Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain

Abstract

Plants harbors complex and variable microbial communities. Endophytic bacteria play an important function and potential role more effectively in developing sustainable systems of crop production. To examine how endophytic bacteria in sugar beet (Beta vulgaris L.) vary across both host growth period and location, PCR-based Illumina was applied to revealed the diversity and stability of endophytic bacteria in sugar beet on the north slope of Tianshan mountain, China. A total of 60.84 M effective sequences of 16S rRNA gene V3 region were obtained from sugar beet samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in sugar beet, that is, 19-121 OTUs in a beet sample, at 3 % cutoff level and sequencing depth of 30,000 sequences. We identified 13 classes from the resulting 449,585 sequences. Alphaproteobacteria were the dominant class in all sugar beets, followed by Acidobacteria, Gemmatimonadetes and Actinobacteria. A marked difference in the diversity of endophytic bacteria in sugar beet for different growth periods was evident. The greatest number of OTUs was detected during rossette formation (109 OTUs) and tuber growth (146 OTUs). Endophytic bacteria diversity was reduced during seedling growth (66 OTUs) and sucrose accumulation (95 OTUs). Forty-three OTUs were common to all four periods. There were more tags of Alphaproteobacteria and Gammaproteobacteria in Shihezi than in Changji. The dynamics of endophytic bacteria communities were influenced by plant genotype and plant growth stage. To the best of our knowledge, this study is the first application of PCR-based Illumina pyrosequencing to characterize and compare multiple sugar beet samples.

Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site

“…However, root-associated microorganisms are also influenced by plant-specific factors, such as plant species (Haichar et al 2008;Aleklett et al 2015), plant genotype (van Overbeek and van Elsas 2008; Shi et al 2014), and plant growth stage (van Overbeek and van Elsas 2008;Shi et al 2014). In this study, similar plant species had largely similar root-associated bacterial composition, despite different sampling locations.…”

Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform

“…bacteria associated with Lucilia spp. (Singh et al 2014), tobacco waste extract (Liu et al 2014a, b14), styrene-degrading biofilters (Portune et al 2014), activated sludge (Zhao et al 2014), high-temperature biogas reactors (Röske et al 2014), phyllosphere of rice (Ren et al 2014), river receiving effluents from swine farm and farmhouse restaurant (Lu and Lu 2014), endophytes of sugar beet (Shi et al 2014), petroleum reservoir , intestinal environment of rats , mine tailings (Liu et al 2014a, b), heavy metals polluted soil (Gołębiewski et al 2014), soil horizons and drain sediments of coastal acid sulfate landscape (Stroud et al 2014). The first 16S rRNA gene-based microbial analysis of mine-water systems was done in the mid-1990s (Goebel and Stackebrandt 1994).…”

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

“…However, these techniques yield unsatisfactory performances in terms of the accurate detection of the changes in ecologically important soil microbial groups under different soil environmental conditions because of resolution limits, fingerprint complexity, and highly abundant indigenous microbes in soil (Bruce et al, 2000;Quince et al, 2009). Conversely, DNA-characterization-based highthroughput methodologies, such as sequencing and subsequent sequence alignment, can directly detect microbial community composition and variations in species with low richness (Shi et al, 2014;Zhao et al, 2014). These methodologies have also been widely adopted to assess the genetic structure and diversity of microbial communities in various environments (Quince et al, 2009;Golebiewski et al, 2014;Liu et al, 2014;Portune et al, 2014;Ren et al, 2014;Singh et al, 2014;Thomson et al, 2015).…”