A Pilot Application of Sedimentary DNA to Reveal Long-Term Fish Diversity Dynamics in an Urbanized Estuary and Adjacent Waters.

Fishery resources are threatened by environmental changes and anthropogenic pressures, particularly in coastal ecosystems. It is crucial to understand the changes of fish communities and their responses to environmental changes and human disturbances to formulate rational fisheries and ecosystem-based management. The Pearl River Estuary (PRE) is a typical sub-tropic coastal ecosystem located in the center of the Guangdong-Hong Kong-Macao Greater Bay Area in the northern South China Sea. The demersal fish in the PRE is traditionally targeted as commercial fishing and severely impacted by overexploitation and hypoxia in the last few decades. In this study, we analyze the fish survey data during the period of 2020~2021 using multivariate statistics to investigate the impacts of human disturbances on the species and functional dynamics of the demersal fish community in the PRE. The results reveal that dissolved oxygen and temperature have significant correlations with the functional traits of the demersal fish community. The impacts of hypoxia on the demersal fish vary with species and locations. We found that the mean functional redundancy of the demersal fish community in the PRE was high across three surveys, but the functional diversity was low in this region. The abundance and richness of the demersal fish community increased during the summer fishing moratorium in the South China Sea in 2021, but the functional diversity did not increase significantly. We conclude that the high functional redundancy in the PRE might not be sufficient to buffer against environmental disturbances because of its low functional diversity. Our study highlights the complicated interactions between the demersal fish community and disturbances in the PRE. Understanding the traits structure and functional diversity of the fish community can help elucidate the factors determining the dynamic responses of the fish community to disturbances.

Suo, A.; Cao, K.; Zhao, J., and Lin, Y., 2015. Study on impacts of sea reclamation on fish community in adjacent sea areas: a case in Caofeidian, North China.To reveal the impacts of sea reclamation on fish communities in adjacent areas, Caofeidian in north China was chosen as a case study in this paper. A total of 19 sample points were set in offshore areas reclaimed in 2004, 2008, and 2010, which represents the beginning, middle and ending phase of reclamation works. Species richness, density, biomass, and biodiversity index were analyzed to describe changes of adjacent fish community during the reclamation process. It is found that the fish density declined by 22.66% from 2004 to 2010 due to sea reclamation. The fish biomass decreased from 46.07 kg·m−2·h−1 in 2004 to 25.35 kg·m−2·h−1 in 2010, which was mainly caused by body miniaturization of dominated fish and increased density of other fish species. The sea reclamation also reduced the eggs and fries in adjacent areas. The density of fish eggs decreased from 5.42 ind·m−3·h−1 to 0.13 ind·m−3·h−1and the density of fries decreased from 2.29 ind·m−3·h−1to 0.19 ind·m−3·h−1. These changes of fish community were mainly due to the plenty of suspended sand diffused to adjacent waters. Besides, the impact of reclamation on fish community was bigger in autumn than in spring.

A three-level nested-grid coastal ocean modeling system was developed recently by Tang et al. (2009) for the Pearl River Estuary (PRE) in South China's Guangdong Province. The modeling system has three downscaling subcomponents: (a) a coarse-resolution outer model for China Seas from Bohai Sea to the northern South China Sea; (b) an intermediate-resolution middle model for coastal waters over the northern shelf of South China Sea; and (c) a fine-resolution inner model for the PRE and adjacent waters. The modeling system is forced by tides, meteorological forcing and buoyancy forcing associated with freshwater runoff from the Pearl River system. Multi-year model results in 1993–95 are used in this study in examining circulation and salinity distributions during the dry (December–March) and wet (May–August) seasons in the PRE. The seasonal mean circulation and salinity distributions in the dry season are affected significantly by freshwater runoff, wind and tides over the northern and western PRE and mainly by wind and tidal forcing over the outer PRE and adjacent inner shelf waters. In the wet season, the estuarine plume extends significantly offshore with river discharge and tides to be the main driving for circulation and salinity distributions inside the PRE, and tides and wind forcing to be the main driving forcing over the inner shelf waters off the PRE.

