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Mihai RA, Terán-Maza VA, Portilla-Benalcazar KA, Ramos-Guaytarilla LE, Vizuete-Cabezas MJ, Melo-Heras EJ, Cubi-Insuaste NS, Catana RD. Secondary Metabolites and Antioxidant Activity against Moko Disease as a Defense Mechanism of Musa spp. from the Ecuadorian Coast Area. Metabolites 2024; 14:307. [PMID: 38921442 PMCID: PMC11206157 DOI: 10.3390/metabo14060307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
The Musa spp. represents the most commonly produced, transitioned, and consumed fruit around the globe, with several important applications in the biotechnology, pharmaceutical, and food industries. Moko disease is produced by Ralstonia solanacearum-a factor with a high impact on all crops in Ecuador, representing one of the biggest phytosanitary problems. Four of the most common varieties of Musa spp. were tested to identify the metabolic reaction of plants facing Moko disease. The phenolic and flavonoid content has been evaluated as a defense system, and the α-diphenyl-α-picrylhydrazyl free-radical-scavenging method (DPPH), free-radical-scavenging activity (ABTS), ferric-reducing antioxidant power (FRAP) assays, and liquid chromatography and mass spectrometry (LC-MS) have been adapted to analyze the active compounds with the antioxidant capacity necessary to counteract the pathogenic attack. Our results indicate that all the studied varieties of Musa spp. react in the same way, such that the diseased samples showed a higher accumulation of secondary metabolites with antioxidant capacity compared with the healthy ones, with high active compound synthesis identified during the appearance of Moko disease symptoms. More than 40 compounds and their derivatives (from kaempferol and quercetin glycosides) with protective roles demonstrate the implication of the Musa spp. defense system against R. solanacearum infection.
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Affiliation(s)
- Raluca A. Mihai
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - Vanessa A. Terán-Maza
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - Karen A. Portilla-Benalcazar
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - Lissette E. Ramos-Guaytarilla
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - María J. Vizuete-Cabezas
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - Erly J. Melo-Heras
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - Nelson S. Cubi-Insuaste
- Army Scientific and Technological Research Center—CICTE, Department of Life Science and Agriculture, Universidad de Las Fuerzas Armadas—ESPE, Av. General Rumiñahui s/n y, Sangolqui 171103, Ecuador; (V.A.T.-M.); (K.A.P.-B.); (L.E.R.-G.); (M.J.V.-C.); (E.J.M.-H.); (N.S.C.-I.)
| | - Rodica D. Catana
- Developmental Biology Department, Institute of Biology Bucharest of Romanian Academy, 296 Splaiul Independenţei, 060031 Bucharest, Romania;
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Ntui VO, Tripathi JN, Shah T, Tripathi L. Targeted knockout of early nodulin-like 3 (MusaENODL3) gene in banana reveals its function in resistance to Xanthomonas wilt disease. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1101-1112. [PMID: 38013635 PMCID: PMC11022791 DOI: 10.1111/pbi.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/09/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Nodulins and nodulin-like proteins play an essential role in the symbiotic associations between legumes and Rhizobium bacteria. Their role extends beyond the leguminous species, as numerous nodulin-like proteins, including early nodulin-like proteins (ENODL), have been identified in various non-leguminous plants, implying their involvement in functions beyond nodulation, such as nutrient transport and growth modulation. Some ENODL proteins have been associated with plant defense against pathogens, as evident in banana infected with Xanthomonas campestris pv. musacearum (Xcm) causing banana Xanthomonas wilt (BXW) disease. Nonetheless, the specific role of ENODL in plant defense remains to be fully elucidated. The MusaENODL3 gene was found to be repressed in BXW-resistant banana progenitor 'Musa balbisiana' and 20-fold upregulated in BXW-susceptible cultivar 'Gonja Manjaya' upon early infection with Xcm. To further unravel the role of the ENODL gene in disease resistance, the CRISPR/Cas9 system was employed to disrupt the MusaENODL3 gene in 'Gonja Manjaya' precisely. Analysis of the enodl3 edited events confirmed the accurate manipulation of the MusaENODL3 gene. Disease resistance and gene expression analysis demonstrated that editing the MusaENODL3 gene resulted in resistance to BXW disease, with 50% of the edited plants remaining asymptomatic. The identification and manipulation of the MusaENODL3 gene highlight its potential as a critical player in plant-pathogen interactions, offering new opportunities for enhancing disease resistance in crops like banana, an important staple food crop and source of income for resource-poor farmers in the tropics. This study provides the first evidence of the direct role of the ENODL3 gene in developing disease-resistant plants.
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Affiliation(s)
| | | | - Trushar Shah
- International Institute of Tropical AgricultureNairobiKenya
| | - Leena Tripathi
- International Institute of Tropical AgricultureNairobiKenya
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Etherton BA, Choudhury RA, Alcalá Briseño RI, Mouafo-Tchinda RA, Plex Sulá AI, Choudhury M, Adhikari A, Lei SL, Kraisitudomsook N, Buritica JR, Cerbaro VA, Ogero K, Cox CM, Walsh SP, Andrade-Piedra JL, Omondi BA, Navarrete I, McEwan MA, Garrett KA. Disaster Plant Pathology: Smart Solutions for Threats to Global Plant Health from Natural and Human-Driven Disasters. PHYTOPATHOLOGY 2024; 114:855-868. [PMID: 38593748 DOI: 10.1094/phyto-03-24-0079-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Disaster plant pathology addresses how natural and human-driven disasters impact plant diseases and the requirements for smart management solutions. Local to global drivers of plant disease change in response to disasters, often creating environments more conducive to plant disease. Most disasters have indirect effects on plant health through factors such as disrupted supply chains and damaged infrastructure. There is also the potential for direct effects from disasters, such as pathogen or vector dispersal due to floods, hurricanes, and human migration driven by war. Pulse stressors such as hurricanes and war require rapid responses, whereas press stressors such as climate change leave more time for management adaptation but may ultimately cause broader challenges. Smart solutions for the effects of disasters can be deployed through digital agriculture and decision support systems supporting disaster preparedness and optimized humanitarian aid across scales. Here, we use the disaster plant pathology framework to synthesize the effects of disasters in plant pathology and outline solutions to maintain food security and plant health in catastrophic scenarios. We recommend actions for improving food security before and following disasters, including (i) strengthening regional and global cooperation, (ii) capacity building for rapid implementation of new technologies, (iii) effective clean seed systems that can act quickly to replace seed lost in disasters, (iv) resilient biosecurity infrastructure and risk assessment ready for rapid implementation, and (v) decision support systems that can adapt rapidly to unexpected scenarios. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Berea A Etherton
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Robin A Choudhury
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Edinburg, TX, U.S.A
| | - Ricardo I Alcalá Briseño
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Romaric A Mouafo-Tchinda
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Aaron I Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Manoj Choudhury
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Ashish Adhikari
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Si Lin Lei
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Nattapol Kraisitudomsook
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
- Department of Biology, Faculty of Science and Technology, Muban Chombueng Rajabhat University, Chom Bueng, Ratchaburi, Thailand
| | - Jacobo Robledo Buritica
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
| | - Vinicius A Cerbaro
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL, U.S.A
| | - Kwame Ogero
- International Potato Center (CIP), Mwanza, Tanzania
| | - Cindy M Cox
- USAID Bureau for Humanitarian Assistance, Washington, DC, U.S.A
| | - Stephen P Walsh
- USAID Bureau for Humanitarian Assistance, Washington, DC, U.S.A
| | | | | | | | - Margaret A McEwan
- International Potato Center (CIP) Africa Regional Office, Nairobi, Kenya
- Wageningen University and Research, Wageningen, the Netherlands
| | - Karen A Garrett
- Plant Pathology Department, University of Florida, Gainesville, FL, U.S.A
- Global Food Systems Institute, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
