Functional redundancy and sensitivity of fish assemblages in European rivers, lakes and estuarine ecosystems

Individual and combined effects of design and inter-operator variability on stream ecological assessment

In the context of long-term monitoring of stream ecological quality at large spatial extent, it is important to assess the overall reliability of a biotic index and to mitigate its uncertainty to ensure the effectiveness of stakeholder assessments and decisions. Only few studies have focused on the uncertainties associated to both the design of the method used to assess ecological status and the different steps of biological data acquisition. In this study we investigated the uncertainty associated with the design of a multimetric index (i.e., the uncertainty related to index parameter values because of the development dataset characteristics and calculation method), as well as the field data uncertainty because of inter-operator variability (i.e., associated with the sampling, sorting and identification steps of the applied protocol). We examined how the combined sources of uncertainty propagate to the index values and the final ecological assessment of water bodies. For this study, we focused on the I2M2, a multimetric index based on benthic macroinvertebrate assemblages and used to assess the ecological quality of French wadeable streams in the context of the European Water Framework Directive. We have shown that inter-operator variability was always the main source of uncertainty. The uncertainty related to the index design remained very limited. This study has highlighted the importance of robust index design combined with standardisation of the field and laboratory steps for the overall reliability of a biotic index, especially for long-term, spatially extensive monitoring of stream ecological health.

Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism

Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.

Stochastic process is main factor to affect plateau river fish community assembly

Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers.

Trait-based insights into sustainable fisheries: A four-decade perspective in Azores archipelago

The trait-based approach provides a powerful perspective for analyzing fisheries and their potential impact on marine ecological processes, offering crucial insights into sustainability and ecosystem functioning. This approach was applied to investigate trends in fish assemblages landed by both local and coastal fishing fleets in the Azores archipelago over the past four decades (1980s, 1990s, 2000s, and 2010s). A matrix of ten traits was built to assess functional redundancy (Fred), functional over-redundancy (FOve), and functional vulnerability (FVul) for the fish assemblages caught by every fishing fleet in each decade. The susceptibility of the Azorean fishery to negative impacts on ecosystem functioning was evidenced by low FRed (<1.5 species per functional entity) and high FVul (exceeding 70 %). However, there is reason for optimism, as temporal trends in the 2000s and 2010s showed an increase in FRed and FOve along with a significant decrease in FVul. These trends indicate the adaptation of the fishery to new target species and, notably, the effectiveness of local fish regulations in mitigating the impacts of targeting functionally important species, such as Elasmobranchii, over the past two decades. These regulations have played a pivotal role in preserving ecological functions within the ecosystem, as well as in managing the removal of high biomass of key important species (e.g., Trachurus picturatus, Pagellus bogaraveo, and Katsuwonus pelamis) from the ecosystem. This study contributes to understanding the delicate balance between fishing pressure, ecological resilience, and sustainable resource management in Azorean waters. It also highlights the importance of continued monitoring, adaptive management, and the enforcement of local fishing regulations to ensure the long-term health and sustainability of the fishery and the broader marine ecosystem.

Interdecadal changes in ichthyofauna in a tropical bay with high anthropogenic influences: functional stability despite turnover predominance

Functional characteristics of species are of great importance for understanding their roles in ecosystems and can be used to detect long-term chances in the environment. We evaluated temporal changes (1983-1985 and 2017-2019) in taxonomic and functional indices of the fish fauna in shallow areas of a tropical bay heavily impacted by anthropogenic activities in recent decades. The hypothesis that functional indices change over time as a result of environmental degradation was tested. Our results showed a significant decrease in species richness and abundance over time, and in functional richness, while others functional diversity indices (divergency, evenness, and originality) remained stable. Thirteen functional groups were detected, some of which contained only one species, raising concerns about the loss of ecosystem functions due to ongoing changes. We also observed an increase in beta diversity over time, which may be the result of a decrease in local richness without leading to regional extinctions. Turnover was the most important process in structuring the fish fauna at the evaluated time scale. The relative stability of the functional structure and the higher levels of turnover seem to be related to the dominance of functional groups, within which species replace each other according to their responses to environmental filters that select for specific functional traits. Incorporating functional diversity indices and beta diversity variations in the fish community helped to enhance the existing information about this coastal system by offering improved estimates of biological diversity through diverse approaches. The predominance of turnover identified in the preset study suggests a dynamic and fluctuating species composition within the habitat. In this sense, habitat preservation should prioritize the protection of diverse habitats to accommodate a broad spectrum of species.

