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Xi DD, Gao L, Miao LM, Ge LA, Zhang DY, Zhang ZH, Li XF, Zhu YY, Shen HB, Zhu HF. Changes in Diversity and Composition of Rhizosphere Bacterial and Fungal Community between Resistant and Susceptible Pakchoi under Plasmodiophora brassicae. Int J Mol Sci 2023; 24:16779. [PMID: 38069101 PMCID: PMC10706474 DOI: 10.3390/ijms242316779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Plasmodiophora brassicae (P. brassicae) is a soil-born pathogen worldwide and can infect most cruciferous plants, which causes great yield decline and economic losses. It is not well known how microbial diversity and community composition change during P. brassicae infecting plant roots. Here, we employed a resistant and a susceptible pakchoi cultivar with and without inoculation with P. brassicae to analyze bacterial and fungal diversity using 16S rRNA V3-V4 and ITS_V1 regions, respectively. 16S rRNA V3-V4 and ITS_V1 regions were amplified and sequenced separately. Results revealed that both fungal and bacterial diversity increased, and composition was changed in the rhizosphere soil of the susceptible pakchoi compared with the resistant cultivar. In the four groups of R_mock, S_mock, R_10d, and S_10d, the most relatively abundant bacterium and fungus was Proteobacteria, accounting for 61.92%, 58.17%, 48.64%, and 50.00%, respectively, and Ascomycota, accounting for 75.11%, 63.69%, 72.10%, and 90.31%, respectively. A total of 9488 and 11,914 bacteria were observed uniquely in the rhizosphere soil of resistant and susceptible pakchoi, respectively, while only 80 and 103 fungi were observed uniquely in the correlated soil. LefSe analysis showed that 107 and 49 differentially abundant taxa were observed in bacteria and fungi. Overall, we concluded that different pakchoi cultivars affect microbial diversity and community composition, and microorganisms prefer to gather around the rhizosphere of susceptible pakchoi. These findings provide a new insight into plant-microorganism interactions.
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Affiliation(s)
- Dan-Dan Xi
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Lu Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Li-Ming Miao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Li-Ao Ge
- Jinshan Agricultural Technology Extension Center, Shanghai 201599, China;
| | - Ding-Yu Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Zhao-Hui Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Xiao-Feng Li
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Yu-Ying Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Hai-Bin Shen
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Hong-Fang Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
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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] [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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Javed MA, Schwelm A, Zamani‐Noor N, Salih R, Silvestre Vañó M, Wu J, González García M, Heick TM, Luo C, Prakash P, Pérez‐López E. The clubroot pathogen Plasmodiophora brassicae: A profile update. MOLECULAR PLANT PATHOLOGY 2023; 24:89-106. [PMID: 36448235 PMCID: PMC9831288 DOI: 10.1111/mpp.13283] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide. DISEASE SYMPTOMS In the advanced stages of clubroot disease wilting, stunting, yellowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club-shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients. HOST RANGE Members of the family Brassicaceae are the primary host of the pathogen, although some members of the family, such as Bunias orientalis, Coronopus squamatus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile. TAXONOMY Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877). DISTRIBUTION Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries. PATHOTYPING Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to understand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 different pathotypes based on the response of a set of 13 hosts. EFFECTORS AND RESISTANCE After the identification and characterization of the clubroot pathogen SABATH-type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide-binding (NB) site leucine-rich-repeat (LRR) receptors (NLRs) clubroot resistance genes validated to date. IMPORTANT LINK Canola Council of Canada is constantly updating information about clubroot and P. brassicae as part of their Canola Encyclopedia: https://www.canolacouncil.org/canola-encyclopedia/diseases/clubroot/. PHYTOSANITARY CATEGORIZATION PLADBR: EPPO A2 list; Annex designation 9E.
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Affiliation(s)
- Muhammad Asim Javed
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Arne Schwelm
- Department of Plant ScienceWageningen University and ResearchWageningenNetherlands
- Teagasc, Crops Research CentreCarlowIreland
| | - Nazanin Zamani‐Noor
- Julius Kühn‐Institute, Institute for Plant Protection in Field Crops and GrasslandBraunschweigGermany
| | - Rasha Salih
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Marina Silvestre Vañó
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Jiaxu Wu
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Melaine González García
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | | | - Chaoyu Luo
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
| | - Priyavashini Prakash
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- K. S. Rangasamy College of TechnologyNamakkalIndia
| | - Edel Pérez‐López
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
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Arnault G, Mony C, Vandenkoornhuyse P. Plant microbiota dysbiosis and the Anna Karenina Principle. TRENDS IN PLANT SCIENCE 2023; 28:18-30. [PMID: 36127241 DOI: 10.1016/j.tplants.2022.08.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/19/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.
