Water diversion and pollution interactively shape freshwater food webs through bottom-up mechanisms

New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary

Environmental DNA (eDNA) metabarcoding is an emerging tool for monitoring biological communities in aquatic ecosystems. The selection of bioinformatic pipelines significantly impacts the results of biodiversity assessments. However, there is currently no consensus on the appropriate bioinformatic pipelines for fish community analysis in eDNA metabarcoding. In this study, we compared three bioinformatic pipelines (Uparse, DADA2, and UNOISE3) using real and mock (constructed with 15/30 known fish) communities to investigate the differences in biological interpretation during the data analysis process in eDNA metabarcoding. Performance evaluation and diversity analyses revealed that the choice of bioinformatic pipeline could impact the biological results of metabarcoding experiments. Among the three pipelines, the operational taxonomic units (OTU)-based pipeline (Uparse) showed the best performance (sensitivity: 0.6250 ± 0.0166; compositional similarity: 0.4000 ± 0.0571), the highest richness (25-102) and minimal inter-group differences in alpha diversity. It suggested the OTU-based pipeline possessed superior capability in fish diversity monitoring compared to ASV/ZOTU-based pipeline. Additionally, the Bray-Curtis distance matrix achieved the highest discriminative effect in the PCoA (43.3%-53.89%) and inter-group analysis (P < 0.01), indicating it was better at distinguishing compositional differences or specific genera of fish community at different sampling sites than other distance matrices. These findings provide new insights into fish community monitoring through eDNA metabarcoding in estuarine environments.

Water quality drives the reconfiguration of riverine planktonic microbial food webs

The food web is a cycle of matter and energy within river ecosystems. River environmental changes resulting from human activities are increasingly threatening the composition and diversity of global aquatic organisms and the multi-trophic networks. How multiple environmental factors influence food web patterns among multi-trophic microbial communities in rivers remains largely unknown. Using water quality evaluation and meta-omics techniques, we investigated the composition, structure and interaction characteristics, and drivers of food webs of microorganisms (archaea, bacteria, fungi, protists, metazoa, viridiplantae and viruses) at multiple trophic levels in different water quality environments (Classes II, III, and IV). First, water quality deterioration led to significant changes in the composition of the microbial community at multiple trophic levels, which were represented by the enrichment of Euryarchaeota in the archaeal community, the increase of r-strategists in the bacterial community, and the increase of the proportion of predators in the protist community. Second, deteriorating water quality resulted in a significant reduction in the dissimilarity of community structure (homogenization of community structure in Class III and IV waters). Of the symbiotic, parasitic, and predatory networks, the community networks in Class II water all showed the most stable symbiotic, parasitic, and predatory correlations (higher levels of modularity in the networks). In Class III and IV waters, nutrient inputs have led to increased reciprocal symbiosis and decreased competition between communities, which may have the risk of a positive feedback loop driving a system collapse. Finally, inputs of phosphorus and organic matter could be the main drivers of changes in the planktonic microbial food web in the Fen River. Overall, the results indicated the potential ecological risks of exogenous nutrient inputs, which were important for aquatic ecosystem conservation.

eDNA-based diversity and multitrophic network reveal the effects of land use and pollutants on the subtropical Dongjiang River systems

Biodiversity and its constituted multitrophic network in rivers are accelerating change under human land use and pollutants. However, due to the lack of complete datasets across taxa limited by traditional morphological biomonitoring, the change patterns of biodiversity and multitrophic networks are still unclear. Here, we used the eDNA approach to capture multitrophic communities (including fish, aquatic insects, protozoa, diatom and bacteria) in the Dongjiang River, a typical subtropical river in southeast China, and analyzed the changing patterns of biodiversity and multitrophic networks in relation to land use and water pollution. First, our data showed that the eDNA approach provided a snapshot of the multitrophic communities in the Dongjiang River, and the monitored 5833 OTUs were annotated to 55 phyla, 144 classes, 329 orders, 521 families, 945 genera and 406 species. Second, the multitrophic diversity index had similar patterns on the longitudinal scale of rivers, with significant decreases from the upstream to the downstream, while individual taxonomic groups exhibited variable spatial patterns. While there were similar spatial patterns between network metrics and diversity index, the former had stronger relationships with the spatial distance. Third, the multitrophic diversity and networks were significantly negatively correlated with land use and water pollution (e.g., CODMn), and network structures often had stronger and non-linear responses. Overall, this study highlights that eDNA biomonitoring of multitrophic communities and networks can provide deeper insights into ecosystem changes and help develop more targeted management strategies.

