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River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.

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.

River ecosystems are superlatives in many respects. Their networks represent the largest biogeochemical nexus between the continents, oceans and atmosphere. River networks span multiple catchments, even biomes, and are highly dynamic in space and time. The world’s rivers contribute relatively little by areal extent, but their CO2 emissions are of the same magnitude as the CO2 sequestration flux by the world’s oceans. Rivers figure among the most heterotrophic ecosystems on Earth, metabolizing terrestrial organic carbon. Owing to their dendritic structure, the biodiversity that river networks host is exceptionally high. Finally, needless to emphasize how critical the ecosystem services are that rivers provide. Central to many of these river superlatives are microbial biofilms that abundantly coat the sedimentary surfaces of the river beds. A microbiome, encompassing all three domains of life, shapes, in conjunction with the turbulent nature of water flow, intriguing biofilm architectures. Biofilms, a hidden beauty emanating from the interactions between biology, physics and chemistry, regulate ecosystem energetics and are therefore an important linchpin between river biodiversity and biogeochemistry.In my lecture, I will attempt to provide the state-of-the-art of global river carbon biogeochemistry and biofilm ecology. An emphasis will be given on the rivers that literally drain the roof of our planet, now at risk because of climate change. It is my hope, that soon we will appreciate the world’s river networks as we do appreciate the oceans and various terrestrial ecosystems.

Quantifying the transfer of organic carbon (OC) from the terrestrial to the riverine ecosystems is of crucial importance to fully appreciate the carbon cycle at the catchment, regional and global scales. Dissolved Organic Carbon (DOC) represents one of the main forms in which terrestrial OC is leached to inland waters and the oceans. Its concentration in streams, rivers and lakes is critical for aquatic metabolism but also for the transport of metals and pollutants. In the past years, several studies in different experimental catchments observed increasing trends in DOC concentration in rivers, possibly linked to changes in land use and hydrologic regime. Moreover, these studies unveiled how hydrologic variability imposes a strong control on DOC transport with streamflow producing events disproportionately contributing to the overall DOC export. In this study, we explore the interaction between water and carbon cycles in the critical zone of an alpine catchment in order to quantify the flux of DOC exported from the soil to the stream via superficial or subsuperficial runoff. We couple the Water Age theory to unravel the time water spends within hillslopes with the Reactivity Continuum model to quantify the degradation of DOC along the transport. The model is applied to the Oberer Seebach basin (Austria) for which extensive time series of streamflow DOC concentration and hydrological variables are available at high-frequency resolution (sub-daily measurements). For a subset of the DOC samples, the excitation emission matrices and the absorbance spectra are also available and allow deriving information on the quality and reactivity of DOC. We reproduce DOC concentration estimating the travel time distribution of water and assuming it dictates the time available for the continuous degradation of the DOC mixture. Results show that the model is able to well reproduce DOC streamflow concentration, capturing its complex relation with streamflow discharge over the three years of observations. In addition, the framework allows the estimation of the reactivity distribution of the exported DOC. To validate these results, we compare the estimated average reactivity with multiple fluorescence and absorbance indexes calculated from data, revealing significant correlations.

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., 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".

Cross-domain interactions are an integral part of the success of complex biofilms in natural environments. Here, we report on cross-domain interactions in biofilms of streams draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterized by multiple environmental gradients and stability that depend on the time since deglaciation. We estimate co-occurrence of prokaryotic and eukaryotic communities along this gradient and show that key community members have disproportionate effects on the stability of co-occurrence networks. The topology of the networks was similar independent of environmental gradients and stability. However, network stability was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that both pro- and eukaryotes are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. These ‘keyplayers’ 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.

