基于宏基因组学的中国沿海密集养殖水域秋季底质细菌多样性研究
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摘要
近年来,随着海水养殖业的迅猛发展,我国沿海水域生态系统遭受了不同程度的污染。选取我国沿海10个典型养殖水域(大连、唐山、蓬莱、连云港、启东、象山、宁德、东山,湛江、陵水),并以美济礁水域作为对照组(无水产养殖活动),采用宏基因组de novo测序方法系统分析了这些水域微生物的多样性,并进行了对比研究。结果发现,我国典型养殖水域微生物多样性与非养殖水域(美济礁)相比差异较大,美济礁水域微生物多样性明显低于各养殖水域;不同的养殖水域之间,微生物的丰度和多样性亦存在较大的差别;厚壁菌门和变形菌门是这些水域丰度最大的门类,其中厚壁菌门中的芽孢杆菌是其优势菌种。研究结果不仅有助于了解中国沿海典型养殖水域微生物的多样性,并可为评估我国海洋生态系统的污染水平提供基础数据。
In recent years,with the rapid development of mariculture,the ecosystem of coastal waters in China has suffered from different degrees of pollution. The scale of mariculture in coastal areas of China is expanding,while sewage entering the sea,illegal exploitation,drug abuse and other problems are prominent,leading to pollution in the coastal waters and frequent occurrence of aquatic diseases. In large marine ecosystems,microorganisms are very important components,and their structural composition and metabolites are indicative of the environment. The composition of the microbial community is closely related to the water quality of the ocean,which can indirectly reflect the characteristics of the water and affect the survival and reproduction of marine species. In this study,10 typical aquaculture waters along the coast of China,including Dalian,Tangshan,Penglai,Lianyungang,Qidong,Xiangshan,Ningde,Dongshan,Zhanjiang and Lingshui were selected,and the Meijijiao was used as a non-mariculture control. Sediment samples were collected from these typical aquaculture waters. The diversity of microbes in these sites was systematically analyzed using the method of macro genome de novo sequencing,and a comparative analysis was carried out.The results showed that the Chao index and ACE index of Ningde were the highest( 652. 0 and 670. 8,respectively),indicating that the community richness in this region was the highest,followed by Dalian; the Simpson index of Ningde was the highest,followed by Dalian,and the highest value of Shannon index was Dalian,followed by Ningde. Principal coordinates analysis( PCoA) used in this experiment showed that there was overlap between Lianyungang and Qidong,indicating that the composition of bacterial community between them was very similar. A variant of principal components analysis was used in this study and showed that the distance between the point of Penglai and other sites was far,suggesting that the bacterial community between PL and other samples was quite different. The heatmap showed that Dalian,Penglai and Xiangshan had obvious and large red regions,indicating that these red regions covered a large number of bacteria,and except for sample of Meijijiao,all other samples had smaller red regions. At the phylum level,the bacterial community was divided into two main groups: Firmicutes and Proteobacteria. In most of samples,the community richness of Firmicutes was higher than that of Proteobacteria. In Firmicutes,the bacteria of Bacteriaceae occupied the main part,and in addition,Planococcaceae and Bacillaceae were the main parts in Bacillates of Bacillus. At the generic level,the dominant group was Bacillus. In the Proteobacteria of Proteus,the most abundant community was Moraxellaceae. Of the family Moralidae,Pseudomonas was the dominant member in the Gammaproteobacteria of Proteus. In summary,the results indicated that the diversity of microorganisms in typical aquaculture waters was different from that in non-cultured waters( Meijijiao),and the abundance and diversity of microorganisms were also different among different mariculture sites. The Firmicutes and Proteobacteria are the most abundant bacterial phylum in these mariculture areas,among which Bacillus is the dominant species in this phylum. The results are not only helpful to understand the diversity of microorganisms in typical mariculture areas along the coast of China,but also to provide basic data for assessing the pollution level of marine ecosystems in China.
