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Flores-Almaraz VS, Truong C, Hernández-Oaxaca D, Reyes-Galindo V, Mastretta-Yanes A, Jaramillo-Correa JP, Salas-Lizana R. Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes. MICROBIAL ECOLOGY 2024; 87:72. [PMID: 38755460 PMCID: PMC11098924 DOI: 10.1007/s00248-024-02387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. & Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.
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Affiliation(s)
- Valeria Stephany Flores-Almaraz
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, Distrito Federal, México
- Instituto de Biología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Camille Truong
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, VIC 3004, Australia.
| | - Diana Hernández-Oaxaca
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, 62210, Cuernavaca, Morelos, México
| | - Verónica Reyes-Galindo
- Depto. de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Alicia Mastretta-Yanes
- Consejo Nacional de Humanidades Ciencias y Tecnología (CONAHCYT), Avenida Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México, 03940, México.
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico.
| | - Juan Pablo Jaramillo-Correa
- Depto. de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Rodolfo Salas-Lizana
- Laboratorios de Micología. Depto. de Biología Comparada, Facultad de Ciencias., Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México.
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Leal CM, Geiger A, Molnár A, Váczy KZ, Kgobe G, Zsófi Z, Geml J. Disentangling the effects of terroir, season, and vintage on the grapevine fungal pathobiome. Front Microbiol 2024; 14:1322559. [PMID: 38298541 PMCID: PMC10829339 DOI: 10.3389/fmicb.2023.1322559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/02/2024] Open
Abstract
The composition, diversity and dynamics of microbial communities associated with grapevines may be influenced by various environmental factors, including terroir, vintage, and season. Among these factors, terroir stands out as a unique possible determinant of the pathobiome, the community of plant-associated pathogens. This study employed high-throughput molecular techniques, including metabarcoding and network analysis, to investigate the compositional dynamics of grapevine fungal pathobiome across three microhabitats (soil, woody tissue, and bark) using the Furmint cultivar. Samples were collected during late winter and late summer in 2020 and 2021, across three distinct terroirs in Hungary's Tokaj wine region. Of the 123 plant pathogenic genera found, Diplodia, Phaeomoniella, and Fusarium displayed the highest richness in bark, wood, and soil, respectively. Both richness and abundance exhibited significant disparities across microhabitats, with plant pathogenic fungi known to cause grapevine trunk diseases (GTDs) demonstrating highest richness and abundance in wood and bark samples, and non-GTD pathogens prevailed soil. Abundance and richness, however, followed distinct patterns Terroir accounted for a substantial portion of the variance in fungal community composition, ranging from 14.46 to 24.67%. Season and vintage also contributed to the variation, explaining 1.84 to 2.98% and 3.67 to 6.39% of the variance, respectively. Notably, significant compositional differences in fungi between healthy and diseased grapevines were only identified in wood and bark samples. Cooccurrence networks analysis, using both unweighted and weighted metrics, revealed intricate relationships among pathogenic fungal genera. This involved mostly positive associations, potentially suggesting synergism, and a few negative relationships, potentially suggesting antagonistic interactions. In essence, the observed differences among terroirs may stem from environmental filtering due to varied edaphic and mesoclimatic conditions. Temporal weather and vine management practices could explain seasonal and vintage fungal dynamics. This study provides insights into the compositional dynamics of grapevine fungal pathobiome across different microhabitats, terroirs, seasons, and health statuses. The findings emphasize the importance of considering network-based approaches in studying microbial communities and have implications for developing improved viticultural plant health strategies.
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Affiliation(s)
- Carla Mota Leal
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Adrienn Geiger
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Molnár
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Kálmán Z. Váczy
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Glodia Kgobe
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary
| | - Zsolt Zsófi
- Institute for Viticulture and Enology, Eszterházy Károly Catholic University, Eger, Hungary
| | - József Geml
- ELKH-EKKE Lendulet Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Eger, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
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Khoshru B, Mitra D, Joshi K, Adhikari P, Rion MSI, Fadiji AE, Alizadeh M, Priyadarshini A, Senapati A, Sarikhani MR, Panneerselvam P, Mohapatra PKD, Sushkova S, Minkina T, Keswani C. Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants. Heliyon 2023; 9:e13825. [PMID: 36873502 PMCID: PMC9981932 DOI: 10.1016/j.heliyon.2023.e13825] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.
