the phylogenetic structure of the subglacial microbial communities using next generation sequencing (NGS) of the 16S rRNA gene and performed bioinformatics analyses. A total of 1409 OTUs (operational taxonomic units) belonged to 40 phyla; mostly Proteobacteria, Gracilibacteria, Bacteroidetes, Actinobacteria and Parcubacteria were identified. Sites located on the edge of Werenskioldbreen forefield (Angell, Kvisla) were mainly dominated by Betaproteobacteria. In the central site (Dusan) domination of Epsilonproteobacteria class was observed. Gracilibacteria (GN02) and Gammaproteobacteria represented the dominant taxa only in the sample Kvisla 2. Principal Coordinate Analysis (PCoA) of beta diversity revealed that phylogenetic profiles grouped in three different clusters according to the sampling site. Moreover, higher similarity of bacterial communities from Angell and Kvisla compared to Dusan was confirmed by cluster analysis and Venn diagrams. The highest alpha index values was measured in Dusan. Richness and phylogenetic diversity indices were significantly (p < .05) and positively correlated with pH values of subglacial water and negatively with concentration of Cl^-, Br^-, and NO₃^- anions. These anions negatively impacted the values of richness indices but positively correlated with abundance of some microbial phyla. Our results indicated that subglacial water from naled ice bodies offer the possibility to study the glacial microbiome. In the studied subglacial water, the microbial community structure was sampling site specific and dependent on the water properties, which in turn were probably influenced by the local bedrock composition.

Over Winter Microbial Processes in a Svalbard Snow Pack: An Experimental Approach

Snow packs cover large expanses of Earth’s land surface, making them integral components of the cryosphere in terms of past climate and atmospheric proxies, surface albedo regulators, insulators for other Arctic environments and habitats for diverse microbial communities such as algae, bacteria and fungi. Yet, most of our current understanding of snow pack environments, specifically microbial activity and community interaction, is limited to the main microbial growing season during spring ablation. At present, little is known about microbial activity and its influence on nutrient cycling during the subfreezing temperatures and 24-h darkness of the polar winter. Here, we examined microbial dynamics in a simulated cold (−5°C), dark snow pack to determine polar winter season microbial activity and its dependence on critical nutrients. Snow collected from Ny-Ålesund, Svalbard was incubated in the dark over a 5-week period with four different nutrient additions, including glacial mineral particles, dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and a combined treatment of DIN plus DIP. Data indicate a consumption of dissolved inorganic nutrients, particularly DIN, by heterotrophic communities, suggesting a potential nitrogen limitation, contradictory to phosphorus limitations found in most aquatic environments. 16S amplicon sequencing also reveal a clear difference in microbial community composition in the particulate mineral treatment compared to dissolved nutrient treatments and controls, suggesting that certain species of heterotrophs living within the snow pack are more likely to associate with particulates. Particulate phosphorus analyses indicate a potential ability of heterotrophic communities to access particulate sources of phosphorous, possibly explaining the lack of phosphorus limitation. These findings have importance for understanding microbial activity during the polar winter season and its potential influences on the abundance and bioavailability of nutrients released to surface ice and downstream environments during the ablation season.

Bacterial community structure of a glacio-marine system in the Arctic (Ny-Ålesund, Svalbard)

The bacterial community composition of a valley glacier in Svalbard, its pro-glacial channels, and the associated downstream fjord ecosystem was investigated so as to figure out the degree to which downslope transport of microbes from the glacier systems along a hydrological continuum impose an effect on the patterns of diversity in the fjord system. A combination of culture based and high-throughput amplicon sequencing approach was followed which resulted in significant variation (R = 0.873, p = 0.001) in the bacterial community structure between these ecosystems. Dominance of sequences belonging to class β-Proteobacteria was seen in the glacier snow, ice and melt waters (MW) while a relatively higher abundance of OTUs belonging to α-Proteobacteria and Verrucomicrobiae demarcated the fjord waters. Similarity percentage (SIMPER) analysis of the Operational Taxonomic Units (OTUs) showed that OTU 1,105,280 (9.15%) and OTU 331 (6.5%) belonging to Burkholderiaceae (β-proteobacteria) and OTU 101,660 (5.76%) and OTU 520 (5.07%) belonging to Rhodobacteraceae (α-proteobacteria) contributed maximum to the overall dissimilarity between the sampling sites. The bacterial community from the MWs were found to be true signatures of the glacier ecosystem while the Kongsfjorden bacterial fraction mostly represented heterotrophic marine taxa influenced by warm Atlantic waters and presence of organic matter. Significant presence of unknown taxa in the MWs suggests the need to study such unexplored, transient niches for a better understanding of the associated microbial processes. Among the various environmental parameters measured, nutrients (NO₃^- and SiO₄^2-) were found to exhibit strong association with the MW bacterial community while temperature, trace metals, Cl^- and SO₄^2- ions were found to influence the fjord bacterial community. The significant differences in the bacterial community composition between the glacier and the fjord ecosystem suggest the unique nature of these systems which in turn is influenced by the associated environmental parameters.

Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria

We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphere continuously onto quartzfiber air filters using a DIGITEL high volume PM10 sampler. The bacterial and fungal communities, sequenced using Illumina MiSeq, as well as the chemical components of the atmosphere were compared to those of a late season snow profile. Results reveal strong dynamics in the composition of bacterial and fungal communities in air and snow. In fall the two compartments were similar, suggesting a strong interaction between them. The overlap diminished as the season progressed due to an evolution within the snowpack throughout winter and spring. Certain bacterial and fungal genera were only detected in air samples, which implies that a distinct air microbiome might exist. These organisms are likely not incorporated in clouds and thus not precipitated or scavenged in snow. Although snow appears to be seeded by the atmosphere, both air and snow showed differing bacterial and fungal communities and chemical composition. Season and alpha diversity were major drivers for microbial variability in snow and air, and only a few chemical markers were identified as important in explaining microbial diversity. Air microbial community variation was more related to chemical markers than snow microbial composition. For air microbial communities Cl^–, TC/OC, SO₄^2–, Mg²⁺, and Fe/Al, all compounds related to dust or anthropogenic activities, were identified as related to bacterial variability while dust related Ca²⁺ was significant in snow. The only common driver for snow and air was SO₄^2–, a tracer for anthropogenic sources. The occurrence of chemical compounds was coupled with boundary layer injections in the free troposphere (FT). Boundary layer injections also caused the observed variations in community composition and chemistry between the two compartments. Long-term monitoring is required for a more valid insight in post-depositional selection in snow.

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.

Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments

Maritime Antarctica has shown the highest increase in temperature in the Southern Hemisphere. Under this scenario, biogeochemical cycles may be altered, resulting in rapid environmental change for Antarctic biota. Microbes that drive biogeochemical cycles often form biofilms or microbial mats in continental meltwater environments. Limnetic microbial mats from the Fildes Peninsula were studied using high-throughput 16S rRNA gene sequencing. Mat samples were collected from 15 meltwater stream sites, comprising a natural gradient from ultraoligotrophic glacier flows to meltwater streams exposed to anthropogenic activities. Our analyses show that microbial community structure differences between mats are explained by environmental NH4+, NO3-, DIN, soluble reactive silicon and conductivity. Microbial mats living under ultraoligotrophic meltwater conditions did not exhibit a dominance of cyanobacterial photoautotrophs, as has been documented for other Antarctic limnetic microbial mats. Instead, ultraoligotrophic mat communities were characterized by the presence of microbes recognized as heterotrophs and photoheterotrophs. This suggests that microbial capabilities for recycling organic matter may be a key factor to dwell in ultra-low nutrient conditions. Our analyses show that phylotype level assemblages exhibit coupled distribution patterns in environmental oligotrophic inland waters. The evaluation of these microbes suggests the relevance of reproductive and structural strategies to pioneer these psychrophilic ultraoligotrophic environments.

Microbial production and consumption of dissolved organic matter in glacial ecosystems on the Tibetan Plateau

Dissolved organic matter (DOM) from alpine glaciers is highly biolabile and plays a vital role in the biogeochemical cycle of meltwater-impacted environments. To unravel the composition and interactions of DOM with the bacterial community in glacier and glacier meltwater, we conducted sampling of two different Tibetan Plateau glaciers and carried out laboratory bio-incubation experiments. The field data revealed that four protein-like components accounted for 86.0 ± 11.9% of the total variability of all six fluorescence components, which suggests a predominantly microbial source of glacial chromophoric DOM (CDOM). The ice and meltwater samples displayed major contributions of molecular formulae associated with lipids and proteins (i.e. high H/C) as revealed by ultrahigh resolution mass spectrometry. Multiple linear regression models revealed that the abundant phyla explain 64.2%, 61.3%, and 65.0% of the variability of microbial and terrestrial humic-like, and protein-like components, respectively. Correlation-based network analysis determined the metabolic niches of the bacterial community members associated with different fluorescence types in biogeochemical processes. Furthermore, laboratory DOM bio-incubation experiments confirmed that sub-components of the CDOM pool differentially participate in bacterial metabolism. We therefore conclude that the bacterial community interacted closely with the compositional variability of DOM in the investigated alpine glacial environments by both producing and consuming of DOM.

