Comparative analysis of microbial community in the sediments from the adjacent area of Yangtze Estuary by 454 pyrosequencing and illumina sequencing
WANG Xun-gong1,2,3, LI Ying1,2,3, ZHEN Yu1,2,3, MI Tie-zhu1,2,3, HE Hui1,3,4, ZHANG Yu1,2,3
1. Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao 266100, China;
2. College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China;
3. Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China;
4. College of Marine Life Science, Ocean University of China, Qingdao 266003, China
Abstract：As the main methods of the second generation high-throughput sequencing technologies, 454 pyrosequencing and Illumina sequencing have been widely utilized in the microbial nucleic acid analysis. In this study, sequence length, microbial compositions, abundance and diversity in the sediments from the adjacent area of Yangtze Estuary were analyzed using 16S rRNA gene-based 454 pyrosequencing and Illumina sequencing technology to compare the advantages and disadvantages of two techniques. The results showed that more sequences and OTUs were obtained by Illumina sequencing, which included many rare species. Illumina sequencing technology had an advantage of microbiological community analysis over 454 pyrosequencing technology, especially in the detection of rare species. In summary, Illumina sequencing technology was better than 454 pyrosequencing technology in the analysis of microbial diversity and community composition. 454 pyrosequencing didn't reflect its advantage in long read length, and it probably underestimated the microbial composition and diversity.
WANG Xun-gong,LI Ying,ZHEN Yu et al. Comparative analysis of microbial community in the sediments from the adjacent area of Yangtze Estuary by 454 pyrosequencing and illumina sequencing[J]. Marine Environmental Science, 2018, 37(5): 766-772,791.
JIANG L,ZHENG Y,PENG X,et al.Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments,Southern China[J].FEMS Microbiology Ecology,2009,70(2):249-262.
[5]
MARDIS ER.Next-generation DNA sequencing methods[J].Annual Review of Genomics and Human Genetics,2008,9:387-402.
[6]
MARDIS E R.The impact of next-generation sequencing technology ongenetics[J].Trends in Genetics,2008,24(3):133-141.
TURCATTI G,ROMIEU A,FEDURCO M,et al.A new class of cleavable fluorescent nucleotides:synthesis and optimization as reversible terminators for DNA sequencing by synthesis[J].Nucleic Acids Research,2008,36(4):e25.
[11]
VARSHNEY R K,KUDAPA H,ROORKIWAL M,et al.Advances in genomics research and molecular breeding applications in SAT legume crops by using next generation sequencing and high-throughput genotyping technologies[J].Journal of Biosciences,2012,37(5):811-820.
JU J Y,KIM D H,BI L R,et al.Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators[J].Proceedings of the National Academy of Sciences of the United States of America,2006,103(52):19635-19640.
[14]
SINCLAIR L,OSMAN O A,BERTILSSON S,et al.Microbial community composition and diversity via 16SrRNA gene amplicons:evaluating the Illumina platform[J].PLoS One,2015,10(2):e0116955.
[15]
MAUGHAN H,WANG P W,CABALLERO J D,et al.Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16SrRNA hypervariable regions[J].PLoS One,2012,7(10):e45791.
[16]
LI M T,XU K Q,WATANABE M,et al.Long-term variations in dissolved silicate,nitrogen,and phosphorus flux from the Yangtze River into the East China Sea and impacts on estuarine ecosystem[J].Estuarine,Coastal and Shelf Science,2007,71(1):3-12.
[17]
CHAI C,YU Z M,SONG X X,et al.The status and characteristics of eutrophication in the Yangtze river (Changjiang) estuary and the adjacent east China sea,China[J].Hydrobiologia,2006,563(1):313-328.
[18]
OLIVER J D.The viable butnonculturable state in bacteria[J].Journal of Microbiology,2005,43(S):93-100.
[19]
CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QⅡME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.
[20]
BLAXTER M,MANN J,CHAPMAN T,et al.Defining operational taxonomic units using DNA barcodedata[J].Philosophical Transactions of the Royal Society B:Biological Sciences,2005,360(1462):1935-1943.
[21]
BOKULICH N A,SUBRAMANIAN S,FAITH JJ,et al.Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing[J].Nature Methods,2013,10(1):57-59.
[22]
BATES S T,CLEMENTE J C,FLORES G E,et al.Global biogeography of highly diverse protistan communities in soil[J].ISME Journal,2013,7(3):652-659.
[23]
CAPORASO J G,LAUBER C L,WALTERS W A,et al.Ultra-high-throughput microbial community analysis on the IlluminaHiSeq and MiSeq platforms[J].ISME Journal,2012,6(8):1621-1624.
[24]
HUSE H M,WELCH D B M,SOGIN M L.Sequencing errors,diversity estimates,and the rare biosphere[M]//CHOFFNES E R,OLSEN L A,WIZEMANN T.The Science and Applications of Microbial Genomics:Workshop Summary.Washington,DC:National Academies Press,2013:188-207.
[25]
ZHU D,TANABE S H,YANG C,et al.Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16SrRNA genes[J].PLoS One,2013,8(10):e78501.
[26]
CLAESSON M J,WANG Q,O'SULLIVAN O,et al.Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions[J].Nucleic Acids Research,2010,38(22):e200.
