1
|
Sondo M, Wonni I, Koïta K, Rimbault I, Barro M, Tollenaere C, Moulin L, Klonowska A. Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data. PLoS One 2023; 18:e0287084. [PMID: 38032916 PMCID: PMC10688718 DOI: 10.1371/journal.pone.0287084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.
Collapse
Affiliation(s)
- Moussa Sondo
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Kadidia Koïta
- Université Joseph Ki Zerbo, Ouagadougou, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Isabelle Rimbault
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Mariam Barro
- INERA, Institut de l’Environnement et de Recherches Agricoles du Burkina Faso, Bobo-Dioulasso, Burkina Faso
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Charlotte Tollenaere
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| | - Lionel Moulin
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Agnieszka Klonowska
- PHIM Plant Health Institute, IRD, CIRAD, INRAE, Institut Agro, Univ. Montpellier, Montpellier, France
- LMI Pathobios, Observatoire des Agents Phytopathogènes en Afrique de l’Ouest, Bobo-Dioulasso, Burkina Faso
| |
Collapse
|
2
|
Liu M, Hu R, Xia M, He X, Jin Y. Novel broad-spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases. Environ Microbiol 2023; 25:2075-2087. [PMID: 37300421 DOI: 10.1111/1462-2920.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Bacterial leaf blight (BLB) and bacterial leaf streak (BLS)-caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively-are two major bacterial diseases that threaten the safe production of rice, one of the most important food crops. Bacteriophages are considered potential biocontrol agents against rice bacterial pathogens, due to their host specificity and environmental safety. It is common for BLB and BLS to occur together in fields, which highlights the need for broad-spectrum phages capable of infecting both Xoo and Xoc. In this study, two lytic broad-spectrum phages (pXoo2106 and pXoo2107) that can infect various strains of Xoo and Xoc were assessed. Both phages belong to the class Caudoviricetes and one of them to the family Autographiviridae, while the other belongs to an unclassified family. Two phages alone or combined in a phage cocktail could effectively inhibit Xoo and Xoc growth in vitro. In an in vivo biocontrol experiment, the phage cocktail reduced the total CFU and significantly eased the symptoms caused by Xoo or Xoc. Our results suggest that pXoo2106 and pXoo2107 have a broad-spectrum host range targeting different X. oryzae strains, and have strong biocontrol potential in field applications against both BLB and BLS.
Collapse
Affiliation(s)
- Mengjiao Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| | - Ran Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| | - Mian Xia
- Hainan Yazhou Bay Seed Laboratory, Hainan, China
| | - Xiaoqing He
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| | - Yi Jin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| |
Collapse
|
3
|
Diversity of transcription activator-like effectors and pathogenicity in strains of Xanthomonas oryzae pv. oryzicola from Yunnan. World J Microbiol Biotechnol 2022; 38:71. [PMID: 35258706 DOI: 10.1007/s11274-022-03230-7] [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: 03/21/2021] [Accepted: 01/07/2022] [Indexed: 10/18/2022]
Abstract
The present study aimed to evaluate transcriptional activator-like effector (TALE) genes in 86 Xanthomonas oryzae pv. oryzicola strains collected from 8 rice-growing regions in Yunnan, and to examine the relationship between TALE genotypes and virulence in 6 differential rice lines. Besides, the geographical areas, distribution of these genotypes were studied in detail. Genetic diversity was analyzed through the number and size of putative TALE genes based on TALE gene avrXa3 as a probe. We found that X. oryzae pv. oryzicola strains consist of variable number (13-27) of avrXa3-hybridizing fragments (putative TALE genes). Test strains were classified into 8 genotypes (G1-G8) with major genotypes G3 and G7 widely distributed in Yunnan. Pathogenicity of X. oryzae pv. oryzicola was evaluated by inoculating 6 differential rice lines with a single resistance gene into 9 pathotypes clusters (I-IX), the dominant Genotypes G3 and G7 consist of pathotypes I, II, and IV. Furthermore, we also detected the known TALE target genes expression in susceptible rice cultivar (cv. nipponbare) after inoculating 8 genotypes-representative X. oryzae pv. oryzicola strain. Correlation between the numbers of putative TALE genes of X. oryzae pv. oryzicola and relevant target genes in nipponbare confirmed up-regulation. Altogether, this study has given insights into the population structure of X. oryzae pv. oryzicola that may inform strategies to control BLS in rice.
