Environmental DNA metabarcoding reveals a decline of fish diversity from 2019 to 2023 in Dongshan Bay, China.

Estuaries and adjacent waters are highly productive ecosystems, but are increasingly stressed by urbanization and climate change. Understanding long-term shifts in fish communities is critical for sustainable management, yet remains limited by scarce historical data. Here, we applied quality-controlled sedimentary DNA (sedDNA) metabarcoding, combining contamination prevention, stringent data filtering, and statistical calibration, to reconstruct ca. 100 years of fish diversity dynamics in the Pearl River Estuary (PRE) area, southern China. The monitored sedDNA data sets revealed that changes in fish communities in the PRE can be categorized into four distinct historical phases: the 1930s-1950s, 1950s-1970s, 1970s-1990s, and 1990s-2020s. Taxonomic and functional richness peaked around the 1970s but declined sharply thereafter. Small-bodied and omnivorous species gradually gave way to larger-bodied and warm-water species, reflecting a shift in trophic and habitat preferences over time. Invasive species, such as Oreochromis niloticus and Coptodon zillii, became increasingly dominant, whereas indigenous species markedly declined. Multivariate analyses showed that urbanization primarily affected taxonomic diversity, while climate drivers shaped functional traits and community structure, with invasive species acting as key mediators of ecological disruption. Overall, these results offer new insights into the century-scale fish diversity dynamics under compounded urbanization and climatic pressures, and highlight sedDNA as a powerful tool for reconstructing historical biomonitoring records.

Extreme droughts caused by current climate changes affect the diversity, composition and function of fish communities in lake ecosystems. Poyang Lake is the largest freshwater lake in China, and it is home to many important avian, fish and aquatic mammals. In 2022, Poyang Lake experienced one of the most severe droughts in recorded history. Understanding how fish communities responded to this event can offer key knowledge in developing strategies for coping with future climatic extremes, particularly given that the local government has been actively posting several middle- to long-term policies on managing the fish diversity of Poyang Lake, including fishery resource supplements and the well-known “ten-year fishing ban”. To understand how the fish diversity of Poyang Lake has been altered by climate change and human interventions, here, we analyzed the α- and β-taxonomic diversity (TD) and functional diversity (FD) of fish species using environmental DNA (eDNA), and we compared the fish diversity and community changes before and after the 2022 drought. In total, 77 native fish species and 4 invasive species were detected. The species richness and Shannon–Wiener index decreased significantly, and Simpson’s index had no significant difference post-drought. Rao’s Quadratic Entropy (Rao’sQE) index increased significantly, and the Functional Evenness (FEve) index decreased significantly. The differences in α- and β-TD and FD in the north part and south part of Poyang Lake also reflect the impact of drought. When calculating biodiversity contribution rates of the different species, we found that small-sized species were dominant pre-drought, while medium- and large-sized species were predominant post-drought. These patterns indicate that the fish community of Poyang Lake is undergoing a reestablishing process after the extreme drought. This fish community reestablishment post-drought does not correspond to the natural process of community recovery; instead, it is the result of human intervention while being affected by drought brought about by climate change.

Trawling the archives: Long-term trends in fish taxonomic and functional diversity in UK coastal community.

ABSTRACT Aim Determine whether changes in fish biogeographic composition and key facets of biodiversity are reversible at short time scales in a high latitude marine ecosystem experiencing ocean warming in the context of a recent short‐term cooling, and an increasing then declining dominant apex predator population. Location Barents Sea. Methods Survey data from an 18‐year time series of demersal fish communities, delineated as Arctic, Arctic‐boreal and boreal assemblages, was used to examine temporal changes in (i) biogeographic composition across the Barents Sea, (ii) taxonomic, functional and phylogenetic (alpha) diversity at a sub‐regional scale and relationships to abiotic and biotic drivers, and (iii) beta diversity at regional and sub‐regional scales. Results Community composition changes across the Barents Sea that were attributed to ocean warming showed signs of a reversal during short‐term cooling. At a sub‐regional scale, several biodiversity measures showed a reversal of changes in the north‐east, but different biodiversity measures as well as abiotic and biotic drivers revealed distinct patterns and trends. Species richness of the Arctic‐boreal group increased but then declined in the north‐east, while species richness of the Arctic group showed a persistent decline. Main Conclusions Our approach of dividing the Barents Sea into sub‐regions and different biogeographical groups revealed patterns that were different from those observed at a large spatial scale and for whole communities. The Barents Sea is heterogeneous regarding temporal changes in diversity, and the recovery potential of fish communities varies among biogeographical groups. Such heterogeneity needs to be accounted for in future conservation strategies and ecosystem‐based management.

