Organic Matter Decomposition and Ecosystem Metabolism as Tools to Assess the Functional Integrity of Streams and Rivers–A Systematic Review

Differential response of multiple stream ecosystem processes to basin- and reach-scale drivers

Stream ecosystems are inherently dependent on their surroundings and, thus, highly vulnerable to anthropogenic impacts, which alter both their structure and functioning. Anchored in biologically-mediated processes, the response of stream ecosystem functioning to environmental conditions exhibits intricate patterns, reflecting both natural dynamics and human-induced changes. Our study aimed at determining the natural and anthropogenic drivers influencing multiple stream ecosystems processes (nutrient uptake, biomass accrual, decomposition, and ecosystem metabolism) at a regional scale. By examining 38 natural and anthropogenic variables across 63 stream reaches in Gipuzkoa (northern Iberian Peninsula), we used structural equation modeling to unravel the cascading effect of basin- and reach-scale drivers onto ecosystem process. The results reveal significant variability in ecosystem processes, with contrasting spatial patterns, suggesting that studied processes respond differently to environmental factors. Urban land-use emerged as a primary basin-scale driver, whereas reach-scale variables reflected both natural and anthropogenic influence. Nutrient uptake rates were primarily driven by nutrient concentrations in stream water, but models for biomass accrual, decomposition, and ecosystem metabolism exhibited more complex cause-effect relationships. Our findings highlight the impact of urban areas on multiple ecosystem processes and services, disproportionate when considering their small land cover. The present study emphasizes the convenience of measuring multiple ecosystem functions simultaneously to get a comprehensive diagnosis of the functional status of rivers.

Rehabilitation of tropical urban streams improves their structure and functioning

Urban streams are affected by a complex combination of stressors, which modify physical habitat structure, flow regime, water quality, biological community composition, and ecosystem processes and services, thereby altering ecosystem structure and functioning. Rehabilitation projects have been undertaken in several countries to rehabilitate urban streams. However, stream rehabilitation is still rarely reported for neotropical regions. In addition, most studies focus on structural aspects, such as water quality, sediment control, and flood events, without considering ecosystem function indicators. Here, we evaluated the structure and functioning of three 15-y old rehabilitated urban stream sites in comparison with three stream sites in the best available ecological condition (reference), three sites with moderate habitat alteration, and three severely degraded sites. Compared to degraded streams, rehabilitated streams had higher habitat diversity, sensitive macroinvertebrate taxa richness, and biotic index scores, and lower biochemical oxygen demand, primary production, sediment deposition, and siltation. However, rehabilitated streams had higher primary production than moderate and reference streams, and lower canopy cover, habitat diversity, sensitive macroinvertebrate taxa richness, and biotic index scores than reference streams. These results indicate that rehabilitated streams have better structural and functional condition than degraded streams, but do not strongly differ from moderately altered streams, nor have they reached reference stream condition. Nonetheless, we conclude that rehabilitation is effective in removing streams from a degraded state by improving ecosystem structure and functioning. Furthermore, the combined use of functional and structural indicators facilitated an integrative assessment of stream ecological condition and distinguished stream conditions beyond those based on water quality indicators.

Assessing the response of an urban stream ecosystem to salinization under different flow regimes

Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.

Improving ecosystem health in highly altered river basins: a generalized framework and its application to the Mississippi-Atchafalaya River Basin

Continued large-scale public investment in declining ecosystems depends on demonstrations of "success". While the public conception of "success" often focuses on restoration to a pre-disturbance condition, the scientific community is more likely to measure success in terms of improved ecosystem health. Using a combination of literature review, workshops and expert solicitation we propose a generalized framework to improve ecosystem health in highly altered river basins by reducing ecosystem stressors, enhancing ecosystem processes and increasing ecosystem resilience. We illustrate the use of this framework in the Mississippi-Atchafalaya River Basin (MARB) of the central United States (U.S.), by (i) identifying key stressors related to human activities, and (ii) creating a conceptual ecosystem model relating those stressors to effects on ecosystem structure and processes. As a result of our analysis, we identify a set of landscape-level indicators of ecosystem health, emphasizing leading indicators of stressor removal (e.g., reduced anthropogenic nutrient inputs), increased ecosystem function (e.g., increased water storage in the landscape) and increased resilience (e.g., changes in the percentage of perennial vegetative cover). We suggest that by including these indicators, along with lagging indicators such as direct measurements of water quality, stakeholders will be better able to assess the effectiveness of management actions. For example, if both leading and lagging indicators show improvement over time, then management actions are on track to attain desired ecosystem condition. If, however, leading indicators are not improving or even declining, then fundamental challenges to ecosystem health remain to be addressed and failure to address these will ultimately lead to declines in lagging indicators such as water quality. Although our model and indicators are specific to the MARB, we believe that the generalized framework and the process of model and indicator development will be valuable in an array of altered river basins.

