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IntroductionThe effects of continuous cropping and rotation cropping, two important tobacco cultivation practices, on soil microbial communities at different stages remain unclear. Different planting patterns have been shown to influence soil physical and chemical properties, which in turn can affect the composition and diversity of soil microbial communities.MethodsIn order to investigate the impact of different planting methods on soil microbial community structure, we selected two representative planting methods: continuous cropping (tobacco) and rotational cropping (tobacco-maize). These methods were chosen as the focal points of our research to explore the potential effects on soil microbial communities. High-throughput sequencing technology was employed to investigate the structure of soil microbial communities, as well as their relationships with soil environmental factors, by utilizing the 16S rRNA, ITS, and 18S genes. Furthermore, the interaction among microorganisms was explored through the application of the Random Matrix Theory (RMT) molecular ecological network approach.ResultsThere was no significant difference in α diversity, but significant difference in β diversity based on Jaccard distance test. Compared to continuous cropping, crop rotation significantly increased the abundance of beneficial prokaryotes Verrucomicrobia and Rhodanobacter. These findings indicate that crop rotation promotes the enrichment of Verrucomicrobia and Rhodanobacter in the soil microbial community. AP and NH4-N had a greater effect on the community structure of prokaryotes and fungi in tobacco soil, while only AP had a greater effect on the community structure of protist. Molecular ecological network analysis showed that the network robustness and Cohesion of rotation were significantly higher than that of continuous cropping, indicating that the complexity and stability of molecular ecological networks were higher in the rotational, and the microbial communities cooperated more effectively, and the community structure was more stable.DiscussionFrom this point of view, rotational cropping is more conducive to changing the composition of soil microbial community, enhancing the stability of microbial network structure, and enhancing the potential ecological functions in soil.

ABSTRACTThe contamination of the plant phyllosphere with antibiotics and antibiotic resistance genes (ARGs), caused by application of antibiotics, is a significant environmental issue in agricultural management. Alternatively, biocontrol agents are environmentally friendly and have attracted a lot of interest. However, the influence of biocontrol agents on the phyllosphere resistome remains unknown. In this study, we applied biocontrol agents to control the wildfire disease in the Solanaceae crops and investigated their effects on the resistome and the pathogen in the phyllosphere by using metagenomics. A total of 250 ARGs were detected from 15 samples, which showed a variation in distribution across treatments of biocontrol agents (BA), BA with Mg2+ (T1), BA with Mn2+ (T2), and kasugamycin (T3) and nontreated (CK). The results showed that the abundance of ARGs under the treatment of BA-Mg2+ was lower than that in the CK group. The abundance of cphA3 (carbapenem resistance), PME-1 (carbapenem resistance), tcr3 (tetracycline antibiotic resistance), and AAC (3)-VIIIa (aminoglycoside antibiotic resistance) in BA-Mg2+ was significantly higher than that in BA-Mn2+ (P < 0.05). The abundance of cphA3, PME_1, and tcr3 was significantly negatively related to the abundance of the phyllosphere pathogen Pseudomonas syringae (P < 0.05). We also found that the upstream and downstream regions of cphA3 were relatively conserved, in which rpl, rpm, and rps gene families were identified in most sequences (92%). The Ka/Ks of cphA3 was 0 in all observed sequences, indicating that under the action of purifying selection, nonsynonymous substitutions are often gradually eliminated in the population. Overall, this study clarifies the effect of biocontrol agents with Mg2+ on the distribution of the phyllosphere resistome and provides evolutionary insights into the biocontrol process.IMPORTANCEOur study applied metagenomics analysis to examine the impact of biocontrol agents (BAs) on the phyllosphere resistome and the pathogen. Irregular use of antibiotics has led to the escalating dissemination of antibiotic resistance genes (ARGs) in the environment. The majority of BA research has focused on the effect of monospecies on the plant disease control process, the role of the compound BA with nutrition elements in the phyllosphere disease, and the resistome is still unknown. We believe BAs are eco-friendly alternatives for antibiotics to combat the transfer of ARGs. Our results revealed that BA-Mg2+ had a lower relative abundance of ARGs compared to the CK group, and the phyllosphere pathogen Pseudomonas syringae was negatively related to three specific ARGs, cphA3, PME-1, and tcr3. These three genes also present different Ka/Ks. We believe that the identification of the distribution and evolution modes of ARGs further elucidates the ecological role and facilitates the development of BAs, which will attract general interest in this field.

Fungi and bacteria coexist assembling complex communities in plant rhizosphere and endosphere that are important for plant health and agricultural productivity, however, the influence of root rot pathogen on bacterial-fungal interactions in plant ecological settings remains unclear. Here, bacterial communities from soil to endophyte of tobacco during Fusarium root rot invasion were comprehensively investigated. The bacterial community diversity and composition of stem endophytes were significantly altered by Fusarium root rot invasion. Molecular ecological network analysis revealed that the interactions among bacterial microbes in infected plant soils exhibit more intricate network structures compared to those found in healthy plants. The pathogens invasion led to changes in the crucial species within both the rhizosphere soil and plant endophytic bacterial communities. Furthermore, the interactions among fungal and bacterial species indicated that diseased samples, encompassing both the rhizosphere and endosphere, exhibited more complicated interdomain networks compared to their healthy counterparts. Importantly, the endophytic bacterial species Bacillus, Paenibacillus, Lactococcus, and two unclassified bacteria (OTU11999 and OTU730) from infected roots, and Bacillus, Raoultella, Leminorella, Pseudomonas, and three unclassified bacteria (OTU12058, OTU3 and OTU11435) from infected stems were negatively correlated with the pathogen Fusarium oxysporum f sp. psidii. It suggested that these endophytic bacteria may be associated with anantagonist effect and resistant against Fusarium root rot.

Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen’s occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.

BackgroundTobacco mosaic virus (TMV) is one famous plant virus responsible for substantial economic losses worldwide. However, the roles of bacterial communities in response to TMV in the tobacco rhizosphere remain unclear.MethodsWe explored the soil physicochemical properties and bacterial community succession of the healthy (YTH) and diseased (YTD) plants with TMV infection by 16S rRNA gene sequencing and bioinformatics analysis.ResultsWe found that soil pH in the YTD group was significantly lower than in the YTH group, and the soil available nutrients were substantially higher. The bacterial community analysis found that the diversity and structure significantly differed post-TMV disease onset. With TMV inoculated, the alpha diversity of the bacterial community in the YTD was markedly higher than that in the YTH group at the early stage. However, the alpha diversity in the YTD group subsequently decreased to lower than in the YTH group. The early bacterial structure of healthy plants exhibited higher susceptibility to TMV infection, whereas, in the subsequent stages, there was an enrichment of beneficial bacterial (e.g., Ramlibacter, Sphingomonas, Streptomyces, and Niastella) and enhanced energy metabolism and nucleotide metabolism in bacteria.ConclusionThe initial soil bacterial community exhibited susceptibility to TMV infection, which might contribute to strengthening resistance of Tobacco to TMV.