Freshwater fish communities in New York State, USA, have been impacted by a variety of threats over the last century, including changes in land cover. Land cover exerts a powerful influence on aquatic communities at multiple spatial scales, and alterations to systems can persist even after restoration actions are taken. Our research examines how land cover changes were correlated with changes in fish species richness in a nearly 100-year dataset from New York's Oswego River Watershed. The watershed was heavily agricultural in the early 1900s and was modified by both reforestation and urbanization in the subsequent century, two changes which we may expect to have opposite effects on biodiversity. Linear mixed effects models showed that species richness correlated positively with natural and urban land cover and negatively with agricultural land cover, with increases in the richness of sediment-tolerant, temperature-tolerant, and nonnative species driving the urban increase. Understanding how historical changes in land cover have affected species richness can help inform predictions about future changes to fish communities as formerly agricultural regions experience the conflicting effects of reforestation and urbanization.

Sediment eDNA reveals damming triggered changes in algal and fish communities at the Three Gorges Reservoir in China.

The ecological consequences of the construction and operation of the Three Gorges Reservoir, particularly its unique operation strategy of storing clear water and releasing turbid water, exerts a profound influence on the composition and dynamics of local fish communities. To date, detailed and comprehensive research on seasonal changes in the fish community across the entire reservoir remains scarce. This study aims to fill this research gap by systematically investigating fish diversity through a comprehensive assessment of six main river reaches and eight major tributaries. The investigation employs environmental DNA (eDNA) technology across three critical life-cycle stages: breeding, feeding, and overwintering periods. A total of 124 fish species were recorded, comprising 10 orders, 20 families, and 80 genera. The comparative analyses of historical data suggest a significant decline in lotic and endemic fish populations, accompanied by a concurrent increase in lentic, eurytopic, and non-native fish species. Notably, the composition of fish communities exhibited similarities between breeding and overwintering periods. This study highlights the occurrence of significant seasonal fluctuations in the fish communities, showing a preference for reservoir tails and tributaries as optimal habitats. Water temperature has a predominant influence on structuring fish communities within aquatic ecosystems. This study investigates variations in the biodiversity of fish communities using historical data, with a focus on changes linked to reservoir operations and water impoundment activities. By integrating historical data, this research examines changes in fish diversity that are associated with water storage processes. It provides foundational data on the current composition and diversity of fish communities within the watershed, elucidating the spatiotemporal variations in fish diversity and the mechanisms by which environmental factors influence these communities. Furthermore, the current study serves as a valuable reference for understanding the changes in fish communities within other large reservoirs.

ABSTRACTAmong lowland fish communities, there is limited knowledge of the importance of headwaters. This information is needed to understand their role in fish communities. We addressed this gap by assessing seasonal changes in fish communities in lowland headwater streams (Arkansas, USA). 16 sites were sampled seasonally (winter, spring, summer and fall) in four events from Jan. to Oct. 2023. Multiple sampling gears (backpack electrofishing, kick nets and seines) were used to increase species detection. Fish presence/absence data, site and survey covariates were analysed using multiseason, community occupancy models to estimate μ, a value between 0 and 1, which represents the likelihood that an individual species is a member of the community and essentially represents that species occupancy (species probability), Ω, a value between 0 and 1, which represents the average occupancy probability across all species in the community across sites (community occupancy mean), and p, a value between 0 and 1, which is the probability of observing a species at a site given that the species is present (detection probability). A total of 37 species from 10 families were observed. Of the many models, we explored the best three: μ (canopy cover), Ω (canopy cover), p (.); μ (catchment area), Ω (catchment area), p (stream flow); μ (catchment area), Ω (catchment area) and p (.). The model incorporating canopy cover suggests that μ varied by species, Ω (± SE) varied by season and that p was constant. Overall, seasonal variation exists at the species and community levels; canopy cover and catchment area are the main drivers of μ and Ω and stream flow is the main driver of p. This research aids in the understanding of fish patterns and species richness on a temporal scale, improving knowledge of lowland headwater stream functionality in South Central Plains watersheds.

