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Shamjana U, Vasu DA, Hembrom PS, Nayak K, Grace T. The role of insect gut microbiota in host fitness, detoxification and nutrient supplementation. Antonie Van Leeuwenhoek 2024; 117:71. [PMID: 38668783 DOI: 10.1007/s10482-024-01970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 04/15/2024] [Indexed: 05/01/2024]
Abstract
Insects are incredibly diverse, ubiquitous and have successfully flourished out of the dynamic and often unpredictable nature of evolutionary processes. The resident microbiome has accompanied the physical and biological adaptations that enable their continued survival and proliferation in a wide array of environments. The host insect and microbiome's bidirectional relationship exhibits their capability to influence each other's physiology, behavior and characteristics. Insects are reported to rely directly on the microbial community to break down complex food, adapt to nutrient-deficit environments, protect themselves from natural adversaries and control the expression of social behavior. High-throughput metagenomic approaches have enhanced the potential for determining the abundance, composition, diversity and functional activities of microbial fauna associated with insect hosts, enabling in-depth investigation into insect-microbe interactions. We undertook a review of some of the major advances in the field of metagenomics, focusing on insect-microbe interaction, diversity and composition of resident microbiota, the functional capability of endosymbionts and discussions on different symbiotic relationships. The review aims to be a valuable resource on insect gut symbiotic microbiota by providing a comprehensive understanding of how insect gut symbionts systematically perform a range of functions, viz., insecticide degradation, nutritional support and immune fitness. A thorough understanding of manipulating specific gut symbionts may aid in developing advanced insect-associated research to attain health and design strategies for pest management.
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Affiliation(s)
- U Shamjana
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Deepa Azhchath Vasu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Preety Sweta Hembrom
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Karunakar Nayak
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Tony Grace
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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Nicoletti R, Russo E, Becchimanzi A. Cladosporium-Insect Relationships. J Fungi (Basel) 2024; 10:78. [PMID: 38276024 PMCID: PMC10820778 DOI: 10.3390/jof10010078] [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: 12/14/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
The range of interactions between Cladosporium, a ubiquitous fungal genus, and insects, a class including about 60% of the animal species, is extremely diverse. The broad case history of antagonism and mutualism connecting Cladosporium and insects is reviewed in this paper based on the examination of the available literature. Certain strains establish direct interactions with pests or beneficial insects or indirectly influence them through their endophytic development in plants. Entomopathogenicity is often connected to the production of toxic secondary metabolites, although there is a case where these compounds have been reported to favor pollinator attraction, suggesting an important role in angiosperm reproduction. Other relationships include mycophagy, which, on the other hand, may reflect an ecological advantage for these extremely adaptable fungi using insects as carriers for spreading in the environment. Several Cladosporium species colonize insect structures, such as galleries of ambrosia beetles, leaf rolls of attelabid weevils and galls formed by cecidomyid midges, playing a still uncertain symbiotic role. Finally, the occurrence of Cladosporium in the gut of several insect species has intriguing implications for pest management, also considering that some strains have proven to be able to degrade insecticides. These interactions especially deserve further investigation to understand the impact of these fungi on pest control measures and strategies to preserve beneficial insects.
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Affiliation(s)
- Rosario Nicoletti
- Council for Agricultural Research and Economics, Research Center for Olive, Fruit and Citrus Crops, 81100 Caserta, Italy
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (E.R.); (A.B.)
| | - Elia Russo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (E.R.); (A.B.)
| | - Andrea Becchimanzi
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy; (E.R.); (A.B.)
- BAT Center—Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Naples Federico II, 80055 Portici, Italy
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Hettiarachchi A, Cnockaert M, Joossens M, Gekière A, Meeus I, Vereecken NJ, Michez D, Smagghe G, Vandamme P. The wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta microbiota are host specific and dominated by endosymbionts and environmental microorganisms. MICROBIAL ECOLOGY 2023; 86:3013-3026. [PMID: 37794084 DOI: 10.1007/s00248-023-02304-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
We characterized the microbial communities of the crop, midgut, hindgut, and ovaries of the wild solitary bees Andrena vaga, Anthophora plumipes, Colletes cunicularius, and Osmia cornuta through 16S rRNA gene and ITS2 amplicon sequencing and a large-scale isolation campaign. The bacterial communities of these bees were dominated by endosymbionts of the genera Wolbachia and Spiroplasma. Bacterial and yeast genera representing the remaining predominant taxa were linked to an environmental origin. While only a single sampling site was examined for Andrena vaga, Anthophora plumipes, and Colletes cunicularius, and two sampling sites for Osmia cornuta, the microbiota appeared to be host specific: bacterial, but not fungal, communities generally differed between the analyzed bee species, gut compartments and ovaries. This may suggest a selective process determined by floral and host traits. Many of the gut symbionts identified in the present study are characterized by metabolic versatility. Whether they exert similar functionalities within the bee gut and thus functional redundancy remains to be elucidated.