Disentangling the effects of different human disturbances on multifaceted biodiversity indices in freshwater fish

Evaluating the effects of anthropogenic pressures on several biodiversity metrics can inform the management and monitoring of biodiversity loss. However, the type of disturbances can lead to different responses in different metrics. In this study, we aimed at disentangling the effects of different types of anthropogenic disturbances on freshwater fish communities. We calculated diversity indices for 1109 stream fish communities across France by computing richness and evenness components for ecological, morphological, and phylogenetic diversity, and used null models to estimate standardized effect sizes. We used generalized linear mixed models to assess the relative effects of environmental and anthropogenic drivers in driving those diversity indices. Our results demonstrated that all diversity indices exhibited significant responses to both climatic conditions and anthropogenic disturbances. While we observed a decrease of ecological and phylogenetic richness with the intensity of disturbance, a weak increase in morphological richness and evenness was apparent. Overall, our results demonstrated the importance of disentangling various types of disturbances when assessing human-induced ecological impacts and highlighted that different facets of diversity are not impacted identically by anthropogenic disturbances in stream fish communities. This calls for further work seeking to integrate biodiversity responses to human disturbances into a multifaceted framework, and could have beneficial implications when planning conservation action in freshwater ecosystems.

Taxonomic and Functional Responses of Species-Poor Riverine Fish Assemblages to the Interplay of Human-Induced Stressors

The effects of human-induced stressors on riverine fish assemblages are still poorly understood, especially in species-poor assemblages such as those of temperate South American rivers. In this study we evaluated the effects of human-induced stressors on the taxonomic and functional facets of fish assemblages of two central-southern Chilean rivers: the Biobío River (flow regulated by multiple dams) and the Valdivia River (free-flowing). The study design considered reference condition, urban polluted, and urban-industrial polluted sites. To evaluate the effects of stressors on fish assemblages we assessed: (i) components of beta diversity; (ii) spatial and temporal patterns of fish structure using a multivariate approach; and (iii) functional diversity (specialization, originality, dispersion, and entropy) using linear models. We found a strong association between taxonomic and functional fish assemblage facets with a predominance of natural processes in the Valdivia River reflected in marked temporal dynamics. In contrast, the Biobío River showed a clear loss of association with seasonal pattern, and both taxonomic and functional facets appeared to respond significantly to pollution zones. Implementation of stricter environmental policies and integrated river basin management are instrumental for conserving species-poor fish assemblages in Chilean temperate rivers characterized by low functional traits redundancy.

Taxonomic and functional homogenization of farmland birds along an urbanization gradient in a tropical megacity

Urbanization is a major driver of land use change and biodiversity decline. While most of the ongoing and future urbanization hotspots are located in the Global South, the impact of urban expansion on agricultural biodiversity and associated functions and services in these regions has widely been neglected. Additionally, most studies assess biodiversity responses at local scale (α-diversity), however, ecosystem functioning is strongly determined by compositional and functional turnover of communities (β-diversity) at regional scales. We investigated taxonomic and functional β-diversity of farmland birds across three seasons on 36 vegetable farms spread along a continuous urbanization gradient in Bangalore, a South Indian megacity. Increasing amount of grey area in the farm surroundings was the dominant driver affecting β-diversity and resulting in taxonomic and functional homogenization of farmland bird communities. Functional diversity losses were higher than expected from species declines (i.e., urbanization acts as an environmental filter), with particular losses of functionally important groups such as insectivores of crop pests. Moreover, urbanization reduced functional redundancy of bird communities, which may further weaken ecosystems resilience to future perturbations. Our study underscores urbanization as a major driver of taxonomic and functional homogenization of species communities in agricultural systems, potentially threatening crucial ecosystem services for food production.

Assessing tropical coastal dynamics across habitats and seasons through different dimensions of fish diversity

Coastal habitat mosaics are among the most productive ecosystems around the globe, with many ecological and social-economic services provided. Their natural challenging conditions have always been a subject of concern for ecologist and conservationist, with a particular interest in understanding how its spatial and temporal dynamics influence ecosystem functioning. In this context, we aimed to assess tropical coastal dynamics using an integrative approach, measuring the different facets of fish diversity across space (habitats) and time (seasons). Three different estuarine systems and their adjacent areas in the southwestern Atlantic were monthly sampled between July 2017 and June 2018, in a sampling design that encompassed three different coastal mosaics with three habitat types (mangroves, seagrass and sandy beaches), and both seasons of the studied region (dry and rainy). Taxonomic, phylogenetic, and functional diversity were then evaluated with equivalent diversity measures to allow comparisons between them. Different patterns of species occurrence and distribution were found between habitats and seasons, which resulted in different effects on the abundance-weighted diversity dimensions. Although taxonomic diversity of habitats was greater during the rainy season (p = 0.03), a seasonal increase in phylogenetic diversity was only observed in the sandy beach habitat (p = 0.04). In contrast for the functional diversity, no significant differences were found among habitats in both seasons (p = 0.15), indicating high levels of redundancy. Our results showed that patterns in the occurrence and abundance of tropical fish species among habitats that comprise a coastal mosaic have different effects on distinct diversity dimensions. More precisely, for tropical coastal systems with marked seasonality, both habitats and season appear to play a synergic role in the maintenance of ecosystem functioning by enhancing functional and phylogenetic redundancy.

