Study on the diversity of epiphytic bacteria on corn and alfalfa using Illumina MiSeq/NovaSeq high-throughput sequencing system

Abstract

Purpose To investigate the diversity of the epiphytic bacteria on corn (Zea mays) and alfalfa (Medicago sativa) collected in Hengshui City and Xingtai City, Hebei Province, China, and explore crops suitable for natural silage. Methods The Illumina MiSeq/NovaSeq high-throughput sequencing system was used to conduct paired-end sequencing of the community DNA fragments from the surface of corn and alfalfa collected in Hengshui and Xingtai. QIIME2 and R software were used to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the alpha and beta diversity indices at of species level were calculated, and the abundance and distribution of taxa were analyzed and compared between samples. Result At phylum level, the dominant groups were Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%), and Bacteroidetes (7%). Meanwhile, the dominant genera were Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), and Hymenobacter (1%). Enterobacteriaceae (24%) were the most predominant bacteria in both the corn and alfalfa samples. Alpha diversity analysis and beta diversity indices revealed that the diversity of epiphytic microbial communities was significantly affected by plant species but not by region. The diversity and richness of the epiphytic bacterial community of alfalfa were significantly higher than those of corn. Conclusion This study contributes to the expanding knowledge on the diversity of epiphytic bacteria in corn and alfalfa silage and provides a basis for the selection of raw materials.

Structure and Ecological Function of Fungal Endophytes from Stems of Different Mulberry Cultivars

“…Studies show that an increase in the diversity of fungal communities enhances the positive colony effect of microorganisms and improves the comprehensive resistance of host plants against pathogens, thereby helping to promote fruit yield and quality [ 30 ]. According to relevant reports [ 23 , 24 , 31 ] and observations on the incidence of sclerotiniosis at the mulberry fruit base of the Chongqing Academy of Agricultural Sciences, TWC is an immune cultivar against sclerotiniosis, and JZS, DBE, NYSJ, and YK display good disease resistance, indicating that a higher microbial community diversity index means higher resistance, which is in line with the results of Allison [ 32 ] and Wu et al [ 17 ].…”

“…Is this difference related to differences in plant endophyte community structure and diversity? Wu et al [ 17 ] analyzed the community structure and diversity of endophytes of four different resistant mulberry cultivars, and the results showed that numerous characteristics and the diversity of endophytes of resistant cultivars were significantly higher than those of susceptible cultivars. Endophytic bacterial populations of two citrus cultivars—the resistant satsuma mandarin and the susceptible Newhall navel orange—were analyzed through high-throughput sequencing, and the results showed that the differences in endophytic bacteria between citrus cultivars might be related to host resistance or susceptibility to citrus canker disease [ 18 ].…”

Effect of Yogurt Acid Whey on the Quality of Maize Silage

“…The epiphytic microflora of forage significantly affects the quality of natural silage fermentation [44,45]. Therefore, an additional purpose of this study was to assess the concentration of various microbial populations, such as total bacteria, Lactobacillus spp., Clostridium spp., yeast and molds and coliforms.…”

Longitudinal Distribution Map of the Active Components and Endophytic Fungi in Angelica sinensis (Oliv.) Diels Root and Their Potential Correlations

“…The original image data file was transformed into sequenced reads using a base-calling analysis, and the results were stored in a FASTQ file format. Data preprocessing was performed in three steps—quality filtering, double-ended sequence splicing, and chimaera removal—to obtain the final effective read length [ 30 ].…”