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. 2022 Aug 3;17(8):e0272500. doi: 10.1371/journal.pone.0272500

Endophytic bacterium Bacillus aryabhattai induces novel transcriptomic changes to stimulate plant growth

Hongli Xu 1, Jingyao Gao 1, Roxana Portieles 1, Lihua Du 1, Xiangyou Gao 1, Orlando Borras-Hidalgo 1,2,*
Editor: Ching-Hong Yang3
PMCID: PMC9348713  PMID: 35921359

Abstract

In nature, plants interact with a wide range of microorganisms, and most of these microorganisms could induce growth through the activation of important molecular pathways. The current study evaluated whether the endophytic bacterium Bacillus aryabhattai encourages plant growth and the transcriptional changes that might be implicated in this effect. The endophytic bacterium promotes the growth of Arabidopsis and tobacco plants. The transcriptional changes in Arabidopsis plants treated with the bacterium were also identified, and the results showed that various genes, such as cinnamyl alcohol dehydrogenase, apyrase, thioredoxin H8, benzaldehyde dehydrogenase, indoleacetaldoxime dehydratase, berberine bridge enzyme-like and gibberellin-regulated protein, were highly expressed. Also, endophytic bacterial genes, such as arginine decarboxylase, D-hydantoinase, ATP synthase gamma chain and 2-hydroxyhexa-2,4-dienoate hydratase, were activated during the interaction. These findings demonstrate that the expression of novel plant growth-related genes is induced by interaction with the endophytic bacterium B. aryabhattai and that these changes may promote plant growth in sustainable agriculture.

Introduction

Plant performance is influenced by the environment and genetic features [1, 2]. Plants are constantly under high pressure from a variety of microbes in their natural environment. Microorganisms and plants establish interesting relationships that are useful for both partners. The cohabitation of microorganisms in a plant exerts an effect on the growth performance of the plant. These interactions effectively enhance the agricultural properties and yields of plants as well as the quality of the soil and nutrient cycling [3–5]. In addition, the extensive application of chemical fertilizer has a negative effect on soil quality and the environment [6]. These negative impacts could be reduced through improved farming practices involving microbial inoculations such as biofertilizers. Bacterial endophytes are used as biofertilizers to enhance crop production and significantly reduce the impact of chemicals in the environment [7–9]. Beneficial microorganisms are also used to improve plant yields and constitute sustainable alternatives to chemical fertilizers [10].

Bacillus species comprise the largest class of plant growth-promoting bacteria [11–13]. Bacillus genus members could survive in adverse environments for extended periods of time. Various Bacillus species produce different secondary metabolites capable of inducing plant growth [11]. The use of Bacillus species as biofertilizers provides an alternative for enhancing plant growth and yield [12]. The application of Bacillus species exerts different effects on plants. Most of these effects are related to increases in the length and biomass of shoots, roots, and leaves [13–15]. Bacillus strains can also enhance fruit and grain yields [16, 17]. In addition, biofertilizers involving Bacillus species are more effective at producing diverse metabolites, forming spores, and maintaining cell viability. These characteristics allow the generation of formulated products suitable for commercial use [18].

Endophytic microorganisms produce different bioactive molecules that have a marked direct or indirect effect on plant growth. An understanding of endophytic microorganism-plant interactions may help clarify mechanisms for promoting plant growth and create a sustainable system for crop production [18]. Previous studies have found that B. methylotrophicus and B. subtilis are involved in hormones synthesis, for instance indole-3-acetic acid, gibberellic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, cytokinins, and spermidines. These proteins are directly involved in the activation of plant growth [15, 19]. Similarly, B. subtilis and B. mojavensis can secrete ACC deaminase to inhibit plant senescence [20, 21].

Recent studies have shown that inoculation with Bacillus aryabhattai impressively improves the nutritional status of wheat crops [22]. The growth and productivity of rice are positively enhanced by treatment with B. aryabhattai. This bacterium improves the salt tolerance of plants through increases in atmospheric nitrogen fixation, phosphate solubilization, and indoleacetic acid production [23]. The B. aryabhattai strain also promotes the growth of cowpea through increases in indole production, siderophore production, phosphate solubilization, and 1-aminocyclopropane-1-carboxylic acid deaminase activity [24].

B. aryabhattai B8W22 can secrete many organic acids, including oxalic acid, malonic acid, citric acid, succinic acid, indole acetic acid (IAA), and siderophores, which can promote plant growth [25]. Most of the studies involving B. aryabhattai have focused on the spectrum of plant growth-promoting secondary metabolites produced by this bacterium. However, additional molecular pathways could be involved in both plants and bacteria during this process.

In general, the understanding of the molecular changes established in plants in response to Bacillus species remains limited. Moreover, investigating the genes expressed in Bacillus during the interaction with plants allows a better understanding of the molecular pathways used by bacteria to induce plant growth. The present study aimed to characterize the effects of the endophytic bacteria B. aryabhattai based on their plant growth-promoting properties and the main molecular pathways involved in their interaction with Arabidopsis plants.

Materials and methods

Endophytic bacterium, plant materials, and growth conditions

The bacterium Bacillus aryabhattai was previously isolated and identified from the wild plant species Glyceria chinensis (Keng) according to Portieles et al. [26]. Samples were collected from the wild plant species G. chinensis (Keng) along the Fu Tuan River (35° 20′ 17″ N, 119° 26′ 8″ E) within 5 km of the coastal region of Rizhao city in Shandong Province, People’s Republic of China. G. chinensis (Keng) was identified according to data on morphological traits from the Flora of China (http://www.iplant.cn/foc/). This experimental study complied with the national and local laws of China, and sample collection was allowed by the Rizhao Administration and Municipal Sciences and Technology Department (Collection information: South China Botanical Garden (IBSC) of the Chinese Academy of Sciences. Source: China Digital Plant Specimens Museum. Identifier: 0114164. Collector: Zhang Zhisong Acquisition number: 401467). The strain was cultivated in Luria-Bertani (LB) agar medium (yeast extract, 5 g/l: peptone, 10 g/l; sodium chloride, 5 g/l; agar, 12 g/l; pH 7) at 37 °C. Seeds of the Arabidopsis thaliana ecotype Columbia were surface-sterilized and placed on Murashige and Skoog (0.5X MS) basal media (Sigma Aldrich, St Louis, MO, USA) supplemented with 1% w/v sucrose. The seeds were maintained in the dark at 4 °C for 2 days and transferred to a growth room with a 16-h light/8-h dark photoperiod and a temperature of 22 °C. Small plants were sown in a substrate composed of peat plugs and vermiculite (1:1) for 14 days. Nicotiana tabacum seeds were also germinated, and plants were cultivated in 6-inch pots with sterilized black turf and rice husk (4:1) substrate and kept at 23 °C in a growth room. All the substrates used in this study were sterilized at 120 °C for 20 minutes.

Plant material (stems and roots) were first cleaned with water to establish the endophytic property and establishment time of B. aryabhattai. The samples were sliced into fragments in an aseptic condition. Each sample was surface sterilized for 1 minute with 70% ethanol before being immersed in a 5% sodium hypochlorite solution for 1 minute. The samples were then washed for 1 minute in sterile distilled water and dried on filter paper. Following adequate drying, plant parts were manually handled for 5 minutes in 1 ml of sterile water in a TissueLyser (Qiagen, Hilden, Germany). The debris was decanted, and 100 l of the remaining water was cultured for three days at 37°C in Luria-Bertani (LB) agar medium (sodium chloride, 5 g/L; peptone, 10 g/L; yeast extract, 5 g/L; agar, 12 g/L and pH 7). In addition, the final wash solution from the surface sterilization operation was spread out onto an MS medium plate as a control. Internally isolated bacterium was exclusively isolated from processed materials. This was the factor for classifying endophytes as contrast to surface contaminants. Furthermore, the roots of the plants that had been infected with the endophytic bacterium used in the studies was processed, and the bacterium was collected and categorized as the original strain using the same methodology described above. The bacterial colonization in the roots was confirmed using the same method followed in the isolation of this strain on LB plates at various time periods. The endophytic bacterium was fully established 72 hours after inoculation.

Greenhouse experiments

Bacillus aryabhattai was grown for one day at 37 °C in the dark in a 250-mL Erlenmeyer flask with 100 mL LB broth medium and 200 rpm shaking. The B. aryabhattai fermentation product’s optical density (OD) was adjusted to 1.0 (4.77 109 CFUs/mL), and 30 mL of the fermentation product was poured to each pot. Five Arabidopsis thaliana and four Nicotiana tabacum plants per plastic pot were cultivated in a growth room at 25 °C and maintained with water without fertilizers, respectively. Five-day-old A. thaliana and N. tabacum plants (seeds previously germinated in MS basal media, transferred to the substrate, and adapted during five days) were treated with the B. aryabhattai fermentation product twice weekly for one month. The plant size and the dry and fresh weights were evaluated after one month of treatment with B. aryabhattai. Whole plants were used for the evaluation of the different parameters. A completely randomized pot experiment with five replicates of each treatment was performed to analyze the influence of B. aryabhattai on the growth of A. thaliana and N. tabacum plants. The data were analyzed using GraphPad Prism software (La Jolla, CA, USA). A “t” test was used to examine the significance of the differences between the mean values, with P<0.05 indicating a significant difference. Five replicates were subjected to each treatment, and the experiments were replicated three times.