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Affiliation(s)
- Gontran Arnault
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35042 Rennes, France
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Mehmood MA, Fu Y, Zhao H, Cheng J, Xie J, Jiang D. Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus. STRESS BIOLOGY 2022; 2:32. [PMID: 37676387 PMCID: PMC10441917 DOI: 10.1007/s44154-022-00049-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/27/2022] [Indexed: 09/08/2023]
Abstract
Rice sheath blight pathogen, Rhizoctonia solani, produces numerous sclerotia to overwinter. As a rich source of nutrients in the soil, sclerotia may lead to the change of soil microbiota. For this purpose, we amended the sclerotia of R. solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points. At the phyla level, Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control. An increased abundance of ammonia-oxidizing bacterium (AOB) Nitrosospira and Nitrite oxidizing bacteria (NOB) i.e., Nitrospira was observed, where the latter is reportedly involved in the nitrifier denitrification. Moreover, Thiobacillus, Gemmatimonas, Anaeromyxobacter and Geobacter, the vital players in denitrification, N2O reduction and reductive nitrogen transformation, respectively, depicted enhanced abundance in R. solani sclerotia-amended samples. Furthermore, asymbiotic nitrogen-fixing bacteria, notably, Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control. Plant growth promoting bacteria, such as Kribbella, Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil. As per our knowledge, this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R. solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.
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Affiliation(s)
- Mirza Abid Mehmood
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
- Plant Pathology, Institute of Plant Protection, MNS University of Agriculture, Multan, 60000, Pakistan
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Huizhang Zhao
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China.
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Hubei Province, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Poveda J, Díaz-González S, Díaz-Urbano M, Velasco P, Sacristán S. Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits. FRONTIERS IN PLANT SCIENCE 2022; 13:932288. [PMID: 35991403 PMCID: PMC9390090 DOI: 10.3389/fpls.2022.932288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.
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Affiliation(s)
- Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Sandra Díaz-González
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - María Díaz-Urbano
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
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Zhao Y, Chen X, Cheng J, Xie J, Lin Y, Jiang D, Fu Y, Chen T. Application of Trichoderma Hz36 and Hk37 as Biocontrol Agents against Clubroot Caused by Plasmodiophora brassicae. J Fungi (Basel) 2022; 8:jof8080777. [PMID: 35893144 PMCID: PMC9331738 DOI: 10.3390/jof8080777] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022] Open
Abstract
Clubroot, a soil-infective disease caused by Plasmodiophora brassicae, is a serious disease affecting cruciferous plants around the world. There is no effective control measure to completely remove this pathogen from fields after infection. Here, we screened and identified two strains (Hz36, Trichoderma guizhouense; Hk37, Trichoderma koningiopsis) of Trichoderma from the gall of clubroot in rapeseed fields with biocontrol potential for clubroot. The fermentation broth of Hz36 could significantly inhibit the germination of resting spores of P. brassicae, and promote the seed germination and root growth of rapeseed. The biocontrol efficiency of Hz36 strain on clubroot for rapeseed and Arabidopsis thaliana was 44.29% and 52.18%, respectively. The qPCR results revealed that strain Hz36 treatment could significantly reduce the content of P. brassicae in root cells, and paraffin section analysis revealed that it could delay the development of P. brassicae. Strain Hk37 showed similar effects to strain Hz36, whose biocontrol efficiency of clubroot could reach 57.30% in rapeseed and 68.01% in A. thaliana. These results indicate that strains Hz36 and Hk37 have the potential for the biocontrol of clubroot.
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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] [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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Wassermann B, Abdelfattah A, Wicaksono WA, Kusstatscher P, Müller H, Cernava T, Goertz S, Rietz S, Abbadi A, Berg G. The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines. Microb Biotechnol 2022; 15:2379-2390. [PMID: 35593114 PMCID: PMC9437892 DOI: 10.1111/1751-7915.14077] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 12/15/2022] Open
Abstract
Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant‐related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.
