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Besze BZ, Borsodi AK, Megyes M, Zsigmond T, Horel Á. Changes in the taxonomic composition of soil bacterial communities under different inter-row tillage managements in a sloping vineyard of the Balaton Uplands (Hungary). Biol Futur 2024:10.1007/s42977-024-00234-2. [PMID: 39073547 DOI: 10.1007/s42977-024-00234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/14/2024] [Indexed: 07/30/2024]
Abstract
The common grape (Vitis vinifera L.) has been cultivated for thousands of years. Nowadays, it is cultivated using a variety of tillage practices that affect the structure of the soil microbial communities and thus the health of the vine. The aim of this study was to explore and compare the effects of tillage (shallow tillage with bare soil) and no-tillage (perennial grass cover) practices on soil physical and chemical properties and soil bacterial community diversities in a small catchment. Soil samples were taken in July and October 2020 at different slope positions of two vineyards exposed to erosion. The two sampling sites were separated by the agricultural inter-row management type: tilled and no-tilled slopes. The taxonomic diversity of bacterial communities was determined using 16S rRNA gene-based amplicon sequencing method on Illumina MiSeq platform. Based on the examined soil properties, the sampling areas were separated from each other according to the positions of the upper and lower slopes and the sampling times. Both the tilled and no-tilled soil samples were dominated by sequences assigned to phyla Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, Actinobacteriota, and Gemmatimonadota. The results showed that tillage had no significant effect compared to the no-tilled samples in the studied area. Water runoff and seasonally changed soil physical and chemical properties affected mainly the bacterial community structures.
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Affiliation(s)
- Balázs Zoltán Besze
- Department of Microbiology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Andrea K Borsodi
- Department of Microbiology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
| | - Melinda Megyes
- Department of Microbiology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
- Doctoral School of Environmental Sciences, ELTE Eötvös Loránd University, Egyetem tér 1-3, Budapest, 1053, Hungary
| | - Tibor Zsigmond
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Ruszti ut 2-4, Budapest, 1022, Hungary
- Doctoral School of Environmental Sciences, ELTE Eötvös Loránd University, Egyetem tér 1-3, Budapest, 1053, Hungary
| | - Ágota Horel
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Ruszti ut 2-4, Budapest, 1022, Hungary
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Han S, An X, He X, Ren X, Sichone J, Wu X, Zhang Y, Wang H, Sun F. Temporal Dynamics of Fungal Communities in Alkali-Treated Round Bamboo Deterioration under Natural Weathering. Microorganisms 2024; 12:858. [PMID: 38792687 PMCID: PMC11124218 DOI: 10.3390/microorganisms12050858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Microbes naturally inhabit bamboo-based materials in outdoor environments, sequentially contributing to their deterioration. Fungi play a significant role in deterioration, especially in environments with abundant water and favorable temperatures. Alkali treatment is often employed in the pretreatment of round bamboo to change its natural elastic and aesthetic behaviors. However, little research has investigated the structure and dynamics of fungal communities on alkali-treated round bamboo during natural deterioration. In this work, high-throughput sequencing and multiple characterization methods were used to disclose the fungal community succession and characteristic alterations of alkali-treated round bamboo in both roofed and unroofed habitats throughout a 13-week deterioration period. In total, 192 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal community richness of roofed bamboo samples declined, whereas that of unroofed bamboo samples increased during deterioration. The phyla Ascomycota and Basidiomycota exhibited dominance during the entire deterioration process in two distinct environments, and the relative abundance of them combined was more than 99%. A distinct shift in fungal communities from Basidiomycota dominant in the early stage to Ascomycota dominant in the late stage was observed, which may be attributed to the increase of moisture and temperature during succession and the effect of alkali treatment. Among all environmental factors, temperature contributed most to the variation in the fungal community. The surface of round bamboo underwent continuous destruction from fungi and environmental factors. The total amount of cell wall components in bamboo epidermis in both roofed and unroofed conditions presented a descending trend. The content of hemicellulose declined sharply by 8.3% and 11.1% under roofed and unroofed environments after 9 weeks of deterioration. In addition, the contact angle was reduced throughout the deterioration process in both roofed and unroofed samples, which might be attributed to wax layer removal and lignin degradation. This study provides theoretical support for the protection of round bamboo under natural weathering.
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Affiliation(s)
- Shuaibo Han
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaojiao An
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xiaolong He
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xin Ren
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - John Sichone
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
| | - Xinxing Wu
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Fangli Sun
- National Engineering & Technology Research Center of Wood-Based Resources Comprehensive Utilization, School of Chemical and Materials Engineering, Zhejiang A&F University, Hangzhou 311300, China; (X.A.); (X.H.); (X.R.); (J.S.); (X.W.); (Y.Z.); (H.W.)
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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Remenyik J, Csige L, Dávid P, Fauszt P, Szilágyi-Rácz AA, Szőllősi E, Bacsó ZR, Szepsy Jnr I, Molnár K, Rácz C, Fidler G, Kállai Z, Stündl L, Dobos AC, Paholcsek M. Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region. PLoS One 2024; 19:e0300563. [PMID: 38626236 PMCID: PMC11020696 DOI: 10.1371/journal.pone.0300563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/29/2024] [Indexed: 04/18/2024] Open
Abstract
A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.