Process study of circulation in the Pearl River Estuary and adjacent coastal waters in the wet season using a triply-nested circulation model

In recent decades, hypoxic areas have rapidly expanded worldwide in estuaries and coastal zones. The Pearl River Estuary (PRE), one of China's largest estuaries, experiences frequent seasonal hypoxia due to intense human activities and eutrophication. However, the ecological effects of hypoxia in the PRE, particularly on fish communities, remain unclear. To explore these effects, we collected fish community and environmental data in July 2021 during the summer hypoxia development period. The results revealed that bottom‐layer dissolved oxygen (DO) in the PRE ranged from 0.08 to 5.71 mg/L, with extensive hypoxic zones (DO ≤ 2 mg/L) observed. Hypoxia has varied effects on fish community composition, distribution, species, and functional diversity in the PRE. A total of 104 fish species were collected in this study, with approximately 30 species (28.6%) exclusively found in hypoxic areas. Species responses to hypoxia varied: species such as Sardinella zunasi, Coilia mystus, and Nuchequula nuchalis were sensitive, while Decapterus maruadsi, Siganus fuscescens, and Lagocephalus spadiceus showed higher tolerance. Within the hypoxia area, dissolved oxygen was the main limiting factor for fish community diversity. Functional diversity (FDiv) decreased with higher dissolved oxygen levels, indicating a potential shift in the functional traits and ecological roles of fish species in response to changing oxygen conditions. Further analysis demonstrated that dissolved oxygen had a significantly stronger effect on fish community structure at hypoxic sites than in the whole PRE. Moreover, other environmental variables also had significant effects on the fish community structure and interacted with dissolved oxygen in the hypoxia area. These findings suggest that maintaining sufficient dissolved oxygen levels is essential for sustaining fish communities and ecosystem health in the PRE. This study provides novel insights into the effects of hypoxia on fish communities in estuarine ecosystems and has significant implications for the ecological health and management of the PRE.

In freshwater ecosystems, invasive salmonid fishes can have a significant impact on native fish species. Detecting the invasion and its negative effects is critical for the conservation of native fish communities. We examined the species composition and seasonal changes in the freshwater fish community, including salmonids, on the Kamikawa Plain, Hokkaido Island, Japan, using environmental DNA (eDNA) metabarcoding. We detected 23 fish species in 176 samples collected from 16 sites over 12 months (October 2018 – August 2019). Between 11 and 20 species were detected at each site, including five native salmonids (Oncorhynchus masou, Oncorhynchus keta, Parahucho perryi, Salvelinus leucomaenis leucomaenis and Salvelinus malma krascheninnikova). The invasive alien rainbow trout Oncorhynchus mykiss was detected at all 16 sites and it was the most commonly detected salmonid. Although we found no obvious competitive exclusion of native salmonids by rainbow trout in the study area, the invasive species occurred more often and at more sites than any of the natives. We also determined the occurrence and seasonal changes in the fish community, classified as native salmonids, invasive rainbow trout, Cypriniformes and other benthic fishes. There were fewer species overall in winter, but the sites with higher species richness in winter were on the lower reaches of the river. In addition, we detected domestic invaders, such as the topmouth gudgeon, Pseudorasbora parva, although they were less prevalent than rainbow trout. These results show the effectiveness of eDNA metabarcoding, which can be used for surveying species richness at an ecosystem scale. In particular, the detection of the early stages of establishment and spread of invasive species can be achieved by eDNA monitoring.

Coastal marine fish populations are in decline due to overfishing, habitat destruction, climate change and invasive species. Seasonal monitoring is important for detecting temporal changes in the composition of fish communities, but current monitoring is often non-existent or limited to annual or semi-annual surveys. In the present study, we investigate the potential of using environmental DNA (eDNA) metabarcoding of seawater samples to detect the seasonal changes in a coastal marine fish community. Water sampling and snorkelling visual census were performed over 1 year (from 23rd of August 2013 to 11th of August 2014) at a temperate coastal habitat in Denmark (55°45′39″N, 12°35′59″E) and compared to long-term data collected over a 7-year period. We used Illumina sequencing of PCR products to demonstrate that seawater eDNA showed compositional changes in accordance with seasonal changes in the fish community. The vast majority of fish diversity observed in the study area by snorkelling was recovered from sequencing, although the overlap between methods varied widely among sampling events. In total, 24 taxa were detected by both methods, while five taxa were only detected using eDNA and three taxa were only detected by snorkelling. A limitation of the applied primers was the lack of resolution to species level in a few diverse families, and varying sequencing depth between samples represents a potential bias. However, our study demonstrates the utility of eDNA for recovering seasonal variation in marine fish communities, knowledge of which is essential for standardised long-term monitoring of marine biodiversity.

