Treeline displacement may affect lake dissolved organic matter processing at high latitudes and altitudes.

Climate change induced shifts in treeline position, both towards higher altitudes and latitudes induce changes in soil organic matter. Eventually, soil organic matter is transported to alpine and subarctic lakes with yet unknown consequences for dissolved organic matter (DOM) diversity and processing. Here, we experimentally investigate the consequences of treeline shifts by amending subarctic and temperate alpine lake water with soil-derived DOM from above and below the treeline. We use ultra-high resolution mass spectrometry (FT-ICR MS) to track molecular DOM diversity (i.e., chemodiversity), estimate DOM decay and measure bacterial growth efficiency. In both lakes, soil-derived DOM from below the treeline increases lake DOM chemodiversity mainly through the enrichment with polyphenolic and highly unsaturated compounds. These compositional changes are associated with reductions in bulk and compound-level DOM reactivity and reduced bacterial growth efficiency. Our results suggest that treeline advancement has the potential to enrich a large number of lake ecosystems with less biodegradable DOM, affecting bacterial community function and potentially altering the biogeochemical cycling of carbon in lakes at high latitudes and altitudes.

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances.

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The functional stability of these communities is critically important for maintaining water quality, productivity, and ecosystem services, such as fishery yields. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. However, little is known about the mechanisms that select these traits under varying nutrient regimes. To study the impact of pulsed disturbances on community assembly and functioning depending on metabolic costs, we performed a 41-day pulse disturbance experiment across two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability-dependent patterns of superordinate community functioning and structural patterns, such as functional resistance in response to disturbances, genomic trait distributions, and species diversity. Predicted genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings are a step toward unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience, and this has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change. IMPORTANCE: Understanding the communities' responses to disturbances is a prerequisite to predicting ecosystem dynamics and, thus, highly relevant considering global change. Microbial communities play key roles in numerous ecosystem functions and services, and the large diversity, rapid growth, and phenotypic plasticity of microorganisms are thought to allow high resistance and resilience. While potential metabolic costs associated with adaptations to fluctuating environments have been debated, little evidence supports trade-offs between resource availability, resistance, and resilience. Here, we experimentally assessed the compositional and functional responses of an aquatic microbial model community to disturbances and systematically manipulated resource availability. Our results demonstrate that the capacity to tolerate environmental fluctuations is constrained by resource availability and reflected in the selection of genomic traits.

The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.

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.

Homogeneous Environmental Selection Structures the Bacterial Communities of Benthic Biofilms in Proglacial Floodplain Streams.

In proglacial floodplains, glacier recession promotes biogeochemical and ecological gradients across relatively small spatial scales. The resulting environmental heterogeneity induces remarkable microbial biodiversity among proglacial stream biofilms. Yet the relative importance of environmental constraints in forming biofilm communities remains largely unknown. Extreme environmental conditions in proglacial streams may lead to the homogenizing selection of biofilm-forming microorganisms. However, environmental differences between proglacial streams may impose different selective forces, resulting in nested, spatially structured assembly processes. Here, we investigated bacterial community assembly processes by unraveling ecologically successful phylogenetic clades in two stream types (glacier-fed mainstems and non-glacier-fed tributaries) draining three proglacial floodplains in the Swiss Alps. Clades with low phylogenetic turnover rates were present in all stream types, including Gammaproteobacteria and Alphaproteobacteria, while the other clades were specific to one stream type. These clades constituted up to 34.8% and 31.1% of the community diversity and up to 61.3% and 50.9% of the relative abundances in mainstems and tributaries, respectively, highlighting their importance and success in these communities. Furthermore, the proportion of bacteria under homogeneous selection was inversely related to the abundance of photoautotrophs, and these clades may therefore decrease in abundance with the future "greening" of proglacial habitats. Finally, we found little effect of physical distance from the glacier on clades under selection in glacier-fed streams, probably due to the high hydrological connectivity of our study reaches. Overall, these findings shed new light on the mechanisms of microbial biofilm assembly in proglacial streams and help us to predict their future in a rapidly changing environment. IMPORTANCE 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. We found that homogeneous selection dominates the structuring of bacterial communities in benthic biofilms in both glacier-fed mainstems and nonglacier tributary streams within three proglacial floodplains in the Swiss Alps. However, differences between glacier-fed and tributary ecosystems may impose differential selective forces. Here, we uncovered nested, spatially structured assembly processes for proglacial floodplain communities. Our analyses additionally provided insights into linkages between aquatic photoautotrophs and the bacterial taxa under homogeneous selection, potentially by providing a labile source of carbon in these otherwise carbon-deprived systems. In the future, we expect a shift in the bacterial communities under homogeneous selection in glacier-fed streams as primary production becomes more important and streams become "greener".

Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters.

Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE 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. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.

Spatial patterns of benthic biofilm diversity among streams draining proglacial floodplains.

Glacier shrinkage opens new proglacial terrain with pronounced environmental gradients along longitudinal and lateral chronosequences. Despite the environmental harshness of the streams that drain glacier forelands, their benthic biofilms can harbor astonishing biodiversity spanning all domains of life. Here, we studied the spatial dynamics of prokaryotic and eukaryotic photoautotroph diversity within braided glacier-fed streams and tributaries draining lateral terraces predominantly fed by groundwater and snowmelt across three proglacial floodplains in the Swiss Alps. Along the lateral chronosequence, we found that benthic biofilms in tributaries develop higher biomass than those in glacier-fed streams, and that their respective diversity and community composition differed markedly. We also found spatial turnover of bacterial communities in the glacier-fed streams along the longitudinal chronosequence. These patterns along the two chronosequences seem unexpected given the close spatial proximity and connectivity of the various streams, suggesting environmental filtering as an underlying mechanism. Furthermore, our results suggest that photoautotrophic communities shape bacterial communities across the various streams, which is understandable given that algae are the major source of organic matter in proglacial streams. Overall, our findings shed new light on benthic biofilms in proglacial streams now changing at rapid pace owing to climate-induced glacier shrinkage.

The microbiome of cryospheric ecosystems.

The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.

Benthic Biofilms in Glacier-Fed Streams from Scandinavia to the Himalayas Host Distinct Bacterial Communities Compared with the Streamwater.

Microbial life in glacier-fed streams (GFSs) is dominated by benthic biofilms which fulfill critical ecosystem processes. However, it remains unclear how the bacterial communities of these biofilms assemble in stream ecosystems characterized by rapid turnover of benthic habitats and high suspended sediment loads. Using16S rRNA gene amplicon sequence data collected from 54 GFSs across the Himalayas, European Alps, and Scandinavian Mountains, we found that benthic biofilms harbor bacterial communities that are distinct from the bacterial assemblages suspended in the streamwater. Our data showed a decrease in species richness in the benthic biofilms compared to the bacterial cells putatively free-living in the water. The benthic biofilms also differed from the suspended water fractions in terms of community composition. Differential abundance analyses highlighted bacterial families that were specific to the benthic biofilms and the suspended assemblages. Notably, source-sink models suggested that the benthic biofilm communities are not simply a subset of the suspended assemblages. Rather, we found evidence that deterministic processes (e.g., species sorting) shape the benthic biofilm communities. This is unexpected given the high vertical mixing of water and contained bacterial cells in GFSs and further highlights the benthic biofilm mode of life as one that is determined through niche-related processes. Our findings therefore reveal a "native" benthic biofilm community in an ecosystem that is currently threatened by climate-induced glacier shrinkage. IMPORTANCE Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble. Our findings from glacier-fed streams from three major mountain ranges across the Himalayas, the European Alps and the Scandinavian Mountains reveal a bacterial community associated with benthic biofilms that is distinct from the assemblage in the overlying streamwater. Our analyses suggest that selection is the underlying process to this differentiation. This is unexpected given that bacterial cells that are freely living or attached to the abundant sediment particles suspended in the water continuously mix with the benthic biofilms. The latter colonize loose sediments that are subject to high turnover owing to the forces of the water flow. Our research unravels the existence of a microbiome specific to benthic biofilms in glacier-fed streams, now under major threats due to global warming.

Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams.

In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.

Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.

