Analysis of bacterial community and diversity in gill tissues of bony fishes in adjacent South China Sea
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摘要: 围绕中国南海丰富的渔业资源，采用16S rDNA扩增子测序技术，分析了南海近岸硬骨鱼类鳃组织微生物群落分布特征，并探讨了7个不同站点细菌群落结构的差异。结果显示，测序共获得有效拼接片段 (Clean tags) 2 952 366条，平均每个文库56 776条。分别在门、属水平对其优势类群进行了分析，其中门水平上变形菌门 (Proteobacteria) 最高 (71.3%)，属水平上变形菌门的不动杆菌属 (Acinetobacter) 最高 (17.2%)。不同站点的α多样性具有显著差异，其中I9和H8站点的物种丰富度 (Chao1指数) 最高，D3站点的多样性 (Shannon指数) 最高。不同站点来源样品之间的β多样性具有显著差异 (P<0.05)，但在宿主分类的目水平上无显著差异 (P>0.05)。中国南海近岸硬骨鱼鳃组织中的细菌群落组成丰富，采样站位相比宿主分类对鳃组织上细菌群落具有更重要的影响，它们可能在辅助宿主营养物质转运及代谢方面发挥积极作用。
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关键词:
- 硬骨鱼鳃 /
- 16S rDNA扩增子 /
- 细菌多样性 /
- 南海
Abstract: Focusing on the abundant fishery resources in the South China Sea, we analyzed the distribution characteristics of the microbial community in the gill tissue of bony fishes in the adjacent South China Sea by using 16S amplicon sequencing technology. In addition, we discussed the differences in the bacterial community structure at different sites. The results show that the sequencing obtained a total of 2 952 366 effective spliced fragments (Clean tags) with an average of 56 776 in each library. The dominant taxa were analyzed at phylum and genus levels. Proteobacteria was the highest (71.3%) at phylum level, and Acinetobacter was the highest at genus level (17.2%). The alpha diversity of different sites was significantly different, and the I9 and H8 sites had the highest species richness (Chao1 index), and the D3 site had the highest diversity (Shannon index). The beta diversity of samples from different sites was significantly different (P<0.05), but there was no significant difference between the host classification (Order level) groups (P>0.05). The composition of bacterial communities in the gill tissues of bony fishes in the South China Sea was abundant. Compared with the classification of the host, the sampling station has more important influence on the community of the bacterial in the gill tissues, and may play an active role in assisting the host's nutrient transport and metabolism.-
Key words:
- Bony fish gill /
- 16S rDNA amplicon /
- Bacterial diversity /
- South China Sea
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图 1 广东近岸南海海域采样站点示意图
Figure 1. Diagram of sampling stations in Guangdong coastal waters in South China Sea
图 3 鱼鳃细菌门水平物种组成相对丰度
Figure 3. Relative abundance of taxonomy composition of bacteria in fish gill at phylum level
图 4 鱼鳃细菌属水平物种组成相对丰度
Figure 4. Relative abundance of taxonomy composition of bacteria in fish gill at genus level
图 5 Alpha多样性指数箱线图
注：a—e. 基于站点分组的Chao1、ACE、Observed、Simpson、Shannon 多样性指数箱线图，不同颜色代表不同站点的样本；f. 基于样本宿主(目水平) 分类分组的Chao1 指数箱线图。
Figure 5. Boxplot of Alpha diversity index
Note: a–e. Boxplot of diversity indexes of Chao1, ACE, Observed, Simpson and Shannon based on site grouping, and different colors represent samples of different sites; f. Boxplot of Chao1 index based on sample host (Order level) classification.
图 6 基于不同分组方式的NMDS分析 [非参数多元方差分析 (PerMANOVA)]
注：a. 基于站点分组的 NMDS 分析； b. 基于样本的目水平分组。图中两个样本点越接近，表示两个样本物种组成越相似。横纵坐标表示样本间的相对距离，无实际意义。图形中的每一个点代表一个样本，不同颜色代表不同的样本分组信息。NMDS 结果的优劣用胁迫系数 (stress) 来衡量，此值越小越好，当小于 0.2 时表示可以用 NMDS 的二维点图表示组间或组内差异。
Figure 6. NMDS analysis based on different grouping modes [Nonparametric multivariate analysis of variance (PerMANOVA)]
Note: a. NMDS analysis based on site grouping; b. Grouping based on the order level of the sample. The closer the two sample points are,the more similar the composition of the two sample species are. The abscissa and ordinate indicate the relative distance between samples, which is of no practical significance. Each point in the graph represents a sample, and different colors represent different sample grouping information. The advantages and disadvantages of testing NMDS results are measured by stress coefficients, the smaller, the better, and the value less than 0.2 indicates that the two-dimensional dot plot of NMDS can be used to represent differences between or within groups.
