Accelerated glacial retreat in Greenland drives increased development of glacial outwash plains. These newly exposed landscapes provide an opportunity to study microbial dynamics during soil development. We explore soil microbial diversity, community assembly, and biogeochemical cycling across the Kiattuut Sermiat glacial chronosequence (southern Greenland) via 16S rRNA gene amplicon analysis paired with microbial abundance, soil physicochemical parameters, and gas flux data. Microbial diversity varied with soil depth, with more acidic topsoils abundant in Cyanobacteriota and Armatimonadota taxa. While aerobic lower soils likely contained relatively more anoxic pore spaces, hosting aerobic nitrifiers such as Nitrospirota, low-oxygen-associated Planctomycetota taxa, and less characterized Gemmatimonadota. Microbial diversity varied across the chronosequence following distance-decay principles, as communities were predominately dispersal limited and shaped by heterogeneous selection, with greater heterogeneous conditions further from the glacier terminus. Soil CO2 fluxes increased with distance from the glacier, following a shift from autotrophic sulfur- and iron-oxidizing taxa towards heterotrophic members. CH4 fluxes demonstrated greater uptake further from the glacier, and CH4-oxidation was associated with the methanotroph Methylocapsa. Considering the climatic relevancy of Greenlandic proglacial environments, we describe the largely unexplored microbial diversity and biogeochemical cycling of greenhouse gases in these developing soils.

Background Alpine permafrost-affected soils, particularly in the European Alps, remain poorly understood despite rapid warming and projected vegetation increase at higher elevations. We investigated how vegetation cover and physicochemical soil properties structure microbial communities across ten high-altitude alpine permafrost-affected sites. Results Soil parameters (pH, soil water content, temperature, and total C and N contents) varied significantly between sites and revealed pH and C:N ratio as key drivers modulated by vegetation cover, highlighting its indirect role in shaping soil environments. Microbial community composition differed significantly across sites, and functional gene profiles mirrored taxonomic patterns, indicating strong coupling between community structure and functional gene potential, without functional redundancy. Microbial abundance increased with vegetation cover, whereas taxonomic and functional gene diversity plateaued at intermediate vegetation cover, suggesting that the presence of vegetation primarily enhances microbial abundance rather than diversity. Genome-resolved metagenomics revealed a shift from generalist-dominated communities in barren soils to increased prevalence of specialist taxa in vegetated soils. Functional gene abundances, particularly for C cycling, were higher in vegetated soils, while N and S cycling gene potentials were associated with soil temperature and water content. A microcosm experiment measuring ex situ CO₂ and CH₄ fluxes from incubated summer soils, identified vegetated soils as modest CO₂ sources. Vegetated soils exhibited lower, pH and C:N ratio, shaping a more abundant microbial community with more specialist members and higher C cycling gene potential. Conclusion Overall, our findings indicate that alpine greening reshapes microbial communities via vegetation-mediated changes in soil properties, with implications for biogeochemical cycling and C emissions under climate warming.

Glacier-fed streams (GFSs) are harsh environments hosting unique, highly specialized communities. Interestingly, glaciers and their GFSs are also present in Earth's tropical regions, where environmental characteristics contrast with GFS conditions elsewhere. Yet, despite the unique and isolated nature of tropical GFSs, little is known about their inhabitants, even though they may disappear later this century with ongoing climate change. Here, we examined diatom communities from one of the last tropical African GFSs in the Rwenzori Mountains, Uganda, to characterize the composition and diversity of this unique system. Six sediment-associated biofilm samples were collected from two reaches of a stream draining the Mt. Stanley Glacier, and the resident diatom communities were studied morphologically using light and scanning electron microscopy, as well as through the sequencing of amplicons from extracted DNA (18S and rbcL). In general, morphological results agree well with barcoding results, but each individually provides irreplaceable insights. In total, we identify 24 morphotypes utilizing light microscopy, 101 diatom Amplicon Sequence Variants (ASVs) using 18S sequences, and 65 ASVs with rbcL. Across approaches, common genera include Achnanthidium, Psammothidium, Neidium, Cymbopleura, Eunotia, and Pinnularia. However, only about half of the diversity could be assigned to the species level across methodologies, including several of the most common taxa, indicating a high level of uniqueness. Accordingly, one of the most common taxa encountered is described here as a new species, Neidium rwenzoriense sp. nov. Our results emphasize the Rwenzori Mountains as a global hotspot for endemism, and the novelty of disappearing tropical GFSs as diatom habitats.