Collapse
|
4
|
Tall H, Lachaux M, Diallo A, Wonni I, Tekete C, Verdier V, Szurek B, Hutin M. Confirmation report of Bacterial Leaf Streak disease of rice caused by Xanthomonas oryzae pv. oryzicola in Senegal. PLANT DISEASE 2022; 106:2253. [PMID: 35100031 DOI: 10.1094/pdis-11-21-2481-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Xanthomonas oryzae pv. X. oryzicola (Xoc), the causal agent of Bacterial Leaf Streak (BLS), is considered as one of the most important emerging pathogens of rice in Africa. This disease is estimated as responsible of 20 to 30% yield loss (Sileshi et Gebeyehu 2021) and has been characterized in several west African countries including Mali and Burkina Faso since 2003 and more recently in Ivory Coast (Wonni et al. 2014, Diallo et al. 2021). Presence of BLS symptoms in Senegal were reported by Trinh in 1980 but, to our knowledge, BLS occurrence has never been validated further and no strain of Xoc have ever been isolated from Senegalese rice fields. Xoc is transmitted by seeds which contribute to its spread through the rice trade (Sileshi et Gebeyehu 2021). To confirm Trinh's observations, we surveyed rice fields between 2014 and 2016 in eight different regions where rice is produced in Senegal. Typical disease symptoms characterized by yellow-brown to black translucent leaf streaks sometimes along with exudates, were detected in fields of several regions and collected. Leaf pieces were successively sanitized, rinsed in sterile water, and symptomatic fragments were ground using the Qiagen Tissue Lyser System (QIAGEN, Courtaboeuf, France). The leaf powder was diluted in 1.5 ml of sterile water and incubated for 30 minutes at room temperature. Ten μl of the suspension was streaked on semi-selective PSA medium and incubated at 28°C for 3 to 7 days. Characteristic round, convex, mucous, straw-yellow Xoc candidate colonies were purified from six individual leaf samples from three distinct sites in the northern Senegal River Valley. To confirm their identity, isolated strains were tested for pathogenicity and molecular characterization. All isolates were subjected to the multiplex PCR developed for the identification of X. oryzae pathovars (Lang et al., 2010) and revealed the same PCR profile (two amplicons of 324 and 691 base pairs) similar to that of the Xoc reference strain BLS256. Leaves of 5-week-old plants of O. sativa cv. Kitaake were infiltrated with a needleless syringe containing a bacterial suspension set at an optical density of 0.5. Upon seven days of incubation under greenhouse conditions (27 ± 1°C with a 12-hour photoperiod), all infiltrated spots (2 spots on 3 plants per isolate) developed water-soaked lesions similar to those caused by control strain BLS256, except when leaves were infiltrated with water. Symptomatic leaf tissues were ground and plated on PSA medium, resulting in colonies with typical Xanthomonas morphology that were diagnosed as Xoc by multiplex PCR typing, thus fulfilling Koch's postulate. At last, four of the isolates were subjected to gyrB sequencing upon PCR amplification using the universal primers XgyrB1F and XgyrB1R (Young et al., 2008). Analysis of 780bp partial gyrB sequences of strains S18-3-4, S23-1-12, S52-1-4 and S52-1-10 highlighted 100% identity with the gyrB sequence of strain BLS256 (Acc. No. CP003057). To our knowledge, this is the first report of BLS in Senegal which is supported by molecular characterization methods. This study validates the presence of BLS in Senegal and will serve as a basis for future efforts of rice breeding for locally adapted resistance. More studies are needed to clarify the spatial distribution and prevalence of BLS in Senegal as rice cultivation is expanding rapidly in the country.
Collapse
Affiliation(s)
- Hamidou Tall
- Institut Sénégalais de Recherches Agricoles, 206826, Kolda, Senegal;
| | - Marlene Lachaux
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| | - Amadou Diallo
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Plant Health Institute of Montpellier Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo Dioulasso, Burkina Faso;
| | - Issa Wonni
- INERA, Institut de l'Environnement et Recherches Agricoles, Plant Pathology, Bobo Dioulasso, Burkina Faso;
| | - Cheick Tekete
- USTTB, 225803, LaboREM-Biotech, Bamako, Bamako, Mali;
| | - Valérie Verdier
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| | - Boris Szurek
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| | - Mathilde Hutin
- Institut de Recherche pour le Développement Centre de Montpellier, 98751, PHIM, Montpellier, Occitanie, France;
| |
Collapse
|
5
|
Diallo A, Zougrana S, Sawadogo M, Kone D, Silué D, Szurek B, Wonni I, Hutin M. First Report of Bacterial Leaf Streak Disease of Rice Caused by Xanthomonas oryzae pv. oryzicola in Ivory Coast. PLANT DISEASE 2021; 105:PDIS04210811PDN. [PMID: 34236215 DOI: 10.1094/pdis-04-21-0811-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo-Dioulasso, Burkina Faso
- IRD, Institut de Recherche pour le Développement UMR PHIM, Plant Health Institute of Montpellier, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- Université de Ouagadougou, Laboratoire de Génétique et Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - S Zougrana
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo-Dioulasso, Burkina Faso
| | - M Sawadogo
- Université de Ouagadougou, Laboratoire de Génétique et Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - D Kone
- Université Félix Houphouët-Boigny, UFR Biosciences, Laboratoire de Physiologie Végétale, Abidjan, Côte d'Ivoire
| | - D Silué
- AfricaRice, Plant Pathology, Bouaké, Ivory Coast
| | - B Szurek
- IRD, Institut de Recherche pour le Développement UMR PHIM, Plant Health Institute of Montpellier, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et Recherches Agricoles, Bobo-Dioulasso, Burkina Faso
| | - M Hutin
- IRD, Institut de Recherche pour le Développement UMR PHIM, Plant Health Institute of Montpellier, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
6
|
Te Molder D, Poncheewin W, Schaap PJ, Koehorst JJ. Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains. BMC Genomics 2021; 22:848. [PMID: 34814827 PMCID: PMC8612006 DOI: 10.1186/s12864-021-08093-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. RESULTS Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. CONCLUSION The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.
