Progress 10/24/16 to 09/30/21
Outputs
Target Audience:The target audicences include undergraduate student, graduate students, postdoctor, the researchers in the related field, extension specialist, farmers, and industry groups. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Altogether, the related project has led to the training of three undergraduate students, three graduate students; one postdoctoral researcher, and three visiting scholars. How have the results been disseminated to communities of interest?Our related research had been presented in local communities, scientific societies, universities, workshops, and conferences for the past five years. The related presentations in 2021: Zhenzhen Zhao, Xianpeng Yang, Shiyou Lü, Jiangbo Fan, Stephen Opiyo, Piao Yang, Jack Mangold, David Mackey, Ye Xia*. Deciphering the novel role of AtMIN7 in cuticle formation and defense against bacterial pathogen infection. American Phytopathology Society (APS) annual meeting online. (2021). Zhenzhen Zhao, Jiangbo Fan, Piao Yang, Zonghua Wang, Stephen Obol Opiyo, David Mackey, Ye Xia*. One Arabidopsis Acyl Carrier Protein is negatively involved in plant defense. Corteva Plant Sciences Symposium, Columbus, USA. (2021). This poster won The First Place of Poster Competition in the related symposium. Piao Yang, Zhenzhen Zhao, Ye Xia. Functional characterizations of bacterial extracellular exudates of three novel Bacillus spp. strains inhibiting the gray mold fungus Botrytis cinerea. Corteva Plant Sciences Symposium and OARDC Annual Meeting, Columbus, USA. (2021). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
For objective 1, (1) The genomes of several beneficial strains had been comparatively analyzed, and the results showed that they all have multiple genes that can contribute to plant growth promotion, such as the genes involved in producing IAA, siderophore, and ammonia. These beneficial strains also have the genes that can contribute to pathogen inhibition, such as the production of acetoin and diacetyl, amylase, pectinase, cellulase, ACC deaminase, and ribonuclease. These data had been further confirmed by the related experimental tests by metabolite analysis and enzyme activity tests. (2) Also, the RNAseq analysis showed that multiple genes involved in different plant pathways, such as the hormone pathways and macronutrient biosynthesis/transportation pathways, had significantly different expression levels between non-beneficial treated- and beneficial treated- Arabidopsis plants. For objective 2, through the 16s rDNA amplicon sequencing results of both leaf and root samples of Arabidopsis plants, it was found that several different plant mutants involved in plant defense also showed different abundance and diversity on the bacterial community compared to the wild-type plants. This indicates that the plant defense pathways are also involved in the interactions with the whole plant-associated microbial community, which may contribute to plants for their growth and health. Altogether, from the project, we discovered the basic mechanisms on how the beneficial bacterial microbes could improve plant growth and health against pathogen infections. We also found that the genes involved in plant defense could be critical for plants' interactions with the whole associated microbial community in addition to the defense against pathogen infections. The related project along a similar vein has been renewed, and more discoveries will help to get deeper understanding on the complex interactions and utilize these beneficial microbes efficiently for enhancing plant growth and health sustainably.
Publications
- Type:
Book Chapters
Status:
Published
Year Published:
2021
Citation:
Kathi J Kemper, Ye Xia, Jeffrey Lakritz, Rattan Lal (2021). Chapter 2: Health of Soil, Plants, Animals, and People. In The Soil-Human Health Nexus. Taylor and Francis Ltd. ISBN-10: 0367422131
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Zhenzhen Zhao, Norbert Bokros, Seth Debolt, Piao Yang, Ye Xia (2021). Genome Sequence Resource of Bacillus sp. RRD69, a Beneficial Bacterial Endophyte Isolated from Switchgrass Plants. Molecular Plant-Microbe Interactions34, 1320-3.