Standard Versus Natural: Assessing the Impact of Environmental Variables on Organic Matter Decomposition in Streams Using Three Substrates

The decomposition of allochthonous organic matter, such as leaves, is a crucial ecosystem process in low-order streams. Microbial communities, including fungi and bacteria, colonize allochthonous organic material, break up large molecules, and increase the nutritional value for macroinvertebrates. Environmental variables are known to affect microbial as well as macroinvertebrate communities and alter their ability to decompose organic matter. Studying the relationship between environmental variables and decomposition has mainly been realized using leaves, with the drawbacks of differing substrate composition and consequently between-study variability. To overcome these drawbacks, artificial substrates have been developed, serving as standardizable surrogates. In the present study, we compared microbial and total decomposition of leaves with the standardized substrates of decotabs and, only for microbial decomposition, of cotton strips, across 70 stream sites in a Germany-wide study. Furthermore, we identified the most influential environmental variables for the decomposition of each substrate from a range of 26 variables, including pesticide toxicity, concentrations of nutrients, and trace elements, using stability selection. The microbial as well as total decomposition of the standardized substrates (i.e., cotton strips and decotabs) were weak or not associated with that of the natural substrate (i.e., leaves, r² < 0.01 to r² = 0.04). The decomposition of the two standardized substrates, however, showed a moderate association (r² = 0.21), which is probably driven by their similar composition, with both being made of cellulose. Different environmental variables were identified as the most influential for each of the substrates and the directions of these relationships contrasted between the substrates. Our results imply that these standardized substrates are unsuitable surrogates when investigating the decomposition of allochthonous organic matter in streams. Environ Toxicol Chem 2023;42:2007-2018. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification

Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.

Functional measures as potential indicators of down-the-drain chemical stress in freshwater ecological risk assessment

Conventional ecological risk assessment (ERA) predominately evaluates the impact of individual chemical stressors on a limited range of taxa, which are assumed to act as proxies to predict impacts on freshwater ecosystem function. However, it is recognized that this approach has limited ecological relevance. We reviewed the published literature to identify measures that are potential functional indicators of down-the-drain chemical stress, as an approach to building more ecological relevance into ERA. We found wide variation in the use of the term "ecosystem function," and concluded it is important to distinguish between measures of processes and measures of the capacity for processes (i.e., species' functional traits). Here, we present a classification of potential functional indicators and suggest that including indicators more directly connected with processes will improve the detection of impacts on ecosystem functioning. The rate of leaf litter breakdown, oxygen production, carbon dioxide consumption, and biomass production have great potential to be used as functional indicators. However, the limited supporting evidence means that further study is needed before these measures can be fully implemented and interpreted within an ERA and regulatory context. Sensitivity to chemical stress is likely to vary among functional indicators depending on the stressor and ecosystem context. Therefore, we recommend that ERA incorporates a variety of indicators relevant to each aspect of the function of interest, such as a direct measure of a process (e.g., rate of leaf litter breakdown) and a capacity for a process (e.g., functional composition of macroinvertebrates), alongside structural indicators (e.g., taxonomic diversity of macroinvertebrates). Overall, we believe that the consideration of functional indicators can add value to ERA by providing greater ecological relevance, particularly in relation to indirect effects, functional compensation (Box 1), interactions of multiple stressors, and the importance of ecosystem context. Environ Assess Manag 2022;18:1135-1147. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

A global synthesis of human impacts on the multifunctionality of streams and rivers