Collapse
Affiliation(s)
- Dennie Te Molder
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Wasin Poncheewin
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- UNLOCK, Wageningen University, Wageningen, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands.
- UNLOCK, Wageningen University, Wageningen, the Netherlands.
| |
Collapse
|
7
|
Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
Collapse
Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
| |
Collapse
|
8
|
Sakthivel K, Kumar A, Gautam RK, Manigundan K, Laha GS, Velazhahan R, Singh R, Yadav IS. Intra-regional diversity of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae, in the Andaman Islands, India: revelation by pathotyping and multilocus sequence typing. J Appl Microbiol 2020; 130:1259-1272. [PMID: 32767623 DOI: 10.1111/jam.14813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
AIM To investigate the genetic and pathogenic variability of Xanthomonas oryzae pv. oryzae causing bacterial blight in rice on the remote Andaman Islands, India. METHODS AND RESULTS A total of 27 yellow-pigmented bacterial isolates representing rice fields of Andaman Islands incited blight on the susceptible-rice cultivar, C14-8. Phenotypic, pathogenic traits and 16S rRNA gene sequences revealed their identity as X. oryzae pv. oryzae. Virulence profiling indicated the prevalence of seven pathotypes of X. oryzae pv. oryzae on the Islands. Pathotypes-VI and -VII were highly virulent, whereas the pathotype-I was less virulent. Multilocus sequence typing based on nucleotide sequence polymorphism in nine housekeeping genes dnaK; fyuA; gyrB (two loci): rpoD; fusA; gapA; gltA and lepA clustered 27 isolates into 17 sequence types (STs) segregated into two clonal-complexes (CC). While CC-I comprised of isolates from Andaman Island, the CC-II is a mixture of isolates representing mainland India and Andaman Island. The data revealed trans-boundary pathogen introduction and a consequent intra-regional diversification on these islands due to the deployment of different rice cultivars in different regions. CONCLUSIONS Genotyping and pathotyping of sland isolates revealed seven pathotypes distributed in two clonal complexes with strong indications for trans-boundary movement and consequent diversification of the bacterial pathogen. Highly virulent pathotypes of X. oryzae pv. oryzae that could overcome combinations of R-genes, xa13+Xa21 as well as xa5+xa13 were found prevalent in the Andaman Islands SIGNIFICANCE AND IMPACT OF THE STUDY: Genetic and virulence analysis of X. oryzae pv. oryzae in the Andaman Islands revealed introduction and host-mediated regional diversification and local adaptation of X oryzae pv. oryzae. The study calls for the need of multi-gene pyramiding for durable disease resistance and establishing stringent quarantine measures for safeguarding island agricultural practices in the future.
Collapse
Affiliation(s)
- K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - A Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - K Manigundan
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - G S Laha
- Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - R Velazhahan
- Center for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - R Singh
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - I S Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| |
Collapse
|
9
|
Bangratz M, Wonni I, Kini K, Sondo M, Brugidou C, Béna G, Gnacko F, Barro M, Koebnik R, Silué D, Tollenaere C. Design of a new multiplex PCR assay for rice pathogenic bacteria detection and its application to infer disease incidence and detect co-infection in rice fields in Burkina Faso. PLoS One 2020; 15:e0232115. [PMID: 32339192 PMCID: PMC7185701 DOI: 10.1371/journal.pone.0232115] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/07/2020] [Indexed: 11/19/2022] Open
Abstract
Crop diseases are responsible for considerable yield losses worldwide and particularly in sub-Saharan Africa. To implement efficient disease control measures, detection of the pathogens and understanding pathogen spatio-temporal dynamics is crucial and requires the use of molecular detection tools, especially to distinguish different pathogens causing more or less similar symptoms. We report here the design a new molecular diagnostic tool able to simultaneously detect five bacterial taxa causing important diseases on rice in Africa: (1) Pseudomonas fuscovaginae, (2) Xanthomonas oryzae, (3) Burkholderia glumae and Burkholderia gladioli, (4) Sphingomonas and (5) Pantoea species. This new detection tool consists of a multiplex PCR, which is cost effective and easily applicable. Validation of the method is presented through its application on a global collection of bacterial strains. Moreover, sensitivity assessment for the detection of all five bacteria is reported to be at 0.5 ng DNA by μl. As a proof of concept, we applied the new molecular detection method to a set of 256 rice leaves collected from 16 fields in two irrigated areas in western Burkina Faso. Our results show high levels of Sphingomonas spp. (up to 100% of tested samples in one field), with significant variation in the incidence between the two sampled sites. Xanthomonas oryzae incidence levels were mostly congruent with bacterial leaf streak (BLS) and bacterial leaf blight (BLB) symptom observations in the field. Low levels of Pantoea spp. were found while none of the 256 analysed samples was positive for Burkholderia or Pseudomonas fuscovaginae. Finally, many samples (up to 37.5% in one studied field) were positive for more than one bacterium (co-infection). Documenting co-infection levels are important because of their drastic consequences on epidemiology, evolution of pathogen populations and yield losses. The newly designed multiplex PCR for multiple bacterial pathogens of rice is a significant improvement for disease monitoring in the field, thus contributing to efficient disease control and food safety.
