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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]

Microbes play a critical role in soil global biogeochemical circulation and microbe-microbe interactions have also evoked enormous interests in recent years. Utilization of green manures can stimulate microbial activity and affect microbial composition and diversity. However, few studies focus on the microbial interactions or detect the key functional members in communities. With the advances of metagenomic technologies, network analysis has been used as a powerful tool to detect robust interactions between microbial members. Here, random matrix theory-based network analysis was used to investigate the microbial networks in response to four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) over two growth cycles from October 2012 to September 2014. The results showed that the topological properties of microbial networks were dramatically altered by green manure fertilization. Microbial network under milk vetch amendment showed substantially more intense complexity and interactions than other fertilization systems, indicating that milk vetch provided a favorable condition for microbial interactions and niche sharing. The shift of microbial interactions could be attributed to the changes in some major soil traits and the interactions might be correlated to plant growth and production. With the stimuli of green manures, positive interactions predominated the network eventually and the network complexity was in consistency with maize productivity, which suggested that the complex soil microbial networks might benefit to plants rather than simple ones, because complex networks would hold strong the ability to cope with environment changes or suppress soil-borne pathogen infection on plants. In addition, network analyses discerned some putative keystone taxa and seven of them had directly positive interactions with maize yield, which suggested their important roles in maintaining environmental functions and in improving plant growth. [ABSTRACT FROM AUTHOR]

The use of green manures in agriculture can provide nutrients, affect soil microbial communities, and be a more sustainable management practice. The activities of soil microbes can effect crop growth, but the extent of this effect on yield remains unclear. We investigated soil bacterial communities and soil properties under four different green manure fertilization regimes ( Vicia villosa, common vetch, milk vetch, and radish) and determined the effects of these regimes on maize growth. Milk vetch showed the greatest potential for improving crop productivity and increased maize yield by 31.3 %. This change might be related to changes in soil microbes and soil properties. The entire soil bacterial community and physicochemical properties differed significantly among treatments, and there were significant correlations between soil bacteria, soil properties, and maize yield. In particular, abundance of the phyla Acidobacteria and Verrucomicrobia was positively correlated with maize yield, while Proteobacteria and Chloroflexi were negatively correlated with yield. These data suggest that the variation of maize yield was related to differences in soil bacteria. The results also indicate that soil pH, alkali solution nitrogen, and available potassium were the key environmental factors shaping soil bacterial communities and determining maize yields. Both soil properties and soil microbes might be useful as indicators of soil quality and potential crop yield. [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]

Plant leaves are colonized by a remarkably diverse fungal microbiome, which contributes to host plant growth and health. However, responses of foliar fungal community to phytopathogen invasion and measures of the fungal community taken to resist or assist pathogens remain elusive. By utilizing high-throughput sequencing of internal transcribed spacer (ITS) amplicons, we studied the relationships between the foliar fungal community around the disease spot and the pathogen of brown spot disease. The pathogenic Alternaria was found to follow a dramatically decreased trend from the disease spot to its surrounding fungal communities, whose community structure also diverged substantially away from the disease spot community. With the increase of pathogenic Alternaria , diversity indexes, including Shannon, Pielou and Simpson, showed a trend of increasing first and then decreasing. Total network links and the average path distance exhibited strong negative and positive correlations with Alternaria , respectively. Five keystone members showed direct interactions with pathogenic Alternaria. Members of Botryosphaeria , Paraphoma and Plectosphaerella might act as key 'pathogen facilitators' to increase the severity and development of brown spot disease, while Pleospora and Ochrocladosporium might be important 'pathogen antagonists' to suppress the expansion of pathogenic Alternaria. Our study provides new insights in developing new strategies for leaf disease prediction or prevention. • The fungal diversity increased firstly and decreased then with Alternaria invasion. • Network characteristics of fungal community were correlated with Alternaria. • Botryosphaeria , Paraphoma and Plectosphaerella may be key 'pathogen facilitators'. • Pleospora and Ochrocladosporium might be vital in suppressing brown spot disease. [ABSTRACT FROM AUTHOR]

