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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.

SUBMITTER: Zhang H

PROVIDER: S-EPMC5209727 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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

Zhang Hongchun H Wang Rui R Chen Shu S Qi Gaofu G He Zhili Z Zhao Xiuyun X

Scientific reports 20170104

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 pathogen ...[more]

PMID: 28051173

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Project description:Bacterial wilt disease is a devastating disease of crops, which leads to huge economic loss worldwide. It is hypothesized that the occurrence of bacterial wilt may be related to changes in soil chemical properties and microbial interactions. In this study, we compared the soil chemical properties and microbial network structures of a healthy soil (HS) and a bacterial wilt-susceptible soil (BWS). The contents of available nitrogen, potassium, and phosphorus and the soil pH in the BWS were significantly lower than those in the HS. BWS showed nutrient deficiency and acidification in comparison with the HS. The structure and composition of the BWS network were quite different from those of the HS network. The BWS network had fewer modules and edges and lower connectivity than the HS network. The HS network contained more interacting species, more key microorganisms, and better high-order organization and thus was more complex and stable than the BWS network. Most nodes and module memberships were unshared by the two networks, while the ones that were shared showed different topological roles. Some generalists in the HS network became specialists in the BWS network, indicating that the topological roles of microbes were changed and key microorganisms were shifted in the BWS. In summary, the composition and structure of the microbial network of the BWS were different from that of the HS. Many microbial network connections were missing in the BWS, which most likely provided conditions leading to higher rates of bacterial wilt disease.IMPORTANCE Bacterial wilt disease is caused by the pathogen Ralstonia solanacearum and is a widespread devastating soilborne disease leading to huge economic losses worldwide. The soil microbial community is crucial to the capacity of soils to suppress soilborne diseases through complex interactions. Network analysis can effectively explore these complex interactions. In this study, we used a random matrix theory (RMT)-based network approach to investigate the changes in microbial network and associated microbial interactions in a bacterial wilt-susceptible soil (BWS) in comparison to a healthy soil (HS). We found that the structure and composition of the microbial network in BWSs were quite different from those of the HS. The BWS network had fewer modules, edges, and key microorganisms and lower connectivity than the HS network. In the BWSs, apparently the topological role of microbes was changed and key microorganisms were shifted to specialists.

Project description:BackgroundBeneficial root-associated microbiomes play crucial roles in enhancing plant growth and suppressing pathogenic threats, and their application for defending against pathogens has garnered increasing attention. Nonetheless, the dynamics of microbiome assembly and defense mechanisms during pathogen invasion remain largely unknown. In this study, we aimed to investigate the diversity and assembly of microbial communities within four niches (bulk soils, rhizosphere, rhizoplane, and endosphere) under the influence of the bacterial plant pathogen Ralstonia solanacearum.ResultsOur results revealed that healthy tobacco plants exhibited more diverse community compositions and more robust co-occurrence networks in root-associated niches compared to diseased tobacco plants. Stochastic processes (dispersal limitation and drift), rather than determinism, dominated the assembly processes, with a higher impact of drift observed in diseased plants than in healthy ones. Furthermore, during the invasion of R. solanacearum, the abundance of Fusarium genera, a known potential pathogen of Fusarium wilt, significantly increased in diseased plants. Moreover, the response strategies of the microbiomes to pathogens in diseased and healthy plants diverged. Diseased microbiomes recruited beneficial microbial taxa, such as Streptomyces and Bacilli, to mount defenses against pathogens, with an increased presence of microbial taxa negatively correlated with the pathogen. Conversely, the potential defense strategies varied across niches in healthy plants, with significant enrichments of functional genes related to biofilm formation in the rhizoplane and antibiotic biosynthesis in the endosphere.ConclusionOur study revealed the varied community composition and assembly mechanism of microbial communities between healthy and diseased tobacco plants along the soil-root continuum, providing new insights into niche-specific defense mechanisms against pathogen invasions. These findings may underscore the potential utilization of different functional prebiotics to enhance plants' ability to fend off pathogens.

Dataset Information

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

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

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