Spatiotemporal Dynamics of Plankton Communities in the Chongqing Section of the National Nature Reserve for Rare and Endemic Fishes in the Upper Yangtze River

Abstract

In order to understand the community structure of plankton and environmental factors in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes (referred to as the “Reserve”) along the upper Yangtze River, this study investigated phytoplankton and zooplankton in the water body from 2021 to 2022. The results revealed a diverse phytoplankton community with 243 species from 105 genera and 8 phyla, dominated by Bacillariophyta and Chlorophyta. Phytoplankton showed average densities of 1.7 × 10⁶ cells/L and biomass of 2.6221 mg/L, following a seasonal pattern of summer > spring > winter. Zooplankton analysis identified 141 species from 77 genera and 4 phyla, with rotifers most abundant, followed by protozoa. Zooplankton displayed average densities of 0.17 × 10⁴ ind./L and biomass of 0.3226 mg/L, also following a seasonal pattern of summer > spring > winter. Total phosphorus (TP) emerged as the primary environmental factor influencing plankton community structure, positively correlating with phytoplankton density and zooplankton biomass. Plankton biodiversity indices classified water quality in the Chongqing section of the “Reserve” as oligo-/mesotrophic. Overall, plankton diversity in this section is notably rich, with similar species composition between mainstems and tributaries but seasonal variations in community structure. While mainstem water quality generally meets standards, some tributaries exhibit varying degrees of pollution, underscoring the need for improved ecological management and protection measures. This is crucial for maintaining the sustainability of the ecosystem.

1. Introduction

Established in 2005, the Upper Yangtze River Rare and Endangered Fish National Nature Reserve (hereinafter referred to as the “Reserve”) spans Sichuan, Yunnan, Guizhou, and Chongqing Municipality. Its primary mission is to safeguard rare and endangered aquatic animals and unique fish species in the upper Yangtze, such as the Chinese sturgeon and red-finned culter [1,2,3]. Plankton, integral to the fish food chain, provide vital nutrients for fish, supporting sustainable use and conservation of fish resources [1,4,5]. However, increased human activities along the coastline have exacerbated water pollution in the basin, posing significant risks to aquatic ecosystems. Thus, continual monitoring of plankton resources in this region is essential to preserve the basin’s aquatic environment and to foster sustainable development of the Yangtze River Economic Belt.

Plankton, which include phytoplankton and zooplankton, are microscopic organisms that drift in water and are essential for maintaining the health and stability of aquatic ecosystems [6,7]. Phytoplankton, as primary producers in water bodies, contribute organic matter through photosynthesis [8,9]. Zooplankton play a crucial role in the aquatic food chain by consuming phytoplankton and other zooplankton, and they are also prey for higher organisms [10]. Additionally, plankton are sensitive indicators of water quality, reflecting changes in aquatic environments [11]. Changes in plankton species composition and abundance can often indicate water quality issues, which may be caused by factors such as nutrient enrichment, excessive heavy metals, or other pollutants [12,13,14,15]. Multiple studies have confirmed this. For example, scholars investigated the community characteristics of phytoplankton and zooplankton in the “protected area” and found that the dominant species were indicators of moderate pollution, revealing that the water environment was somewhat polluted [16]. Scholars assessed the biodiversity index of phytoplankton in the Chongqing section of the main stream of the “protected area,” and the results showed that the investigated waters were slightly polluted or unpolluted [17]. Scholars evaluated the water quality of the Yibin to Jiangjin section of the upper Yangtze River using the biodiversity index and found that most sampling points were slightly polluted or unpolluted [18]. These studies highlight the crucial role of plankton in water quality monitoring and environmental protection.

The Yangtze River Basin, with its rich biodiversity and ecological significance, is a key area for sustainable development. To ensure the sustainable development of aquatic biological resources in the Yangtze River Basin, understanding the current status of aquatic life in the basin is extremely important. In light of this, the main research question of this study is: How do the spatial and temporal distribution patterns of plankton reflect the health status of the water in the Chongqing section of the “Reserve”? By answering this question, we aim to provide fundamental data for the “Ten-Year Fishing Ban” initiative in the Yangtze River, offer scientific management and planning for the sustainable development of aquatic life, and further advance knowledge in this field based on existing research.

2. Materials and Methods

2.1. Study Area and Time

In December 2021 (winter), April 2022 (spring), and August 2022 (summer), eleven sampling sites were considered in the “Reserve,” including five in tributaries (S2, S5, S8, S9, and S11) and six in the mainstem (S1, S3, S4, S6, S7, and S10), as depicted in Figure 1.

2.2. Survey Methods

2.2.1. Environmental Factor Measurements

Transparency (SD) was measured using a Secchi disk (SD20, MRD, Shanghai, China) at the site. Temperature (WT) and dissolved oxygen (DO) were measured using a dissolved oxygen meter (HI98193, HANNA, Villafranca Padovana, Italy). Conductivity (EC) was assessed using a high-precision conductivity testing pen (LS310, Linshang, Shenzhen, China), and pH was determined using a pH meter (PH828, Xima, Huaian, China). Furthermore, total phosphorus (TP) and ammonia nitrogen (NH₃-N) in the water samples were analyzed indoors using a Lianhua water quality analyzer (LH—MUP230, Lianhua, Beijing, China) on the same day. All instruments used to record environmental variables are calibrated and verified before use.

2.2.2. Phytoplankton Survey Method

Qualitative Sample Collection: Qualitative specimens of phytoplankton were collected using a plankton net (PN-219, Yutaiheng, Wuhan, China) with a diameter of 64 μm, which was maneuvered in a back-and-forth ”∞” pattern for 3–5 min. The filtered samples were then transferred into prepared specimen bottles and preserved with 1–1.5% Lugol’s solution. These samples were subsequently transported to the laboratory for microscopic observation and species identification.

Quantitative Sample Collection: Prior to qualitative sampling, water was collected using a water sampler, with 1 L of water sample taken at each sampling point. The samples were promptly fixed with 1–1.5% Lugol’s solution. Upon returning to the laboratory, all quantitative samples were allowed to settle and concentrate for more than 24 h before counting [19].

