4.1. Composition of the Fish Assemblages
In the present study, a total of 64 fish species were caught in the offshore waters of the Yangtze Estuary during the autumns of 2012–2016, which is clearly at a low level compared to the autumns of 2002–2005 [
17]. The number of fish species caught in our study also decreases from 41 in 2012 to 29 in 2016. This is closely related to the effects of high-intensity fishing and changes in the offshore marine environment on fish spawning and bait grounds in the last decade [
7,
23]. The ichthyoplankton assemblage in the Yangtze Estuary has also declined from 94 species in the 1980s to 26 species in 2013–2020, and the replenishment capacity of the fishery resources has decreased substantially [
24,
25]. Tropical and subtropical estuaries have higher species richness than temperate systems [
26]. The number of fish species in the waters of the Pearl River Estuary is much greater than in the waters of the Yangtze River estuary [
27]. In Zuari, a well-mixed tropical estuary located along the southwest coast of India, the number of fish species can reach 224 in the same period [
28].
Combinations of a large number of rare species and a few highly abundant species are common features of temperate estuarine faunae [
29,
30]. Due to the mixed water masses in the Yangtze Estuary, not all of the species are adapted to the local conditions [
31]. The sensu stricto freshwater and marine species do not occur in the offshore waters of the Yangtze Estuary or occur in small numbers at very few stations for only a short period of time. For example, the Yangtze River’s abundant freshwater fish such as
Mylopharyngodon piceus and
Ctenopharyngodon idella do not appear in the offshore waters of the Yangtze Estuary, while
Johnius distinctus, which is a marine fish, only occurs in two stations in 2015 [
32]. In the present study, only six of the species caught in the Yangtze Estuary dominate with IRI values > 500. The dominant species account for a significant proportion of total abundance (96.72%) and total biomass (95.88%), and species homogeneity is low. In comparison with the autumn fish in the Yangtze River estuary from 2002 to 2005, the dominant species do not differ much, but the dominance of the traditionally dominant species decreases, and the species with absolute dominance changes from
Trichiurus japonicus to
Harpadon nehereus [
17]. The structure of fishery resources in the Yangtze Estuary has changed significantly, with the decline in traditional fishery resources and the miniaturization of fish [
33]. This phenomenon is manifested in the offshore waters of the Yangtze Estuary by the decline in traditional large economic species resources and the gradual dominance of small secondary economic species fish [
34]. The protection and restoration of fishery resources urgently need to be strengthened.
4.2. Annual Variation in Fish Assemblages
Estuaries are highly dynamic ecosystems with complex physical, chemical, and hydrological conditions that change dramatically over time [
26,
35,
36]. In this study, all environmental factors except depth exhibit significant interannual differences, which further influences the abundance, biomass, and composition structure of the fish communities. In the autumns of 2002–2005, water temperature and salinity were the main environmental factors causing the interannual variation of fish in the Yangtze Estuary [
17]. In the spring of 2004 and 2007, the temperature was still the main environmental factor driving fish community variation in the Yangtze Estuary [
1]. In addition to the Yangtze Estuary, in a small macrotidal estuary (the Canche, France), temperature, salinity, and
Crangon crangon (a potential predator for young-of-the-year fish or prey for older ones) were the three most important factors influencing fish species richness and abundance [
37]. Temperature and salinity have relatively strong effects on the temporal variation of most estuarine fish, but there are exceptions. In a sample survey of the subtidal fish assemblage of the Tagus estuary coastal area, depth and sediment type were the main structural factors in the fish assemblage. Temperature and salinity were less important to the overall assemblage structure, although this may be due to the particular climatic regime of the sampling year [
38]. In this survey, due to the fixed sampling season, temperature and salinity show little difference in the autumn and do not become the main influencing factors. Total suspended particles and dissolved oxygen are the main environmental driving factors for the temporal variation of fish assemblage structure in the offshore waters of the Yangtze Estuary during the autumns of 2012–2016, and the correlation between them is not strong.
During the spring and fall of 1998–2001 and the autumn of 2001, there was no significant intervention effect of total suspended particles on the variations in fish assemblages [
15,
39]. In this study, total suspended particles are the dominant environmental factor driving fish assemblages in the Yangtze Estuary in the autumn. Total suspended particle concentrations are mainly influenced by benthic sediment resuspension, riverine inputs, upwelling, and plankton [
40,
41]. Wind direction also plays a significant role in the dispersal of total suspended particle concentrations, with southerly winds favoring the dispersal of high total suspended particle concentrations offshore and easterly winds inhibiting expansion [
42]. In 2012–2016, the cumulative effect of Yangtze River input and the diffusion effect of higher wind speeds and southerly winds resulted in the highest level of total suspended particles in 2013 [
42]. There was a good log–linear relationship between the total suspended matter concentration and turbidity in the offshore waters of the Yangtze Estuary, and the influencing mechanism on fish distribution was consistent [
43]. High turbidity increases the survival rate of estuarine fish by keeping juveniles and small adults away from visual predators and providing more available food [
44]. There are many small fish in the turbidity waters, which are an important food for marine carnivorous fish. Carnivorous fish may choose their habitat based on a balance of factors such as the consumption and time of predation in turbidity waters [
45]. The changing trend of fish biomass in the autumns of 2012–2016 is basically consistent with the change in total suspended particles, that is, the higher the concentration of total suspended matter, the higher the fish biomass, which is consistent with the above results. In terms of fish assemblage structure, RDA shows that fish such as
Harpadon nehereus and
Collichthys lucidus are associated with high total suspended matter concentrations.