Spatial Variability of Antarctic Surface Snow Bacterial Communities

It was once a long-held view that the Antarctic was a pristine environment with low biomass, low biodiversity and low rates of microbial activity. However, as the intensity of scientific investigation has increased, so these views have started to change. In particular, the role and impact of human activity toward indigenous microbial communities has started to come under more intense scrutiny. During the Subglacial Lake Ellsworth exploration campaign in December 2012, a microbiological survey was conducted to determine the extent and likelihood of exogenous input into the subglacial lake system during the hot-water drilling process. Snow was collected from the surface to represent that used for melt water production for hot-water drilling. The results of this study showed that snow used to provide melt water differed in its microbiological composition from that of the surrounding area and raised the question of how the biogeography of snow-borne microorganisms might influence the potential outcome of scientific analyses. In this study, we investigated the biogeography of microorganisms in snow around a series of Antarctic logistic hubs, where human activity was clearly apparent, and from which scientific investigations have been undertaken. A change in microbial community structure with geographical location was apparent and, notably, a decrease in alpha diversity at more remote southern latitudes. Soil-related microorganisms dominated microbial assemblages suggesting terrestrial input, most likely from long-range aeolian transport into continental Antarctica. We also observed that relic DNA was not a major issue when assessing snow samples. Overall, our observations might have profound implications for future scientific activities in Antarctica, such as the need to establish "no-go" protected areas, the need for better characterization of field sites and improved protocols for sterilization and verification of ice drilling equipment.

Environmental characteristics of a tundra river system in Svalbard. Part 1: Bacterial abundance, community structure and nutrient levels

The Arctic hosts a set of unique ecosystems, characterised by extreme environmental conditions and undergoing a rapid change resulting from the average temperature rising. We present a study on an aquatic ecosystem of the Revelva catchment (Spitsbergen), based on samples collected from the lake, river and their tributaries, in the summer of 2016. The landscape variety of the study site and the seasonal change in the hydrological regime modify the availability of nutrients. In general, the upper part of the catchment consists of the mountain rocky slopes which are especially abundant in iron minerals, sulphides and phosphorus minerals. The lower part of the catchment is covered by plants - lichens, saxifrages and bryophytes, which are a different source of nutrients. In the analysed water samples, the maximum concentrations of nutrients such as iron, boron and phosphorus were 0.28 μg L^-1, 4.52 μg L^-1 and 1.91 μg L^-1, respectively, in June, while in September, Fe and B reached the concentrations of 1.32 μg L^-1 and 2.71 μg L^-1, respectively. The concentration of P in September was below the detection limit of 1.00 μg L^-1, which may be explained by the necessity of bacteria to consume it immediately on current needs. We noted also an increase in TOC concentration between the June and September samples, which could originate both from the biomass accumulation in the catchment and the permafrost melting contributing to the hydrological regime of the river. The bacterial community developed in this environment consisted mainly of Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes phylum, while the presence of Acidobacteria was less pronounced than in other tundra-related environments. The described catchment shows that despite the relatively small amount of bioavailable nutrients, the Revelva system is biodiverse and one of the most significant biogeochemical changes occurs there in response to seasonally switching water sources.

Microbial metabolism directly affects trace gases in (sub) polar snowpacks

Concentrations of trace gases trapped in ice are considered to develop uniquely from direct snow/atmosphere interactions at the time of contact. This assumption relies upon limited or no biological, chemical or physical transformations occurring during transition from snow to firn to ice; a process that can take decades to complete. Here, we present the first evidence of environmental alteration due to in situ microbial metabolism of trace gases (methyl halides and dimethyl sulfide) in polar snow. We collected evidence for ongoing microbial metabolism from an Arctic and an Antarctic location during different years. Methyl iodide production in the snowpack decreased significantly after exposure to enhanced UV radiation. Our results also show large variations in the production and consumption of other methyl halides, including methyl bromide and methyl chloride, used in climate interpretations. These results suggest that this long-neglected microbial activity could constitute a potential source of error in climate history interpretations, by introducing a so far unappreciated source of bias in the quantification of atmospheric-derived trace gases trapped within the polar ice caps.

