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To investigate the community structure and macromolecular substances degradation function of surface microorganisms on different aged cigarette raw materials, the structures of microorganism communities in the samples of flue-cured tobacco stems and strips and oriental tobacco aged for two years were analyzed using metagenomic sequencing technology, and the correlation analysis between the contents of pectin, cellulose, starch, protein and lignin and the community composition of surface microorganisms of the samples were carry out. The results showed that among the three types of aged samples, the contents of starch and protein in aged flue-cured tobacco stems and those of pectin, cellulose, and lignin in aged flue-cured tobacco strips were the lowest. The dominant bacteria in aged flue-cured tobacco stems were Pantoea, Acinetobacter, Klebsiella, and Pseudomonas, those in aged oriental tobacco were Pantoea, Pseudomonas, and Acinetobacter, and those in aged flue-cured tobacco strips were Pantoea, Bacillus, and Terribacillus. Sphingomonas had more genes involved in starch degradation, and its relative abundance was negatively correlated with the starch content in the aged samples. Sphingomonas, Stenotrophomonas, and Klebsiella had more genes involved in protein degradation, and their relative abundances were negatively correlated with the protein content in the aged samples. Bacillus had more genes involved in pectin degradation, and its relative abundance was negatively correlated with the pectin content in the aged samples. [ABSTRACT FROM AUTHOR]

Carbon nanosol (CNS) is a carbon-based nanomaterial that promotes plant growth; however, its functional mechanisms and effects on the microbiome are not fully understood. Here, we explored the effects of CNS on the relationship between the soil, endophytic microbiomes and plant productivity. CNS treatment increased the fresh biomass of tobacco (Nicotiana tabacum L.) plants by 27.4% ± 9.9%. Amplicon sequencing analysis showed that the CNS treatment significantly affected the composition and diversity of the microbial communities in multiple ecological niches associated with tobacco, especially the bulk soil and stem endophytic microbiome. Furthermore, the application of CNS resulted in enhanced network connectivity and stability of the microbial communities in different niches, particularly in the soil, implying a strengthening of certain microbial interactions. Certain potentially growth-promoting root endophytic bacteria were more abundant under the CNS treatment. In addition, CNS increased the abundance of some endophytic microbial functional genes known to enhance plant growth, such as those associated with nutrient metabolism and the plant hormone biosynthesis pathways. We isolated two bacterial strains (Sphingopyxis sp. and Novosphingobium sp.) that were enriched under CNS treatment, and they were confirmed to promote tobacco plant growth in vitro. These results suggested that CNS might, at least in part, promote plant growth by enriching beneficial bacteria in the microbiome. [ABSTRACT FROM AUTHOR]

Summary: Alicyclobacillus species inhabit diverse environments and have adapted to broad ranges of pH and temperature. However, their adaptive evolutions remain elusive, especially regarding the role of mobile genetic elements (MGEs). Here, we characterized the distributions and functions of MGEs in Alicyclobacillus species across five environments, including acid mine drainage (AMD), beverages, hot springs, sediments, and soils. Nine Alicyclobacillus strains were isolated from AMD and possessed larger genome sizes and more genes than those from other environments. Four AMD strains evolved to be mixotrophic and fell into distinctive clusters in phylogenetic tree. Four types of MGEs including genomic island (GI), insertion sequence (IS), prophage, and integrative and conjugative element (ICE) were widely distributed in Alicyclobacillus species. Further, AMD strains did not possess CRISPR‐Cas systems, but had more GI, IS, and ICE, as well as more MGE‐associated genes involved in the oxidation of iron and sulfide and the resistance of heavy metal and low temperature. These findings highlight the differences in phenotypes and genotypes between strains isolated from AMD and other environments and the important role of MGEs in rapid environment niche expansions. [ABSTRACT FROM AUTHOR]

Bacterial wilt, caused by Ralstonia solanacearum, occurs occasionally during tobacco planting and potentially brings huge economic losses in affected areas. Soil microbes in different management stages play important roles in influencing bacterial wilt incidence. Studies have focused on the impacts of species diversity and composition during cropping periods on disease morbidity; however, the effects of the soil bacterial biomass, species diversity, species succession, and population interactions on morbidity remain unclear during non-cropping periods. In this study, we explored the soil bacterial communities in the non-cropping winter fallow (WF) and cropping late growing (LG) periods under consecutive monoculture systems using 16S ribosomal RNA gene sequencing and qPCR and further analyzed their effects on tobacco bacterial wilt incidence. We found that the bacterial communities in the WF period were significantly different from those in the LG period based on detrended correspondence analysis and dissimilarity tests. Crop morbidity was significantly related to bacterial community structure and to the presence of some genera during WF and LG periods. These genera, such as Arthrobacter, Pseudomonas, Acidobacteria GP6, and Pasteuria, may be potential biological control agents for bacterial wilt. Further analysis indicated that low soil bacterial diversity during the WF period, decrease of bacterial interactions from the WF to LG periods, and low soil biomass during the LG period all have the potential to increase morbidity. In conclusion, an increase of soil bacterial diversity and control of some bacterial abundances in the WF period might be an effective approach in controlling bacterial wilt incidence. [ABSTRACT FROM AUTHOR]

Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China. Genomic analysis revealed that strain has a gene repertoire for metal-resistance, e.g., genes coding for the mer operon and a variety of transporters/efflux proteins, and for low pH adaptation, such as genes for hopanoid-synthesis and the sodium:proton antiporter. Genes for various DNA repair enzymes and synthesis of UV-absorbing mycosporine-like amino acids precursor indicated hypothetical UV radiation—resistance mechanisms in strain YL15. In addition, it has two types of the acquired immune system–type III-B and type I-F CRISPR/Cas modules against invasion of foreign genetic elements. RNA-seq based analysis uncovered that strain YL15 uses a set of mechanisms to adapt to low temperature. Genes involved in protein synthesis, transmembrane transport, energy metabolism and chemotaxis showed increased levels of RNA transcripts. Furthermore, a bacterioferritin Dps gene had higher RNA transcript counts at 6°C, possibly implicated in protecting DNA against oxidative stress at low temperature. The study represents the first to comprehensively unveil the adaptation mechanisms of an acidophilic bacterium to the acid mine drainage in alpine regions. [ABSTRACT FROM AUTHOR]

Microbial degradation of organic compounds is an environmentally benign and energy efficient part in product processing. Fermentation of plant leaves involves enzymatic actions of many microorganisms. However, microbes and enzymes discovered from natural degradation communities were still limited by cultural methods. In this study, we used a metagenomics sequence-guided strategy to identify the microbes and enzymes involved in compound degradation and explore the potential synergy among community members in fermented tobacco leaves. The results showed that contents of protein, starch, pectin, lignin, and cellulose varied in fermented leaves from different growing sites. The different compound contents were closely related to taxonomic composition and functional profiles of foliar microbial communities. Microbial communities showed significant correlations with protein, lignin, and cellulose. Vital species for degradations of protein (Bacillus cereus and Terribacillus aidingensis), lignin (Klebsiella pneumoniae and Pantoea ananatis) and cellulose (Pseudomonas putida and Sphingomonas sp. Leaf20) were identified and relating hydrolytic enzymes were annotated. Further, twenty-two metagenome-assembled genomes (MAGs) were assembled from metagenomes and six potential cellulolytic genomes were used to reconstruct the cellulose-degrading process, revealing the potential metabolic cooperation related to cellulose degradation. Our work should deepen the understanding of microbial roles in plant fermentation and provide a new viewpoint for applying microbial consortia to convert plant organic components to small molecules. • Metagenome of fermented leaves microbial communities was sequenced. • Compound degradation potential of microbial communities were revealed. • Vital species involving in compound degradation were identified and verified. • High-quality MAGs were obtained to reconstruct the cellulose-degrading process. • Microbial cellulolytic cooperation was uncovered from a genomic perspective. [ABSTRACT FROM AUTHOR]

Bioleaching has been widely applied to recover sulfide minerals, however, little is known about the bioleaching behavior and mechanism of mixed oxide-sulfide copper ore with high-oxidative ratio. The leaching efficiency of artificial indigenous and exogenous microbial communities on a mixed oxide-sulfide copper ore with and without energy substrate was investigated. The results indicated that extra energy substrate was needed when bioleaching was applied to this kind of ore. The variation of leaching parameters caused by indigenous community was inferior to that caused by exogenous ones due to its lower activity. The leaching efficiency of sulfide part induced by indigenous strains was superior to that induced by exogenous ones, due to the stronger colonization ability of indigenous strains. It verified that both microbial activity and colonization ability were important properties affecting leaching efficiency. Sulfur oxidizers, which can oxidize sulfur or polysulfide formed on mineral surface and decrease leachate pH, played a more important role than ferrous oxidizers in bioleaching of high-oxidative oxide-sulfide ore. [ABSTRACT FROM AUTHOR]

Growth of multicellular organisms relies on diversity in gene expression between cells of different functions. Single-cell transcriptomes can facilitate analysis of cell specific response to different environmental stress. By performing single-nucleus sequencing of tobacco (Nicotiana tabacum) seedlings, 13,028 single cells were profiled. We identified 29 clusters corresponding to 18 cell types, some of which were verified by in situ hybridization. Developmental trajectory results and comparisons of ligand-receptor repertoires revealed cell specific functions of different cell types in tobacco seedlings. Divergent and conserved genes between tobacco and rice (Oryza sativa) highlighted some cell specific and species specific gene features. Our study generated the first single-cell transcriptome atlas of tobacco seedling, providing a wide range of information into the role and functions of different cell types. • It was first singe-cell atlas of tobacco seedling, including 13,028 cells. • 29 clusters corresponding to 18 cell types were identified. • Cell-specific functions for different cell types were revealed. • Some species-cell specific features were identified by conservation analysis. [ABSTRACT FROM AUTHOR]