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Zhang J, Zhou X, Zhang Y, Dai Z, He Z, Qiu Y, Alharbi SA, Wei F, Wei L, Ahmed W, Ji G. Pre-soil fumigation with ammonium bicarbonate and lime modulates the rhizosphere microbiome to mitigate clubroot disease in Chinese cabbage. Front Microbiol 2024; 15:1376579. [PMID: 38686113 PMCID: PMC11057235 DOI: 10.3389/fmicb.2024.1376579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Background Plasmodiophora brassicae is an ever-increasing threat to cruciferous crop production worldwide. Aims and methods This study investigated the impact of pre-soil fumigation with ammonium bicarbonate (N) and lime (NB) to manage clubroot disease in Chinese cabbage through 16S rRNA gene amplification sequencing. Results We found that soil fumigation with N and NB suppressed disease incidence by reducing the soil acidity and population of P. brassicae in the rhizosphere. Minimum disease incidence and maximum relative control effect of about 74.68 and 66.28% were achieved in greenhouse and field experiments, respectively, under the combined application of ammonium bicarbonate and lime (LNB) as compared with N, NB, and control (GZ). Microbial diversity analysis through Miseq sequencing proved that pre-soil fumigation with N, NB, and LNB clearly manipulated rhizosphere microbial community composition and changed the diversity and structure of rhizosphere microbes compared with GZ. Bacterial phyla such as Proteobacteria, Bacteriodetes, and Acidobacteria and fungal phyla including Olpidiomycota and Ascomycota were most dominant in the rhizosphere of Chinese cabbage plants. Soil fumigation with N and NB significantly reduced the abundance of clubroot pathogen at genus (Plasmodiophora) level compared with GZ, while decreased further under combined application LNB. Microbial co-occurrence network analysis showed a highly connected and complex network and less competition for resources among microbes under combined application LNB. Conclusion We conclude that for environmentally friendly and sustainable agriculture, soil fumigation with combined ammonium bicarbonate and lime plays a crucial role in mitigating Chinese cabbage clubroot disease by alleviating soil pH, reducing pathogen population, and manipulating the rhizosphere microbiome.
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Affiliation(s)
- Jinhao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Xinghai Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yu Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning Guangxi, China
| | - Zhenlin Dai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Zulei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yue Qiu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Sulaiman Ali Alharbi
- Department of Botany and Microbiology College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fangjun Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Lanfang Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Agricultural Foundation Experiment Teaching Center, Yunnan Agricultural University, Kunming, China
| | - Waqar Ahmed
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Guanghai Ji
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, China
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Ye T, Su H, Zheng G, Meng H, Wang W, Guo Y. Multiomics Reveals the Key Microorganisms and Metabolites in the Resistance to Root Rot Disease of Paris polyphylla. Genes (Basel) 2023; 15:21. [PMID: 38254911 PMCID: PMC10815090 DOI: 10.3390/genes15010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Root rot of Paris polyphylla has received widespread attention due to its threat to yield and leads to serious economic losses. However, the relationship among the rhizosphere microbial community, metabolites and root rot disease remained largely unexplored. Herein, we used integrated 16S rRNA, ITS, RNA sequencing and UPLC-MS/MS to systematically investigate the differences between healthy and diseased P. polyphylla. We found that root rot reduced the microbial diversity in the diseased P. polyphylla compared with the healthy control. The relative abundance of the bacterial phylum Actinobacteria increased in the diseased rhizome of P. polyphylla. For the fungal community, root rot disease contributed to an increased relative abundance of Ascomycota and decreased Glomeromycota at the phylum level. The transcriptomic results showed that the differently expressed genes were significantly enriched in the "Biosynthesis of various alkaloids", "flavonoid biosynthesis" and "isoflavonoid biosynthesis" and "Phenylpropanoid biosynthesis" was dramatically enriched in healthy P. polyphylla compared with that in diseased P. polyphylla. Likewise, the metabolomic results showed that the biosynthesis of secondary metabolites and metabolic pathways was found to be significantly enriched by differential metabolites. Taken together, the study of combining metabolomics with microbiomes can help us enhance our understanding of the mechanisms of plant resistance to root rot disease, thereby discovering specific metabolites and microorganisms that can resist pathogen infection in P. polyphylla.