Microbial connectivity and sorting in a High Arctic watershed

Aquatic ecosystems in the High Arctic are facing unprecedented changes as a result of global warming effects on the cryosphere. Snow pack is a central feature of northern landscapes, but the snow microbiome and its microbial connectivity to adjacent and downstream habitats have been little explored. To evaluate these aspects, we sampled along a hydrologic continuum at Ward Hunt Lake (latitude 83°N) in the Canadian High Arctic, from snow banks, water tracks in the permafrost catchment, the upper and lower strata of the lake, and the lake outlet and its coastal marine mixing zone. The microbial communities were analyzed by high-throughput sequencing of 16 and 18S rRNA to determine the composition of potentially active Bacteria, Archaea and microbial Eukarya. Each habitat had distinct microbial assemblages, with highest species richness in the subsurface water tracks that connected the melting snow to the lake. However, up to 30% of phylotypes were shared along the hydrologic continuum, showing that many taxa originating from the snow can remain in the active fraction of downstream microbiomes. The results imply that changes in snowfall associated with climate warming will affect microbial community structure throughout all spatially connected habitats within snow-fed polar ecosystems.

Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants

An updated sul1 gene sequence database was constructed and new degenerate primers were designed to better investigate the abundance, diversity, and variation of a ubiquitous antibiotic resistance gene, sul1, with PCR-based methods in activated sludge from wastewater treatment plants (WWTPs). The newly designed degenerate primers showed high specificity and higher coverage in both in-silico evaluations and activated sludge samples compared to previous sul1 primers. Using the new primers, the abundance and diversity of sul1 gene, together with 16S rRNA gene, in activated sludge from five WWTPs in summer and winter were determined by quantitative PCR and MiSeq sequencing. The sul1 gene was found to be prevalent and displayed a comparable abundance (0.081 copies per bacterial cell in average) to the total bacteria across all samples. However, compared to the significant seasonal and geographical divergences in the quantity and diversity of bacterial communities in WWTPs, there were no significant seasonal or geographical variations of representative clusters of sul1 gene in most cases. Additionally, the representative sul1 clusters showed fairly close phylogeny and there was no obvious correlation between sul1 gene and the dominant bacterial genera, as well as the int1 gene, suggesting that bacterial hosts of sul1 gene is not stable, the sul1 gene may be carried by mobile genetic elements, sometimes integrated with class 1 integrons and sometimes not. Thus mobile genetic elements likely play a greater role than specific microbial taxa in determining the composition of sul1 gene in WWTPs.

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing

Motivation

The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis.

Results

To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models.

Availability and implementation

A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.

Contact

taijo@flatironinstitute.org or rb113@nyu.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica

Cryoconite holes (cylindrical melt-holes on the glacier surface) are important hydrological and biological systems within glacial environments that support diverse microbial communities and biogeochemical processes. This study describes retrievable heterotrophic microbes in cryoconite hole water from three geographically distinct sites in Antarctica, and a Himalayan glacier, along with their potential to degrade organic compounds found in these environments. Microcosm experiments (22 days) show that 13-60% of the dissolved organic carbon in the water within cryoconite holes is bio-available to resident microbes. Biodegradation tests of organic compounds such as lactate, acetate, formate, propionate and oxalate that are present in cryoconite hole water show that microbes have good potential to metabolize the compounds tested. Substrate utilization tests on Biolog Ecoplate show that microbial communities in the Himalayan samples are able to oxidize a diverse array of organic substrates including carbohydrates, carboxylic acids, amino acids, amines/amides and polymers, while Antarctic communities generally utilized complex polymers. In addition, as determined by the extracellular enzyme activities, majority of the microbes (82%, total of 355) isolated in this study (Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Basidiomycota) had ability to degrade a variety of compounds such as proteins, lipids, carbohydrates, cellulose and lignin that are documented to be present within cryoconite holes. Thus, microbial communities have good potential to metabolize organic compounds found in the cryoconite hole environment, thereby influencing the water chemistry in these holes. Moreover, microbes exported downstream during melting and flushing of cryoconite holes may participate in carbon cycling processes in recipient ecosystems.