2.2.3. Zooplankton Survey Method

Qualitative Sample Collection: Protozoa and rotifers were collected using a plankton net with a diameter of 64 μm, while cladocerans and copepods were collected using a plankton net with a diameter of 112 μm. The nets were slowly maneuvered back and forth in an “∞” pattern for 3–5 min, and samples retrieved from the net heads were transferred into water sample bottles. Protozoa and rotifer samples were fixed with 1–1.5% Lugol’s solution, while cladocerans and copepods were preserved using a 5% formaldehyde solution. After labeling and recording, the samples were transported back to the laboratory and allowed to settle for more than 24 h before microscopic examination.

Quantitative Sample Collection: Water samples, ranging from 10 to 50 L each, were collected using a water sampler and filtered through a 13# plankton net. Subsequently, the filtered samples were immediately preserved with a 5% formaldehyde solution. Upon returning to the laboratory, all quantitative samples were left to settle and concentrate for over 24 h before they were enumerated [19].

2.3. Data Processing and Analysis

2.3.1. Species Identification

Microscopic examination, species identification, and plankton counting procedures were conducted in accordance with historical literature [19,20,21,22], complemented by the Wanshen Algae C intelligent identification and counting instrument for both quantitative and qualitative analysis purposes.

2.3.2. Dominance Index

The formula for calculating the McNaughton dominance index (Y) of plankton is as follows:

Y = (n_i/N) × f_i

where N is the total number of planktonic species in the sample, n_i is the number of individuals of the i-th species, and f_i is the occurrence frequency of the i-th species. A species is considered dominant in the community when Y > 0.02.

2.3.3. Biodiversity Index

The analysis utilized the Sorensen similarity index to assess the similarity of biological communities and species composition between mainstem and tributary communities [23]. The formula is stated below:

Sorensen = 2a/(b + c)

where a represents the number of shared species, and b and c represent the respective species numbers. Values ranging from 0.75 to 1.00 indicate very high similarity, values ranging from 0.50 to 0.74 indicate moderate similarity, values ranging from 0.25 to 0.49 indicate low similarity, and values ranging from 0 to 0.24 indicate very low similarity.

2.3.4. Biodiversity Index

This study analyzed plankton diversity in the “Reserve” using the Shannon-Wiener diversity index (H′), Pielou index (J), and Margalef index (D), as outlined in

Table 1. Relationship between the diversity index and degree of water pollution.

Evaluation Standard	Diversity Indices
	H′	J	D
Oligo-pollution	>3	>0.5	>3
β-medium pollution	>2~3	>0.4~0.5	>2~3
α-medium pollution	>1~2	>0.3~0.4	>1~2
Severe pollution	≤1	≤0.3	≤1

[24,25,26]. The Shannon index assesses species diversity in biological communities, with higher values indicating greater diversity [26]. The Pielou index measures the evenness of species distribution within a community [25]. The Margalef index indicates species richness within a community, reflecting the abundance of species [24]. Formulas for each index are as follows:

Shannon index: H′ = ∑P_ilog₂P_i, P_i = n_i/N

Margalef index: D = (S − 1)/log₂N

Pielou index: J = H′/H_max

The variables are defined as follows: N represents the total count of individuals or sequences detected, n_i denotes the count of individuals or sequences of the i-th species, S signifies the total number of species present, and H_max indicates the highest Shannon index attainable given the same species richness across all community species.

2.3.5. Statistical Analysis

This study is based on temporal and spatial scales. The data of environmental factors were sorted out and averaged. One-way analysis of variance (ANOVA) was used to test the significance between the data. A pie chart is drawn to display the results of species identification and their proportions. Draw pie charts of the density and biomass of phytoplankton and zooplankton, and use variance analysis to test whether the differences between the mainstem and tributaries in different seasons are significant. At the same time, based on the density of planktonic organisms, draw a Principal Coordinate Analysis (PCoA) chart based on the Bray–Curtis distance. The biodiversity index was presented in a line chart and one-way ANOVA was performed. All data are subjected to normality and homogeneity of variance tests using SPSS, and one-way ANOVA is conducted on data that meet the prerequisites. Conduct a Detrended Correspondence Analysis (DCA), and if the length of the DCA axis is greater than 3, proceed with a Redundancy Analysis (RDA). Use this method to explain the relationship between phytoplankton and zooplankton and environmental factors. Analyze whether there are any significant differences between the biological communities at different sampling sections and various environmental factors. Statistical analyses are performed using IBM SPSS Statistics 26 software and Excel 2021.

3. Results

3.1. Differences in Environmental Factors between the Mainstem and Tributaries

The environmental test results for the “Reserve” are detailed in

Table 2. Temporal and spatial variation in environmental factors (significant analysis of variance was carried out among different sections in the same season (Mean 1), different seasons in the same section (Mean 2), and seasonal mainstem and tributaries (Mean 3) for each environmental factor).