• Effects of microbial types and diversity on chalcopyrite bioleaching were studied. • Community with more sulfur oxidizers and high diversity showed high Cu recovery. • Microbial types showed greater influences on mineral dissolution than biodiversity. • A. caldus enhanced CuFeS 2 extraction greatly by regulating physicochemical factors. Six artificial communities with different function or biodiversity were reconstructed by six typical bioleaching species for chalcopyrite leaching. Absence of sulfur oxidizers in communities significantly reduced copper extraction rates, and low diversity communities also exhibited slightly poor bioleaching performances. The variations of pH, redox potential, ferrous and copper ions indicated that the community with both sulfur oxidizers and high diversity showed fast adaptation to the environment and rapid dissolution of chalcopyrite. Integrated analysis of mineralogical and microbial parameters demonstrated that functional types of microorganisms made more contributions in mediating chalcopyrite dissolution than microbial diversity. Further correlation analysis between microbial types and chalcopyrite dissolution performances showed that sulfur oxidizers, especially Acidithiobacillus caldus , could greatly accelerate chalcopyrite dissolution by regulating solution physicochemical factors, such as redox potential and pH. This study provided a theoretical basis for improving bioleaching efficiency by balancing microbial functional types and biodiversity. [ABSTRACT FROM AUTHOR]

The phyllosphere supports a tremendous diversity of microbes, which have the potential to influence plant biogeography and ecosystem function. Although biocontrol agents (BCAs) have been used extensively for controlling plant diseases, the ecological effects of BCAs on phyllosphere bacteria and the relationships between phyllosphere community and plant health are poorly understood. In this study, we explored the control efficiency of two BCA communities on bacterial wildfire disease by repeatedly spraying BCAs on tobacco leaves. The results of field tests showed that BCAs used in our study, especially BCA_B, had remarkable control effects against tobacco wildfire disease. The higher control efficiency of BCA_B might be attributed to a highly diverse and complex community in the phyllosphere. By 16S ribosomal RNA gene sequencing, we found that phyllosphere microbial community, including community diversity, taxonomic composition and microbial interactions, changed significantly by application of BCAs. According to the correlation analysis, it showed that wildfire disease infection of plants was negatively related to phyllosphere microbial diversity, indicating a highly diverse community in the phyllosphere might prevent pathogens invasion and colonization. In addition, we inferred that a more complex network in the phyllosphere might be beneficial for decreasing the chances of bacterial wildfire outbreak, and the genera of Pantoea and Sphingomonas might play important roles in wildfire disease suppression. These correlations between phyllosphere community and plant health will improve our understanding on the ecological function of phyllosphere community on plants. [ABSTRACT FROM AUTHOR]

Background: WD40 proteins, which are highly prevalent in eukaryotes, play important roles in plant development and stress responses. However, systematic identification and exploration of WD40 proteins in tobacco have not yet been conducted. Results: In this study, a total of 399 WD40 regulatory genes were identified in common tobacco (Nicotiana tabacum). Gene structure and motif analysis revealed structural and functional diversity among different clades of tobacco WD40 regulatory genes. The expansion of tobacco WD40 regulatory genes was mainly driven by segmental duplication and purifying selection. A potential regulatory network of NtWD40s suggested that NtWD40s might be regulated by miRNAs and transcription factors in various biological processes. Expression pattern analysis via transcriptome analysis and qRT-PCR revealed that many NtWD40s exhibited tissue-specific expression patterns and might be involved in various biotic and abiotic stresses. Furthermore, we have validated the critical role of NtTTG1, which was located in the nuclei of trichome cells, in enhancing the drought tolerance of tobacco plants. Conclusions: Our study provides comprehensive information to better understand the evolution of WD40 regulatory genes and their roles in different stress responses in tobacco. [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]

Toxic ions accumulation in leachate is one of the limitations for bioleaching application. The effects of fluoride ions on microbial growth relevant to bioleaching have been extensively emphasized. However, the reasons that the microorganisms present different fluoride tolerance in bioleaching of different minerals have not yet been proposed. A fundamental exploration on the differential fluoride tolerance of sulfur- and ferrous iron-grown Acidithiobacillus ferrooxidans was performed. The results showed that the critical fluoride concentration for sulfur-grown A. ferrooxidans was less than 0.1 mM whenever fluoride was introduced. The critical fluoride concentration for ferrous iron-grown A. ferrooxidans was 1.0 mM when fluoride was introduced prior to the lag phase, but it was higher than 10.0 mM when fluoride was introduced at the log phase. The ferric ions generated from ferrous oxidation could significantly decrease the concentration of HF and finally reduce the toxicity of fluoride to A. ferrooxidans . The changes of concentration of metal ions with strong complex ability to fluoride ions, resulted in an illusion of high fluorine-resistant strain in industrial bioleaching heap. Finally, the feasibility of fluoride removal by ferric ion was put forward. This work has meaningful implications for the industrial bioleaching of high-fluorine containing uranium ore. [ABSTRACT FROM AUTHOR]