The rapid recession of glaciers is exposing large zones to the development of embryonic phototrophic ecosystems and eventual ecological succession. Traditionally, succession patterns in glacial forefields have been seen as a response to time since deglaciation, but nowadays forefield exposure is so rapid that this theory may be less applicable. In this suc-cession process, periphyton are potential pioneer organisms because of their role in modifying the local environment (e.g. access to water) to create conditions conducive to plant colonization. In this paper, we aim to decrypt the physical properties of the habitats that define the spatial and temporal assemblage of periphyton during the melt-season of an Alpine temperate glacier in the context of rapid climate change. We show that periphyton develop in glacial flood -plains throughout the melt-season and could extend to cover significant surfaces. However, development is only pos-sible when the combined conditions of stability and water accessibility are met. In glacial floodplains, stable zones exist and are typically located on terraces; but they can also be locally found for much shorter periods in the more ac-tive, glacial-stream reworked zone. On terraces, water accessibility can be a limit due to well-drained sediments, but when present, often aided by the role that biofilms play in creating an impermeable layer, it provides a stable and clear water source that biofilms could exploit. In the active part of the braid plain, whilst water availability is very high, the water is harsh (low temperature, high turbidity) and erosive. Therein, periphyton can rapidly exploit short windows of opportunity but the habitat conditions rarely remain stable for long enough for continuous periphyton cover to develop. Thus, the role of periphyton in ecosystem succession is strongly conditioned by the spatial extent of the active zone, itself a function of high rates of glacier melt and sediment supply associated with rapid glacier retreat.

Bacterial gut commensals experience a biologically and physically complex mucosal environment. While many chemical factors mediate the composition and structure of these microbial communities, less is known about the role of mechanics. Here, we demonstrate that fluid flow impacts the spatial organization and composition of gut biofilm communities by shaping how different species interact metabolically. We first demonstrate that a model community composed of Bacteroides thetaiotaomicron (Bt) and Bacteroides fragilis (Bf), two representative human commensals, can form robust biofilms in flow. We identified dextran as a polysaccharide readily metabolized by Bt but not Bf, but whose fermentation generates a public good enabling Bf growth. By combining simulations with experiments, we demonstrate that in flow, Bt biofilms share dextran metabolic by-products, promoting Bf biofilm formation. By transporting this public good, flow structures the spatial organization of the community, positioning the Bf population downstream from Bt. We show that sufficiently strong flows abolish Bf biofilm formation by limiting the effective public good concentration at the surface. Physical factors such as flow may therefore contribute to the composition of intestinal microbial communities, potentially impacting host health., Proceedings of the National Academy of Sciences of the United States of America, 120 (25), ISSN:10916490, ISSN:0027-8424, ISSN:1091-6490

1) Primary production is a fundamental ecosystem process that influences nutrient and carbon cycling, and trophic structure in streams. The magnitude and timing of gross primary production (GPP) are typically controlled by hydrology, light, nutrient availability and grazers. Estimates of GPP and its drivers in high-mountain streams remain elusive at present. 2) We estimated GPP in streams typical for high-mountain catchments, namely a glacier-fed, groundwater-fed (krenal) and a snowmelt-fed (nival) stream. Using high-resolution sensor data over 2 years in combination with numerical simulations of stream hydraulics, we studied the periods of GPP characteristic for these streams, as well as their major drivers. 3) Favourable windows for GPP were constrained to periods at the onset of the snowmelt and its recession, when photosynthetic active radiation at the streambed and streambed stability facilitated GPP. 4) During these windows of opportunity, GPP was higher in the nival stream (3.7 ± 3.4 g O2 m−2 day−1), followed by the glacier-fed (1.5 ± 1.6 g O2 m−2 day−1) and the krenal streams (0.6 ± 0.6 g O2 m−2 day−1). GPP was largely controlled by photosynthetic active radiation at the stream bottom, however, we were not able to establish an unequivocal relationship between flow-induced bed movement and GPP. 5) Our results highlight the capacity of primary producers to exploit the discrete and relatively predictable windows of opportunities in high-mountain streams. We propose that climate-driven change in snow and glacier melt reduction may ameliorate stream environmental conditions, thereby enhancing the potential autochthonous organic matter supply within the catchment.