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Aghdam SA, Lahowetz RM, Brown AMV. Divergent endophytic viromes and phage genome repertoires among banana ( Musa) species. Front Microbiol 2023; 14:1127606. [PMID: 37362937 PMCID: PMC10288200 DOI: 10.3389/fmicb.2023.1127606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Viruses generally cause disease, but some viruses may be beneficial as resident regulators of their hosts or host microbiomes. Plant-associated viruses can help plants survive by increasing stress tolerance or regulating endophytic communities. The goal of this study was to characterize endophytic virus communities in banana and plantain (Musa spp.) genotypes, including cultivated and wild species, to assess virome repertoires and detect novel viruses. Methods DNA viral communities were characterized by shotgun sequencing of an enriched endosphere extract from leaves and roots or corm of 7 distinct Musa genotypes (M. balbisiana, Thai Black, M. textilis, M. sikkimensis, Dwarf Cavendish, Williams Hybrid, and FHIA-25 Hybrid). Results Results showed abundant virus-like contigs up to 108,191 bp long with higher relative abundance in leaves than roots. Analyses predicted 733 phage species in 51 families, with little overlap in phage communities among plants. Phage diversity was higher in roots and in diploid wild hosts. Ackermanniviridae and Rhizobium phage were generally the most abundant taxa. A Rhizobium RR1-like phage related to a phage of an endophytic tumor-causing rhizobium was found, bearing a holin gene and a partial Shiga-like toxin gene, raising interest in its potential to regulate endophytic Rhizobiaceae. Klebsiella phages were of interest for possible protection against Fusarium wilt, and other phages were predicted with potential to regulate Erwinia, Pectobacterium, and Ralstonia-associated diseases. Although abundant phage-containing contigs were functionally annotated, revealing 1,038 predicted viral protein domains, gene repertoires showed high divergence from database sequences, suggesting novel phages in these banana cultivars. Plant DNA viruses included 56 species of Badnavirus and 26 additional non-Musa plant viruses with distributions that suggested a mixture of resident and transient plant DNA viruses in these samples. Discussion Together, the disparate viral communities in these plants from a shared environment suggest hosts drive the composition of these virus communities. This study forms a first step in understanding the endophytic virome in this globally important food crop, which is currently threatened by fungal, bacterial, and viral diseases.
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Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
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Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
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Lim JA, Yaacob JS, Mohd Rasli SRA, Eyahmalay JE, El Enshasy HA, Zakaria MRS. Mitigating the repercussions of climate change on diseases affecting important crop commodities in Southeast Asia, for food security and environmental sustainability—A review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1030540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Southeast Asia is a fertile land with a warm and humid climate which tends to accommodate various food crops. The development and advancement of the agricultural sector not only allows the countries in the region to feed the increasing population, but are also able to boost the nation's economy through exportation of the crops. Some of the well-known and economically-significant plant commodities found in the region include rice, oil palm, rubber, coconut, banana, sugarcane, pineapple, black pepper, maize, cocoa, durian, and jackfruit. Due to the high production of crops, Southeast Asia is able to stand among the top world producers of these commodities. Nevertheless, the widespread of pathogenic microorganisms has posed a serious threat to the industry over the years; with hundreds of millions of money wasted and total yield being lost due to the devastating diseases associated with each type of the plants. A lot of attention and effort have been continuously devoted to find effective plant management strategies to combat plant diseases, starting from traditional physical and chemical methods to the increasing discoveries on biological approaches made in recent decades. Due to the challenges and limitations faced by conventional approaches and the rising awareness toward the environment, more work has been focused on establishing the application of beneficial microorganisms to tackle plant diseases through direct mechanisms. Thus, by bringing the common plant commodities in Southeast Asia, their associated diseases and various physical, chemical and biological control measures together, this review aims to provide clearer insights and practical information to those who seek to limit the damages caused by plant diseases.
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Pais AKL, dos Santos LVS, Albuquerque GMR, de Farias ARG, Silva WJ, Balbino VDQ, Silva AMF, da Gama MAS, de Souza EB. Comparative genomics and phylogenomics of the Ralstonia solanacearum Moko ecotype and its symptomatological variants. Genet Mol Biol 2022; 45:e20220038. [PMID: 36469480 PMCID: PMC9731368 DOI: 10.1590/1678-4685-gmb-2022-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/14/2022] [Indexed: 12/04/2022] Open
Abstract
Banana tree bacterial wilt is caused by the Ralstonia solanacearum Moko ecotype. These strains vary in their symptom progression in banana, and are classified as typical Moko variants (phylotype IIA and IIB strains from across Central and South America), Bugtok variant (Philippines), and Sergipe facies (the states of Sergipe and Alagoas, Brazil). This study used comparative genomic and phylogenomic approaches to identify a correlation between the symptom progression of the Moko ecotypes based on the analysis of 23 available genomes. Average nucleotide identity and in silico DNA-DNA hybridization revealed a high correlation (>96% and >78%, respectively) between the genomes of Moko variants. Pan-genome analysis identified 21.3% of inheritable regions between representatives of the typical Moko and Sergipe facies variants, which could be traced to an abundance of exclusive homolog clusters. Moko ecotype genomes shared 1,951 orthologous genes, but representatives with typical symptoms did not display unique orthologues. Moreover, Bugtok disease and Sergipe facies genomes did not share any unique genes, suggesting convergent evolution to a shared symptom progression. Overall, genomic and phylogenomic analyses were insufficient to differentiate the Moko variants based on symptom progression.
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Affiliation(s)
- Ana Karolina Leite Pais
- Universidade Federal Rural de Pernambuco (UFRPE), Departamento de
Agronomia, Recife, PE, Brazil
| | | | | | | | - Wilson José Silva
- Universidade Federal de Pernambuco (UFPE), Departamento de Genética,
Recife, PE, Brazil
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Birt HWG, Pattison AB, Skarshewski A, Daniells J, Raghavendra A, Dennis PG. The core bacterial microbiome of banana (Musa spp.). ENVIRONMENTAL MICROBIOME 2022; 17:46. [PMID: 36076285 PMCID: PMC9461194 DOI: 10.1186/s40793-022-00442-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Bananas (Musa spp.) are a globally significant crop and are severely afflicted by diseases for which there are no effective chemical controls. Banana microbiomes may provide novel solutions to these constraints but are difficult to manage due to their high diversity and variability between locations. Hence 'common core' taxa, which are a subset of the microbiome that frequent all, or most, individuals of a host species, represent logical targets for the development of microbiome management approaches. Here, we first performed a pot experiment to characterise the effects of two factors that are likely to differ between farms (viz. edaphic conditions and host genotype) on bacterial diversity in bulk soil and seven plant compartments. From this experiment, we created shortlisted core 'candidates' that were then refined using a survey of 52 field-grown Musa spp. We confirmed the importance of the core through network analysis and by comparing the sequences of our core taxa with those reported in 22 previous studies. RESULTS Diversity was found to differ between plant compartments and soils, but not genotypes. Therefore, we identified populations that were frequent across most plants irrespective of the soil in which they were grown. This led to the selection of 36 'common core' bacteria, that represented 65-95% of the dominant taxa in field-grown plants and were identified as highly interconnected 'hubs' using network analysis - a characteristic shown to be indicative of microbes that influence host fitness in studies of other plants. Lastly, we demonstrated that the core taxa are closely related to banana-associated bacteria observed on five other continents. CONCLUSIONS Our study provides a robust list of common core bacterial taxa for Musa spp. Further research may now focus on how changes in the frequencies and activities of these most persistent taxa influence host fitness. Notably, for several of our core taxa, highly similar populations have already been isolated in previous studies and may be amenable to such experimentation. This contribution should help to accelerate the development of effective Musa spp. microbiome management practices.
