Continuous cropping leads to the development of serious fungal diseases in tobacco plants and depleted yield of tobacco (Nicotiana tabacum), which can be mitigated by organic fertilization. Yet, we know little about how organic fertilizers affect the fungal community of continuous cropping tobacco soil. In this study, we investigated the soil fungal community after 11 years of tobacco planting with chemical fertilization (CF) or chemical fertilization combined with organic fertilizers obtained from plant or animal origin, including oil cake (CFO), straw (CFS), and farmyard fertilizer (CFM). The predominant phyla of Ascomycota (70%) and Mortierellomycota (15%) were identified in all the treatments. A significantly higher proportion of Pyrenochaetopsis and lower relative abundance of Sordariomycetes were observed in the CFM group compared to the controls. Compared to CF and non-fertilized control (CK), CFO and CFS led to higher species richness (P < 0.05), while CFM led to a less uniform fungal community, indicated by lower Shannon and higher Simpson diversity indices (P < 0.05). Pearson’s correlation and redundancy analysis suggested that fertilizations primarily influenced the fungal community by altering the soil nutrient conditions, among which soil organic carbon and total phosphorus significantly correlated with the fungal diversity and community composition (P < 0.05). Notably, FUNGuild annotation suggested that while other treatments showed no significant effect on the fungal trophic modes, CFM strongly increased the abundance of saprotrophic fungi by more than 30% (P < 0.05), thus preventing the prevalence of potential pathotypes and symbionts. The results suggest that the type of organic fertilizers is essential to the long-term effects of organic application on the fungal community, and the animal-origin manure seems to be a better choice than plant-origin materials in continuous cropping tobacco fields.

Remediation of soil contaminated with cadmium (Cd) and lead (Pb) is critical for tobacco production. Silicon (Si) fertilizer can relieve heavy metal stress and promote plant growth, however, it remains unknown whether fertilization with Si can mitigate the effects of Cd and Pb on tobacco growth and alter microbial community composition in polluted soils. Here we assessed the effect of two organic (OSiFA, OSiFB) and one mineral Si fertilizer (MSiF) on Cd and Pb accumulation in tobacco plants, together with responses in plant biomass, physiological parameters and soil bacterial communities in pot experiments. Results showed that Si fertilizer relieved Cd and Pb stress on tobacco, thereby promoting plant growth: Si fertilizer reduced available Cd and Pb in the soil by 37.3 % and 28.6 %, respectively, and decreased Cd and Pb contents in the plant tissue by 42.0-55.5 % and 17.2-25.6 %, resulting in increased plant biomass by 13.0-30.5 %. Fertilization with Si alleviated oxidative damage by decreasing malondialdehyde content and increasing peroxidase and ascorbate peroxidase content. In addition, Si fertilization increased photosynthesis, chlorophyll and carotenoid content. Microbial community structure was also affected by Si fertilization. Proteobacteria and Actinobacteria were the dominant phylum in the Cd and Pb contaminated soils, but Si fertilization reduced the abundance of Actinobacteria. Si fertilization also altered microbial metabolic pathways associated with heavy metal resistance. Together, our results suggest that both organic and mineral Si fertilizers can promote tobacco growth by relieving plant physiological stress and favoring a heavy metal tolerant soil microbial community.

Despite many studies on the influence of cropping practices on soil microbial community structure, little is known about ecological patterns of rare and abundant microbial communities in response to different tobacco cropping systems. Here, using the high-throughput sequencing technique, we investigated the impacts of two different cropping systems on soil biochemical properties and the microbial community composition of abundant and rare taxa and its driving factors in continuous and rotational tobacco cropping systems in the mountain lands of Yunnan, China. Our results showed that distinct co-occurrence patterns and driving forces for abundant and rare taxa across the different cropping systems. The abundant taxa were mainly constrained by stochastic processes in both cropping systems. In contrast, rare taxa in continuous cropping fields were mainly influenced by environmental perturbation (cropping practice), while governed by deterministic processes under rotational cropping. The α-diversity indices of rare taxa tended to be higher than those of the abundant ones in the two cropping systems. Furthermore, the network topologies of rare taxa were more complex than those of the abundant taxa in the two cropping systems. These results highlight that rare taxa rather than abundant ones play important roles in maintaining ecosystem diversity and sustaining the stability of ecosystem functions, especially in continuous cropping systems.

Soil sickness a severe problem in tobacco production, leading to soil-borne diseases and reduce in tobacco yield. This occurs as a result of the interaction between root exudates and rhizosphere microorganisms, which is however, little studied until now. By combining the field investigation and pot experiment, we found the output yield consistently decreased during the first 10 years of continuous cropping in a tobacco field, but increased at the 15th year (15Y). The root exudate and rhizosphere bacterial community was further analyzed to reveal the underlying mechanism of the suppressive soil formation. Root exudate of 15Y tobacco enriched in amino acids and derivatives, while depleted in the typical autotoxins including phenolic acids and alkaloids. This was correlated to the low microbial diversity in 15Y, but also the changes in community composition and topological properties of the co-occurrence network. Especially, the reduced autotoxins were associated with low Actinobacteria abundance, low network complexity and high network modularity, which significantly correlated with the recovered output yield in 15Y. This study revealed the coevolution of rhizosphere microbiota and root exudate as the soil domesticated by continuous cropping of tobacco, and indicated a potential role of the autotoxins and theirs effect on the microbial community in the formation of suppressive soil.

Introduction: Tobacco root-knot nematode (TRKN) disease is a soil-borne disease that presents a major hazard to the cultivation of tobacco, causing significant reduction in crop quality and yield, and affecting soil microbial diversity and metabolites. However, differences in rhizosphere soil microbial communities and metabolites between healthy tobacco soils and tobacco soils with varying degrees of TRKN infection remain unclear.Methods: In this study, diseased rhizosphere soils of tobacco infected with different degrees of TRKN [severally diseased (DH) soils, moderately diseased (DM) soils, and mildly diseased (DL) soils] and healthy (H) rhizosphere soils were collected. Here, we combined microbiology with metabolomics to investigate changes in rhizosphere microbial communities and metabolism in healthy and TRKN-infected tobacco using high-throughput sequencing and LC-MS/MS platforms.Results: The results showed that the Chao1 and Shannon indices of bacterial communities in moderately and mildly diseased soils were significantly higher than healthy soils. The Proteobacteria, Actinobacteria, Ascomycota, Burkholderia, Bradyrhizobium and Dyella were enriched in the rhizosphere soil of healthy tobacco. Basidiomycota, Agaricales, Pseudeurotiaceae and Ralstonia were enriched in severally diseased soils. Besides, healthy soils exhibited a relatively complex and interconnected network of bacterial molecular ecologies, while in severally and moderately diseased soils the fungal molecular networks are relatively complex. Redundancy analysis showed that total nitrogen, nitrate nitrogen, available phosphorus, significantly affected the changes in microbial communities. In addition, metabolomics results indicated that rhizosphere soil metabolites were significantly altered after tobacco plants were infected with TRKNs. The relative abundance of organic acids was higher in severally diseased soils. Spearman’s analyses showed that oleic acid, C16 sphinganine, 16-hydroxyhexadecanoic acid, D-erythro-3-methylmalate were positively correlated with Basidiomycota, Agaricales, Ralstonia.Discussion: In conclusion, this study revealed the relationship between different levels of TRKN invasion of tobacco root systems with bacteria, fungi, metabolites and soil environmental factors, and provides a theoretical basis for the biological control of TRKN disease.