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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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Root microbiota affect the host plant's adaptation to adverse environments. The structure and function of plant root bacterial communities are affected by soil physicochemical properties and plant genotypes. Distant hybridization is a common breeding strategy to introgress the excellent genes of wild relatives into the crop genome. The effect of distant hybridization on the crop root microbiota has not been reported. In this study, the structure and function of root bacterial community of the somatic hybrid wheat introgression lines SR3 and SR4, which have been respectively reported to be tolerant to salt and saline-alkali stress, and their parent wheat cultivar JN177 as well as common wheat cultivar Chinese Spring (CS) were analyzed using 16S rRNA high-throughput sequencing technology. The results showed that distant hybridization altered the structure and function of wheat (Triticum aestivum L.) root bacterial community. Compared with the parent JN177, some bacterial genera related to plant growth and stress resistance showed higher abundance in SR3 and SR4. Intriguingly, compared with parent JN177, the root bacterial communities of SR3 and SR4 are more similar to that of CS. This indicated that the process of distant hybridization may alter key genes regulating wheat root microbiota.