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Affiliation(s)
- Birgit Wassermann
- ACIB GmbH, Petersgasse 14, 8010, Graz, Austria.,Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Henry Müller
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Simon Goertz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Steffen Rietz
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria.,Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany.,Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam OT Golm, Germany
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10
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Durán P, Tortella G, Sadowsky MJ, Viscardi S, Barra PJ, Mora MDLL. Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change. BIOLOGY 2021; 10:865. [PMID: 34571742 PMCID: PMC8472835 DOI: 10.3390/biology10090865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.
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Affiliation(s)
- Paola Durán
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.J.B.); (M.d.l.L.M.)
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Gonzalo Tortella
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA-BIOREN), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco 4811230, Chile;
| | - Michael J. Sadowsky
- BioTechnology Institute, University of Minnesota, Minneapolis, MN 55108, USA;
| | - Sharon Viscardi
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, P.O. Box 15-D, Temuco 4813302, Chile;
| | - Patricio Javier Barra
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.J.B.); (M.d.l.L.M.)
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Maria de la Luz Mora
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.J.B.); (M.d.l.L.M.)
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11
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Bacillus amyloliquefaciens FH-1 significantly affects cucumber seedlings and the rhizosphere bacterial community but not soil. Sci Rep 2021; 11:12055. [PMID: 34103586 PMCID: PMC8187646 DOI: 10.1038/s41598-021-91399-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) inoculants have been applied worldwide. However, the ecological roles of PGPB under different soil conditions are still not well understood. The present study aimed to explore the ecological roles of Bacillus amyloliquefaciens FH-1 (FH) on cucumber seedlings, rhizosphere soil properties, and the bacterial community in pot experiments. The results showed that FH had significant effects on cucumber seedlings and the rhizosphere bacterial community but not on soil properties. The FH promoted cucumber seedlings growth, reduced the rhizosphere bacterial diversity, increased Proteobacteria, and decreased Acidobacteria. Linear discriminant analysis (LDA) effect size (LEfSe) revealed that FH enriched two taxa (GKS2_174 and Nannocystaceae) and inhibited 18 taxa (mainly Acidobacteria, Actinobacteria, BRC1, Chloroflexi, Plantctomycetes, and Verrucomicrobia). Co-occurrence network analysis demonstrated that FH increased bacteria-bacteria interactions and that Bacillus (genus of FH) had few interactions with the enriched and inhibited taxa. This might indicate that FH does not directly affect the enriched and inhibited taxa. Correlation analysis results displayed that cucumber seedlings’ weight and height/length (except root length) were significantly correlated with the 18 inhibited taxa and the enriched taxa Nannocystaceae. It was speculated that FH might promote cucumber seedling growth by indirectly enriching Nannocystaceae and inhibiting some taxa from Acidobacteria, Actinobacteria, BRC1, Chloroflexi, Plantctomycetes, and Verrucomicrobia.
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12
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Solís-García IA, Ceballos-Luna O, Cortazar-Murillo EM, Desgarennes D, Garay-Serrano E, Patiño-Conde V, Guevara-Avendaño E, Méndez-Bravo A, Reverchon F. Phytophthora Root Rot Modifies the Composition of the Avocado Rhizosphere Microbiome and Increases the Abundance of Opportunistic Fungal Pathogens. Front Microbiol 2021; 11:574110. [PMID: 33510714 PMCID: PMC7835518 DOI: 10.3389/fmicb.2020.574110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/15/2020] [Indexed: 02/01/2023] Open
Abstract
The structure and function of rhizosphere microbial communities are affected by the plant health status. In this study, we investigated the effect of root rot on the avocado rhizosphere microbiome, using 16S rDNA and ITS sequencing. Furthermore, we isolated potential fungal pathogens associated with root rot symptoms and assessed their pathogenic activity on avocado. We found that root rot did not affect species richness, diversity or community structure, but induced changes in the relative abundance of several microbial taxa. Root rot increased the proportion of Pseudomonadales and Burkholderiales in the rhizosphere but reduced that of Actinobacteria, Bacillus spp. and Rhizobiales. An increase in putative opportunistic fungal pathogens was also detected in the roots of symptomatic trees; the potential pathogenicity of Mortierella sp., Fusarium spp., Lasiodiplodia sp. and Scytalidium sp., is reported for the first time for the State of Veracruz, Mexico. Root rot also potentially modified the predicted functions carried out by rhizobacteria, reducing the proportion of categories linked with the lipid and amino-acid metabolisms whilst promoting those associated with quorum sensing, virulence, and antibiotic resistance. Altogether, our results could help identifying microbial taxa associated to the disease causal agents and direct the selection of plant growth-promoting bacteria for the development of biocontrol microbial consortia.