A trawl survey of the south-eastern Gulf of Carpentaria carried out at the beginning of a commercial prawn fishery in the 1960s provided data on the demersal fish of an unexploited tropical fish community. The extent of temporal variation in this community was investigated using abundance data on 359 taxa of fish and cephalopods over 13 months in 1963-1964. Seasonal changes in water temperature and salinity were large, particularly in nearshore waters. Catch rates and species richness in nearshore waters were highest during summer, and in offshore waters during autumn or winter. Shannon diversity was variable, with no clear seasonal component. Temporal changes in community composition resulted in large changes between different seasons in the structure of site groups derived by classification; temporal effects within seasons were also found. The numerically dominant species were the leatherjackets Paramonacanthus spp., the ponyfish Equulites leuciscus, the tripodfish Tripodichthys blochii, and the saury Saurida undosquamis. Squid, the ponyfish Leiognathus sp. nr blochi, the butterfly-bream Nemipterus tolu and the grunter Pomadasys maculatus were seasonally abundant. Although species were restricted in their depth range, discrete communities that maintained their identity in different seasons were apparently absent. The relative abundance of many species varied substantially wirh season and probably also over a longer period. Small changes in local abundance were often associated with movement to deeper water at times of high nearshore water temperature (summer) or of reduced nearshore salinity (autumn). Large seasonal changes occurred in the local abundance of estuarine and semidiadromous species. The community shared many species with the demersal fish community of the Gulf of Thailand. It is suggested that similar structural changes in the fish community of the Gulf of Carpentaria may occur in response to intensive fishing. Further research on the effects of demersal fishing and on the interactions of the demersal fish community with commercially important crustaceans is necessary.

Understanding the biodiversity of aquatic communities and the underlying mechanisms that shape biodiversity patterns and community dynamics is crucial for the effective conservation and management of freshwater ecosystems. However, traditional survey methods often fail to comprehensively capture species diversity, particularly for low-abundance taxa. Moreover, studies integrating both metazoan and fish communities at fine spatial scales remain limited. To address these gaps, we employed a multi-marker eDNA metabarcoding approach, targeting both the 12S and 18S rRNA gene regions, to comprehensively investigate the composition of metazoan and fish communities in the Yujiang River. A total of 12 metazoan orders were detected, encompassing 15 families, 21 genera, and 19 species. For the fish community, 32 species were identified, belonging to 25 genera, 10 families, and 7 orders. Among these, Adula falcatoides and Coptodon zillii were identified as the most prevalent and abundant metazoan and fish species, respectively. Notably, the most prevalent fish species, C. zillii and Oreochromis niloticus, are both recognized as invasive species. The Bray–Curtis distance of metazoa (average: 0.464) was significantly lower than that of fish communities (average: 0.797), suggesting higher community heterogeneity among fish assemblages. Beta-diversity decomposition indicated that variations in the metazoan and fish communities were predominantly driven by species replacement (turnover) (65.4% and 70.9% for metazoa and fish, respectively) rather than nestedness. Mantel tests further revealed that species turnover in metazoan communities was most strongly influenced by water temperature, while fish community turnover was primarily affected by water transparency, likely reflecting the physiological sensitivity of metazoans to thermal gradients and the dependence of fish on visual cues for foraging and habitat selection. In addition, a co-occurrence network of metazoan and fish species was constructed, highlighting potential predator-prey interactions between native species and Corbicula fluminea, which emerged as a potential keystone species. Overall, this study demonstrates the utility of multi-marker eDNA metabarcoding in characterizing aquatic community structures and provides new insights into the spatial dynamics and species interactions within river ecosystems.

