Bacillus amyloliquefaciens PDR1 from root of karst adaptive plant enhances Arabidopsis thaliana resistance to alkaline stress through modulation of plasma membrane H+-ATPase activity

Li, Fēi; Shi, Tianlong; Tang, Xin; Tang, Ming; Gong, Jirui; Yi, Yin

doi:10.1016/j.plaphy.2020.08.019

Cited by 10 publications

(8 citation statements)

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“…Similarly to our findings, a large number of studies ( Qin et al, 2017 ; Wang et al, 2021 ) have shown that B. amyloliquefaciens strains are rhizosphere-promoting bacteria and that inoculation of these strains can promote plant growth, prevent soil-borne diseases and improve plant resistance to stress. As demonstrated in our previous review ( Li et al, 2019b ) and research works ( Li et al, 2019a , 2020a , b ), some of bacillus species are able to produce volatile organic compounds (VOCs) which affect the changes of metabolism in their symbiotic plants. Thus, in the present study, since the LZ04 and A. thaliana were cultivated on the medium separated by a separator, we stipulated that the mechanism of the effect of LZ04 on A. thaliana may be through the production of VOCs which may probably affect gene regulation and phenotypic changes in A. thaliana .…”

Section: Discussionmentioning

confidence: 95%

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

et al. 2021

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Several gene families involved in calcium signaling have been detected in plants, including calmodulin (CaM), calcium dependent protein kinases (CDPK), calcineurin B-like (CBL) and cyclic nucleotide-gated channels (CNGCs). In our previous study, we demonstrated that Bacillus amyloliquefaciens LZ04 (B. amyloliquefaciens LZ04) regulate genes involved in calcium stress in Arabidopsis thaliana (A. thaliana). Here, we aimed to explore the potential involvement of calcium-related gene families in the response of A. thaliana to calcium stress and the potential regulatory effects of B. amyloliquefaciens LZ04 on these genes. The structure, duplication, synteny, and expression profiles of 102 genes in calcium-related gene families in A. thaliana were investigated. Hidden Markov Models (HMMs) and BLASTP were used to predict candidate genes and conserved domains of the candidate genes were confirmed in SMART and NCBI CDD databases. Gene duplications and synteny were uncovered by BLASTP and phylogenetic analysis. The transcriptome expression profiles of candidate genes were investigated by strand-specific sequencing. Cluster analysis was used to find the expression profiles of calcium-related genes families under different treatment conditions. A total of 102 genes in calcium-related gene families were detected in A. thaliana genome, including 34 CDPK genes, 20 CNGC genes, 18 CIPK genes, 22 IQD genes, and 10 CBP genes. Additionally, of the 102 genes, 33 duplications (32.35%) and 26 gene pairs including 48 genes (47.06%) were detected. Treatment with B. amyloliquefaciens LZ04 enhanced the resistance of A. thaliana under high calcium stress by regulating some of the genes in the calcium-related gene families. Functional enrichment analysis revealed that the genes clustered in the 42nd expression profile which may be B. amyloliquefaciens-responsive genes under calcium stress were enriched in protein phosphorylation and protein modification process. Transcriptome data was validated by RT-PCR and the results generally corroborated the transcriptome sequencing results. These results may be useful for agricultural improvement in high calcium stress regions.

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Section: Discussionmentioning

confidence: 95%

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

et al. 2021

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“…For nitrogen limitation treatment, KNO3 in half-strength Hoagland’s nutrient solution was replaced by KCl for 5 days of nitrogen starvation (NS) treatment. Strain treatment was by inoculating 1 mL of B. amyloliquefaciens PDR1 bacterial suspension culture at an optical density (OD) of 0.5 OD at 600 nm near the roots of each seedling or liquid LB medium which served as a control ( Li et al., 2020 ). The treatment groups were as follows: Control (cultivation a control soil), Control+PDR1 (control soil + bacteria treatment), N limitation (cultivation on a low nitrogen soil), and N limitation + PDR1 (low nitrogen soil + bacteria treatment).…”

Section: Methodsmentioning

confidence: 99%

“…Studies indicated that PGPB could mobilize organic and mineral-bound nutrients and are essential players in nitrogen fixation in plants; nitrogen-fixing bacteria have been reported to be involved in the improvement of root growth, reduction of N losses from agricultural ecosystems and increase of plant resilience to environmental stresses in wheat ( Kant et al., 2010 ; Dal Cortivo et al., 2017 ; Di Benedetto et al., 2017 ; Maenhout et al., 2018 ; Wang et al., 2020 ). Our recent study reported that B. amyloliquefaciens PDR1 interacts with Arabidopsis thaliana and provides beneficial effects for this plant ( Li et al., 2020 ). Specifically, B. amyloliquefaciens PDR1 enhanced the resistance of A. thaliana to alkaline stress by modulating the activity of plasma membrane H+-ATPase in the roots.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of transmembrane 9 superfamily genes in wheat (Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions

Li,

Xi,

et al. 2024

Front. Plant Sci.

