Endophytic bacterial communities of Jingbai Pear trees in north China analyzed with Illumina sequencing of 16S rDNA
- 99 Downloads
Plant endophytes play a crucial role in plant growth, health and ecological function. Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has important ecological and economic value in north China. Conversation of its genetics has great meanings to pear genus (Pyrus L.). However, the bacterial community associated with the cultivar remains unknown. In this study, the structure of endophytic bacterial communities associated with different tissues and soil of Jingbai Pear trees was analyzed with Illumina Miseq sequencing of bacterial 16S rDNA. This is the first report on bacterial microbiome associated with Jingbai pear. Our results demonstrated that different tissues harbored a unique bacterial assemblage. Interestingly, Cyanobacteria was the most abundant phylum, followed by Proteobacteria and Actinobacteria. Samples from three different sites (soils) had significant differences in microbial communities structure. Redundancy analysis (RDA) showed that the bacterial community structure correlated significantly with soil properties—temperature, pH, nitrogen and carbon contents. The conclusion could facilitate to understand the interaction and ecological function of endophytic bacteria with host Jingbai pear trees, so as to benefit the pear variety genetic resource conservation and protection.
KeywordsEndophytic bacterial community Metagenomic analysis Jingbai pear
The Fundamental Research Funds for the Central Non-profit Research Institution of Chinese Academy of Forestry is gratefully acknowledged for research funding (Project CAFYBB2017MA019).
FR, DHY conceived the study and contributed in the experimental design of the study; FR, WD and DHY collected the samples; FR did the experiment; FR, WD performed the statistical analysis; FR wrote the first draft of the manuscript; All authors contributed to manuscript revision, read and approved the submitted version.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
- Araújo WL, Marcon J, Maccheroni W, van Elsas JD, van Vuurde JWL, Azevedo JL (2002) Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 68:4906–4914. https://doi.org/10.1128/AEM.68.10.4906-4914.2002 CrossRefGoogle Scholar
- Bremner JM (1965) Total nitrogen. In: Black CA (ed) Methods of soil analysis part 2: chemical and microbial properties. American Society of Agronomy Publisher Inc., Madison, pp 1049–1178Google Scholar
- Campisano A, Pancher M, Puopolo G, Puddu A, Lòpez-Fernàndez S, Biagini B, Yousaf S, Pertot I (2015) Diversity in endophyte populations reveals functional and taxonomic diversity between wild and domesticated grapevines. Am J Enol Vitic 66(1):12–21. https://doi.org/10.5344/ajev.2014.14046 CrossRefGoogle Scholar
- Carvalho TL, Ballesteros HG, Thiebaut F, Ferreira PC, Hemerly AS (2016) Nice to meet you: genetic, epigenetic and metabolic controls of plant perception of beneficial associative and endophytic diazotrophic bacteria in non-leguminous plants. Plant Mol Biol 90(6):561–574. https://doi.org/10.1007/s11103-016-0435-1 CrossRefGoogle Scholar
- Fidalgo C, Henriques I, Rocha J, Tacao M, Alves A (2016) Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal (loid) contamination. Environ Sci Pollut Res Int 23(10):10200–10214CrossRefGoogle Scholar
- Garbeva P, Van Overbeek LS, Van Vuurde JWL, Van Elsas JD (2001) Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA based PCR fragments. Microb Ecol 41(4):369–383. https://doi.org/10.1007/s002480000096 CrossRefGoogle Scholar
- Hortova B, Novotny D (2011) Endophytic fungi in branches of sour cherry trees: a preliminary study. Czech Mycol 63(1):77–82Google Scholar
- Kovalchuk A, Mukrimin M, Zeng Z, Raffaello T, Liu MX, Kasanen R, Sun H, Asiegbu FO (2018) Mycobiome analysis of asymptomatic and symptomatic Norway spruce trees naturally infected by the conifer pathogens Heterobasidion spp. Environ Microbiol Rep. https://doi.org/10.1111/1758-2229.12654 Google Scholar
- Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2011) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112–5120. https://doi.org/10.1128/AEM.01043-13 CrossRefGoogle Scholar
- Liu Y, Li YH, Yao S, Wang H et al (2015) Diversity and distribution of endophytic bacterial community in the Noni (Morinda citrifolia L.) plant. Afr J Microbiol Res 24 9:1649–1657Google Scholar
- Masoud W, Takamiya M, Vogensen FK, Lillevang S et al (2011) Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing. Int Dairy J 21:142–148. https://doi.org/10.1016/j.idairyj.2010.10.007 CrossRefGoogle Scholar
- Mûller DB, Vogel C, Bai Y, Vorholt JA (2016) The plant microbiota: systems-level insights and perspectives. Annu Rev Genet 50:211–234. https://doi.org/10.1146/annurev-genet-120215-034952 CrossRefGoogle Scholar
- Nelson DW, Sommers LE (1996) Total carbon, organic carbon, and organic matter. In: Sparks DL (ed) Methods of soil analysis part 3: chemical methods (methodsofsoilan3). Soil Science Society of America Publisher Inc, Madison, pp 961–1010Google Scholar
- Porras-Alfaro A, Bayman P (2011) Hidden fungi, emergent properties: endophytes and microbiomes. Annu Rev Phytopathol 49:291–315. https://doi.org/10.1146/annurev-phyto-080508-081831 CrossRefGoogle Scholar
- R Core Team (2013) R: a language and environment for statistical computing. R foundation for Statistical Computing, ViennaGoogle Scholar
- Stanier RY, Cohen-Bazire G (1977) Phototrophic prokaryotes: the cyanobacteria. Annu Rev Microbiol 31:225–274. https://doi.org/10.1146/annurev.mi.31.100177.001301 CrossRefGoogle Scholar