Coastal lagoons are dynamic systems where the mode of nutrient input, continuous or pulsed, or a combination, can significantly affect plankton community structure and function. We conducted a spring field microcosm experiment in a Mediterranean lagoon to evaluate how three nutrient delivery regimes influence planktonic dynamics, using biomass measurements and extracellular enzyme activity (EEA) as functional indicators. Continuous nutrient additions promoted sustained phytoplankton and bacterioplankton growth, indicating bottom-up control and microbial stability. In contrast, pulse treatments saw a brief bacterioplankton bloom followed by delayed phytoplankton increase and a marked decline in zooplankton, suggesting disrupted trophic succession and food quality limitations. The pulse–continuous treatment yielded intermediate responses, confirming that delivery mode, not just nutrient load, modulates ecosystem processes. Elevated β-glucosidase (GLU) and leucine aminopeptidase (LAP) activity under nutrient addition, particularly in continuous treatments, signaled intensified carbon and nitrogen demand and active organic matter mineralization, even when nutrient concentrations appeared low. These findings suggest that, during stable spring conditions, microbial communities rapidly assimilate nutrients, potentially obscuring short-term biogeochemical changes from traditional concentration-based monitoring. Crucially, the timing and frequency of nutrient supply are as influential as total input, with continuous inputs supporting a more stable and efficient microbial loop. This work underscores the ecological importance of recognizing diffuse, low-level nutrient sources, such as groundwater seepage, which may be underrepresented in lagoon management strategies. Integrating functional indicators with delivery mode assessments can improve predictions of eutrophication risks and support more effective conservation planning in shallow coastal systems.

Urban wastewater treatment has significantly improved in recent decades, reducing the environmental impacts of their effluents and improving the chemical and ecological status of receiving water bodies. However, specific treatments, focused on nitrogen and phosphorus removal, have been implemented principally in large urban wastewater treatment plants (UWWTPs) serving over 10,000 population equivalents (P.E). In contrast, small UWWTPs (<10,000 P.E.) are generally not required to meet nutrient discharge limits despite the revised Urban Wastewater Treatment Directive. Nature-Based Solutions (NBS) offer cost-effective alternatives for small facilities as potential tertiary treatments. This research evaluated a pond-stream system, based on the biological activity of benthic (biofilms) and planktonic microbial communities (biofilm-plankton reactor, BPR), as an additional treatment step for activated sludge UWWTPs. The BPR achieved removal efficiencies for nitrogen (67.4 ± 11.1 %) and Escherichia coli (75.4 ± 37.3 %), while phosphorus, carbon, and targeted contaminants of emerging concern were highly variable and were not consistently removed. Microbial communities' structure and functions were assessed through algal biomass, stoichiometry, and extracellular enzymatic activities, providing a distinctive perspective into the BPR's microbial ecological dynamics related to removal efficiencies. Shotgun metagenomics identified a broad range of nitrogen functional genes, mainly involved in biodegradation and biosynthesis processes. This next-generation sequencing approach complemented conventional E. coli count methods, offering a deeper understanding of potential pathogen hotspots in treated effluents. Overall, the BPR system demonstrated a promising NBS for nitrogen and microbiological contaminant removal in small UWWTPs, whereas further investigation is needed to optimise the removal of other important water quality parameters.

Increasing aridity poses a threat to soil functionality, as it affects the key players -prokaryotes and fungiresponsible for these functions. Studying microbial diversity and functions in soils from different aridity conditions is crucial to understanding potential adaptations and response mechanisms to climate change, which may ultimately affect soil ecosystem multifunctionality. Here, we used a natural humid-to-arid climate gradient to determine: (1) if and how soil functions and microbial communities change across the aridity gradient; and (2) the main drivers of soil function variability along the gradient. We sampled soils (0-10 cm depth) from 12 sites across the Iberian Peninsula and analyzed their prokaryotic and fungal diversity and biomass as well as soil functions (aerobic respiration and extracellular enzyme activities linked to organic carbon, nitrogen and phosphorus degradation), together with soil physicochemical characteristics. Our results showed that increasing aridity resulted in a gradual change in the microbial community structure and a decrease in fungal diversity. However, soil functions did not show clear changes in response to aridity itself. Instead, microbial respiration and enzyme activities depended mainly on the local soil properties (i.e. organic matter quantity and quality, soil texture and pH) rather than on aridity. Overall, results indicated that in long-term climate-adapted soils, microbial functions are primarily driven by soil edaphology with aridity influencing them indirectly by shaping the microbial community composition and the intrinsic soil characteristics.

