The trait-based partitioning of species plays a critical role in biodiversity-ecosystem function relationships. This niche partitioning drives and depends on community structure, yet this link remains elusive in the context of a metacommunity, where local community assembly is dictated by regional dispersal alongside local environmental conditions. Hence, elucidating the coupling of niche partitioning and community structure needs spatially explicit studies. Such studies are particularly necessary in river networks, where local habitats are highly connected by unidirectional water flow in a spatially complex network structure and frequent disturbance makes community structure strongly dependent on recolonization. Here, we show that taxonomic turnover among periphyton communities colonizing deployed bricks (microhabitats) at multiple sampling sites (local habitats) in a river network came along with a turnover in traits. This niche partitioning showed a hump-shaped relationship with richness of periphyton communities, which increased along river size. Our observations suggest downstream dispersal along the river network to increase the regional metacommunity pool, which then ensures local colonization by taxa possessing diverse traits allowing them to efficiently partition into environmentally different microhabitats. However, at the most downstream sites, the excessive dispersal of widespread generalists drove mass effects which inflated richness with taxa that co-occupied several microhabitats and swamped niche partitioning. Further, efficient niche partitioning depended on communities rich in rare taxa, an indication for the importance of specialists. Alarmingly, richness and rare taxa declined with high phosphorus concentrations and conductivity, respectively, two environmental variables which potentially reflected anthropogenic activity.

Meta-ecosystem theory predicts that cross-ecosystem flows of energy, nutrients, and organisms have important implications for local community assembly and ecosystem functioning. Developments in the theory also have the potential to enhance our under-standing of biodiversity-ecosystem functioning relationships. Meta-ecosystem theory is particularly well-suited to the study of rivers, because water flow forces strong spatial interrelationships among connected ecosystems. However, models that address flows of both resources and organisms and explicitly link both are lacking. We present a model and associated R-package for cross-ecosystem flows of both resources and organisms that can be used to predict their distribution in river networks, as well as meta-ecosystem functioning. The model incorporates feedbacks between these two crucial components. To illustrate the capabilities of the model, we present an in silico experiment and analysis, as well as providing sample code.### Competing Interest StatementThe authors have declared no competing interest.

Benthic bacteria in stream ecosystems drive organic matter mineralization. However, knowledge on how this ecosystem function is driven by bacterial community composition in interaction with environmental conditions and organic matter resources is poor. This is especially true when considering the regional scale of river networks, at which environmental conditions vary in a scale-dependent manner and are spatially structured due to asymmetrical water flow. Similarly, organic matter resources may have a terrestrial origin in remote headwaters or be sourced locally from algae living in close proximity to bacteria in benthic biofilms. We investigated benthic biofilm meta-community structure and function across the > 6700 km2 river network of the near-natural Vjosa in Albania and Greece and found a strong control of the benthic algal community on bacterial community composition (13.4% of variability explained). In addition, bacterial community composition has linkages to water chemistry, which itself is strongly shaped by the diverse geology in the catchment, and to dispersal, shaping metacommunity structure as a neutral process. Notably, bacterial community composition explained the largest single fraction of variability (31.5%) in extracellular enzymatic activities, while there was no dependency of enzyme ratios on organic matter nor environmental conditions. Synergistic effects between bacteria and algae accounted for additional 47.3% of variability in heterotrophic functioning, emphasizing the importance of algal-bacterial interactions in benthic biofilms. Our findings shed new light on bacterial structure-function coupling highlighting the importance of algal-bacterial interactions at the river network scale.