Microbial biofilms have received great attention in the last few decades from both aquatic ecologists and biogeomorphologists. Most recently, this has focused on mapping biofilms to understand their spatial distributions and ecosystem services. Such studies often involve the use of satellite imagery, which typically provides large temporal and spatial scales and wide-range spectral information. Although satellites have the advantage of multi- and hyper-spectral sensors, images often have low spatial resolution that limits their use in river studies, where both rivers are narrower and stream processes occur at resolutions smaller than the footprint of satellite sensors. Spatial resolution is sensor quality dependent but also controlled by sensor elevation above the ground. Hence, high resolutions can be achieved either by using a very expensive sensor or by decreasing the distance between the target area and the sensor itself. To date, sensor technology has advanced to a point where multi- or even hyper-spectral cameras can be easily carried out by an Uncrewed Aerial Vehicle (UAV) at unprecedented spatial resolutions. Where such sensors have high spectral resolution, they are often prohibitively expensive, especially as their use in extreme environments such as glacial forefields risks UAV damage. In this paper, we test the performance of visible band ratios in mapping biofilms in an Alpine glacier forefield characterized by a well-developed and heterogeneous stream ecosystem but using a low-cost UAV. The paper shows that low-cost and consumer grade UAVs can be easily deployed in such extreme environments, delivering both quality RGB images for photogrammetric (SfM-MVS) processing and sufficient spectral information for benthic biofilm mapping at high temporal and spatial resolution. RGB cameras are an alternative to expensive multi- or hyper-spectral cameras.Phototrophic biofilms can be detected and mapped through visible band ratios.High-temporal and high-resolution imagery can be collected by consumer-grade UAVs.Biofilm presence is restricted to stable and water-fed terraces in summer. RGB cameras are an alternative to expensive multi- or hyper-spectral cameras. Phototrophic biofilms can be detected and mapped through visible band ratios. High-temporal and high-resolution imagery can be collected by consumer-grade UAVs. Biofilm presence is restricted to stable and water-fed terraces in summer.

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., Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble.

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.

BackgroundAntimicrobial resistance (AMR) is a universal phenomenon whose origins lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. However, the ecological and evolutionary processes shaping AMR need to be better understood in view of better antimicrobial stewardship. Resolving antibiotic biosynthetic pathways, including biosynthetic gene clusters (BGCs), and corresponding antimicrobial resistance genes (ARGs) may therefore help in understanding the inherent mechanisms. However, to study these phenomena, it is crucial to examine the origins of AMR in pristine environments with 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.ResultsWe 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, 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, etc.) including representatives of the superphylum Patescibacteria encode both ARGs and BGCs within close proximity of each other, thereby demonstrating their capacity to simultaneously influence and compete within the microbial community.ConclusionsOur findings highlight the presence and abundance of AMR in epilithic biofilms within GFSs. Additionally, we identify their role in the complex intra- and inter-domain competition and the underlying mechanisms influencing microbial survival in GFS epilithic biofilms. We demonstrate that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. We also find that the taxonomic affiliation of the AMR and the BGCs are congruent. Importantly, our findings allow for understanding how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Importantly, these observations may be generalizable and potentially extended to other environments which may be more or less impacted by human activity.

The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires., 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.

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

1. Understanding how different food resources sustain stream food webs is fundamental towards increasing our knowledge on trophic structure and energy flow pathways in fluvial ecosystems. 2. Food webs in small mountain streams are sustained by autochthonous (instream primary production) and allochthonous (inputs from the terrestrial ecosystem) organic resources, with their relative importance highly dependent on catchment land cover. 3. This study aimed to understand how catchment land cover determines food resource type (autochthonous, allochthonous) and quantity in mountain streams, and how this affects energy flow pathways and food web structure. We hypothesised that food resource type and quantity would reflect catchment land cover. Thus, changes in food resources would lead to shifts in macroinvertebrate assimilation of autochthonous and allochthonous food resources and consequently in dominant energy flow pathways. We further hypothesised that changes in food resources will have strong effects on dominant feeding groups and community biomass distribution among taxa in food webs. 4. Energy flow pathways were quantified by combining macroinvertebrate biomass measures and assimilation of food resources estimated from δ2H and δ15N in 10 streams along a forest cover gradient, located in the Cantabrian Mountains (northern Spain). 5. Results showed that grassland/shrub dominated streams had a higher proportion autochthonous food resources and a lower proportion of allochthonous food resources, whereas forested streams showed the opposite pattern. Changes in food resources with forest cover resulted in shifts in food resource assimilation and dominant energy flow pathways. Forested streams were mainly sustained by allochthonous resources, while streams flowing through grassland/shrub landscapes were mostly sustained by autochthonous resources. 6. Food resource assimilation differed between feeding groups. Detritivores showed a fixed assimilation of allochthonous resources independent of resource quantity, while omnivore assimilation was determined by the dominant food resource. This