Soil microorganisms, crucial players of soil organic matter degradation, contribute substantially to global carbon and nitrogen biogeochemical cycles. Although microbial community structure and diversity have been extensively studied at different latitudes worldwide, the relationship between microbial communities, environmental drivers, and ecosystem functions across latitudes has yet to be explored. Here we investigate soil bacterial and fungal community structure and diversity, and ecosystem multifunctionality across different biomes of the European continent from southern Spain (37°N) to Sweden (60°N). Bacterial alpha-diversity increased with increasing the latitude, while fungal alpha-diversity showed an opposite pattern. Fungal communities were more geographically dispersed than bacterial communities. Microbial communities were structured by soil temperature, water content, and resources (TOC, C/N ratio and phosphate). While multifunctionality index related to N cycling functions decreased linearly and significantly with increasing bacterial diversity, it increased significantly with the increases in fungal diversity indices. Our study sheds light on the soil microbial complexity, microbial diversity and function relationship across latitudes and biomes, and highlights the importance of microbial diversity and community structure in driving soil multifunctionality.

Providing endogenous labile carbon (C) is crucial when designing constructed wetlands (CWs) to treat C-limited but nitrate rich-wastewater. In subsurface flow CWs, the main sources of C are the bed substrate and vegetation. When senescent plant leaves fall on the CW bed surfaces, they release C and nutrients during decomposition, fuelling microbial reactions and enhancing CW performance. However, the type of bed substrate not only influences plant and microbial growth but may also affect the chemical composition of leaves and their role as a C-source. To study this, we designed an experiment to analyze the effect of different bed substrates (gravel only, gravel + soil and gravel + biochar) on i) leaf litter decomposition rates and ii) the chemical quality and potential microbial uptake of leaf leachates. Our goal was to advance in the selection of a CW substrate that promotes leaf litter decomposition as a suitable and effective source of labile C for microorganisms. We observed varying decomposition rates among substrates, which appeared to result from differences in environmental conditions at the habitat scale rather than differences in leaf chemical composition. Photodegradation mechanisms dominated in gravel beds, driving decomposition at rates similar to those observed with soil addition, where microbial activity played a major role. In contrast, the addition of biochar inhibited decomposition. C leached from plants growing in soil and biochar substrates exhibited the highest microbial uptake, likely due to the presence of essential nutrients. This study supports that adding natural soil to gravel is the most favourable option for promoting labile C supply via plant decomposition, thereby enhancing microbial activity. Furthermore, our results suggest that management strategies allowing leaf litter to remain on CW bed surfaces would provide a valuable supply of DOC, helping to mitigate labile C limitation in the treatment of irrigated agricultural drainage water.

Benthic biofilms on cobbles (i.e., epilithic biofilms) control the uptake of soluble reactive phosphorus (SRP) and ammonium (NH 4 + ) in headwater streams. However, nutrient uptake by biofilms in higher‐order rivers, particularly those affected by anthropogenic nutrient inputs and hydrological regulation, remains poorly understood. To address this gap, we examined the spatial and temporal variability of SRP and NH 4 + uptake by epilithic biofilms, as well as their main drivers under light and dark conditions, along the main stem of a fifth‐order human‐regulated Mediterranean river. In situ light–dark incubations were conducted in open recirculating chambers at six sites across four dates, using dual nutrient additions to quantify gross uptake ( U ) of SRP and NH 4 + . Uptake of NH 4 + was consistently higher than U SRP across sites and dates, particularly under light conditions, with both nutrients showing rates similar to those reported in previous reach‐scale studies. Uptake of SRP was consistent under light and dark conditions, with spatial and temporal variability contributing similarly to the explained variation in uptake. In contrast, U NH4 differed markedly between light and dark conditions and exhibited site‐specific temporal patterns, suggesting a stronger dependence on photoautotrophic demand and greater influence on local environmental conditions. Finally, U SRP was primarily associated with biofilm metabolic activity, while U NH4 was more strongly related to ambient nutrient concentrations. Overall, this study expands our understanding of spatial and temporal variability in biofilm nutrient uptake and highlights the importance of considering light availability to better understand the role of biofilms in P and N retention.