The shrinking of glaciers is among the most iconic consequences of climate change. Despite this, the downstream consequences for ecosystem processes and related microbiome structure and function remain poorly understood. Here, using a space-for-time substitution approach across 101 glacier-fed streams (GFSs) from six major regions worldwide, we investigated how glacier shrinkage is likely to impact the organic matter (OM) decomposition rates of benthic biofilms. To do this, we measured the activities of five common extracellular enzymes and estimated decomposition rates by using enzyme allocation equations based on stoichiometry. We found decomposition rates to average 0.0129 (% d-1 ), and that decreases in glacier influence (estimated by percent glacier catchment coverage, turbidity, and a glacier index) accelerates decomposition rates. To explore mechanisms behind these relationships, we further compared decomposition rates with biofilm and stream water characteristics. We found that chlorophyll-a, temperature, and stream water N:P together explained 61% of the variability in decomposition. Algal biomass, which is also increasing with glacier shrinkage, showed a particularly strong relationship with decomposition, likely indicating their importance in contributing labile organic compounds to these carbon-poor habitats. We also found high relative abundances of chytrid fungi in GFS sediments, which putatively parasitize these algae, promoting decomposition through a fungal shunt. Exploring the biofilm microbiome, we then sought to identify bacterial phylogenetic clades significantly associated with decomposition, and found numerous positively (e.g., Saprospiraceae) and negatively (e.g., Nitrospira) related clades. Lastly, using metagenomics, we found evidence of different bacterial classes possessing different proportions of EEA-encoding genes, potentially informing some of the microbial associations with decomposition rates. Our results, therefore, present new mechanistic insights into OM decomposition in GFSs by demonstrating that an algal-based "green food web" is likely to increase in importance in the future and will promote important biogeochemical shifts in these streams as glaciers vanish.

Biophysical properties at patch scale shape the metabolism of biofilm landscapes.

Phototrophic biofilms form complex spatial patterns in streams and rivers, yet, how community patchiness, structure and function are coupled and contribute to larger-scale metabolism remains unkown. Here, we combined optical coherence tomography with automated O2 microprofiling and amplicon sequencing in a flume experiment to show how distinct community patches interact with the hydraulic environment and how this affects the internal distribution of oxygen. We used numerical simulations to derive rates of community photosynthetic activity and respiration at the patch scale and use the obtained parameter to upscale from individual patches to the larger biofilm landscape. Our biofilm landscape approach revealed evidence of parallels in the structure-function coupling between phototrophic biofilms and their streambed habitat.

Viral diversity is linked to bacterial community composition in alpine stream biofilms.

Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied the spatiotemporal turnover of dsDNA viruses associated with stream biofilms and found an astounding diversity to be structured by seasons and along the longitudinal gradient in the stream. While some vOTUs were region- or season-specific, we also identified a large group of permanent biofilm phages, taxonomically dominated by Myoviridae. Comparison of the observed viral distribution with predictions based on neutral community assembly indicated that chance and dispersal may be important for structuring stream biofilm viral communities. Deviation from neutral model predictions suggests that certain phages distribute efficiently across distant locations within the stream network. This dispersal capacity appears to be linked to EPS depolymerases that enable phages to efficiently overcome the biofilm barrier. Other phages, particularly vOTUs classified as Siphoviridae, appear locally overrepresented and to rely on a lysogenic life cycle, potentially to exploit the spatial distribution of bacterial populations in stream biofilms. Overall, biofilm viral and bacterial community turnover were significantly coupled. Yet, viral communities were linked to the presence of the most abundant bacterial community members. With this work, we provide a foundational ecological perspective on factors that structure viral diversity in stream biofilms and identify potentially important viral traits related to the biofilm mode of life.

Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome.

Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, "phyloscore analysis", to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.

Controlling the calcium carbonate microstructure of engineered living building materials.

The fabrication of responsive soft materials that enable the controlled release of microbial induced calcium carbonate (CaCO3) precipitation (MICP) would be highly desirable for the creation of living materials that can be used, for example, as self-healing construction materials. To obtain a tight control over the mechanical properties of these materials, needed for civil engineering applications, the amount, location, and structure of the forming minerals must be precisely tuned; this requires good control over the dynamic functionality of bacteria. Despite recent advances in the self-healing of concrete cracks and the understanding of the role of synthesis conditions on the CaCO3 polymorphic regulation, the degree of control over the CaCO3 remains insufficient to meet these requirements. We demonstrate that the amount and location of CaCO3 produced within a matrix, can be controlled through the concentration and location of bacteria; these parameters can be precisely tuned if bacteria are encapsulated, as we demonstrate with the soil-dwelling bacterium Sporosarcina pasteurii that is deposited within biocompatible alginate and carboxymethyl cellulose (CMC) hydrogels. Using a competitive ligand exchange mechanism that relies on the presence of yeast extract, we control the timing of the release of calcium ions that crosslink the alginate or CMC without compromising bacterial viability. With this novel use of hydrogel encapsulation of bacteria for on-demand release of MICP, we achieve control over the amount and structure of CaCO3-based composites and demonstrate that S. pasteurii can be stored for up to 3 months at an accessible storage temperature of 4 °C, which are two important factors that currently limit the applicability of MICP for the reinforcement of construction materials. These composites thus have the potential to sense, respond, and heal without the need for external intervention.