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Affiliation(s)
- Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Antoine Gekière
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Plants of Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Nicolas J Vereecken
- Agroecology Lab, Université libre de Bruxelles (ULB), Boulevard du Triomphe CP 264/02, 1050, Brussels, Belgium
| | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Place du parc 20, 7000, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants of Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Gent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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Picciotti U, Araujo Dalbon V, Ciancio A, Colagiero M, Cozzi G, De Bellis L, Finetti-Sialer MM, Greco D, Ippolito A, Lahbib N, Logrieco AF, López-Llorca LV, Lopez-Moya F, Luvisi A, Mincuzzi A, Molina-Acevedo JP, Pazzani C, Scortichini M, Scrascia M, Valenzano D, Garganese F, Porcelli F. "Ectomosphere": Insects and Microorganism Interactions. Microorganisms 2023; 11:microorganisms11020440. [PMID: 36838405 PMCID: PMC9967823 DOI: 10.3390/microorganisms11020440] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
This study focuses on interacting with insects and their ectosymbiont (lato sensu) microorganisms for environmentally safe plant production and protection. Some cases help compare ectosymbiont microorganisms that are insect-borne, -driven, or -spread relevant to endosymbionts' behaviour. Ectosymbiotic bacteria can interact with insects by allowing them to improve the value of their pabula. In addition, some bacteria are essential for creating ecological niches that can host the development of pests. Insect-borne plant pathogens include bacteria, viruses, and fungi. These pathogens interact with their vectors to enhance reciprocal fitness. Knowing vector-phoront interaction could considerably increase chances for outbreak management, notably when sustained by quarantine vector ectosymbiont pathogens, such as the actual Xylella fastidiosa Mediterranean invasion episode. Insect pathogenic viruses have a close evolutionary relationship with their hosts, also being highly specific and obligate parasites. Sixteen virus families have been reported to infect insects and may be involved in the biological control of specific pests, including some economic weevils. Insects and fungi are among the most widespread organisms in nature and interact with each other, establishing symbiotic relationships ranging from mutualism to antagonism. The associations can influence the extent to which interacting organisms can exert their effects on plants and the proper management practices. Sustainable pest management also relies on entomopathogenic fungi; research on these species starts from their isolation from insect carcasses, followed by identification using conventional light or electron microscopy techniques. Thanks to the development of omics sciences, it is possible to identify entomopathogenic fungi with evolutionary histories that are less-shared with the target insect and can be proposed as pest antagonists. Many interesting omics can help detect the presence of entomopathogens in different natural matrices, such as soil or plants. The same techniques will help localize ectosymbionts, localization of recesses, or specialized morphological adaptation, greatly supporting the robust interpretation of the symbiont role. The manipulation and modulation of ectosymbionts could be a more promising way to counteract pests and borne pathogens, mitigating the impact of formulates and reducing food insecurity due to the lesser impact of direct damage and diseases. The promise has a preventive intent for more manageable and broader implications for pests, comparing what we can obtain using simpler, less-specific techniques and a less comprehensive approach to Integrated Pest Management (IPM).
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Affiliation(s)
- Ugo Picciotti
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
- Department of Marine Science and Applied Biology, University of Alicante, 03690 Alicante, Spain
| | | | - Aurelio Ciancio
- Institute for Sustainable Plant Protection, National Research Council (CNR), Via G. Amendola 122/D, 70126 Bari, Italy
| | - Mariantonietta Colagiero
- Institute for Sustainable Plant Protection, National Research Council (CNR), Via G. Amendola 122/D, 70126 Bari, Italy
| | - Giuseppe Cozzi
- Institute of Food Production Sciences, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | | | - Davide Greco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Antonio Ippolito
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Nada Lahbib
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
- Faculty of Sciences of Tunis, University of Tunis El-Manar, Tunis 1002, Tunisia
| | - Antonio Francesco Logrieco
- Institute of Food Production Sciences, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | | | - Federico Lopez-Moya
- Department of Marine Science and Applied Biology, University of Alicante, 03690 Alicante, Spain
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Annamaria Mincuzzi
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Juan Pablo Molina-Acevedo
- Colombian Corporation for Agricultural Research Agrosavia C. I. Turipana-AGROSAVIA, Km. 13, Vía Montería-Cereté 230558, Colombia
| | - Carlo Pazzani
- Dipartimento di Bioscienze, Biotecnologie e Ambiente (DBBA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Marco Scortichini
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), 00134 Roma, Italy
| | - Maria Scrascia
- Dipartimento di Bioscienze, Biotecnologie e Ambiente (DBBA), University of Bari Aldo Moro, 70126 Bari, Italy
| | - Domenico Valenzano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
| | - Francesca Garganese
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
- Correspondence:
| | - Francesco Porcelli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, 70126 Bari, Italy
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Hladnik M, Unković N, Janakiev T, Grbić ML, Arbeiter AB, Stanković S, Janaćković P, Gavrilović M, Rančić D, Bandelj D, Dimkić I. An Insight into an Olive Scab on the "Istrska Belica" Variety: Host-Pathogen Interactions and Phyllosphere Mycobiome. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02131-4. [PMID: 36307735 DOI: 10.1007/s00248-022-02131-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
The olive tree is one of the most important agricultural plants, affected by several pests and diseases that cause a severe decline in health status leading to crop losses. Olive leaf spot disease caused by the fungus Venturia oleaginea can result in complete tree defoliation and consequently lower yield. The aim of the study was to obtain new knowledge related to plant-pathogen interaction, reveal mechanisms of plant defense against the pathogen, and characterize fungal phyllosphere communities on infected and symptomless leaves that could contribute to the development of new plant breeding strategies and identification of novel biocontrol agents. The highly susceptible olive variety "Istrska Belica"' was selected for a detailed evaluation. Microscopy analyses led to the observation of raphides in the mesophyll and parenchyma cells of infected leaves and gave new insight into the complex V. oleaginea pathogenesis. Culturable and total phyllosphere mycobiota, obtained via metabarcoding approach, highlighted Didymella, Aureobasidium, Cladosporium, and Alternaria species as overlapping between infected and symptomless leaves. Only Venturia and Erythrobasidium in infected and Cladosporium in symptomless samples with higher abundance showed statistically significant differences. Based on the ecological role of identified taxa, it can be suggested that Cladosporium species might have potential antagonistic effects on V. oleaginea.
