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Background: Tobacco 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., Methods: We 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., Results: We 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., Conclusion: The initial soil bacterial community exhibited susceptibility to TMV infection, which might contribute to strengthening resistance of Tobacco to TMV., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Zhao, Liu, Wu, Zhang, Xiao, Ren, Li, Liu, Xiao and Tang.)

Understanding the signaling pathways activated in response to these combined stresses and their crosstalk is crucial to breeding crop varieties with dual or multiple tolerances. However, most studies to date have predominantly focused on individual stress factors, leaving a significant gap in understanding plant responses to combined biotic and abiotic stresses. The bHLH family plays a multifaceted regulatory role in plant response to both abiotic and biotic stresses. In order to comprehensively identify and analyze the bHLH gene family in rice, we identified putative OsbHLHs by multi-step homolog search, and phylogenic analysis, molecular weights, isoelectric points, conserved domain screening were processed using MEGAX version 10.2.6. Following, integrative transcriptome analysis using 6 RNA-seq data including Xoo infection, heat, and cold stress was processed. The results showed that 106 OsbHLHs were identified and clustered into 17 clades. Os04g0301500 and Os04g0489600 are potential negative regulators of Xoo resistance in rice. In addition, Os04g0301500 was involved in non-freezing temperatures (around 4°C) but not to 10°C cold stresses, suggesting a complex interplay with temperature signaling pathways. The study concludes that Os04g0301500 may play a crucial role in integrating biotic and abiotic stress responses in rice, potentially serving as a key regulator of plant resilience under changing environmental conditions, which could be important for further multiple stresses enhancement and molecular breeding through genetic engineering in rice., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Zhang, Teng, Yuan, Sheng, Xiao, Deng, Tang and Wang.)

Background: Tobacco bacterial wilt (TBW) and black shank (TBS) are responsible for substantial economic losses worldwide; however, microbial interactions and metabolisms in response to TBW and TBS pathogens in the tobacco rhizosphere remain unclear., Methods: We explored and compared the response of rhizosphere microbial communities to these two plant diseases with the incidences in moderate and heavy degrees by sequencing of 16S rRNA gene amplicons and bioinformatics analysis., Results and Discussions: We found that the structure of rhizosphere soil bacterial communities was significantly ( p < 0.05) changed from the incidences of TBW and TBS, which also led to decreased Shannon diversity and Pielou evenness. Compared with the healthy group (CK), the OTUs with significantly ( p < 0.05) decreased relative abundances were mostly affiliated with Actinobacteria (e.g., Streptomyces and Arthrobacter ) in the diseased groups, and the OTUs with significantly ( p < 0.05) increased relative abundances were mainly identified as Proteobacteria and Acidobacteria. Also, molecular ecological network analysis showed that the nodes (<467) and links (<641) were decreased in the diseased groups compared with the control group (572; 1056), suggesting that both TBW and TBS weakened bacterial interactions. In addition, the predictive functional analysis indicated that the relative abundance of genes related to the biosynthesis of antibiotics (e.g., ansamycins and streptomycin) was significantly ( p < 0.05) decreased due to incidences of TBW and TBS, and antimicrobial tests showed that some Actinobacteria strains (e.g., Streptomyces ) and their secreted antibiotics (e.g., streptomycin) could effectively inhibit the growth of these two pathogens., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Tang, Liu, Teng, Xiao, Cai, Wang, Xiao and Chen.)

Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica . In this study, we investigated the transcriptome information of IR64 ( indica , IR) and Koshihikari ( japonica , Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Wang, Wang, Chen, Dong, Zhang, Deng, Liu, Lu, Wang, Chen, Xiao and Tang.)

Heavy metals (HMs) contamination and vegetation destruction in the mining area caused by mining activities are severely increasing. It is urgent to restore vegetation and stabilize HMs. In this study, we compared the ability of HMs phytoextraction/phytostabilization of three dominant plants, including Artemisia argyi (LA) , Miscanthus floridulus (LM), and Boehmeria nivea (LZ) in a lead-zinc mining area in Huayuan County (China). We also explored the role of the rhizosphere bacterial community in assisting phytoremediation using 16S rRNA sequencing technology. Bioconcentration factor (BCF) and translocation factor (TF) analysis showed that LA preferred accumulating Cd, LZ preferred accumulating Cr and Sb, and LM preferred accumulating Cr and Ni. Significant ( p < 0.05) differences were found among the rhizosphere soil microbial communities of these three plants. The key genera of LA were Truepera and Anderseniella , that of LM were Paracoccus and Erythrobacter , and of LZ was Novosphingobium . Correlation analysis showed some rhizosphere bacterial taxa (e.g., Actinomarinicola , Bacillariophyta and Oscillochloris ) affected some soil physicochemical parameters (e.g., organic matter and pH) of the rhizosphere soil and enhanced the TF of metals. Functional prediction analysis of soil bacterial community showed that the relative abundances of genes related to the synthesis of some proteins (e.g., manganese/zinc-transporting P-type ATPase C, nickel transport protein and 1-aminocyclopropane-1-carboxylate deaminase) was positively correlated with the phytoextraction/phytostabilization capacity of plants for heavy metals. This study provided theoretical guidance on selecting appropriate plants for different metal remediation applications. We also found some rhizosphere bacteria might enhance the phytoremediation of multi-metals, which could provide a reference for subsequent research., Competing Interests: The authors declare that this study received funding from Science and Technology of Hunan Branch of China National Tobacco Corporation. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication., (Copyright © 2023 Xiao, Chen, Li, Ma, Chen, Yang, Liu, Liu and Fang.)

