基于Miseq测序的长江中游枯水季水体菌群结构
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摘要
采用基于16S rRNA基因的Illumina Miseq测序方法,对长江中游枯水季冬季的水质及水体细菌群落多样性进行系统分析。研究发现,所测长江水段当季属于《地表水环境质量标准》(GB 3838—2002)Ⅲ类水。长江中菌群多样性高,变形菌门(Proteobacteria,44. 9%)、β-变形菌纲(Betaproteobacteria,32. 9%)以及丛毛单胞菌科(Comamonadaceae,30. 6%)分别在门、纲、科上为优势菌。除此之外,长江水体中大量的优势菌科与生物除氮相关,其中具有好氧反硝化功能的丛毛单胞菌科(Comamonadaceae)相对丰度最大,对于控制水体中氮素的污染指标,促进水体自净修复有积极的作用。PICRUSt功能预测分析表明水体中菌群在碳水化合物代谢和氨基酸代谢方面功能最强。在菌种关联网络中,拟杆菌属(Bacteroides)、黄杆菌属(Luteolibacter)、Pseudarcicella等在共存网络菌群中具有正相关的关系,可以抑制微囊藻的生长。研究揭示了长江枯水季的水质与其微生物群落结构的内在关系,可以为长江枯水季饮用水源地水质安全保障提供理论依据。
The water quality and the diversity of bacteria community in the dry season and winter of the Yangtze river were systematically analyzed by using the Illumina Miseq sequencing method based on 16 S rRNA gene. The show that the test of the Yangtze River water belongs to the Ⅲ GB 3838—2002 class. The diversity of the bacteria community in the Yangtze River is high,with Proteobacteria( 44. 9%),protein-proteobacteria( 32. 9%) and Comamonadaceae( 30. 6%) as dominant species in the phylum,class and family. In addition,a large number of dominant bacteria families in the water of the Yangtze River are related to biological nitrogen removal. Among them,Comamonadaceae with aerobic denitrification has the largest relative abundance,which plays a positive role in controlling the pollution index of nitrogen in water and promoting the self-purification and repair of water.PICRUSt function prediction showed that bacteria in water had the strongest function in carbohydrate and amino acid metabolism. Bacteroides,Luteolibacter and Pseudarcicella are positively correlated in the network of bacterial species association,which can inhibit the growth of microcystis. The results reveal the internal relationship between the water quality of the Yangtze River dry season and the microbial community structure,which can provide theoretical basis for the water quality security of the drinking water sources of the Yangtze River dry season.
The water quality and the diversity of bacteria community in the dry season and winter of the Yangtze river were systematically analyzed by using the Illumina Miseq sequencing method based on 16 S rRNA gene. The show that the test of the Yangtze River water belongs to the Ⅲ GB 3838—2002 class. The diversity of the bacteria community in the Yangtze River is high,with Proteobacteria( 44. 9%),protein-proteobacteria( 32. 9%) and Comamonadaceae( 30. 6%) as dominant species in the phylum,class and family. In addition,a large number of dominant bacteria families in the water of the Yangtze River are related to biological nitrogen removal. Among them,Comamonadaceae with aerobic denitrification has the largest relative abundance,which plays a positive role in controlling the pollution index of nitrogen in water and promoting the self-purification and repair of water.PICRUSt function prediction showed that bacteria in water had the strongest function in carbohydrate and amino acid metabolism. Bacteroides,Luteolibacter and Pseudarcicella are positively correlated in the network of bacterial species association,which can inhibit the growth of microcystis. The results reveal the internal relationship between the water quality of the Yangtze River dry season and the microbial community structure,which can provide theoretical basis for the water quality security of the drinking water sources of the Yangtze River dry season.