Gas exchange across the air–water interface drives the flux of climate-relevant gases and is critical for biogeochemical processes in aquatic ecosystems. Despite the presence of mountain streams worldwide, we lack basic understanding of gas exchange through their turbulent surfaces, making global estimates of outgassing from streams and rivers difficult to constrain. Here we combine new estimates of gas transfer velocities from tracer gas additions in mountain streams with published data to cover streams differing in geomorphology and hydraulics. We find two different scaling relationships between the turbulence-induced energy dissipation rate and gas transfer velocity for low- and high-channel slope streams, indicating that gas exchange in streams exists in two states. We suggest that turbulent diffusion drives gas transfer velocity in low-energy streams; whereas turbulence entrains air bubbles in high-energy streams, and the resulting bubble-mediated gas exchange accelerates with energy dissipation rate. Gas transfer velocities in the high-energy streams are among the highest reported. Our findings offer a framework to include mountain streams in future estimates of gas fluxes from streams and rivers at the global scale. Bubble-mediated gas exchange in high-energy streams accelerates faster as energy dissipation intensifies than does turbulent-diffusion-driven gas exchange in low-energy streams, according to an analysis of new measurements and published data.

Lakes receive large amounts of carbon (C) from the surrounding catchment and, together with the connecting streams, play an important and active role in the global C cycle. The received C can either be lost through the outflow and eventually transported to the ocean, or transformed and stored in sediments or outgassed to the atmosphere. Globally, lakes are estimated to emit 0.3 – 0.64 Pg C m-2 in form of CO2 annually. Although subalpine and alpine lakes were observed to be supersaturated with CO2, long-term measurements of lake-atmosphere CO2 exchange are sparse. Several methods to quantify water-atmosphere gas exchange exist, like chambers, eddy covariance (EC), mass-balance or gradient based methods including boundary layer models (BLM), each having its own advantages and disadvantages. However, quantifying CO2 exchange in aquatic ecosystems has often proved to be challenging. Here, both the BLM and the EC methods were used to estimate the air-water CO2 exchange of Lake Lunz, a small lake situated in complex mountainous topography of the Austrian Alps. The results indicated that the lake was a small source of CO2. Fluxes were affected by the thermo-topographic flow regime of the field site and its surroundings which drove the local wind pattern but also determined the local atmospheric CO2 concentration. During most nights, a significant increase in atmospheric CO2 was observed which decreased the differential CO2 concentration at the air-water interface and therefore led to decreased nocturnal CO2 efflux. This diurnal pattern, however, was obscured in the EC measurements, because the method itself highly depends on the local wind regime. Because lakes are an integral part of mountain ranges which are characterized by catchments with complex topography, our findings are most likely of broader impact.

Streams and rivers emit substantial amounts of nitrous oxide (N2O) and are therefore an essential component of global nitrogen (N) cycle. Permafrost soils store a large reservoir of dormant N that, upon thawing, can enter fluvial networks and partly degrade to N2O, yet the role of waterborne release of N2O in permafrost regions is unclear. Here we report N2O concentrations and fluxes during different seasons between 2016 and 2018 in four watersheds on the East Qinghai-Tibet Plateau. Thawing permafrost soils are known to emit N2O at a high rate, but permafrost rivers draining the East Qinghai-Tibet Plateau behave as unexpectedly minor sources of atmospheric N2O. Such low N2O fluxes are associated with low riverine dissolved inorganic N (DIN) after terrestrial plant uptake, unfavorable conditions for N2O generation via denitrification, and low N2O yield due to a small ratio of nitrite reductase: nitrous oxide reductase in these rivers. We estimate fluvial N2O emissions of 0.432 − 0.463 Gg N2O-N yr−1 from permafrost landscapes on the entire Qinghai-Tibet Plateau, which is marginal (~0.15%) given their areal contribution to global streams and rivers (0.7%). However, we suggest that these permafrost-affected rivers can shift from minor sources to strong emitters in the warmer future, likely giving rise to the permafrost non-carbon feedback that intensifies warming.