Environmental Factors	Season	Sampling Sections											Mean 2	Mean 3
		S1	S2	S3	S4	S5	S6	S7	S8	S9	S10	S11		Tributary	Mainstem
pH	Winter	8.32	8.24	8.3	8.43	8.28	8.27	8.25	8.38	8.39	8.33	8.27	8.31 a	8.31 a	8.32 a
	Spring	8.45	8.31	8.22	8.06	8.18	8.21	8.24	7.99	8.2	8.18	8.12	8.20 b	8.16 a	8.23 a
	Summer	8.62	8.46	8.38	8.5	8.33	8.49	8.58	8.71	8.41	8.56	8.72	8.52 c	8.53 a	8.52 a
Mean 1		8.46 a	8.34 a	8.30 a	8.33 a	8.26 a	8.32 a	8.36 a	8.36 a	8.33 a	8.36 a	8.37 a
WT (°C)	Winter	15.6	13.6	15.5	15.7	14.7	14.9	15.6	13.4	19	15.5	12.7	15.11 a	14.7 a	15.5 a
	Spring	19.4	22.2	17.8	18.1	20.8	17.8	18.2	22.4	24.8	18	19.7	19.93 b	22.0 b	18.2 b
	Summer	28.5	35.1	28.1	28.7	35.3	28.3	29.7	33.2	32.3	26.4	35.9	31.05 c	34.4 c	28.3 b
Mean 1 (°C)		21.17 a	23.63 a	20.47 a	20.83 a	23.60 a	20.33 a	21.17 a	23.00 a	25.37 a	19.97 a	22.77 a
SD (m)	Winter	0.9	0.12	0.7	0.8	0.1	0.13	0.9	0.6	0.2	0.12	0.75	0.48 a	0.4 a	0.6 a
	Spring	0.9	1.2	1.1	1	0.6	0.8	0.8	0.7	0.6	0.5	0.7	0.81 b	0.8 a	0.9 a
	Summer	1.2	1	1.1	1.5	0.7	1.9	1	0.9	0.7	1.5	0.9	1.13 c	0.8 a	1.4 b
Mean 1 (m)		1.00 a	0.77 a	0.97 a	1.10 a	0.47 a	0.94 a	0.90 a	0.73 a	0.50 a	0.71 a	0.78 a
DO (mg/L)	Winter	10.77	12.33	11.84	13.15	12.92	11.56	11.44	12.59	9.68	10.7	11.91	11.72 a	11.89 a	11.58 a
	Spring	9.43	9.69	9.87	10.08	10.14	9.66	9.86	9.34	7.53	9.09	9.01	9.43 b	9.14 a	9.67 a
	Summer	6.26	6.21	5.96	6.85	6.69	7.16	8.58	8.71	8.41	8.56	8.72	7.46 c	7.75 a	7.23 a
Mean 1 (mg/L)		8.82 a	9.41 a	9.22 a	10.03 a	9.92 a	9.46 a	9.96 a	10.21 a	8.54 a	9.45 a	9.88 a
EC (μS/cm)	Winter	344	384	350	352	624	398	370	664	1800	394	197	534 a	734 a	368 a
	Spring	374	302	402	404	422	404	392	578	1246	388	140	459 a	538 a	394 a
	Summer	284	450	340	332	634	314	332	614	1934	332	148	519 a	756 a	322 a
Mean 1 (μS/cm)		334 ac	379 ab	364 abc	363 abc	560 bd	372 ab	365 abc	619 d	1660 e	371 ab	162 c
TP (mg/L)	Winter	0.054	0.038	0.052	0.047	0.06	0.13	0.064	0.111	0.039	0.048	0.021	0.060 ab	0.054 a	0.066 a
	Spring	0.07	0.075	0.057	0.076	0.166	0.064	0.061	0.219	0.045	0.063	0.034	0.085 a	0.108 a	0.065 a
	Summer	0.031	0.035	0.024	0.091	0.03	0.032	0.078	0.045	0.023	0.037	0.04	0.042 b	0.035 a	0.049 a
Mean 1 (mg/L)		0.052 a	0.049 a	0.044 a	0.071 ab	0.085 ab	0.075 ab	0.068 ab	0.125 b	0.036 a	0.049 a	0.032 a
NH3-N (mg/L)	Winter	0.186	0.48	0.306	0.162	0.384	0.114	0.102	0.522	1.896	0.12	0.336	0.419 a	0.724 a	0.165 a
	Spring	0.204	0.48	0.114	0.078	1.092	0.198	0.276	3.558	1.314	0.252	0.276	0.713 a	1.344 a	0.187 a
	Summer	0.036	0.222	0.132	0.032	0.276	0.18	0.45	0.588	2.264	0.498	0.348	0.457 a	0.740 a	0.221 a
Mean 1 (mg/L)		0.142 a	0.394 a	0.184 a	0.091 a	0.584 a	0.164 a	0.276 a	1.556 b	1.825 b	0.290 a	0.320 a

Note: Different lowercase letters represent no significant difference (p > 0.05) among different means under the same environmental factor (distinguished rows and columns), while the absence of the same letter indicates a significant difference (p < 0.05). The bold is the mean value.

. One-way ANOVA was performed on space (Mean1) and time (Mean2) of different environmental factors (Table 2). It was found that the pH, water temperature, transparency, dissolved oxygen, and total phosphorus were significantly different between different seasons. Specifically, pH levels were notably higher in summer compared to winter (p < 0.01), and pH values in winter exceeded those of spring (p < 0.05). Summer water temperatures were significantly higher than those in spring (p < 0.01), while spring temperatures were notably higher than those in winter (p < 0.01). Transparency in summer was significantly greater than that in spring (p < 0.05). The dissolved oxygen concentration in winter and spring was significantly greater than that in summer (p < 0.05). The total phosphorus in spring was significantly greater than that in summer (p < 0.05). The conductivity, total phosphorus, and ammonia nitrogen significantly differed among the sampling sections. The conductivity in section S9 was significantly greater than that in the other sections (p < 0.01), and the total phosphorus in section S8 was significantly greater than that in the other sections (p < 0.05). The ammonia nitrogen in sections S8 and S9 was significantly greater than that in the other sections (p < 0.05). Additionally, the conductivity and ammonia nitrogen in the tributaries were significantly greater than those in the mainstem (p < 0.05), while the transparency in the mainstem was significantly greater than that in the tributaries (p < 0.05). Differences in environmental factors between the mainstem and tributaries were observed across seasons. In summer, tributary water temperature was significantly higher than that of the mainstem (p < 0.01), and tributary water transparency was significantly lower than that of the mainstem (p < 0.01). Similarly, in spring, tributary water temperature was significantly higher than that of the mainstem (p < 0.01).

According to the “Surface Water Environmental Quality Standards” (GB 3838-2002) [27], water quality in this area is Class II during winter and summer, and Class III in spring. A comparison between the mainstem and tributaries reveals that the mainstem consistently maintains Class II water quality throughout all seasons. In contrast, the tributaries exhibit Class III water quality during winter and summer, and Class IV water quality in spring. Among the tributaries, the Qijiang River and Tang River maintain Class II water quality in all seasons. The Binan River maintains Class II water quality in winter and summer, but drops to Class IV in spring. The Linjiang River has Class III water quality in winter and summer, and worsens to exceed Class V standards in spring. The Daluxi River has Class V water quality in winter, Class IV in spring, and exceeds Class V in summer.