Human impacts, particularly nutrient pollution and land-use change, have caused significant declines in the quality and quantity of freshwater resources. Most global assessments have concentrated on species diversity and composition, but effects on the multifunctionality of streams and rivers remain unclear. Here, we analyse the most comprehensive compilation of stream ecosystem functions to date to provide an overview of the responses of nutrient uptake, leaf litter decomposition, ecosystem productivity, and food web complexity to six globally pervasive human stressors. We show that human stressors inhibited ecosystem functioning for most stressor-function pairs. Nitrate uptake efficiency was most affected and was inhibited by 347% due to agriculture. However, concomitant negative and positive effects were common even within a given stressor-function pair. Some part of this variability in effect direction could be explained by the structural heterogeneity of the landscape and latitudinal position of the streams. Ranking human stressors by their absolute effects on ecosystem multifunctionality revealed significant effects for all studied stressors, with wastewater effluents (194%), agriculture (148%), and urban land use (137%) having the strongest effects. Our results demonstrate that we are at risk of losing the functional backbone of streams and rivers if human stressors persist in contemporary intensity, and that freshwaters are losing critical ecosystem services that humans rely on. We advocate for more studies on the effects of multiple stressors on ecosystem multifunctionality to improve the functional understanding of human impacts. Finally, freshwater management must shift its focus toward an ecological function-based approach and needs to develop strategies for maintaining or restoring ecosystem functioning of streams and rivers.

The combination of chemical, structural, and functional indicators to evaluate the anthropogenic impacts on agricultural stream ecosystems

Freshwater contamination by pesticides in agricultural landscapes is of increasing concern worldwide, with strong pesticide impacts on biodiversity, ecosystem functions, and ultimately human health (drinking water, fishing). In addition, the excessively large number of substances, as well as their low - and temporally variable - concentrations in water, make the chemical monitoring by grab sampling very demanding and not fully representative of the actual contamination. Tools that integrate temporal variations and that are ecologically relevant are clearly needed to improve the monitoring of freshwater contamination and assess its biological effects. Here, we studied pesticide contamination and its biological impacts in 10 stream sections (sites) belonging to 3 agricultural catchments in France. In each site, we deployed a combination of pesticide integrative samplers, biocenotic indicators based on benthic macroinvertebrates, and functional indicators based on leaf litter decomposition and associated fungal communities. The 3 approaches largely proved complementary: structural and functional indicators did not respond equally to different agricultural impacts such as pesticide contamination (as revealed by integrative samplers), nutrients, or oxygen depletion. Combining chemical, structural, and functional indicators thus seems an excellent strategy to provide a comprehensive picture of agricultural impacts on stream ecosystems.

Organic-matter decomposition as a bioassessment tool of stream functioning: A comparison of eight decomposition-based indicators exposed to different environmental changes

Organic-matter decomposition has long been proposed as a tool to assess stream functional integrity, but this indicator largely depends on organic-matter selection. We assessed eight decomposition-based indicators along two well-known environmental gradients, a nutrient-enrichment gradient (0.2-1.4 mg DIN/L) in central Portugal and an acidification gradient (pH: 4.69-7.33) in north-eastern France to identify the most effective organic-matter indicator for assessing stream functional integrity. Functional indicators included natural leaf litter (alder and oak) in 10-mm and 0.5-mm mesh bags, commercial tea (Lipton green and rooibos teas in 0.25-mm mesh bags), wood sticks (wood tongue depressors) and cotton strips. Biotic indices based on benthic macroinvertebrates (IPtI_N for Portugal and IBGN for France) were calculated to compare the effectiveness of structural and functional indicators in detecting stream impairment and to assess the relationship between both types of indicators. The effectiveness of organic-matter decomposition rates as a functional indicator depended on the stressor considered and the substrate used. Decomposition rates generally identified nutrient enrichment and acidification in the most acidic streams. Decomposition rates of alder and oak leaves in coarse-mesh bags, green and rooibos teas and wood sticks were positively related with pH. Only decomposition rates of rooibos tea and wood sticks were related with DIN concentration; decomposition rates along the nutrient-enrichment gradient were confounded by differences in shredder abundance and temperature among streams. Stream structural integrity was good to excellent across streams; the IPtI_N index was unrelated to DIN concentration, while the IBGN index was positively related with pH. The relationships between decomposition rates and biotic indices were loose in most cases, and only decomposition rates of alder leaves in coarse-mesh bags and green tea were positively related with the IBGN. Commercial substrates may be a good alternative to leaf litter to assess stream functional integrity, especially in the case of nutrient enrichment.