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题名: The effect of depth on microbial communities from mesotrophic lake sediments as measured by two DNA extraction methods
作者: Xiong, Wei1; Xie, Ping2; Wang, Shengrui3; Niu, Yuan3
通讯作者: Wang, SR (reprint author), Chinese Res Inst Environm Sci, State Environm Protect Key Lab Lake Pollut Contro, Res Ctr Lake Ecoenvironm, Beijing 100012, Peoples R China.
关键词: DNA extraction ; lake sediment ; bacterial diversity ; organic matter content ; denaturing gradient gel electrophoresis ; bacterial community structure
刊名: JOURNAL OF FRESHWATER ECOLOGY
发表日期: 2015-04-03
DOI: 10.1080/02705060.2014.915587
卷: 30, 期:2, 页:215-228
收录类别: SCI
文章类型: Article
部门归属: [Xiong, Wei] Huazhong Agr Univ, Coll Fisheries, Wuhan 430070, Peoples R China ; [Xie, Ping] Chinese Acad Sci, Inst Hydrobiol, Donghu Expt Stn Lake Ecosyst, State Key Lab Freshwater Ecol & Biotechnol China, Wuhan 430072, Peoples R China ; [Wang, Shengrui ; Niu, Yuan] Chinese Res Inst Environm Sci, State Environm Protect Key Lab Lake Pollut Contro, Res Ctr Lake Ecoenvironm, Beijing 100012, Peoples R China
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
类目[WOS]: Ecology ; Limnology
研究领域[WOS]: Environmental Sciences & Ecology ; Marine & Freshwater Biology
英文摘要: We evaluated the effect of depth on microbial communities from mesotrophic lake sediments as measured by two DNA extraction methods. DNA yields and the number of ribotypes differed significantly by depth. The mean yields at the depth interval of 0-8cm from the two extraction methods were both higher than those within the depth range of 10-44cm. Significant differences were also observed between the two methods in DNA yields from the deeper (10-44cm) samples. An analysis of denaturing gradient gel electrophoresis (DGGE) profiles demonstrated that the choice of the DNA extraction method has a profound effect on the bacterial community profiles generated, which was reflected in the number of bands or ribotypes detected from samples from all depths. Higher DNA yield did not lead to a higher diversity of phylotypes. In almost all cases, extraction method 2 (M2, soil DNA test kit) resulted in a greater diversity of phylotypes compared to method 1 (M1, liquid nitrogen/cetyl trimethylammonium bromide extraction). Moreover, notable changes in bacterial diversity were detected in the uppermost layers (0-5cm). The results of canonical correspondence analysis illustrated that the DNA extraction method did not affect the evaluation of the relationship between bacterial community structure and environmental variables in lake sediments at multiple depths, and the differences in community structure in the two extraction methods were both related to the same environmental variables (pH, total phosphorus concentration) and depth. Vertically, the community structure of sediment layers formed several separate clusters along the depth gradient. This study expands our understanding of the depth-related microbial community structure in lake sediments.
关键词[WOS]: GRADIENT GEL-ELECTROPHORESIS ; 16S RIBOSOMAL-RNA ; RAPID METHOD ; PURIFICATION METHODS ; ENVIRONMENTAL DNA ; HUMIC SUBSTANCES ; SOIL ; DIVERSITY ; PCR ; QUANTIFICATION
语种: 英语
WOS记录号: WOS:000353953700002
ISSN号: 0270-5060
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/23860
Appears in Collections:淡水生态学研究中心_期刊论文

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作者单位: 1.Huazhong Agr Univ, Coll Fisheries, Wuhan 430070, Peoples R China
2.Chinese Acad Sci, Inst Hydrobiol, Donghu Expt Stn Lake Ecosyst, State Key Lab Freshwater Ecol & Biotechnol China, Wuhan 430072, Peoples R China
3.Chinese Res Inst Environm Sci, State Environm Protect Key Lab Lake Pollut Contro, Res Ctr Lake Ecoenvironm, Beijing 100012, Peoples R China
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