Collapse
Affiliation(s)
- Martine Bangratz
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| | - Issa Wonni
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| | - Kossi Kini
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- AfricaRice, Plant Pathology, Bouaké, Ivory Coast
| | - Moussa Sondo
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| | - Christophe Brugidou
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| | - Gilles Béna
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
| | - Fatoumata Gnacko
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| | - Mariam Barro
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| | - Ralf Koebnik
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
| | - Drissa Silué
- AfricaRice, Plant Pathology, Bouaké, Ivory Coast
| | - Charlotte Tollenaere
- IRD, Cirad, Univ Montpellier, IPME, Montpellier, France
- INERA, Laboratoire de Phytopathologie, LMI PathoBios, Bobo-Dioulasso, Burkina Faso
| |
Collapse
|
10
|
Lang JM, Pérez-Quintero AL, Koebnik R, DuCharme E, Sarra S, Doucoure H, Keita I, Ziegle J, Jacobs JM, Oliva R, Koita O, Szurek B, Verdier V, Leach JE. A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. FRONTIERS IN PLANT SCIENCE 2019; 10:507. [PMID: 31114597 PMCID: PMC6503118 DOI: 10.3389/fpls.2019.00507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Xanthomonas oryzae (Xo) are globally important rice pathogens. Virulent lineages from Africa and Asia and less virulent strains from the United States have been well characterized. Xanthomonas campestris pv. leersiae (Xcl), first described in 1957, causes bacterial streak on the perennial grass, Leersia hexandra, and is a close relative of Xo. L. hexandra, a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo. We used long read, single molecule real time (SMRT) genome sequences of five strains of Xcl from Burkina Faso, China, Mali, and Uganda to determine the genetic relatedness of this organism with Xo. Novel transcription activator-like effectors (TALEs) were discovered in all five strains of Xcl. Predicted TALE target sequences were identified in the Leersia perrieri genome and compared to rice susceptibility gene homologs. Pathogenicity screening on L. hexandra and diverse rice cultivars confirmed that Xcl are able to colonize rice and produce weak but not progressive symptoms. Overall, based on average nucleotide identity (ANI), type III (T3) effector repertoires, and disease phenotype, we propose to rename Xcl to X. oryzae pv. leersiae (Xol) and use this parallel system to improve understanding of the evolution of bacterial pathogenicity in rice agroecosystems.
Collapse
Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Alvaro L. Pérez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Elysa DuCharme
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Soungalo Sarra
- Centre Régional de Recherche Agronomique de Niono, Institut d’Economie Rural, Bamako, Mali
| | - Hinda Doucoure
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Ibrahim Keita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Janet Ziegle
- Pacific Biosciences, Menlo Park, CA, United States
| | - Jonathan M. Jacobs
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
- Department of Plant Pathology, Infectious Disease Institute, Ohio State University, Columbus, OH, United States
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| |
Collapse
|
11
|
Draft Genome Sequences of Pathotype Strains for Three Pathovars Belonging to Three Xanthomonas Species. Microbiol Resour Announc 2018; 7:MRA00923-18. [PMID: 30533651 PMCID: PMC6256674 DOI: 10.1128/mra.00923-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/02/2018] [Indexed: 11/20/2022] Open
Abstract
We present here the draft genome sequences of type/pathotype strains for three Xanthomonas species and pathovars with different host specificities, the Hedera helix L. pathogen Xanthomonas hortorum pv. We present here the draft genome sequences of type/pathotype strains for three Xanthomonas species and pathovars with different host specificities, the Hedera helix L. pathogen Xanthomonas hortorum pv. hederae WHRI 7744 (NCPPB 939T), the rice pathogen X. oryzae pv. oryzicola WHRI 5234 (NCPPB 1585), and the cotton pathogen X. citri subsp. malvacearum WHRI 5232 (NCPPB 633).