Since the opening of the Suez Canal, the Eastern Mediterranean has been continuously affected by the influx of non-indigenous species (NIS), leading to significant changes in species composition. In this study, we focus on the temporal changes in marine teleost fish communities within one of the most heavily invaded shelf ecosystems. To examine changes in species assemblages, we integrated historical seasonal trawl data from the 1980s with recent data collected in 2022 along the Northeastern Mediterranean coast at depths of 0–25 m, 25–50 m, and 50–100 m. As a result, we identified 130 fish species, consisting of 37 NIS and 93 native species. Cluster analysis and Non-metric Multidimensional Scaling (NMDS) results revealed three main groups: a shallow water group, a deeper water group, and a western group, along with additional groups exhibiting sporadic occurrences. The western group, influenced by the presence of Posidonia oceanica meadows, has consistently been dominated by native biomass. However, the ratio of NIS to the total number of species has notably increased since the 1980s. The shallow water group, considered Por’s “Lessepsian Province”, is predominantly composed of NIS biomass and spans a depth range of 7 to 60 meters. In contrast, the deeper water group, which extends up to 82 meters, has maintained a relatively stable community dominated by native biomass over the years. However, since the 1980s, there has been a recorded increase in the contribution of NIS biomass and the overall proportion of NIS in the total species count within this group. Significant differences in community structure were correlated with depth and the spatially defined subregions within the study area. This study elucidates the dynamic nature of species assemblages in the continental shelf of the Northeastern Mediterranean and emphasizes the need for continuous monitoring to understand the ongoing transformations in these heavily impacted regions.

Abstract Small fish, including species with small adult sizes and juveniles of larger species, play a central role in marine food webs as prey for top predators, such as seabirds, marine mammals, and piscivorous fish. However, reliable data on small fish are lacking as conventional fisheries surveys primarily focus on larger, commercially important species and underestimate small fish. Consequently, little is known about absolute biomasses, and fine-scale distribution patterns of this important trophic group. Based on 1307 quantitative Triple-D samples from the Dutch Exclusive Economic Zone and the UK sector of the Dogger Bank, biomass densities were estimated for pooled small demersal fish and for the most abundant species individually. Our estimates suggest that small demersal fish biomass is at least twice as high as reported in trawl-based studies. Uniformly distributed species such as dab (Limanda limanda) and plaice (Pleuronectes platessa) contributed most to the overall small fish biomass, while sandeels (Ammodytidae) showed particularly high local densities. These new prey biomass estimates might change our understanding of the North Sea ecosystem's carrying capacity, and establishes a baseline for monitoring changes in small fish communities driven by climate change and human impacts.

Abstract Despite efforts to minimize human impact on rivers, native teleost fish and lamprey species communities in Germany remain threatened. The aim of the study was to quantify current species diversity in the study area, identify the level of deviation from realistic reference conditions, and characterize relevant drivers of diversity loss. Site-specific survey data were consolidated with reference fish community data, and selected biodiversity metrics were calculated and compared for 390 river sections. A novel species deviation index was implemented that reflects the level at which a community deviates from a presumptive natural state. The obtained biodiversity data were cross-linked with environmental factors using generalized linear mixed modeling. A significant decline in biodiversity was revealed when comparing results of the recent surveys with the corresponding reference conditions. Non-native species, transverse structures, and human land use were identified as important drivers of low native species diversity. The deviation index was especially effective in quantifying changes in fish communities and revealed ongoing dynamic environmental influences, such as bioclimatic change, that do not necessarily affect biodiversity metrics but lead to significant deviation from reference conditions. Authorities and stakeholders are encouraged to establish site-specific reference data to develop more targeted species conservation measures.