Identification of novel differentially expressed genes by RNA sequencing

Arabidopsis plants (five-day-old) were treated with 30 mL (4.77 × 109 CFUs/mL) of B. aryabhattai. Previously, the bacterium was well established 72 h post inoculation according to the protocol mentioned above, and leaves, stems, and roots from five plants were collected after establishment. Plants treated with water were used as a control. The treatments, including the control treatment, were repeated three times per group. In total three libraries were constructed as follow: 1) bacterium; 2) Arabidopsis and 3) Arabidopsis treated with bacterium. The Qiagen RNeasy Midi Kit (Hilden, Germany) was used to extract total RNA, and the concentration of total RNA was measured using spectrometry. Following total RNA extraction and DNase I treatment, magnetic beads containing oligo (dT) were used to isolate mRNA (for eukaryotes) or rRNA (for prokaryotes) using the QIAseq FastSelect 5S/16S/23S Kit (Qiagen, Germany). The samples were sequenced using an Illumina HiSeq™ 2000 (Personalbio Co., Shanghai, People’s Republic of China). High-quality reads were processed using the Perl script, and the differentially expressed genes were identified using the edgeR package (https://bioconductor.org/packages/edgeR/) [27]. Genes with a fold change ≥ 2 were considered significantly differentially expressed genes. The differentially expressed genes were characterized using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (www.genome.jp/kegg) pathway enrichment analyses [28, 29]. Blast2GO software (www.blast2go.com) was also used to assess the GO annotations [30, 31]. The prokaryote genetic analysis process involved filtering the raw data to obtain a high-quality sequence and comparing the filtered sequences to the reference genome for the species (http://www.tigr.org/softlab, http://sourceforge.net/projects/ngopt) [32, 33].

The read count values of each gene were compared to the gene’s original expression level using HTSeq (https://pypi.python.org/pypi/HTSeq) [34]. To make the gene expression levels comparable between different genes and samples, we normalized the sequencing depth and gene length based on fragments per kilobase of transcript per million (FPKM). The FPKM values consider that two reads can map to the same transcript. In the reference transcription group, FPKM > 1 indicated that the gene was expressed. To test the reliability of the experiments and determine whether sample selection was reasonable, Pearson correlation coefficients were calculated to indicate the correlation between the expression levels of genes in the sample and used. The correlation of gene expression levels between samples is an important index indicating the reliability of experiments and whether sample selection was reasonable. The log2-fold change for the up and down regulated plant genes was computed by dividing the FPKM values of Arabidopsis plants treated with the bacterium by the FPKM values of Arabidopsis plants treated with water. While the log2-fold change for the up and down regulated bacterial genes was calculated by dividing the FPKM values of bacterium during the interaction with the plant by the FPKM values of the bacterium grown in LB medium. The 2-fold change cutoff FPKM value was established.

Analysis of RNA sequencing results

In a second experiment, the transcripts with the largest expression levels from RNA sequencing were confirmed using quantitative real-time polymerase chain reaction. The experiment was done in accordance with the procedure described above. Primer 5.0 was used to generate the oligonucleotides (S1 Table). Total RNA was extracted with a Qiagen RNeasy kit, and cDNA was prepared with oligo-dT primers and a SuperScript III kit (Invitrogen, Carlsbad, CA, USA). A Rotor-Gene Q PCR equipment (Hilden, Germany) and the QuantiTect SYBR Green PCR Kit were used for real-time quantitative PCR (Qiagen). During RT-qPCR gene quantification, the B. aryabhattai 16S rRNA and A. thaliana -actin genes were selected as internal controls. The real-time PCR reaction conditions were as follows: an initial denaturation step at 95 °C for 15 minutes, followed by denaturation at 95 °C for 15 seconds, an alignment step at 58 °C for 30 seconds, and an extension step at 72 °C for 40 cycles. Q-Gene software was used to calculate relative gene expression as mean normalized expression [35]. The relative fold-change (log2) values were calculated in relation to the control treatment. All quantitative PCR experiments were replicated three times for biological and technical considerations.

Results

B. aryabhattai enhances the growth of Arabidopsis and Nicotiana tabacum plants

The promotion of the growth of Arabidopsis and N. tabacum plants by B. aryabhattai was tested in the growth room. Arabidopsis plants treated with B. aryabhattai showed increased growth compared with the control plants (Fig 1A). The analysis indicated that bacterial inoculation significantly increased the size of Arabidopsis plants (4.55 cm) compared with that of the control plants (3.10 cm) (Fig 1B). At 20 days posttreatment, bacterial inoculation significantly enhanced the fresh and dry weights of the treated Arabidopsis plants (0.97/0.08 g) compared with those of the control plants (0.47/0.034 g; Fig 1C and 1D). Moreover, B. aryabhattai induced the growth of N. tabacum plants (Fig 2A). The heights of the inoculated N. tabacum plants were significantly greater (4.05 cm) than those of the uninoculated plants (2.25 cm; Fig 2B). A data analysis showed that N. tabacum plants inoculated with the endophytic bacterium presented higher fresh and dry weights than the control plants (0.13/0.010 and 0.05/0.003 g, respectively: Fig 2C and 2D). The nutrients from the LB broth medium were a key aspect. In terms of the volume and frequency of LB broth medium applied, this could have a substantial impact factor on the growth of little Arabidopsis plants. However, this had not significant impact on Arabidopsis and tobacco plants. There were not statistically significant changes between the two treatments (S2 Table).

Fig 1. The endophytic bacterium B. aryabhattai enhances Arabidopsis plant growth.

Fig 1

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A) Phenotype (at 20 days post inoculation) of mock-treated (control) Arabidopsis plants and those treated with B. aryabhattai. Plant size (B), fresh (C), and dry weight (D) of mock-treated and B. aryabhattai-treated Arabidopsis plants. The mean results with standard errors from two separate experiments (n = 15) are represented by each bar.

Fig 2. The endophytic bacterium B. aryabhattai enhances Nicotiana tabacum plant growth.

Fig 2

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A) Phenotype (at 20 days post inoculation) of mock-treated N. tabacum plants (control) and those treated with B. aryabhattai. Plant size (B), fresh (C), and dry weight (D) of mock-treated and B. aryabhattai-treated N. tabacum plants. The mean results with standard errors from two separate experiments (n = 15) are represented by each bar.

B. aryabhattai induces transcriptional changes in genes involved in plant growth

Endophytic bacterial species frequently exert important beneficial effects on plant growth. The genes generally associated with the beneficial effects of endophytic bacteria on plant productivity encode proteins involved in different molecular pathways. To determine whether B. aryabhattai induces genes associated with the promotion of plant growth, the interactions between B. aryabhattai and Arabidopsis were evaluated by RNA-seq. The range of gene expression changes during the B. aryabhattai-Arabidopsis interaction was determined. During the interaction, 21,416 transcripts were identified and annotated (S3 Table), and from this set, 6,943 new transcripts were annotated (S4 Table). The highest number of transcripts (33.05%) showed a fold change in expression between 1 and 10, and the lowest number of transcripts exhibited the highest expression level (>100-fold change) (Fig 3).

Fig 3. Plant gene expression during the interaction with B. aryabhattai.

Fig 3

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The X-axis represents the range of gene expression values, and the Y-axis represents the number of genes in each expression interval.

An analysis of RNA-seq data obtained during the interaction identified 363 differentially expressed transcripts, which included 268 upregulated and 95 downregulated transcripts (Fig 4). Among these transcripts, cinnamyl alcohol dehydrogenase (14983.5-fold), apyrase (2685.5-fold), thioredoxin H8 (2444.5-fold), benzaldehyde dehydrogenase (2166.9-fold), indoleacetaldoxime dehydratase (2092.8-fold), berberine bridge enzyme-like (2018.8-fold), gibberellin-regulated protein (1666.9-fold), maturase K (12.3-fold), tetratricopeptide repeats (TPR)-like superfamily protein (12.0-fold), BTB/POZ, TAZ domain-containing protein (10.8-fold) and auxin-responsive GH3 family protein (10.4-fold) showed the highest differential expression during the B. aryabhattai-Arabidopsis interaction. In contrast, zinc finger C-x8-C-x5-C-x3-H type family protein (-293.1-fold), ankyrin repeat/KH domain protein (-119.8-fold), CAPRICE-like MYB3 (-109.6-fold), HSP20-like chaperone superfamily protein (-80.4-fold), gibberellin-regulated protein (-78.8-fold), abscisic acid 8’-hydroxylase (-74.5-fold), pectinesterase (-70.1-fold), agamous-like MADS-box protein (-57.2-fold), and ethylene-responsive transcription factor (-51.8-fold) were significantly repressed during the interaction (Table 1).

Fig 4. During the B. aryabhattai-Arabidopsis interaction, a volcano plot of differential gene expression was established.

Fig 4

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The log2-transformed fold changes are on the X-axis, while the -log10-transformed p values are on the Y-axis. The horizontal dashed lines represent the P value thresholds, while the vertical dashed lines show the difference thresholds (0.05). The scale was set based on the log2-transformed lowest and maximum values (between -7.60 and 15.70).

Table 1. Significantly differentially expressed genes during the B. aryabhattai-Arabidopsis interaction.

