Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer
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Abstract: Microorganisms are fundamental for the functioning of marine ecosystems and are involved in the decomposition of organic matter, transformation of nutrients and circulation of biologically-important chemicals. Based on the complexity of the natural geographic characteristics of the Changjiang River Estuary, the geographic distribution of sedimentary microorganisms and the causes of this distribution are largely unexplored. In this work, the surface sediment samples from the adjacent sea area of the Changjiang River Estuary were collected. Their prokaryotic diversity was examined by high-throughput sequencing technology, and the environmental factors of the bacterial community were investigated. The results indicated that the distribution of prokaryotic communities in the sediments of the study areas showed obvious spatial heterogeneity. The sampling sequences divided the sample regions into three distinct clusters. Each geographic region had a unique community structure, although Proteobacteria, Bacteroidota, Desulfobacterota, Acidobacteriota, and Actinobacteriota all existed in these three branches. Canonical correspondence analysis demonstrated that prokaryotic diversity and community distribution were significantly correlated with the geographic location of sediment, seawater depth, and in particular, nutrient content (e.g., total phosphorus, total organic carbon and dissolved oxygen). Moreover, it was found for the first time that the metal ions obviously affected the composition and distribution of the prokaryotic community in this area. In general, this work provides new insights into the structural characteristics and driving factors of prokaryotic communities under the background of the ever-changing Changjiang River Estuary.
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Figure 2. Clustering of surface sediment prokaryotic communities of sampling sites (a) and of each sample (b) by Unweighted Pair-group Method with Arithmetic Mean.
Figure 3. Principal coordinate analysis plots. The first principal coordinate (PC1) clearly separates the samples according to their collection positions, as indicated by the ovals around pooled samples from the same collection site.
Figure 4. Identification of the distinct bacterial taxa from different sampling regions using LEfSe. Only bacterial taxa with linear discriminant analysis influence values greater than 4 are displayed in this cladogram. Differences in the most abundant taxa are represented by colors (red, blue, and green indicate Group A, Group B, and Group C, respectively). The diameter of each circle is proportional to the corresponding taxon’s abundance. Circles represent phylogenetic levels from phylum to genus. Labels are shown from phylum to genus level.
Figure 5. Canonical correspondence analysis diagram illustrating the relationships between the OTU-level community structures of different sampling sites. The angle between the arrow line and the sorting axis represents the correlation between a certain environmental factor and the sorting axis. The smaller angle represents the higher the correlation is, on the contrary, the lower the correlation is.
Figure 6. Spearman analysis of the effects of geochemical parameters on the phylogenetic structure of the prokaryotic communities. a. Cluster analysis between main environmental factor and community abundance; b. cluster analysis between main environmental factor and diversity indices. In Spearman correlation analysis, the intermediate heat map corresponding value is the Spearman correlation coefficient r, r > 0 is the positive correlation, r < 0 is the negative correlation.* indicates the significance test p < 0.05, ** indicates the significance test p < 0.01, *** indicates the significance test p < 0.001. The contents of the metal elements are represented by symbols Mg, Ca, and Ba, while TP, TON, and DO represent the concentrations of total phosphorus, total organic nitrogen and dissolved oxygen.
Table 1. Sample sites description of the 15 surface sediment samples from the Changjiang River Estuary adjacent sea area
