Illumina MiSeq investigations on the changes of microbial community in the Fusarium oxysporum f.sp. cubense infected soil during and after reductive soil disinfestation

Abstract

Although reductive soil disinfestation (RSD) is increasingly used for the control of soil-borne diseases, its impact on the soil microbial community during and after RSD remains poorly understood. MiSeq pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the changes of microbial community in the Fusarium oxysporum f. sp. cubense (FOC) infected soil during RSD and at the simulative banana cultivation after RSD. The results showed that RSD significantly increased soil microbial populations and a different microbial community with the pathogenic soil was established after RSD. Specifically, the number of Firmicutes mainly containing Ruminococcus and Coprococcus followed by a small part of Clostridium which were the dominant bacterial genera significantly increased during RSD. In contrast, Symbiobacterium and Flavisolibacter were the dominant genera in the flooding soil. When the soils were recovered under aerobic condition, the relative abundances of the bacteria belonging to the phylum Bacteroidetes, Acidobacteria, Planctomycetes increased as alternatives to the reducing Firmicutes. For fungi, the population of F. oxysporum significantly decreased during RSD accompanied with the pH decline, which resulted in the significant decrease of relative abundance in the phylum Ascomycota. Alternatively, the relative abundances of some other fungal species increased, such as Chaetomium spp. and Penicillium spp. belonging to Ascomycota and the family Clavulinaceae belonging to Basidiomycota. Then, the relative abundance of Ascomycota re-increased after RSD with Podospora and Zopfiella as dominant genera, whereas the relative abundance of Fusarium further decreased. Overall, the microbial populations and community re-established by RSD made the soil more disease-suppressive and beneficial to the soil nutrient cycling and plant growth compared with the previous pathogenic soil.

Genetic and Metabolic Diversity of Soil Microbiome in Response to Exogenous Organic Matter Amendments

“…The Biolog system has been used for environmental research by many researchers [20,43], allowing for the monitoring of changes in the population of microorganisms in the soil and other ecosystems under the influence of various factors. The assessment of the impact of fertilizer (organic or mineral) addition on the population of microorganisms is important due to the functions they perform in the soil [44]. The results of our study show, that all of the tested wastes affected the functional diversity of soil microbial communities, including bacteria, fungi and anaerobes in a characteristic way.…”

Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation

“…Previous studies (Bhat and Bhat, 1997;Biddle et al, 2013;Del Rio et al, 2010;Eichorst et al, 2013;Kumar et al, 2015) have indicated that they also can break down less-degradable organic carbon. Therefore, these TOC decomposers and organic acid producers could collaborate to control FOC (Huang et al, 2015a).…”

Comparison of prokaryotic communities among fields exhibiting different disinfestation effects by anaerobic soil disinfestation

“…Clostridia are gram-positive anaerobic bacteria. Several studies have reported that the abundance of Clostridia species increases and it becomes the dominant bacteria after ASD treatment using plant material or low-concentration ethanol as a substrate [13,14,27]. During ASD, decreased oxygen utilization promotes the increased prevalence of anaerobic microbes [6,12,27].…”