Collapse
|
12
|
Bossa‐Castro AM, Tekete C, Raghavan C, Delorean EE, Dereeper A, Dagno K, Koita O, Mosquera G, Leung H, Verdier V, Leach JE. Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1559-1568. [PMID: 29406604 PMCID: PMC6097120 DOI: 10.1111/pbi.12895] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/22/2018] [Accepted: 01/26/2018] [Indexed: 05/19/2023]
Abstract
Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub-Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar-specific QTL. The most promising BSR QTL (qXO-2-1, qXO-4-1 and qXO-11-2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes.
Collapse
Affiliation(s)
- Ana M. Bossa‐Castro
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
| | - Cheick Tekete
- IRDCiradIPMEUniv MontpellierMontpellierFrance
- Faculté des Sciences et TechniquesLBMAUniversité des Sciences Techniques et TechnologiquesBamakoMali
| | - Chitra Raghavan
- Division of Plant Breeding, Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
- Present address:
Horticulture and Forestry SciencesQueensland Department of Agriculture and FisheriesCairnsQLDAustralia
| | - Emily E. Delorean
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Plant PathologyKansas State UniversityManhattanKSUSA
| | | | - Karim Dagno
- Plant ProtectionInstitute of Rural EconomySotubaMali
| | - Ousmane Koita
- Faculté des Sciences et TechniquesLBMAUniversité des Sciences Techniques et TechnologiquesBamakoMali
| | | | - Hei Leung
- Division of Plant Breeding, Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
| | | | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsCOUSA
| |
Collapse
|
13
|
Shidore T, Broeckling CD, Kirkwood JS, Long JJ, Miao J, Zhao B, Leach JE, Triplett LR. The effector AvrRxo1 phosphorylates NAD in planta. PLoS Pathog 2017; 13:e1006442. [PMID: 28628666 PMCID: PMC5491322 DOI: 10.1371/journal.ppat.1006442] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/29/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity. Most characterized effectors work through modification of host proteins or transcriptional regulators, although a few are known to modify small molecule targets. The Xanthomonas type III secreted avirulence factor AvrRxo1 is a structural homolog of the zeta toxin family of sugar-nucleotide kinases that suppresses bacterial growth. AvrRxo1 was recently reported to phosphorylate the central metabolite and signaling molecule NAD in vitro, suggesting that the effector might enhance bacterial virulence on plants through manipulation of primary metabolic pathways. In this study, we determine that AvrRxo1 phosphorylates NAD in planta, and that its kinase catalytic sites are necessary for its toxic and resistance-triggering phenotypes. A global metabolomics approach was used to independently identify 3'-NADP as the sole detectable product of AvrRxo1 expression in yeast and bacteria, and NAD kinase activity was confirmed in vitro. 3'-NADP accumulated upon transient expression of AvrRxo1 in Nicotiana benthamiana and in rice leaves infected with avrRxo1-expressing strains of X. oryzae. Mutation of the catalytic aspartic acid residue D193 abolished AvrRxo1 kinase activity and several phenotypes of AvrRxo1, including toxicity in yeast, bacteria, and plants, suppression of the flg22-triggered ROS burst, and ability to trigger an R gene-mediated hypersensitive response. A mutation in the Walker A ATP-binding motif abolished the toxicity of AvrRxo1, but did not abolish the 3'-NADP production, virulence enhancement, ROS suppression, or HR-triggering phenotypes of AvrRxo1. These results demonstrate that a type III effector targets the central metabolite and redox carrier NAD in planta, and that this catalytic activity is required for toxicity and suppression of the ROS burst.
Collapse
Affiliation(s)
- Teja Shidore
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| | - Corey D. Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States of America
| | - Jay S. Kirkwood
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States of America
| | - John J. Long
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Jiamin Miao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Bingyu Zhao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| |
Collapse
|
14
|
Tollenaere C, Lacombe S, Wonni I, Barro M, Ndougonna C, Gnacko F, Sérémé D, Jacobs JM, Hebrard E, Cunnac S, Brugidou C. Virus-Bacteria Rice Co-Infection in Africa: Field Estimation, Reciprocal Effects, Molecular Mechanisms, and Evolutionary Implications. FRONTIERS IN PLANT SCIENCE 2017; 8:645. [PMID: 28507553 PMCID: PMC5410622 DOI: 10.3389/fpls.2017.00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/10/2017] [Indexed: 05/04/2023]
Abstract
Simultaneous infection of a single plant by various pathogen species is increasingly recognized as an important modulator of host resistance and a driver of pathogen evolution. Because plants in agro-ecosystems are the target of a multitude of pathogenic microbes, co-infection could be frequent, and consequently important to consider. This is particularly true for rapidly intensifying crops, such as rice in Africa. This study investigated potential interactions between pathogens causing two of the major rice diseases in Africa: the Rice yellow mottle virus (RYMV) and the bacterium Xanthomonas oryzae pathovar oryzicola (Xoc) in order to: 1/ document virus-bacteria co-infection in rice in the field, 2/ explore experimentally their consequences in terms of symptom development and pathogen multiplication, 3/ test the hypothesis of underlying molecular mechanisms of interactions and 4/ explore potential evolutionary consequences. Field surveys in Burkina Faso revealed that a significant proportion of rice fields were simultaneously affected by the two diseases. Co-infection leads to an increase in bacterial specific symptoms, while a decrease in viral load is observed compared to the mono-infected mock. The lack of effect found when using a bacterial mutant for an effector specifically inducing expression of a small RNA regulatory protein, HEN1, as well as a viral genotype-specific effect, both suggest a role for gene silencing mechanisms mediating the within-plant interaction between RYMV and Xoc. Potential implications for pathogen evolution could not be inferred because genotype-specific effects were found only for pathogens originating from different countries, and consequently not meeting in the agrosystem. We argue that pathogen-pathogen-host interactions certainly deserve more attention, both from a theoretical and applied point of view.