Open riparian canopy and nutrient pollution interactively decrease trophic redundancy and allochthonous resource in streams

Riparian deforestation, which leads to increase in light intensity and excessive nutrient loading in waterways, are two pervasive environmental stressors in the stream ecosystems. Both have been found to alter basal resource availability and consequently stream food webs. However, their interactive effects on trophic structure in stream food webs are unclear. Here, we manipulated light intensity and nutrient availability in three headwater streams to evaluate their effects on consumer diet composition and food web characteristics (i.e., trophic diversity and redundancy) with stable isotope analysis. Dietary analysis revealed that the relative contribution of stream periphyton to the diets of macroinvertebrates increased, while that of allochthonous resources, specifically leaf litter from the terrestrial ecosystems in the catchment, decreased in response to open canopy and nutrient enrichment in the streams. The trophic diversity also increased with the elevated light intensity and nutrient availability, while the trophic redundancy decreased, suggesting a reduced ability of the stream ecosystems to resist environmental changes. Nutrient enrichment also increased the δ15N ratios of periphyton and macroinvertebrates, indicating potential δ15N enrichment of stream benthos by nitrogen pollution. Our results suggested that an increase in light intensity due to riparian canopy openness and stream water nutrient enrichment primarily from human activities have interactive effects on resource flow and trophic structure in stream food webs.

Key factors driving dissolved organic matter composition and bioavailability in lakes situated along the Eastern Route of the South-to-North Water Diversion Project, China

The Eastern Route of the South-to-North Water Diversion Project (SNWDP-ER) is a large scale multi-decade infrastructure project aiming to divert substantial amounts of water (≈45 billion m³ yr^-1) to alleviate water shortage in comparatively arid regions of northern China. The project has ramifications for hydrological connectivity and biogeochemical cycling of dissolved organic matter (DOM) in regional lakes affected by the project. We carried out an extensive field sampling campaign along the SNWDP-ER in different hydrological seasons of 2018 and monthly observations in Lake Hongze and Lake Luoma from April 2018 to June 2021. We found the lakes connecting to the SNWDP-ER had higher mean DOC, specific UV absorbance, higher ratio of humic-like to protein-like fluorophores (Humic : Protein), and shallower spectral slope (S_275-295) in the wet season compared to the wet-to-dry transition, and dry seasons. The southern lakes and Yangtze River had lower DOC concentration, bioavailable DOC (BDOC), and higher DOM aromaticity compared to the northern two downstream lakes. Ultrahigh-resolution mass spectrometry (FT-ICR MS) revealed higher relative abundance of CHO-containing and aromatic compounds in the Yangtze River and the southern three upstream lakes compared to the northern two lakes. The data from Lake Hongze and Lake Luoma, studied in different hydrological seasons, suggest that water delivery had high consistency in DOM composition and BDOC over the season. We conclude that positioning along the watercourse and seasonally variable hydrological conditions play an important role in influencing the DOM composition and bioavailability of key lakes connecting to the SNWDP-ER. Our results indicated that the water diversion project delivers water with low DOC concentration and higher aromaticity and thus is of higher quality since it has higher DOM removal potential during drinking water treatment.

Environmental DNA Biomonitoring Reveals the Interactive Effects of Dams and Nutrient Enrichment on Aquatic Multitrophic Communities

Dam construction and nutrient enrichment are two pervasive stressors in rivers worldwide, which trigger a sharp decline in biodiversity and ecosystem services. However, the interactive effects of both stressors on multitrophic taxonomic groups remain largely unclear. Here, we used the multitrophic datasets captured by the environmental DNA (eDNA) approach to reveal the interactions between dams and nutrient enrichment on aquatic communities from the aspects of taxonomic α diversity, β diversity, and food webs. First, our data showed that dams and nutrient enrichment jointly shaped a unique spatial pattern of aquatic communities across the four river systems, and the dissimilarity of community structure significantly declined (i.e., structural homogenization) under both stressors. Second, dams and nutrients together explained 40-50% of the variations in aquatic communities, and dams had a stronger impact on fish, aquatic insects, and bacteria, yet nutrients had a stronger power to drive protozoa, fungi, and eukaryotic algae. Finally, we found that additive, synergistic, and antagonistic interactions of dams and nutrient enrichment were common and coexisted in river systems and led to significantly simplified aquatic food webs, with decreases in modularity (synergistic) and robustness (additive) and an increase in coherence (synergistic). Overall, our study highlights that eDNA-based datasets can provide multitrophic perspectives for fostering the understanding of the interactive effects of multiple stressors on rivers.