Nelson Lake, a moderately acidic (pH 5.7), metal-contaminated (Cu 22 μg L−1; Zn 18 ug L−1) lake, 28 km from the smelters at Sudbury, had a degraded fish community in the early 1970's, with lake trout (Salvelinus namaycush) scarce, smallmouth bass (Micropterus dolomieui) extinct, and the littoral zone dominated by the acid-tolerant yellow perch (Perca flavescens). Liming of the lake in 1975–76 increased pH to 6.4, and decreased metal concentrations. Chemical conditions have remained relatively stable in the 10 yr following base addition. Initially, it appeared that neutralization produced dramatic changes in the resident fish community. Yellow perch abundance declined rapidly after neutralization, lake trout abundance increased to the extent that 3.26 kg ha−1 were caught in the winter of 1980, and reintroduced smallmouth bass reproduced and established a large population. However, these changes in the fish community can not be directly attributed to liming, as water quality and the sport fisheries of an unlimed nearby lake also improved. Reduced emissions from Sudbury smelters were responsible for improvements in the untreated lake. Recovery of the lake trout population in Nelson Lake appears to have begun prior to liming. Of the lake trout sampled during the 1980 winter fishery, 65.8% were present prior to the chemical treatment. Predation by lake trout was the likely cause of the perch decline. Our results suggest that chemical conditions producing population level responses in fish have abrupt thresholds and that neutralization of lakes above these thresholds may not produce distinguishable effects.

Seasonal variation in the functional structure of demersal fish communities and response to the environmental changes in the Pearl River Estuary, China

Temporal and spatial distribution of dissolved oxygen in the Pearl River Estuary and adjacent coastal waters

Ecological thresholds that lead to alternative community states can be exceeded through gradual perturbation or as a result of sudden disturbance. Many Great Plains streams have experienced dramatic changes in their hydrologic regime resulting from water and landuse changes that began as early as 1880. These changes, combined with the presence of many invasive species, have substantially altered the fish communities in this area. We quantified temporal changes in fish communities in 3 large river basins in relation to putative anthropogenic stressors, including increased sediment supply derived from row-crop agriculture (beginning in 1880), habitat fragmentation caused by reservoir construction (beginning in the 1950s), and reduced discharge caused by groundwater withdrawal (beginning in the 1960s). We hypothesized that these abiotic regime shifts, coupled with species invasions, would shift the system from a fish community dominated by lotic (flowing water) species to one dominated by lentic (still water) species. Further, we predicted that the timing and intensity of community change would vary across basins that experienced different types and levels of stressors. Restructuring of fish communities across the 3 river basins was driven primarily by similar increases in lentic species, with only a few declines in several large-river species. Current fish communities in these basins share ,50% of the species recorded in historic collections, and these differences were driven by species extirpations and invasions. The greatest levels of community divergence over time occurred in western Kansas basins that experienced the most intense groundwater withdrawals and fragmentation by reservoirs. An alarming result from this analysis was the recent (after 1991) expansion of several invasive species in the Arkansas and lower Kansas River basins and the decline or extirpation of several native species where flow regimes are less heavily altered. Accelerating changes in the biota and habitat identified by our retrospective analysis highlight potential complications for restoring the habitat and native fish communities to a previous state.

We describe and explain some of the changes in the fish community as reflected by the catches of the commercial fishery, and evaluate the efforts to restore the trout (Salvelinus spp.) in Georgian Bay. The changes in the fish community were caused in part by excessive fishing for lake trout (S. namaycush), lake whitefish (Coregonus clupcaformis) and deepwater ciscoes (Coregonus spp.), and the introduction of new species such as sea lamprey (Petromyzon marinus), alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax) and salmonids (Oncorhynchus spp.). The most striking changes were the near extinction of the lake trout, reductions in lake herring (Coregonus artedii), deepwater ciscoes and lake whitefish, and the increase in abundance of smelt and alewife. In an effort to replace the low of yield from the cold-water habitat, a fast growing and early maturing hybrid trout (splake [S. namaycush x S. fontinalis]) and its backcross to lake trout were selectively bred for stocking in Georgian Bay. Splake did poorly because of low survival immediately after planting. The survival of backcross after planting was better, but adult mortality was still high. Adult survival of backcross improved considerably after restrictions were placed on the commercial fishery in 1984. The first naturally produced backcross larvae were collected in 1985.

Food web structure and trophic diversity for the fishes of four islands in the Pearl River Estuary, China