图 7 22个KEGG-L2功能层级相对丰度热图
注：横坐标代表不同的样本，纵坐标代表不同的功能层级，图片上方色条表示不同分组，并按照样本聚类。
Figure 7. Heatmap of relative abundance of 22 KEGG-L2 functional levels
Note: The abscissa represents different samples; the ordinate represents different functional levels; the color bars indicate different groups, which are clustered according to samples.
表 1 样品分类信息
Table 1. Taxonomy information of samples
站点
Sampling station样品编号
Sample ID目
Order物种
SpeciesD3 D3.1S 鲈形目 条纹䱨 Terapon theraps D3 D3.2S 鲈形目 日本金线鱼 Nemipterus japonicus D3 D3C.2S 鲈形目 列牙䱨 Pelates quadrilineatus F3 F3.2S 鲈形目 鹿斑鲾 Leiognathus ruconius F3 F3.4S 鲽形目 少牙斑鲆 Pseudorhombus oligodon F3 F3.5S 鲈形目 带鱼 Trichiurus lepturus D8 D8.1S 鲈形目 蓝圆鲹 Decapterus maruadsi D8 D8.3S 鳗鲡目 网纹裸胸鳝 Gymnothorax reticularis D8 D8.5S 鮟目 黑鮟 Lophiomus setigerus D8 D8.6S 鲉形目 环纹蓑鲥 Pterois lunulata D8 D8.8S 鲈形目 深水金线鱼 Nemipterus bathybius D8 D8.12S 鲉形目 深海红娘鱼 Lepidotrigla abyssalis F8 F8.1S 鲉形目 环纹蓑鲥 Pterois lunulata F8 F8.4S 鲉形目 单棘豹鲂鮄 Daicocus peterseni F8 F8.8S 鲈形目 二长棘鲷 Parargyrops edita F8 F8.11S 鮟目 棘茄鱼 Halieutaea stellata F8 F8.16S 鲉形目 日本红娘鱼 Lepidotrigla japonice F8 F8.17S 鲉形目 拟蓑鲉 Parapterois heterurus F8 F8.18S 海龙鱼目 鳞烟管鱼 Fistularia petimba H3 H3.3S 鲈形目 翼红娘鱼 Lepidotrigla alata H3 H3.4S 鲈形目 中华䲢 Uranoscopus chinensis H3 H3.5S 鳗鲡目 大鳞鳞头鲉 Sebastapistes megalepis H3 H3.7S 鮟目 无备虎鲉 Minous inermis H8 H8.1S 鲉形目 大鳞短额鲆 Engyprosopon grandisquama H8 H8.2S 鲈形目 鳞烟管鱼 Fistularia petimba H8 H8.3S 鲉形目 繁星鲆 Bothus myriaster H8 H8.7S 鲉形目 孔鰕虎鱼 Trypauchen vagina H8 H8.10S 鲉形目 斑鰶 Konosirus punctatus H8 H8.12S 鲈形目 皮氏叫姑鱼 Johnius belangerii H8 H8.15S 鮟目 短吻鲾 Leiognathus brevirostris H8 H8.24S 鲉形目 大头狗母鱼 Trachinocephalus myops H8 H8.25S 鲉形目 大头狗母鱼 Trachinocephalus myops I9 I9.1S 海龙鱼目 大鳞鳞头鲉 Sebastapistes megalepis I9 I9.5S 鲉形目 黄纹拟鲈 Parapercis xanthozona I9 I9.7S 鲈形目 寿鱼 Banjos banjos I9 I9.8S 鲉形目 棕斑宽吻鲀 Amblyrhynchotes rufopunctatus I9 I9.9S 鲉形目 单棘豹鲂鮄 Daicocus peterseni I9 I9.10S 鲽形目 松球鱼 Monocentris japonica I9 I9.11S 海龙鱼目 新平鲉 Neosebastes entaxis I9 I9.12S 鲽形目 二长棘鲷 Parargyrops edita I9 I9.13S 鲈形目 横带眶棘鲈 Scolopsis inermis I9 I9.14S 鲱形目 盔蓑鲉 Ebosia bleekeri I9 I9.15S 鲈形目 冠鲽 Samaris cristatus I9 I9.16S 鲈形目 叉斑狗母鱼 Synodus macrops I9 I9.17S 海龙鱼目 美尾䲗 Calliurichthys japonicus I9 I9.18S 鲉形目 瑞氏红鲂鮄 Satyrichthys rieffeli I9 I9.20S 鲉形目 虻鲉 Erisphex pottii I9 I9.21S 鲉形目 红鲬 Bembras japonicus I9 I9.22S 鲈形目 六带拟鲈 Parapercis sexfasciata I9 I9.23S 鲈形目 黄纹拟鲈 Parapercis xanthozona I9 I9.24S 鲈形目 尖牙鲈 Synagrops japonicus I9 I9.25S 鲈形目 水珍鱼 Argentina kagoshimae 
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