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Affiliation(s)
- Itzel A Solís-García
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Xalapa, Mexico.,Escuela Nacional de Estudios Superiores Unidad Morelia, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Oscar Ceballos-Luna
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Xalapa, Mexico
| | | | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología, A.C., Xalapa, Mexico
| | - Edith Garay-Serrano
- CONACYT - Red de Diversidad Biológica del Occidente Mexicano, Instituto de Ecología, A.C., Pátzcuaro, Mexico
| | - Violeta Patiño-Conde
- Escuela Nacional de Estudios Superiores Unidad Morelia, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Edgar Guevara-Avendaño
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Xalapa, Mexico.,Instituto de Agroindustrias, Universidad Tecnológica de la Mixteca, Heroica Ciudad de Huajuapan de Leon, Mexico
| | - Alfonso Méndez-Bravo
- CONACYT - Escuela Nacional de Estudios Superiores Unidad Morelia, Laboratorio Nacional de Análisis y Síntesis Ecológica, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Frédérique Reverchon
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Pátzcuaro, Mexico
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13
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Daval S, Gazengel K, Belcour A, Linglin J, Guillerm‐Erckelboudt A, Sarniguet A, Manzanares‐Dauleux MJ, Lebreton L, Mougel C. Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes. Microb Biotechnol 2020; 13:1648-1672. [PMID: 32686326 PMCID: PMC7415369 DOI: 10.1111/1751-7915.13634] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
The contribution of surrounding plant microbiota to disease development has led to the 'pathobiome' concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defence-related genes (glucosinolate metabolism) in B. napus.
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Affiliation(s)
- Stéphanie Daval
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
| | - Kévin Gazengel
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
| | | | - Juliette Linglin
- INRAEAgrocampus OuestUniversité de RennesIGEPPPloudanielF‐29260France
| | | | - Alain Sarniguet
- INRAEAgrocampus OuestUniversité d'AngersIRHSBeaucouzéF‐49071France
| | | | - Lionel Lebreton
- INRAEAgrocampus OuestUniversité de RennesIGEPPLe RheuF‐35650France
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14
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Wang D, Sun T, Zhao S, Pan L, Liu H, Tian X. Physiological change alters endophytic bacterial community in clubroot of tumorous stem mustard infected by Plasmodiophora brassicae. BMC Microbiol 2020; 20:244. [PMID: 32762653 PMCID: PMC7412676 DOI: 10.1186/s12866-020-01930-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Endophytic bacteria are considered as symbionts living within plants and are influenced by abiotic and biotic environments. Pathogen cause biotic stress, which may change physiology of plants and may affect the endophytic bacterial communiy. Here, we reveal how endophytic bacteria in tumorous stem mustard (Brassica juncea var. tumida) are affected by plant physiological changes caused by Plasmodiophora brassicae using 16S rRNA high-throughput sequencing. RESULTS The results showed that Proteobacteria was the dominant group in both healthy roots and clubroots, but their abundance differed. At the genus level, Pseudomonas was dominant in clubroots, whereas Rhodanobacter was the dominant in healthy roots. Hierarchical clustering, UniFrac-weighted principal component analysis (PCA), non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) indicated significant differences between the endophytic bacterial communities in healthy roots and clubroots. The physiological properties including soluble sugar, soluble protein, methanol, peroxidase (POD) and superoxide dismutase (SOD) significantly differed between healthy roots and clubroots. The distance-based redundancy analysis (db-RDA) and two-factor correlation network showed that soluble sugar, soluble protein and methanol were strongly related to the endophytic bacterial community in clubroots, whereas POD and SOD correlated with the endophytic bacterial community in healthy roots. CONCLUSIONS Our results illustrate that physiologcial changes caused by P. brassicae infection may alter the endophytic bacterial community in clubroots of tumorous stem mustard.