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Affiliation(s)
- Matjaž Hladnik
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, Sl-6000, Koper, Slovenia
| | - Nikola Unković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11158, Belgrade, Serbia
| | - Tamara Janakiev
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11158, Belgrade, Serbia
| | | | - Alenka Baruca Arbeiter
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, Sl-6000, Koper, Slovenia
| | - Slaviša Stanković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11158, Belgrade, Serbia
| | - Peđa Janaćković
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11158, Belgrade, Serbia
| | - Milan Gavrilović
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11158, Belgrade, Serbia
| | - Dragana Rančić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade, Zemun, Serbia
| | - Dunja Bandelj
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, Sl-6000, Koper, Slovenia
| | - Ivica Dimkić
- Faculty of Biology, University of Belgrade, Studentski Trg 16, 11158, Belgrade, Serbia.
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Hobi S, Cafarchia C, Romano V, Barrs VR. Malassezia: Zoonotic Implications, Parallels and Differences in Colonization and Disease in Humans and Animals. J Fungi (Basel) 2022; 8:jof8070708. [PMID: 35887463 PMCID: PMC9324274 DOI: 10.3390/jof8070708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022] Open
Abstract
Malassezia spp. are commensals of the skin, oral/sinonasal cavity, lower respiratory and gastrointestinal tract. Eighteen species have been recovered from humans, other mammals and birds. They can also be isolated from diverse environments, suggesting an evolutionary trajectory of adaption from an ecological niche in plants and soil to the mucocutaneous ecosystem of warm-blooded vertebrates. In humans, dogs and cats, Malassezia-associated dermatological conditions share some commonalities. Otomycosis is common in companion animals but is rare in humans. Systemic infections, which are increasingly reported in humans, have yet to be recognized in animals. Malassezia species have also been identified as pathogenetic contributors to some chronic human diseases. While Malassezia species are host-adapted, some species are zoophilic and can cause fungemia, with outbreaks in neonatal intensive care wards associated with temporary colonization of healthcare worker’s hands from contact with their pets. Although standardization is lacking, susceptibility testing is usually performed using a modified broth microdilution method. Antifungal susceptibility can vary depending on Malassezia species, body location, infection type, disease duration, presence of co-morbidities and immunosuppression. Antifungal resistance mechanisms include biofilm formation, mutations or overexpression of ERG11, overexpression of efflux pumps and gene rearrangements or overexpression in chromosome 4.
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Affiliation(s)
- Stefan Hobi
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University, Tat Chee Avenue, Kowloon, Hong Kong, China
- Correspondence: (S.H.); (V.R.B.)
| | - Claudia Cafarchia
- Department of Veterinary Medicine, University of Bari, Str. prov. per Casamassima Km 3, Valenzano, (Bari), 70010, Italy; (C.C.); (V.R.)
| | - Valentina Romano
- Department of Veterinary Medicine, University of Bari, Str. prov. per Casamassima Km 3, Valenzano, (Bari), 70010, Italy; (C.C.); (V.R.)
| | - Vanessa R. Barrs
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University, Tat Chee Avenue, Kowloon, Hong Kong, China
- Centre for Animal Health and Welfare, City University of Hong Kong, Kowloon Tong, Hong Kong, China
- Correspondence: (S.H.); (V.R.B.)
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Aluja M, Zamora-Briseño JA, Pérez-Brocal V, Altúzar-Molina A, Guillén L, Desgarennes D, Vázquez-Rosas-Landa M, Ibarra-Laclette E, Alonso-Sánchez AG, Moya A. Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota. Front Microbiol 2021; 12:685937. [PMID: 34413837 PMCID: PMC8367737 DOI: 10.3389/fmicb.2021.685937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/21/2021] [Indexed: 12/17/2022] Open
Abstract
We studied the microbiota of a highly polyphagous insect, Anastrepha ludens (Diptera: Tephritidae), developing in six of its hosts, including two ancestral (Casimiroa edulis and C. greggii), three exotic (Mangifera indica cv. Ataulfo, Prunus persica cv. Criollo, and Citrus x aurantium) and one occasional host (Capsicum pubescens cv. Manzano), that is only used when extreme drought conditions limit fruiting by the common hosts. One of the exotic hosts (“criollo” peach) is rife with polyphenols and the occasional host with capsaicinoids exerting high fitness costs on the larvae. We pursued the following questions: (1) How is the microbial composition of the larval food related to the composition of the larval and adult microbiota, and what does this tell us about transience and stability of this species’ gut microbiota? (2) How does metamorphosis affect the adult microbiota? We surveyed the microbiota of the pulp of each host fruit, as well as the gut microbiota of larvae and adult flies and found that the gut of A. ludens larvae lacks a stable microbiota, since it was invariably associated with the composition of the pulp microbiota of the host plant species studied and was also different from the microbiota of adult flies indicating that metamorphosis filters out much of the microbiota present in larvae. The microbiota of adult males and females was similar between them, independent of host plant and was dominated by bacteria within the Enterobacteriaceae. We found that in the case of the “toxic” occasional host C. pubescens the microbiota is enriched in potentially deleterious genera that were much less abundant in the other hosts. In contrast, the pulp of the ancestral host C. edulis is enriched in several bacterial groups that can be beneficial for larval development. We also report for the first time the presence of bacteria within the Arcobacteraceae family in the gut microbiota of A. ludens stemming from C. edulis. Based on our findings, we conclude that changes in the food-associated microbiota dictate major changes in the larval microbiota, suggesting that most larval gut microbiota is originated from the food.