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Progress 10/01/19 to 09/30/20
Outputs
Target Audience:The target audicences include undergraduate students, graduate students, postdoctors, the researchers in the related field, extension specialist, farmers, and industry groups. Changes/Problems:The covid-19 situation led to the closure of the lab and greenhouse for several months; and even now we have limited time allowed for researchers to carry out research experiments in our universityfor safety and health concerns. We all collaborate to cope with this very difficult situation. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?1. A novel Bacillus spp. strain contributes to the plant defense against the biotic and abiotic stresses. The related poster was presented at OARDC Annual Conference and OSU Plant Sciences Symposium, Columbus, USA. (2020). 2. The novel role of Atmin7 in cuticle formation and related defense against bacterial pathogen infection. The related poster was presented at OSU Plant Sciences Symposium, Columbus, USA. (2020). The related invited talk had also been presented in the Annual Meeting of American Phytopathological Society on line. 3. Oxathiapiprolin, a novel chemical inducer activates plant resistance. The related poster was presented at OSU Plant Sciences Symposium, Columbus, USA. (2020). 4. Identification of Alternaria tenuissima from tomato plants and its biocontrol by the beneficial bacteria. The related poster was presented at OSU Plant Sciences Symposium, Columbus, USA. (2020). This poster won First Place in the Poster Competition. What do you plan to do during the next reporting period to accomplish the goals?For objective 1, The genome sequences of several identified beneficial microbes for the related beneficial function will be further studied and compared with the several published strains. The UP LC-MS/MS will be applied to screen and identify the related compounds/small molecules from the beneficial microbes that potentially involve indirect pathogen inhibition, plant growth promotion, and the activation of the induced systemic resistance (ISR). The RNAseq and real-time PCR will be applied to target the activated plant genes/pathways that contribute to ISR. For objective 2, The 16s rDNA amplicon sequencing results from both the leaf and root samples will be further analyzed to obtain more insights into the related functional mechanisms. The root exudate metabolites from wild type (Col-0) vs. those in the related mutant plants will be extracted and analyzed comparatively. The potential metabolites from the roots that could be involved in the Arabidopsis-microbiome interaction will be identified. The plant defense-related phenotypes will be further studied.
Impacts
What was accomplished under these goals?
For objective 1: (1) More beneficial bacterial strains, which can inhibit diverse pathogens directly or/and activate Arabidopsis and Tomato plants' induced resistance to Pto and diverse fungal pathogen infections, have been identified and further studied. (2) The genome sequence of several related beneficial bacterial strains was obtained and analyzed. (3) The RNAseq or/and Real-time PCR analysis of Arabidopsis leaf and root tissues, treated with the above-mentioned beneficial bacterial strains, had been carried out and analyzed to target the genes/ pathways that were either up-regulated or down-regulated compared to the water control treatment. (4) Arabidopsis plant leaf samples treated with the above-mentionedbeneficial bacterial strains and water control had been collected and prepared for the analysis of the secondary metabolite production, such as the hormone SA, JA, ABA by UPLC-MS/MS. For objective 2: (1) The 16s rDNA amplicon sequencing results of root and rhizosphere samples from different Arabidopsis mutants and wild type (Col-0) plants had been further analyzed for the bacterial community composition, abundance, and diversity. (2) Multiple genes of Arabidopsis plants involved in regulating their associated microbial community had been identified and further analyzed. (3)The plant defense-related phenotypes were studied.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Zhenzhen Zhao, Xianpeng Yang, Shiyou L�, Jiangbo Fan, Stephen Opiyo, Piao Yang, Jack Mangold, J., David Mackey, *Ye Xia (2020). Deciphering the Novel Role of AtMIN7 in Cuticle Formation and Defense against the Bacterial Pathogen Infection. International Journal of Molecular Sciences. 21, 5547.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Qin Peng, Zhiwen Wang, Pengfei Liu, Yinping Liang, Zhenzhen Zhao, Wenhui Li, * Xili Liu and *Ye Xia (2020). Oxathiapiprolin, a novel chemical inducer activates the plant disease resistance. International Journal of Molecular Sciences. 21(4), 1223; https://doi.org/10.3390/ijms21041223.