ID Log2(Fold Change) a Description
Upregulated genes
AT4G37990 14983.5 Cinnamyl alcohol dehydrogenase
AT1G14250 2685.5 Apyrase
AT1G69880 2444.7 Thioredoxin H8
AT1G04580 2166.9 Benzaldehyde dehydrogenase
AT2G30770 2092.8 Indoleacetaldoxime dehydratase
AT1G26390 2018.8 Berberine bridge enzyme-like
AT3G02885 1666.9 Gibberellin-regulated protein
ATCG00040 12.3 Maturase K
ATCG00360 12.0 Tetratricopeptide repeat (TPR)-like superfamily protein
AT3G48360 10.8 BTB/POZ and TAZ domain-containing protein
AT4G37390 10.4 Auxin-responsive GH3 family protein
AT4G37540 9.9 LOB domain-containing protein
AT4G28040 9.7 WAT1-related protein
AT5G09730 9.4 Beta-D-xylosidase
AT1G61120 8.6 (E,E)-geranyllinalool synthase
AT1G52400 7.8 Beta-D-glucopyranosyl abscisate beta-glucosidase
AT4G21680 7.8 Protein NRT1/PTR FAMILY
AT4G17470 7.7 Alpha/beta-hydrolase superfamily protein
AT1G73220 7.5 Organic cation/carnitine transporter
AT3G45140 7.3 Lipoxygenase
AT4G15210 7.2 Beta-amylase
AT1G54020 7.2 GDSL esterase/lipase
ATMG00570 7.2 Sec-independent periplasmic protein translocase
AT2G25900 6.1 Zinc finger CCCH domain-containing protein
AT1G21310 5.8 Extensin-3
AT2G23170 5.7 Indole-3-acetic acid-amido synthetase
AT3G04070 5.6 NAC transcription factor
AT5G67480 4.8 BTB and TAZ domain protein
AT1G44350 4.7 IAA-amino acid hydrolase
AT1G52000 4.4 Jacalin-related lectin
Downregulated genes
AT1G29560 -293.1 Zinc finger C-x8-C-x5-C-x3-H type family protein
AT1G12320 -119.8 Ankyrin repeat/KH domain protein
AT4G01060 -109.6 CAPRICE-like MYB3
AT1G76780 -80.4 HSP20-like chaperones superfamily protein
AT1G74670 -78.8 Gibberellin-regulated protein
AT2G29090 -74.5 Abscisic acid 8’-hydroxylase
AT2G47030 -70.1 Pectinesterase
AT5G60440 -57.2 Agamous-like MADS-box protein
AT4G16750 -51.8 Ethylene-responsive transcription factor
AT5G26749 -48.5 C2H2 and C2HC zinc fingers superfamily protein
AT2G40330 -47.5 Abscisic acid receptor
AT2G36270 -43.7 Basic-leucine zipper (bZIP) transcription factor
AT5G15800 -42.6 MADS-box transcription factor family protein
AT5G03680 -33.4 Trihelix transcription factor
AT1G13920 -32.9 Remorin family protein
AT3G28830 -31.3 Mucin-like protein
AT4G31370 -28.6 Fasciclin-like arabinogalactan protein
AT1G16060 -23.7 AP2-like ethylene-responsive transcription factor
AT1G01380 -23.2 MYB-like transcription factor
AT5G57640 -22.1 GCK domain-containing protein
AT4G33970 -22.1 Pollen-specific leucine-rich repeat extensin-like protein
AT4G31620 -18.3 Transcription factor B3 family protein
AT5G28640 -17.8 GRF1-interacting factor
AT3G27650 -17.2 LOB domain-containing protein
AT4G31380 -14.0 Flowering-promoting factor 1-like protein
AT5G46530 -13.4 AWPM-19-like family protein
AT2G45760 -11.3 BON1-associated protein
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a All the genes with a log2 (fold change) value between -11.3 and 14983.5 were added.

The differentially expressed transcripts were analyzed to determine their function. A GO enrichment analysis was performed using the annotated differentially expressed genes to generate a list of key genes and the number of genes related to each term. The transcripts showing the largest increases in expression were NADH dehydrogenase (quinone) activity, NADH dehydrogenase (ubiquinone) activity, NADH dehydrogenase activity, and oxidoreductase activity (Fig 5). Based on the KEGG pathways, we categorized the most significant transcripts into the indole alkaloid biosynthesis and linoleic acid metabolism pathways (Fig 6). The expression profile of transcription factor genes revealed the transcription-related activities that are enhanced by these genes. To determine their important roles, the transcription factor genes involved in the B. aryabhattai-Arabidopsis interaction were analyzed. The largest transcription factor gene families detected in our study were LOB domain-containing proteins (9.9-fold), zinc finger CCCH domain-containing proteins (6.1-fold), NAC transcription factors (5.6-fold), and BTB and TAZ domain proteins (4.7-fold) (Table 1).

Fig 5. Gene Ontology (GO) enrichment analysis of the differentially expressed genes during the interaction between B. aryabhattai and Arabidopsis.

Fig 5

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The rich factor, false discovery rate (FDR) values, and the number of genes with the associated GO term were used to determine the level of enrichment based on the GO enrichment analysis results. The number of distinct genes with the appropriate GO term to the number of annotated genes is referred to as the rich factor. The number of enriched genes is shown by the size of each dot. Each dot is colored differently: red dots represent pathways with high concentration, whereas green dots suggest pathways with low concentration.

Fig 6. KEGG pathway analysis of differentially expressed genes during the B. aryabhattai-Arabidopsis interaction.

Fig 6

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The chart shows the enrichment of signaling pathways with differentially expressed genes. The Y-axis label represents the pathway, and the X-axis label represents the rich factor (rich factor = number of differentially expressed genes enriched in the pathway/number of genes in the background gene set). The size and color of the bubble represent the number of differentially expressed genes enriched in the pathway and the enrichment significance, respectively.

During the interaction, a total of 4,305 B. aryabhattai genes were annotated, and the genes from this set that exhibited a log2-fold change in expression between -2.1 and 5.1 were analyzed. Nine and six B. aryabhattai genes were up- and downregulated during the interaction with Arabidopsis plants, respectively. The remaining genes had undefined functions, were repeated, had less significant fold changes in expression, or were involved in the primary metabolism of the bacterium. Arginine decarboxylase (5.1-fold), D-hydantoinase (4.9-fold), membrane protein (4.9-fold), ATP synthase gamma chain (4.8-fold), and 2-hydroxyhexa-2,4-dienoate hydratase (4.7-fold) exhibited the highest expression levels in B. aryabhattai during the interaction with Arabidopsis plants. Moreover, putative universal stress protein (-3.6-fold), L-lactate dehydrogenase (12.8-fold), succinate dehydrogenase flavoprotein subunit (12.7-fold), and glycolate permease (12.6-fold) were highly downregulated in the bacterium (Table 2 and S5 Table).

Table 2. Highly differentials expressed genes in B. aryabhattai during its interaction with Arabidopsis plants.

ID Log2(Fold Change) a Swiss-Prot
Upregulated genes
gene3107 5.1 Arginine decarboxylase
gene1769 4.9 D-hydantoinase
gene1522 4.9 Membrane protein
gene4310 4.8 ATP synthase gamma chain
gene1091 4.7 2-hydroxyhexa-2,4-dienoate hydratase
gene5616 3.2 Transcriptional regulatory protein
gene3481 2.6 Microcystinase C
gene2400 2.4 4,4’-diapolycopen-4-al dehydrogenase
gene1987 2.1 Succinate-CoA ligase [ADP-forming] subunit beta
Downregulated genes
gene4030 -3.6 Putative universal stress protein
gene5157 -2.8 L-lactate dehydrogenase
gene1475 -2.7 Succinate dehydrogenase flavoprotein subunit
gene5156 -2.6 Glycolate permease
gene4267 -2.1 Betaine aldehyde dehydrogenase
gene4268 -2.1 Alcohol dehydrogenase
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a All the genes with a log2 (fold change) value between -2.1 and 5.1 were added.

Analysis of RNA sequencing results

Even though RNA-Seq is the fundamental basis for gene expression profiling, qPCR is the main tool for validation. qRT-PCR analysis was done to validate the data generated by RNA sequencing. The expression levels of plant and bacterium genes matched the RNA-Seq data, indicating that the RNA-Seq results are trustworthy (Fig 7). Cinnamyl alcohol dehydrogenase (106-log2 ratio), apyrase (57-log2 ratio) and thioredoxin H8 (35- log2 ratio) were highest expressed genes in Arabidopsis plants inoculated with B. aryabhattai in a different replication of the experiment. While the zinc finger C-x8-C-x5-C-x3-H type family protein gene (-27-log2 ratio) was highest repressed during the interaction (Fig 7A). Besides, arginine decarboxylase (8-log2) and D-hydantoinase (6-log2) were highest expressed bacterium genes in planta. Meantime, the putative universal stress protein gene (-3-log2) had the most reduced expression (Fig 7B).

Fig 7. Analysis of differential expressed genes using qRT-PCR.

Fig 7

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A) Expression levels of Arabidopsis plants genes during the interaction with B. aryabhattai. B) Expression of bacterium genes in planta.

Discussion

In the current study, we elucidated the mechanism through which B. aryabhattai promotes the growth of Arabidopsis and N. tabacum plants. N. tabacum plants were included to evaluate their influence on other plant species. The bacterium increases the plant size and fresh and dry weights. Notably, although this endophytic bacterium was isolated from wild plant species, it exerts a robust impact on the growth of nonhost plants. The findings indicate that B. aryabhattai can stimulate growth in a range of plant species. However, these effects should be studied in a natural context and with other crop species. Regardless of the context, based on the effect of B. aryabhattai on plants, this bacterium could be used as a biofertilizer to boost growth and agricultural production.

The beneficial effect of different Bacillus species on various plant species was previously established [11, 13, 15]. Bacillus species are the most common type of growth-promoting bacterium, and these bacterial usually promote growth via growth-responsive genes, proteins, phytohormones, and metabolites [11]. Additionally, Bacillus is reportedly effective in increasing the biomass and height of important crops through increases in plant N uptake, phosphate solubilization and root-promoting phytohormones [36–38]. Additionally, most of these effects are associated with the production of phytohormones such as indole-3-acetic acid (IAA), cytokinins, gibberellic acid (GA), and spermidines [9, 15, 19]. Furthermore, the induction of endogenous proteins, amino acids, and minerals by Bacillus species could promote plant growth [15, 39].