Root-knot nematode (RKN) disease is a destructive soil disease that affects crop health and causes huge losses in crop production. To explore the relationships between soil environments, rhizobacterial communities, and plant health, rhizosphere bacterial communities were analyzed using metagenomic sequencing in tobacco samples with different grades of RKN disease. The results showed that the community structure and function of the plant rhizosphere were significantly correlated to the RKN disease. RKN density and urease content were key factors affecting the rhizosphere bacterial community. Urease accelerated the catabolism of urea and led to the production of high concentrations of ammonia, which directly suppressed the development of RKNs or by improving the nutritional and growth status of microorganisms that were antagonistic to RKNs. Further experiments showed that the suppression role of ammonia should be attributed to the direct inhibition of NH 3. The bacterial members that were positively correlated with RKN density, contained many plant cell wall degrading enzymes, which might destroy plant cell walls and promote the colonization of RKN in tobacco roots. The analysis of metatranscriptome and metabolism demonstrated the role of these cell wall degrading enzymes. This study offers a comprehensive insight into the relationships between RKNs, bacteria, and soil environmental factors and provides new ideas for the biological control of RKNs. • RKN density and urease content were key factors affecting the rhizosphere community. • Some functional gene categories had strong relationships with the infection of RKN. • Urease might have significant impacts on RKN disease. • Bacteria with cell wall degrading enzymes might promote the colonization of RKNs. [ABSTRACT FROM AUTHOR]

Carbon nanosol (CNS) is a carbon-based nanomaterial capable of promoting plant growth while the underlying mechanism involved in this process remains unknown. This study demonstrates that CNS promotes rice seedling growth under restricted concentrations. Macroelement transporter mutants were investigated to further investigate the CNS-mediated promotion of rice seedling growth. The genetic and physiological findings revealed that nitrate transporter 1.1B (NRT1.1B) and ammonium transporter 1 (AMT1) mutants inhibited the CNS-induced growth development of rice seedlings, whereas potassium transporter (AKT1) and phosphate transporter 8 (PT8) did not exhibit any inhibitory effects. Further investigations demonstrated the inhibition of CNS-mediated growth promotion via glutamine synthetase 1;1 (gs1;1) mutants. Additionally, the administration of CNS resulted in enhanced accumulation of chlorophyll in plants, and the promotion of CNS-induced growth was inhibited by yellow-green leaf 8 (YGL8) mutants and the chlorophyll biosynthetic gene divinyl reductase (DVR) mutants. According to these findings, the CNS promotes plant growth by stimulating chlorophyll biosynthesis. Furthermore, the presence of CNS enhanced the ability of rice to withstand blast, sheath blight (ShB), and bacterial blight. The nrt1.1b , amt1 , dvr , and ygl8 mutants did not exhibit a broad spectrum effect. The positive regulation of broad-spectrum resistance in rice by GS1;1 suggests the requirement of N assimilation for CNS-mediated broad-spectrum resistance. In addition, an in vitro assay demonstrated that CNS inhibits the growth of pathogens responsible for blast, ShB, and bacterial blight, namely Magnaporthe oryzae , Rhizoctonia solani AG1-IA, and Xanthomonas oryzae pv. Oryzae , respectively. CNS application may also induce broad-spectrum resistance against bacterial and fungal pathogens, indicating that in addition to its antifungal and antibacterial properties, CNS application may also stimulate N assimilation. Collectively, the results indicate that CNS may be a potential nano-therapeutic agent for improved plant growth promotion while also providing broad-spectrum resistance. [Display omitted] • Carbon nanosol promote rice seedling growth under restricted concentrations. • Carbon nanosol activates chlorophyll biosynthesis to promote plant growth. • Nitrogen assimilation is required for Carbon nanosol-mediated broad-spectrum resistance. • Carbon nanosol is a potential nano-therapeutic agent for plant growth promotion and broad-spectrum resistance. [ABSTRACT FROM AUTHOR]

The root phenotypic traits have been considered as important factors in shaping the rhizosphere microbiome and regulating plant growth. However, the relationships between root phenotypic traits and the rhizosphere bacterial community remain unclear. We investigated two fields with different developing tobacco roots by a long-term positioning test in Hengshi. The well-developed root system (WDR) showed much more superiority in root phenotypic traits, including total root length, total projection area, surface area, and root tip number, than the underdeveloped root system. The specific root traits in WDR provided more ecological niches for the rhizosphere microorganisms, contributing to a more diverse microbial community and a more complex microbial network. The total root length and root tip number were the key factors shaping bacterial communities in the rhizosphere. In turn, the phyla Acidobacteria and Bacteroidetes might play vital roles in modifying root development and promoting plant growth according to their positive correlation with root phenotypic traits. Linking root phenotypic traits to the microbiome may enhance our understanding of rhizospheric interactions and their roles in developing rhizosphere ecosystems. [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]

