基于高通量测序的陕西花马池和苟池微生物群落多样性分析
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摘要
目的:研究陕西花马池和苟池盐湖嗜盐细菌和古菌的群落多样性特征。方法:从两地盐湖采集卤水样品,提取总DNA后对其16S rRNA基因进行PCR扩增,通过Miseq高通量测序和生物信息学分析得到花马池和苟池微生物群落结构。结果:细菌优化序列被分入222个操作分类单位(OTU),花马池细菌优化序列经筛选后得到26 698个序列,其中厚壁菌门(Firmicutes)占主要地位,占总序列数的24.13%,其次20.02%的序列归入变形菌门(Proteobacteria);苟池细菌优化序列经筛选得到31 329个序列,拟杆菌门(Bacteroidetes)是样品中最主要的门类,占总数的60.56%。古菌优化序列经筛选后有81 286条,被归入86个OTU中,绝大多数属于广古菌门(Euryarchaeota)。在属水平上,2个盐湖共有的优势古菌群落包括Halonotius、盐红菌属(Halorubrum)、盐杆状菌属(Halorhabdus)和Halobellus等。花马池特有Halolamina、盐杆菌属(Halobacterium)、Halobellus和Halovenus。结论:研究揭示了陕西花马池和苟池嗜盐细菌和古菌群落组成,表明陕西花马池和苟池盐湖微生物群落分布具有相似性和独特性,同时存在丰富的嗜盐菌资源和潜在的新类群,为新种的挖掘及嗜盐菌的开发提供了理论数据。
Objective: To explore the halophilic bacteria and haloarchaea from Huama Lake(HMC) and GouLake(GC) in Shaanxi province. Methods: High-throughput sequencing and bioinformatics analysis were used forthe investigation of microbial communities and species diversity of the two lakes. Results: 222 operational taxonom-ic units(OTU) were generated from bacterial reads. The bacterial community in HMC sample was dominated bythe Firmicutes(24.13%) and Proteobacteria(20.02%) in phylum level while Bacteroidetes(60.56%) was the mostphylum of 31 329 trimmed bacterial reads in GC sample. Archaea reads were devided into 86 OTU, and the mostof 81 286 trimmed reads was Euryarchaeota. On genera level, results showed that archaea reads found from boththe sample were mainly composed of Halonotius, Halorubrum, Halorhabdus and Halobellus, while Halolamina, Halobacterium, Halobellus and Halovenus were isolated from HMC only. Conclusion: The study of the halophiles rich-ness and species diversity of the salt lakes revealed that the halophilic bacterial and haloarchaeal types from boththe lakes were similar, but each lake had its distinctive species and there were abundant halophiles resources andnew species in the HMC and GC salt lake. Apart from that, we can also provide important information that is use-ful for further investigation and application of halophiles of salt lakes.
Objective: To explore the halophilic bacteria and haloarchaea from Huama Lake(HMC) and GouLake(GC) in Shaanxi province. Methods: High-throughput sequencing and bioinformatics analysis were used forthe investigation of microbial communities and species diversity of the two lakes. Results: 222 operational taxonom-ic units(OTU) were generated from bacterial reads. The bacterial community in HMC sample was dominated bythe Firmicutes(24.13%) and Proteobacteria(20.02%) in phylum level while Bacteroidetes(60.56%) was the mostphylum of 31 329 trimmed bacterial reads in GC sample. Archaea reads were devided into 86 OTU, and the mostof 81 286 trimmed reads was Euryarchaeota. On genera level, results showed that archaea reads found from boththe sample were mainly composed of Halonotius, Halorubrum, Halorhabdus and Halobellus, while Halolamina, Halobacterium, Halobellus and Halovenus were isolated from HMC only. Conclusion: The study of the halophiles rich-ness and species diversity of the salt lakes revealed that the halophilic bacterial and haloarchaeal types from boththe lakes were similar, but each lake had its distinctive species and there were abundant halophiles resources andnew species in the HMC and GC salt lake. Apart from that, we can also provide important information that is use-ful for further investigation and application of halophiles of salt lakes.