Lakes and streams in mountain regions are important contributors to carbon (C) fluxes. However, detailed carbon balances of the stream‐lake continuum are rare. Combining eddy covariance (EC) measurements of lake‐atmosphere net ecosystem CO2 exchange with measurements of fluvial C fluxes (dissolved organic C, DOC; particulate organic C, POC; dissolved inorganic C, DIC), and in‐lake sedimentation, we here present a detailed annual C balance of an oligotrophic clearwater lake in the eastern European Alps. The C flux into the lake was 1522 Mg C year−1 by DIC (93%), DOC (6%), and POC (0.7%). The largest C losses were fluvial exports (1595 Mg C year−1) of DIC (93%), DOC (6%), and POC (0.8%), while sedimentation accounted for 7.3 Mg C year−1. The residual of all fluvial and sedimentation fluxes revealed the lake as a net sink of atmospheric CO2 of 77 Mg C year−1. The EC measurement confirmed a small positive or negative contribution of atmospheric exchange to the lake C balance. In‐lake transfer among C pools was only significant for the flux from DIC to POC (8.4 Mg C year−1), which, following our model, is the transfer through primary production in summer. Fluvial DOC and DIC fluxes were controlled by discharge; POC retention and sedimentation depended on the meteorological season and in‐lake residence time. Following our findings, we conclude that hydrology acted as the most important control for the C balance of this clearwater mountain lake by controlling inflow, outflow, and sedimentation fluxes.

Streams and rivers form dense networks that drain the terrestrial landscape and are relevant for biodiversity dynamics, ecosystem functioning, and transport and transformation of carbon. Yet, resolving in both space and time gross primary production (GPP), ecosystem respiration (ER) and net ecosystem production (NEP) at the scale of entire stream networks has been elusive so far. Here, combining Random Forest (RF) with time series of sensor data in 12 reach sites, we predicted annual regimes of GPP, ER, and NEP in 292 individual stream reaches and disclosed properties emerging from the network they form. We further predicted available light and thermal regimes for the entire network and expanded the library of stream metabolism predictors. We found that the annual network-scale metabolism was heterotrophic yet with a clear peak of autotrophy in spring. In agreement with the River Continuum Concept, small headwaters and larger downstream reaches contributed 16% and 60%, respectively, to the annual network-scale GPP. Our results suggest that ER rather than GPP drives the metabolic stability at the network scale, which is likely attributable to the buffering function of the streambed for ER, while GPP is more susceptible to flow-induced disturbance and fluctuations in light availability. Furthermore, we found large terrestrial subsidies fueling ER, pointing to an unexpectedly high network-scale level of heterotrophy, otherwise masked by simply considering reach-scale NEP estimations. Our machine learning approach sheds new light on the spatiotemporal dynamics of ecosystem metabolism at the network scale, which is a prerequisite to integrate aquatic and terrestrial carbon cycling at relevant scales. Supplementary Information The online version contains supplementary material available at (10.1007/s10021-021-00618-8)

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.

Microdiversity, the organization of microorganisms into groups with closely related but ecologically different sub-types, is widespread and represents an important linchpin between microbial ecology and evolution. However, the drivers of microdiversification remain largely unknown. Here we show that selection promotes microdiversity in the microbiome associated with sediments in glacier-fed streams (GFS). Applying a novel phylogenetic framework, we identify several clades that are under homogeneous selection and that contain genera with higher levels of microdiversity than the rest of the genera. Overall these clades constituted ∼44% and ∼64% of community α-diversity and abundance, and both percentages increased further in GFS that were largely devoid of primary producers. Our findings show that strong homogeneous selection drives the microdiversification of specialized microbial groups putatively underlying their success in the extreme environment of GFS. This microdiversity could be threatened as glaciers shrink, with unknown consequences for microbial diversity and functionality in these ecosystems.