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]

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]

Acidophilic microorganisms involved in uranium bioleaching are usually suppressed by dissolved fluoride ions, eventually leading to reduced leaching efficiency. However, little is known about the regulation mechanisms of microbial resistance to fluoride. In this study, the resistance of Acidithiobacillus ferrooxidans ATCC 23270 to fluoride was investigated by detecting bacterial growth fluctuations and ferrous or sulfur oxidation. To explore the regulation mechanism, a whole genome microarray was used to profile the genome-wide expression. The fluoride tolerance of A. ferrooxidans cultured in the presence of FeSO was better than that cultured with the S substrate. The differentially expressed gene categories closely related to fluoride tolerance included those involved in energy metabolism, cellular processes, protein synthesis, transport, the cell envelope, and binding proteins. This study highlights that the cellular ferrous oxidation ability was enhanced at the lower fluoride concentrations. An overview of the cellular regulation mechanisms of extremophiles to fluoride resistance is discussed. [ABSTRACT FROM AUTHOR]

Continuous cropping has become the most common system in intensive, modern agricultural production; however, obstacles often appear in continuous cropping patterns after a few years of use. There have been several studies about the impacts of continuous cropping on soil microbial, but few about differences between soil experiencing continuous cropping obstacles and those where such obstacles had been resisted. Here, after ten or twenty years of continuous tobacco cropping, we collected soil samples investigating discrepancies in soil property and bacterial community between soils experiencing continuous cropping obstacles and soils where the obstacles were resisted providing insight into preventing and controlling continuous cropping obstacles. Results showed that soil organic matter (SOM), available phosphorus (AP), total nitrogen (TN), nitrate-N (NO 3 −-N), and bacterial diversity of samples where continuous cropping obstacles had been resisted were significantly higher than those where continuous cropping obstacles were present. Besides, SOM, AP, TN, and Ammonium-N (NH 4 +-N) considerably affected the bacterial community. Among all variables, NH 4 +-N explained the largest proportion of bacterial community variation. Molecular ecological networks were used to putatively identify keystone taxa, including Acidobacteria Gp1 , Acidobacteria Gp2 , Acidobacteria Gp16, and WPS-1_genera_incertae_sedis. Their relative abundance significantly changed between the two conditions. Overall, our results indicate that decreases in soil nutrient content and bacterial diversity, and significant changes in some keystone taxa abundances may be important factors leading to increased soil-borne diseases and reduced tobacco production potential or quality. Thus, during agricultural production, we could regulate the stability of the soil-crop-microbial ecological system via crop rotation, intercropping, or the use of specialized bio-fertilizers and soil conditioners to mitigate continuous cropping obstacles. • The SOM, AP, TN, NO 3 −-N, and bacterial diversity of RCCO were significantly higher than CCO. • The SOM, AP, TN, and NH 4 +-N had a considerable effect on RCCO and CCO bacterial communities. • Soil NH 4 +-N explained the largest proportion of bacterial community variation. • The relative abundance of keystone taxa significantly changed between the two conditions. [ABSTRACT FROM AUTHOR]

• Typical low-grade copper ores and their corresponding pure isolates were obtained. • Cross bioleaching of low-grade copper ores was firstly conducted. • Longitudinal domestication was an effective way to improve bioleaching performance. • Population regulation was another effective way to improve bioleaching efficiency. The interaction between microorganisms and minerals was a hot topic to reveal the transformation of key elements that affecting bioleaching efficiency. Three typical low-grade copper ores, the main copper-bearing components of which were primary sulfide, secondary sulfide and high-oxidative sulfide copper, were obtained from Dexing, Zijinshan and Luanshya copper mine, respectively. Meanwhile, six typical microorganisms were isolated from each of the three habitats, and assembled as communities based on their origins. Cross bioleaching was carried out under identical conditions. The leaching parameters showed that native strains played excellent roles in their corresponding ore bioleaching process, and community structure was greatly determined by mineral composition, indicating that domestication for longitudinal adaption was an effective way to improve microbial leaching performance. Leptospirillum ferriphilum and Acidithiobacillus ferrooxidans promoted copper release by shifting redox potential and pH of the leachate, respectively, indicating that microbial population regulation was another effective way to improve bioleaching efficiency. [ABSTRACT FROM AUTHOR]