Harpadon nehereus show stronger feeding in the autumn, with the highest stomach fullness coefficient, and, therefore, prefer areas with higher bait organisms [
10,
31]. In the present study, high total suspended matter concentrations in the Yangtze Estuary in the autumn of 2013 provide more feeding opportunities for
Harpadon nehereus, and, thus, their abundance and biomass reach their highest values in 2013.
Dissolved oxygen is another main factor driving the interannual variation of fish aggregation in the Yangtze Estuary from 2012 to 2016. Dissolved oxygen content in seawater is an important reference item to determine the biological growth level and seawater pollution level in the sea area [
46]. Dissolved oxygen, as a basic condition for the survival of aquatic animals, is an important environmental factor affecting the growth, respiration, material, and energy metabolism of aquatic animals [
47]. When the dissolved oxygen concentrations drop to 5.0 mg/L, some fish experience respiratory distress, and when dissolved oxygen levels fall below 2.0 mg/L or below 3.0 mg/L, low-dissolved-oxygen sea zones can form [
48]. The hypoxic zone in the Yangtze Estuary is mostly formed in the summer, and the hypoxic phenomenon soon subsides after September, and dissolved oxygen content increases, so there is no hypoxic zone in the autumn [
49]. Hajisamae et al. found a significant positive correlation between dissolved oxygen in the water and fish biomass [
50]. Keller et al. reported a significant decrease in biomass and species diversity of benthic organisms along a low oxygen gradient [
51]. Hypoxia may also reduce growth, reproductive success, and recruitment success [
52]. In this study, dissolved oxygen reaches its highest value in 2012 and its lowest value in 2015, with significant differences. There is no positive correlation between dissolved oxygen and fish biomass, which may be influenced by the synergistic effect of other environmental factors and human activities. The different preferences and adaptability of different fish species to dissolved oxygen also affect the species composition of fish in the different years [
53,
54,
55]. The RDA shows that fish such as
Benthosema pterotum,
Vespicula trachinoides,
Decapterus maruadsi, and
Lateolabrax japonicus are associated with high dissolved oxygen levels.
Benthosema pterotum and
Decapterus maruadsi, as pelagic fish, require higher dissolved oxygen content [
10,
56].
Lateolabrax japonicus is sensitive to dissolved oxygen, and low oxygen stress can cause significant oxidative damage to the juvenile
Lateolabrax japonicus organism; therefore,
Lateolabrax japonicus prefers areas of high dissolved oxygen, which in the Yangtze Estuary only occurred in 2012 when dissolved oxygen was high [
57].
In addition to environmental changes, high-intensity fishing is also an important reason for the interannual variation of fish assemblages. With the increase in fishing efforts, fishing intensity far exceeds resource replenishment capacity, and major economic fish in the Yangtze River estuary are now overfished [
10]. In this study, fish total abundance decreases year by year after reaching its peak in 2013, and it reaches its lowest value in 2016, which is only 19.25% of the abundance in 2013. Therefore, it is imperative to protect the ecological environment of the Yangtze Estuary, limit the fishing intensity, and standardize the use of fishing gear.
4.3. Spatial Characteristics of the Fish Assemblages
Coastal areas are important habitats for many marine fish, and there are often large gradients in environmental conditions that result in different species assemblages [
58]. Depth is an important variable in estuarine ecosystems and is closely related to the distribution of marine organisms, light intensity, food availability, and temperature [
59]. In this study, the range of depths in the Yangtze Estuary is 23–62 m, with large spatial variation driving spatial variation in fish assemblages, but no significant interannual variation in time. This spatial variability is largely a product of the different spatial patterns exhibited by different species [
60]. The fish are classified into shallow assemblage and deep assemblage according to depth. The species have their own preferences for the water layers, with 19 species preferring to live in the deeper areas, 13 species preferring shallow areas, and deep assemblage having a higher species diversity.
Depth has historically been an important factor, but it is not the only factor driving spatial variability in the Yangtze Estuary. In this study, total suspended matter also differs significantly in the deep areas and shallow areas, suggesting that total suspended matter drives interannual variation along with spatial variation in fish assemblages. Total suspended matter concentrations are lower in the deep area near the outer sea and higher in the shallow area near the estuary. In 2004 and 2007, depth, salinity, and total suspended matter together drove variation in the spatial structure of spring fish assemblages in the Yangtze Estuary, dividing fish into southern and northern assemblages [
1]. The invertebrate assemblage in the Yangtze Estuary was also divided into shallow assemblage and deep assemblage according to depth [
61]. In addition to depth, the spatial variation in fish assemblages in the Yangtze Estuary is also driven by other environmental factors at different times. In 2018, the spatial variation in fish in the Yangtze Estuary was driven by salinity, which was divided into high-salt assemblage and low-salt assemblage depending on salinity [
18]. With the exception of the Yangtze Estuary, significant spatial variability is an essential feature of most estuaries (except those with high mixing uniformity) [
28,
62,
63]. On the Alaska Beaufort Shelf, significant interactions between depth and along-shelf position helped define six geographic regions [
64]. Continuously changing environmental gradients underlie the spatial variability in estuarine fish communities.
Biotic interactions and human activities may act in conjunction with environmental preferences in the spatial selection of fish. Fish select their preference for environmental conditions while also integrating the effects of solicitations, interspecific competition, predator avoidance, and human activities [
58]. Flow alterations caused by dam construction, pollution, habitat destruction, and other human activities can all lead to variations in fish biomass and community structure. Therefore, further studies should quantify the importance of biological effects and human activities on the spatial and temporal distribution of fish to generate more reliable assessments of fish assemblage dynamics and facilitate our development of more rational and effective fisheries conservation strategies.