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Affiliation(s)
- Martín Aluja
- Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Vicente Pérez-Brocal
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Alma Altúzar-Molina
- Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Larissa Guillén
- Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Damaris Desgarennes
- Red de Biodiversidad y Sistemática, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Mirna Vázquez-Rosas-Landa
- Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Alexandro G Alonso-Sánchez
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, AC-INECOL, Clúster Científico y Tecnológico BioMimic®, Xalapa, Mexico
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain.,Instituto de Biología Integrativa de Sistemas (I2Sysbio), Universidad de Valencia-CSIC, Valencia, Spain
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Choudhary P, Singh BN, Chakdar H, Saxena AK. DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance. World J Microbiol Biotechnol 2021; 37:54. [PMID: 33604719 DOI: 10.1007/s11274-021-03019-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.
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Affiliation(s)
- Prassan Choudhary
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Bansh Narayan Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
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9
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Insects' potential: Understanding the functional role of their gut microbiome. J Pharm Biomed Anal 2020; 194:113787. [PMID: 33272789 DOI: 10.1016/j.jpba.2020.113787] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.
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Masoudi A, Wang M, Zhang X, Wang C, Qiu Z, Wang W, Wang H, Liu J. Meta-Analysis and Evaluation by Insect-Mediated Baiting Reveal Different Patterns of Hypocrealean Entomopathogenic Fungi in the Soils From Two Regions of China. Front Microbiol 2020; 11:1133. [PMID: 32595616 PMCID: PMC7303310 DOI: 10.3389/fmicb.2020.01133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/05/2020] [Indexed: 01/16/2023] Open
Abstract
A survey was carried out on forest soils and grassland soils from Hebei and Sichuan provinces using Tenebrio molitor larvae as a bait, and high-throughput DNA sequencing (HTS) of the fungal internal transcribed spacer-2 ribosomal DNA was used to monitor the natural distribution of three leading hypocrealean families of insect fungal pathogens (Clavicipitaceae, Cordycipitaceae, and Ophiocordycipitaceae). The occurrence of insect fungal pathogens in soil samples from 98 different sites was compared. The use of insect bait indicated that entomopathogenic fungi of the genus Metarhizium were predominant, followed by Beauveria and Isaria. Molecular characterization using the Mz_FG543 intergenic region revealed that the Metarhizium species pool was phylogenetically composed of three closely related species as follows; Metarhizium pingshaense (n = 74), Metarhizium robertsii (n = 51), and Metarhizium brunneum (n = 26), as well as one isolate which clustered with Metarhizium flavoviride. Nine potentially new phylogenetic species were delimited within the M. flavoviride species complex by sequencing of the 5′ elongation factor-1 alpha region locus. The Beauveria (n = 64) and Isaria (n = 5) isolates were characterized via sequence analyses of the Bloc region. An intergenic spacer phylogeny of the Beauveria isolate assemblage revealed the phylogenetic species within the Beauveria bassiana clade. Interestingly, the individuals of M. pingshaense (n = 18) and M. brunneum (n = 12) exhibited the presence of both mating types in Sichuan Province. Similarly, for the Beauveria isolates, reproductive mode assays demonstrated that all four B. bassiana subclades possessed bipolar outcrossing mating systems. Of these, 19 isolates contained two mating types, and the rest were fixed for single mating types, revealing opportunities for intra-lineage heterothallic mating. The HTS results showed a significantly higher occurrence of the Clavicipitaceae family and the Metarhizium genus in the soil samples. The Venn diagram showed Metarhizium anisopliae (senso lato), Isaria farinose, and B. bassiana as frequently abundant fungal pathogen operational taxonomic units (core) across sampling sites, while the baiting method showed that the genus of Isaria was isolated locally. The Mantel test verified that community dissimilarity increased significantly with geographical distance, suggesting that geographical coordinates are possible factors that influence the insect fungal pathogen community composition in the studied sites. This study is the first to highlight the usefulness of utilizing soil baiting and deep sequencing to investigate the population dynamics of entomopathogens in soil.
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Affiliation(s)
- Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xiaoli Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhaoxi Qiu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Wenying Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hui Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Olive fruit volatiles route intraspecific interactions and chemotaxis in Bactrocera oleae (Rossi) (Diptera: Tephritidae) females. Sci Rep 2020; 10:1666. [PMID: 32015351 PMCID: PMC6997409 DOI: 10.1038/s41598-020-58379-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/14/2020] [Indexed: 12/05/2022] Open
Abstract
Plant nutritional quality and chemical characteristics may affect the fitness of phytophagous insects. Here, the olfactory preferences of Bactrocera oleae (Rossi) females toward olives with different maturation and infestation status were evaluated in three cultivars: Ottobratica, Roggianella and Sinopolese. Volatile profiles from olives were identified by SPME/GC-MS. Choice tests were performed to determine the responses of B. oleae adult females toward fruits and pure chemicals linked to infestation degree. Cultivar was the main source of variability explaining the differences recorded in volatile emissions. Moreover, three VOCs [β-myrcene, limonene and (E)-β-ocimene] were associated to infestation status across all olive varieties. In choice-tests, B. oleae females always preferred the olfactory cues from low-infested over high-infested fruits. Therefore, choice-tests using synthetic VOCs, emitted in greater amount by high-infested fruit, were arranged in order to identify putative B. oleae kairomones. While females were indifferent to β-myrcene, the highest dosages of limonene and (E)-β-ocimene were unfavoured by the tested flies, which preferentially moved toward the empty arm of the Y-tube. Furthermore, females preferred the lowest concentration of β-ocimene compared to the highest one. These results supported our hypothesis that fruit VOCs may serve as kairomones for female flies.