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Affiliation(s)
- Ting Ye
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
| | - Hailan Su
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Germplasm Resources Center, Fuzhou 350000, China;
| | - Guohua Zheng
- Plant Introduction & Quarantine Base and Plant Product Key Laboratory of Xiamen City, Xiamen Overseas Chinese Subtropical Plant Introduction Garden, Xiamen 361002, China;
| | - Hongyan Meng
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
| | - Wenhua Wang
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
| | - Ying Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen 361006, China; (T.Y.); (H.M.); (W.W.)
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Ding L, Zhou H, Liang HD, Tan L, Zhao H, Chen XJ, Ren ZH. Efficacy of Streptomyces melanosporofaciens strain X216 at controlling clubroot disease on oilseed rape. Front Microbiol 2023; 14:1249813. [PMID: 37795295 PMCID: PMC10546314 DOI: 10.3389/fmicb.2023.1249813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
Oilseed rape (Brassica napus L.) is highly susceptible to infection from the soilborne pathogen Plasmodiophora brassicae Woronin that causes clubroot disease and deleteriously affects production throughout the world. In this study, biological control resources were explored by isolating 237 strains of bacteria from fields of oilseed rape using the gradient dilution coating method. A strain with strong antagonistic ability was screened using a plate confrontation test and designated X216. It was identified as Streptomyces melanosporofaciens owing to its morphological characteristics and 16S rRNA gene sequence. This study also examined the lethality of strain X216 to the resting spores of P. brassicae, its influence on infection in root hairs, and its ability to control clubroot on oilseed rape. The corrected lethality rate on resting spores after strain X216 had been used for 14 days was 56.59% ± 1.97%, which was significantly higher than the use of 75% of the fungicides chlorothalonil WP and 20% Fluazinam SC. Significantly fewer root hairs were infected after this treatment. A pot test showed that X216 was 62.14% effective at controlling the disease, which was not significantly different from that of the fungicide 100 g L-1 cyazofamid SC diluted 1,000-fold but significantly higher than those of 75% chlorothalonil and 50% carbendazim WP. Strain X216 controlled 43.16% of the incidence of clubroot in the field, which could significantly reduce the disease index of oilseed rape clubroot. Therefore, strain X216 is promising to study for the biological control of oilseed rape clubroot.
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Affiliation(s)
- Lin Ding
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Hu Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Yueyang Inspection and Testing Center, Yueyang, China
| | - Hai-di Liang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Lin Tan
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Hui Zhao
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Xiao-jun Chen
- College of Agricultural, Hunan Agricultural University, Changsha, China
| | - Zuo-hua Ren
- College of Plant Protection, Hunan Agricultural University, Changsha, China
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Wei X, Fu T, He G, Zhong Z, Yang M, Lou F, He T. Characteristics of rhizosphere and bulk soil microbial community of Chinese cabbage ( Brassica campestris) grown in Karst area. Front Microbiol 2023; 14:1241436. [PMID: 37789857 PMCID: PMC10542900 DOI: 10.3389/fmicb.2023.1241436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/24/2023] [Indexed: 10/05/2023] Open
Abstract
Understanding the rhizosphere soil microbial community and its relationship with the bulk soil microbial community is critical for maintaining soil health and fertility and improving crop yields in Karst regions. The microbial communities in the rhizosphere and bulk soils of a Chinese cabbage (Brassica campestris) plantation in a Karst region, as well as their relationships with soil nutrients, were examined in this study using high-throughput sequencing technologies of 16S and ITS amplicons. The aim was to provide theoretical insights into the healthy cultivation of Chinese cabbage in a Karst area. The findings revealed that the rhizosphere soil showed higher contents of organic matter (OM), alkaline hydrolyzable nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), total potassium (TK), total nitrogen (TN), catalase (CA), urease (UR), sucrase (SU), and phosphatase (PHO), in comparison with bulk soil, while the pH value showed the opposite trend. The diversity of bacterial and fungal communities in the bulk soil was higher than that in the rhizosphere soil, and their compositions differed between the two types of soil. In the rhizosphere soil, Proteobacteria, Acidobacteriota, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla, while Olpidiomycota, Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungal phyla. In contrast, the bulk soil was characterized by bacterial dominance of Proteobacteria, Acidobacteriota, Chloroflexi, and Actinobacteriota and fungal dominance of Ascomycota, Olpidiomycota, Mortierellomycota, and Basidiomycota. The fungal network was simpler than the bacterial network, and both networks exhibited less complexity in the rhizosphere soil compared with the bulk soil. Moreover, the rhizosphere soil harbored a higher proportion of beneficial Rhizobiales. The rhizosphere soil network was less complicated than the network in bulk soil by building a bacterial-fungal co-occurrence network. Furthermore, a network of relationships between soil properties and network keystone taxa revealed that the rhizosphere soil keystone taxa were more strongly correlated with soil properties than those in the bulk soil; despite its lower complexity, the rhizosphere soil contains a higher abundance of bacteria which are beneficial for cabbage growth compared with the bulk soil.
