High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

PLOS ONE, Nov 2019

In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine.

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High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

March High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China Yu-jie Wei 0 1 Yun Wu 0 1 Yin-zhuo Yan 1 Wan Zou 0 1 Jie Xue 1 Wen-rui Ma 0 1 Wei Wang 0 1 Ge Tian 0 1 Li-ye Wang 0 1 0 College of Food Science and Pharmacy, Xinjiang Agricultural University , Urumqi , China , 2 China National Research Institute of Food & Fermentation Industries , Beijing , China 1 Editor: Luca Cocolin, University of Torino , ITALY In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine. - Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: This work was supported by the Xinjiang Autonomous Region Science and Technology Plan (201431113), by the Major Technology Projects of Xinjiang (2017A01001-2 to YW), and by the Natural Science Foundation of China-regional fund (31360406 to YW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Introduction Microbial biodiversity is highly essential for harboring a healthy environment with sustainable economy, especially at agricultural field. In recent years, several studies on biodiversity tried to characterize the microbiome in different agricultural ecosystems, as to understand the dynamics of plant and microbe interaction. It is discovered that plant-associated bacteria and fungi colonize on both exterior (epiphytes) and interior surfaces (endophytes) of plants, while the surrounding soil around the plant acts as the major resource for these microbes [ 1 ]. As plant species and soil type play a predominant role in soil microbial community, the interaction between plant and soil microbes are highly complex. Vitis vinifera (wine grape) is an economically important agricultural crop. V. vinifera phyllosphere is easy to be colonized by both Competing interests: The authors have declared that no competing interests exist. bacteria and fungi, which in-turn modulates grapevine health, development, and grape qualities [ 2 ]. In this case, microbial activity plays a critical role on grape production and quality [2± 3]. Due to its nutritive contents like organic acids, amino acids, and trace elements, wine does have beneficial effects on human health. Studies have shown that long term in-take of wine in diet could prevent chronic diseases and cardiovascular diseases [4±7]. The winemaking is a composite process where numerous microorganisms were involved, especially yeast and bacteria [8±11]. Understanding the composition and population dynamics of the microbial population throughout brewing is highly essential for controlling the process, thereby improving the quality and safety of the wine [12±13]. Microbes in wine brewing is mainly from wine grapes, vineyards, brewing equipment, and surrounding environment, impacts the quality of the wine at a larger level [14±15]. In recent years, studies have shown that the unique flavor in wine is mainly generated from the microbial metabolic process during wine making process [16±17]. Therefore, selecting specific microbes for wine fermentation can help to crease the flavor, thereby enhancing the taste and quality of wine. Current methods for microbial diversity analysis mainly include traditional culture method and non-culture methods. Traditional culture methods such as restriction fragment length polymorphism (RFLP) and random amplified polymorphic analysis (RAPD) are based on polymerase chain reaction (PCR) techniques. Compare to non-culture methods, they are laborious and time consuming, also poor in reliability. Non-culture methods mainly involve denaturing gradient gel electrophoresis (DGGE), real-time fluorescence PCR, and fluorescence in situ hybridization (FISH). They have the capability to detect the dynamic changes of microorganisms in the fermentation proc (...truncated)


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Yu-jie Wei, Yun Wu, Yin-zhuo Yan, Wan Zou, Jie Xue, Wen-rui Ma, Wei Wang, Ge Tian, Li-ye Wang. High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China, PLOS ONE, 2018, Volume 13, Issue 3, DOI: 10.1371/journal.pone.0193097