Diversity and space–time dynamics of endophytic archaea from sugar beet in the north slope of Tianshan Mountain revealed by 454 pyrosequencing and T-RFLP

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• 作者：YingWu Shi ; MuSi TaPa ; Chun Li ; HongMei Yang…
• 关键词：Sugar beet ; Endophytic archaea ; Diversity ; Growth period ; Biogeography ; Pyrosequencing ; T ; RFLP
• 刊名：World Journal of Microbiology & Biotechnology
• 出版年：2015
• 出版时间：July 2015
• 年：2015
• 卷：31
• 期：7
• 页码：1031-1039
• 全文大小：769 KB
• 参考文献：Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-69
  Bley T (2011) From single cells to microbial population dynamics: modelling in biotechnology based on measurements of individual cells. In High resolution microbial single cell analytics, p. 211-27
  Bolhuis H, Stal LJ (2011) Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing. ISME J 5:1701-712View Article
  Chelius MK, Triplett EW (2001) The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41:252-63View Article
  Chen HB (2012) Venn diagram: generate high-resolution venn and euler plots. Rpackage version 113
  Conn VM, Franco CMM (2004) Analysis of the endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol 70:1787-794View Article
  de Melo Pereira GV, Magalhaes KT, Lorenzetii ER, Souza TP, Schwan RF (2012) A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion. Microb Ecol 63:405-17View Article
  Ding T, Palmer MW, Melcher U (2013) Community terminal restriction fragment length polymorphisms reveal insights into the diversity and dynamics of leaf endophytic bacteria. BMC Microbiol 13:1View Article
  Ferrando L, Fernandez Manay J, Fernandez Scavino A (2012) Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties. FEMS Microbiol Ecol 80:696-08View Article
  Kolde R (2012) Pheatmap: pretty heatmaps. Rpackage version 061
  Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442:806-09View Article
  Ma B, Lv X, Warren A, Gong J (2013) Shifts in diversity and community structure of endophytic bacteria and archaea across root, stem and leaf tissues in the common reed, Phragmites australis, along a salinity gradient in a marine tidal wetland of northern China. Antonie Van Leeuwenhoek 104:759-68View Article
  Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD (2012) PANDAseq: paired-end assembler for illumina sequences. BMC Bioinform 13:31View Article
  Mirzaei MZ, Rezvani SMAD, Gohari J (2005) Effect of drought stress in different growth stages on yield and some physiological properties of sugar beet. J Sugar Beet 21(1):1-4
  Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:3518-525
  Qin S, Chen HH, Zhao GZ, Li J, Zhu WY, Xu LH, Jiang JH, Li WJ (2012) Abundant and diverse endophytic actinobacteria associated with medicinal plant Maytenus austroyunnanensis in Xishuangbanna tropical rainforest revealed by culture-dependent and culture-independent methods. Environ Microbiol Rep 4:522-31View Article
  Riesenfeld CS, Schloss PD, Handelsman J (2004) Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 38:525-52View Article
  Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-541View Article
  Shen JP, Zhang LM, He JZ (2011) Abundance of archaea, crenarchaea and bacteria in selected agricultural soils of China. Chin J Appl Ecol 22:2996-002
  Shi YW, Lou K, Li C (2009) Promotion of plant growth by phytohormone-producing endophytic microbes of sugar beet. Biol Fertil Soils 45:645-53View Article
  Shyu C, Soule T, Bent SJ, Foster JA, Forney LJ (2007) MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol 53:562-70View Article
  Song ZQ, Wang FP, Zhi XY, Chen JQ, Zhou EM, Liang F, Xiao X, Tang SK, Jiang HC, Zhang CL, Dong H, Li WJ (2013) Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China. Environ Microbiol 15:1160-175View Article
  Sun L, Qiu F, Zhang X, Dai X, Dong X, Song W (2008) Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis. Microb Ecol 55:415-24View Article
  Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805-14View Article
  von Mering C, Hugenholtz P, Raes
• 作者单位：YingWu Shi (1) (2)
  MuSi TaPa (1) (2)
  Chun Li (1) (2)
  HongMei Yang (1) (2)
  Tao Zhang (1) (2)
  Yan Gao (1) (2)
  Jian Sun (1) (2)
  Jun Zeng (1) (2)
  Qing Lin (1) (2)
  ZhenHua Cao (1) (2)
  KuEr OuTi (1) (2)
  YuGuo Li (1) (2)
  Kai Lou (1) (2)
  
  1. Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, Xinjiang, China
  2. Xinjiang Laboratory of Special Enviromental Microbiology, Urumqi, 830091, Xinjiang, China
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Applied Microbiology
  Biotechnology
  Biochemistry
  Environmental Biotechnology
  Microbiology
  
• 出版者：Springer Netherlands
• ISSN：1573-0972

文摘

Plants harbor complex and variable microbial communities. Using molecular-based techniques targeting the 16S rRNA gene, we studied the developmental stages and geographical location diversity of endophytic archaea in two locations (Shihezi and Changji) and four periods (the seedling growth, rosette formation, tuber growth and sucrose accumulation sampling periods) in the north slope of Tianshan Mountain, China. Community structure of mixed sample from 60 sugar beet plants was examined using PCR-based 454 pyrosequencing and terminal restriction fragment length polymorphism (T-RFLP). In total, 5290 archaea 16S rRNA sequences were obtained from all sugar beet samples. The most abundant archaea groups in all sugar beet were Methanococci, the miscellaneous Crenarchaeotic Group and Thermoplasmata. There was a marked difference in diversity of endophytic archaea in sugar beet for different growth periods. The greatest number of Operational T-RFLP Units (OTUs) was detected during sucrose accumulation (298) and rosette formation (282). Endophytic archaea diversity was reduced during seedling growth (128 OTUs) and tuber growth (55 OTUs). Nine OTUs were common to all four periods of growth. There were more OTUs in Shihezi than in Changji. Clustering analysis and principal component analysis of T-RFLP data revealed distinct shifts in endophytic archaea community profiles that corresponded to plant growth stage rather than geographical location. The dynamics of endophytic archaea communities were influenced by plant growth stage. To our knowledge, this is the first report that archaea has been identified as endophytes associated with sugar beet by the culture-independent approach. The results suggest that the diversity of endophytic archaea is abundant in sugar beet.