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Affiliation(s)
- Bahman Khoshru
- Department of Soil Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj - 733 134, West Bengal, India
| | - Kuldeep Joshi
- G.B. Pant National Institute of Himalayan Environment, Kosi-Katarmal, Almora-263643, Uttarakhand, India
| | - Priyanka Adhikari
- Centre for Excellence on GMP Extraction Facility (DBT, Govt. of India), National Institute of Pharmaceutical Education and Research. Guwahati-781101, Assam, India
| | | | - Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho 2735, South Africa
| | - Mehrdad Alizadeh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ankita Priyadarshini
- Crop Production Division, ICAR – National Rice Research Institute, Cuttack, 753006, Odisha, India
| | - Ansuman Senapati
- Crop Production Division, ICAR – National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Periyasamy Panneerselvam
- Crop Production Division, ICAR – National Rice Research Institute, Cuttack, 753006, Odisha, India
| | | | - Svetlana Sushkova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Chetan Keswani
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don 344090, Russia
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Kanetis LI, Taliadoros D, Makris G, Christoforou M. A Novel Seimatosporium and Other Sporocadaceae Species Associated with Grapevine Trunk Diseases in Cyprus. PLANTS (BASEL, SWITZERLAND) 2022; 11:2733. [PMID: 36297757 PMCID: PMC9608602 DOI: 10.3390/plants11202733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Besides well-known grapevine trunk disease (GTD)-related pathogens, there is an increased interest in wood-colonizing fungi that infect grapevines. During 2017-2018, a survey was conducted in Cyprus and wood samples were collected from vines exhibiting typical GTD symptoms. Based on morphological and multilocus phylogenetic analyses (ITS, LSU, bt2, tef1-a), four species in the Sporocadaceae family were described and typified; two in the genus of Seimatosporium: Seim. cyprium sp. nov. and Seim. vitis-viniferae and two in Sporocadus: Spo. kurdistanicus and Spo. rosigena. The teleomorph of Seim. cyprium sp. nov. was also described. Pathogenicity trials with representative isolates of each species were performed on woody stems of two-year-old potted grapevines for 12 months under field conditions. All isolates were pathogenic, causing dark brown to black vascular discoloration, extending upward and downward from the inoculation point. Sporocadus isolates were significantly more aggressive than Seimatosporium with lesion lengths ranging from 9.24 to 6.90 and 4.13 to 4.00 cm, respectively. Successful re-isolations were also evident for all species and isolates. Seim. cyprium sp. nov. is a newly described species, while Spo. kurdistanicus and Spo. rosigena are reported for the first time in Europe on Vitis vinifera, suggesting the potential role of Sporocadaceae in the GTDs complex.
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Affiliation(s)
- Loukas I. Kanetis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus
| | - Demetris Taliadoros
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
- Department of Biology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Georgios Makris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus
| | - Michalis Christoforou
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol 3036, Cyprus
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Molnár A, Geml J, Geiger A, Leal CM, Kgobe G, Tóth AM, Villangó S, Mézes L, Czeglédi M, Lőrincz G, Zsófi Z. Exploring Relationships among Grapevine Chemical and Physiological Parameters and Leaf and Berry Mycobiome Composition. PLANTS 2022; 11:plants11151924. [PMID: 35893628 PMCID: PMC9331551 DOI: 10.3390/plants11151924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022]
Abstract
Improving our knowledge on biotic and abiotic factors that influence the composition of the grapevine mycobiome is of great agricultural significance, due to potential effects on plant health, productivity, and wine characteristics. Here, we assessed the influence of scion cultivar on the diversity and composition of fungal communities in the berries and leaves of three different cultivars. We generated DNA metabarcoding data, and statistically compared the richness, relative abundance, and composition of several functional groups of fungi among cultivars, which are partly explained by measured differences in chemical composition of leaves and berries and physiological traits of leaves. Fungal communities in leaves and berries show contrasting patterns among cultivars. The richness and relative abundance of fungal functional groups statistically differ among berry and leaf samples, but less so among cultivars. Community composition of the dominant functional groups of fungi, i.e., plant pathogens in leaves and saprotrophs in berries, differs significantly among cultivars. We also detect cultivar-level differences in the macro- and microelement content of the leaves, and in acidity and sugar concentration of berries. Our findings suggest that there appears to be a relatively diverse set of fungi that make up the grapevine mycobiome at the sampled terroir that spans several cultivars, and that both berry and leaf mycobiomes are likely influenced by the chemical characteristics of berries and leaves, e.g., pH and the availability of nutrients and simple carbohydrates. Finally, the correlation between fungal community composition and physiological variables in leaves is noteworthy, and merits further research to explore causality. Our findings offer novel insights into the microbial dynamics of grapevine considering plant chemistry and physiology, with implications for viticulture.