Beneficial plant-bacteria interactions have been extensively analyzed. However, the specific molecular pathways that are associated with these interactions are unclear. This knowledge is critical for maximizing the potential of these microbes in the field. In the current study, we done RNA sequencing to analyze the genes expressed during the Arabidopsis-B. aryabhattai interaction. We conducted an analysis of the RNA-seq dataset and found various types of genes that might be ideal candidates for characterizing the host pathway governing this essential plant-microbe relationship. A high number of novel genes involved in metabolite biosynthesis were differentially expressed in our dataset. The results reveal new insights into plant and bacterial gene expression and improve our understanding of the molecular events involved in the Arabidopsis-B. aryabhattai interaction. Notably, GO and KEGG analyses revealed significant changes between treated and nontreated plants. Our data indicate that B. aryabhattai triggers important molecular pathways related to plant growth.

Interestingly, the KEGG pathway analysis revealed that the most significant transcripts were involved in the indole alkaloid biosynthesis and linoleic acid metabolism pathways. These pathways have been related to resistance and tolerance to biotic and abiotic factors [40, 41]. Most likely, the bacterium can induce plant protection against pathogens and abiotic factors through the production of jasmonic acid and secondary metabolites associated with the defense responses of plants. The synthesis of indole-alkaloids in plants causes consistent alterations of the microbiota surviving at the barley root-soil interface while having no discernible detrimental influence on plant growth performance in two elite barley types [42]. These results indicate that the application of indole-alkaloids modulates the proliferation of a subset of soil microbes with relatively broad phylogenetic assignments [42].

In contrast, bacteria can undergo symbiotic or pathogenic interactions with plants. Membrane lipids and lipid-derived molecules from the plant or microbial organism play important roles during the infection process [43]. For example, lipids are involved in establishing the membrane interface between the two organisms [43]. Furthermore, lipid-derived molecules are crucial for intracellular signaling in plant cells, and lipids serve as signals during plant-microbe communication [43]. Linolenic acid is released from several complex fatty acids mainly located in the membranes of organelles such as chloroplasts and is a precursor of jasmonic acid [44, 45]. The involvement of this hormone in different biological processes of plants, such as responses to biotic and abiotic stress conditions, indicates the possible use of this bacterium to activate plant defense.

Surprisingly, during the Arabidopsis-B. aryabhattai interaction, the expression of genes encoding cinnamyl alcohol dehydrogenase, apyrase, thioredoxin H8, benzaldehyde dehydrogenase, indoleacetaldoxime dehydratase, berberine bridge enzyme-like, gibberellin-regulated protein, maturase K, tetratricopeptide repeat (TPR)-like superfamily protein, BTB/POZ and TAZ domain-containing protein and auxin-responsive GH3 family protein genes were highly induced. Some identified genes from our dataset are addressed here, as well as their roles in other plant-microbe relationships. B. aryabhattai most likely promotes the synthesis of lignin during the growing phase of Arabidopsis and N. tabacum plants, which results in the robust phenotype observed in the plants treated with the bacterium. Cinnamyl alcohol dehydrogenase is a key enzyme involved in lignin synthesis and is closely related to plant growth and development. This enzyme is expressed in the lateral roots and root tips of sweet potato, and its activity is induced by abscisic acid [46].

Similarly, apyrases play a crucial role in regulating the growth of Arabidopsis plants treated with the bacterium. Specifically, apyrases influence auxin transport and stomatal aperture, and the removal of apyrase activity can lead to growth inhibition [47]. A previous study revealed that silencing of the apyrase gene induces significant phenotypic changes, growth retardation, an increase in the tuber number per plant, and an effect on the tuber morphology of potato plants [48]. Moreover, the expression of apyrase genes in Arabidopsis plants exerts a marked effect on the growth of plant tissues and the accumulation of auxin [49, 50].

Interestingly, B. aryabhattai can indirectly induce plant growth through benzaldehyde dehydrogenase, which plays a key role in the benzoic acid pathway. In addition, benzaldehyde dehydrogenase is involved in the processing of benzaldehyde to benzoic acid. The growth, mineral composition, and chlorophyll content of soybean plants are influenced by benzoic acid [51]. Herein, benzoic acid exerts a marked effect on the growth and yield of tomato plants. Similarly, benzoic acid exerts a positive effect on fruit yield [52].

We observed high induction of maturase K gene expression during the interaction. Recent studies revealed that the maturase K gene is induced during the Arabidopsis-Bacillus altitudinis interaction [53]. In addition, the maturase K gene is highly expressed in Anoectochilus roxburghii plants treated with endophytic fungi [54]. Most likely, this gene could be related to the Bacillus-plant association, but a functional analysis of Arabidopsis mutants could provide a clear understanding of the real function of this gene during Bacillus-plant interactions.

Furthermore, tetratricopeptide repeat (TPR)-like superfamily protein genes might have indirect effects on the activation of phytohormones related to plant growth. This gene was found to be expressed during the interaction and constitutes a basic component of gibberellin and ethylene responses. The silencing of an Arabidopsis chloroplast-localized tetratricopeptide repeat protein gene affects plant growth, leaf greening, chloroplasts, and photosynthesis genes [55].

We also predicted that hormone-related genes and transcription factors would be modulated during this interaction. The bacterium B. aryabhattai induced plant growth by triggering key molecular pathways involved in the production of phytohormones and transcription factors. Root development, shoot growth, and fruit ripening are regulated by Aux/IAA family genes [56]. Auxin influences numerous stages of plant development and growth by regulating the expression of auxin-activated genes [57], and auxin controls plant development and growth by altering the expression of different genes [58]. This finding could be directly correlated with the phenotype observed in the Arabidopsis plants treated with the bacteria.

Many of the processes that occur in a plant during interactions with endophytic bacteria are known. It is also important to understand the processes that take place in a bacterium during its interaction with a plant, such as the specific genes that are expressed in the bacterium that may contribute to the growth phenotype of treated plants. This point is more complex, as demonstrated by the low proportion of bacterial transcripts found during the interaction. A functional analysis of these types of genes would elucidate the actual role of these genes during the interaction. Interestingly, the expression of arginine decarboxylase, D-hydantoinase, ATP synthase gamma chain and 2-hydroxyhexa-2,4-dienoate hydratase genes was highly induced in B. aryabhattai during its interaction with the plant, and this finding constitutes the first line of evidence indicating that these types of genes are expressed in this species. We speculate that the overexpression of these genes in B. aryabhattai might enhance plant growth. Based on the same principles, we discuss some bacterial genes expressed during the interaction.

For example, the activity of arginine decarboxylase has been implicated in the effect of hormones on plant growth [59]. The expression of this enzyme is correlated with cell growth and stress responses in apple plants [60]. Additionally, this enzyme is involved in efficient ROS elimination and its influence on root growth, which is conducive to drought tolerance [61]. Most of the effects of these genes could be indirectly implicated in enhancement of the plant physiological status and thus in a better growing environment.

Contradictorily, the expression of the D-hydantoinase gene was induced in the bacterium during its interaction with the plant. These D-amino acids (D-AAs) exert a growth-inhibiting effect on plants [62–64]. The exogenous administration of various D-AAs to growth media has a deleterious or favorable effect on the growth and development of many plant species, and these effects depend on the D-AAs used [63, 65]. However, the mechanism responsible for the finding that its expression is correlated with growth stimulation but not growth inhibition. Although some D-AAs impede seedling growth, some lines of evidence show that D-AAs can also promote plant growth. Recent studies found that the application of 0.1 mM d-Leu, d-Val, and d-Cys increases the growth of pepper plants [66]. Additionally, Arabidopsis seedlings treated with d-Lys and d-Ile at a range of 1–10 mM exhibit superior growth. This ostensible inconsistency has been resolved through functional studies. Another conclusion is that D-AAs should not be considered a class of chemicals with uniform features but rather that each D-AA should be evaluated separately.

Among the identified group of plant genes and those showing the most differential expression, the zinc finger C-x8-C-x5-C-x3-H type family protein, ankyrin repeat/KH domain protein, CAPRICE-like MYB3, HSP20-like chaperone superfamily protein and gibberellin-regulated protein were downregulated during the interaction. Additionally, bacterial genes such as putative universal stress protein, L-lactate dehydrogenase, and succinate dehydrogenase flavoprotein subunit showed the strongest repression during the interaction.

For example, the zinc finger C-x8-C-x5-C-x3-H type family protein functions as a transcriptional activator and is involved in secondary wall biosynthesis. Additionally, some evidence shows that this type of protein is involved in ABA-, GA- and phytochrome-mediated seed germination responses [67]. Furthermore, the ankyrin repeat protein family plays a crucial role in plant growth and development and in the responses to biotic and abiotic stresses [68, 69]. In addition, CAPRICE-like MYB3 encodes a small protein with an R3 MYB motif and promotes root hair cell differentiation in Arabidopsis plants. The overexpression of this protein results in the suppression of trichomes and the overproduction of root hairs and exerts pleiotropic effects on flowering development, epidermal cell size and trichome branching [70, 71]. Similarly, HSP20-like chaperone superfamily proteins mediate protein folding and are associated with abiotic stresses and death [72]. Gibberellin-regulated proteins are important endogenous plant growth regulators involved in different physiological processes, and these types of proteins are sometimes up- or downregulated depending on the developmental stages of the plants [73]. Recent studies have shown that orange gibberellin-regulated proteins are involved in allergy reactions [74].

Among the downregulated bacterial genes, putative universal stress proteins are important elements for survival under anaerobic conditions and during persistent colonization and infection with pathogenic bacteria [75]. In addition, lactate dehydrogenase plays an important role in the anaerobic metabolic pathway and catalyzes the reversible conversion of lactate to pyruvate with the reduction of NAD+ to NADH [76, 77]. Interestingly, the succinate dehydrogenase flavoprotein subunit is involved in cellular energetics and is needed for the virulence of many important bacterial pathogens [78]. Certainly, most of these genes could play an important role during the interaction, but functional analyses are needed to draw a conclusion.