Mountain ecosystems, contributing substantially to the global carbon (C) and nitrogen (N) biogeochemical cycles, are heavily impacted by global changes. Although soil respiration and microbial activities have been extensively studied at different elevation, little is known on the relationships between environmental drivers, microbial functions, and greenhouse gas fluxes (GHGs; carbon dioxide [CO2], methane [CH4] and nitrous oxide [N2O]) in soils of different elevation. Here, we measured how in situ GHG fluxes were linked to soil properties, soil organic matter (SOM) quantity and composition (the proportion of humic-like vs. protein-like OM), microbial biomass, enzyme activities and functional gene abundances in natural soils spanning an elevational gradient of ∼2400 m in Switzerland. Soil CO2 fluxes did not significantly vary from low (lowland zone) to higher (montane and subalpine zones) elevation forests, but decreased significantly (P<0.001) from the treeline to the mountain summit. Multivariate analyses revealed that CO2 fluxes were controlled by C-acquiring enzymatic activities which were mainly controlled by air mean annual temperature (MAT) and SOM quantity and composition. CH4 fluxes were characterized by uptake of atmospheric CH4, but no trend was observed along the elevation. N2O fluxes were also dominated by uptake of atmospheric N2O. The flux rates remained stable with increasing elevation below the treeline, but decreased significantly (P<0.001) from the treeline to the summit. N2O fluxes were driven by specific nitrifying and denitrifying microbial genes (ammonia-oxidizing amoA and N2O-producing norB), which were again controlled by SOM quantity and composition. Our study indicates the treeline as a demarcation point changing the patterns of CO2 and N2O fluxes along the elevation, highlighting the importance of SOM quantity and composition in controlling microbial enzyme activities and GHG fluxes.

Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.

A significant fraction of Earth's ecosystems undergoes periodic wet-dry alternating transitional states. These globally distributed water-driven transitional ecosystems, such as intermittent rivers and coastal shorelines, have traditionally been studied as two distinct entities, whereas they constitute a single, interconnected meta-ecosystem. This has resulted in a poor conceptual and empirical understanding of water-driven transitional ecosystems. Here, we develop a conceptual framework that places the temporal availability of water as the core driver of biodiversity and functional patterns of transitional ecosystems at the global scale. Biological covers (e.g., aquatic biofilms and biocrusts) serve as an excellent model system thriving in both aquatic and terrestrial states, where their succession underscores the intricate interplay between these two states. The duration, frequency, and rate of change of wet-dry cycles impose distinct plausible scenarios where different types of biological covers can occur depending on their desiccation/hydration resistance traits. This implies that the distinct eco-evolutionary potential of biological covers, represented by their trait profiles, would support different functions while maintaining similar multifunctionality levels. By embracing multiple alternating transitional states as interconnected entities, our approach can help to better understand and manage global change impacts on biodiversity and multifunctionality in water-driven transitional ecosystems, while providing new avenues for interdisciplinary studies. Our framework proposes that water-driven transitional ecosystems experience periodic shifts between aquatic and terrestrial states within a single interconnected meta-ecosystem, driven by temporal water availability. Biological covers like aquatic biofilms and biocrusts play a central role, undergoing successional dynamics in response to wet-dry transitions, impacting biodiversity and ecosystem functioning. These impacts, especially considering the risk to become a stable dry ecosystem under the global change context, pose threats to the contribution of water-driven transitional ecosystems to global biogeochemical cycles, climatic stability, and human welfare.image

We present a comprehensive, customizable workflow for inferring prokaryotic phenotypic traits from marker gene sequences and modelling the relationships between these traits and environmental factors, thus overcoming the limited ecological interpretability of marker gene sequencing data. We created the trait sequence database ampliconTraits, constructed by cross-mapping species from a phenotypic trait database to the SILVA sequence database and formatted to enable seamless classification of environmental sequences using the SINAPS algorithm. The R package MicEnvMod enables modelling of trait - environment relationships, combining the strengths of different model types and integrating an approach to evaluate the models' predictive performance in a single framework. Traits could be accurately predicted even for sequences with low sequence identity (80 %) with the reference sequences, indicating that our approach is suitable to classify a wide range of environmental sequences. Validating our approach in a large trans-continental soil dataset, we showed that trait distributions were robust to classification settings such as the bootstrap cutoff for classification and the number of discrete intervals for continuous traits. Using functions from MicEnvMod, we revealed precipitation seasonality and land cover as the most important predictors of genome size. We found Pearson correlation coefficients between observed and predicted values up to 0.70 using repeated split sampling cross validation, corroborating the predictive ability of our models beyond the training data. Predicting genome size across the Iberian Peninsula, we found the largest genomes in the northern part. Potential limitations of our trait inference approach include dependence on the phylogenetic conservation of traits and limited database coverage of environmental prokaryotes. Overall, our approach enables robust inference of ecologically interpretable traits combined with environmental modelling allowing to harness traits as bioindicators of soil ecosystem functioning.