Collapse
Affiliation(s)
- Charlotte Tollenaere
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Bactériologie, Institut de l'Environnement et de Recherches Agricoles (INERA)Bobo-Dioulasso, Burkina Faso
| | - Severine Lacombe
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| | - Issa Wonni
- Laboratoire Mixte International Patho-Bios, Laboratoire de Bactériologie, Institut de l'Environnement et de Recherches Agricoles (INERA)Bobo-Dioulasso, Burkina Faso
| | - Mariam Barro
- Laboratoire Mixte International Patho-Bios, Laboratoire de Bactériologie, Institut de l'Environnement et de Recherches Agricoles (INERA)Bobo-Dioulasso, Burkina Faso
| | - Cyrielle Ndougonna
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Fatoumata Gnacko
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| | - Drissa Sérémé
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| | - Jonathan M. Jacobs
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Eugénie Hebrard
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Sebastien Cunnac
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
| | - Christophe Brugidou
- Interactions Plantes-Microorganismes-Environnement, Institut de Recherche pour le Développement (IRD), Cirad, Univ MontpellierMontpellier, France
- Laboratoire Mixte International Patho-Bios, Laboratoire de Virologie et de Biotechnologies Végétales, Institut de l'Environnement et de Recherches Agricoles (INERA)Kamboinsé, Burkina Faso
| |
Collapse
|
15
|
Nagel R, Turrini PCG, Nett RS, Leach JE, Verdier V, Van Sluys MA, Peters RJ. An operon for production of bioactive gibberellin A 4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola. THE NEW PHYTOLOGIST 2017; 214:1260-1266. [PMID: 28134995 PMCID: PMC5388578 DOI: 10.1111/nph.14441] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/10/2016] [Indexed: 05/19/2023]
Abstract
Phytopathogens have developed elaborate mechanisms to attenuate the defense response of their host plants, including convergent evolution of complex pathways for production of the GA phytohormones, which were actually first isolated from the rice fungal pathogen Gibberella fujikuroi. The rice bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) has been demonstrated to contain a biosynthetic operon with cyclases capable of producing the universal GA precursor ent-kaurene. Genetic (knock-out) studies indicate that the derived diterpenoid serves as a virulence factor for this rice leaf streak pathogen, serving to reduce the jasmonic acid-mediated defense response. Here the functions of the remaining genes in the Xoc operon are elucidated and the distribution of the operon in X. oryzae is investigated in over 100 isolates. The Xoc operon leads to production of the bioactive GA4 , an additional step beyond production of the penultimate precursor GA9 mediated by the homologous operons recently characterized from rhizobia. Moreover, this GA biosynthetic operon was found to be widespread in Xoc (> 90%), but absent in the other major X. oryzae pathovar. These results indicate selective pressure for production of GA4 in the distinct lifestyle of Xoc, and the importance of GA to both fungal and bacterial pathogens of rice.
Collapse
Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Paula C. G. Turrini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Ryan S. Nett
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Valérie Verdier
- IRD – Cirad – Univ. Montpellier, UMR Interactions Plantes Microorganismes Environnement (IPME), 34399 Montpellier, France
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
16
|
Djedatin G, Ndjiondjop MN, Sanni A, Lorieux M, Verdier V, Ghesquiere A. Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2016; 9:18. [PMID: 27107993 PMCID: PMC4842194 DOI: 10.1186/s12284-016-0090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 03/20/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains. RESULTS The reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map. CONCLUSION We characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease.