Morphogenesis and oxygen dynamics in phototrophic biofilms growing across a gradient of hydraulic conditions.

Biofilms are surface-attached and matrix-enclosed microbial communities that dominate microbial life in numerous ecosystems. Using flumes and automated optical coherence tomography, we studied the morphogenesis of phototrophic biofilms along a gradient of hydraulic conditions. Compact and coalescent biofilms formed under elevated bed shear stress, whereas protruding clusters separated by troughs formed under reduced shear stress. This morphological differentiation did not linearly follow the hydraulic gradient, but a break point emerged around a shear stress of ~0.08 Pa. While community composition did not differ between high and low shear environments, our results suggest that the morphological differentiation was linked to biomass displacement and reciprocal interactions between the biofilm structure and hydraulics. Mapping oxygen concentrations within and around biofilm structures, we provide empirical evidence for biofilm-induced alterations of oxygen mass transfer. Our findings suggest that architectural plasticity, efficient mass transfer, and resistance to shear stress contribute to the success of phototrophic biofilms.

Combining Fluidic Devices with Microscopy and Flow Cytometry to Study Microbial Transport in Porous Media Across Spatial Scales.

Understanding the transport, dispersion and deposition of microorganisms in porous media is a complex scientific task comprising topics as diverse as hydrodynamics, ecology and environmental engineering. Modeling bacterial transport in porous environments at different spatial scales is critical to better predict the consequences of bacterial transport, yet current models often fail to up-scale from laboratory to field conditions. Here, we introduce experimental tools to study bacterial transport in porous media at two spatial scales. The aim of these tools is to obtain macroscopic observables (such as breakthrough curves or deposition profiles) of bacteria injected into transparent porous matrices. At the small scale (10-1000 µm), microfluidic devices are combined with optical video-microscopy and image processing to obtain breakthrough curves and, at the same time, to track individual bacterial cells at the pore scale. At larger scale, flow cytometry is combined with a self-made robotic dispenser to obtain breakthrough curves. We illustrate the utility of these tools to better understand how bacteria are transported in complex porous media such as the hyporheic zone of streams. As these tools provide simultaneous measurements across scales, they pave the way for mechanism-based models, critically important for upscaling. Application of these tools may not only contribute to the development of novel bioremediation applications but also shed new light on the ecological strategies of microorganisms colonizing porous substrates.

Patterns and Drivers of Extracellular Enzyme Activity in New Zealand Glacier-Fed Streams.

Glacier-fed streams (GFSs) exhibit near-freezing temperatures, variable flows, and often high turbidities. Currently, the rapid shrinkage of mountain glaciers is altering the delivery of meltwater, solutes, and particulate matter to GFSs, with unknown consequences for their ecology. Benthic biofilms dominate microbial life in GFSs, and play a major role in their biogeochemical cycling. Mineralization is likely an important process for microbes to meet elemental budgets in these systems due to commonly oligotrophic conditions, and extracellular enzymes retained within the biofilm enable the degradation of organic matter and acquisition of carbon (C), nitrogen (N), and phosphorus (P). The measurement and comparison of these extracellular enzyme activities (EEA) can in turn provide insight into microbial elemental acquisition effort relative to environmental availability. To better understand how benthic biofilm communities meet resource demands, and how this might shift as glaciers vanish under climate change, we investigated biofilm EEA in 20 GFSs varying in glacier influence from New Zealand's Southern Alps. Using turbidity and distance to the glacier snout normalized for glacier size as proxies for glacier influence, we found that bacterial abundance (BA), chlorophyll a (Chl a), extracellular polymeric substances (EPS), and total EEA per gram of sediment increased with decreasing glacier influence. Yet, when normalized by BA, EPS decreased with decreasing glacier influence, Chl a still increased, and there was no relationship with total EEA. Based on EEA ratios, we found that the majority of GFS microbial communities were N-limited, with a few streams of different underlying bedrock geology exhibiting P-limitation. Cell-specific C-acquiring EEA was positively related to the ratio of Chl a to BA, presumably reflecting the utilization of algal exudates. Meanwhile, cell-specific N-acquiring EEA were positively correlated with the concentration of dissolved inorganic nitrogen (DIN), and both N- and P-acquiring EEA increased with greater cell-specific EPS. Overall, our results reveal greater glacier influence to be negatively related to GFS biofilm biomass parameters, and generally associated with greater microbial N demand. These results help to illuminate the ecology of GFS biofilms, along with their biogeochemical response to a shifting habitat template with ongoing climate change.