Depletion of coastal predatory fish sub-stocks coincided with the largest sea urchin grazing event observed in the NE Atlantic

In this contribution, we propose fishery driven predator release as the cause for the largest grazing event ever observed in the NE Atlantic. Based on the evolving appreciation of limits to population connectivity, published and previously unpublished data, we discuss whether overfishing caused a grazer bloom of the sea urchin (Strongylocentrotus droebachiensis) resulting in overgrazing of more than 2000 km² kelp (Laminaria hyperborea) forest along Norwegian and Russian coasts during the 1970 s. We show that coastal fisheries likely depleted predatory coastal fish stocks through modernization of fishing methods and fleet. These fish were important predators on urchins and the reduction coincided with the urchin bloom. From this circumstantial evidence, we hypothesize that coastal predatory fish were important in regulating sea urchins, and that a local population dynamics perspective is necessary in management of coastal ecosystems.

Temporal Dynamics of Fish Assemblages as a Reflection of Policy Shift from Fishing Concession to Co-Management in One of the World’s Largest Tropical Flood Pulse Fisheries

Inland fisheries management in Cambodia has undergone two major policy reforms over the last two decades. These reforms led to the abolishment of a century-old commercial fishing lot system in 2012 and the establishment of new fish sanctuary and community fishing areas. However, the status of fisheries and fish assemblages following the reforms is not well understood. Here, we investigated the temporal changes in fish catch weight and fish assemblage structure for the period 1995–2000 before fishing lot abolishment (BLA) and for the period 2012–2015 after the removal of all fishing lots (after lot abolishment-ALA) using time-series fish catch data recorded from the Tonle Sap Lake (TSL), one of the world largest inland fisheries. We found (i) mean catch trends vary seasonally, with stable catch trends during the BLA and decreasing catch trends during the ALA and (ii) significant shifts in fish assemblage composition, notably a shift from large-bodied, migratory, and/or predatory species during the BLA toward more short-distance migratory and/or floodplain, small-bodied species during the ALA. Fishing lot abolishment coincided with substantial changes to floodplain habitats and increases in fishing pressure, threatening TSL fish stocks. Flow alterations caused by dams and climate change may exacerbate the problem. Therefore, to realize the fisheries reform objectives, it is imperative to strengthen the fisheries’ governance and management system, including effective law enforcement, institutional strengthening, improved planning, cooperation, and coordination as well as clearly defined roles and responsibilities among concerned stakeholders at all levels.

Functional response of fish communities in a multistressed freshwater world

Freshwater fish communities are impacted by multiple pressures, determining loss of functional diversity and redundancy. Our aim was to disentangle the roles and relevancies of different pressures in shaping fish communities in small streams of the Po plain (North Italy). Long term trend (1998-2018) of functional diversity of 31 fish communities was assessed and modeled in respect to three potential pressures: temperature increase, intensity of exotic fish invasion, and habitat quality degradation. Ecological traits mostly influenced by the pressures were also identified. Reduction of functional richness mostly due to local extinction or contraction of cold adapted predators, such as salmonids, was linked to increasing temperatures. Warming probably also led to a shift of generalist and dominant species, which became more abundant in streams hosting mixed communities of salmonids and cyprinids, and determined the increase of functional dispersion and uniqueness. Reduction of functional redundancy and increasing functional dispersion were both also related to the introduction of new ecological traits brought by expanding exotic species. Low functional overlap was found among native and exotic species, indicating that the invasion process was mainly controlled by competitive interactions and/or resource opportunism. Functional response to habitat quality was not clearly evident. In conclusion, the impact of temperature increase and exotic species on fish functional diversity was effective, idiosyncratic and mediated by the scale of analysis and by the intensity of pressures.

Diversity patterns of reef fish along the Brazilian tropical coast

Causal mechanisms for broad-scale reef fish diversity patterns are poorly understood and current knowledge is limited to trends of species richness. This work compared the effects of ecological drivers on components of fish diversity across reefs spanning over 2.000 km of the tropical Brazilian coastline. A quarter of communities' diversity is accountable to common and dominant species, while remaining species are rare. Low-latitude sites were more diverse in rare species. Communities along the coast share common and dominant species, which display high densities across all reefs, but differ in rare species that show abundance peaks in particular reef morphotypes. The disproportionate distribution of rare species reveals a higher vulnerability of these communities to impacts and stochastic density fluctuations. Uneven conservation efforts directed to these morphotypes pose a threat to the maintenance of a paramount component of the reef fish diversity represented by rare species.