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Affiliation(s)
- Henry W. G. Birt
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Anthony B. Pattison
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
- Department of Agriculture and Fisheries, Centre for Wet Tropics Agriculture, 24 Experimental Station Road, South Johnstone, QLD 4859 Australia
| | - Adam Skarshewski
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Jeff Daniells
- Department of Agriculture and Fisheries, Centre for Wet Tropics Agriculture, 24 Experimental Station Road, South Johnstone, QLD 4859 Australia
| | - Anil Raghavendra
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Paul G. Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
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Prakoso AB, Joko T, Soffan A, Sari JP, Ray JD, Drenth A, Subandiyah S. Draft Genome Sequence of Ralstonia syzygii subsp. celebesensis from Indonesia, the Causal Agent of Blood Disease of Banana. PHYTOPATHOLOGY 2022; 112:1584-1586. [PMID: 35522569 DOI: 10.1094/phyto-10-21-0443-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Ady B Prakoso
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Tri Joko
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Alan Soffan
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Juli P Sari
- Dinas Pangan, Tanaman Pangan dan Hortikultura Provinsi Riau, Pekanbaru, 28142, Indonesia
| | - Jane D Ray
- Centre for Horticultural Science, University of Queensland, Brisbane, 4001, Australia
| | - André Drenth
- Centre for Horticultural Science, University of Queensland, Brisbane, 4001, Australia
| | - Siti Subandiyah
- Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
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Tripathi L, Dhugga KS, Ntui VO, Runo S, Syombua ED, Muiruri S, Wen Z, Tripathi JN. Genome Editing for Sustainable Agriculture in Africa. Front Genome Ed 2022; 4:876697. [PMID: 35647578 PMCID: PMC9133388 DOI: 10.3389/fgeed.2022.876697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- *Correspondence: Leena Tripathi,
| | | | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Easter D. Syombua
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Kenyatta University, Nairobi, Kenya
| | - Zhengyu Wen
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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11
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Development of a Highly Sensitive Loop-Mediated Isothermal Amplification Incorporated with Flocculation of Carbon Particles for Rapid On-Site Diagnosis of Blood Disease Bacterium Banana. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bananas are one of the most crucial fruit crops worldwide and significantly contribute to food security in developing countries. However, blood disease of bananas caused by Ralstonia syzygii subspecies celebensensis has become a threat to banana production. Rapid and accurate diagnosis of BDB for on-site detection is pivotal at an early stage for an effective disease control strategy. This study developed LAMP with specific primers targeting BDB, followed by a flocculation assay for visualising positive amplification in the LAMP assay. The assay was sensitive to picogram amounts of gDNA (0.5 pg). LAMP assay on BDB gDNA showed flocculation, but negative results on Fusarium oxysporus cubense and Ralstonia solanacaerum confirming the specificity of the assays. Field testing conducted at MARDI headquarters and Taman Pertanian Universiti discovered that the LAMP-flocculation assays were successful in detecting BDB on symptomatic samples as well as on samples from a healthy plot with no symptom observed at the sampling stage, revealing that this assay can detect BDB at an early infection stage. The validation results showed that the LAMP-flocculation assay was comparable with the PCR technique. This newly developed technique is highly specific and sensitive for the early detection of BDB for the adoption of precautionary control measures.
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12
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Tamrat S, Borrell JS, Shiferaw E, Wondimu T, Kallow S, Davies RM, Dickie JB, Nuraga GW, White O, Woldeyes F, Demissew S, Wilkin P. Reproductive biology of wild and domesticated Ensete ventricosum: Further evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:482-491. [PMID: 35137516 PMCID: PMC9303740 DOI: 10.1111/plb.13390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Loss of sexual reproductive capacity has been proposed as a syndrome of domestication in vegetatively propagated crops, but there are relatively few examples from agricultural systems. In this study, we compare sexual reproductive capacity in wild (sexual) and domesticated (vegetative) populations of enset (Ensete ventricosum (Welw.) Cheesman), a tropical banana relative and Ethiopian food security crop. We examined floral and seed morphology and germination ecology across 35 wild and domesticated enset. We surveyed variation in floral and seed traits, including seed weight, viability and internal morphology, and germinated seeds across a range of constant and alternating temperature regimes to characterize optimum germination requirements. We report highly consistent floral allometry, seed viability, internal morphology and days to germination in wild and domesticated enset. However, seeds from domesticated plants responded to cooler temperatures with greater diurnal range. Shifts in germination behaviour appear concordant with a climatic envelope shift in the domesticated distribution. Our findings provide evidence that sexual reproductive capacity has been maintained despite long-term near-exclusive vegetative propagation in domesticated enset. Furthermore, certain traits such as germination behaviour and floral morphology may be under continued selection, presumably through rare sexually reproductive events. Compared to sexually propagated crops banked as seeds, vegetative crop diversity is typically conserved in living collections that are more costly and insecure. Improved understanding of sexual propagation in vegetative crops may have applications in germplasm conservation and plant breeding.
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Affiliation(s)
- S. Tamrat
- Department of Plant Biology and Biodiversity ManagementAddis Ababa UniversityAddis AbabaEthiopia
- Department of BiologyDilla UniversityDillaSouthern Ethiopia
| | | | - E. Shiferaw
- Ethiopian Biodiversity InstituteAddis AbabaEthiopia
| | - T. Wondimu
- Department of Plant Biology and Biodiversity ManagementAddis Ababa UniversityAddis AbabaEthiopia
| | - S. Kallow
- Royal Botanic Gardens KewMillennium Seed BankWakehurst, ArdinglySussexUK
- Department of BiosystemsKatholieke Universiteit LeuvenLeuvenBelgium
| | - R. M. Davies
- Royal Botanic Gardens KewMillennium Seed BankWakehurst, ArdinglySussexUK
| | - J. B. Dickie
- Royal Botanic Gardens KewMillennium Seed BankWakehurst, ArdinglySussexUK
| | - G. W. Nuraga
- Department of Plant Biology and Biodiversity ManagementAddis Ababa UniversityAddis AbabaEthiopia
| | - O. White
- Royal Botanic GardensKew, RichmondSurreyUK
| | - F. Woldeyes
- Ethiopian Biodiversity InstituteAddis AbabaEthiopia
| | - S. Demissew
- Department of Plant Biology and Biodiversity ManagementAddis Ababa UniversityAddis AbabaEthiopia
| | - P. Wilkin
- Royal Botanic GardensKew, RichmondSurreyUK
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13
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Control of Bacterial Diseases of Banana Using CRISPR/Cas-Based Gene Editing. Int J Mol Sci 2022; 23:ijms23073619. [PMID: 35408979 PMCID: PMC8998688 DOI: 10.3390/ijms23073619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/30/2022] Open
Abstract
Banana is an important staple food crop and a source of income for smallholder farmers in about 150 tropical and sub-tropical countries. Several bacterial diseases, such as banana Xanthomonas wilt (BXW), blood, and moko disease, cause substantial impacts on banana production. There is a vast yield gap in the production of bananas in regions where bacterial pathogens and several other pathogens and pests are present together in the same field. BXW disease caused by Xanthomonas campestris pv. musacearum is reported to be the most destructive banana disease in East Africa. The disease affects all the banana varieties grown in the region. Only the wild-type diploid banana, Musa balbisiana, is resistant to BXW disease. Developing disease-resistant varieties of bananas is one of the most effective strategies to manage diseases. Recent advances in CRISPR/Cas-based gene editing techniques can accelerate banana improvement. Some progress has been made to create resistance against bacterial pathogens using CRISPR/Cas9-mediated gene editing by knocking out the disease-causing susceptibility (S) genes or activating the expression of the plant defense genes. A synopsis of recent advancements and perspectives on the application of gene editing for the control of bacterial wilt diseases are presented in this article.