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12
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Guégan M, Tran Van V, Martin E, Minard G, Tran FH, Fel B, Hay AE, Simon L, Barakat M, Potier P, Haichar FEZ, Valiente Moro C. Who is eating fructose within the Aedes albopictus gut microbiota? Environ Microbiol 2020; 22:1193-1206. [PMID: 31943686 DOI: 10.1111/1462-2920.14915] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 12/18/2022]
Abstract
The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito-borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies have emerged from the study of mosquito-associated microorganisms. Although the role of the microbiota in insect biology does not require further proof, much remains to be deciphered in mosquitoes, especially the contribution of the microbiota to host nutrient metabolism. Mosquitoes feed on plant nectar, composed of mostly fructose. We used stable isotope probing to identify bacteria and fungi assimilating fructose within the gut of Ae. albopictus. Mosquitoes were fed a 13 C-labelled fructose solution for 24 h. Differences in the active microbial community according to the sex of mosquitoes were highlighted. The bacterium Lelliottia and the fungi Cladosporium and Aspergillus dominated the active microbiota in males, whereas the bacterium Ampullimonas and the yeast Cyberlindnera were the most active in females. This study is the first to investigate trophic interactions between Ae. albopictus and its microbiota, thus underscoring the importance of the microbial component in nectar feeding in mosquitoes.
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Affiliation(s)
- Morgane Guégan
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Van Tran Van
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Edwige Martin
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Guillaume Minard
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Florence-Hélène Tran
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Benjamin Fel
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France.,Université de Lyon, Université Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, CESN Centre d'Etude des Substances Naturelles, 43 Bd du 11 novembre 1918, 69622, Villeurbanne Cedex, France
| | - Anne-Emmanuelle Hay
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France.,Université de Lyon, Université Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, CESN Centre d'Etude des Substances Naturelles, 43 Bd du 11 novembre 1918, 69622, Villeurbanne Cedex, France
| | - Laurent Simon
- UMR 5023 LEHNA, CNRS, Univ Lyon, Université Claude Bernard Lyon 1, Université Lyon 1, ENTPE, Villeurbanne, France
| | - Mohamed Barakat
- Laboratory for Microbial Ecology of the Rhizosphere and Extreme Environment, CNRS, UMR 7265 BIAM, CEA, Aix Marseille University, Saint-Paul-lès-Durance, France
| | - Patrick Potier
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Feth El Zahar Haichar
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
| | - Claire Valiente Moro
- Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, Univ Lyon, Université Claude Bernard Lyon 1, UMR INRA, 1418, Villeurbanne, France
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Hamelin RC, Roe AD. Genomic biosurveillance of forest invasive alien enemies: A story written in code. Evol Appl 2020; 13:95-115. [PMID: 31892946 PMCID: PMC6935587 DOI: 10.1111/eva.12853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 06/30/2019] [Accepted: 07/19/2019] [Indexed: 12/15/2022] Open
Abstract
The world's forests face unprecedented threats from invasive insects and pathogens that can cause large irreversible damage to the ecosystems. This threatens the world's capacity to provide long-term fiber supply and ecosystem services that range from carbon storage, nutrient cycling, and water and air purification, to soil preservation and maintenance of wildlife habitat. Reducing the threat of forest invasive alien species requires vigilant biosurveillance, the process of gathering, integrating, interpreting, and communicating essential information about pest and pathogen threats to achieve early detection and warning and to enable better decision-making. This process is challenging due to the diversity of invasive pests and pathogens that need to be identified, the diverse pathways of introduction, and the difficulty in assessing the risk of establishment. Genomics can provide powerful new solutions to biosurveillance. The process of invasion is a story written in four chapters: transport, introduction, establishment, and spread. The series of processes that lead to a successful invasion can leave behind a DNA signature that tells the story of an invasion. This signature can help us understand the dynamic, multistep process of invasion and inform management of current and future introductions. This review describes current and future application of genomic tools and pipelines that will provide accurate identification of pests and pathogens, assign outbreak or survey samples to putative sources to identify pathways of spread, and assess risk based on traits that impact the outbreak outcome.