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:The target audicences include undergraduate students, graduate students, postdoctors, the researchers in the related field, extension specialist, farmers, and industry groups. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?The related project has led to the training of three under-graduate students (Jack A. Mangold, Madison Cahill, Happy Kwok);two graduate students (Zhenzhen Zhao and Piao Yang); one postdoctor researcher (Jiangbo fan). How have the results been disseminated to communities of interest?Our related research had been presented in local communities, scientific societies, universities, workshops, and conferences. Selected presentation list: The roles of plant surface in plant defense against diverse pathogens. Mississippi State University, MS, USA (2019). The bio-control activity of a Bacillus strain against diverse destructive plant pathogens. American Phytopathological Society Annual Meeting, Cleveland, OH, USA. (2019). Functional characterization of a novel Bacillus strain in promoting Arabidopsis plant root growth. OARDC Annual Conference and DuPont Plant Sciences Symposium, Columbus, OH, USA. (2019). Deciphering the role of a novel Pseudomonas poae strain in enhancing Arabidopsis plant root development and defense against diverse pathogens. OARDC Annual Conference and DuPont Plant Sciences Symposium, Columbus, OH, USA. The role of a fatty acid synthesis related protein in plant defense. Plant Lipids: Structure, Metabolism and Function Conference GRC - Gordon Research Conferences, USA. Galveston, Texas, USA. (2019). What do you plan to do during the next reporting period to accomplish the goals?For objective 1, (1) Further analyze the genome sequences of several identified beneficial microbes for the related beneficial function study. (2) The compounds/small molecules from the beneficial microbes that potentially involved in pathogen inhibition, promoting plant growth, and the induced systemic resistance (ISR)activation will be screened and identified by LC-MS/MS. (3) The activated plant genes/pathways that contribute to ISR will be further identified and the related phenotypes will be characterized. For objective 2, (1) Further analyze the 16s rDNA amplicon sequencing results to obtain more insights for the related mechanisms. (2) For the identified genes involved in regulating the Arabidopsis plants' associated microbial community, the root exudate metabolite analysis for wild type (Col-0) and related mutant plants will be extracted and compared comparatively, the potential metabolites from the roots that could be involved in the Arabidopsis-microbiome interaction will be identified. (3) The plant defense related phenotypes will be further studied.
Impacts
What was accomplished under these goals?
For objective 1: (1) More beneficial bacterial strains, which can inhibit diverse pathogens directly or/and activate Arabidopsis and Tomato plants' induced resistance to Pto and diverse fungal pathogen infections, have been identified. (2) Genome sequenceof several related beneficial bacterial strains was carried out. (3) The RNAseq or/and Real time PCR analysis of Arabidopsis leaf and root tissues, treated with two above mentioned beneficial bacterial strains, had been carried out to target the genes/ pathways that were either up-regulated or down-regulated compared with the water control treatment. (4) Arabidopsis plant samples treated with two beneficial bacterial strains and water control, including the leave samples, had been collected and further analyzed for the secondary metabolite production, such as the hormone SA, JA, ABA by UPLC-MS /MS. For objective 2: (1) The 16s rDNA amplicon sequencing results of root and rhizosphere samples from different Arabidopsis mutants and wild type (Col-0) plants had been analyzed for the bacterial community composition, abundance, and diversity. (2) Several genes of Arabidopsis plants involved in regulating their associated microbial community had been identified. (3) The real time PCR analysis for the related genes of Arabidopsis plant samples had been carried out.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
* corresponding author
Sahib MR, Piao Yang, Norbert Bokros, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides, *Ye Xia, *Seth DeBolt (2019) (*Co-corresponding author). Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. Microbiology Resource Announcements. 8 (45) e00927-19; DOI: 10.1128/MRA.00927-19
*Ye Xia, Seth DeBolt, Qin Ma, Adam McDermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides (2019). Improved Draft Genome Sequence of Bacillus sp. YF23 with plant growth promoting activity. Microbiology Resource Announcements. DOI: 10.1128/MRA.00099-19.