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Affiliation(s)
- Xiaoliao Wei
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tianling Fu
- Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Institute of New Rural Development, Guizhou University, Guiyang, China
| | - Guandi He
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhuoyan Zhong
- College of Agriculture, Guizhou University, Guiyang, China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Fei Lou
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tengbing He
- College of Agriculture, Guizhou University, Guiyang, China
- Engineering Key Laboratory for Pollution Control and Resource Reuse Technology of Mountain Livestock Breeding, Institute of New Rural Development, Guizhou University, Guiyang, China
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Xie Q, Wei X, Liu Y, Han F, Li Z. Germplasm Enhancement and Identification of Loci Conferring Resistance against Plasmodiophora brassicae in Broccoli. Genes (Basel) 2022; 13:1600. [PMID: 36140766 PMCID: PMC9498593 DOI: 10.3390/genes13091600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
In order to breed broccoli and other Brassica materials to be highly resistant to clubroot disease, 41 Brassicaceae varieties were developed and identified between 2020 and 2021. Seven known clubroot genes were used for screening these materials. In addition, the resistant and susceptible broccoli cultivars were designed for observing their differences in the infection process with Plasmodiophora brassicae. The results showed that 90% of total materials had carried more than two clubroot resistance genes: one material carried two disease resistance genes, four materials carried seven genes for clubroot resistance, two materials carried six genes for clubroot resistance, and in total 32% of these materials carried five genes for clubroot resistance. As a result, several new genotypes of Brassicaceae germplasm were firstly created and obtained based on distant hybridization and identification of loci conferring resistance against Plasmodiophora brassicae in this study. We found and revealed that similar infection models of Plasmodiophora brassicae occurred in susceptible and resistant cultivars of broccoli, but differences in infection efficiency of Plasmodiophora brassicae also existed in both materials. For resistant broccoli plants, a small number of conidia formed in the root hair, and only a few spores could enter the cortex without forming sporangia while sporangia could form in susceptible plants. Our study could provide critical Brassica materials for breeding resistant varieties and new insight into understanding the mechanism of plant resistance.
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Ni H, Zong R, Sun J, Wu Y, Yu L, Liu Y, Liu J, Ju R, Sun X, Zheng Y, Tan L, Liu L, Dong Y, Li T, Zhang Y, Tu Q. Response of Bacterial Community to the Occurrence of Clubroot Disease in Chinese Cabbage. Front Microbiol 2022; 13:922660. [PMID: 35875525 PMCID: PMC9298529 DOI: 10.3389/fmicb.2022.922660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clubroot disease is a common soilborne disease caused by Plasmodiophora brassicas Wor. and widely occurs in Chinese cabbage. Soil microorganisms play vital roles in the occurrence and development of plant diseases. The changes in the soil bacterial community could indicate the severity of plant disease and provide the basis for its control. This study focused on the bacterial community of the clubroot disease-infected soil-root system with different severity aiming to reveal the composition and structure of soil bacteria and identified potential biomarker bacteria of the clubroot disease. In the clubroot disease-infected soil, the bacterial community is mainly composed of Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacilli, Thermolrophilia, Bacteroidia, Gemmatimonadetes, Subgroup_6, Deltaproteobacteria, KD4-96, and some other classes, while the major bacterial classes in the infected roots were Oxyphotobacteria, Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacilli, Bacteroidia, Saccharimonadia, Thermoleophilia, Clostridia, Chloroflexia, and some other classes. The severe clubroot disease soil-root system was found to possess a poorer bacterial richness, evenness, and better coverage. Additionally, a significant difference was observed in the structure of the bacterial community between the high-severity (HR) and healthy (LR) soil-root system. Bacillus asahii and Noccaea caerulescens were identified as the differential bacteria between the LR and HR soil and roots, respectively. pH was demonstrated as a vital factor that was significantly associated with the abundance of B. asahii and N. caerulescens. This study provides novel insight into the relationship between soil bacteria and the pathogen of clubroot disease in Chinese cabbage. The identification of resistant species provides candidates for the monitoring and biocontrol of the clubroot disease.