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Affiliation(s)
- Anna Molnár
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
| | - József Geml
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
- ELKH–EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary;
- Correspondence: ; Tel.: +36-365204004406
| | - Adrienn Geiger
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Páter K. u. 1, 2100 Gödöllő, Hungary;
| | - Carla Mota Leal
- ELKH–EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary;
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Páter K. u. 1, 2100 Gödöllő, Hungary;
| | - Glodia Kgobe
- Doctoral School of Environmental Sciences, Hungarian University of Agricultural and Life Sciences, Páter K. u. 1, 2100 Gödöllő, Hungary;
| | - Adrienn Mária Tóth
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
| | - Szabolcs Villangó
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
| | - Lili Mézes
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
| | - Márk Czeglédi
- Food and Wine Research Institute, Research and Development Center, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.); (A.G.); (L.M.); (M.C.)
| | - György Lőrincz
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
| | - Zsolt Zsófi
- Institute for Viticulture and Enology, Faculty of Natural Sciences, Eszterházy Károly Catholic University, Leányka u. 6, 3300 Eger, Hungary; (A.M.T.); (S.V.); (G.L.); (Z.Z.)
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Metagenomic Assessment Unravels Fungal Microbiota Associated to Grapevine Trunk Diseases. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Grapevine trunk diseases (GTDs) are among the most important problems that affect the longevity and productivity of vineyards in all the major growing regions of the world. They are slow-progression diseases caused by several wood-inhabiting fungi with similar life cycles and epidemiology. The simultaneous presence of multiple trunk pathogens in a single plant together with the inconsistent GTDs symptoms expression, their isolation in asymptomatic plants, and the absence of effective treatments make these diseases extremely complex to identify and eradicate. Aiming to gain a better knowledge of GTDs and search sustainable alternatives to limit their development, the present work studied the fungal community structure associated with GTDs symptomatic and asymptomatic grapevines, following a metagenomic approach. Two important cultivars from the Alentejo region with different levels of susceptibility to GTDs were selected, namely, ‘Alicante Bouschet’ and ‘Trincadeira’. Deep sequencing of fungal-directed ITS1 amplicon led to the detection of 258 taxa, including 10 fungi previously described as responsible for GTDs. Symptomatic plants exhibited a lower abundance of GTDs-associated fungi, although with significantly higher diversity of those pathogens. Our results demonstrated that trunk diseases symptoms are intensified by a set of multiple GTDs-associated fungi on the same plant. The composition of fungal endophytic communities was significantly different according to the symptomatology and it was not affected by the cultivar. This study opens new perspectives in the study of GTDs-associated fungi and their relation to the symptomatology in grapevines.
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Bettenfeld P, Cadena i Canals J, Jacquens L, Fernandez O, Fontaine F, van Schaik E, Courty PE, Trouvelot S. The microbiota of the grapevine holobiont: A key component of plant health. J Adv Res 2021; 40:1-15. [PMID: 36100319 PMCID: PMC9481934 DOI: 10.1016/j.jare.2021.12.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/08/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
Grapevine interacts different microbiota living around and within its tissues Addition of microbial genes to plant genome gives supplementary functions to the holobiont The composition of grapevine microbiota varies according to endogenous and exogenous factors Microbiota variations can lead to perturbations of grapevine metabolism The link between symptom emergence of dieback and microbial imbalance is currently studied
Background Grapevine is a woody, perennial plant of high economic importance worldwide. Like other plants, it lives in close association with large numbers of microorganisms. Bacteria, fungi and viruses are structured in communities, and each individual can be beneficial, neutral or harmful to the plant. In this sense, microorganisms can interact with each other and regulate plant functions (including immunity) and even provide new ones. Thus, the grapevine associated with its microbial communities constitutes a supra-organism, also called a holobiont, whose functioning is linked to established plant-microorganism interactions. Aim of review The overall health of the plant may be conditioned by the diversity and structure of microbial communities. Consequently, an optimal microbial composition will consist of a microbial balance allowing the plant to be healthy. Conversely, an imbalance of microbial populations could lead to (or be generated by) a decline of the plant. The microbiome is an active component of the host also responsive to biotic and abiotic changes; in that respect, a better understanding of the most important drivers of the composition of plant microbiomes is needed. Key scientific concepts of review This article presents the current state of the art about the grapevine microbiota and its composition according to the plant compartments and the influencing factors. We also focus on situations of imbalance, in particular during plant disease or decline. Finally, we discuss the possible interest of microbial engineering in an agrosystem such as viticulture.
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