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Affiliation(s)
- Richard C. Hamelin
- Department of Forest and Conservation SciencesThe University of British ColumbiaVancouverBCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département des sciences du bois et de la forêt, Faculté de Foresterie et GéographieUniversité LavalQuébecQCCanada
| | - Amanda D. Roe
- Great Lakes Forestry CenterNatural Resources CanadaSault Ste. MarieONCanada
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Morales-Cruz A, Figueroa-Balderas R, García JF, Tran E, Rolshausen PE, Baumgartner K, Cantu D. Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding. BMC Microbiol 2018; 18:214. [PMID: 30547761 PMCID: PMC6295080 DOI: 10.1186/s12866-018-1343-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/15/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND DNA metabarcoding, commonly used in exploratory microbial ecology studies, is a promising method for the simultaneous in planta-detection of multiple pathogens associated with disease complexes, such as the grapevine trunk diseases. Profiling of pathogen communities associated with grapevine trunk diseases is particularly challenging, due to the presence within an individual wood lesion of multiple co-infecting trunk pathogens and other wood-colonizing fungi, which span a broad range of taxa in the fungal kingdom. As such, we designed metabarcoding primers, using as template the ribosomal internal transcribed spacer of grapevine trunk-associated ascomycete fungi (GTAA) and compared them to two universal primer widely used in microbial ecology. RESULTS We first performed in silico simulations and then tested the primers by high-throughput amplicon sequencing of (i) multiple combinations of mock communities, (ii) time-course experiments with controlled inoculations, and (iii) diseased field samples from vineyards under natural levels of infection. All analyses showed that GTAA had greater affinity and sensitivity, compared to those of the universal primers. Importantly, with GTAA, profiling of mock communities and comparisons with shotgun-sequencing metagenomics of field samples gave an accurate representation of genera of important trunk pathogens, namely Phaeomoniella, Phaeoacremonium, and Eutypa, the abundances of which were over- or under-estimated with universal primers. CONCLUSIONS Overall, our findings not only demonstrate that DNA metabarcoding gives qualitatively and quantitatively accurate results when applied to grapevine trunk diseases, but also that primer customization and testing are crucial to ensure the validity of DNA metabarcoding results.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Jadran F. García
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Eric Tran
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Kendra Baumgartner
- United States Department of Agriculture, Agricultural Research Service, Crops Pathology and Genetics Research Unit, Davis, CA 95616 USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
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15
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Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes. PLoS One 2018; 13:e0199403. [PMID: 30496186 PMCID: PMC6264826 DOI: 10.1371/journal.pone.0199403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/11/2018] [Indexed: 11/18/2022] Open
Abstract
The olive fruit fly (OFF), Bactrocera oleae is the most devastating pest affecting olive fruit worldwide. Previous investigations have addressed the fungal microbiome associated with olive drupes or B. oleae, but the impact of the insect on fungal communities of olive fruit remains undescribed. In the present work, the fungal microbiome of olive drupes, infested and non-infested by the OFF, was investigated in four different localities and cultivars. Olive fruit fly infestations caused a general reduction of the fungal diversity, a higher quantity of the total DNA and an increase in taxa that remained unidentified or had unknown roles. The infestations led to imbalanced fungal communities with the growth of taxa that are usually outcompeted. While it was difficult to establish a cause-effect link between fly infestation and specific fungi, it is clear that the fly alters the natural microbial balance, especially the low abundant taxa. On the other hand, the most abundant ones, were not significantly influenced by the insect. In fact, despite the slight variation between the sampling locations, Aureobasidium, Cladosporium, and Alternaria, were the dominant genera, suggesting the existence of a typical olive fungal microbiome.
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16
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Meta-Omics Tools in the World of Insect-Microorganism Interactions. BIOLOGY 2018; 7:biology7040050. [PMID: 30486337 PMCID: PMC6316257 DOI: 10.3390/biology7040050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/16/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023]
Abstract
Microorganisms are able to influence several aspects of insects’ life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies are now available at a lower cost per base, and bioinformatic procedures are becoming more user-friendly. This is triggering a huge effort in studying the microbial diversity associated to insects, and especially to economically important insect pests. The importance of the microbiome has been widely acknowledged for a wide range of animals, and also for insects this topic is gaining considerable importance. In addition to bacterial-associates, the insect-associated fungal communities are also gaining attention, especially those including plant pathogens. The use of meta-omics tools is not restricted to the description of the microbial world, but it can be also used in bio-surveillance, food safety assessment, or even to bring novelties to the industry. This mini-review aims to give a wide overview of how meta-omics tools are fostering advances in research on insect-microorganism interactions.
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18
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Aguayo J, Fourrier-Jeandel C, Husson C, Ioos R. Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities. Appl Environ Microbiol 2018; 84:e02637-17. [PMID: 29572213 PMCID: PMC5960964 DOI: 10.1128/aem.02637-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/19/2018] [Indexed: 11/20/2022] Open
Abstract
Techniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.IMPORTANCE The advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.
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Affiliation(s)
- Jaime Aguayo
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| | - Céline Fourrier-Jeandel
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
| | - Claude Husson
- UMR IAM, INRA, Université de Lorraine, Nancy, France
| | - Renaud Ioos
- ANSES, Laboratoire de la Santé des Végétaux-LSV, Unité de Mycologie. Domaine de Pixérécourt, Malzéville, France
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Banchi E, Ametrano CG, Stanković D, Verardo P, Moretti O, Gabrielli F, Lazzarin S, Borney MF, Tassan F, Tretiach M, Pallavicini A, Muggia L. DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy. PLoS One 2018; 13:e0194489. [PMID: 29558527 PMCID: PMC5860773 DOI: 10.1371/journal.pone.0194489] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/05/2018] [Indexed: 01/13/2023] Open
Abstract
Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments. The microscopic method used to analyze aerobiological samples and the inconspicuous fungal characters do not allow a in depth taxonomical identification. Here, we present a first assessment of fungal diversity from airborne samples using a DNA metabarcoding analysis. The nuclear ITS2 region was selected as barcode to catch fungal diversity in mixed airborne samples gathered during two weeks in four sites of North-Eastern and Central Italy. We assessed the taxonomic composition and diversity within and among the sampled sites and compared the molecular data with those obtained by traditional microscopy. The molecular analyses provide a tenfold more comprehensive determination of the taxa than the traditional morphological inspections. Our results prove that the metabarcoding analysis is a promising approach to increases quality and sensitivity of the aerobiological monitoring. The laboratory and bioinformatic workflow implemented here is now suitable for routine, high-throughput, regional analyses of airborne fungi.