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.

Saline shallow lakes in arid and semi-arid regions frequently undergo drying episodes, leading to significant variations in salinity and water availability. Research on the impacts of salinity and drought on the structure and function of biofilms in hypersaline shallow lakes is limited. This study aimed to understand the potential changes of biofilms in playa-lake sediments during the drying process. Sediments were sampled at different depths (surface, subsurface) and hydrological periods (wet, retraction, and dry), which included a decrease in water activity (aw, the availability of water for microbial use) from 0.99 to 0.72. aw reduction caused a greater effect on functional variables compared to structural variables, indicating the high resistance of the studied biofilms to changes in salinity and water availability. Respiration and hydrolytic extracellular enzyme activities exhibited higher values under high aw, while phenol oxidase activity and prokaryote biomass increased at lower aw. This shift occurred at both depths but was more pronounced at the surface, possibly due to the more extreme conditions (up to 0.7 aw). The increased levels of extracellular polymeric substances and carotenoids developed at low aw may help protect microorganisms in high salinity and drought environments. However, these harsh conditions may interfere with the activity of hydrolytic enzymes and their producers, while promoting the growth of resistant prokaryotes and their capacity to obtain C and N sources from recalcitrant compounds. The resilience of biofilms in hypersaline lakes under extreme conditions is given by their resistant biochemichal structure and the adaptability of their microbial functioning.

Proper bed substrate selection is essential for the growth of microorganisms and plants, which are key elements in constructed wetlands (CWs) performance. This is even more important in CWs that treat irrigated agricultural drainage water characterised by a high nitrogen (N), but low carbon (C) and phosphorus (P) concentration. This nutrient imbalance compromises biota activity and limits water treatment processes. Three substrates were tested in a CW field-scale pilot plant for 2 years: gravel (100%) and two mixed substrates, gravel + 30% natural wetland soil and gravel + 10% biochar. While gravel is one of the most commonly used substrates in subsurface flow CWs, soil has hardly been employed, and field-scale biochar application studies are scarce. We analysed the effect of adding a C-rich substrate to gravel on both nutrient imbalance correction and the biotic performance of CWs. Adding natural soil or biochar increased P availability in beds. However, the dissolved organic C concentration in interstitial water was only enhanced by soil addition. Unlike gravel, microbial density and activity, and Phragmites australis plant growth, were higher in beds with soil, followed by those with biochar. A similar pattern was observed for plant tissue quality. Although biochar proved positive for biota, it had a short-term effect as a source of C and P. Therefore, employing a suitable gravel-soil mixture provides notable advantages for the irrigated agricultural water treatment challenge. Even after considering some limitations, our results represent an important step to design CWs that treat this wastewater type and for eutrophication control in sustainable agroecosystems.

&lt;p&gt;Changes in temperature and water availability under global warming will alter soil bacterial and fungal community structures and thus ecosystem functioning across the globe. We sampled large-scale temperature and aridity gradients across Greenland, Europe, Spain, the Swiss Alps and South Africa to understand microbial long-term adaptation to climatic conditions in soils and to predict microbial responses to climate change. We found that bacterial communities from South African soils were distinct from those in European and Greenlandic soils, largely explained by high relative abundances of Firmicutes. Conversely, fungal communities additionally differed between European and Greenlandic soils and thus seem to be more affected by oceans acting as geographical barrier compared to bacteria. Interestingly, bacterial communities in hyperarid soils from Northern Greenland clustered with hyperarid soils from Southern Spain and South Africa indicating that these communities share taxa adapted to low water availability despite their distinct geographical origin and temperature regimes. Within regional gradients in Europe and Greenland microbial community structures sequentially shifted along the gradients of temperature and aridity, whereas in the South African gradient soil physicochemical properties such as pH and texture that were not related with aridity were important drivers of microbial community structures. Shifts in fungal and bacterial community structures along climatic gradients occurred in parallel with changes in microbial functions, such as extracellular enzyme activities, greenhouse gas fluxes as well as abundances of functional genes involved in soil carbon and nitrogen cycling. Collectively, our results suggest that alterations in microbial community structures along climatic gradients, which serve as a proxy for climate change over time, translate into an alteration in ecosystem services provided by the community members. Moreover, at the global scale our study indicates that bacterial communities are mainly controlled by environmental conditions whereas fungal communities are more influenced by geographic barriers.&lt;/p&gt;