The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.

The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth’s major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem. Leveraging metabarcoding and metagenomics, a survey of bacteria in the benthic microbiome across 152 glacier-fed streams (GFSs) provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

Glacier-fed streams (GFS) feature among Earth’s most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change. Thousands of metagenome-assembled genomes from the Vanishing Glaciers project showcase the interactions between prokaryotes, algae, fungi and viruses in glacier-fed stream environments.

The factors and processes that shape microbial genomes and determine the success of microbes in different environments have long attracted scientific interest. Here, leveraging 2855 metagenome-assembled genomes sampled by the Vanishing Glacier Project from glacier-fed streams (GFSs), we shed light on the genomic architecture of the benthic microbiome in these harsh ecosystems-now vanishing because of climate change. Owing to glacial influence, the GFS benthic habitat is unstable, notoriously cold, and ultra-oligotrophic. Along gradients of glacial influence and concomitant variation in benthic algal biomass across 149 GFSs draining Earth's major mountain ranges, we show how genomes of GFS bacteria vary in terms of size, coding density, gene redundancy, and translational machinery. We develop a novel, phylogeny-rooted analytical framework that allows pinpointing the phylogenetic depth at which patterns in genomic trends occur. These analyses reveal both deep- and shallow-rooting phylogenetic patterns in genomic features associated with key GFS taxa and functional potential relevant to live in these ecosystems. Additionally, we highlight the role of several clades of Gammaproteobacteria in shaping community-level genomic architecture. Our work shows how genome architecture is shaped by selective environmental constraints in an extreme environment. These insights are important as they reveal putatively important adaptations to the GFS environment which is now changing at rapid pace due to climate change.

Cross-domain interactions are an integral part of the success of biofilms in natural environments but remain poorly understood. Here, we describe cross-domain interactions in stream biofilms draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterised by multiple environmental gradients and perturbations (e.g., changes in channel geomorphology, discharge) that depend on the time since deglaciation. We evaluate co-occurrence of bacteria and eukaryotic communities along streams and show that key community members have disproportionate effects on the stability of community networks. The topology of the networks, here quantified as the arrangement of the constituent nodes formed by specific taxa, was independent of stream type and their apparent environmental stability. However, network stability against fragmentation was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that bacteria, eukaryotic photoautotrophs, and fungi are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. Key taxa are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.

Cross-domain interactions are an integral part of the success of biofilms in natural environments but remain poorly understood. Here, we describe cross-domain interactions in stream biofilms draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterised by multiple environmental gradients and perturbations (e.g., changes in channel geomorphology, discharge) that depend on the time since deglaciation. We evaluate co-occurrence of bacteria and eukaryotic communities along streams and show that key community members have disproportionate effects on the stability of community networks. The topology of the networks, here quantified as the arrangement of the constituent nodes formed by specific taxa, was independent of stream type and their apparent environmental stability. However, network stability against fragmentation was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that bacteria, eukaryotic photoautotrophs, and fungi are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. Key taxa are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.

Most cryospheric ecosystems are energy limited. How their energetics will respond to climate change remains largely unknown. This is particularly true for glacier-fed streams, which interface with the cryosphere and initiate some of Earth’s largest river systems. Here, by studying resource stoichiometry and microbial energetics in 154 glacier-fed streams sampled by the Vanishing Glaciers project across Earth’s major mountain ranges, we show that these ecosystems and their benthic microbiome are overall carbon and phosphorus limited. Threshold elemental ratios and low carbon use efficiencies (median: 0.15) modelled from extracellular enzymatic activities corroborate resource limitation in agreement with maintenance metabolism of benthic microorganisms. Space-for-time substitution analyses suggest that glacier shrinkage will stimulate benthic primary production in glacier-fed streams, thereby relieving microbial metabolism from carbon limitation. Concomitantly, we find that increasing streamwater temperature will probably stimulate microbial growth (temperature sensitivity: 0.62 eV). Consequently, elevated microbial demands for phosphorus, but diminishing inputs from subglacial sources, may intensify phosphorus limitation as glaciers shrink. Our study thus unveils a ‘green transition’ towards autotrophy in the world’s glacier-fed streams, entailing shifts in the energetics of their microorganisms.