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Affiliation(s)
- Elisa Banchi
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | | | - David Stanković
- Department of Life Sciences, University of Trieste, Trieste, Italy
- Marine Biology Station, National Institute of Biology, Piran, Slovenia
| | - Pierluigi Verardo
- Regional Agency for Environmental Protection Friuli Venezia Giulia, Department of Pordenone, Pordenone, Italy
| | - Olga Moretti
- Regional Agency for Environmental Protection Umbria, Terni, Italy
| | | | | | | | - Francesca Tassan
- Regional Agency for Environmental Protection Friuli Venezia Giulia, Department of Trieste, Trieste, Italy
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | | | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
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Theelen B, Cafarchia C, Gaitanis G, Bassukas ID, Boekhout T, Dawson TL. Malassezia ecology, pathophysiology, and treatment. Med Mycol 2018. [DOI: 10.1093/mmy/myx134] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Bart Theelen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Claudia Cafarchia
- Dipartimento di Medicina Veterinaria, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Georgios Gaitanis
- Department of Skin and Venereal Diseases, Faculty of Medicine, School of Health Sciences, University of Ioannina, Greece
| | - Ioannis Dimitrios Bassukas
- Department of Skin and Venereal Diseases, Faculty of Medicine, School of Health Sciences, University of Ioannina, Greece
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Thomas L Dawson
- Agency for Science, Technology, and Research (A*STAR), Institute for Medical Biology, (IMB), Singapore
- Center for Cell Death, Injury and Regeneration, Departments of Drug Discovery and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
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Talhinhas P, Loureiro A, Oliveira H. Olive anthracnose: a yield- and oil quality-degrading disease caused by several species of Colletotrichum that differ in virulence, host preference and geographical distribution. MOLECULAR PLANT PATHOLOGY 2018; 19:1797-1807. [PMID: 29517840 PMCID: PMC6638118 DOI: 10.1111/mpp.12676] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/24/2018] [Accepted: 03/05/2018] [Indexed: 05/26/2023]
Abstract
Olive anthracnose causes fruit rot leading to its drop or mummification, resulting in yield losses and the degradation of oil quality. TAXONOMY AND DISTRIBUTION The disease is caused by diverse species of Colletotrichum, mostly clustering in the C. acutatum species complex. Colletotrichum nymphaeae and C. godetiae are the prevalent species in the Northern Hemisphere, whereas C. acutatum sensu stricto is the most frequent species in the Southern Hemisphere, although it is recently and quickly emerging in the Northern Hemisphere. The disease has been reported from all continents, but it attains higher incidence and severity in the west of the Mediterranean Basin, where it is endemic in traditional orchards of susceptible cultivars. LIFE CYCLE The pathogens are able to survive on vegetative organs. On the fruit surface, infections remain quiescent until fruit maturity, when typical anthracnose symptoms develop. Under severe epidemics, defoliation and death of branches can also occur. Pathogen species differ in virulence, although this depends on the cultivar. CONTROL The selection of resistant cultivars depends strongly on pathogen diversity and environmental conditions, posing added difficulties to breeding efforts. Chemical disease control is normally achieved with copper-based fungicides, although this may be insufficient under highly favourable disease conditions and causes concern because of the presence of fungicide residues in the oil. In areas in which the incidence is high, farmers tend to anticipate harvest, with consequences in yield and oil characteristics. CHALLENGES Olive production systems, harvest and post-harvest processing have experienced profound changes in recent years, namely new training systems using specific cultivars, new harvest and processing techniques and new organoleptic market requests. Changes are also occurring in both the geographical distribution of pathogen populations and the taxonomic framework. In addition, stricter rules concerning pesticide use are likely to have a strong impact on control strategies. A detailed knowledge of pathogen diversity, population dynamics and host-pathogen interactions is basal for the deployment of durable and effective disease control strategies, whether based on resistance breeding, agronomic practices or biological or chemical control.
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Affiliation(s)
- Pedro Talhinhas
- LEAF‐Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda1349‐017 LisboaPortugal
| | - Andreia Loureiro
- LEAF‐Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda1349‐017 LisboaPortugal
| | - Helena Oliveira
- LEAF‐Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda1349‐017 LisboaPortugal
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Strano CP, Malacrinò A, Campolo O, Palmeri V. Influence of Host Plant on Thaumetopoea pityocampa Gut Bacterial Community. MICROBIAL ECOLOGY 2018; 75:487-494. [PMID: 28735425 DOI: 10.1007/s00248-017-1019-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
Microbial communities associated to the gut of insects are attracting an increasing interest, mainly because of their role in influencing several host life-traits. The characterization of the gut microbial community is pivotal for understanding insect ecology and, thus, to develop novel pest management strategies. The pine processionary moth, Thaumetopoea pytiocampa (Denis & Schiff.) (Lepidoptera: Thaumetopoeidae), is a severe defoliator of pine forests, able to feed on several pine species. In this work, we performed a metabarcoding analysis to investigate, for the first time, the diversity of the gut bacterial community of pine processionary larvae associated with three different host pine species (Pinus halepensis, Pinus nigra subsp. laricio, and Pinus pinaster). We found that the gut microbial community of T. pityocampa larvae collected on P. halapensis was different from that associated with larvae collected from P. nigra and P. pinaster. Moreover, the high presence of bacteria belonging to the genera Modestobacter, Delftia, and unidentified Methylobacteriaceae retrieved in larvae feeding on P. halapensis suggested that specific interactions can occur. Our results provide the evidence that different host plant differently impact on the microbiota diversity of T. pityocampa larvae, contributing to the general knowledge of this pest with information that could be useful in shaping the next generation of pest control strategies.