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14
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Banana Fusarium Wilt Disease Detection by Supervised and Unsupervised Methods from UAV-Based Multispectral Imagery. REMOTE SENSING 2022. [DOI: 10.3390/rs14051231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Banana Fusarium wilt (BFW) is a devastating disease with no effective cure methods. Timely and effective detection of the disease and evaluation of its spreading trend will help farmers in making right decisions on plantation management. The main purpose of this study was to find the spectral features of the BFW-infected canopy and build the optimal BFW classification models for different stages of infection. A RedEdge-MX camera mounted on an unmanned aerial vehicle (UAV) was used to collect multispectral images of a banana plantation infected with BFW in July and August 2020. Three types of spectral features were used as the inputs of classification models, including three-visible-band images, five-multispectral-band images, and vegetation indices (VIs). Four supervised methods including Support Vector Machine (SVM), Random Forest (RF), Back Propagation Neural Networks (BPNN) and Logistic Regression (LR), and two unsupervised methods including Hotspot Analysis (HA) and Iterative Self-Organizing Data Analysis Technique Algorithm (ISODATA) were adopted to detect the BFW-infected canopies. Comparing to the healthy canopies, the BFW-infected canopies had higher reflectance in the visible region, but lower reflectance in the NIR region. The classification results showed that most of the supervised and unsupervised methods reached excellent accuracies. Among all the supervised methods, RF based on the five-multispectral-band was considered as the optimal model, with higher overall accuracy (OA) of 97.28% and faster running time of 22 min. For the unsupervised methods, HA reached high and balanced OAs of more than 95% based on the selected VIs derived from the red and NIR band, especially for WDRVI, NDVI, and TDVI. By comprehensively evaluating the classification results of different metrics, the unsupervised method HA was recommended for BFW recognition, especially in the late stage of infection; the supervised method RF was recommended in the early stage of infection to reach a slightly higher accuracy. The results found in this study could give advice for banana plantation management and provide approaches for plant disease detection.
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15
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Rincón-Flórez VA, Ray JD, Carvalhais LC, O'Dwyer CA, Subandiyah S, Zulperi D, Drenth A. Diagnostics of Banana Blood Disease. PLANT DISEASE 2022; 106:947-959. [PMID: 34668403 DOI: 10.1094/pdis-07-21-1436-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Blood disease in bananas caused by Ralstonia syzygii subsp. celebesensis is a bacterial wilt disease that causes major yield losses of banana in Indonesia and peninsular Malaysia. The disease has significantly increased its geographic distribution in the past decade. Diagnostic methods are an important component of disease management in vegetatively propagated crops such as banana to constrain incursions of plant pathogens. Therefore, the objectives of this study were (i) to design and rigorously validate a novel banana Blood disease (BBD) real-time PCR assay with a high level of specificity and sensitivity of detection and (ii) to validate published PCR-based diagnostic methods targeting the intergenic region in the megaplasmid ("121 assay" with primer set 121) or the phage tail protein-coding sequence in the bacterial chromosome ("Kubota assay" and "BDB2400 assay" with primer set BDB2400). Assay validation included 339 samples (174 Blood disease bacteria, 51 bacteria associated with banana plants, 51 members of the Ralstonia solanacearum species complex, and 63 samples from symptomatic and healthy plant material). Validation parameters were analytical specificity (inclusivity and exclusivity), selectivity, limit of detection, accuracy, and ruggedness. The 121 assay and our newly developed BBD real-time PCR assay detected all R. syzygii subsp. celebesensis strains with no cross-specificity during validation. Two different PCR assays using the primer set BDB2400 lacked specificity and selectivity. This study reveals that our novel BBD real-time PCR assay and the conventional PCR 121 assay are reliable methods for Blood disease diagnostics, as they comply with all tested validation parameters.
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Affiliation(s)
- Vivian A Rincón-Flórez
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jane D Ray
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cecilia A O'Dwyer
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Siti Subandiyah
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Department of Entomology and Plant Pathology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Dzarifah Zulperi
- Department of Plant Protection, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - André Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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16
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Gemeda B, Tesfaye G, Simachew A, Andualem B, Wang A, Guadie A. Microbial community shifts association with physicochemical parameters: Visualizing enset bacterial wilt from different states of enset health. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114084. [PMID: 34773777 DOI: 10.1016/j.jenvman.2021.114084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/13/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Bacterial wilt of enset caused by Xanthomonas campestris is a devastating disease in Ethiopia, where enset is domesticated and served as a staple food for about 20 million people in the country. While enset is infected by bacteria, it shows different wilting stages. However, the microbial community shifts at the different stages of enset infection and associated physicochemical parameter changes remain poorly understood. This study was aimed to visualize the proportion of enset wilt bacterium from other microbial community and its association with physicochemical parameter at different states of enset health. Soil and enset (zero, first, second and third stages) samples were collected from three districts in Gamo Highlands for physicochemical and biological (culture dependent and16S rRNA gene sequence) analysis. The results of culture dependent analysis which has been complemented by 16S rRNA gene sequence confirmed that increasing trends were observed for Xanthomonadaceae, Pseudomonadaceae, Lactobacillaceae and Flavobacteriaceae, while Bacillaceae and Enterobacteriaceae showed progressive decrease from zero to the third stage. Particularly, the 16S rRNA data showed that Xanthomonadaceae increased significantly from zero to different (2.5 × 102 times at the onset of disease and 1.0-2.0 × 104 times at the second and third) stages of enset infection. Most physicochemical results showed that a decreasing trends from zero to third stage, while few parameters are showing an increasing trend. Moisture content (R2 ≥ 0.951, P ≤ 0.049) of the soil and plant samples positively influenced Xanthomonas abundance, while this bacterium showed a strongly negative significant correlation with pH (R2 ≥ -0.962, P ≤ 0.038), temperature (R2 ≥ -0.958, P ≤ 0.042), OM (R2 ≥ -0.952, P ≤ 0.048), and TN (R2 ≥ -0.951, P ≤ 0.049). A strongly negative significant correlation (R2 ≥ -0.948, P ≤ 0.050) was also observed between Xanthomonas and nutrients (K, Mg, Ca, and Cu). Overall, this study implies that different environmental factors found a key driving force of Xanthomonas proportional increment from low abundance at zero stage to higher abundance at the last stage of enset infection suggesting that considering these factors help to design an effective enset disease management strategy, for which further studies will be needed.