Organic carbon availability limiting microbial denitrification in the deep vadose zone

Microbes in the deep vadose zone play an essential role in the mitigation of nitrate leaching; however, limited information is available on the mechanisms of microbial denitrification due to sampling difficulties. We experimentally studied the factors that affect denitrification in soils collected down to 10.5 meters deep along the soil profile. After an anoxic pre-incubation, denitrification rates moderately increased and the N₂ O/(N₂ O + N₂ ) ratios declined while the microbial abundance and diversity did not change significantly in most of the layers. Denitrification rate was significantly enhanced and the abundance of the denitrification genes was simultaneously elevated by the increased availability of organic carbon in all studied layers, to a greater extent in the subsurface layers than in the surface layers, suggesting the severe scarcity of carbon in the deep vadose zone. The genera Pseudomonas and Bacillus, which are made up of a number of species that have been previously identified as denitrifiers in soil, were the major taxa that respond to carbon addition. Overall, our results suggested that the limited denitrification in the deep vadose zone is not because of the lack of denitrifiers, but due to the low abundance of denitrifiers which is caused by low carbon availability.

Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture

Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km² of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. We found that Betaproteobacteria dominated bacterial communities, with large abundance of genera Polaromonas, probably thanks to its highly versatile metabolism, and Limnohabitans, which may have been favoured by the presence of supraglacial lakes in the area where cryoconite holes were sampled. Variation in bacterial communities among different sampling areas of the glacier could be explained by divergent selective processes driven by variation in environmental conditions, particularly pH, which was the only environmental variable that significantly affected the structure of bacterial communities. This variability may be due to both temporal and spatial patterns of variation in environmental conditions.

Primary productivity of snow algae communities on stratovolcanoes of the Pacific Northwest

The majority of geomicrobiological research conducted on glacial systems to date has focused on glaciers that override primarily carbonate or granitic bedrock types, with little known of the processes that support microbial life in glacial systems overriding volcanic terrains (e.g., basalt or andesite). To better constrain the role of the supraglacial ecosystems in the carbon and nitrogen cycles, to gain insight into microbiome composition and function in alpine glacial systems overriding volcanic terrains, and to constrain potential elemental sequestration or release through weathering processes associated with snow algae communities, we examined the microbial community structure and primary productivity of snow algae communities on stratovolcanoes in the Cascade Range of the Pacific Northwest. Here, we present the first published values for carbon fixation rates of snow algae communities on glaciers in the Pacific Northwest. We observed varying levels of light-dependent carbon fixation on supraglacial and periglacial snowfields at Mt. Hood, Mt. Adams, and North Sister. Recovery of abundant 18S rRNA transcripts affiliated with photoautotrophs and 16S rRNA transcripts affiliated with heterotrophic bacteria is consistent with previous studies indicating the majority of primary productivity on snow and ice can be attributed to photoautotrophs. In contrast to previous observations of glacial ecosystems, our geochemical, isotopic, and microcosm data suggest these assemblages are not limited by phosphorus or fixed nitrogen availability. Furthermore, our data indicate these snow algae communities actively sequester Fe, Mn, and P leached from minerals sourced from the local rocks. Our observations of light-dependent primary productivity on snow are consistent with similar studies in polar ecosystems; however, our data may suggest that DIC may be a limiting nutrient in contrast to phosphorus or fixed nitrogen as has been observed in other glacial ecosystems. Our data underscore the need for similar studies on glacier surfaces and seasonal snowfields to better constrain the role of local bedrock and nutrient delivery on carbon fixation and biogeochemical cycling in these ecosystems.

Bacterial Community Structures in Freshwater Polar Environments of Svalbard

Two thirds of Svalbard archipelago islands in the High Arctic are permanently covered with glacial ice and snow. Polar bacterial communities in the southern part of Svalbard were characterized using an amplicon sequencing approach. A total of 52,928 pyrosequencing reads were analyzed in order to reveal bacterial community structures in stream and lake surface water samples from the Fuglebekken and Revvatnet basins of southern Svalbard. Depending on the samples examined, bacterial communities at a higher taxonomic level mainly consisted either of Bacteroidetes, Betaproteobacteria, and Microgenomates (OP11) or Planctomycetes, Betaproteobacteria, and Bacteroidetes members, whereas a population of Microgenomates was prominent in 2 samples. At the lower taxonomic level, bacterial communities mostly comprised Microgenomates, Comamonadaceae, Flavobacteriaceae, Legionellales, SM2F11, Parcubacteria (OD1), and TM7 members at different proportions in each sample. The abundance of OTUs shared in common among samples was greater than 70%, with the exception of samples in which the proliferation of Planctomycetaceae, Phycisphaeraceae, and Candidatus Methylacidiphilum spp. lowered their relative abundance. A multi-variable analysis indicated that As, Pb, and Sb were the main environmental factors influencing bacterial profiles. We concluded that the bacterial communities in the polar aquatic ecosystems examined mainly consisted of freshwater and marine microorganisms involved in detritus mineralization, with a high proportion of zooplankton-associated taxa also being identified.