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Affiliation(s)
- Cinzia P Strano
- Dipartimento di Agraria, Università degli Studi "Mediterranea" di Reggio Calabria, Reggio Calabria, Italy
| | - Antonino Malacrinò
- Dipartimento di Agraria, Università degli Studi "Mediterranea" di Reggio Calabria, Reggio Calabria, Italy
- Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping, Sweden
| | - Orlando Campolo
- Dipartimento di Agraria, Università degli Studi "Mediterranea" di Reggio Calabria, Reggio Calabria, Italy
| | - Vincenzo Palmeri
- Dipartimento di Agraria, Università degli Studi "Mediterranea" di Reggio Calabria, Reggio Calabria, Italy.
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23
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Pangallo S, Nicosia MGLD, Agosteo GE, Abdelfattah A, Romeo FV, Cacciola SO, Rapisarda P, Schena L. Evaluation of a Pomegranate Peel Extract as an Alternative Means to Control Olive Anthracnose. PHYTOPATHOLOGY 2017; 107:1462-1467. [PMID: 28766401 DOI: 10.1094/phyto-04-17-0133-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Olive anthracnose is caused by different species of Colletotrichum spp. and may be regarded as the most damaging disease of olive fruit worldwide, greatly affecting quality and quantity of the productions. A pomegranate peel extract (PGE) proved very effective in controlling the disease. The extract had a strong in vitro fungicidal activity against Colletotrichum acutatum sensu stricto, was very effective in both preventive and curative trials with artificially inoculated fruit, and induced resistance in treated olive tissues. In field trials, PGE was significantly more effective than copper, which is traditionally used to control the disease. The highest level of protection was achieved by applying the extract in the early ascending phase of the disease outbreaks because natural rots were completely inhibited with PGE at 12 g/liter and were reduced by 98.6 and by 93.0% on plants treated with PGE at 6 and 3 g/liter, respectively. Two treatments carried out 30 and 15 days before the expected epidemic outbreak reduced the incidence of the disease by 77.6, 57.0, and 51.8%, depending on the PGE concentration. The analysis of epiphytic populations showed a strong antimicrobial activity of PGE, which sharply reduced both fungal and bacterial populations. Because PGE was obtained from a natural matrix using safe chemicals and did not have any apparent phytotoxic effect on treated olive fruit, it may be regarded as a safe and effective natural antifungal preparation to control olive anthracnose and improve olive productions.
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Affiliation(s)
- Sonia Pangallo
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Maria G Li Destri Nicosia
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Giovanni E Agosteo
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Ahmed Abdelfattah
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Flora V Romeo
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Santa O Cacciola
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Paolo Rapisarda
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
| | - Leonardo Schena
- First, second, third, fourth, and eighth authors: Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria 89122, Italy; fifth and seventh authors: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di Ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Corso Savoia 190, 95024 Acireale (CT) 95024; and sixth author: Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123 Catania, Italy
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24
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Abdelfattah A, Cacciola SO, Mosca S, Zappia R, Schena L. Analysis of the Fungal Diversity in Citrus Leaves with Greasy Spot Disease Symptoms. MICROBIAL ECOLOGY 2017; 73:739-749. [PMID: 27752718 DOI: 10.1007/s00248-016-0874-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
Citrus greasy spot (CGS) is a disease of citrus with worldwide distribution and recent surveys have revealed a high level of incidence and severity of symptoms of the disease in Sicily, southern Italy. Although Mycosphaerel la citri (anamorph Zasmidium citri-griseum) and other related species are generally considered as causal agents, the etiology of CGS is still unclear. Here, we report the use of an amplicon metagenomic approach to investigate the fungal communities on citrus leaves symptomatic or asymptomatic for CGS from an orchard in Sicily showing typical CGS symptoms. A total of 35,537 high-quality chimeric free reads were obtained and assigned to 176 operational taxonomic units (OTUs), clustered at 99 % similarity threshold. Data revealed a dominating presence of the phylum Ascomycota (92.6 %) over other fungal phyla. No significant difference was observed between symptomatic and asymptomatic leaves according to both alpha and beta diversity analyses. The family Mycosphaerellaceae was the most abundant and was represented by the genera Ramularia, Mycosphaerella, and Septoria with 44.8, 2.4, and 1.7 % of the total detected sequences, respectively. However, none of the species currently reported as causal agents of CGS was detected in the present study. The most abundant sequence type (ST) was associated to Ramularia brunnea, a species originally described to cause leaf spot in a perennial herbaceous plant of the family Asteraceae. Results exclude that CGS symptoms observed in Sicily are caused by Z. citri-griseum and, moreover, they indicate that a considerable part of the fungal diversity in citrus leaves is still unknown.
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Affiliation(s)
- Ahmed Abdelfattah
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria, 89122, Italy
| | - Santa O Cacciola
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi, Via S. Sofia 100, 95123, Catania, Italy
| | - Saveria Mosca
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria, 89122, Italy
| | - Rocco Zappia
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria, 89122, Italy
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, Reggio Calabria, 89122, Italy.
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