引文
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27 Dong Q,Shi H C,Liu Y C.Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system[J].Frontiers in Microbiology,2017,8:64
2 Zhang J,Li S Y,Dong R Z,et al.Influences of land use metrics at multi-spatial scales on seasonal water quality:a case study of river systems in the Three Gorges Reservoir Area,China[J].Journal of Cleaner Production,2019,206:76-85
3顾胜,李思悦,张全发.汉江堵河流域地表水质时空变化特征[J].长江流域资源与环境,2009,18(1):41-46Gu Sheng,Li Siyue,Zhang Quanfa.Spatial-temporal distribution of surface water quality in the Du River Basin[J].Resources and Environment in the Yangtze Basin,2009,18(1):41-46
4 Ramanan R,Kim B,Cho D,et al.Algae-bacteria interactions:evolution,ecology and emerging applications[J].Biotechnology Advances,2016,34(1):14-29
5 Bai YAOHUI,Shi Q,Wen D H,et al.Bacterial communities in the sediments of Dianchi Lake,a partitioned eutrophic waterbody in China[J].Plos One,2012,7(5):e37796
6 Newton R J,Mcmahon K D.Seasonal differences in bacterial community composition following nutrient additions in a eutrophic lake[J].Environmental Microbiology,2011,13(4):887-899
7 Rimoldi S,Terova G,Ascione C,et al.Next generation sequencing for gut microbiome characterization in rainbow trout(Oncorhynchus mykiss)fed animal by-product meals as an alternative to fishmeal protein sources[J].Plos One,2018,13(3):e193652
8任丽娟,何聃,邢鹏,等.湖泊水体细菌多样性及其生态功能研究进展[J].生物多样性,2013,21(4):421-432Ren Lijuan,He Dan,Xing Peng,et al.Bacterial diversity and ecological function in lake water bodies[J].Biodiversity Science,2013,21(4):421-432
9 Drury B,Rosimarshall E,Kelly J J.Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers[J].Applied&Environmental Microbiology,2013,79(6):1897-1905
10 Liu S,Coyne M S,Grove J H,et al.Nitrogen,season,and tillage management influence ammonia oxidizing bacterial communities in long-term maize[J].Applied Soil Ecology,2018,129:98-106
11 MagoT,Salzberg S L.Flash:fast length adjustment of short reads to improve genome assemblies[J].Bioinformatics,2011,27(21):2957-2963
12 Ja 6)zd 6)zewska A M,Corbari L,Driskell A,et al.A genetic fingerprint of Amphipodafrom Icelandic waters-the baseline for further biodiversity and biogeography studies[J].Zookeys,2018,731:55-73
13 Zhang Z M,Li D P,Refaey M M,et al.Host age affects the development of southern catfish gut bacterial community divergent from that in the food and rearing water[J].Frontiers in Microbiology,2018,9:495
14 Shannon P,Markiel A,Ozier O,et al.Cytoscape:a software environment for integrated models of biomolecular interaction networks[J].Genome Research,2003,13:2498-2504
15 Quach-Cu J,Herrera-Lynch B,Marciniak C,et al.The effect of primary,secondary,and tertiary wastewater treatment processes on antibiotic resistance gene(ARG)concentrations in solid and dissolved wastewater fractions[J].Water,2018,10(1):37
16李军.高通量测序技术及其在地下水污染研究中的应用[D].北京:中国地质科学院,2018Li Jun.High throughput sequencing technology and its application in groundwater pollution research[D].Beijing:Chinese Academy of Geological Sciences,2018
17傅爽.长江武汉段地表水指示微生物与致病菌相关关系的研究与分析[D].武汉:华中科技大学,2012Fu Shuang.The researchand analysisa of the relationship between bacteriology indexand microbial pathogensin Wuhan YangtzeRiver[D].Wuhan:Huazhong University of Science and Technology,2012
18 Jiang Y,Yang Y,Wu Y,et al.Microcystin bioaccumulation in freshwater fish at different trophic levels from the eutrophic Lake Chaohu,China[J].Bulletin of Environmental Contamination and Toxicology,2017,99(1):69-74
19 Song H,Xu J H,Lavoie M,et al.Biological and chemical factors driving the temporal distribution of cyanobacteria and heterotrophic bacteria in a eutrophic lake(West Lake,China)[J].Applied Microbiology and Biotechnology,2017,101(4):1685-1696
20 Li Z,Lu L H,Guo J S,et al.Responses of spatial-temporal dynamics of bacterioplankton community to large-scale reservoir operation:a case study in the Three Gorges Reservoir,China[J].Scientific Reports,2017,7:42469
21范可旭,张晶.长江流域地表水水质演变趋势分析[J].人民长江,2008,39(17):82-84Fan Kexu,Zhang Jing.Analysis of surface water quality evolution trend in the Yangtze River Basin[J].Yangtze River,2008,39(17):82-84
22 Luo W S,Peng X X,Jing F,et al.Simultaneous microbial removal of carbon,nitrogen,and phosphorus in a modified anaerobic/aerobic(A/O)bioreactor with no phosphorus release:simultaneous microbial removal of carbon,nitrogen,and phosphorus[J].Water&Environment Journal,2017,31(2):158-167
23 Gupta R S.The phylogeny and signature sequences characteristics of Fibrobacteres,Chlorobi,and Bacteroidetes[J].Critical Reviews in Microbiology,2004,30(2):123-143
24 De Vos P,Kersters K,Falsen E,et al.Comamonas Davis and Park1962 gen.nov.,nom.rev.emend.,and Comamonas terrigena Hugh 1962 sp.nov.,nom.rev[J].International Journal of Systematic and Evolutionary Microbiology,1985,35(4):443-453
25刘志培,杨惠芳.食酸丛毛单胞菌AN3菌株降解苯胺代谢途径的研究[J].微生物学报,1999,5(5):448-453Liu Zhipei,Yang Huifang.Studies on the metabolism pathway of aniline degradation by Comamonas acidovorans AN3[J].Acta Microbiologica Sinica,1999,5(5):448-453
26 Wei Y M,Wang J Q,Liu T T,et al.Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16SrRNA gene[J].Environmental Science and Pollution Research,2015,22:12605-12614
27 Dong Q,Shi H C,Liu Y C.Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system[J].Frontiers in Microbiology,2017,8:64