Functional stability despite anthropogenic influences on the ichthyofauna of a tropical bay

Classifying species into groups based on taxonomic relationship and functions are objective approaches to evaluate environmental and anthropogenic influences on coastal fishes. We evaluated temporal (1993-1995 and 2012-2015) changes in the taxonomic and functional indices in three zones of a tropical bay heavily impacted over the recent decades. We tested the hypothesis that both indices decrease over time as result of the environmental degradation. A decrease in the taxonomic richness and abundance was observed mainly of the inner zone. The functional structure remained relatively stable, but the functional originality decreased significantly between the two periods. This functional loss is of particular concern because the loss of species with unique treats may generate a series of ecosystem damage. This information tells us that the use of functional indices is essential to complement taxonomic assessments and to detect a more detailed understanding of the real dimension of biodiversity loss in impacted environments.

Functional diversity of marine megafauna in the Anthropocene

Marine megafauna, the largest animals in the oceans, serve key roles in ecosystem functioning. Yet, one-third of these animals are at risk of extinction. To better understand the potential consequences of megafaunal loss, here we quantify their current functional diversity, predict future changes under different extinction scenarios, and introduce a new metric [functionally unique, specialized and endangered (FUSE)] that identifies threatened species of particular importance for functional diversity. Simulated extinction scenarios forecast marked declines in functional richness if current trajectories are maintained during the next century (11% globally; up to 24% regionally), with more marked reductions (48% globally; up to 70% at the poles) beyond random expectations if all threatened species eventually go extinct. Among the megafaunal groups, sharks will incur a disproportionate loss of functional richness. We identify top FUSE species and suggest a renewed focus on these species to preserve the ecosystem functions provided by marine megafauna.

How Do Eutrophication and Temperature Interact to Shape the Community Structures of Phytoplankton and Fish in Lakes?

Freshwater ecosystems are among the systems most threatened and impacted by anthropogenic activities, but there is still a lack of knowledge on how this multi-pressure environment impacts aquatic communities in situ. In Europe, nutrient enrichment and temperature increase due to global change were identified as the two main pressures on lakes. Therefore, we investigated how the interaction of these two pressures impacts the community structure of the two extreme components of lake food webs: phytoplankton and fish. We modelled the relationship between community components (abundance, composition, size) and environmental conditions, including these two pressures. Different patterns of response were highlighted. Four metrics responded to only one pressure and one metric to the additive effect of the two pressures. Two fish metrics (average body-size and biomass ratio between perch and roach) were impacted by the interaction of temperature and eutrophication, revealing that the effect of one pressure was dependent on the magnitude of the second pressure. From a management point of view, it appears necessary to consider the type and strength of the interactions between pressures when assessing the sensitivity of communities, otherwise their vulnerability (especially to global change) could be poorly estimated.

Beyond classic ecological assessment: The use of functional indices to indicate fish assemblages sensitivity to human disturbance in estuaries

Assessing ecological health of aquatic ecosystems is crucial in the current context of biodiversity loss to guide and prioritize management actions. Although several fish-based indices were developed to assess the ecological status of estuarine ecosystems, they do not provide guidance on the causal responses of communities to disturbances. The functional trait-based approach provides an understanding of how human disturbance affects the composition of biological and ecological traits in assemblages, as well as their consequences for ecosystem functioning. Here, we evaluate the responses of fish assemblages to human disturbance in 30 French estuaries using several taxonomic and functional indices (e.g. diversity, evenness or redundancy). We tested whether these indices can provide additional information on the human impacts and health of assemblages that are not reflected by the ecological indicator (fish-based index ELFI). Results indicated that high values of local human disturbances were associated to a decrease in fish abundance, decrease in species richness and reduced functional redundancy, whereas taxonomic and functional evenness increased. In contrast, the functional richness remained stable suggesting that the functional traits of species removed by stressors were maintained by more tolerant species. Indeed, we found that the local disturbances mainly resulted in a decrease in the proportions of small benthic species feeding on macro-invertebrates, which were dominant in the studied estuaries. Some functional alterations were detected by the fish-based index, but the decline of functional redundancy was not reflected, highlighting a serious concern for management. Indeed, the abrupt collapse of functional redundancy in response to local disturbances can decrease the ability of assemblages to maintain certain species traits in the face of future environmental disturbance, including climate change. From a management perspective, the application of such functional redundancy measure in monitoring programs can help stakeholders identify sensitive areas where conservation efforts need to be planned.