Collapse
Affiliation(s)
| | | | | | - Mathias Lorieux
- UMR Diversité, Adaptation et Développement des plantes (DIADE), Institut de Recherche pour le Développement, 911 Avenue Agropolis BP 64501, 34394, Montpellier Cedex 5, France
| | - Valérie Verdier
- IPME Interactions Plantes Microorganismes, Environnement, IRD - Cirad - University Montpellier, 34394, Montpellier, France
| | - Alain Ghesquiere
- UMR Diversité, Adaptation et Développement des plantes (DIADE), Institut de Recherche pour le Développement, 911 Avenue Agropolis BP 64501, 34394, Montpellier Cedex 5, France
| |
Collapse
|
17
|
Triplett LR, Shidore T, Long J, Miao J, Wu S, Han Q, Zhou C, Ishihara H, Li J, Zhao B, Leach JE. AvrRxo1 Is a Bifunctional Type III Secreted Effector and Toxin-Antitoxin System Component with Homologs in Diverse Environmental Contexts. PLoS One 2016; 11:e0158856. [PMID: 27391081 PMCID: PMC4938570 DOI: 10.1371/journal.pone.0158856] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/22/2016] [Indexed: 11/18/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous bacterial systems that may function in genome maintenance and metabolic stress management, but are also thought to play a role in virulence by helping pathogens survive stress. We previously demonstrated that the Xanthomonas oryzae pv. oryzicola protein AvrRxo1 is a type III-secreted virulence factor that has structural similarities to the zeta family of TA toxins, and is toxic to plants and bacteria in the absence of its predicted chaperone Arc1. In this work, we confirm that AvrRxo1 and its binding partner Arc1 function as a TA system when expressed in Escherichia coli. Sequences of avrRxo1 homologs were culled from published and newly generated phytopathogen genomes, revealing that avrRxo1:arc1 modules are rare or frequently inactivated in some species and highly conserved in others. Cloning and functional analysis of avrRxo1 from Acidovorax avenae, A. citrulli, Burkholderia andropogonis, Xanthomonas translucens, and Xanthomonas euvesicatoria showed that some AvrRxo1 homologs share the bacteriostatic and Rxo1-mediated cell death triggering activities of AvrRxo1 from X. oryzae. Additional distant putative homologs of avrRxo1 and arc1 were identified in genomic or metagenomic sequence of environmental bacteria with no known pathogenic role. One of these distant homologs was cloned from the filamentous soil bacterium Cystobacter fuscus. avrRxo1 from C. fuscus caused watersoaking and triggered Rxo1-dependent cell collapse in Nicotiana benthamiana, but no growth suppression in E. coli was observed. This work confirms that a type III effector can function as a TA system toxin, and illustrates the potential of microbiome data to reveal new environmental origins or reservoirs of pathogen virulence factors.
Collapse
Affiliation(s)
- Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| | - Teja Shidore
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| | - John Long
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO, United States of America
| | - Jiamin Miao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Shuchi Wu
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Qian Han
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
- Laboratory of Tropical Veterinary Medicine and Vector Biology, College of Agriculture, Hainan University, Haikou, 570228, Hainan, China
| | - Changhe Zhou
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Hiromichi Ishihara
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO, United States of America
| | - Jianyong Li
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Bingyu Zhao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO, United States of America
| |
Collapse
|
18
|
The Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01450-15. [PMID: 26659686 PMCID: PMC4675951 DOI: 10.1128/genomea.01450-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report the draft genome sequence of Xanthomonas sp. strain Mitacek01, isolated from an indoor environment vending machine surface with frequent human use in Stillwater, Oklahoma, USA, as part of the Student-Initiated Microbial Discovery project. The genome has a total size of 3,617,426 bp and a contig N50 of 1,906,967 bp.
Collapse
|
19
|
Niu XN, Wei ZQ, Zou HF, Xie GG, Wu F, Li KJ, Jiang W, Tang JL, He YQ. Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola. BMC Microbiol 2015; 15:233. [PMID: 26498126 PMCID: PMC4619425 DOI: 10.1186/s12866-015-0562-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. METHODS The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays. RESULTS The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5α. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99A to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids. CONCLUSIONS pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.
Collapse
Affiliation(s)
- Xiang-Na Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Zhi-Qiong Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Hai-Fan Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Gui-Gang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Feng Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Kang-Jia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| |
Collapse
|
20
|
Booher NJ, Carpenter SCD, Sebra RP, Wang L, Salzberg SL, Leach JE, Bogdanove AJ. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships. Microb Genom 2015; 1. [PMID: 27148456 PMCID: PMC4853030 DOI: 10.1099/mgen.0.000032] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33–35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.
Collapse
Affiliation(s)
- Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robert P Sebra
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jan E Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
21
|
Booher NJ, Carpenter SCD, Sebra RP, Wang L, Salzberg SL, Leach JE, Bogdanove AJ. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships. Microb Genom 2015. [PMID: 27148456 DOI: 10.1099/mgen.000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33-35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution.