*Ye Xia, Seth DeBolt, Qin Ma, Adam McDermaid, Cankun Wang, Nicole Shapiro, Tanja Woyke, Nikos C. Kyrpides (2019). Improved Draft Genome Sequence of Pseudomonas poae strain A2-S9 with plant growth promoting activity. Microbiology Resource Announcements. DOI: 10.1128/MRA.00275-19.
*Ye Xia, Sahib MR, Amna A, Opiyo SO, Zhao Z, Gao YG (2019). Culturable endophytic fungal communities associated with plants in organic and conventional farming systems and their effects on plant growth. Scientific Reports 9:1669.
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The target audience may be undergraduate students, graduate students, postdoctors,researchers in the related field, extension specialist, farmers,industries, and other stakeholders. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The related project has led to the training of three under-graduate students (Caleb Mathia, Jack A. Mangold, Madison Cahill); two graduate students (Zhenzhen Zhao and Piao Yang); one postdoctor researcher (Jiangbo fan). How have the results been disseminated to communities of interest?Our related research has been presented in local communities, scientific societies, institutes, universities, workshops, and conferences. What do you plan to do during the next reporting period to accomplish the goals?For objective 1: (1) The RNAseq or/and Real time PCR analysis of Arabidopsis leaf and root tissues will be carried out to target the genes and pathways that could be up-regulated or down-regulated by the associated beneficial microbes compared with the water control. (2) Arabidopsis plant samples treated with beneficial microbes and water control, including the leaves and roots, will be collected and further analyzed for their primary and secondary metabolites production by UPLC-MS or/and GC-MS. (3) The compounds/small molecules from the beneficial microbes that potentially involved in promoting plant growth and activate plant immunity will be screened and identified by LC-MS. For objective 2: (1a) The 16s rDNA amplicon sequencing result of rhizosphere samples from different Arabidopsis mutants and wild type (Col-0) control will be further analyzed for the bacterial community composition, abundance, and diversity. The genes involved in regulating the microbial community associated with Arabidopsis plants will be identified. (1b) For the identified genes, the root exudate metabolite analysis for wild type (Col-0) and related mutant plants will be extracted and compared comparatively, the potential metabolites from the roots that could be involved in the Arabidopsis-microbiome interaction will be identified. (2) The RNAseq or/and real time PCR analysis of Arbidopsis plant root samples will be carried out, the potential genes/pathways involved in plant and Bacillus species interactions will be identified.
Impacts
What was accomplished under these goals?
For objective 1: (1) Our results show that the studied Pfu strain promotes the Arabidopsis lateral root and root hair growth. By screening different Arabidopsis plant hormone mutants for their response to the Pfu, we identify that the auxin pathway is involved in this Arabidopsis- Pfu interaction. The manuscript is in preparation and will be submitted shortly. (2) The RNA samples of Arabidopsis plants treated with the Pfu strain and water control have been extracted and sent for RNAseq analysis. (3) The comparative analysis of this targeted Pfu strain has been carried out to compare with some other reported Pfu strains. For objective 2: (1) The rhizosphere samples from different Arabidopsis mutants and wild type (Col-0) control had been collected, the microbial DNA in the rhizosphere soil had been extracted, the 16s rDNA amplicon sequencing had been carried out, and the related data has been obtained and needs to be further analyzed. (2a) The genome sequence for one Bacillus strain has been done and further analyzed and the genome DNA of the other Bacillus strain has been extracted and sent for sequencing. (2b) The RNA samples of Arabidopsis plants treated with two Bacillus strains and water controls have been extracted and sent for RNAseq analysis.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Carmit Ziv, Zhenzhen Zhao, Yu Gary Gao, and *Ye Xia (2018). The multifunctional roles of plant cuticle during plant-pathogen interactions. Invited review. Frontiers in Plant-Microbe Interaction.
doi: 10.3389/fpls.2018.01088
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Ye Xia, Amna Amna, Stephen Opiyo (2018). The culturable endophytic fungal communities of switchgrass grown on a coal-mining site and their effects on plant growth. PLOS ONE 13(6): e0198994. https://doi.org/10.1371/journal.pone.0198994.
