Application of PCR-Denaturing-Gradient Gel Electrophoresis (DGGE) Method to Examine Microbial Community Structure in Asparagus Fields with Growth Inhibition due to Continuous Cropping

Abstract

Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE.

Effects of cultivation ages and modes on microbial diversity in the rhizosphere soil of Panax ginseng

“…5 ). In previous studies, the cultivation age was assumed to be an important factor that influenced microbial activity and diversity in the rhizosphere of plants [9] , [46] , [47] . In addition, soil characteristics had a significant influence on soil microbial communities [48] , of which soil pH was thought to exert primary domination on the composition of soil bacterial communities [49] .…”

“…Therefore, many investigations on discontinuous cultivation were focused on the evaluation of soil quality and the microbial community. Interestingly, several findings from previous studies have demonstrated that continuous farming resulted in an imbalance in soil ecology and alterations of microbial diversity in rhizosphere soil [8] , [9] . Although a number of microbial strains (comprising < 1% in total) have been isolated from successive cultivation soil [10] , [11] , [12] , most of the microbial communities and their composition in rhizosphere soil are still difficult to analyze.…”

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach

“…These methods are laborious, time consuming and only detect a relatively small number of clones (Pace ; Urashima et al . ). Therefore, the detailed effects of continuous tea cropping on soil microbial communities remain unclear.…”

Analyses of the community compositions of root rot pathogenic fungi in the soybean rhizosphere soil

“…For example, continuous cropping may cause significant decreases in pH, making the soil switch from neutral to acidic, which favors the growth of fungi (Urashima et al, 2012), inhibits the breeding of bacteria and actinomycete (Helgason et al, 2009;Page et al, 2013) and leads to the dominance of fungi. At the same time, continuous cropping results in the enrichment of root exudates, which also increases the quantity of soil fungi (Suyker and Verma, 2009 …”