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, 17, 1091-1100
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A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among Different Mulberry Cultivars

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A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among Different Mulberry Cultivars

Ting Ou et al. Comput Struct Biotechnol J.

Abstract

Knowledge of seasonal shifts in the bacterial community composition among different mulberry (Morus L.) cultivars will facilitate to develop the biocontrol phytopathogens strategy using endophytic bacteria. The present study investigated the endophytic bacterial communities of four mulberry cultivars that have different resistance to mulberry fruit sclerotiniosis using Illumina-based sequencing of the 16S rRNA gene fragment in spring and autumn. The results indicated that spring samples harbor higher bacterial operational taxonomic units (OTUs), α-diversity, and bacterial community complexity in comparison with autumn samples. The taxonomic composition analysis showed that the majority of endophytes were composed of Proteobacteria (genus level: Methylobaterium) and Actinobacteria in spring, while sequences classified as Proteobacteria (genus level: Pantoea and Pseudomonas) were abundant in autumn. Analysis of β-diversity also revealed endophytic bacteria were divided into two main groups by season. By comparison among different mulberry cultivars, we found that Pantoea, Methylobaterium, and Pseudomonas were the three major bacterial genera in all cultivars, while their relative abundances varied with cultivars and appeared no obvious relationship with resistance level of mulberry fruit sclerotiniosis. The complex correlation of the endophytic communities in susceptible mulberry cultivars was higher than that of the resistant cultivars. Overall, the findings suggested that season plays a key role in determining the mulberry endophytic bacterial communities, followed by host cultivar, and Proteobacteria was the predominant phylum in both seasons and different mulberry cultivars.

Keywords: Endophytic bacteria; Microbial diversity; Mulberry cultivar; Seasonal variation.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Unlabelled Image
Fig. 1
Fig. 1
Richness and diversity analysis of the endophytic bacterial communities in different seasons and in different mulberry cultivars. Richness based on the number of observed OTUs (A) and Chao index (B), and diversity based on Shannon index (C) and Simpson index (D). CSQ, CGS, XLJ and HGE represent bacterial communities from ‘Chuan Sang No.7637’, ‘Changguo Sang’, ‘Xin Lunjiao’ and ‘Hong Guo No.2’, respectively. Bars with the different letters indicate a significant difference between means by one-way analysis of variance (ANOVA) and least significant difference (LSD) tests (p < 0.05). Values represent the mean. Error bars indicate ± standard deviation.
Fig. 2
Fig. 2
Venn diagram of the number of OTUs obtained in different cultivars and in different seasons (spring and fall). Values represent the number of OTUs. (A) grouping by season. Spring and autumn represent spring bacterial communities and autumn bacterial communities, respectively. (B) grouping by cultivar. CSQ, CGS, XLJ and HGE represent bacterial communities from ‘Chuan Sang No.7637’, ‘Changguo Sang’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’, respectively. (C) cultivars in spring. SC, SQ, SX and SH represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’ in spring, respectively. (D) cultivars in autumn. AC, AQ, AX and AH represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’ in autumn, respectively.
Fig. 3
Fig. 3
Relative abundance of endophytic bacteria from different communities at the phylum level. Taxa with an abundance <0.01 are included in “others”. The x-axis represents different communities (cultivars × season) and the y-axis represents the relative abundance of all communities. SC, SQ, SX and SH represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’ in spring, respectively. AC, AQ, AX and AH represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’ in autumn, respectively. Each column represents the mean of three biological replicates per cultivar.
Fig. 4
Fig. 4
Comparison in the abundance of the top 5 dominant bacterial genera in different seasons and mulberry cultivars. *** indicates a significant difference at p < 0.001, ** p < 0.01, * p < 0.05. The x-axis represents the genus mean proportions and the y-axis represents the top 5 dominant bacterial genera. CGS, CSQ, XLJ, and HGE represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’, respectively.
Fig. 5
Fig. 5
PCoA plot of the relationship between samples on the basis of similarity in the community composition of bacterial OTUs. Two first components (PCoA 1 and PCoA 2) are plotted and represent 70.55% of the variation. SC, SQ, SX and SH represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’ in spring, respectively. AC, AQ, AX and AH represent bacterial communities from ‘Changguo Sang’, ‘Chuan Sang No.7637’, ‘Xin Lunjiao’, and ‘Hong Guo No.2’ in autumn, respectively.
Fig. 6
Fig. 6
Correlation network analysis of microbial communities in different seasons (A) and in different mulberry cultivars (B). The size of the node is proportional to the richness of bacteria. Node color corresponds to phylum classification. Edge color represents positive (red) and negative (blue) correlations, and the edge thickness is equivalent to the correlation values.

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