Conclusions

In summary, our results show that the endophytic bacterium B. aryabhattai significantly promotes the growth of Arabidopsis and N. tabacum plants. Notably, the expression of novel genes involved in different plant growth pathways is involved identified during the Arabidopsis-B. aryabhattai interaction. In contrast, the bacterial genes expressed during the interaction could produce some proteins, enzymes, and secondary metabolites capable of inducing plant growth-promoting genes, but further investigation of this finding is needed. Similarly, the effect of this bacterium on important crops and field conditions needs to be evaluated. The potential beneficial effects of B. aryabhattai identified in this study suggest that this bacterium is an appropriate and efficient candidate for use in sustainable agriculture.

Supporting information

S1 Table. List of oligonucleotides used for RNA sequencing validation.

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Click here for additional data file. (12.1KB, xlsx)
S2 Table. Evaluation of the effect of LB broth medium on Arabidopsis and tobacco growth experiment.

(XLSX)

Click here for additional data file. (136.6KB, xlsx)
S3 Table. Plant gene annotation during Arabidopsis-Bacillus aryabhattai interaction.

(XLSX)

Click here for additional data file. (5.5MB, xlsx)
S4 Table. Plant new gene annotation during Arabidopsis-Bacillus aryabhattai interaction.

(XLSX)

Click here for additional data file. (1.3MB, xlsx)
S5 Table. Bacillus aryabhattai gene annotation during the interaction.

(XLSX)

Click here for additional data file. (579.6KB, xlsx)

Data Availability

Data relevant to this study are available from the BioProject at accession numbers PRJNA781678 and PRJNA781727

Funding Statement

This study was supported by the Special Funds for Guiding Local Science and Technology Development of Central Government of Shandong Province (No. YDZX20193700004362).