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Affiliation(s)
- Birhanu Gemeda
- Department of Biology, College of Natural Sciences, Arba Minch University, Arba Minch, 21, Ethiopia; Biodiversity Research and Conservation Center, Arba Minch University, Arba Minch, 21, Ethiopia
| | - Getaneh Tesfaye
- Department of Biology, College of Natural Sciences, Arba Minch University, Arba Minch, 21, Ethiopia
| | - Addis Simachew
- Addis Ababa University, Institute of Biotechnology, Industrial Biotechnology Unit, Ethiopia
| | - Berhanu Andualem
- University of Gonder, Institute of Biotechnology, Department of Industrial Biotechnology, Ethiopia
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China
| | - Awoke Guadie
- Department of Biology, College of Natural Sciences, Arba Minch University, Arba Minch, 21, Ethiopia; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, PR China.
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17
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Dato KMG, Dégbègni MR, Atchadé MN, Zandjanakou Tachin M, Hounkonnou MN, Aman Omondi B. Spatial parameters associated with the risk of banana bunchy top disease in smallholder systems. PLoS One 2021; 16:e0260976. [PMID: 34860836 PMCID: PMC8641891 DOI: 10.1371/journal.pone.0260976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/20/2021] [Indexed: 11/18/2022] Open
Abstract
The Banana Bunchy Top Disease (BBTD), caused by the Banana Bunchy Top Virus (BBTV) is the most important and devastating in many tropical countries. BBTD epidemiology has been little studied, mixed landscape smallholder systems. The relative risks associated with this disease vary between geographical areas and landscapes. This work analyzed the management and vegetation conditions in smallholder gardens to assess the factors linked to landscape-level BBTV transmission and management. Mapping was done in this study area which is in a BBTD-endemic region, involving farmers actively managing the disease, but with household-level decision making. A spatial scanning statistic was used to detect and identify spatial groups at the 5% significance threshold, and a Poisson regression model was used to explore propagation vectors and the effect of surrounding vegetation and crop diversity. Spatial groups with high relative risk were identified in three communities, Dangbo, Houéyogbé, and Adjarra. Significant associations emerged between the BBTD prevalence and some crop diversity, seed systems, and BBTD management linked factors. The identified factors form important candidate management options for the detailed assessment of landscape-scale BBTD management in smallholder communities.
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Affiliation(s)
- Kéladomé Maturin Géoffroy Dato
- International Chair in Mathematical Physics and Applications (ICMPA-UNESCO CHAIR), University of Abomey-Calavi, Cotonou, Benin Republic
| | - Mahougnon Robinson Dégbègni
- International Chair in Mathematical Physics and Applications (ICMPA-UNESCO CHAIR), University of Abomey-Calavi, Cotonou, Benin Republic
| | - Mintodê Nicodème Atchadé
- International Chair in Mathematical Physics and Applications (ICMPA-UNESCO CHAIR), University of Abomey-Calavi, Cotonou, Benin Republic
- National Higher School of Mathematics Genius and Modelization, National University of Sciences, Technologies, Engineering and Mathematics, Abomey, Republic of Benin
| | - Martine Zandjanakou Tachin
- Doctorate School of Agriculture and Water Sciences, National University of Agriculture, Kétou, Benin Republic
| | - Mahouton Norbert Hounkonnou
- International Chair in Mathematical Physics and Applications (ICMPA-UNESCO CHAIR), University of Abomey-Calavi, Cotonou, Benin Republic
| | - Bonaventure Aman Omondi
- Bioversity International (Alliance of Bioversity International and CIAT), Abomey Calavi, Cotonou, Benin
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18
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Abstract
Banana cultivation has increased significantly over the last century to meet the growing demand for this popular fruit. Originating in Southeast Asia, bananas are now produced in >135 different countries in tropical and subtropical regions of the world. Most of this expansion of production is based on a single banana variety, Cavendish, which makes up almost all the export trade grown in large-scale monocultures and a large part of the local trade and represents >40% of all bananas grown globally. Over the last century several major diseases of the banana have emerged and widely expanded their geographic ranges. Cultivars within the Cavendish variety are highly susceptible to these diseases, including yellow Sigatoka, black leaf streak, Eumusae leaf spot, freckle, Fusarium wilt tropical race 4, banana bunchy top, and the bacterial wilts Moko, Xanthomonas wilt, and banana Blood disease. This review graphically illustrates the emergence and rapid intercontinental spread of these diseases and discusses several major disease epidemics in bananas. Evidently, the large-scale monoculture based on the single variety Cavendish has resulted in an extreme level of genetic vulnerability. The resistance to diversification in the Cavendish production chain and the lack of investment in genetics and plant breeding in the recent past means that currently limited genetic solutions are available to replace the Cavendish banana with a set of market acceptable resistant varieties from a range of different genetic backgrounds.
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Affiliation(s)
- André Drenth
- Centre for Horticultural Science, The University of Queensland, Brisbane, QLD, Australia
| | - Gert Kema
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
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19
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Ray JD, Subandiyah S, Rincon-Florez VA, Prakoso AB, Mudita IW, Carvalhais LC, Markus JER, O'Dwyer CA, Drenth A. Geographic Expansion of Banana Blood Disease in Southeast Asia. PLANT DISEASE 2021; 105:2792-2800. [PMID: 33973808 DOI: 10.1094/pdis-01-21-0149-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Blood disease in bananas caused by Ralstonia syzygii subsp. celebesensis is a bacterial wilt causing significant crop losses in Indonesia and Malaysia. Disease symptoms include wilting of the plant and red-brown vascular staining, internal rot, and discoloration of green banana fruit. There is no known varietal resistance to this disease in the Musa genus, although variation in susceptibility has been observed, with the popular Indonesian cooking banana variety Kepok being highly susceptible. This study established the current geographic distribution of Blood disease in Indonesia and confirmed the pathogenicity of isolates by Koch's postulates. The long-distance distribution of the disease followed an arbitrary pattern indicative of human-assisted movement of infected banana materials. In contrast, local or short-distance spread radiated from a single infection source, indicative of dispersal by insects and possibly contaminated tools, water, or soil. The rapid expansion of its geographical range makes Blood disease an emerging threat to banana production in Southeast Asia and beyond.
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Affiliation(s)
- Jane D Ray
- Centre for Horticultural Science, The University of Queensland, Brisbane, QLD 4001, Australia
| | - Siti Subandiyah
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
- Department of Entomology and Plant Pathology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Vivian A Rincon-Florez
- Centre for Horticultural Science, The University of Queensland, Brisbane, QLD 4001, Australia
| | - Ady B Prakoso
- Department of Entomology and Plant Pathology, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - I W Mudita
- Agricultural Faculty, University of Nusa Cendana, Kupang 85001, Indonesia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, The University of Queensland, Brisbane, QLD 4001, Australia
| | - Jenny E R Markus
- Agricultural Faculty, University of Nusa Cendana, Kupang 85001, Indonesia
| | - Cecilia A O'Dwyer
- Centre for Horticultural Science, The University of Queensland, Brisbane, QLD 4001, Australia
| | - André Drenth
- Centre for Horticultural Science, The University of Queensland, Brisbane, QLD 4001, Australia
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20
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Nakato GV, Studholme DJ, Blomme G, Grant M, Coutinho TA, Were EM, Wicker E, Mahuku G. SNP-based genotyping and whole-genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin. PLANT PATHOLOGY 2021; 70:534-543. [PMID: 33776147 PMCID: PMC7984043 DOI: 10.1111/ppa.13308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/19/2020] [Indexed: 05/16/2023]
Abstract
For decades, Xanthomonas vasicola pv. musacearum (Xvm) has been an economically important bacterial pathogen on enset in Ethiopia. Since 2001, Xvm has also been responsible for significant losses to banana crops in several East and Central African countries, with devastating consequences for smallholder farmers. Understanding the genetic diversity within Xvm populations is essential for the smart design of transnationally reasoned, durable, and effective management practices. Previous studies have revealed limited genetic diversity in Xvm, with East African isolates from banana each falling into one of two closely related clades previously designated as sublineages SL 1 and SL 2, the former of which had also been detected on banana and enset in Ethiopia. Given the presumed origin of Xvm in Ethiopia, we hypothesized that both clades might be found in that country, along with additional genotypes not seen in Central and East African bananas. Genotyping of 97 isolates and whole-genome sequencing of 15 isolates revealed not only the presence of SL 2 in Ethiopia, but additional diversity beyond SL 1 and SL 2 in four new clades. Moreover, SL 2 was detected in the Democratic Republic of Congo, where previously SL 1 was the only clade reported. These results demonstrate a greater range of genetic diversity among Xvm isolates than previously reported, especially in Ethiopia, and further support the hypothesis that the East/Central Africa xanthomonas wilt epidemic has been caused by a restricted set of genotypes drawn from a highly diverse pathogen pool in Ethiopia.