Abstract Mountain and polar glaciers are melting worldwide. However, the downstream impacts of this unprecedented environmental change on elemental fluxes and microbial energetics in the glacier-fed streams (GFS) remains poorly understood at a global scale. This contrasts the relevance of GFSs in initiating the flow of some of the world’s largest river networks and providing clean water to large human populations. Here, by studying resource stoichiometry in 154 GFSs from Earth’s major mountain ranges, we show that these ecosystems are potentially carbon (C) and phosphorus (P) limited, where P limitation may become exacerbated and C limitation alleviated as glaciers shrink. Modeling threshold elemental ratios from extracellular enzymatic activities, we show that the microbial metabolism in GFSs is indeed C and P limited. This is consistent with low microbial carbon use efficiencies (CUE; median: 0.15) indicative of maintenance metabolism. Using space-for-time substitution approaches, we found increasing biomass of benthic primary producers potentially relieving the microbial metabolism from resource limitation as glaciers shrink. Furthermore, increasing streamwater temperature will stimulate microbial growth (temperature sensitivity: 0.62 electronvolts) in GFSs. Our study unveils responses of the microbial energetics to a greening and warming GFS environment, shifting ecosystem metabolism to autotrophy with consequences for related ecosystem C cycling.

The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.

Abstract Nearly 60% of the world’s glaciers are predicted to be lost by the end of the century because of global warming1. The impacts of this environmental change on the glacier-fed stream (GFS) ecosystems are profound, putting their ecological communities at risk2–4. Life in GFSs is dominated by benthic microbial biofilms, which regulate key ecosystem processes and form the basis of the food web5 . However, the biodiversity and biogeography of the biofilm microbiome of the world’s GFSs remain unknown, precluding a mechanistic understanding of its responses to glacier shrinkage. Here, applying metabarcoding to the benthic biofilm bacteria from 148 GFSs draining the world’s major mountain ranges, we unveil their global biodiversity and biogeography. We find that the global GFS benthic microbiome differs from other cryospheric microbiomes and is unexpectedly diverse. A large microbiome fraction (58% of the total amplicon sequence variants) is endemic to single mountain ranges, while 0.4% are disproportionately abundant and form a cosmopolitan core. These microbiome components have overlapping taxonomies, but their compositional turnover is differently shaped by dispersal limitation and environmental selection. Phylogenetic analyses relate prevalent clades to endemicity and microdiversity, the latter potentially buffering the GFS microbiome against climate-change impacts. Our global survey provides the basis for future climate-change microbiology studies6 on a rapidly changing ecosystem.

Abstract Mountain and polar glaciers are melting worldwide. However, the downstream impacts of this unprecedented environmental change on elemental fluxes and microbial energetics in the glacier-fed streams (GFS) remains poorly understood at a global scale. This contrasts the relevance of GFSs in initiating the flow of some of the world’s largest river networks and providing clean water to large human populations. Here, by studying resource stoichiometry in 154 GFSs from Earth’s major mountain ranges, we show that these ecosystems are potentially carbon (C) and phosphorus (P) limited, where P limitation may become exacerbated and C limitation alleviated as glaciers shrink. Modeling threshold elemental ratios from extracellular enzymatic activities, we show that the microbial metabolism in GFSs is indeed C and P limited. This is consistent with low microbial carbon use efficiencies (CUE; median: 0.15) indicative of maintenance metabolism. Using space-for-time substitution approaches, we found increasing biomass of benthic primary producers potentially relieving the microbial metabolism from resource limitation as glaciers shrink. Furthermore, increasing streamwater temperature will stimulate microbial growth (temperature sensitivity: 0.62 electronvolts) in GFSs. Our study unveils responses of the microbial energetics to a greening and warming GFS environment, shifting ecosystem metabolism to autotrophy with consequences for related ecosystem C cycling.