3.2. Phytoplankton

3.2.1. Overall Composition of Phytoplankton Species

In the “Reserve”, a total of 243 phytoplankton species belonging to 105 genera and distributed among 8 phyla were identified (Appendix A). The phylum Bacillariophyta exhibited the highest species count, with 119 species found in 38 genera. Following this, Chlorophyta had 66 species across 37 genera. Other phyla included Cyanobacteria with 31 species in 17 genera, Euglenophyta with 15 species in 4 genera, Pyrrophyta with 4 species in 3 genera, Chrysophyta with 4 species in 3 genera, Cryptophyta with 3 species in 2 genera, and Xanthophyta with 1 species in 1 genus (Figure 2).

In different seasons, the highest species count was observed in spring, totaling 194 species across 90 genera. Bacillariophyta had the most species with 113, followed by Chlorophyta with 49. Summer showed the next highest diversity, with 182 species across 87 genera. Bacillariophyta dominated with 98 species, followed by Chlorophyta with 45. Winter exhibited the lowest species count, with 161 species across 71 genera. Bacillariophyta had the highest number with 97 species, followed by Chlorophyta with 28.

3.2.2. Composition of Phytoplankton Species in the Mainstem and Tributaries

In the mainstem of the “Reserve” across three seasons, a total of 211 species from 92 genera and 7 phyla of phytoplankton were identified (Appendix A). Of these, 113 species were Bacillariophyta, representing 53.55% of the total species, and 50 species were Chlorophyta, constituting 23.70% of the total species. Specifically, in winter, 135 species were observed in the mainstem, with 83 species of Bacillariophyta, making up 61.48% of the total, and 25 species of Chlorophyta, comprising 18.52% of the total. In spring, 154 species were observed, with Bacillariophyta comprising the majority at 89 species, followed by 34 species of Chlorophyta. In summer, 143 species were noted, with Bacillariophyta again having the most at 88 species, followed by 30 species of Chlorophyta.

In the tributaries of the “Reserve” during the same seasons, 211 species from 96 genera and 8 phyla were recorded (Appendix A). Bacillariophyta dominated with 106 species, accounting for 50.24% of the total, followed by 54 species of Chlorophyta, which constituted 25.60% of the total. In winter, 127 species were recorded in the tributaries, with 85 species of Bacillariophyta, representing 66.93% of the total, and 16 species of Chlorophyta. In spring, 161 species were detected, with Bacillariophyta again leading at 89 species, followed by 38 species of Chlorophyta. In summer, 151 species were observed, with 75 species of Bacillariophyta and 40 species of Chlorophyta.

A total of 179 species were identified as common between the mainstem and tributaries, with 32 species exclusive to the mainstem and another 32 to the tributaries. The Sorensen similarity index results (

Table 3. Sorensen similarity index of phytoplankton in the mainstem and tributaries.

Index	Between the Mainstem and Tributaries	Between Each Tributary and the Mainstem
		S2	S5	S8	S9	S11
a	179	122	127	115	117	128
b	213	133	139	127	125	141
c	211	211	211	211	211	211
Sorensen	0.8443	0.7093	0.7257	0.6805	0.6923	0.7273
Degree of similarity	very high similarity	moderate similarity	moderate similarity	moderate similarity	moderate similarity	moderate similarity

Note: “a” represents the number of shared phytoplankton species between the main and tributary streams; “b” and “c” represent the number of phytoplankton species in the tributary and mainstems, respectively.

) revealed a very high similarity of 0.8443 in phytoplankton species composition between the mainstem and tributaries. The similarity indices for tributaries S2, S5, S8, S9, and S11 in comparison to the mainstem were 0.7093, 0.7257, 0.6805, 0.6923, and 0.7273, respectively, indicating moderate similarity in species composition.

3.2.3. Dominant Species of Phytoplankton in Each Season

A total of 23 dominant phytoplankton species were identified across three seasons (

Table 4. Dominant species of phytoplankton in different seasons. The “Y” value is the dominant value of this species in all sampling sections.

Category	Dominant Species	Y
		Spring	Summer	Winter
Bacillariophyta	Cyclotella meneghiniana	0.0220	0.0424	0.0304
	C. stelligera	—	0.0955	—
	Gomphonema intricatum	—	—	0.0386
	G. parvulum	0.0284	—	0.0477
	Melosira granulata var. angustissima	—	—	0.0225
	M. granulata	—	0.0600	0.0479
	M. varians	0.0515	—	0.0913
	Nitzschia amphibia	—	—	0.0288
	N. actinastroides	—	0.0298	—
	N. palea	—	0.0240	—
	N. paradoxa	0.0380	—	0.1098
	N. palea	0.0301	—	0.0220
	N. exigua	0.0368	—	—
	Synedra acus	0.0289	—	—
	S. ulna	0.0284	—	0.0210
Chlorophyta	Chlorella vulgaris	0.0570	0.0453	0.0383
	Ankistrodesmus angustus	0.0247	—	—
Cyanophyta	Anabaena azotica	—	0.0347	—
	Phormidium tenus	—	—	0.0230
	Microcystis aeruginosa	—	0.0218	—
	Oscillatoria irrigua	—	0.1275	—
Cryptophyta	Cryptomonas erosa	0.0225	—	—
	C. ovata	0.0217	—	—

Note: “—” indicates that the dominance is less than 0.02.

), distributed among 4 phyla (15 species from Bacillariophyta, 2 from Chlorophyta, 4 from Cyanobacteria, and 2 from Cryptophyta). In spring, 12 dominant species were detected, with Bacillariophyta having the highest count of 8 species, followed by Chlorophyta and Cryptophyta, each with 2 species. Summer showed 9 dominant species, primarily Bacillariophyta with 5 species, followed by Cyanobacteria with 3 species and Chlorophyta with 1 species. In winter, 12 dominant species were recorded, Bacillariophyta leading with 10 species, followed by Chlorophyta and Cyanobacteria, each with 1 species.