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Affiliation(s)
- Haiping Ni
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China.,Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Rui Zong
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Jianjun Sun
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Yuxia Wu
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China.,Shandong Agricultural Technology Extension Center, Jinan, China
| | - Lei Yu
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Yuanyuan Liu
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Jin Liu
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Ruicheng Ju
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Xianli Sun
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Yulian Zheng
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Lekun Tan
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Lumin Liu
- Qingdao Hexie Biotechnology Co., Ltd., Qingdao, China
| | - Yachao Dong
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tao Li
- Shandong Agricultural Technology Extension Center, Jinan, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, China.,Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiang Tu
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Zhang J, Ahmed W, Dai Z, Zhou X, He Z, Wei L, Ji G. Microbial Consortia: An Engineering Tool to Suppress Clubroot of Chinese Cabbage by Changing the Rhizosphere Bacterial Community Composition. Biology (Basel) 2022; 11:biology11060918. [PMID: 35741438 PMCID: PMC9219690 DOI: 10.3390/biology11060918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022]
Abstract
Clubroot disease, caused by Plasmodiophora brassicae, is a serious threat to Chinese cabbage (Brassica rapa subsp. pekinensis) production, which results in extensive yield losses. At present, clubroot control mainly depends upon pesticides, which provoke food-safety concerns, and the application of sole biocontrol agents cannot successfully control the disease. In this study, we investigated the effect of Bacillus cereus BT-23, Lysobacter antibioticus 13-6, and Lysobacter capsici ZST1-2 as sole strains, intra-/inter-genus co-culture, and microbial consortia on clubroot disease, plant growth, and rhizosphere bacterial diversity in a field experiment. The microbial consortia efficiently controlled the incidence of clubroot disease, with a biocontrol effect of about 65.78%, by decreasing the soil acidity and enhancing the yield (17,662.49 kg/acre). The high-throughput sequencing results demonstrated that the phyla Proteobacteria and Bacteroidetes were present in high relative abundance in the rhizosphere soil of the Chinese cabbage. Furthermore, Firmicutes was found as a unique phylum in the rhizosphere soil of CK-H and T1-T7, except for CK-D. The application of microbial consortia recovers the imbalance in indigenous microbial communities. Therefore, we conclude that microbial consortia can reduce the clubroot incidence in Chinese cabbage by decreasing the soil acidity and altering the diversity and structure of rhizosphere bacterial communities. This study highlights the potential of microbial consortia as an engineering tool to control devastating soilborne diseases in commercial crops.
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Affiliation(s)
- Jinhao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Waqar Ahmed
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Zhenlin Dai
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Xinghai Zhou
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Zulei He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Lanfang Wei
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Agricultural Foundation Experiment Teaching Center, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (L.W.); (G.J.)
| | - Guanghai Ji
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (J.Z.); (W.A.); (Z.D.); (X.Z.); (Z.H.)
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (L.W.); (G.J.)