References

  • 1.Kleinwechter U, Gastelo M, Ritchie J, Nelson G, Asseng S. Simulating cultivar variations in potato yields for contrasting environments. Agric Syst. 2016; 145: 51–63. [Google Scholar]
  • 2.Li C, Sun B, Li Y, Liu C, Wu X, Zhang D, et al. Numerous genetic loci identified for drought tolerance in the maize nested association mapping populations. BMC Genomic. 2016; 17: 894. doi: 10.1186/s12864-016-3170-8 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Soliman M, Alhaithloul HA, Hakeem KR, Alharbi BM, El-Esawi M, Elkelish A. Exogenous nitric oxide mitigates nickel-induced oxidative damage in Eggplant by upregulating antioxidants, osmolyte metabolism, and glyoxalase systems. Plants. 2019; 8: 562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Habib N, Ali Q, Ali S, Javed MT, Zulqurnain Haider M, Perveen R, et al. Use of nitric oxide and hydrogen peroxide for better yield of wheat (Triticum aestivum L.) under water deficit conditions: growth, osmoregulation, and antioxidative defense mechanism. Plants. 2020; 9: 285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Elkelish A, Qari SH, Mazrou YSA, Abdelaal KAA, Hafez YM, Abu-Elsaoud AM, et al. Exogenous ascorbic acid induced chilling tolerance in tomato plants through modulating metabolism, osmolytes, antioxidants, and transcriptional regulation of catalase and heat shock proteins. Plants. 2020; 9: 431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Azab E, Elsalam H, Sharnouby M. Performance of Catharanthus roseus Plants in Response to Gamma Irradiation. J Biol Chem. Res. 2016; 33: 130–140. [Google Scholar]
  • 7.Afzal I, Shinwari ZK, Sikandar S, Shahzad S. Plant beneficial endophytic bacteria: Mechanisms, diversity, host range and genetic determinants. Microbiol Res. 2019; 221: 36–49. doi: 10.1016/j.micres.2019.02.001 [DOI] [PubMed] [Google Scholar]
  • 8.Alkahtani MD, Fouda A, Attia KA, Al-Otaibi F, Eid AM, Ewais EED, et al. Isolation and characterization of plant growth promoting endophytic bacteria from desert plants and their application as bio-inoculants for sustainable agriculture. Agronomy. 2020; 10: 1325. [Google Scholar]
  • 9.Fouda A, Eid AM, Elsaied A, El-Belely EF, Barghoth MG, Azab E, et al. Plant growth-promoting endophytic bacterial community inhabiting the leaves of Pulicaria incisa (Lam.) DC inherent to arid regions. Plants. 2021; 10: 76. doi: 10.3390/plants10010076 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Ke J, Wang B, Yoshikuni Y. Microbiome engineering: synthetic biology of plant-associated microbiomes in sustainable agriculture. Trends Biotechnol. 2021; 39: 244–261. doi: 10.1016/j.tibtech.2020.07.008 [DOI] [PubMed] [Google Scholar]
  • 11.Radhakrishnan R, Hashem A and Abd Allah EF. Bacillus: a biological tool for crop improvement through bio-molecular changes in adverse environments. Front Physiol. 2017; 8 667. doi: 10.3389/fphys.2017.00667 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Choudhary DK. Plant growth promotion (PGP) activities and molecular characterization of rhizobacterial strains isolated from soybean (Glycine max L. Merril) plants against charcoal rot pathogen, Macrophomina phaseolina. Biotechnol Lett. 2011; 33: 2287–2295. doi: 10.1007/s10529-011-0699-0 [DOI] [PubMed] [Google Scholar]
  • 13.Ashraf M, Hasnain S, Berge O, Mahmood T. Inoculating wheat seedlings with exopolysaccharide-producing bacteria restricts sodium uptake and stimulates plant growth under salt stress. Biol Fertil Soils. 2004; 40: 157–162. [Google Scholar]
  • 14.Barnawal D, Maji D, Bharti N, Chanotiya CS, Kalra A. ACC deaminase-containing Bacillus subtilis reduces stress ethylene-induced damage and improves mycorrhizal colonization and rhizobial nodulation in Trigonella foenumgraecum under drought stress. J Plant Growth Regul. 2013; 32: 809–822. [Google Scholar]
  • 15.Radhakrishnan R, Lee IJ. Gibberellins producing Bacillus methylotrophicus KE2 supports plant growth and enhances nutritional metabolites and food values of lettuce. Plant Physiol Biochem. 2016; 109: 181–189. doi: 10.1016/j.plaphy.2016.09.018 [DOI] [PubMed] [Google Scholar]
  • 16.Kilian M, Steiner U, Krebs B, Junge H, Schmiedeknecht G, Hain R. FZB24R Bacillus subtilis—mode of action of a microbial agent enhancing plant vitality. Pflanzenschutz Nachr Bayer. 2000; 1: 72–93. [Google Scholar]
  • 17.Dursun A, Ekinci M, Donmez MF. Effects of foliar application of plant growth promoting bacterium on chemical contents, yield and growth of tomato (Lycopersicon esculentum L.) and cucumber (Cucumis sativus L.). Pak J Bot. 2010; 42: 3349–3356. [Google Scholar]
  • 18.Hassan SED. Plant growth-promoting activities for bacterial and fungal endophytes isolated from medicinal plant of Teucrium polium L. J Adv Res. 2017; 8: 687–695. doi: 10.1016/j.jare.2017.09.001 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Xie S, Wu HJ, Zang H, Wu L, Zhu Q, Gao X. Plant growth promotion by spermidine-producing Bacillus subtilis OKB105. Mol. Plant Microbe Interact. 2014; 27: 6556663. doi: 10.1094/MPMI-01-14-0010-R [DOI] [PubMed] [Google Scholar]
  • 20.Xu M, Sheng J, Chen L, Men Y, Gan L, Guo S, et al. Bacterial community compositions of tomato (Lycopersicum esculentum Mill.) seeds and plant growth promoting activity of ACC deaminase producing Bacillus subtilis (HYT-12-1) on tomato seedlings. World J Microbiol Biotechnol. 2014; 30: 835–845. doi: 10.1007/s11274-013-1486-y [DOI] [PubMed] [Google Scholar]
  • 21.Pourbabaee AA, Bahmani E, Alikhani HA, Emami S. Promotion of wheat growth under salt stress by halotolerant bacteria containing ACC deaminase. J Agric Sci. Technol. 2016; 18: 855–864. [Google Scholar]
  • 22.Hussain A, Ahmad M, Nafees M, Iqbal Z, Luqman M, Jamil M, et al. Plant-growth-promoting Bacillus and Paenibacillus species improve the nutritional status of Triticum aestivum L. PLoS One. 2020; 15: e0241130. doi: 10.1371/journal.pone.0241130 [DOI] [PMC free article] [PubMed] [Google Scholar] [Retracted]
  • 23.Sultana S, Paul SC, Parveen S, Alam S, Rahman N, Jannat B, et al. Isolation and identification of salt-tolerant plant-growth-promoting rhizobacteria and their application for rice cultivation under salt stress. Can J Microbiol. 2020; 66: 144–160. doi: 10.1139/cjm-2019-0323 [DOI] [PubMed] [Google Scholar]
  • 24.Inthama P, Pumas P, Pekkoh J, Pathom-Aree W, Pumas C. Plant growth and drought tolerance-promoting bacterium for bioremediation of Paraquat pesticide residues in agriculture soils. Front Microbiol. 2021; 12: 604662. doi: 10.3389/fmicb.2021.604662 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Song S, Liu Y, Wang NR, Haney CH. Mechanisms in plant-microbiome interactions: lessons from model systems. Curr Opin Plant Biol. 2021; 2: 102003. doi: 10.1016/j.pbi.2021.102003 [DOI] [PubMed] [Google Scholar]
  • 26.Portieles R, Xu H, Yue Q, Zhao L, Zhang D, Du L, et al. Heat-killed endophytic bacterium induces robust plant defense responses against important pathogens. Sci Rep. 2021; 11: 12182. doi: 10.1038/s41598-021-91837-5 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26: 139–140. doi: 10.1093/bioinformatics/btp616 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Ashburner M, Ball C, Blake J, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25: 25–29. doi: 10.1038/75556 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000; 28: 27–30. doi: 10.1093/nar/28.1.27 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997; 25: 3389–3402. doi: 10.1093/nar/25.17.3389 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21: 3674–6. doi: 10.1093/bioinformatics/bti610 [DOI] [PubMed] [Google Scholar]
  • 32.Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic acids research. 1999; 27: 4636–4641. doi: 10.1093/nar/27.23.4636 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Coil D, Jospin G, Darling AE. A5-MiSeq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2014; 31: 587–589. doi: 10.1093/bioinformatics/btu661 [DOI] [PubMed] [Google Scholar]
  • 34.Simon A, Theodor P, Huber W. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015; 31: 166–169. doi: 10.1093/bioinformatics/btu638 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Muller PY, Janovjak H, Miserez AR, Dobbie Z. Processing of gene expression data generated by quantitative real-time RT-PCR. Biotechniques 2002, 32: 1372–1380. [PubMed] [Google Scholar]
  • 36.Montañez A, Abreu C, Gill PR, Hardarson G, Siracdi M. Biological nitrogen fixation in maize (Zea mays L.) by 15N isotope-dilution and identification of associated culturable diazotrophs. Biol Fertil Soils. 2009; 45: 253–263. [Google Scholar]
  • 37.Piromyou P, Buranabanyat B, Tantasawat P, Tittabutr P, Boonkerd N, Teaumroong N. Effect of plant growth promoting rhizobacteria (PGPR) inoculation on microbial community structure in rhizosphere of forage corn cultivated in Thailand. Eur J Soil Biol. 2011; 47: 44–54. [Google Scholar]
  • 38.Wu SC, Cao ZH, Li ZG, Cheung KC, Wong MH. Effects of biofertilizer containing N-fixer, P and K solubilizers and AM fungi on maize growth: a greenhouse trial. Geoderma. 2005; 125: 155–166. [Google Scholar]
  • 39.Kang SM, Radhakrishnan R, You YH, Joo GJ, Lee IJ, Lee KE, et al. Phosphate solubilizing Bacillus megaterium mj1212 regulates endogenous plant carbohydrates and amino acids contents to promote mustard plant growth. Indian J Microbiol. 2014; 54: 427–433. doi: 10.1007/s12088-014-0476-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Okada K, Abe H, Arimura G. Jasmonates induce both defense responses and communication in monocotyledonous and dicotyledonous plants. Plant Cell Physiol. 2015; 56: 16–27. doi: 10.1093/pcp/pcu158 [DOI] [PubMed] [Google Scholar]
  • 41.Matsuura HN, Rau MR, Fett-Neto AG. Oxidative stress and production of bioactive monoterpene indole alkaloids: biotechnological implications. Biotechnol Lett. 2014; 36: 191–200. doi: 10.1007/s10529-013-1348-6 [DOI] [PubMed] [Google Scholar]
  • 42.Maver M, Escudero-Martinez C, Abbott J, Morris J, et al. Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota. PeerJ. 2021; 9: e12498. doi: 10.7717/peerj.12498 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Siebers M, Brands M, Wewer V, Duan Y, Hölzl G, Dörmann P. Lipids in plant-microbe interactions. Biochim Biophys Acta. 2016; 1861:1379–1395. doi: 10.1016/j.bbalip.2016.02.021 [DOI] [PubMed] [Google Scholar]
  • 44.Mata-Pérez C, Sánchez-Calvo B, Begara-Morales JC, Luque F, et al. Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis. Front Plant Sci. 2015; 6: 122. doi: 10.3389/fpls.2015.00122 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 45.Wasternack C. Action of jasmonates in plant stress responses and development-applied aspects. Biotechnol Adv. 2014; 32: 31–39. doi: 10.1016/j.biotechadv.2013.09.009 [DOI] [PubMed] [Google Scholar]
  • 46.Kim YH, Bae JM, Huh GH. Transcriptional regulation of the cinnamyl alcohol dehydrogenase gene from sweet potato in response to plant developmental stage and environmental stress. Plant Cell Rep. 2010; 29: 779–91. doi: 10.1007/s00299-010-0864-2 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Clark GB, Morgan RO, Fernandez MP, Salmi ML, Roux SJ. Breakthroughs spotlighting roles for extracellular nucleotides and apyrases in stress responses and growth and development. Plant Sci. 2014; 225: 107–16. doi: 10.1016/j.plantsci.2014.06.002 [DOI] [PubMed] [Google Scholar]
  • 48.Riewe D, Grosman L, Fernie AR, Wucke C, Geigenberger P. The potato-specific apyrase is apoplastically localized and has influence on gene expression, growth, and development. Plant Physiol. 2008; 147: 1092–109. doi: 10.1104/pp.108.117564 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Wu J, Steinebrunner I, Sun Y, Butterfield T, Torres J, Arnold D, et al. Apyrases (nucleoside triphosphate-diphosphohydrolases) play a key role in growth control in Arabidopsis. Plant Physiol. 2007; 144: 961–75. doi: 10.1104/pp.107.097568 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 50.Liu X, Wu J, Clark G, Lundy S, Lim M, Arnold D, et al. Role for apyrases in polar auxin transport in Arabidopsis. Plant Physiol. 2012; 160: 1985–95. doi: 10.1104/pp.112.202887 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Baziramakenga R, Simard RR, Leroux GD. Effects of benzoic and cinnamic acids on growth, mineral composition, and chlorophyll content of soybean. J Chem Ecol. 1994; 20: 2821–2833. doi: 10.1007/BF02098391 [DOI] [PubMed] [Google Scholar]
  • 52.Benavides-Mendoza A, Burgos-Limón D, Ramirez H, Robledo-Torres V, Sandoval-Rangel A. Benzoic acid effect in the growth and yield of tomato in calcareous soil. Acta Horticulturae. 2012; 938: 251–256 [Google Scholar]
  • 53.Zhang D, Xu H, Gao J, Portieles R, Du L, Gao X, et al. Endophytic Bacillus altitudinis strain uses different novelty molecular pathways to enhance plant growth. Front Microbiol. 2021; 12: 692313. doi: 10.3389/fmicb.2021.692313 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 54.Ye B, Wu Y, Zhai X, Zhang R, Wu J, Zhang C, et al. Beneficial effects of endophytic fungi from the Anoectochilus and Ludisia Species on the growth and secondary metabolism of Anoectochilus roxburghii. ACS Omega. 2020; 5: 3487–3497. doi: 10.1021/acsomega.9b03789 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 55.Ma F, Hu Y, Ju Y, Jiang Q, Cheng Z, Zhang Q, et al. A novel tetratricopeptide repeat protein, WHITE TO GREEN1, is required for early chloroplast development and affects RNA editing in chloroplasts. J Exp Bot. 2017; 68: 5829–5843. doi: 10.1093/jxb/erx383 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 56.Luo J, Zhou JJ, Zhang JZ. Aux/IAA gene family in plants: molecular structure, regulation, and function. Int J Mol Sci. 2018; 19: 259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 57.Jiang W, Yin J, Zhang H, He Y, Shuai S, Chen S, et al. Genome-wide identification, characterization analysis and expression profiling of auxin-responsive GH3 family genes in wheat (Triticum aestivum L.). Mol Biol Rep. 2020; 47: 3885–3907. doi: 10.1007/s11033-020-05477-5 [DOI] [PubMed] [Google Scholar]
  • 58.Jain M, Kaur N, Tyagi AK, Khurana JP. The auxin-responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genomics. 2006; 6: 36–46. doi: 10.1007/s10142-005-0142-5 [DOI] [PubMed] [Google Scholar]
  • 59.Apelbaum A, Goldlust A, Icekson I. Control by ethylene of arginine decarboxylase activity in pea seedlings and its implication for hormonal regulation of plant growth. Plant Physiol. 1985; 79: 635–40. doi: 10.1104/pp.79.3.635 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 60.Hao YJ, Kitashiba H, Honda C, Nada K, Moriguchi T. Expression of arginine decarboxylase and ornithine decarboxylase genes in apple cells and stressed shoots. J Exp Bot. 2005; 56: 1105–15. doi: 10.1093/jxb/eri102 [DOI] [PubMed] [Google Scholar]
  • 61.Wang J, Sun PP, Chen CL, Wang Y, Fu XZ, Liu JH. An arginine decarboxylase gene PtADC from Poncirus trifoliata confers abiotic stress tolerance and promotes primary root growth in Arabidopsis. J Exp Bot. 2011; 62: 2899–914. doi: 10.1093/jxb/erq463 [DOI] [PubMed] [Google Scholar]
  • 62.Xu GC, Li L, Han RZ, Dong JJ, Ni Y. Characterization and soluble expression of D-hydantoinase from Pseudomonas fluorescens for the synthesis of D-amino acids. Appl Biochem Biotechnol. 2016; 179: 1–15. doi: 10.1007/s12010-015-1975-6 [DOI] [PubMed] [Google Scholar]
  • 63.Kolukisaoglu Ü. D-amino acids in plants: sources, metabolism, and functions. Int J Mol Sci. 2020; 21: 5421. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 64.Hener C, Hummel S, Suarez J, Stahl M, Kolukisaoglu Ü. d-Amino acids are exuded by Arabidopsis thaliana roots to the rhizosphere. Int J Mol Sci. 2018; 19: 1109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 65.Gordes D, Kolukisaoglu U, Thurow K. Uptake and conversion of d-amino acids in Arabidopsis thaliana. Amino Acids. 2011; 40: 553–563. doi: 10.1007/s00726-010-0674-4 [DOI] [PubMed] [Google Scholar]
  • 66.Serralta-Interian AA, Miranda-Ham MDL, Echevarría-Machado I. Stimulation of root growth and enhanced nitrogenous metabolite content in habanero pepper (Capsicum chinense Jacq.) treated with a d-amino acid mixture. Theor Exp Plant Physiol. 2020; 32: 31–47. [Google Scholar]
  • 67.Bogamuwa S, Jang JC. Plant Tandem CCCH Zinc finger proteins interact with ABA, drought, and stress response regulators in processing-bodies and stress granules. PLoS One. 2016; 11 (3): e0151574. doi: 10.1371/journal.pone.0151574 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 68.Yuan X, Zhang S, Qing X, Sun M, Liu S, Su H, et al. Superfamily of ankyrin repeat proteins in tomato. Gene. 2013; 523: 126–36. doi: 10.1016/j.gene.2013.03.122 [DOI] [PubMed] [Google Scholar]
  • 69.Vo KTX, Kim CY, Chandran AKN, Jung KH, An G, Jeon JS. Molecular insights into the function of ankyrin proteins in plants. J Plant Biol. 2015; 58: 271–284 [Google Scholar]
  • 70.Tominaga R, Iwata M, Sano R, Inoue K, Okada K, Wada T. Arabidopsis CAPRICE-LIKE MYB 3 (CPL3) controls endo reduplication and flowering development in addition to trichome and root hair formation. Development. 2008; 135: 1335–45. doi: 10.1242/dev.017947 [DOI] [PubMed] [Google Scholar]
  • 71.Wada T, Tominaga-Wada R. CAPRICE family genes control flowering time through both promoting and repressing CONSTANS and FLOWERING LOCUS T expression. Plant Sci. 2015; 241: 260–5. doi: 10.1016/j.plantsci.2015.10.015 [DOI] [PubMed] [Google Scholar]
  • 72.Gugger PF, Peñaloza-Ramírez JM, Wright JW, Sork VL. Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata. Tree Physiol. 2017; 37: 632–644. doi: 10.1093/treephys/tpw122 [DOI] [PubMed] [Google Scholar]
  • 73.Hardtke CS. Dispatch. Gibberellin signaling: GRASs growing roots dispatch. Curr Biol. 2003; 13: R366–7. doi: 10.1016/s0960-9822(03)00279-3 [DOI] [PubMed] [Google Scholar]
  • 74.Inomata N, Miyakawa M, Ikeda N, Oda K, Aihara M. Identification of gibberellin-regulated protein as a new allergen in orange allergy. Clin Exp Allergy. 2018; 48: 1509–1520. doi: 10.1111/cea.13247 [DOI] [PubMed] [Google Scholar]
  • 75.Boes N, Schreiber K, Härtig E, Jaensch L, Schobert M. The Pseudomonas aeruginosa universal stress protein PA4352 is essential for surviving anaerobic energy stress. J Bacteriol. 2006; 188: 6529–38. doi: 10.1128/JB.00308-06 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 76.Farhana A, Lappin SL. Biochemistry, Lactate Dehydrogenase. 2021. In: StatPearls. Treasure Island (FL): StatPearls Publishing. [PubMed] [Google Scholar]
  • 77.Chen W, Wei L, Zhang Y, Shi D, Ren W, Zhang Z, et al. Involvement of the two L-lactate dehydrogenase in development and pathogenicity in Fusarium graminearum. Curr Genet. 2019; 65: 591–605. doi: 10.1007/s00294-018-0909-6 [DOI] [PubMed] [Google Scholar]
  • 78.McNeil MB, Hampton HG, Hards KJ, Watson BN, Cook GM, Fineran PC. The succinate dehydrogenase assembly factor, SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria. FEBS Lett. 2014; 588: 414–21. doi: 10.1016/j.febslet.2013.12.019 [DOI] [PubMed] [Google Scholar]