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Affiliation(s)
| | - Tingting Sun
- Henan engineering research center of biological pesticide & fertilizer development and synergistic application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Songyu Zhao
- Henan engineering research center of biological pesticide & fertilizer development and synergistic application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Limei Pan
- Yangtze Normal University, Fuling, Chongqing, China
| | - Hongfang Liu
- Henan engineering research center of biological pesticide & fertilizer development and synergistic application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xueliang Tian
- Henan engineering research center of biological pesticide & fertilizer development and synergistic application, Henan Institute of Science and Technology, Xinxiang, Henan, China.
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15
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Morvan S, Meglouli H, Lounès-Hadj Sahraoui A, Hijri M. Into the wild blueberry (Vaccinium angustifolium) rhizosphere microbiota. Environ Microbiol 2020; 22:3803-3822. [PMID: 32623832 DOI: 10.1111/1462-2920.15151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022]
Abstract
The ability of wild blueberries to adapt to their harsh environment is believed to be closely related to their symbiosis with ericoid mycorrhizal fungi, which produce enzymes capable of organic matter mineralization. Although some of these fungi have been identified and characterized, we still know little about the microbial ecology of wild blueberry. Our study aims to characterize the fungal and bacterial rhizosphere communities of Vaccinium angustifolium (the main species encountered in wild blueberry fields). Our results clearly show that the fungal order Helotiales was the most abundant taxon associated with V. angustifolium. Helotiales contains most of the known ericoid mycorrhizal fungi which are expected to dominate in such a biotope. Furthermore, we found the dominant bacterial order was the nitrogen-fixing Rhizobiales. The Bradyrhizobium genus, whose members are known to form nodules with legumes, was among the 10 most abundant genera in the bacterial communities. In addition, Bradyrhizobium and Roseiarcus sequences significantly correlated with higher leaf-nitrogen content. Overall, our data documented fungal and bacterial community structure differences in three wild blueberry production fields.
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Affiliation(s)
- Simon Morvan
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, QC, Canada
| | - Hacène Meglouli
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, QC, Canada
| | - Anissa Lounès-Hadj Sahraoui
- Université du Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV), SFR Condorcet FR CNRS 3417, Calais Cedex, France
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Département de sciences biologiques, Université de Montréal, QC, Canada.,AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Morocco
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16
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Wu Y, Qu M, Pu X, Lin J, Shu B. Distinct microbial communities among different tissues of citrus tree Citrus reticulata cv. Chachiensis. Sci Rep 2020; 10:6068. [PMID: 32269258 PMCID: PMC7142118 DOI: 10.1038/s41598-020-62991-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/18/2020] [Indexed: 11/17/2022] Open
Abstract
Plant microbiota colonize all organs of a plant and play crucial roles including supplying nutrients to plants, stimulating seed germination, promoting plant growth, and defending plants against biotic and abiotic stress. Because of the economic importance, interactions between citrus and microbes have been studied relatively extensively, especially citrus-pathogen interactions. However, the spatial distribution of microbial taxa in citrus trees remains under-studied. In this study, Citrus reticulata cv. Chachiensis was examined for the spatial distribution of microbes by sequencing 16S rRNA genes. More than 2.5 million sequences were obtained from 60 samples collected from soil, roots, leaves, and phloem. The dominant microbial phyla from all samples were Proteobacteria, Actinobacteria and Acidobacteria. The composition and structure of microbial communities in different samples were analyzed by PCoA, CAP, Anosim and MRPP methods. Variation in microbial species between samples were analyzed and the indicator microbes of each sample group were identified. Our results suggested that the microbial communities from different tissues varied significantly and the microenvironments of tree tissues could affect the composition of its microbial community.