Surveys of fish diversity in complex heterogeneous environments are highly challenging to perform using traditional survey methods. Although environmental DNA (eDNA) metabarcoding has been effectively used to evaluate fish diversity, studies exploring the spatial and temporal variability of fish communities in mosaic habitats and their connection to water quality after ecological project implementation are still scarce. Here, we evaluated the changes in water quality and fish assembles using the traditional method and environmental DNA (eDNA) metabarcoding after Ecological water replenishment (EWR) and the links between fish communities and water quality were established in the Baiyangdian (BYD) ecosystem in the North China Plain. All water quality variables including TN, NH3-N, CODMn and TP showed a conspicuous improvement pattern, and the number of fish species increased notably after EWR. In addition, 6 more introduced fish species were recorded when compared with the historical data before the implementation of the EWR project. Furthermore, the species richness showed a highly significant difference among the four habitats in the summer 2020 and spring 2021 (spring: P = 0.000; summer: P = 0.002), and obvious discrimination of fish communities across two seasons was observed (P = 0.001) with eDNA metabarcoding. The water quality variables driving the changes of fish communities during the same period varied significantly across different habitats, while not all showed noticeable discrepancy in driving cross-seasonal fish community changes. Thus, our study highlights that the continuous EWR improves the water quality and fish richness but potential ecological issues associated with introduced species should be carefully considered after EWR. Our results also confirm that eDNA is a reliable tool for assessing fish diversity and distinguishing spatiotemporal variability of fish communities in mosaic habitat ecosystems.

Dam construction alters river hydrology, influencing the temporal and spatial heterogeneity of fish communities. This study utilized environmental DNA (eDNA) sequencing to analyze seasonal variations in fish communities in the Duliu River, Guizhou Province, and to assess the impact of hydrological regulation on biodiversity. High-throughput sequencing revealed that sequence reads were significantly higher in the dry season than in the wet season (P < 0.05), while operational taxonomic unit (OTU) richness was greater in the wet season. A total of 69 fish species (6 orders, 18 families) were detected in the dry season, with only 23 species matching historical records. eDNA sequencing identified an additional 46 species, primarily from the order Cypriniformes. In the wet season, 82 species (7 orders, 17 families) were recorded, including 44 species not found in historical data. Cypriniformes dominated in both seasons, comprising 94% of the community in the dry season and 82% in the wet season. Spatial heterogeneity analysis using principal coordinates analysis (PCoA) indicated significant differences among river sections (PC1 = 65.2% in the dry season; 83.65% in the wet season). Beta diversity analysis (NMDS) confirmed significant temporal and spatial variation in fish communities (P < 0.05). This study highlights the ecological impact of dam construction on fish communities and underscores the need for conservation strategies to protect biodiversity in regulated mountain rivers.

BackgroundFluvial fish habitat in the Northeastern and Midwestern U.S. is substantially affected by natural landscape factors and anthropogenic stressors, with climate change expected to alter natural influences and exacerbate stressor effects. To conserve fluvial fish species in the future, it is crucial to understand which fish habitats will be most strongly influenced by changing climate, which species are most sensitive to climate change, and how changes in individual species will affect entire assemblages. To answer these questions, we modeled fluvial fish distributions under projected changes in climate to understand how climate could affect suitability of fish habitat for 55 widely distributed fluvial fishes with differing thermal preferences in the region. Using boosted regression tree models, we predicted distributions of fishes at a stream reach scale using four contemporary climate variables including annual mean air temperature, annual precipitation, and variation in monthly air temperature and precipitation along with seven natural landscape and anthropogenic stressor variables. We then used projected values from eight general circulation models (GCMs) during 2041–2080 to evaluate potential patterns in species richness, turnover, and range shifts under climate change across the study region.ResultsMost cold-water and cool-water species were projected to lose habitat; however, projected habitat loss also occurred for certain small-bodied warm-water species. The percentage change in species richness of all 55 species across reaches ranged from − 40.4 to 33.93%, with regions of major species richness losses occurring across southern portions of the Northeastern coast and southern Midwest regions. Species turnover ranged from 0 to 43.5% with substantial turnover occurring along the Northeastern coast and upper Midwest.ConclusionsTemperature and precipitation variation will influence fish species distribution substantially. Our findings provide multiple measures describing patterns of fish community change under climate change to aid management and conservation of stream fishes in the future.

Real-time biodiversity monitoring should provide more resolved data to quantify shifts in ecological communities progressively altered by anthropogenic disturbances. Identifying biodiversity trends requires a rapid and efficient inventory method that enables the collection and delivery of high-resolution data within short intervals. Using aquatic environmental DNA (eDNA), we investigated spatiotemporal changes in fish and mammal communities along the Maroni River in French Guiana. We compared spatial biodiversity trends between two years, separated by a four-year interval, during which an increase in anthropogenic disturbances was observed. To evaluate biodiversity changes, we examined the impact of these disturbances on both taxonomic and functional diversity. Our findings revealed that, while the increase in disturbances did not result in major biodiversity decline, it continued to drive alterations in community taxonomic and functional richness. Communities underwent changes in their functional structure, with mammal communities experiencing a decline in extreme functional traits, while fish communities lost functional redundancy in generalist functions and experienced a reduction in extreme functional strategies. In a context of small-scale anthropogenic disturbances, these changes highlight the necessity of long-term, short-interval monitoring to capture rapid reorganisation of ecological communities under stress.