Sampling site ID Sampling site description Latitude Longitude Layer/cm Collected method Sample amount/g Water depth/m Collected time CJ-02 31.792 86°N 122.996 90°E 0–2 sediment box corer 50 38.6 2020-08-17 3100-1 30.902 66°N 122.452 16°E 0–2 sediment box corer 50 14.5 2020-08-18 3100-2a 31.010 40°N 123.250 10°E 0–2 sediment box corer 50 60.0 2020-08-18 3100-3 31.000 56°N 123.501 38°E 0–2 sediment box corer 50 55.0 2020-08-18 3050-2 30.494 22°N 123.016 68°E 0–2 sediment box corer 50 61.0 2020-08-16 3000-2 30.000 98°N 122.999 94°E 0–2 sediment box corer 50 52.0 2020-08-16 DH4-0 29.631 02°N 122.830 10°E 0–2 sediment box corer 50 51.0 2020-08-14 DH45 29.363 42°N 122.678 72°E 0–2 sediment box corer 50 51.0 2020-08-14 DH5-0 29.136 61°N 122.480 70°E 0–2 sediment box corer 50 44.0 2020-08-14 DH5-1a 29.017 12°N 122.668 46°E 0–2 sediment box corer 50 57.0 2020-08-14 DH5-2 28.897 74°N 122.868 94°E 0–2 sediment box corer 50 64.0 2020-08-15 DH5-2a 28.781 67°N 123.070 78°E 0–2 sediment box corer 50 68.0 2020-08-15 DH5-3 28.650 79°N 123.276 02°E 0–2 sediment box corer 50 72.0 2020-08-15 DH56 28.809 90°N 122.361 22°E 0–2 sediment box corer 50 47.0 2020-08-15 DH6-1 28.450 96°N 122.179 00°E 0–2 sediment box corer 50 43.0 2020-08-15 
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Table 2. Geochemical parameters of the 15 surface sediment samples from the Changjiang River Estuary adjacent sea area
Sample
IDSample geochemical factors characteristic TN/
(μg·g−1)TP/
(μg·g−1)TON/
(μg·g−1)TOP/
(μg·g−1)TOC/
(mg·g−1)DO/
(mg·L−1)Mg/% Al/(%) K/(%) Ca/(%) Fe/% Mn/
(mg·kg−1)Cu/
(mg·kg−1)Zn/
(mg·kg−1)As/
(mg·kg−1)Ba/
(mg·kg−1)Pb/
(mg·kg−1)Cd/
(mg·kg−1)CJ-02 171.30 214.20 155.71 118.17 3.05 2.29 1.90 11.03 2.23 3.56 3.89 504.1 8.2 48.3 3.1 418 17.8 0.12 3100-1 395.27 245.21 382.54 135.70 4.32 4.71 2.69 14.42 2.65 4.13 5.57 763.5 28.8 91.1 9.4 425 28.1 0.20 3100-2a 400.76 193.65 385.41 149.30 3.43 3.12 2.46 13.78 2.55 4.29 4.24 475.4 12.0 59.9 4.6 400 20.0 0.13 3100-3 362.86 210.42 350.85 116.99 2.25 3.22 2.36 12.51 2.35 5.17 3.98 573.6 11.7 59.5 3.3 398 16.2 0.12 3050-2 437.76 246.53 425.94 85.46 2.38 1.76 2.84 14.95 2.73 4.34 5.16 618.1 18.8 79.0 5.5 428 25.0 0.14 3000-2 416.37 81.16 402.16 58.53 1.99 4.23 2.75 14.65 2.71 4.60 4.93 761.1 15.9 73.8 5.1 426 19.6 0.12 DH4-0 570.39 231.32 555.69 214.63 4.00 4.26 2.90 15.42 2.92 4.11 5.96 624.1 27.3 97.3 7.2 432 31.1 0.18 DH45 719.52 246.42 702.14 161.07 6.66 4.35 3.10 16.35 3.07 3.63 6.62 841.7 35.0 113.9 10.6 441 32.4 0.19 DH5-0 904.97 192.60 889.69 158.24 8.50 4.33 3.13 16.63 3.13 3.37 6.91 1 154.3 37.1 119.1 12.0 458 36.3 0.21 DH5-1a 696.37 202.97 684.89 143.71 4.87 5.14 3.04 16.40 3.08 3.78 6.34 845.8 28.1 106.4 8.8 459 30.2 0.16 DH5-2 766.00 187.82 727.64 125.48 7.20 5.41 2.94 16.39 3.14 4.10 6.54 859.2 25.9 110.9 7.0 450 31.9 0.16 DH5-2a 552.91 36.92 537.40 31.92 3.02 5.16 2.73 15.07 2.83 6.22 5.41 749.9 17.7 85.0 3.7 415 26.1 0.11 DH5-3 550.00 148.94 533.17 138.84 2.21 4.83 2.69 15.18 2.86 5.63 5.32 644.4 17.7 83.1 4.1 417 23.4 0.11 DH56 795.04 216.08 774.52 204.57 7.20 4.18 3.10 16.69 3.22 3.42 7.17 1 012.1 40.2 124.0 11.8 458 38.7 0.21 DH6-1 847.24 87.20 835.40 80.09 5.35 4.99 3.11 16.64 3.16 3.37 7.07 1 179.0 38.0 121.9 12.7 448 37.0 0.21 Note: The contents of Mg、Al、K、 Ca and Fe are presented by the percentages of their related oxides (MgO, Al2O3, K2O, CaO and Fe2O3) in sediment. TN: total nitrogen; TP: total phosphorus; TON: total organic nitrogen; TOP: total organic phosphorus; TOC: total organic carbon; DO: dissolved oxygen.
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Table 3. Biodiversity parameters of the 15 locations of surface Changjiang River Estuary adjacent sea area
Sample ID Effective sequence Base number Operational Taxonomic Shannon index ACE estimator Coverage/% CJ-02 49959 21112433 2781 6.31 3446.88 0.98 3100-1 54373 22949506 2811 6.21 3694.29 0.977 3100-2a 44908 18883844 2517 6.04 3452.74 0.98 3100-3 53385 22541097 3003 6.42 3874.58 0.98 3050-2 66852 28235313 3296 6.40 4452.27 0.98 3000-2 55133 23327239 2768 6.08 3836.63 0.98 DH4-0 51194 21682724 3123 6.37 4336.89 0.97 DH45 60438 25475554 3096 6.27 4359.16 0.97 DH5-0 58946 24869661 2973 6.20 4330.02 0.97 DH5-1a 41935 17703747 2757 6.32 4975.49 0.96 DH5-2 68649 28984752 3310 6.43 4490.64 0.98 DH5-2a 54684 23052855 3138 6.53 4319.96 0.97 DH5-3 54545 22973489 2953 6.56 3721.15 0.98 DH56 52897 22363027 3064 6.33 4267.99 0.97 DH6-1 63476 26841604 3387 6.40 4688.09 0.97 Note: ACE: Abundance-based Coverage Estimator.
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