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IntroductionTransmembrane 9 superfamily (TM9SF) proteins play significant roles in plant physiology. However, these proteins are poorly characterized in wheat (Triticum aestivum). The present study aimed at the genome-wide analysis of putative wheat TM9SF (TraesTM9SF) proteins and their potential involvement in response to nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatments.MethodsTraesTM9SF genes were retrieved from the wheat genome, and their physiochemical properties, alignment, phylogenetic, motif structure, cis-regulatory element, synteny, protein-protein interaction (PPI), and transcription factor (TF) prediction analyses were performed. Transcriptome sequencing and quantitative real-time polymerase reaction (qRT-PCR) were performed to detect gene expression in roots under single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1.Results and discussionForty-seven TraesTM9SF genes were identified in the wheat genome, highlighting the significance of these genes in wheat. TraesTM9SF genes were absent on some wheat chromosomes and were unevenly distributed on the other chromosomes, indicating that potential regulatory functions and evolutionary events may have shaped the TraesTM9SF gene family. Fifty-four cis-regulatory elements, including light-response, hormone response, biotic/abiotic stress, and development cis-regulatory elements, were present in the TraesTM9SF promoter regions. No duplication of TraesTM9SF genes in the wheat genome was recorded, and 177 TFs were predicted to target the 47 TraesTM9SF genes in a complex regulatory network. These findings offer valued data for predicting the putative functions of uncharacterized TM9SF genes. Moreover, transcriptome analysis and validation by qRT-PCR indicated that the TraesTM9SF genes are expressed in the root system of wheat and are potentially involved in the response of this plant to single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1, suggesting their functional roles in plant growth, development, and stress responses.ConclusionThese findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.

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“…Then, the seedlings were placed in a Petri dish filled with clear water so that the roots could be fully elongated, and the number of lateral roots was counted and recorded. The root hair of A. thaliana was photographed with a Zeiss stereomicroscope (Zeiss Microscope System Standard 16; Carl Zeiss Ltd.; Wetzlar, Germany) ( Bhattacharyya et al, 2015 ; Perez-Flores et al, 2017 ; Li F. et al, 2020 ). Each treatment was composed of ten replicates, and the experiment was repeated twice.…”

Section: Methodsmentioning

confidence: 99%

Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion

et al. 2022

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Genomic information for bacteria within the genus Rahnella remains limited. Rahnella sp. JZ-GX1 was previously isolated from the Pinus massoniana rhizosphere in China and shows potential as a plant growth-promoting (PGP) bacterium. In the present work, we combined the GridION Nanopore ONT and Illumina sequencing platforms to obtain the complete genome sequence of strain JZ-GX1, and the application effects of the strain in natural field environment was assessed. The whole genome of Rahnella sp. JZ-GX1 comprised a single circular chromosome (5,472,828 bp, G + C content of 53.53%) with 4,483 protein-coding sequences, 22 rRNAs, and 77 tRNAs. Based on whole genome phylogenetic and average nucleotide identity (ANI) analysis, the JZ-GX1 strain was reidentified as R. victoriana. Genes related to indole-3-acetic acid (IAA), phosphorus solubilization, nitrogen fixation, siderophores, acetoin, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, gamma-aminobutyric acid (GABA) production, spermidine and volatile organic compounds (VOCs) biosynthesis were present in the genome of strain JZ-GX1. In addition, these functions were also confirmed by in vitro experiments. Importantly, compared to uninoculated control plants, Pyrus serotina, Malus spectabilis, Populus euramericana (Dode) Guinier cv. “San Martino” (I-72 poplar) and Pinus elliottii plants inoculated with strain JZ-GX1 showed increased heights and ground diameters. These findings improve our understanding of R. victoriana JZ-GX1 as a potential biofertilizer in agriculture.

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Bacillus amyloliquefaciens PDR1 from root of karst adaptive plant enhances Arabidopsis thaliana resistance to alkaline stress through modulation of plasma membrane H+-ATPase activity

Cited by 10 publications

References 58 publications

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

Genome-wide analysis of transmembrane 9 superfamily genes in wheat (Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions

Genome Sequencing of Rahnella victoriana JZ-GX1 Provides New Insights Into Molecular and Genetic Mechanisms of Plant Growth Promotion

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