<p> </p><p>Glacier-fed streams (GFSs) serve as headwaters to many of the world’s largest river networks. Although being characterized by extreme environmental conditions (i.e., low water temperatures, oligotrophy) GFSs host an underappreciated microbial biodiversity, especially within benthic biofilms which play pivotal roles in downstream biogeochemical cycles. Yet, we still lack a global overview of the GFS biofilm microbiome. In addition, little is known on how environmental conditions shape bacterial diversity, and how these relationships drive global distribution patterns. This is particularly important as mountain glaciers are currently vanishing at a rapid pace due to global warming. Here, we used 16S rRNA gene sequencing data from the Vanishing Glaciers project to conduct a first comprehensive analysis of the benthic microbiome from 148 GFSs across 11 mountain ranges. Our analyses revealed marked biogeographic patterns in the GFS microbiome, mainly driven by the replacement of phylogenetically closely related taxa. Strikingly, the GFS microbiome was characterized by pronounced level of endemism, with >58% of the Amplicon Sequence Variants (ASVs) being specific to one mountain range. Consistent with the marked dissimilarities across mountain ranges, we found a very small taxonomic core including only 200 ASVs, yet accounting for >25% of the total relative abundance of the ASVs. Finally, we found that spatial effects such as dispersal limitation, isolation and spatially autocorrelated environmental conditions overwhelmed the effect of the environment by itself on benthic biofilm beta diversity. Our findings shed light on the previously unresolved global diversity and biogeography of the GFS microbiome now at risk across the world’s major mountain ranges because of rapidly shrinking glaciers.</p>

Glaciers are receding worldwide because of climate change, and as a consequence, glacier-fed streams are expected to undergo deep physical and chemical changes in the future, potentially inducing dramatic ecological shifts. At the base of glacier-fed stream ecosystems are bacteria, which, along with eukaryotic algae, form biofilms that drive biogeochemical transformations and fluxes of global relevance. Despite this importance, relatively little is known about the glacier-fed stream microbiome and even less on how it may be affected by climate change. The Vanishing Glaciers Project offers a novel and powerful opportunity to investigate this idea, with 16S rRNA amplicon data, shotgun metagenome sequencing, and physicochemical parameters assessed for glacier-fed streams distributed globally. Here, using data from 161 of the sampled streams, combined with glaciological modelling, we examined a) how the environmental template of these ecosystems will change according to several scenarios of climate change; b) how these changes will alter species distributions for the most prevalent bacterial community members; and c) how the ecological properties of abundant taxa vary along the gradient of glacier influence. We predict, that glacier-fed streams will undergo a process analogous to the “greening” of terrestrial alpine ecosystems, as benthic algal abundance is forecasted to significantly increase. Models based on 16s rRNA amplicon data predict the total bacterial abundance to greatly expand, but differences across taxa reveal unique responses to the modelled environmental changes. Corroborative evidence for shifts in bacterial communities along the gradient of glacier influence was found using metagenome assembled genomes, where we identified genomic features putatively adaptive to cryospheric conditions. Within these changes in taxa abundance, we highlight the shifting role of specialists within the community. Overall, this work sheds light on how bacteria adapt to the extreme environmental conditions of glacier-fed streams, and how climate change will impact these unique communities.

Glaciers are receding at an unprecedented rate with expected losses of up to half their masses by 2100. Such changes will profoundly effect the physicochemical characteristics of glacier-fed stream (GFS) water, such as the composition of organic matter, turbidity, conductivity, and patterns in discharge. Hence, direct effects are anticipated for the microbial communities and assemblages inhabiting these environments. High-elevation tropical glaciers are already responding to these enhanced changes (e.g. temperature) and thus are a proxy to study the ecology of GFSs in the future. Here, we sampled and studied the Mt Stanley glacier in Africa’s ‘Mountains of the Moon’ (Rwenzori National Park, Uganda). We showed that the benthic microbiome from this GFS is distinct at several levels from other GFSs worldwide. Specifically, several novel taxa were present, and usually, common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while >80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.

Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown.

Streams draining proglacial floodplains harbor benthic biofilms comprised of diverse microbial communities. These high-mountain ecosystems are rapidly changing with climate warming, and it is therefore critical to better understand the mechanisms underlying the assembly of their microbial communities.