High temperature is one of the main constraints affecting plant growth and development. It has been reported that abscisic acid (ABA) synthesis gene 9-cis-epoxycarotenoid dioxygenase ( NCED ) positively regulates plant resistance to salt, cold, and drought stresses. However, little is known about the function of the NCED gene in heat tolerance of rice. Here, we found that OsNCED1 was a heat stress inducible gene. Rice seedlings overexpressing OsNCED1 showed enhanced heat tolerance with more abundant ABA content, whereas the knockout mutant osnced1 accumulated less ABA and showed more sensitive to heat stress. Under heat stress, increased expression of OsNCED1 could reduce membrane damage and reactive oxygen species (ROS) level of plants, and elevate the activity of antioxidant enzymes. Moreover, real time-quantitative PCR (RT-qPCR) analysis showed that overexpression of OsNCED1 significantly activated the expression of genes involved in antioxidant enzymes, ABA signaling pathway, heat response, and defense. Together, our results indicate that OsNCED1 positively regulates heat tolerance of rice seedling by raising endogenous ABA contents, which leads to the improved antioxidant capacity and activated expression of heat and ABA related genes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Liu, Su, Xiao, Deng, Lu, Wang, Chen, Tang and Zhang.)

Plant cell wall is a complex and changeable structure, which is very important for plant growth and development. It is clear that cell wall polysaccharide synthases have critical functions in rice growth and abiotic stress, yet their role in plant response to pathogen invasion is poorly understood. Here, we describe a dwarf and narrowed leaf in Hejiang 19 ( dnl19 ) mutant in rice, which shows multiple growth defects such as reduced plant height, enlarged lamina joint angle, curled leaf morphology, and a decrease in panicle length and seed setting. MutMap analysis, genetic complementation and gene knockout mutant show that cellulose synthase-like D4 ( OsCSLD4 ) is the causal gene for DNL19 . Loss function of OsCSLD4 leads to a constitutive activation of defense response in rice. After inoculation with rice blast and bacterial blight, dnl19 displays an enhanced disease resistance. Widely targeted metabolomics analysis reveals that disruption of OsCSLD4 in dnl19 resulted in significant increase of L-valine, L-asparagine, L-histidine, L-alanine, gentisic acid, but significant decrease of L-aspartic acid, malic acid, 6-phosphogluconic acid, glucose 6-phosphate, galactose 1-phosphate, gluconic acid, D-aspartic acid. Collectively, our data reveals the importance of OsCSLD4 in balancing the trade-off between rice growth and defense., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Liu, Yin, Wang, Cao, Yao, Liu, Lu, Wang, Zhang, Xiao, Tang and Deng.)

Cadmium (Cd) speciation ratio in arable land determines the Cd exposure risk and Cd uptake in crops. However, the driving mechanisms of Cd speciation change on the vertical scale of paddy fields remain poorly understood. In this study, the effects of plow layer and plow pan on Cd speciation distribution were investigated in a long-term Cd-contaminated rice ecosystem. The Cd accumulative effect within rice grain was enhanced with high levels of activated Cd speciation ratios in soils. Activated Cd speciation ratios were higher in plow layer soils, while stabilized Cd speciation ratios were elevated in plow pan soils. Soil physicochemical properties and soil microbes synergistically affected the Cd speciation changes in different ways between the two soil layers. Soil pH and organic elements in plow layer environment directly hindered the transformation of stabilized Cd speciation, while in plow pan environment, soil pH and organic elements indirectly decreased activated Cd speciation ratios and resulted in the accumulation of stabilized Cd speciation via regulating the predominant bacterial taxa. This study will improve our understanding of how soil environments regulate Cd speciation distributions in rice ecosystems and help to seek effective remediation methods of Cd-contaminated paddy fields to reduce the Cd accumulation in rice., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Hao, Bai, Liu, Zhu, Liu, Xiao, Geng, Liu, Huang and Jiang.)