Nitrogen loadings affect trophic structure in stream food webs on the Tibetan Plateau, China

Anthropogenic activities, such as agricultural and industrial development, have increased nutrient inputs into waterways, which affect trophic interactions and the flow of energy through food webs in the aquatic ecosystems. However, the responses of food web structure and function to specific anthropogenic stressors in the alpine stream systems remain unclear. Here, we studied the stream food webs in the Lhasa River on the Tibetan Plateau, China. We measured the isotopic ratios (δ¹³C and δ¹⁵N) of macroinvertebrate and fish functional feeding groups (FFGs) and their basal resources in the streams. Dietary contributions of basal resources to consumers and food web metrics including trophic length, diversity, and redundancy were used to quantify changes in stream food webs in response to anthropogenic disturbance. Dietary analysis showed that allochthonous resources contributed more than autochthonous resources to macroinvertebrate primary consumers regardless of the disturbance intensity in the adjacent land areas. Anthropogenic activities increased the δ¹⁵N values in epilithic algae and isotopic variation in basal resources and fish but reduced the trophic length and redundancy (i.e., fewer species or taxon at each trophic level) in food webs. Additionally, the total nitrogen concentration in waters was the most important environmental variable affecting trophic diversity and redundancy. Therefore, the reduction of nitrogen inputs into streams is critical for sustainable river management and biodiversity conservation in the streams on the Tibetan Plateau.

Water diversion and pollution interactively shape freshwater food webs through bottom-up mechanisms

Water diversion and pollution are two pervasive stressors in river ecosystems that often co-occur. Individual effects of both stressors on basal resources available to stream communities have been described, with diversion reducing detritus standing stocks and pollution increasing biomass of primary producers. However, interactive effects of both stressors on the structure and trophic basis of food webs remain unknown. We hypothesized that the interaction between both stressors increases the contribution of the green pathway in stream food webs. Given the key role of the high-quality, but less abundant, primary producers, we also hypothesized an increase in food web complexity with larger trophic diversity in the presence of water diversion and pollution. To test these hypotheses, we selected four rivers in a range of pollution subject to similar water diversion schemes, and we compared food webs upstream and downstream of the diversion. We characterized food webs by means of stable isotope analysis. Both stressors directly changed the availability of basal resources, with water diversion affecting the brown food web by decreasing detritus stocks, and pollution enhancing the green food web by promoting biofilm production. The propagation of the effects at the base of the food web to higher trophic levels differed between stressors. Water diversion had little effect on the structure of food webs, but pollution increased food chain length and trophic diversity, and reduced trophic redundancy. The effects at higher trophic levels were exacerbated when combining both stressors, as the relative contribution of biofilm to the stock of basal resources increased even further. Overall, we conclude that moderate pollution increases food web complexity and that the interaction with water abstraction seems to amplify this effect. Our study shows the importance of assessing the interaction between stressors to create predictive tools for a proper management of ecosystems.

The role of cladocerans in green and brown food web coupling

ABSTRACT Cladocerans, an important zooplankton community, are consumers from the base of the food web of aquatic environments. We investigated the contribution of producers (phytoplankton and periphytic biofilm) and particulate organic carbon (POC). Collections were carried out in lakes of the Upper Paraná River Floodplain, the last stretch free of dams in the second-largest South American basin. Isotope ratios (δ13C and δ15N) were measured, besides the contributions of probable food sources to the cladocerans biomass. The phytoplankton constituted the source of carbon for cladocerans, followed by POC. Thus this work, in addition to emphasizing the importance of cladocerans in nutrient cycling, highlighted the need for the conservation of environments surrounding the lakes as they are the sources of organic matter for aquatic communities. Besides, the analyzed zooplanktonic organisms demonstrated their role in the interconnection between the green and brown food webs, which have been studied separately for a long time.