Research Article: Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity

Date Published: September 18, 2017

Publisher: Springer Berlin Heidelberg

Author(s): Shuting Zhang, Xiaojiao Liu, Qipeng Jiang, Guihua Shen, Wei Ding.


Chloropicrin is widely used to control ginger wilt in China, which have an enormous impact on soil microbial diversity. However, little is known on the possible legacy effects on soil microbial community composition with continuous fumigation over different years. In this report, we used high throughput Illumina sequencing and Biolog ECO microplates to determine the bacterial community and microbial metabolic activity in ginger harvest fields of non-fumigation (NF), chloropicrin-fumigation for 1 year (F_1) and continuous chloropicrin-fumigation for 3 years (F_3). The results showed that microbial richness and diversity in F_3 were the lowest, while the metabolic activity had no significant difference. With the increase of fumigation years, the incidence of bacterial wilt was decreased, the relative abundance of Actinobacteria and Saccharibacteria were gradually increased. Using LEfSe analyses, we found that Saccharibacteria was the most prominent biomarker in F_3. Eight genera associated with antibiotic production in F_3 were screened out, of which seven belonged to Actinobacteria, and one belonged to Bacteroidetes. The study indicated that with the increase of fumigation years, soil antibacterial capacity may be increased (possible reason for reduced the incidence of bacterial wilt), and Saccharibacteria played a potential role in evaluating the biological effects of continuous fumigation.

Partial Text

Soil fumigants are used extensively to control soil-borne pests including nematodes, pathogens, and weeds, so that increasing the yields of many crops (Mao et al. 2013; Wang et al. 2014; Ibekwe 2004). For instance, bacterial wilt on ginger, caused by the soil-borne bacterial pathogen Ralstonia solanacearum, is a major disease responsible for enormous yield losses (Yang et al. 2012). Without soil fumigation, it can cause an 80% crop failure in ginger (Li et al. 2014). Therefore, in order to ensure a better crop yield and provide greater benefits to farmers, soil fumigation has become an important global agricultural practice (Ajwa et al. 2010). Methyl bromide (MB) is mainly used for pre-planting fumigation of vegetables to manage many kinds of phytopathogenic organisms including R. solanacearum (Paret et al. 2010). However, MB had been phased out in developing countries owing to its detrimental effects on the stratospheric ozone layer (Bell et al. 2000). Chloropicrin is a potential replacement for MB, which has been widely used to control ginger bacterial wilt in China (Mao et al. 2013).

Soil fumigation can significantly impact the soil microbial communities (Ibekwe et al. 2001). Fumigants can reduce the bacterial population in the early stage and create a temporary “biological vacuum”. The temporary vacant niche can be easily and quickly recolonized by many bacteria (Yakabe et al. 2010). The effects on the bacterial population structure are short-lived and become non-significant difference compared to non-fumigation after fumigating 2–3 months (Liu et al. 2015; Wei et al. 2016). In this study, with the increase of fumigation years, the richness and diversity were significantly reduced. Although the soil microbial population structure could be restored after fumigation, the microbial richness and diversity can not be restored to the original state.




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