Different Continuous Cropping Spans Significantly Affect Microbial Community Membership and Structure in a Vanilla-Grown Soil as Revealed by Deep Pyrosequencing

Abstract

In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

Effects of <i>Bacillus cereus</i> F-6 on Promoting Vanilla (<i>Vanilla planifolia</i> Andrews.) Plant Growth and Controlling Stem and Root Rot Disease

“…Vanilla growth had been almost entirely decimated in this field [3]. The field was located in the Spice and Beverage Research Institute of the Chinese Academy of Tropical Agricultural Sciences, Xinglong, Hainan Province (110˚20'E, 18˚73'N); the soil contained 35.9 g•kg −1 of organic matter, 82.52 mg•kg −1 of available N, 336.36 mg•kg −1 of available P (Olsen), and 98.85 mg•kg −1 of available K (NH 4 OAc).…”

“…vanilla, causes heavy economic losses in numerous vanilla-planting regions [7]. On long-term monoculture vanilla plantations, this disease has spread widely; the plant symptoms have worsened and the soil microbial community structure is out of balance [3]. In addition, the intensive growth of vanilla requires a very high consumption of chemical fertilizers and pesticides, resulting in serious environmental and food safety problems.…”

“…However, vanilla plants are typically slow growing and suffer from successive cropping obstacles when they are replanted after a previous crop is removed [3], similar to apple [4], cotton [5], melon [6]. A number of soilborne diseases can cause successive cropping obstacles, and stem and root rot disease, which is caused by the fungal pathogen Fusarium oxysporum f. sp.…”

Microbiome engineering: Current applications and its future

“…Navarrete et al [7] reported taxonomic and functional adaptations in soil microbiome after deforestation in the Amazon region and these adaptations typically result in increased soil fertility. Other agricultural practices, such as logging [43], tillage [44] and cropping systems [45,46], also play roles in effecting structural and functional changes in soil microbiome that lead to changes in soil functions. As many of the discussed agricultural management practices have been implemented for decades with success, recent efforts in understanding their effects on soil microbiota composition would enable rational engineering of the soil microbiome to optimize these practices for improved crops.…”

“…Agricultural management Soil Organic farming, changing land usage, logging, tillage, cropping [7,[41][42][43][44][45][46] Improve soil fertility • Alter structure and function of soil microbiome;…”