3.2.4. Density and Biomass of Phytoplankton in the Mainstem and Tributaries

The density of phytoplankton in the “Reserve” is illustrated in Figure 3a. In this section, the average phytoplankton density was 1.70 × 10⁶ cells/L. Specifically, during spring, it averaged 1.33 × 10⁶ cells/L, ranging from 0.22 × 10⁶ cells/L to 5.94× 10⁶ cells/L; during summer, it peaked at 3.23 × 10⁶ cells/L, ranging from 0.35 × 10⁶ cells/L to 20.39 × 10⁶ cells/L; and during winter, it was lowest at 0.54 × 10⁶ cells/L, with a range of 0.21 to 1.87 × 10⁶ cells/L. Based on the Bray–Curtis distance, PCoA was conducted, with the first two axes explaining 59% and 16% of the variance, respectively (Figure 4). It can be observed from the Figure 3 that there is a very high degree of overlap in the confidence intervals for the three seasons, and, similarly, the confidence intervals for the tributaries and mainstem during winter, spring, and summer also show a very high degree of overlap. Statistical analysis indicated no significant differences (p > 0.05) in phytoplankton density between mainstem and tributaries during winter, spring, or summer. However, phytoplankton density at S8 was significantly higher than at other sampling sections, except S5 (p < 0.05). Overall, phytoplankton density followed the trend of summer > spring > winter in this section, with no significant differences observed between seasons (p > 0.05).

The biomass of phytoplankton in the “Reserve” is shown in Figure 3b. In this section, the average biomass was 2.6221 mg/L. Specifically, during spring, it averaged 2.3032 mg/L, ranging from 0.1090 to 8.4507 mg/L; during summer, it peaked at 4.4126 mg/L, ranging from 0.6197 to 30.7315 mg/L; and during winter, it was lowest at 1.1504 mg/L, ranging from 0.1542 to 3.3360 mg/L. Statistical analysis indicated no significant differences (p > 0.05) in phytoplankton biomass between the mainstem and tributaries during winter, spring, or summer. However, phytoplankton biomass at S8 was significantly higher than at other sampling sections, except S5 and S4 (p < 0.05). Overall, the biomass of phytoplankton followed the trend of summer > spring > winter in this section, with no significant differences observed between seasons (p > 0.05).

3.2.5. Diversity Indices of Phytoplankton in the Mainstem and Tributaries

The diversity indices H′, J, and D of phytoplankton in the “Reserve” are depicted in Figure 5. During spring, H′, J, and D were 3.4447, 0.8590, and 10.1130, respectively, with values ranging from 3.2582 to 3.8390 for H′, 0.7933 to 0.9046 for J, and 7.9651 to 12.7820 for D. In summer, these indices measured 3.1550, 0.8361, and 8.4249, respectively, with ranges of 2.4446 to 3.5829 for H′, 0.6315 to 0.9023 for J, and 5.5207 to 10.8524 for D. In winter, H′, J, and D were 3.1638, 0.8549, and 8.0175, respectively, with ranges of 2.9129 to 3.3978 for H′, 0.7745 to 0.8979 for J, and 6.3989 to 9.1092 for D. Overall, H′ and J followed the sequence of spring>winter>summer, while D followed the pattern of spring. H′ and D were significantly higher in spring than in winter and summer (p < 0.05), while no significant differences were observed in J between seasons (p > 0.05). Single-factor analysis of variance showed no significant differences (p > 0.05) in H′, J, or D between the mainstem and tributaries during winter and summer, and no significant differences in H′ or J between them during spring (p > 0.05). However, D in spring for tributaries was significantly higher than in the mainstem (p < 0.05). According to evaluation criteria (Table 2), H′, J, and D correspond to oligotrophic water quality types in the “Reserve” across all seasons. Additionally, these indices in both mainstem and tributaries reflect oligotrophic water quality types.

3.3. Zooplankton

3.3.1. Overall Composition of Zooplankton Species

In the “Reserve”, a total of 141 zooplankton species from 77 genera were identified (Appendix B). Rotifers were the most abundant, comprising 64 species in 31 genera, followed by protozoa with 50 species in 26 genera. Cladocera accounted for 17 species across 12 genera, while Copepoda had the fewest species, totaling 10 in 8 genera (Figure 6). When comparing seasons, spring exhibited the highest species diversity with 107 species in 63 genera. Rotifers were the dominant group with 48 species, followed by protozoa with 36 species. Summer recorded 101 species in 57 genera, mainly rotifers with 54 species, followed by protozoa with 29 species. Winter had 80 species in 44 genera, with rotifers being the most abundant at 34 species, followed by protozoa with 32 species.

3.3.2. Composition of Zooplankton Species in the Mainstem and Tributaries

In the “Reserve”, the mainstems were found to host a total of 121 zooplankton species belonging to 68 genera across all three seasons (Appendix B). Rotifers were the dominant group, comprising 57 species, making up 47.11% of the total species, followed by protozoa with 42 species, accounting for 34.71% of the total. Specifically, during winter, 73 mainstems were identified, with rotifers being the most prevalent at 32 species (43.84%), followed by protozoa with 30 species (41.10%). In spring, 87 mainstems were recorded, with rotifers leading at 39 species (44.83%), followed by protozoa with 29 species (33.33%). During summer, 74 mainstems were observed, with rotifers once again dominating at 41 species (55.41%), followed by protozoa with 23 species (31.08%).

In the tributary streams of the “Reserve”, a total of 112 zooplankton species from 61 genera were identified across all three seasons (Appendix B). Rotifers were the dominant species, comprising 55 species, which accounted for 49.11% of the total species, followed by protozoa with 38 species, representing 33.93% of the total. Specifically, during winter, the tributary streams harbored 52 species, with both protozoa and rotifers equally prevalent at 20 species each (38.46%), followed by Cladocera with 7 species (13.46%). In spring, the tributary streams recorded 81 species, with rotifers being the most numerous at 37 species (45.68%), followed by protozoa with 29 species (35.80%). During summer, the tributary streams observed 73 species, with rotifers again dominating at 44 species (60.27%), followed by protozoa with 16 species (21.92%).

The main and tributary streams shared 92 species (

Table 5. Sorensen similarity index of zooplankton between the mainstem and tributaries.

Index	Between the Mainstem and Tributaries	Between each Tributary and the Mainstem
		S2	S5	S8	S9	S11
a	92	59	53	53	55	53
b	112	67	59	61	58	57
c	121	121	121	121	121	121
Sorensen	0.7897	0.6277	0.5889	0.5824	0.6145	0.5955
Degree of similarity	very high similarity	moderate similarity	moderate similarity	moderate similarity	moderate similarity	moderate similarity

), with 29 species exclusive to the mainstems and 20 species exclusive to the tributary streams. The Sorensen similarity index for zooplankton species composition between them was 0.7897, indicating a high similarity. Between tributary streams (S2, S5, S8, S9, and S11) and mainstems, Sorensen similarity indices ranged from 0.5824 to 0.6277, showing moderate similarity in zooplankton species composition between each tributary and the mainstems.