引文
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[15]Wang Y,Sheng H F,He Y,et al.Comparison of the levels of bacterial diversity in freshwater,intertidal wetland,and marine sediments by using millions of illumina tags[J].Appl Environ Microbiol,2012,78(23):8264-8271.
[16]柴丽红,崔晓龙,彭谦,等.青海两盐湖细菌多样性研究[J].微生物学报,2006,44(3):271-275.
[17]潘媛媛,黄海鹏,孟婧,等.松嫩平原盐碱地中耐(嗜)盐菌的生物多样性[J].微生物学报,2012,52(10):1187-1194.
[18]何敏艳,邹正中,蔡林,等.连云港台北和盐城三圩盐田土壤嗜盐菌多样性研究[J].微生物学报,2008,35(5):737-742.
[19]Walsh D A,Papke R T,Doolittle W F.Archaeal diversity along a soil salinity gradient prone to disturbance[J].Environ Microbiol,2005,7(10):1655-1666.
[2]郑喜玉,张明刚,徐昶,等.中国盐湖志[M].北京:科学出版社,2002:3-6.
[3]曾章仁,雷建年,康高峰.定边盐湖地质特征及其形成条件[J].西安地质学院学报,1992,14(1):21-26.
[4]何若凡,李永棋.嗜盐细菌的研究进展[J].海洋通报,1993,(5):84-88.
[5]Wen Hongyu,Yang Liu,Shen Lulu,et al.Isolation and characterization of culturable halophilic microorganisms of salt ponds in Lianyungang,China[J].World J Microbiol Biotechnol,2009,25:1727-1732.
[6]柴丽红,崔晓龙,彭谦,等.青海两盐湖细菌多样性研究[J].微生物学报,2004,44(3):271-275.
[7]赵婉雨,杨渐,董海良,等.柴达木盆地达布逊盐湖微生物多样性研究[J].地球与环境,2013,41(4):398-405.
[8]黄勇.基于高通量测序的微生物基因组学研究[D].北京:军事医学科学院,2013:9-10.
[9]Guan L,Cho K H,Lee J H.Analysis of the cultivable bacterial community in jeotgal,a Korean salted and fermented seafood,and identification of its dominant bacteria[J].Food Microbiol,2011,28(1):101-113.
[10]Wu Liyou,Wen Chongqing,Qin Yujia,et al.Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis[J].BMC Microbiol,2015,15:125.
[11]You Jing,Wu Gang,Ren Fuping,et al.Microbial community dynamics in Baolige oilfield during MEOR treatment,revealed by Illumina Mi Seq sequencing[J].Environ Biotechnol,2016,100:1469-1478.
[12]熊丽.运用第二代测序技术对母体血浆中胎儿游离进行β地中海贫血无创性产前诊断的应用性研究[D].广州:南方医科大学,2014:31-45
[13]白学让.定边盐湖盐类沉积特征[J].西北大学学报,1992,22(4):457-463.
[14]郑喜玉,张明刚,徐昶,等.中国盐湖志[M].北京:科学出版社,2002:403-405.
[15]Wang Y,Sheng H F,He Y,et al.Comparison of the levels of bacterial diversity in freshwater,intertidal wetland,and marine sediments by using millions of illumina tags[J].Appl Environ Microbiol,2012,78(23):8264-8271.
[16]柴丽红,崔晓龙,彭谦,等.青海两盐湖细菌多样性研究[J].微生物学报,2006,44(3):271-275.
[17]潘媛媛,黄海鹏,孟婧,等.松嫩平原盐碱地中耐(嗜)盐菌的生物多样性[J].微生物学报,2012,52(10):1187-1194.
[18]何敏艳,邹正中,蔡林,等.连云港台北和盐城三圩盐田土壤嗜盐菌多样性研究[J].微生物学报,2008,35(5):737-742.
[19]Walsh D A,Papke R T,Doolittle W F.Archaeal diversity along a soil salinity gradient prone to disturbance[J].Environ Microbiol,2005,7(10):1655-1666.