Cytokinins (CKs) are a class of phytohormones playing essential roles in various biological processes. However, the mechanisms underlying CK transport as well as its function in plant growth and development are far from being fully elucidated. Here, we characterize the function of PURINE PERMEASE1 (OsPUP1) in rice ( Oryza sativa L.). OsPUP1 was predominantly expressed in the root, particularly in vascular cells, and CK treatment can induce its expression. Subcellular localization analysis showed that OsPUP1 was predominantly localized to the endoplasmic reticulum (ER). Overexpression of OsPUP1 resulted in growth defect of various aerial tissues, including decreased leaf length, plant height, grain weight, panicle length, and grain number. Hormone profiling revealed that the CK content was decreased in the shoot of OsPUP1 -overexpressing seedling, but increased in the root, compared with the wild type. The CK content in the panicle was also decreased. Quantitative reverse transcription-PCR (qRT-PCR) analysis using several CK type-A response regulators ( OsRRs ) as the marker genes suggested that the CK response in the shoot of OsPUP1 -overexpressing seedling is decreased compared to the wild type when CKs are applied to the root. Genetic analysis revealed that BG3/OsPUP4, a putative plasma membrane-localized CK transporter, overcomes the function of OsPUP1. We hypothesize that OsPUP1 might be involved in importing CKs into ER to unload CKs from the vascular tissues by cell-to-cell transport., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Xiao, Zhang, Yu, Lu, Mei, Deng, Zhang, Chen, Chu, Tong and Tang.)

Background: Black shank, caused by the oomycete pathogen Phytophthora nicotianae , is responsible for huge economic losses worldwide. Research has focused on biocontrol to prevent disease and to minimize the use of synthetic fungicides., Methods: We explored and compared the efficacy of suppressive microflora cultured from soil and roots on the growth of P. nicotianae for controlling the incidence of black shank., Results: We found that 31 microfloral communities, enriched from 40 root samples but only 18 microfloral communities from soil samples, were antagonistic to P. nicotianae. In the field experiment, the root functional microflora (RFM) showed a greater suppressiveness of black shank than the soil functional microflora (SFM), while both RFM and SFM altered diversity, composition, structure, and interaction of soil bacterial communities during plant growth. Although the inoculation of RFM onto roots significantly ( p < 0.05) decreased microbial diversity, molecular ecological network analysis indicated more possible interactions among soil microbes, while an opposite trend was observed with SFM inoculation. Linear regression analysis revealed that diversity indices were negatively correlated with suppression on the black shank, suggesting that specific taxa (e.g., OTU&#95;322 and OTU&#95;6478) could colonize and be active during plant growth at the expense of microbial diversity. In addition, 18 functional strains, isolated and screened from 3 RMF (12 strains) and 3 SMF (6 strains), were identified as bacterial genera Acinetobacter (12), Enterobacter (1), Bacillus (1), Stenotrophomonas (2), and Citrobacter (2). Spearman's ranked correlation tests revealed that relative abundances of some OTUs affiliated with genera Acinetobacter , Enterobacter , and Bacillus were significantly ( p < 0.05) and positively correlated with the level of disease suppression., Conclusion: Microfloral communities or key functional species isolated from plant roots might be more effective in controlling black shank than those from soil, and they may be developed for disease control., (Copyright © 2020 Liu, Xiao, Yin, Yi, Zhou, Hsiang, Tang and Chen.)

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into 'healthy' and 'infected' samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health.

Brassinosteroids (BRs) regulate important agronomic traits in rice, including plant height, leaf angle, and grain size. However, the underlying mechanisms remain not fully understood. We previously showed that GSK2, the central negative regulator of BR signaling, targets DLT, the GRAS family protein, to regulate BR responses. Here, we identified Ovate Family Protein 1 (OFP1) as a DLT interacting protein. OFP1 was ubiquitously expressed and the protein was localized in both cytoplasm and nucleus. Overexpression of OFP1 led to enlarged leaf angles, reduced plant height, and altered grain shape, largely resembled DLT overexpression plants. Genetic analysis showed that the regulation of plant architecture by OFP1 depends on DLT function. In addition, we found OFP1 was greatly induced by BR treatment, and OsBZR1, the critical transcription factor of BR signaling, was physically associated with the OFP1 promoter. Moreover, we showed that gibberellin synthesis was greatly repressed in OFP1 overexpression plants, suggesting OFP1 participates in the inhibition of plant growth by high BR or elevated BR signaling. Furthermore, we revealed that OFP1 directly interacts with GSK2 kinase, and inhibition of the kinase activity significantly promotes OFP1 protein accumulation in plant. Taken together, we identified OFP1 as an additional regulator of BR responses and revealed how BRs promote OFP1 at both transcription and protein levels to modulate plant architecture and grain morphology in rice.

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members ( Acidithiobacillus caldus, Leptospirillum ferriphilum , and Sulfobacillus thermosulfidooxidans ) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.