Biodiversity and functioning often follow spatial gradients, yet with unclear causal linkage. In spatially complex rivers, regional-scale factors associated with hydrological connections and catchment properties control downstream transport of material and dispersal of organisms, both being crucial for ecosystem functioning. In a single snapshot study, we here show how a river's network structure interacts with its terrestrial matrix to control key environmental conditions and periphyton community composition at the local habitat scale, which in turn drive primary production. We found the high geodiversity of the Vjosa River network to promote high periphyton beta-biodiversity through regional (dispersal) and local (species sorting) processes. Community turnover driven by species sorting rather than purely by dispersal was identified as relevant for production rates, suggesting a match between environment and community composition to be conditional for functioning. Hence, anthropogenic perturbation of regional mechanisms by river modification may affect ecosystem functions through interfering with metacommunity structure. In the natural Vjosa River network in Europe, the high geodiversity in the catchment and the structure of the river network control algae periphyton biodiversity and its function through regional dispersal and local species sorting, suggests an analysis of environmental and ecological data from 46 river sites.

In many regions of the world, large populations of native wildlife have declined or been replaced by livestock grazing areas and farmlands, with consequences for terrestrial-aquatic ecosystem connectivity and trophic resources supporting food webs in aquatic ecosystems. The river continuum concept (RCC) and the riverine productivity model (RPM) predict a shift of energy supplying aquatic food webs along rivers: from terrestrial inputs in low-order streams to autochthonous production in mid-sized rivers. In Afromontane-savanna landscapes, the shifting numbers of large mammalian wildlife present a physical continuum whose ecological implications for rivers is not clearly understood. Here, we studied the influence of replacing large wildlife (mainly hippos) with livestock on the fractional contribution of C3 vegetation, C4 grasses and periphyton on macroinvertebrates in the Mara River, which is an African montane-savanna river known to receive large subsidy fluxes of terrestrial organic matter and nutrients mediated by large mammalian herbivores (LMH), both wildlife and livestock, in its middle and lower reaches. Using stable carbon (δ13C) and nitrogen (δ15N) isotopes, we identified spatial patterns in the fractional contribution of allochthonous organic matter from C3 and C4 plants (woody vegetation and grasses, respectively) and autochthonous energy from periphyton for macroinvertebrates at various sites of the Mara River and its tributaries. Potential energy sources and invertebrates were sampled at 80 sites spanning stream orders 1 to 7, various catchment land uses (forest, agriculture and grasslands) and different loading rates of organic matter and nutrients by LMH (livestock and wildlife, i.e., hippopotamus). The fractional contribution of different sources of energy for macroinvertebrates along the river did not follow predictions of the RCC and RPM. First, the fractional contribution of C3 and C4 carbon was not related to river order or location along the fluvial continuum but to the loading of organic matter (dung) by both wildlife and livestock. Notably, C4 carbon was important for macroinvertebrates even in large river sections inhabited by hippos. Second, even in small 1st -3rd order forested streams, periphyton was a major source of energy for macroinvertebrates, and this was fostered by livestock inputs fuelling aquatic primary production throughout the river network. Importantly, our results show that replacing wildlife (hippos) with livestock shifts river systems towards greater reliance on autochthonous sources of energy through an algae-grazer pathway as opposed to reliance on allochthonous inputs of C4 carbon through a detrital pathway.

Globally, inland waters emit over 2 Pg of carbon (C) per year as carbon dioxide (CO2), of which the majority originates from streams and rivers. Despite the global significance of fluvial CO2 emissions, little is known about their diel dynamics. We present the first large-scale assessment of day- and night-time CO2 fluxes at the water-air interface across European streams. Fluxes were directly measured four times throughout one year using drifting chambers. Median CO2 fluxes amounted to 1.4 and 2.1 mmol m-2 h-1 at midday and midnight, respectively, with night fluxes exceeding those during the day by 39%. Diel CO2 flux variability was mainly attributed to changes in the water partial pressure of CO2 (pCO2) but no consistent drivers could be identified across sites. Our results highlight widespread day-night changes in fluvial CO2 fluxes and that the time of day greatly influences measured CO2 fluxes across European streams.