3.3.3. Dominant Species of Zooplankton in Each Season

A total of 11 dominant zooplankton species were identified across the three seasons (

Table 6. Dominant species of zooplankton in different seasons. The “Y” value is the dominant value of this species in all sampling sections.

Category	Dominant Species	Y
		Spring	Summer	Winter
Protozoa	Arcella vulgaris	0.0999	—	—
	Centropyxis aerophila	—	—	0.0342
	Difflugia acuminata	—	—	0.0383
	D. globulosa	0.0496	0.0315	0.2599
	D. mammilaris	0.0344	—	0.0731
	D. pyriformis	0.0327	—	—
	Tintinnopsis wangi	0.0285	—	0.0223
	Vorticella sp.	—	0.0558	—
Rotifera	Brachionus  calyciflorus	—	0.0245	—
	B. angularis	—	0.0211	—
	Keratella cochlearis	0.0240	—	—

), categorized into two main groups; protozoa (8 species) and rotifers (3 species). In spring, there were 6 dominant species, primarily consisting of 5 protozoa species, with 1 species from rotifers. In summer, 4 dominant species were observed, evenly split between 2 species each from protozoa and rotifers. Winter showed 5 dominant species, all belonging to protozoa. Notably, no dominant species were identified from Cladocera or Copepoda. Difflugia globulosa, a protozoan species, was notably dominant across all three seasons.

3.3.4. Zooplankton Density and Biomass in the Mainstem and Tributaries

The average zooplankton density in the “Reserve” plots was 0.17 × 10⁴ ind./L (Figure 7a). In spring, it was 0.23 × 10⁴ ind./L, ranging from 0.01 × 10⁴ ind./L to 0.66 × 10⁴ ind./L; in summer, it measured 0.17 × 10⁴ ind./L, ranging from 0.01 × 10⁴ ind./L to 0.84 × 10⁴ ind./L; and in winter, it was 0.10 × 10⁴ ind./L, ranging from 0.03 × 10⁴ ind./L to 0.30 × 10⁴ ind./L. Based on the Bray–Curtis distance, PCoA was conducted, with the first two axes explaining 47% and 23% of the variance, respectively (Figure 8). It can be observed from the Figure 7 that there is a very high degree of overlap in the confidence intervals for the two seasons, and, similarly, the confidence intervals for the tributaries and mainstem during winter and spring also show a very high degree of overlap. However, the confidence intervals between the mainstem and tributaries in summer do not overlap. One-way analysis of variance (ANOVA) comparing zooplankton density between main and tributary streams indicated no significant differences in spring and winter (p > 0.05). However, during summer, zooplankton density in tributary streams was notably higher than in the mainstems (p < 0.05). There were no significant differences in zooplankton density among different sampling sections (p > 0.05). Overall, zooplankton density showed a trend of summer > spring > winter, with no significant seasonal differences (p > 0.05).

The average zooplankton biomass in the “Reserve” treatment was 0.3226 mg/L (Figure 7b). In spring, it was 0.4239 mg/L, ranging from 0.0180 to 1.1621 mg/L; in summer, it measured 0.3311 mg/L, ranging from 0.0282 to 0.8859 mg/L; and in winter, it was 0.2127 mg/L, ranging from 0.0223 to 0.5487 mg/L. One-way ANOVA comparing zooplankton biomass between main and tributary streams indicated no significant differences in any season (p > 0.05). Similarly, there were no significant differences in zooplankton biomass among different sampling sections (p > 0.05). Overall, zooplankton biomass showed a trend of summer > spring > winter, with no significant seasonal variations (p > 0.05).

3.3.5. Diversity Index of Zooplankton in the Mainstem and Tributaries

In the “Reserve”, the diversity indices H′, J, and D of zooplankton were 2.0988, 0.8080, and 2.0231, respectively (Figure 9). Specifically, in spring, H′, J, and D were 2.1998, 0.7771, and 2.3565, with values ranging from 1.6058 to 2.8338 for H′, 0.6740 to 0.8578 for J, and 1.3139 to 4.1371 for D. In summer, H′, J, and D measured 2.1839, 0.8434, and 2.0774, with values ranging from 1.3500 to 2.9806 for H′, 0.6764 to 0.9108 for J, and 0.7545 to 3.6218 for D. In winter, H′, J, and D were 1.9128, 0.8035, and 1.6352, with values ranging from 0.9644 to 2.4366 for H′, 0.6957 to 0.8600 for J, and 0.5137 to 3.0178 for D. Overall, H′ and D showed a pattern of spring > summer > winter, while J followed summer > winter > spring. There were no significant differences in H′ or D between seasons (p > 0.05), but J in summer was significantly higher than in spring (p < 0.05).

One-way ANOVA conducted on the zooplankton diversity indices between the main and tributary streams indicated significant findings. Specifically, during spring, J was notably higher in the tributary streams compared to the mainstream (p < 0.01), while no significant differences were observed in H′ and D (p > 0.05). In summer, J did not show significant differences between the main and tributary streams (p > 0.05), but H′ and D were significantly greater in the tributary streams than in the mainstem (p < 0.05). During winter, there were no significant differences in H′, J, or D between the main and tributary streams (p > 0.05).

According to the assessment criteria (Table 2), diversity indices H′ and D consistently indicated β-medium pollution across all seasons, while J consistently indicated oligo-pollution. Specifically, during spring and summer, both H′ and D were classified as β-medium pollution, whereas in winter, they shifted to α-medium pollution. J consistently reflected oligo-pollution throughout all seasons. Comparing the main and tributary streams, the overall H′ and D of the tributary streams were categorized as β-medium pollution, contrasting with the mainstems that showed α-medium pollution tendencies. In both main and tributary streams across all seasons, J consistently indicated oligo-pollution. Specifically, in spring, H′ and D for both main and tributary streams were classified as β-medium pollution. In summer, while H′ of the mainstems shifted to α-medium pollution, that of the tributary streams remained β-medium pollution. During winter, H′ for the mainstems indicated β-medium pollution, while for the tributary streams, it indicated α-medium pollution.