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Affiliation(s)
- Gloria V. Nakato
- Plant PathologyInternational Institute of Tropical AgricultureKampalaUganda
- Department of Microbiology and Plant PathologyCentre for Microbial Ecology and Genomics (CMEG), Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | | | - Guy Blomme
- Bioversity International, c/o ILRIAddis AbabaEthiopia
| | | | - Teresa A. Coutinho
- Department of Microbiology and Plant PathologyCentre for Microbial Ecology and Genomics (CMEG), Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Evans M. Were
- Plant PathologyInternational Institute of Tropical AgricultureKampalaUganda
| | - Emmanuel Wicker
- CIRADUMR Interactions Plantes‐Microorganismes‐Environnement (IPME)Montpellier cedex 5France
- IPMEUniversity of MontpellierCIRADMontpellier cedex 5France
| | - George Mahuku
- Plant PathologyInternational Institute of Tropical AgricultureKampalaUganda
- International Institute of Tropical Agriculture (IITA)Dar es SalaamTanzania
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21
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The Changing Face of the Family Enterobacteriaceae (Order: " Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes. Clin Microbiol Rev 2021; 34:34/2/e00174-20. [PMID: 33627443 DOI: 10.1128/cmr.00174-20] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.
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Rasoamanana H, Ravelomanantsoa S, Yahiaoui N, Dianzinga N, Rébert E, Gauche MM, Pecrix Y, Costet L, Rieux A, Prior P, Robène I, Cellier G, Guérin F, Poussier S. Contrasting genetic diversity and structure among Malagasy Ralstonia pseudosolanacearum phylotype I populations inferred from an optimized Multilocus Variable Number of Tandem Repeat Analysis scheme. PLoS One 2020; 15:e0242846. [PMID: 33290390 PMCID: PMC7723262 DOI: 10.1371/journal.pone.0242846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
The Ralstonia solanacearum species complex (RSSC), composed of three species and four phylotypes, are globally distributed soil-borne bacteria with a very broad host range. In 2009, a devastating potato bacterial wilt outbreak was declared in the central highlands of Madagascar, which reduced the production of vegetable crops including potato, eggplant, tomato and pepper. A molecular epidemiology study of Malagasy RSSC strains carried out between 2013 and 2017 identified R. pseudosolanacearum (phylotypes I and III) and R. solanacearum (phylotype II). A previously published population biology analysis of phylotypes II and III using two MultiLocus Variable Number of Tandem Repeats Analysis (MLVA) schemes revealed an emergent epidemic phylotype II (sequevar 1) group and endemic phylotype III isolates. We developed an optimized MLVA scheme (RS1-MLVA14) to characterize phylotype I strains in Madagascar to understand their genetic diversity and structure. The collection included isolates from 16 fields of different Solanaceae species sampled in Analamanga and Itasy regions (highlands) in 2013 (123 strains) and in Atsinanana region (lowlands) in 2006 (25 strains). Thirty-one haplotypes were identified, two of them being particularly prevalent: MT007 (30.14%) and MT004 (16.44%) (sequevar 18). Genetic diversity analysis revealed a significant contrasting level of diversity according to elevation and sampling region. More diverse at low altitude than at high altitude, the Malagasy phylotype I isolates were structured in two clusters, probably resulting from different historical introductions. Interestingly, the most prevalent Malagasy phylotype I isolates were genetically distant from regional and worldwide isolates. In this work, we demonstrated that the RS1-MLVA14 scheme can resolve differences from regional to field scales and is thus suited for deciphering the epidemiology of phylotype I populations.
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Affiliation(s)
- Hasina Rasoamanana
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
| | - Santatra Ravelomanantsoa
- Centre National de la Recherche Appliquée au Développement Rural FOFIFA, Antananarivo, Madagascar
| | - Noura Yahiaoui
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
| | - Niry Dianzinga
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
| | - Emeline Rébert
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
| | - Miharisoa-Mirana Gauche
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
| | - Yann Pecrix
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, Réunion, France
| | - Laurent Costet
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, Réunion, France
| | - Adrien Rieux
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, Réunion, France
| | - Philippe Prior
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, Réunion, France
| | - Isabelle Robène
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, Réunion, France
| | - Gilles Cellier
- Anses - Plant Health Laboratory - Tropical Pests and Diseases Unit, Saint-Pierre, Réunion, France
| | - Fabien Guérin
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
| | - Stéphane Poussier
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Université de La Réunion, Saint-Pierre, Réunion, France
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Allometric models for above and below-ground biomass of wild Musa stands in tropical semi evergreen forests. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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An SQ, Potnis N, Dow M, Vorhölter FJ, He YQ, Becker A, Teper D, Li Y, Wang N, Bleris L, Tang JL. Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas. FEMS Microbiol Rev 2020; 44:1-32. [PMID: 31578554 PMCID: PMC8042644 DOI: 10.1093/femsre/fuz024] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/29/2019] [Indexed: 01/15/2023] Open
Abstract
Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.
