Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

Abstract

Background Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented. Results We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil’s previous fumigation exposure. Conclusions The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

Artificial network inference analysis reveals the impact of biostimulant on bacterial communities in fumigated soil for potato production against common scab

“…Our findings highlight the significant influence of both the treatments (biostimulant and fumigation) and the time periods on specific ASVs that were positively or negatively affected in the treated soils. Our results are consistent with those reported by Li et al (64), who found that chloropicrin fumigation exposure enriched the abundance of Pseudarthrobacter, Sphingomonas, Pseudomonas, Domibacillus, Nocardioides, and Paenibacillus at the genus level, many of which have known beneficial functions in promoting crop growth, antagonizing plant pathogens, and interacting with soil nitrogen cycling.…”

“…Previous studies have found that in bacterial community, Proteobacteria, Actinobacteriota and Firmicutes were more abundant while Acidobacteriota were less abundant in soils exposed to chloropicrin (17, 25, 65). Also, our findings are consistent with previous studies that reported that chloropicrin fumigation altered bacterial phyla relative abundance and sustained changes of bacterial community compared to the effects of other non-fumigated treatments (22,64).…”

Metagenomic Analyses Reveal Gut Microbial Profiles of Cnaphalocrocis medinalis Driven by the Infection of Baculovirus CnmeGV

“…The interaction circle diagram of species composition was drawn by Krona [43]. Alphadiversity indexes, including the Chao 1, Shannon, and Simpson, were calculated in QIIME 2 [44], and the statistical significance was calculated using the two-tailed, unpaired Student's t-test, followed by the Benjamini, Krieger and Yekutieli procedure for false discovery rate (FDR) correction. We used the Non-Metric Multi-Dimensional Scaling (NMDS) method to evaluate the difference in beta diversity between treatments [45].…”

Effects of Soil Amendments on Soil Properties, Soil-Borne Pathogens, and Strawberry Growth after Dazomet Fumigation

“…Soil fumigation can control and kill root-knot nematodes, soil-borne pathogens, and weeds [43]. Wang et al [44] reported that the inhibition rate of Phytophthora spp.…”