3.4. Relationships between Plankton and Environmental Factors

Detrended Correspondence Analysis (DCA) of the plankton community structure in the “Reserve” indicated a maximum gradient length of the sorting axis less than 3, prompting the adoption of a linear model (RDA) to analyze environmental drivers of plankton community characteristics. Axis I and Axis II explained 98.43% and 1.33% of the relationships for phytoplankton and environmental factors (Figure 10a), and 77.28% and 18.8% for zooplankton (Figure 10b), respectively, illustrating effective explanation of plankton–environment relationships. Upon screening, total phosphorus emerged as the primary environmental factor influencing variation in both phytoplankton community structure (r = 0.87, p < 0.05) and zooplankton community structure (r = 0.80, p < 0.05). The study highlighted a significant positive correlation between total phosphorus levels and phytoplankton density, as well as zooplankton biomass. Additionally, plankton community structures at S8 and S5 exhibited significant correlations with total phosphorus levels.

4. Discussion

4.1. Composition of Plankton in the Mainstem and Tributaries

In the “Reserve”, a total of 243 species of phytoplankton from 105 genera and 8 classes were identified, primarily Bacillariophyta and Chlorophyta, consistent with historical records [16,17,18]. Winter showed the fewest species, likely due to lower water temperatures and reduced light, which can hinder phytoplankton growth and reproduction [28,29]. Cold temperatures may limit survival of certain species, notably Chlorophyta, with only 28 species detected in winter compared to over 40 in spring and summer. Zooplankton analysis found 141 species from 7 genera, with rotifers predominating over protozoa, indicating a shift in community structure from earlier surveys [16,18]. Rotifers thrive in the “Reserve” due to favorable conditions such as water temperature, quality, and nutrient content [30]. Bacillariophyta and Chlorophyta dominated phytoplankton in both main and tributary streams across all seasons, while rotifers were the predominant zooplankton. The Sorensen similarity index indicated moderate to high community similarity between main and tributary streams throughout the seasons, suggesting effective dispersal and synchronization of plankton communities [31]. However, comparisons across seasons revealed higher phytoplankton species diversity in spring and summer tributaries compared to the mainstem, likely due to warmer tributary temperatures during these seasons, which promote plankton diversity. Temperature is recognized as a critical factor influencing plankton community dynamics [32]. Overall, plankton composition in both main and tributary streams in the region exhibits significant similarity and synchronization, with tributaries contributing to the ecological role of the mainstem to some extent. This has laid a certain foundation for the sustainable development of the ecosystem.

4.2. Dominant Species of Plankton

Among the prominent species identified in the “Reserve“, species such as Melosira varians, Oscillatoria irrigua, and Brachionus calyciflorus serve as indicators of pollution [33], suggesting potential anthropogenic disturbances or pollution in the water quality of the “Reserve” [34]. Bacillariophyta predominates among the dominant phytoplankton species, consistent with findings from previous surveys [16]. The silica shells of Bacillariophyta provide them with resilience, shielding cells from mechanical damage and predators, allowing adaptation to various environmental pressures [35]. During summer, there was an uptick in dominant Cyanophyta species, whereas their presence waned in winter. Cyanobacteria generally exhibit robust tolerance to high temperatures, thriving under warmer conditions in summer [36,37]. Conversely, lower winter temperatures constrain extensive cyanobacterial reproduction, fostering the growth of Bacillariophyta, dinoflagellates, and other organisms [38].

The predominant zooplankton species in the area are primarily protozoa and rotifers, with no single dominant species identified among copepods and cladocerans. Protozoa exhibited the highest number of dominant species during spring and winter, while they were comparable to rotifers in summer. Spring and winter water bodies are comparatively nutrient-poor, providing protozoa with more resources and a competitive edge in nutrient-limited environments [39,40]. Within this group, the genus Difflugia emerged as a dominant taxon across all seasons, likely due to its omnivorous feeding habits, which include organic matter, phytoplankton, and bacteria [41,42], facilitating rapid reproduction and development. Rotifers, characterized by their sexual reproduction and ability to form resting eggs under adverse conditions, also contribute to their dominance in the water body [43,44]. In contrast, copepods and cladocerans have simpler diets primarily consisting of phytoplankton and other zooplankton, coupled with limited swimming abilities that hinder their rapid proliferation in flowing water bodies [45], thereby preventing them from establishing dominance in this aquatic ecosystem.

4.3. Plankton Density and Biomass in the Mainstem and Tributary

The density and biomass of phytoplankton and zooplankton in the “Reserve” show a consistent pattern of summer > spring > winter, without significant seasonal variations. This trend reflects the favorable conditions for phytoplankton growth and reproduction in summer, characterized by higher water temperatures and stronger light intensity. In contrast, lower temperatures and reduced light intensity during spring and winter limit phytoplankton densities and biomass [28,29]. Since zooplankton primarily feed on phytoplankton, their densities and biomass also follow this seasonal pattern [46].

Comparative examination of plankton density and biomass between the mainstem and tributaries indicated that only the zooplankton density in tributaries significantly exceeded that in the mainstem during summer. This disparity is likely influenced by robust water exchange between the mainstem and tributaries, fostering a high degree of similarity in planktonic community composition [31]. Additionally, total phosphorus emerged as the primary environmental factor limiting plankton in this basin, with no notable distinction observed between the mainstem and tributaries, thereby maintaining relatively consistent plankton density and biomass across these water bodies. During summer, zooplankton dynamics may also be affected by factors such as water temperature and transparency. Tributaries typically exhibit higher transparency and water temperature compared to the mainstem during this season, conditions likely conducive to enhanced reproductive and foraging activities of zooplankton [47,48].

Furthermore, the density and biomass of phytoplankton in the S8 section were significantly higher compared to other sections. This could be attributed to its proximity to a river tributary where the riverbed and adjacent sediment are composed of soil. Fertilizers from nearby farmlands and domestic sewage from surrounding towns enter the water through surface runoff, leading to eutrophication of the water body. Additionally, the slower water flow rate in this section supports the reproduction and growth of phytoplankton [49,50]. Moreover, plankton play a crucial role as a primary food source for fish. Thus, variations in plankton density and biomass across time and space within the “Reserve” might influence the feeding behavior and ecological distribution of fish.