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Affiliation(s)
- Yongxian Wu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Mengqiu Qu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xinhua Pu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jintian Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
| | - Benshui Shu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
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17
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Mehmood MA, Zhao H, Cheng J, Xie J, Jiang D, Fu Y. Sclerotia of a phytopathogenic fungus restrict microbial diversity and improve soil health by suppressing other pathogens and enriching beneficial microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 259:109857. [PMID: 32072956 DOI: 10.1016/j.jenvman.2019.109857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum, a notorious soil-borne pathogen of various important crops, produces numerous sclerotia to oversummer in the soil. Considering that sclerotia may also be attacked by other microbes in the soil, we hypothesized that sclerotia in soil may affect the community of soil microbes directly and/or indirectly. In this study, we inoculated sclerotia of S. sclerotiorum in soil collected from the field to observe changes in microbial diversity over three months using 16S rRNA and ITS2 sequencing techniques. Alpha diversity indices exhibited a decline in the diversity of microbial communities, while permanova results confirmed a significant difference in the microbial communities of sclerotia-amended and non-amended soil samples. In sclerotia-amended soil, fungal diversity showed enrichment of antagonists such as Clonostachys, Trichoderma, and Talaromyces and a drastic reduction in the plant pathogenic microbes compared to the non-amended soil. Sclerotia not only activated the antagonists but also enhanced the abundance of plant growth-promoting bacteria, such as Chitinophaga, Burkholderia, and Dyella. Moreover, the presence of sclerotia curtailed the growth of several notorious plant pathogenic fungi belonging to various genera such as Fusarium, Colletotrichum, Cladosporium, Athelia, Alternaria, and Macrophomina. Thus, we conclude that S. sclerotiorum when dormant in soil can reduce the diversity of soil microbes, including suppressing plant pathogens and enriching beneficial microbes. To the best of our knowledge, this is the first time a plant pathogen has been found in soil that can significantly suppress other pathogens. Our findings may provide novel cues to understand the ecology of crop pathogens in soil and maintaining soil conditions that could be beneficial for constructing a healthy soil microorganism community required for mitigating soil-borne diseases.
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Affiliation(s)
- Mirza Abid Mehmood
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Department of Plant Pathology, Muhammad Nawaz Shareef University of Agriculture, Multan, Punjab, Pakistan
| | - Huizhang Zhao
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Jiatao Xie
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China.
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18
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Impact of plant genotype and plant habitat in shaping bacterial pathobiome: a comparative study in olive tree. Sci Rep 2020; 10:3475. [PMID: 32103149 PMCID: PMC7044170 DOI: 10.1038/s41598-020-60596-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 12/02/2022] Open
Abstract
Plant-inhabiting microorganisms interact directly with each other affecting disease progression. However, the role of host plant and plant habitat in shaping pathobiome composition and their implication for host susceptibility/resistance to a particular disease are currently unknown. For the elucidation of these questions, both epiphytic and endophytic bacterial communities, present in asymptomatic and symptomatic twigs from olive cultivars displaying different susceptibilities to olive knot (OK) disease, were investigated using culturing methods. OK disease was the main driver of the bacterial community, causing changes on their diversity, abundance and composition. OK disease effect was most notorious on OK-susceptible cultivar and when considering the endophytic communities. Plant habitat (epiphytes vs. endophytes) also contributed to the bacterial community assembling, in particular on symptomatic twigs (knots) of OK-susceptible cultivar. In contrast, host cultivar had little effect on the bacterial community composition, but OK-symptomatic twigs (knots) revealed to be more affected by this driver. Overall, the pathobiome seems to result from an intricate interaction between the pathogen, the resident bacteria, and the plant host. Specific bacterial genera were associated to the presence or absence of OK disease in each cultivar. Their ability to trigger and/or suppress disease should be studied in the future.
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19
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Kavamura VN, Robinson RJ, Hayat R, Clark IM, Hughes D, Rossmann M, Hirsch PR, Mendes R, Mauchline TH. Land Management and Microbial Seed Load Effect on Rhizosphere and Endosphere Bacterial Community Assembly in Wheat. Front Microbiol 2019; 10:2625. [PMID: 31803160 PMCID: PMC6873152 DOI: 10.3389/fmicb.2019.02625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/29/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial community ecology studies have traditionally utilized culture-based methodologies, though the advent of next-generation amplicon sequencing has facilitated superior resolution analyses of complex microbial communities. Here, we used culture-dependent and -independent approaches to explore the influence of land use as well as microbial seed load on bacterial community structure of the wheat rhizosphere and root endosphere. It was found that niche was an important factor in shaping the microbiome when using both methodological approaches, and that land use was also a discriminatory factor for the culture-independent-based method. Although culture-independent methods provide a higher resolution of analysis, it was found that in the rhizosphere, particular operational taxonomic units (OTUs) in the culture-dependent fraction were absent from the culture-independent fraction, indicating that deeper sequence analysis is required for this approach to be exhaustive. We also found that the microbial seed load defined the endosphere, but not rhizosphere, community structure for plants grown in soil which was not wheat adapted. Together, these findings increase our understanding of the importance of land management and microbial seed load in shaping the root microbiome of wheat and this knowledge will facilitate the exploitation of plant-microbe interactions for the development of novel microbial inoculants.