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Affiliation(s)
- Shi-Qi An
- National Biofilms Innovation Centre (NBIC), Biological Sciences, University of Southampton, University Road, Southampton SO17 1BJ, UK
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Rouse Life Science Building, Auburn University, Auburn AL36849, USA
| | - Max Dow
- School of Microbiology, Food Science & Technology Building, University College Cork, Cork T12 K8AF, Ireland
| | | | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Anke Becker
- Loewe Center for Synthetic Microbiology and Department of Biology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, Marburg 35032, Germany
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Yi Li
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred 33850, USA
| | - Leonidas Bleris
- Bioengineering Department, University of Texas at Dallas, 2851 Rutford Ave, Richardson, TX 75080, USA.,Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, 800 W Campbell Road, Richardson, TX75080, USA
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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Studholme DJ, Wicker E, Abrare SM, Aspin A, Bogdanove A, Broders K, Dubrow Z, Grant M, Jones JB, Karamura G, Lang J, Leach J, Mahuku G, Nakato GV, Coutinho T, Smith J, Bull CT. Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov. PHYTOPATHOLOGY 2020; 110:1153-1160. [PMID: 31922946 DOI: 10.1094/phyto-03-19-0098-le] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
| | - Emmanuel Wicker
- IPME, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Sadik Muzemil Abrare
- Southern Agricultural Research Institute (SARI), Areka Agricultural Research Center, Areka, Ethiopia
| | | | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Zoe Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Murray Grant
- School of Life Sciences, Gibbet Hill, University of Warwick, Coventry, CV4 7AL, U.K
| | - Jeffrey B Jones
- University of Florida, Plant Pathology Department, 1453 Fifield Hall, Gainesville, FL 32611, U.S.A
| | | | - Jillian Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Jan Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - George Mahuku
- International Institute of Tropical Agiculture (IITA), East Africa Hub, IITA-Tanzania, P.O. Box 34441, Dar es Salaam, Tanzania
| | - Gloria Valentine Nakato
- International Institute of Tropical Agriculture (IITA), Plot 15B, Naguru East Road, Upper Naguru, P.O. Box 7878, Kampala, Uganda
| | - Teresa Coutinho
- Department of Microbiology and Plant Pathology, Centre for Microbial Ecology and Genomics (CMEG), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X28, Pretoria 0028, South Africa
| | | | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, PA, U.S.A
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Kikulwe EM, Asindu M. A contingent valuation analysis for assessing the market for genetically modified planting materials among banana producing households in Uganda. GM CROPS & FOOD 2020; 11:113-124. [PMID: 32009531 PMCID: PMC7289523 DOI: 10.1080/21645698.2020.1720498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Banana is an important livelihood source for more than 12 million smallholder farmers in Uganda. Despite this contribution, its productivity continues to decline due to Banana Xanthomonas wilt (BXW). Cultural practices have been deployed to effectively control BXW but require a continuous and timely application, thus, prompting scientists to develop genetically modified (GM) bananas which display BXW resistance or tolerance. With prospects for commercialization of these GM bananas on the agenda, this paper applied a Contingent Valuation Method to assess producer acceptance of GM banana suckers among 233 banana producing households. Results show that producers were willing to pay between Ugandan shillings (UGX) 1100 to 1700 (US$0.28–0.44) per GM banana sucker Annual demand for GM banana suckers ranged from 70 to 82 million suckers. The results suggest that, in the event of not commercializing BXW-resistant GM bananas, Uganda loses an annual revenue ranging from UGX 76 to 139 billion (US$ 19.51 to 35.70 million).
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Affiliation(s)
| | - Marsy Asindu
- Development Impact Unit, Bioversity International, Kampala, Uganda.,Department of Agribusiness and Natural Resources Economics, Makerere University, Kampala, Uganda
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27
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Borrell JS, Biswas MK, Goodwin M, Blomme G, Schwarzacher T, Heslop-Harrison JS(P, Wendawek AM, Berhanu A, Kallow S, Janssens S, Molla EL, Davis AP, Woldeyes F, Willis K, Demissew S, Wilkin P. Enset in Ethiopia: a poorly characterized but resilient starch staple. ANNALS OF BOTANY 2019; 123:747-766. [PMID: 30715125 PMCID: PMC6526316 DOI: 10.1093/aob/mcy214] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/16/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. SCOPE Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. CONCLUSION Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop.
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Affiliation(s)
| | - Manosh K Biswas
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Mark Goodwin
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Guy Blomme
- Bioversity International, Addis Ababa, Ethiopia
| | | | | | | | - Admas Berhanu
- Department of Biology and Biotechnology, Wolkite University, Hawassa, Ethiopia
| | - Simon Kallow
- Conservation Science Department, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex, UK
- Division of Crop Biotechnics, Katholieke Universiteit Leuven, Willem de Croylaan, Leuven, Belgium
| | - Steven Janssens
- Laboratory of Plant Systematics, Institute of Botany and Microbiology, Katholieke Universiteit Leuven, Kasteelpark, Arenberg, Leuven, Belgium
| | - Ermias L Molla
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Kathy Willis
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | - Sebsebe Demissew
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Gullele Botanic Garden, Addis Ababa, Ethiopia
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
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Ocimati W, Bouwmeester H, Groot JCJ, Tittonell P, Brown D, Blomme G. The risk posed by Xanthomonas wilt disease of banana: Mapping of disease hotspots, fronts and vulnerable landscapes. PLoS One 2019; 14:e0213691. [PMID: 30939129 PMCID: PMC6445462 DOI: 10.1371/journal.pone.0213691] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Banana production landscapes in the African Great Lakes Region (AGLR) have been under immense pressure from Xanthomonas wilt (XW) disease over the past two decades. XW, first reported on banana in central Uganda and eastern DR Congo in 2001, has since spread to the entire AGLR. XW is currently spreading westwards from hot spots in eastern DR Congo highlands, putting the plantain (Musa AAB genome) belt of central and west Africa at risk. In-depth understanding of the key variables responsible for disease spread, current hotspots, and vulnerable landscapes is crucial for disease early warning and management. We mapped aggregated disease distribution and hotspots in the AGLR and identified vulnerable landscapes across African banana production zones. Available data on disease prevalence collected over 11 years was regressed against environmental and expert developed covariates to develop the AGLR XW hotspots map. For the Africa-wide risk map, precipitation, distance to hotspots, degree of trade in fresh banana products, production zone interconnectedness and banana genotype composition were used as covariates. In the AGLR, XW was mainly correlated to precipitation and disease/banana management. Altitude and temperature had unexpectedly low effects, possibly due to an overriding impact of tool-mediated spread which is part of the management covariate. In the AGLR, the eastern part of DR Congo was a large hotspot with highest vulnerability. Apart from endemic zones in the AGLR and Ethiopia, northern Mozambique was perceived as a moderate risk zone mainly due to the predominance of 'Bluggoe' (Musa ABB type) which is highly susceptible to insect-vectored transmission. Presence of XW hotspots (e.g. eastern DR Congo) and vulnerable areas with low (e.g. north-western Tanzania) or no disease (e.g. Congo basin, western DR Congo and northern Mozambique) pressure suggest key areas where proactive measures e.g. quarantines and information sharing on XW diagnosis, epidemiology, and control could be beneficial.
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Affiliation(s)
- Walter Ocimati
- Bioversity International, Kampala, Uganda
- Farming Systems Ecology, Wageningen University & Research, Wageningen, The Netherlands
- * E-mail:
| | | | - Jeroen C. J. Groot
- Farming Systems Ecology, Wageningen University & Research, Wageningen, The Netherlands
| | - Pablo Tittonell
- Agroecology, Environment and Systems Group, Instituto de Investigaciones Forestales y Agropecuarias de Bariloche (IFAB), INTA-CONICET, San Carlos de Bariloche, Río Negro, Argentina
- Groningen Institute of Evolutionary Life Sciences, Groningen University, Groningen, The Netherlands
| | - David Brown
- Bioversity International, Turrialba, Cartago, Costa Rica
| | - Guy Blomme
- Bioversity International, Addis Ababa, Ethiopia
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Merga IF, Tripathi L, Hvoslef-Eide AK, Gebre E. Application of Genetic Engineering for Control of Bacterial Wilt Disease of Enset, Ethiopia's Sustainability Crop. FRONTIERS IN PLANT SCIENCE 2019; 10:133. [PMID: 30863414 PMCID: PMC6399475 DOI: 10.3389/fpls.2019.00133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/28/2019] [Indexed: 05/05/2023]
Abstract
Enset (Ensete ventricosum (Welw.) Cheesman) is one of the Ethiopia's indigenous sustainability crops supporting the livelihoods of about 20 million people, mainly in the densely populated South and Southwestern parts of the country. Enset serves as a food security crop for humans, animal feed, and source of fiber for the producers. The production of enset has been constrained by plant pests, diseases, and abiotic factors. Among these constraints, bacterial wilt disease has been the most important limiting factor for enset production since its outbreak five decades ago. There is no known bacterial wilt disease resistant genetic material in the enset genetic pool to transfer this trait to susceptible enset varieties through conventional breeding. Moreover, the absence of effective chemicals against the disease has left farmers without means to combat bacterial wilt for decades. Genetic engineering has been the alternative approach to develop disease resistant plant materials in other crops where traditional breeding tools are ineffective. This review discusses enset cultivation and recent developments addressing the control of bacterial wilt disease in enset and related crops like banana to help design effective strategies.