4.4. Plankton Diversity Indices of the Mainstem and Tributaries

In evaluations of water quality, higher biodiversity indices are typically linked to better water conditions, while lower indices may indicate pollution or disruptions in the ecosystem [28,51]. During spring, the diversity indices H′, J, and D of phytoplankton were at their peak, with H′ and D significantly higher in spring compared to winter and summer. This likely reflects the more stable and abundant environmental conditions in spring, which support the reproduction, growth, and balanced distribution of various algal species without any one species dominating excessively. This results in a more diverse species composition. Previous research has also noted greater diversity of algal species in the “reserve” community during spring compared to summer and winter [52]. Similarly, the diversity indices H′ and D for zooplankton were also highest in spring, showing similar trends to phytoplankton. Comparative analysis between the main and tributary streams revealed that the diversity index D of phytoplankton in the tributaries was significantly greater than that in the mainstem during spring, indicating a greater species richness of phytoplankton in the tributaries and possibly greater habitat heterogeneity. During summer, the diversity indices H′ and D of zooplankton in tributaries are notably higher than those in the mainstream, which could be influenced by distinct differences in water temperature and transparency between these two types of streams [47,48].

The diversity indices H′, J, and D of phytoplankton across all seasons indicate oligo-pollution, suggesting minimal pollution inputs and relatively clean water conditions. For zooplankton, H′ and D correspond to β-medium pollution, while J indicates oligo-pollution, reflecting a uniform distribution of zooplankton with a loss of sensitive species, indicative of some degree of water pollution [53]. Comprehensive biodiversity index evaluations classify the water quality of the “Reserve” as oligo-moderate pollution overall, with sections exhibiting α-medium pollution and tributaries showing β-medium pollution. This suggests richer community diversity and lower pollution levels in the tributaries compared to the mainstream. According to surface water environmental quality criteria, the “Reserve” is Class II water in winter and summer, and Class III water in spring. Winter and summer exhibit more abundant ecological functions, supporting the conservation goals of rare aquatic habitats. The mainstem consistently shows cleaner water quality than the tributaries across all seasons. The conclusions drawn from different water quality evaluation methods vary between seasons and main versus tributary streams, indicating potential discrepancies. Physicochemical methods focus on water properties such as dissolved oxygen and nutrient levels, directly reflecting pollution levels. Diversity index evaluation considers organism distribution and ecosystem complexity, providing insights into ecosystem stability. However, the adaptability of some plankton species to adverse conditions may lead diversity indices to inaccurately reflect current water quality status [34]. Therefore, integrating multiple evaluation methods is crucial for comprehensive and accurate water quality monitoring, ensuring a more holistic assessment of specific water bodies.

4.5. Relationships between Plankton and Environmental Factors

In this study, total phosphorus emerged as the predominant environmental factor influencing plankton community structure. It exhibited a significant positive correlation with both phytoplankton density and zooplankton biomass. The community structure of zooplankton at sites S8 (the Lingjiang River) and S5 (the Binan River) showed notable associations with total phosphorus levels. Total phosphorus is a critical nutrient known to enhance photosynthesis and growth of phytoplankton [54,55]. Elevated phosphorus concentrations can stimulate phytoplankton proliferation, thereby increasing their density and biomass. Since phytoplankton serve as the primary food source for zooplankton, higher phytoplankton densities often lead to increased zooplankton biomass. Notably, except at site S5, total phosphorus levels at site S8 were significantly higher than those at other sites. Both S5 and S8 are likely influenced more by anthropogenic activities, with increased nutrient inputs from nearby coastal towns and extensive agricultural areas. These inputs contribute to higher total phosphorus concentrations, thereby influencing zooplankton community structures in these areas.

5. Conclusions

In summary, the “Reserve” and its tributaries harbor diverse planktonic ecosystems. Phytoplankton analysis revealed a total of 243 species from 8 phyla and 105 genera, predominantly Bacillariophyta followed by Chlorophyta. The average phytoplankton density was 1.7 × 10⁶ cells/L, with an average biomass of 2.6221 mg/L, showing a seasonal abundance pattern of summer > spring > winter. Zooplankton analysis identified 141 species from 4 phyla and 77 genera, with rotifers as the dominant group, followed by protozoans. The average zooplankton density was 0.17 × 10⁴ ind./L, with an average biomass of 0.3226 mg/L, following the same seasonal abundance pattern as phytoplankton.

Comparative analysis between the mainstem and tributaries showed comparable species compositions of plankton, with seasonal fluctuations. In spring, phytoplankton diversity was notably higher in the tributaries compared to the mainstem, while during summer, zooplankton diversity in the tributaries outstripped that in the mainstem. Notably, only during summer did the density of zooplankton in the tributaries significantly surpass that in the mainstem.

Additionally, total phosphorus was identified as the primary environmental factor influencing plankton community structure, demonstrating a significant positive correlation with phytoplankton density and zooplankton biomass. Planktonic diversity indices indicated oligo-mesotrophic water quality, with higher biodiversity observed in tributaries. According to physicochemical indicator standards, water quality in winter and summer met Class II standards, while spring met Class III standards. Overall, the planktonic community exhibited high diversity, with similar species compositions between the mainstem and tributaries. However, seasonal variations in community structure were evident, with most areas meeting water quality standards, although some tributaries showed signs of pollution, highlighting the need for enhanced management and protection measures for tributary ecological environments.

This research underscores the importance of monitoring plankton communities as indicators of aquatic ecosystem health. The high diversity and seasonal variations observed provide critical insights into the ecological dynamics of the “Reserve” and its tributaries. Understanding these patterns is essential for effective water resource management and conservation strategies. The study highlights the role of total phosphorus as a key environmental factor affecting plankton communities, emphasizing the need for targeted nutrient management to maintain water quality. Despite the comprehensive nature of this study, several limitations should be acknowledged. The research focused primarily on phytoplankton and zooplankton, potentially overlooking other important components of the aquatic ecosystem. Additionally, the study’s seasonal scope may not capture all temporal variations in plankton communities. Future research could benefit from a broader temporal and spatial scope, as well as a more integrated approach that includes other biotic and abiotic factors influencing water quality.