Decision Letter 0

Ching-Hong Yang

27 May 2022

PONE-D-22-09489Endophytic bacterium Bacillus aryabhattai induces novel transcriptomic changes to stimulate plant growth.PLOS ONE

Dear Dr. Borras-Hidalgo,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the major points raised during the review process.

==============================

Especially,Comments 1, 2, 3, and 4 from reviewers #1. It is important to give analysis and conclusion of the RNAseq data.As suggested from reviewer #2, qRT-PCR assay is required  to prove the RNA seq data. This can be focused on keys genes from your RNA seq result. 

==============================

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PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Partly

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: Yes

**********

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Reviewer #2: Yes

**********

5. Review Comments to the Author

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Reviewer #1: This manuscript addresses the Endophytic bacterium Bacillus aryabhattai promotes the growth of Arabidopsis thaliana and Nicotiana tabacum. Although the great potential of various Bacillus spp. in plant growth promotion has been demonstrated in several important crop plants, the molecular mechanism underlying the gene regulation is still unclear. In this study, the RNAseq assay was performed and differentially expressed genes (DEGs) were analyzed in the plant as well as Bacillus aryabhattai. RNAseq data might provide a new highlight into the plant growth promotion under the mutual reaction between the plant and bacteria. Unfortunately, the manuscript has flaws in experiments design, data collection, and interpretation that will prevent publication in its current form.

Major concerns:

1. 30 ml of LB culture with Bacillus aryabhattai was applied to Arabidopsis seedlings twice a week. However, “Plants treated with water were used as a control.” Based on this experiment design, the nutrient from LB broth was a significant impact factor for the growth of tiny Arabidopsis seedlings in terms of the volume and frequency of LB applied.

2. What is the method for RNA extraction from Bacillus aryabhattai? What are the control and treatment of Bacillus aryabhattai?

3. Please clarify the cutoff RPKM value. Could you explain the data from Table 1 “AT4G37990, log2(Fold change) = 14983.5”?

4. In the results part, there is no analysis and conclusion for the RNAseq data. It is not helpful for readers to understand the meanings of RNAseq data by simply listing gene, GO, and KEGG names.

5. Information is not consistent. For example,

A. “Three plants were grown per plastic pot” was claimed but five plants were shown in Figure 1A.

B. “Small plants were sown in a substrate composed of peat plugs and vermiculite (1:1) for 14 days.” “Five-day-old Arabidopsis thaliana and Nicotiana tabacum plants were treated with the B. aryabhattai fermentation product twice weekly for one month.” “At 20 days posttreatment, bacterial inoculation significantly enhanced the fresh and dry weights of the treated Arabidopsis plants.” It is very confused about the days from these statements. How did the author define Five-day-old Arabidopsis thaliana? The seeds were germinated on the 1/2MS plates and transferred into pots. When did the author start to count days?

6. “The bacterium was well established 72 h post inoculation, and leaves, stems, and roots from five plants were collected after establishment.”

A. Is there any evidence to support the statement “The bacterium was well established 72 h post inoculation”?

B. Does this statement imply tissues were collected after 72 h?

Reviewer #2: The MS showed that the endophytic bacterium promotes the growth of Arabidopsis and tobacco plants. The RNA seq data showed that various genes were highly expressed in Arabidopsis plants treated with the bacterium and also some genes of the endophytic bacterial were activated during the interaction. However, no qPCR to prove the RNA seq data.

**********

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Reviewer #2: No

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PLoS One. 2022 Aug 3;17(8):e0272500. doi: 10.1371/journal.pone.0272500.r002

Author response to Decision Letter 0

14 Jun 2022

Dear Prof. Dr. Ching-Hong Yang

Academic Editor

PLOS ONE

This study was supported by the Special Funds for Guiding Local Science and Technology Development of Central Government of Shandong Province (No. YDZX20193700004362). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

With this revision we would like to submit a revised version of our manuscript entitled "Endophytic bacterium Bacillus aryabhattai induces novel transcriptomic changes to stimulate plant growth". We would like to thank you and the referees for the excellent comments made to our manuscript and we feel the comments helped to prepare an improved version of our manuscript.

Here, we would like to address all comments made by the reviewers and the changes we have made to meet those comments. A revised version of the manuscript was submitted in which all changes are indicated in “Red Font” to facilitate the revision procedure.

Best regards

Prof. Orlando Borras-Hidalgo

Reviewers' comments:

Reviewer #1: This manuscript addresses the Endophytic bacterium Bacillus aryabhattai promotes the growth of Arabidopsis thaliana and Nicotiana tabacum. Although the great potential of various Bacillus spp. in plant growth promotion has been demonstrated in several important crop plants, the molecular mechanism underlying the gene regulation is still unclear. In this study, the RNAseq assay was performed and differentially expressed genes (DEGs) were analyzed in the plant as well as Bacillus aryabhattai. RNAseq data might provide a new highlight into the plant growth promotion under the mutual reaction between the plant and bacteria. Unfortunately, the manuscript has flaws in experiments design, data collection, and interpretation that will prevent publication in its current form.

Major concerns:

1. 30 ml of LB culture with Bacillus aryabhattai was applied to Arabidopsis seedlings twice a week. However, “Plants treated with water were used as a control.” Based on this experiment design, the nutrient from LB broth was a significant impact factor for the growth of tiny Arabidopsis seedlings in terms of the volume and frequency of LB applied.

Authors: Excellent observation. We agreed with the reviewer. In the previous version of our manuscript this analysis previously done was not included. We have included this point requested by the reviewer as supporting information in the current version. Basically, we also evaluated the effect of LB medium on Arabidopsis and tobacco plants. We did not find significant differences between the treatment with water and LB medium. Taking account, the reviewer remark, we have included this in the “Results” section as follow:

“The nutrients from the LB broth medium were a key aspect. In terms of the volume and frequency of LB broth medium applied, this could have a substantial impact factor on the growth of little Arabidopsis plants. However, this had not significant impact on Arabidopsis and tobacco plants. There were not statistically significant changes between the two treatments (S2 Table).”

2. What is the method for RNA extraction from Bacillus aryabhattai? What are the control and treatment of Bacillus aryabhattai?

Authors: We agree with the reviewer. This is not clarified in the manuscript. We have included this information in “Materials and Methods” section.