Linking microbial diversity and functionality of arctic glacial surface habitats

Distinct microbial habitats on glacial surfaces are dominated by snow and ice algae, which are the critical players and the dominant primary colonisers and net producers during the melt season. Here for the first time we have evaluated the role of these algae in association with the full microbial community composition (i.e., algae, bacteria, archaea) in distinct surface habitats and on 12 glaciers and permanent snow fields in Svalbard and Arctic Sweden. We cross-correlated these data with the analyses of specific metabolites such as fatty acids and pigments, and a full suite of potential critical physico-chemical parameters including major and minor nutrients, and trace metals. It has been shown that correlations between single algal species, metabolites, and specific geochemical parameters can be used to unravel mixed metabolic signals in complex communities, further assign them to single species and infer their functionality. The data also clearly show that the production of metabolites in snow and ice algae is driven mainly by nitrogen and less so by phosphorus limitation. This is especially important for the synthesis of secondary carotenoids, which cause a darkening of glacial surfaces leading to a decrease in surface albedo and eventually higher melting rates.

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier

Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub- and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N.

The biogeography of red snow microbiomes and their role in melting arctic glaciers

The Arctic is melting at an unprecedented rate and key drivers are changes in snow and ice albedo. Here we show that red snow, a common algal habitat blooming after the onset of melting, plays a crucial role in decreasing albedo. Our data reveal that red pigmented snow algae are cosmopolitan as well as independent of location-specific geochemical and mineralogical factors. The patterns for snow algal diversity, pigmentation and, consequently albedo, are ubiquitous across the Arctic and the reduction in albedo accelerates snow melt and increases the time and area of exposed bare ice. We estimated that the overall decrease in snow albedo by red pigmented snow algal blooms over the course of one melt season can be 13%. This will invariably result in higher melt rates. We argue that such a ‘bio-albedo' effect has to be considered in climate models.

The Arctic is melting at an unprecedented rate and key drivers are changes in snow and ice albedo. Here, the authors show that red pigmented snow algae play a crucial role in decreasing surface albedo and their patterns for diversity, pigmentation, and consequently albedo, are ubiquitous across the Arctic.

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.

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps

Seasonally, snow environments cover up to 50% of the land's surface, yet the microbial diversity and ecosystem functioning within snow, particularly from alpine regions are not well described. This study explores the bacterial diversity in snow using next-generation sequencing technology. Our data expand the global inventory of snow microbiomes by focusing on two understudied regions, the Swiss Alps and the Australian Alps. A total biomass similar to cell numbers in polar snow was detected, with 5.2 to 10.5 × 10(3) cells mL(-1) of snow. We found that microbial community structure of surface snow varied by country and site and along the altitudinal range (alpine and sub-alpine). The bacterial communities present were diverse, spanning 25 distinct phyla, but the six phyla Proteobacteria (Alpha- and Betaproteobacteria), Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes, accounted for 72%-98% of the total relative abundance. Taxa such as Acidobacteriaceae and Methylocystaceae, associated with cold soils, may be part of the atmospherically sourced snow community, while families like Sphingomonadaceae were detected in every snow sample and are likely part of the common snow biome.

Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow

The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic

Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7)  cells ml(-1) (mean 3.12 × 10(6)  cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research.

Snow and ice ecosystems: not so extreme

Snow and ice environments cover up to 21% of the Earth's surface. They have been regarded as extreme environments because of their low temperatures, high UV irradiation, low nutrients and low water availability, and thus, their microbial activity has not been considered relevant from a global microbial ecology viewpoint. In this review, we focus on why snow and ice habitats might not be extreme from a microbiological perspective. Microorganisms interact closely with the abiotic conditions imposed by snow and ice habitats by having diverse adaptations, that include genetic resistance mechanisms, to different types of stresses in addition to inhabiting various niches where these potential stresses might be reduced. The microbial communities inhabiting snow and ice are not only abundant and taxonomically diverse, but complex in terms of their interactions. Altogether, snow and ice seem to be true ecosystems with a role in global biogeochemical cycles that has likely been underestimated. Future work should expand past resistance studies to understanding the function of these ecosystems.