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Ludwig-Müller J. What Can We Learn from -Omics Approaches to Understand Clubroot Disease? Int J Mol Sci 2022; 23:ijms23116293. [PMID: 35682976 PMCID: PMC9180986 DOI: 10.3390/ijms23116293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
Clubroot is one of the most economically significant diseases worldwide. As a result, many investigations focus on both curing the disease and in-depth molecular studies. Although the first transcriptome dataset for the clubroot disease describing the clubroot disease was published in 2006, many different pathogen-host plant combinations have only recently been investigated and published. Articles presenting -omics data and the clubroot pathogen Plasmodiophora brassicae as well as different host plants were analyzed to summarize the findings in the richness of these datasets. Although genome data for the protist have only recently become available, many effector candidates have been identified, but their functional characterization is incomplete. A better understanding of the life cycle is clearly required to comprehend its function. While only a few proteome studies and metabolome analyses were performed, the majority of studies used microarrays and RNAseq approaches to study transcriptomes. Metabolites, comprising chemical groups like hormones were generally studied in a more targeted manner. Furthermore, functional approaches based on such datasets have been carried out employing mutants, transgenic lines, or ecotypes/cultivars of either Arabidopsis thaliana or other economically important host plants of the Brassica family. This has led to new discoveries of potential genes involved in disease development or in (partial) resistance or tolerance to P. brassicae. The overall contribution of individual experimental setups to a larger picture will be discussed in this review.
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Pang Z, Mao X, Xia Y, Xiao J, Wang X, Xu P, Liu G. Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain. Microbiol Spectr 2022; 10:e0238521. [PMID: 35225655 PMCID: PMC9045327 DOI: 10.1128/spectrum.02385-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 01/19/2023] Open
Abstract
Root (rhizome) rot of Polygonatum plants has received substantial attention because it threatens yield and sustainable utilization in the polygonati rhizome industry. However, the potential pathogens that cause rhizome rot as well as the direct and indirect (via root-associated microbes) strategies by which Polygonatum defends against pathogens remain largely unknown. Herein, we used integrated multiomics of plant-targeted metabolomics and transcriptomics, microbiome, and culture-based methods to systematically investigate the interactions between the Polygonatum cyrtonema Hua root-associated microbiota and pathogens. We found that root rot inhibited P. cyrtonema rhizome growth and that the fresh weight significantly decreased (P < 0.001). The transcriptomic and metabonomic results showed that the expression of differentially expressed genes (DEGs) related to specialized metabolic and systemic resistance pathways, such as glycolysis/gluconeogenesis and flavonoid biosynthesis, cycloartenol synthase activity (related to saponin synthesis), mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction, was particularly increased in diseased rhizomes. Consistently, the contents of lactose, d-fructose, sarsasapogenin, asperulosidic acid, botulin, myricadoil, and other saponins, which are functional medicinal compounds present in P. cyrtonema rhizomes, were also increased in diseased plants infected with rhizome rot. The microbiome sequencing and culture results showed that root rot disrupted the P. cyrtonema bacterial and fungal communities and reduced the microbial diversity in the rhizomes and rhizosphere soil. We further found that a clear enrichment of Streptomyces violascens XTBG45 (HJB-XTBG45) in the healthy rhizosphere could control the root rot caused by Fusarium oxysporum and Colletotrichum spaethianum. Taken together, our results indicate that P. cyrtonema can modulate the plant immune system and metabolic processes and enrich beneficial root microbiota to defend against pathogens. IMPORTANCE Root (rhizome or tuber) reproduction is the main method for the agricultural cultivation of many important cash crops, and infected crop plants rot, exhibit retarded growth, and experience yield losses. While many studies have investigated medicinal plants and their functional medicinal compounds, the occurrence of root (rhizome) rot of plant and soil microbiota has received little attention. Therefore, we used integrated multiomics and culture-based methods to systematically study rhizome rot on the famous Chinese medicine Polygonatum cyrtonema and identify pathogens and beneficial microbiota of rhizome rot. Rhizome rot disrupted the Polygonatum-associated microbiota and reduced microbial diversity, and rhizome transcription and metabolic processes significantly changed. Our work provides evidence that rhizome rot not only changes rhizome transcription and functional metabolite contents but also impacts the microbial community diversity, assembly, and function of the rhizome and rhizosphere. This study provides a new friendly strategy for medicinal plant breeding and agricultural utilization.
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Affiliation(s)
- Zhiqiang Pang
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, China
| | - Xinyu Mao
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Xia
- Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Jinxian Xiao
- School of Biological and Chemical Science, Pu’er University, Puer, China
| | - Xiaoning Wang
- Key Laboratory for Crop Breeding of Hainan Province, Haikou, China
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, China
| | - Peng Xu
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, China
| | - Guizhou Liu
- Crops Conservation and Breeding Base, CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
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