Changes in Fish Communities in the Lower Nakdong River

Abstract Northern Snakehead Channa argus an invasive freshwater piscivore discovered in the Potomac River in 2004, has spread throughout the Chesapeake Bay (Maryland, USA). The first incidental reports of Northern Snakehead in Blackwater National Wildlife Refuge (Chesapeake Bay) occurred during 2012. Since that time, Northern Snakehead have become established and has formed the basis for a popular harvest fishery in the Blackwater River drainage. This increase in abundance has caused concern about competition and predation on other species. To determine whether the fish community has changed in composition or relative abundance in Blackwater River drainage (Blackwater River and Little Blackwater River) since the introduction of Northern Snakehead, we replicated fish community surveys from 2006 and 2007 (pre-snakehead) and compared those fish community composition with data collected from 2018 to 2019 (post-snakehead). Subsequent seasonal surveys of fishes between 2021 and 2023 helped to substantiate our findings. Including pre-snakehead and post-snakehead survey periods, we caught 35 species (32 fish species and three invertebrate species) totaling 51,781 individuals. With few exceptions, species richness was similar between periods, with 27 fishes caught pre-snakehead and 26 species caught post-snakehead. However, of 22 species that we captured during both pre-snakehead and post-snakehead survey periods, 19 declined in relative abundance, which was supported during subsequent seasonal surveys. These changes led to four of six sites having significantly different fish communities between survey periods. Fish communities experienced declines in relative abundances of popular prey species for Northern Snakehead: White Perch Morone americana, sunfish Lepomis, and killifishes Fundulus. Our study is among the first to document long-term fish community changes following establishment of Northern Snakehead in its introduced range.

To understand biodiversity change and support conservation decision-making, estimates of species' long-term population trends at regional and national scales are essential. However, such estimates are missing for many freshwater taxa, despite the diverse range of threats that they face. For this study, we mobilised monitoring data on riverine freshwater fish abundance collected across different regions of Germany. We applied generalized mixed effect models to estimate the population trends for 55 native species and 11 non-native species between 2004 and 2020. In addition, we used boosted regression trees to identify trait-based predictors of species trends and assessed their predictive ability. We found evidence of increasing abundance trends for 14 species and decreasing trends for 15 species; while the remaining species were mostly stable (26 species). Native species were more typically decreasing than increasing (14 vs 10 species); while non-native species were more often increasing (4 vs 1 species). Important traits associated with trends were maximum length, spawning temperature, and water quality tolerance, with small species, those spawning at high temperatures, and those preferring unpolluted waters, being most likely to have positive trends. Despite these associations, overall trait-based models showed limited power to predict trends in terms of direction as well as magnitude. Our results highlight the ongoing change in riverine fish communities and the importance of on-going species-level monitoring. The trait-based associations also indicate climate change and invasive species as important drivers of change in European freshwater rivers.

The expansion of northern Pike Esox lucius outside its native range into the western states of North America is a growing problem due to their negative effects on fish communities. Illegally introduced E. lucius were first detected in Box Canyon Reservoir in northeast Washington in 2004. By 2010, the E. lucius population was estimated at more than 10,000 individuals. Between 2012 and 2019, a gillnet suppression programme was conducted, which reduced the E. lucius catch per unit effort in Box Canyon Reservoir by 97% and their biomass by 98%. Between 2004 and 2019, four standardized surveys were conducted to characterize changes in the Box Canyon Reservoir fish community. Even after E. lucius were effectively suppressed, native species showed no signs of recovery during the study. The relative abundance of all native species decreased 82% in total number and 56% in total biomass between 2004 and 2019. Conversely, the relative abundance of non-native species increased 26% in total number and 33% in total biomass over the same period. As an apex predator, E. lucius had a significant impact on the fish community in Box Canyon Reservoir over a relatively short period of time (7 years), and appeared to act as a catalyst to increase the rate of replacement of native species with non-native species, which likely increased the pace of taxonomic homogenization in the reservoir.