“In total three libraries were constructed as follow: 1) bacterium; 2) Arabidopsis and 3) Arabidopsis treated with bacterium. The Qiagen RNeasy Midi Kit (Hilden, Germany) was used to extract total RNA, and the concentration of total RNA was measured using spectrometry. Following total RNA extraction and DNase I treatment, magnetic beads containing oligo (dT) were used to isolate mRNA (for eukaryotes) or rRNA (for prokaryotes) using the QIAseq FastSelect 5S/16S/23S Kit (Qiagen, Germany).”

3. Please clarify the cutoff FPKM value. Could you explain the data from Table 1 “AT4G37990, log2(Fold change) = 14983.5”?

Authors: We agree with the reviewer. This is not clear in the manuscript. This remark was added as follow in the “Materials and Methods” section.

“The log2-fold change for the up and down regulated plant genes was computed by dividing the FPKM values of Arabidopsis plants treated with the bacterium by the FPKM values of Arabidopsis plants treated with water. While the log2-fold change for the up and down regulated bacterial genes was calculated by dividing the FPKM values of bacterium during the interaction with the plant by the FPKM values of the bacterium grown in LB medium. The 2-fold change cutoff FPKM value was established.”

4. In the results part, there is no analysis and conclusion for the RNAseq data. It is not helpful for readers to understand the meanings of RNAseq data by simply listing gene, GO, and KEGG names.

Authors: We agree with the reviewer and a remark based on his comment has been added in the “Results” section.

“Even though RNA-Seq is the fundamental basis for gene expression profiling, qPCR is the main tool for validation. qRT-PCR analysis was done to validate the data generated by RNA sequencing. The expression levels of plant and bacterium genes matched the RNA-Seq data, indicating that the RNA-Seq results are trustworthy (Fig 7). Cinnamyl alcohol dehydrogenase (106-log2 ratio), apyrase (57-log2 ratio) and thioredoxin H8 (35- log2 ratio) were highest expressed genes in Arabidopsis plants inoculated with B. aryabhattai in a different replication of the experiment. While the zinc finger C-x8-C-x5-C-x3-H type family protein gene (-27-log2 ratio) was highest repressed during the interaction (Fig 7A). Besides, arginine decarboxylase (8-log2) and D-hydantoinase (6-log2) were highest expressed bacterium genes in planta. Meantime, the putative universal stress protein gene (-3-log2) had the most reduced expression (Fig 7B).”

5. Information is not consistent. For example,

A. “Three plants were grown per plastic pot” was claimed but five plants were shown in Figure 1A.

Authors: We agree with the reviewer. It was a mistake. This point was clarified in the document as follow in the “Materials and Methods” section:

“Five Arabidopsis thaliana and four Nicotiana tabacum plants per plastic pot were cultivated in a growth room at 25 °C and maintained with water without fertilizers, respectively.”

B. “Small plants were sown in a substrate composed of peat plugs and vermiculite (1:1) for 14 days.” “Five-day-old Arabidopsis thaliana and Nicotiana tabacum plants were treated with the B. aryabhattai fermentation product twice weekly for one month.” “At 20 days posttreatment, bacterial inoculation significantly enhanced the fresh and dry weights of the treated Arabidopsis plants.” It is very confused about the days from these statements. How did the author define Five-day-old Arabidopsis thaliana? The seeds were germinated on the 1/2MS plates and transferred into pots. When did the author start to count days?

Authors: We agree with the reviewer. This point was clarified in the document as follow in the “Materials and Methods” section:

“Five-day-old A. thaliana and N. tabacum plants (seeds previously germinated in MS basal media, transferred to the substrate, and adapted during five days) were treated with the B. aryabhattai fermentation product twice weekly for one month.”

6. “The bacterium was well established 72 h post inoculation, and leaves, stems, and roots from five plants were collected after establishment.”

A. Is there any evidence to support the statement “The bacterium was well established 72 h post inoculation”?

Authors: We agree with the reviewer. We have clarified this point in the manuscript in the “Material and Methods” section as follow:

“Plant material (stems and roots) were first cleaned with water to establish the endophytic property and establishment time of B. aryabhattai. The samples were sliced into fragments in an aseptic condition. Each sample was surface sterilized for 1 minute with 70% ethanol before being immersed in a 5% sodium hypochlorite solution for 1 minute. The samples were then washed for 1 minute in sterile distilled water and dried on filter paper. Following adequate drying, plant parts were manually handled for 5 minutes in 1 ml of sterile water in a TissueLyser (Qiagen, Hilden, Germany). The debris was decanted, and 100 l of the remaining water was cultured for three days at 37°C in Luria-Bertani (LB) agar medium (sodium chloride, 5 g/L; peptone, 10 g/L; yeast extract, 5 g/L; agar, 12 g/L and pH 7). In addition, the final wash solution from the surface sterilization operation was spread out onto an MS medium plate as a control. Internally isolated bacterium was exclusively isolated from processed materials. This was the factor for classifying endophytes as contrast to surface contaminants. Furthermore, the roots of the plants that had been infected with the endophytic bacterium used in the studies was processed, and the bacterium was collected and categorized as the original strain using the same methodology described above. The bacterial colonization in the roots was confirmed using the same method followed in the isolation of this strain on LB plates at various time periods. The endophytic bacterium was fully established 72 hours after inoculation.”

B. Does this statement imply tissues were collected after 72 h?

Authors: Yes, considering that we already knew when the bacterium was well-established in the interior tissue.

Reviewer #2: The MS showed that the endophytic bacterium promotes the growth of Arabidopsis and tobacco plants. The RNA seq data showed that various genes were highly expressed in Arabidopsis plants treated with the bacterium and also some genes of the endophytic bacterial were activated during the interaction. However, no qPCR to prove the RNA seq data.

Authors: We agree with the reviewer. Now, we have included this information in detail in “Materials and Methods” and “Results” section as follow:

“In a second experiment, the transcripts with the largest expression levels from RNA sequencing were confirmed using quantitative real-time polymerase chain reaction. The experiment was done in accordance with the procedure described above. Primer 5.0 was used to generate the oligonucleotides (S1 Table). Total RNA was extracted with a Qiagen RNeasy kit, and cDNA was prepared with oligo-dT primers and a SuperScript III kit (Invitrogen, Carlsbad, CA, USA). A Rotor-Gene Q PCR equipment (Hilden, Germany) and the QuantiTect SYBR Green PCR Kit were used for real-time quantitative PCR (Qiagen). During RT-qPCR gene quantification, the B. aryabhattai 16S rRNA and A. thaliana -actin genes were selected as internal controls. The real-time PCR reaction conditions were as follows: an initial denaturation step at 95 °C for 15 minutes, followed by denaturation at 95 °C for 15 seconds, an alignment step at 58 °C for 30 seconds, and an extension step at 72 °C for 40 cycles. Q-Gene software was used to calculate relative gene expression as mean normalized expression [35]. The relative fold-change (log2) values were calculated in relation to the control treatment. All quantitative PCR experiments were replicated three times for biological and technical considerations.”

“Even though RNA-Seq is the fundamental basis for gene expression profiling, qPCR is the main tool for validation. qRT-PCR analysis was done to validate the data generated by RNA sequencing. The expression levels of plant and bacterium genes matched the RNA-Seq data, indicating that the RNA-Seq results are trustworthy (Fig 7). Cinnamyl alcohol dehydrogenase (106-log2 ratio), apyrase (57-log2 ratio) and thioredoxin H8 (35- log2 ratio) were highest expressed genes in Arabidopsis plants inoculated with B. aryabhattai in a different replication of the experiment. While the zinc finger C-x8-C-x5-C-x3-H type family protein gene (-27-log2 ratio) was highest repressed during the interaction (Fig 7A). Besides, arginine decarboxylase (8-log2) and D-hydantoinase (6-log2) were highest expressed bacterium genes in planta. Meantime, the putative universal stress protein gene (-3-log2) had the most reduced expression (Fig 7B).”

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Decision Letter 1

Ching-Hong Yang

21 Jul 2022

Endophytic bacterium Bacillus aryabhattai induces novel transcriptomic changes to stimulate plant growth.

PONE-D-22-09489R1

Dear Dr. Borras-Hidalgo,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. There is an additional comment from the review below.

"when G. chinensis (Keng) was firstly appeared, the full name of genus is required to provide."

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Ching-Hong Yang

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: (No Response)

Reviewer #2: When G. chinensis (Keng) was firstly appeared in the M&M, the full name of genus is required to provide.

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Reviewer #1: Yes: Jian Huang

Reviewer #2: No

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Acceptance letter

Ching-Hong Yang

25 Jul 2022

PONE-D-22-09489R1

Endophytic bacterium Bacillus aryabhattai induces novel transcriptomic changes to stimulate plant growth.

Dear Dr. Borras-Hidalgo:

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on behalf of

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Table. List of oligonucleotides used for RNA sequencing validation.

    (XLSX)

    Click here for additional data file. (12.1KB, xlsx)
    S2 Table. Evaluation of the effect of LB broth medium on Arabidopsis and tobacco growth experiment.

    (XLSX)

    Click here for additional data file. (136.6KB, xlsx)
    S3 Table. Plant gene annotation during Arabidopsis-Bacillus aryabhattai interaction.

    (XLSX)

    Click here for additional data file. (5.5MB, xlsx)
    S4 Table. Plant new gene annotation during Arabidopsis-Bacillus aryabhattai interaction.

    (XLSX)

    Click here for additional data file. (1.3MB, xlsx)
    S5 Table. Bacillus aryabhattai gene annotation during the interaction.

    (XLSX)

    Click here for additional data file. (579.6KB, xlsx)
    Attachment

    Submitted filename: Response to Reviewers.docx

    Click here for additional data file. (26.8KB, docx)

    Data Availability Statement

    Data relevant to this study are available from the BioProject at accession numbers PRJNA781678 and PRJNA781727

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