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Affiliation(s)
- Ibsa Fite Merga
- International Institute of Tropical Agriculture, Nairobi, Kenya
- Norwegian University of Life Sciences, Ås, Norway
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | | | - Endale Gebre
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
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Ocimati W, Were E, Groot JCJ, Tittonell P, Nakato GV, Blomme G. Risks Posed by Intercrops and Weeds as Alternative Hosts to Xanthomonas campestris pv. musacearum in Banana Fields. FRONTIERS IN PLANT SCIENCE 2018; 9:1471. [PMID: 30364243 PMCID: PMC6192450 DOI: 10.3389/fpls.2018.01471] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
Alternative host plants are important in the survival and perpetuation of several crop pathogens and have been suspected to play a role in the survival of Xanthomonas campestris pv. musacearum (Xcm) and perpetuation of Xanthomonas wilt (XW) disease of banana and enset. This study determined the potential risk posed by two weeds (Canna spp. and wild sorghum) and common banana intercrops (maize, millet, sorghum, taro, and sugarcane) as alternative hosts to Xcm. The study employed screenhouse experiments, laboratory procedures and diagnosis of banana fields in XW-affected landscapes. Typical XW symptoms were only observed in artificially inoculated Canna sp., with an incidence of 96%. Leaf lesions characteristic of xanthomonads occurred on millet (50%) and sorghum (35%), though the plants recovered. No symptoms occurred in maize, sugarcane, taro or wild sorghum. However, Xcm was recovered from all these plant species, with higher recoveries in Canna sp. (47%), millet (27%), sugarcane (27%), and wild sorghum (25%). Only isolates recovered from Canna sp., millet, sorghum and wild sorghum caused disease in banana plantlets. The presence and incidence of XW on-farm was positively associated with the presence of susceptible ABB Musa genotypes and negatively with number of banana cultivars on farm and household access to training on XW management. Only 0.02% of field sampled Canna spp. plants had Xcm. Risk posed by Canna spp. on-farm could be limited to tool transmission as it has persistent floral bracts that prevent insect-mediated infections. Given the high susceptibility, perennial nature and propagation through rhizomes of Canna sp., it could pose a moderate-high risk, thus warranting some attention in the management of XW disease. Sugarcane could offer a low-moderate risk due to its perennial nature and propagation through rhizomes while risk from maize, millet, and sorghum was deemed zero-low due to their annual nature, wind-mediated mode of pollination and propagation through seed. Understanding the interactions of a crop pathogen with other plants is thus important when diversifying agroecosystems. The study findings also suggest other factors such as cultivar composition and management of the disease at farm and landscape level to be important in the perpetuation of XW disease.
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Affiliation(s)
- Walter Ocimati
- Farming Systems Ecology Group, Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
- Bioversity International, Kampala, Uganda
| | - Evans Were
- International Institute of Tropical Agriculture, Kampala, Uganda
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute) (490), University of Hohenheim, Stuttgart, Germany
| | - Jeroen C. J. Groot
- Farming Systems Ecology Group, Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Pablo Tittonell
- Agroecology, Environment and Systems Group, Instituto de Investigaciones Forestales y Agropecuarias de Bariloche (IFAB), INTA-CONICET, San Carlos de Bariloche, Río Negro, Argentina
- Groningen Institute of Evolutionary Life Sciences, Groningen University, Netherlands
| | | | - Guy Blomme
- Bioversity International, Addis Ababa, Ethiopia
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Fernández-Ruiz I, Coutinho FH, Rodriguez-Valera F. Thousands of Novel Endolysins Discovered in Uncultured Phage Genomes. Front Microbiol 2018; 9:1033. [PMID: 29867909 PMCID: PMC5968864 DOI: 10.3389/fmicb.2018.01033] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/01/2018] [Indexed: 12/05/2022] Open
Abstract
Bacteriophages express endolysins toward the end of their replication cycle to degrade the microbial cell wall from within, allowing viral progeny to be released. Endolysins can also degrade the prokaryotic cell wall from the outside, thus have potential to be used for biotechnological and medical purposes. Multiple endolysins have been identified within the genomes of isolated phages, but their diversity in uncultured phages has been overlooked. We used a bioinformatics pipeline to identify novel endolysins from nearly 200,000 uncultured viruses. We report the discovery of 2,628 putative endolysins, many of which displayed novel domain architectures. In addition, several of the identified proteins are predicted to be active against genera that include pathogenic bacteria. These discoveries enhance the diversity of known endolysins and are a stepping stone for developing medical and biotechnological applications that rely on bacteriophages, the most diverse biological entities on Earth.
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Affiliation(s)
- Iris Fernández-Ruiz
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Felipe H Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
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Abstract
In this paper, I describe the genomic characteristics of a Ralstonia phage infecting Ralstonia solanacearum. The Ralstonia phage RPSC1 was isolated from a soil sample collected in Sichuan Province, in southwestern China. The complete genome of RPSC1 is composed of a linear double-stranded DNA 39,628 bp in length, with G+C content of 61.55%, and 43 putative protein-coding genes. All the putative protein-coding genes were on the same strand. No tRNA-encoding genes were identified. Phylogenetic and comparative genomics analyses indicate that Ralstonia phage RPSC1 should be considered a new member of the family Podoviridae. The wide host range contributes to the potential of Ralstonia phage RPSC1 as a biocontrol agent.
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Affiliation(s)
- Min Liao
- College of Life Science & Biotechnology, Mianyang Teachers' College, 166# Mianxingdong Rd, Mianyang, 621000, Sichuan, China.
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33
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Moore MD, Jaykus LA. Virus-Bacteria Interactions: Implications and Potential for the Applied and Agricultural Sciences. Viruses 2018; 10:E61. [PMID: 29393885 PMCID: PMC5850368 DOI: 10.3390/v10020061] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/28/2018] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic virus-bacteria interactions have recently become an emerging topic of study due to multiple significant examples related to human pathogens of clinical interest. However, such omnipresent and likely important interactions for viruses and bacteria relevant to the applied and agricultural sciences have not been reviewed or compiled. The fundamental basis of this review is that these interactions have importance and deserve more investigation, as numerous potential consequences and applications arising from their discovery are relevant to the applied sciences. The purpose of this review is to highlight and summarize eukaryotic virus-bacteria findings in the food/water, horticultural, and animal sciences. In many cases in the agricultural sciences, mechanistic understandings of the effects of virus-bacteria interactions remain unstudied, and many studies solely focus on co-infections of bacterial and viral pathogens. Given recent findings relative to human viral pathogens, further research related to virus-bacteria interactions would likely result in numerous discoveries and beneficial applications.
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Affiliation(s)
- Matthew D Moore
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
| | - Lee-Ann Jaykus
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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