In recent years,with the rapid development of mariculture,the ecosystem of coastal waters in China has suffered from different degrees of pollution. The scale of mariculture in coastal areas of China is expanding,while sewage entering the sea,illegal exploitation,drug abuse and other problems are prominent,leading to pollution in the coastal waters and frequent occurrence of aquatic diseases. In large marine ecosystems,microorganisms are very important components,and their structural composition and metabolites are indicative of the environment. The composition of the microbial community is closely related to the water quality of the ocean,which can indirectly reflect the characteristics of the water and affect the survival and reproduction of marine species. In this study,10 typical aquaculture waters along the coast of China,including Dalian,Tangshan,Penglai,Lianyungang,Qidong,Xiangshan,Ningde,Dongshan,Zhanjiang and Lingshui were selected,and the Meijijiao was used as a non-mariculture control. Sediment samples were collected from these typical aquaculture waters. The diversity of microbes in these sites was systematically analyzed using the method of macro genome de novo sequencing,and a comparative analysis was carried out.The results showed that the Chao index and ACE index of Ningde were the highest( 652. 0 and 670. 8,respectively),indicating that the community richness in this region was the highest,followed by Dalian; the Simpson index of Ningde was the highest,followed by Dalian,and the highest value of Shannon index was Dalian,followed by Ningde. Principal coordinates analysis( PCoA) used in this experiment showed that there was overlap between Lianyungang and Qidong,indicating that the composition of bacterial community between them was very similar. A variant of principal components analysis was used in this study and showed that the distance between the point of Penglai and other sites was far,suggesting that the bacterial community between PL and other samples was quite different. The heatmap showed that Dalian,Penglai and Xiangshan had obvious and large red regions,indicating that these red regions covered a large number of bacteria,and except for sample of Meijijiao,all other samples had smaller red regions. At the phylum level,the bacterial community was divided into two main groups: Firmicutes and Proteobacteria. In most of samples,the community richness of Firmicutes was higher than that of Proteobacteria. In Firmicutes,the bacteria of Bacteriaceae occupied the main part,and in addition,Planococcaceae and Bacillaceae were the main parts in Bacillates of Bacillus. At the generic level,the dominant group was Bacillus. In the Proteobacteria of Proteus,the most abundant community was Moraxellaceae. Of the family Moralidae,Pseudomonas was the dominant member in the Gammaproteobacteria of Proteus. In summary,the results indicated that the diversity of microorganisms in typical aquaculture waters was different from that in non-cultured waters( Meijijiao),and the abundance and diversity of microorganisms were also different among different mariculture sites. The Firmicutes and Proteobacteria are the most abundant bacterial phylum in these mariculture areas,among which Bacillus is the dominant species in this phylum. The results are not only helpful to understand the diversity of microorganisms in typical mariculture areas along the coast of China,but also to provide basic data for assessing the pollution level of marine ecosystems in China.
引文
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[2]臧红梅,樊景凤,王斌,等.海洋微生物多样性的研究进展[J].海洋环境科学,2006,35(3):96-100.ZANG H M,FAN J F,WANG B,et al. Research progress on marine microbial diversity[J]. Marine Environmental Science,2006,35(3):96-100.
[3]程豹,望雪,徐雅倩,等.澜沧江流域浮游细菌群落结构特征及驱动因子分析[J].环境科学,2018,39(8):3649-3659.CHENG B, WANG X, XU Y Q, et al.Bacterioplankton community structure in the lancang river basin and analysis of driving environmental factors[J]. Environmental Science,2018,39(8):3649-3659.
[4] WAN Y,RUAN X H,ZHANG Y P,et al. Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes[J]. Microbiology Open, 2017, 6(4):e450.
[5] CHEN D,QIAN Z Y,WANG Z M,et al. Ecological distribution of heterotrophic bacteria in the Continental Shelf of East China Sea[J]. Studia Marine Sinica,1982(19):3-9.
[6]戴欣,周惠,陈月琴,等.中国南海南沙海区沉积物中细菌16S r DNA多样性的初步研究[J].自然科学进展,2002,12(5):479-484.DAI X,ZHOU H,CHEN Y Q,et al. A preliminary study on bacterial 16S r DNA diversity in sediments from Nansha Sea area, South China Sea[J].Progress in Natural Science,2002,12(5):479-484.
