Microbial taxa and functional genes shift in degraded soil with bacterial wilt

Abstract

Soil degradation is a serious global problem, but little is known about how soil microbial communities respond to soil degradation as well as their feedback to ecosystem functioning. In this study, we found the microbial community composition, structure and functional potential significantly altered in the degraded soils with bacterial wilt (termed as degraded soils). Compared with healthy soils, OTU richness of beneficial microorganisms were significantly decreased, but OTU richness of pathogenic microorganisms were significantly increased in the degraded soils. Functional gene array (GeoChip 5.0) analysis showed the functional metabolic potential of genes involved in stress, virulence, sulfur cycle, metal resistance, degradation of plant cell wall was significantly increased in the degraded soils. Increased functional metabolic potential of these genes may be related to the acidification and severe plant disease of degraded soils. Biological activity of degraded soils was obviously decreased with weakened soil enzyme activities when compared to the healthy soils. Soil pH and enzyme activities were negatively correlated with the abundance of genes involved in sulfur cycle, virulence, and stress responses. This study provides new insights into our understanding of soil microbial community responses to soil degradation.

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

“…The soil fungal community of lotus ( Nelumbo nucifera ) in healthy and Fusarium wilt‐infected fields showed significant differences, indicating reduction of beneficial microorganism and accumulation of fungal pathogens under continuous lotus cultivation (Cui, Wang, Zeng, & Sun, ). These results are in line with the above cited observations on microbial dysbiosis in pea (Xu et al, ; Yu et al, ), peanut (Li et al, ), and tobacco (Zhang et al, ). Such an approach will allow to select plant genotypes that associate with a disease‐suppressive or “healthy” microbiome that can restrict the virulence of predominant pathogens.…”

“…Similar observations were made for long‐term peanut monocultures, where plant pathogenic fungi accumulated in the soil at the expense of beneficial fungi (Li et al, ). Zhang et al () took microbiome analysis a step further in their study on the sick soil phenomenon in monocropped tobacco fields. Combining amplicon sequencing with a functional gene analysis, the authors showed a shift in the microbial community composition to be accompanied by changes in the metabolic potential of genes involved in stress, virulence, and plant cell wall degradation in the sick soil.…”

New Soil, Old Plants, and Ubiquitous Microbes: Evaluating the Potential of Incipient Basaltic Soil to Support Native Plant Growth and Influence Belowground Soil Microbial Community Composition

“…Land degradation reduces soil microbial biomass and microbial activity [11], with reports of significant decrease in beneficial microorganisms and increase in pathogenic ones in degraded soils [12]. Another study [13] found higher bacterial richness and diversity in restored soils and soils under native vegetation in comparison to degraded soils.…”

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

“…For example, Addy et al () reported a filamentous phage (φRSM) of the wilt‐causing bacterial pathogen Ralstonia solanacearum : φRSM infection made the pathogen less virulent and thus prevented damage to its host plants (Yamada, ). Ecologists have also been interested in φRSM because R. solanacearum is a serious threat to phytorestoration programs (Zhang et al, ), for example to programs to grow tobacco for ecorestoration of nutrient‐deficient and contaminant‐rich soils. In fact, degraded soils show greater abundance of not only R. solanacearum but also of pathogenic members of Pseudomonas , Erwinia , and Xanthomonas .…”

“…Also, silverized antimicrobial phage fibers developed with E3 modified M13 kill bacterial contaminants in water during filtration through phage-coated fibers (Mao et al, 2010; (Yamada, 2013). Ecologists have also been interested in φRSM because R. solanacearum is a serious threat to phytorestoration programs (Zhang et al, 2017), for example to programs to grow tobacco for ecorestoration of nutrient-deficient and contaminant-rich soils.…”