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Progress 10/24/16 to 09/30/17
Outputs
Target Audience:The target audicences include undergraduate student, graduate students, postdoctor, the researchers in the related field, extension specialist, farmers, and industry groups. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided the traning for one postdoctor, four graduate students, and one undergraduate student. They have been trained on project development and skills in using the integrated molecular, genetic/genomic, metabolic approaches for related resaerch. How have the results been disseminated to communities of interest?Yes, the results have been disseminated to the scientific community, extention specialist, and farmers through oral and poster presentations: (1). 2017. Beneficial microbes and soil-plant microbiomes. Conservation Tillage and Technology Conference, Ada, OH, USA. (2). 2017. Plant endophytes and their effects on plant growth and defense. Presented at Northeast Forestry University, Harbin, China (3). 2017. Plant associated micorbiome and their roles in plant health and growth. Presented at Northeast Agricultural University, Harbin, China (4). 2017. Mobile signals and regulation of plant systemic immunity. Presented at Fujian Agriculture and Forestry University, Fuzhou, China (5). 2017. Priming and mobile signals of plant systemic acquired resistance. Presented at University of Hawaii, Honolulu, USA (6).2017. Systemic signaling of plant systemic acquired resistance. Presented at China Agricultural University, Beijing, China (7). 2017. Current advances of the plant systemic resistance (SAR). Presented at Chinese Ministry of Agriculture Summer Workshop, Beijing, China (8) 2016. Plant associated microbiome for plant yield and health. OARDC (Ohio Agricultural Research and Education Center) Annual meeting, Wooster, OH, USA (9) 2016. The importance of beneficial microbes for plant growth and soil health. Ohio Ecological Food and Farm Association Annual Meeting, Granville, OH, USA What do you plan to do during the next reporting period to accomplish the goals? · We will make further progress on the related experiments, publish our data and finding in scientific journals/books, present our results in professional communities, and develop further collaboration with farmers and industry. · For object 1, we will further investigate the related genes and pathways of arabidopsis plants involved in the beneficial interaction with thePseudomonas strain for plant growth and disease resistance; on the other hand, the components of Pseudomonas strain that could contribute to the related beneficial effects on plants will be further studied by genetic modification and metabolite/enzyme analysis. The expected results will lead to further understanding of the multiple scale interactions among plant, pathogen, and beneficial microbes. · For object 2, we will further investigate the genes/pathways of arabidopsis plants involved in recruiting associated microbial community from the soil for their growth and health and contributing to the beneficial interactions with the identified two Bacillus spp. strains by integrating the genetic, molecular, and metabolic approaches. The components contributing to the beneficial effects of two Bacillus spp. strains will also be further investigated.
Impacts
What was accomplished under these goals?