Aim Although running waters are getting recognized as important methane sources, large-scale geographical patterns of microorganisms controlling the net methane balance of streams are still unknown. Here we aim at describing community compositions of methanogenic and methanotrophic microorganisms at large spatial scales and at linking their abundances to potential sediment methane production (PMP) and oxidation rates (PMO). Location The study spans across 16 European streams from northern Spain to northern Sweden and from western Ireland to western Bulgaria. Taxon Methanogenic archaea and methane-oxidizing microorganisms. Methods To provide a geographical overview of both groups in a single approach, microbial communities and abundances were investigated via 16S rRNA gene sequencing, extracting relevant OTUs based on literature; both groups were quantified via quantitative PCR targeting mcrA and pmoA genes and studied in relation to environmental parameters, sediment PMP and PMO, and land use. Results Diversity of methanogenic archaea was higher in warmer streams and of methanotrophic communities in southern sampling sites and in larger streams. Anthropogenically altered, warm and oxygen-poor streams were dominated by the highly efficient methanogenic families Methanospirillaceae, Methanosarcinaceae and Methanobacteriaceae, but did not harbour any specific methanotrophic organisms. Contrastingly, sediment communities in colder, oxygen-rich waters with little anthropogenic impact were characterized by methanogenic Methanosaetaceae, Methanocellaceae and Methanoflorentaceae and methanotrophic Methylococcaceae and Cd. Methanoperedens. Representatives of the methanotrophic Crenotrichaceae and Methylococcaceae as well as the methanogenic Methanoregulaceae were characteristic for environments with larger catchment area and higher discharge. PMP increased with increasing abundance of methanogenic archaea, while PMO rates did not show correlations with abundances of methane-oxidizing bacteria. Main conclusions Methanogenic and methanotrophic communities grouping into three habitat types suggest that future climate- and land use changes may influence the prevailing microbes involved in the large-scale stream-related methane cycle, favouring the growth of highly efficient hydrogenotrophic methane producers. Based on these results, we expect global change effect on PMP rates to especially impact rivers adjacent to anthropogenically disturbed land uses.

Large-scale studies are needed to identify the drivers of total mercury (THg) and monomethyl-mercury (MeHg) concentrations in aquatic ecosystems. Studies attempting to link dissolved organic matter (DOM) to levels of THg or MeHg are few and geographically constrained. Additionally, stream and river systems have been understudied as compared to lakes. Hence, the aim of this study was to examine the influence of DOM concentration and composition, morphological descriptors, land uses and water chemistry on THg and MeHg concentrations and the percentage of THg as MeHg (%MeHg) in 29 streams across Europe spanning from 41°N to 64 °N. THg concentrations (0.06-2.78 ng L-1) were highest in streams characterized by DOM with a high terrestrial soil signature and low nutrient content. MeHg concentrations (7.8-159 pg L-1) varied non-systematically across systems. Relationships between DOM bulk characteristics and THg and MeHg suggest that while soil derived DOM inputs control THg concentrations, autochthonous DOM (aquatically produced) and the availability of electron acceptors for Hg methylating microorganisms (e.g. sulfate) drive %MeHg and potentially MeHg concentration. Overall, these results highlight the large spatial variability in THg and MeHg concentrations at the European scale, and underscore the importance of DOM composition on mercury cycling in fluvial systems.