Collapse
Affiliation(s)
- Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Robert P Sebra
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jan E Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
22
|
Wilkins KE, Booher NJ, Wang L, Bogdanove AJ. TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. FRONTIERS IN PLANT SCIENCE 2015; 6:536. [PMID: 26257749 PMCID: PMC4508525 DOI: 10.3389/fpls.2015.00536] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/30/2015] [Indexed: 05/19/2023]
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription activator-like (TAL) effectors to upregulate host susceptibility genes. By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains. TAL effector content is surprisingly conserved overall, yet distinguishes Asian from African isolates. Five TAL effectors are conserved across all strains. In a prior laboratory assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the strict conservation indicates all five may be important, in different rice genotypes or in the field. Concatenated and aligned, TAL effector content across strains largely reflects relationships based on housekeeping genes, suggesting predominantly vertical transmission. Rice transcriptional responses did not reflect these relationships, and on average, only 28% of genes upregulated and 22% of genes downregulated by a strain are up- and down- regulated (respectively) by all strains. However, when only known TAL effector targets were considered, the relationships resembled those of the TAL effectors. Toward identifying new targets, we used the TAL effector-DNA recognition code to predict effector binding elements in promoters of genes upregulated by each strain, but found that for every strain, all upregulated genes had at least one. Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes. Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.
Collapse
Affiliation(s)
- Katherine E. Wilkins
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
- Graduate Field of Computational Biology, Cornell UniversityIthaca, NY, USA
| | - Nicholas J. Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
- Graduate Field of Computational Biology, Cornell UniversityIthaca, NY, USA
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell UniversityIthaca, NY, USA
| |
Collapse
|
23
|
Characterization of a novel clade of Xanthomonas isolated from rice leaves in Mali and proposal of Xanthomonas maliensis sp. nov. Antonie Van Leeuwenhoek 2015; 107:869-81. [PMID: 25588569 DOI: 10.1007/s10482-015-0379-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
Four bacterial strains, designated M89, M92, M97(T), and M106, were isolated in a previous study from surface-sterilized leaves of rice (Oryza sativa) or murainagrass (Ischaemum rugosum) at three sites in Mali, Africa. Here they were examined by a polyphasic taxonomic approach and analysis of a whole-genome sequence. Phylogenetic analyses based on 16S rRNA sequence and multilocus sequence analysis of seven genes showed that these four strains formed a distinct lineage representing a novel species within the genus Xanthomonas. This was supported by whole-genome average nucleotide identity values calculated from comparisons of strain M97(T) with established Xanthomonas species. The strains can be differentiated from the known Xanthomonas species on the basis of their fatty acid and carbohydrate utilization profiles. Population growth studies on rice confirmed that these bacteria multiply in rice leaves without causing symptoms. Identification of this novel species can be accomplished by using diagnostic primer sets or by gyrB gene sequence analysis. We propose to classify these rice- and grass-associated bacteria as Xanthomonas maliensis sp. nov. with strain M97(T) = CFBP7942(T) = LMG27592(T) as the type strain.
Collapse
|
24
|
Poulin L, Grygiel P, Magne M, Gagnevin L, Rodriguez-R LM, Forero Serna N, Zhao S, El Rafii M, Dao S, Tekete C, Wonni I, Koita O, Pruvost O, Verdier V, Vernière C, Koebnik R. New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Appl Environ Microbiol 2015; 81:688-98. [PMID: 25398857 PMCID: PMC4277570 DOI: 10.1128/aem.02768-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/04/2014] [Indexed: 12/12/2022] Open
Abstract
Multilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales.
Collapse
Affiliation(s)
- L Poulin
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - P Grygiel
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - M Magne
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - L Gagnevin
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - L M Rodriguez-R
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - N Forero Serna
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - S Zhao
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - M El Rafii
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - S Dao
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - C Tekete
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - I Wonni
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France Institut de l'Environnement et de Recherches Agricoles, Bobo Dioulasso, Burkina Faso
| | - O Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques (FAST), Université des Sciences Techniques et Technologie, Bamako, Mali
| | - O Pruvost
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - V Verdier
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - C Vernière
- UMR PVBMT, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Saint-Pierre, La Réunion, France
| | - R Koebnik
- UMR 186 Résistance des Plantes aux Bio-Agresseurs, Institut de Recherche pour le Développement, Montpellier, France
| |
Collapse
|
25
|
Lang JM, Langlois P, Nguyen MHR, Triplett LR, Purdie L, Holton TA, Djikeng A, Vera Cruz CM, Verdier V, Leach JE. Sensitive detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by loop-mediated isothermal amplification. Appl Environ Microbiol 2014; 80:4519-30. [PMID: 24837384 PMCID: PMC4148787 DOI: 10.1128/aem.00274-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 05/06/2014] [Indexed: 11/20/2022] Open
Abstract
Molecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 10(4) to 10(5) CFU ml(-1), while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens.
Collapse
Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Paul Langlois
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | | | - Lindsay R. Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| | - Laura Purdie
- Biosciences eastern and central Africa, Nairobi, Kenya
| | | | | | | | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs, IRD-CIRAD-UM2, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|