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Affiliation(s)
| | | | - Rifat Hayat
- Department of Soil Science and Soil and Water Conservation, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Ian M. Clark
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - David Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Penny R. Hirsch
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, United Kingdom
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20
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Cordero J, de Freitas JR, Germida JJ. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can J Microbiol 2019; 66:71-85. [PMID: 31658427 DOI: 10.1139/cjm-2019-0330] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhizosphere and root associated bacteria are key components of plant microbiomes and influence crop production. In sustainable agriculture, it is important to investigate bacteria diversity in various plant species and how edaphic factors influence the bacterial microbiome. In this study, we used high-throughput sequencing to assess bacterial communities associated with the rhizosphere and root interior of canola, wheat, field pea, and lentil grown at four locations in Saskatchewan, Canada. Rhizosphere bacteria communities exhibited distinct profiles among crops and sampling locations. However, each crop was associated with distinct root endophytic bacterial communities, suggesting that crop species may influence the selection of root bacterial microbiome. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in the root interior, whereas Gemmatimonadetes, Firmicutes, and Acidobacteria were prevalent in the rhizosphere soil. Pseudomonas and Stenotrophomonas were predominant in the rhizosphere and root interior, whereas Acinetobacter, Arthrobacter, Rhizobium, Streptomyces, Variovorax, and Xanthomonas were dominant in the root interior of all crops. The relative abundance of specific bacterial groups in the rhizosphere correlated with soil pH and silt and organic matter contents; however, there was no correlation between root endophytes and analyzed soil properties. These results suggest that the root microbiome may be modulated by plant factors rather than soil characteristics.
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Affiliation(s)
- Jorge Cordero
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - J Renato de Freitas
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.,Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - James J Germida
- Department of Soil Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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21
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Tian X, Wang D, Mao Z, Pan L, Liao J, Cai Z. Infection of Plasmodiophora brassicae changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods. PLoS One 2019; 14:e0214975. [PMID: 31188828 PMCID: PMC6561537 DOI: 10.1371/journal.pone.0214975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/28/2019] [Indexed: 01/12/2023] Open
Abstract
Diverse fungal endophytes live in plants and are shaped by some abiotic and biotic stresses. Plant disease as particular biotic stress possibly gives an impact on the communities of fungal endophytes. In this study, clubroot disease caused by an obligate biotroph protist, Plasmodiophora brassicae, was considered to analyze its influence on the fungal endophyte community using an internal transcribed spacer (ITS) through high-throughput sequencing and culture-dependent methods. The results showed that the diversity of the endophyte community in the healthy roots was much higher than the clubroots. Ascomycota was the dominant group of endophytes (Phoma, Mortierella, Penicillium, etc.) in the healthy roots while P. brassicae was the dominant taxon in the clubroots. Hierarchical clustering, principal component analysis (PCA), principal coordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated significant differences between the endophyte communities in the healthy roots and clubroots. Linear discriminant analysis effect size (LefSe) analysis showed that the dominant genera could be regarded as potential biomarkers. The endophyte community in the healthy roots had a more complex network compared with the clubroots. Also, many plant pathogenic Fusarium were isolated from the clubroots by the culture-dependent method. The outcome of this study illustrates that P. brassicae infection may change the fungal endophyte community associated with the roots of tumourous stem mustard and facilitates the entry of soil pathogen into the roots.