Optimised biomolecular extraction for metagenomic analysis of microbial biofilms from high-mountain streams.

Glacier-fed streams (GFS) are harsh ecosystems dominated by microbial life organized in benthic biofilms, yet the biodiversity and ecosystem functions provided by these communities remain under-appreciated. To better understand the microbial processes and communities contributing to GFS ecosystems, it is necessary to leverage high throughput sequencing. Low biomass and high inorganic particle load in GFS sediment samples may affect nucleic acid extraction efficiency using extraction methods tailored to other extreme environments such as deep-sea sediments. Here, we benchmarked the utility and efficacy of four extraction protocols, including an up-scaled phenol-chloroform protocol. We found that established protocols for comparable sample types consistently failed to yield sufficient high-quality DNA, delineating the extreme character of GFS. The methods differed in the success of downstream applications such as library preparation and sequencing. An adapted phenol-chloroform-based extraction method resulted in higher yields and better recovered the expected taxonomic profile and abundance of reconstructed genomes when compared to commercially-available methods. Affordable and straight-forward, this method consistently recapitulated the abundance and genomes of a mock community, including eukaryotes. Moreover, by increasing the amount of input sediment, the protocol is readily adjustable to the microbial load of the processed samples without compromising protocol efficiency. Our study provides a first systematic and extensive analysis of the different options for extraction of nucleic acids from glacier-fed streams for high-throughput sequencing applications, which may be applied to other extreme environments.

Microbial Ecology of Methanotrophy in Streams Along a Gradient of CH4 Availability.

Despite the recognition of streams and rivers as sources of methane (CH4) to the atmosphere, the role of CH4 oxidation (MOX) in these ecosystems remains poorly understood to date. Here, we measured the kinetics of MOX in stream sediments of 14 sites to resolve the ecophysiology of CH4 oxidizing bacteria (MOB) communities. The streams cover a gradient of land cover and associated physicochemical parameter and differed in stream- and porewater CH4 concentrations. Michealis-Menten kinetic parameter of MOX, maximum reaction velocity (V max ), and CH4 concentration at half V max (K S ) increased with CH4 supply. K S values in the micromolar range matched the CH4 concentrations measured in shallow stream sediments and indicate that MOX is mostly driven by low-affinity MOB. 16S rRNA gene sequencing identified MOB classified as Methylococcaceae and particularly Crenothrix. Their relative abundance correlated with pmoA gene counts and MOX rates, underscoring their pivotal role as CH4 oxidizers in stream sediments. Building on the concept of enterotypes, we identify two distinct groups of co-occurring MOB. While there was no taxonomic difference among the members of each cluster, one cluster contained abundant and common MOB, whereas the other cluster contained rare operational taxonomic units (OTUs) specific to a subset of streams. These integrated analyses of changes in MOB community structure, gene abundance, and the corresponding ecosystem process contribute to a better understanding of the distal controls on MOX in streams.

Trait-specific dispersal of bacteria in heterogeneous porous environments: from pore to porous medium scale.

The dispersal of organisms controls the structure and dynamics of populations and communities, and can regulate ecosystem functioning. Predicting dispersal patterns across scales is important to understand microbial life in heterogeneous porous environments such as soils and sediments. We developed a multi-scale approach, combining experiments with microfluidic devices and time-lapse microscopy to track individual bacterial trajectories and measure the overall breakthrough curves and bacterial deposition profiles: we, then, linked the two scales with a novel stochastic model. We show that motile cells of Pseudomonas putida disperse more efficiently than non-motile mutants through a designed heterogeneous porous system. Motile cells can evade flow-imposed trajectories, enabling them to explore larger pore areas than non-motile cells. While transported cells exhibited a rotation in response to hydrodynamic shear, motile cells were less susceptible to the torque, maintaining their body oriented towards the flow direction and thus changing the population velocity distribution with a significant impact on the overall transport properties. We also found, in a separate set of experiments, that if the suspension flows through a porous system already colonized by a biofilm, P. putida cells are channelled into preferential flow paths and the cell attachment rate is increased. These two effects were more pronounced for non-motile than for motile cells. Our findings suggest that motility coupled with heterogeneous flows can be beneficial to motile bacteria in confined environments as it enables them to actively explore the space for resources or evade regions with unfavourable conditions. Our study also underlines the benefit of a multi-scale approach to the study of bacterial dispersal in porous systems.