For objective 1, we isolated and identified one Pseudomonas strain that could activate the Arabidopsis and tomato plants' ISR against Pseudomonas syringae pv. tomato (Pto) infection. This strain also has direct inhibition effects on the growth of Pto by in-vitro plate assay. In addition, this strain could also promote Arabidopsis root growth and may help the plants to take up more nutrients. We have been working on the genome, metabolite, and enzyme activity analysis of this strain, which is focused on the potential components contributing to the growth promotion, pathogen inhibition, and induced disease resistance against Pto. It was found that this strain did not have the metabolite gene clusters related with the antibiotic production, such as hydrogen cyanide (HCN), 2,4-diacetylphloroglucinol (DAPG), pyoverdine, and pyrrolnitrin for direct inhibition of the pathogen. Our metabolite analysis of bacterial assay also showed that this strain did not produce HCN and organic acid, which could contribute to the pathogen inhibition effects. But this strain has the gene cluster homolog to mangotoxin biosynthesis, which may be involved in the pathogen inhibition and needs to be further investigated. In addition, this strain has catalase activity and could produce siderophore, which may be associated with its pathogen inhibition activities. Our result also showed that this strain could produce IAA, which may be associated with its beneficial effects on promoting plant root growth. Now we are working on identifying the related genes and signaling pathways of Arabidopsis plants that could be involved in the beneficial interactions with this beneficial bacteria strain for both growth promotion and ISR. By using mutant screening two Arabidopsis genes have been identified to affect the root development upon this bacteria interaction, the related mechanism needs to be further investigated. For objective two, we already screened and obtained diverse Arabidopsis homozygous mutant lines defective in diverse pathways associated with plant defense and we are working on the investigation of their associated endophytic and rhizosphere microbiome compared with wild type plants in green house controlled environment. Our aim is to target certain genes/pathways of Arabidopsis that play critical roles in recruiting the associated microbial community from the soil for their growth and health, which may lead to develop the strategy to engineer the plants to gain their favorite microbiome for their growth and health. Also we identified two different Bacillus spp. strains, which show high similarity based on their genome sequence. Both of them could induce plants' resistance against Pto and increase the whole plant biomass. These two strains did not show direct inhibition activity on Pto by in-vitro plate assay, but show direct inhibition activities on fungal Botrytis cinerea. It was found that these two strains both show the catalase, amylase, glucanase, and cellulase activities, which may contribute to fungal pathogen inhibition. One strain could produce organic acid, but not the other; one could produce dark brown color pigment, but not the other. Also both of them could produce IAA and siderophore, which may be related with growth promotion activity. The comparative genomic and metabolomic analysis are under investigation and more details on how these two beneficial microbes interact with the host plants to confer beneficial effects on plant growth and disease resistance will be discovered. Arabidopsis genes and pathways involved in the associated beneficial interactions are also under the investigation. The project presented here will facilitate both the basic study on the beneficial and harmful interactions of plants with beneficial microbes and pathogens on both sides, it will also contribute to develop strategy to utilize the beneficial microbes and interactions to improve crop growth, health, and yield in real agricultural practices by using the sustainable approach to reduce the chemical application, which are harmful to environment and human health.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
1. Ye Xia, 2017. Beneficial microbes and soil-plant microbiomes. Conservation Tillage and Technology Conference, Ada, OH, USA
2. Ye Xia, 2017. Plant endophytes and their effects on plant growth and defense. Presented at Northeast Forestry University, Harbin, China
3. Ye Xia, 2017. Plant associated micorbiome and their roles in plant health and growth. Presented at Northeast Agricultural University, Harbin, China
4. Ye Xia, 2017. Mobile signals and regulation of plant systemic immunity. Presented at Fujian Agriculture and Forestry University, Fuzhou, China
5. Ye Xia, 2017. Priming and mobile signals of plant systemic acquired resistance. Presented at University of Hawaii, Honolulu, USA
6. Ye Xia, 2017. Systemic signaling of plant systemic acquired resistance. Presented at China Agricultural University, Beijing, China
7. Ye Xia, 2017. Current advances of the plant systemic resistance (SAR). Presented at Chinese Ministry of Agriculture Summer Workshop, Beijing, China
8. Ye Xia, 2016. Plant associated microbiome for plant yield and health. OARDC (Ohio Agricultural Research and Education Center) Annual meeting, Wooster, OH, USA
9. Ye Xia, 2016. The importance of beneficial microbes for plant growth and soil health. Ohio Ecological Food and Farm Association Annual Meeting, Granville, OH, USA
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