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Affiliation(s)
- Xueliang Tian
- Henan institute of science and technology, Xinxiang, Henan, China
| | | | - Zhenchuan Mao
- Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Pan
- Yangtze Normal University, Fuling, Chongqing, China
| | | | - Zhaoming Cai
- Yangtze Normal University, Fuling, Chongqing, China
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22
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Zhang Q, Acuña JJ, Inostroza NG, Mora ML, Radic S, Sadowsky MJ, Jorquera MA. Endophytic Bacterial Communities Associated with Roots and Leaves of Plants Growing in Chilean Extreme Environments. Sci Rep 2019; 9:4950. [PMID: 30894597 PMCID: PMC6426880 DOI: 10.1038/s41598-019-41160-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
Several studies have demonstrated the relevance of endophytic bacteria on the growth and fitness of agriculturally-relevant plants. To our knowledge, however, little information is available on the composition, diversity, and interaction of endophytic bacterial communities in plants struggling for existence in the extreme environments of Chile, such as the Atacama Desert (AD) and Patagonia (PAT). The main objective of the present study was to analyze and compare the composition of endophytic bacterial communities associated with roots and leaves of representative plants growing in Chilean extreme environments. The plants sampled were: Distichlis spicate and Pluchea absinthioides from the AD, and Gaultheria mucronata and Hieracium pilosella from PAT. The abundance and composition of their endophytic bacterial communities was determined by quantitative PCR and high–throughput sequencing of 16S rRNA, respectively. Results indicated that there was a greater abundance of 16S rRNA genes in plants from PAT (1013 to 1014 copies g−1 DNA), compared with those from AD (1010 to 1012 copies g−1 DNA). In the AD, a greater bacterial diversity, as estimated by Shannon index, was found in P. absinthioides, compared with D. spicata. In both ecosystems, the greater relative abundances of endophytes were mainly attributed to members of the phyla Proteobacteria (14% to 68%), Firmicutes (26% to 41%), Actinobacteria (6 to 23%) and Bacteroidetes (1% to 21%). Our observations revealed that most of operational taxonomic units (OTUs) were not shared between tissue samples of different plant species in both locations, suggesting the effect of the plant genotype (species) on the bacterial endophyte communities in Chilean extreme environments, where Bacillaceae and Enterobacteriacea could serve as keystone taxa as revealed our linear discriminant analysis.
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Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - María Luz Mora
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile
| | - Sergio Radic
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad de Magallanes, Ave. Bulnes 01855, Punta Arenas, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Ave., St Paul, MN, 55108-6106, USA.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMAlab), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile. .,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Ave. Francisco Salazar 01145, Temuco, Chile.
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23
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Niederwerder MC, Constance LA, Rowland RRR, Abbas W, Fernando SC, Potter ML, Sheahan MA, Burkey TE, Hesse RA, Cino-Ozuna AG. Fecal Microbiota Transplantation Is Associated With Reduced Morbidity and Mortality in Porcine Circovirus Associated Disease. Front Microbiol 2018; 9:1631. [PMID: 30083142 PMCID: PMC6064930 DOI: 10.3389/fmicb.2018.01631] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/29/2018] [Indexed: 12/12/2022] Open
Abstract
Porcine circovirus associated disease (PCVAD) is a term used to describe the multi-factorial disease syndromes caused by porcine circovirus type 2 (PCV-2), which can be reproduced in an experimental setting through the co-infection of pigs with PCV-2 and porcine reproductive and respiratory syndrome virus (PRRSV). The resulting PCVAD-affected pigs represent a subpopulation within the co-infected group. In co-infection studies, the presence of increased microbiome diversity is linked to a reduction in clinical signs. In this study, fecal microbiota transplantation (FMT) was investigated as a means to prevent PCVAD in pigs co-infected with PRRSV and PCV-2d. The sources of the FMT material were high-parity sows with a documented history of high health status and robust litter characteristics. The analysis of the donated FMT material showed the absence of common pathogens along with the presence of diverse microbial phyla and families. One group of pigs (n = 10) was administered the FMT while a control group (n = 10) was administered a sterile mock-transplant. Over the 42-day post-infection period, the FMT group showed fewer PCVAD-affected pigs, as evidenced by a significant reduction in morbidity and mortality in transplanted pigs, along with increased antibody levels. Overall, this study provides evidence that FMT decreases the severity of clinical signs following co-infection with PRRSV and PCV-2 by reducing the prevalence of PCVAD.
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Affiliation(s)
- Megan C Niederwerder
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Laura A Constance
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Raymond R R Rowland
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Waseem Abbas
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Samodha C Fernando
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Maureen A Sheahan
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Thomas E Burkey
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Richard A Hesse
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States.,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, United States
| | - Ada G Cino-Ozuna
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States.,Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS, United States
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Ourry M, Lebreton L, Chaminade V, Guillerm-Erckelboudt AY, Hervé M, Linglin J, Marnet N, Ourry A, Paty C, Poinsot D, Cortesero AM, Mougel C. Influence of Belowground Herbivory on the Dynamics of Root and Rhizosphere Microbial Communities. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00091] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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