[7] SPRING S. Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes:Molecular and cultivation studies[J]. FEMS Microbiology Reviews,2000,24(5):573.
[8]李筠,周宏霞,刘佳琳,等.青岛近岸特征环境中海洋异养细菌的分布规律及其分子鉴定[J].中国海洋大学学报,2006,36(6):965-970.LI J,ZHOU H X,LIU J L,et al. Distribution and identification of marine heterotrophic bacteria in different sea areas close to the shore of Qingdao[J]. Periodical of Ocean University of China,2006,36(6):965-970.
[9] YOZA B A,HARADA M,NIHOUS G C,et al.Impact of mariculture on microbial diversity in sediments near open ocean farming of polydactylus sexfilis[J]. Ecological Indicators,2007,7(1):108-122.
[10] FREY K G,HERRERA-GALEANO J E,REDDEN C L, et al. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood[J]. BMC Genomics,2014,15(1):1-14.
[11]宣丽霞,戴文芳,郁维娜,等.有机污染物对杭州湾海域浮游细菌群落的影响[J].环境科学,2018,39(8):3640-3648.XUAN L X,DAI W F,YU W N,et al. Effects of organic pollutants on bacterioplankton community in Hangzhou Bay[J]. Environmental Science,2018,39(8):3640-3648.
[12]李云莉,高权新,张晨捷,等.养殖水域抗生素抗性基因污染的研究概况与展望[J].海洋渔业,2017,39(3):351-360.LI Y L,GAO Q X,ZHANG C J,et al. Current status and prospect ofantibiotic resistance genes(ARGs)pollution in the aquaculture[J]. Marine Fisheries,2017,39(3):351-360.
[13]戴文芳,郭永豪,郁维娜,等.三门湾近海有机污染对浮游细菌群落的影响[J].环境科学,2017,38(4):1414-1422.DAI W F,GUO Y H,YU W N,et al. Effects of coastal organic pollution on bacterioplankton community in Sanmen Bay[J]. Environmental Science,2017,38(4):1414-1422.
[14]肖伟.南海水体中颗粒物特性对颗粒附着细菌和浮游细菌群落的影响[D].厦门:厦门大学,2016.XIAO W. Linking biochemical properties of particles to particle-attached and free-living bacterial community structure along the particle density gradient from freshwater to open ocean[D].Xiamen:Xiamen University,2016.
[15] CATANIA V, SARA G, SETTANNI L, et al.Bacterial communities in sediment of a Mediterranean marine protected area[J]. Canadian Journal of Microbiology,2017,63(4):303-311.
[16]徐亚岩,柏育材,王云龙,等.长江口临近海域沉积物中Cu和Zn赋存形态的分异及对潜在生态风险的影响[J].海洋渔业,2017,39(6):619-628.XU Y Y, BAI Y C, WANG Y L, et al.Differentiation characteristics and influence on potential ecological risk of Cu and Zn in labile fractions from sediments in the Yangtze River Estuary[J]. Marine Fisheries,2017,39(6):619-628.
[17] YU S X,PANG Y L,WANG Y C,et al. Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay[J]. Marine Pollution Bulletin,2017,120(1-2):90-98.
[18]季凤云.珠江口海水和辽河口沉积物中微生物丰度及群落结构分析[D].大连:大连海洋大学,2016.JI F Y. Microbial community composition of Liaohein seawater and Pearl river estuary in sediment[D].Dalian:Dalian Ocean University,2016.
[19]马继波.粤东大规模增养殖区柘林湾海洋微生物的生态学研究[D].汕头:汕头大学,2016.MA J B. An ecological study on marine microorganisms in a large-scale mariculture-Zhelin Bay,Eastern Guangdong[D]. Shantou:Shantou University,2016.
[20]原雅纬,傅莲英,刘国生,等.海水养殖沉积环境细菌多样性PCR-DGGE分析[J].河南师范大学学报(自然科学版),2010,38(5):150-155.YUAN Y W,FU L Y,LIU G S,et al. Influence of hygromycin on leaf formation of arabidopsis thaliana seedling[J]. Journal of Henan Normal University(Natural Science),2010,38(5):150-155.
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