Mountain ecosystems contribute substantially to global carbon and nitrogen biogeochemical cycles. Although soil respiration, and microbial biomass, activities and diversity have been extensively studied at different altitudes worldwide, little is known on causal link between environmental drivers, microbial functions and emissions of greenhouse gases (GHGs) in soils of different elevation. Here, by measuring in-situ GHG fluxes, soil properties, organic matter (OM) quality, microbial enzyme activities, biomass and gene abundances, we investigate factors that control long-term GHG fluxes (carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)) in natural soils with an elevational gradient of ~2400 m across Switzerland with different vegetation covers. Results showed that CO2 and N2O fluxes increased significantly with elevation from top to the treeline, but slightly decreased from the treeline to bottom. Contrastingly, no significantly patterns of CH4 fluxes across the whole elevation were observed. Spearman correlations revealed that the increased CO2 and N2O fluxes were highly correlated to the significant increases in soil temperature, moisture, organic matter (OM) quantity and quality (increases in the relative contribution of humic-like vs. fresh-like OM), bacterial and fungal biomass and gene abundances. Structural equation model, hierarchical partitioning and random forest regression further confirmed that, in addition to soil temperature and moisture, SOM quantity and quality are the most driving factors of microbial activity and respiration. Our study highlights the importance of OM quality as a driving factor of soil microbial metabolic activities in Alpine soils across the elevation, and predicts a potential increase in GHG emissions in high-altitudinal soils with the expected upwarding-shifting treeline under climate warming.

To evaluate the effects of hydrological variability on pesticide dissipation capacity by stream biofilms, we conducted a microcosm study. We exposed biofilms to short and frequent droughts (daily frequency), long and less frequent droughts (weekly frequency) and permanently immersed controls, prior to test their capacities to dissipate a cocktail of pesticides composed of tebuconazole, terbuthylazine, imidacloprid, glyphosate and its metabolite aminomethylphosphonic acid. A range of structural and functional descriptors of biofilms (algal and bacterial biomass, extracellular polymeric matrix (EPS) concentration, microbial respiration, phosphorus uptake and community-level physiological profiles) were measured to assess drought effects. In addition, various parameters were measured to characterise the dynamics of pesticide dissipation by biofilms in the different hydrological treatments (% dissipation, peak asymmetry, bioconcentration factor, among others). Results showed higher pesticide dissipation rates in biofilms exposed to short and frequent droughts, despite of their lower biomass and EPS concentration, compared to biofilms in immersed controls or exposed to long and less frequent droughts. High accumulation of hydrophobic pesticides (tebuconazole and terbuthylazine) was measured in biofilms despite the short exposure time (few minutes) in our open-flow microcosm approach. This research demonstrated the stream biofilms capacity to adsorb hydrophobic pesticides even in stressed drought environments.

Plastic pollution represents a threat for biological communities and the ecological functions they provide in river ecosystems. In this study, we compared the microbial colonization of two plastics (biodegradable and non-biodegradable) and three natural substrata (leaves, sediment, and rocks) in two study sites of an urbanized watershed differing in their plastic-contamination degree (upstream and downstream). The density and diversity of bacterial, fungal, and algal communities, as well as the extracellular enzymatic activities β-glucosidase (GLU), N-acetyl-glucosaminidase (NAG), and phosphatase (PHO), were analysed in each substrata and site over a 4-week colonization experiment. Results showed higher microbial densities and enzymatic activities in leaves and sediment compared to plastics and rocks, probably due to the greater availability of organic carbon and nutrients in the former substrata. However, the microbial colonization of the two plastics was only different in the downstream site, where bacterial density and enzymatic activities were higher in the biodegradable plastic compared to the non-biodegradable plastic. Accordingly, the presence of biodegradable plastics would enhance the heterotrophic metabolism in plastic-polluted rivers.