Summary Stream ecosystem metabolism integrates production and respiration of organic matter and plays a fundamental role in the global carbon (C) cycle. Several studies have identified distal and proximal physical controls, for example, land use and transient storage, or the effects of water chemistry, that is, organic matter and nutrient availability, on stream metabolism. In parallel, research on organic matter quality has identified conspicuous gradients of chemical composition, yet mostly without demonstrating any functional implications. We hypothesise that organic matter holds a key position in a more comprehensive causal framework of stream ecosystem metabolism, and that a concurrent study can improve mechanistic understanding. Specifically, we here postulate that dissolved organic matter (DOM) quality, that is, its chemical composition, acts as a control of ecosystem respiration (ER) as much as it is a result of gross primary production (GPP). As such, DOM quality likely forms a central link between land use and stream metabolism, besides known physical controls including transient storage and light availability. To examine these hypotheses, we studied 33 streams in north‐eastern Austria, a region with diverse land use ranging from semi‐natural, forested areas to agricultural areas and settlements. We analysed DOM composition by absorbance and fluorescence spectroscopy, including modelling excitation–emission matrices with parallel factor analysis. We then opposed these data to GPP and ER estimated by fitting a metabolism model to single‐station diurnal oxygen records. Structural equation modelling revealed land use as a control on light conditions, DOM composition and concentration and nutrient concentrations, which together ultimately shaped GPP and ER. In particular, humified, coloured and aromatic DOM of predominantly terrestrial origin was prevalent in coniferous forest catchments and increased stream ER. Agricultural and urban areas enriched streams with phosphorous and nitrogen, which increased ER and GPP. Besides nutrients, GPP seemed to be weakly correlated with light availability and – in contrast to our hypothesis – left only a weak imprint on DOM composition. Land‐use change is rated as the most pervasive human influence on natural ecosystems and our results highlight its impact on aquatic GPP and ER in streams. To understand the role of inland waters in the global C cycle will require mechanistic understanding of ecosystem metabolism, which notably includes organic matter quality as a hitherto underappreciated key player.

Metabolismus in Fliesgewassern integriert die Produktion und die Respiration von organischem Material auf der Ebene eines Okosystems. Gelostes organisches Material (dissolved organic matter, DOM) in aquatischen Lebensraumen ist ein komplexer, extrem diverser Mix aus in-situ produzierten und von terrestrischen Okosystemen stammenden chemischen Substanzen. Ich untersuchte Auswirkungen der Landnutzung auf die DOM-Zusammensetzung und Nahrstoff- und Kohlenstoffkonzentrationen im Fliesgewasser und stellte dies in Bezug zum Metabolismus des gesamten Fliesgewassers, d.h. Bruttoprimarproduktion (BPP) und Gesamtrespiration des Okosystems. Dafur untersuchte ich 33 Fliesgewasser im Norden Osterreichs, deren Einzugsgebiete einen Landnutzungsgradienten von landwirtschaftlich und urban gepragten zu bewaldeten und naturnahen Flachen umspannten. Zur Charakterisierung der DOM-Zusammensetzung wurden Absorptions- und Fluoreszenzindizes, sowie DOM-Komponenten identifiziert durch parallele Faktorenanalyse (PARAFAC), verwendet. Zur Metabolismusberechnung wurde sowohl der 1-Station- als auch 2-Stationen-Ansatz verfolgt, welche beide auf den taglichen Sauerstoffdynamiken im Fliesgewasser basieren. Raten der BPP und der Respiration wurden durch Anpassung eines mathematischen Modells an die empirischen Sauerstoffdaten berechnet. Die DOM-Zusammensetzung, Phosphor-Konzentrationen und Kohlenstoffquantitat wurden stark von der Landnutzung beeinflusst. Die DOM-Zusammensetzung und Phosphor-Konzentrationen hatten weiteren Einfluss auf die Respiration. Die DOM-Zusammensetzung wurde nicht von der BPP beeinflusst, welche ihrerseits hauptsachlich von Lichtverfugbarkeit abhangig war. Diese Studie zeigt deutlich, welche Schlusselrolle anthropogene Landnutzung in der Kontrolle des Kohlenstoff-Kreislaufes der Binnengewasser einnimmt. Landnutzung wird als die tiefgreifendste vom Menschen verursachte Auswirkung auf die naturlichen Okosysteme dieser Erde angesehen und Binnengewasser geraten zunehmend als bedeutende Umsatzorte fur das klimatisch wirksame Treibhausgas CO2 in den Fokus wissenschaftlicher Betrachtung. In Anbetracht dieser Tatsachen ist es wichtig DOM-Dynamiken sowohl als Kontrollen als auch als Indikatoren von Metabolismus mit Bedacht auf die Landnutzung zu untersuchen, um die Rolle der Binnengewasser in gegenwartigen Landschaften genauer einordnen zu konnen.