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Affiliation(s)
- Judit Remenyik
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - László Csige
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - Péter Dávid
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Péter Fauszt
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Anna Anita Szilágyi-Rácz
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Erzsébet Szőllősi
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Zsófia Réka Bacsó
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - István Szepsy Jnr
- Research Laboratory and Wine Academy of Mad, University of Debrecen, Mád, Hungary
| | - Krisztina Molnár
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Csaba Rácz
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Gábor Fidler
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Zoltán Kállai
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - László Stündl
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Attila Csaba Dobos
- Centre for Precision Farming R&D Services, Faculty of Agriculture, Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary
| | - Melinda Paholcsek
- Center for Complex Systems and Microbiome Innovations, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Debrecen, Hungary
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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Kolařík M, Vrublevskaya M, Kajzrová S, Kulišová M, Kolouchová IJ. Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic. Folia Microbiol (Praha) 2023; 68:961-975. [PMID: 37289415 DOI: 10.1007/s12223-023-01066-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/20/2023] [Indexed: 06/09/2023]
Abstract
This paper represents the results of screening a diversity of fungal endophytes associated with Vitis vinifera leaves and canes in the Czech Republic. The characterization of strains is based on morphological and phylogenetic analyses of ITS, EF1α and TUB2 sequence data. Our strain selection covers 16 species and seven orders belonging to Ascomycota and Basidiomycota. Together with ubiquitous fungi, we report on several poorly known plant-associated fungi, Angustimassarina quercicola (= A. coryli, a synonym proposed in this study) and Pleurophoma pleurospora. Other species, such as Didymella negriana, D. variabilis, Neosetophoma sp. (species identical or sister to N. rosae), Phragmocamarosporium qujingensis and Sporocadus rosigena, have so far been little known and rarely found, but are frequent on V. vinifera in different parts of the world and obviously belong to a microbiota with a strong preference for this plant. Detailed taxonomical identification allowed us to identify species with apparent stable associations with V. vinifera, for which further interactions with V. vinifera can be expected. Our study is the first to focus on V. vinifera endophytes in Central Europe and expands the knowledge about their taxonomy, ecology and geography.
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Affiliation(s)
- Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Maria Vrublevskaya
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
| | - Soňa Kajzrová
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 14220, Prague, Czech Republic
| | - Markéta Kulišová
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
| | - Irena Jarošová Kolouchová
- Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28, Prague, Czech Republic
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de Menezes Souza J, de Menezes Fonseca D, Pinheiro de Souza J, Cordeiro do Nascimento L, Mendes Hughes F, Pereira Bezerra JD, Góes-Neto A, Ferreira-Silva A. Cactus Endophytic Fungi and Bioprospecting for their Enzymes and Bioactive Molecules: A Systematic Review. Chem Biodivers 2023; 20:e202301413. [PMID: 37934008 DOI: 10.1002/cbdv.202301413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
Endophytic fungi are associated with plant health and represent a remarkable source of potential of enzymes and bioactive compounds, but the diversity of endophytes remains uncertain and poorly explored, especially in Cactaceae, one of the most species-rich families adapted to growing in arid and semi-arid regions. The aim of this study was to conduct a systematic review on the diversity and bioprospecting of endophytic fungi from Cactaceae. We analysed peer-reviewed articles from seven databases using PRISMA guidelines. The results showed that the Cactaceae family is a source of new taxa, but the diversity of endophytic fungi of Cactaceae is little explored, mainly the diversity among tissues and by metagenomics. Bioprospecting studies have shown that these microorganisms can be used in the production of enzymes and larvicidal and antifungal compounds. Our results are relevant as a starting point for researchers to develop studies that expand the knowledge of plant mycobiota in arid and semi-arid ecosystems, as well as comprising a remarkable source of fungal compounds with several biotechnological applications.
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Affiliation(s)
- Jeferson de Menezes Souza
- Graduate Program in Biotechnology, Universidade Estadual de Feira de Santana, Feira de Santana City, 44036-900, Bahia State, Brazil
| | | | - Jaciara Pinheiro de Souza
- Graduate Program in Pharmaceutical Sciences, Universidade Federal de Sergipe, Aracaju City, 41100-000, Sergipe State, Brazil
| | - Luciana Cordeiro do Nascimento
- Agricultural Sciences Center, Department of Phytotechnics and Environmental Sciences, Universidade Federal da Paraíba, Areia City, 58397-000, Paraíba State, Brazil
| | - Frederic Mendes Hughes
- Conselho de Curadores das Coleções Científicas and Graduate Program in Zoology, Universidade Estadual de Santa Cruz, Ilhéus City, 45662-900, Bahia State, Brazil
| | - Jadson Diogo Pereira Bezerra
- Departament of Biosciences and Technology, Institute of Tropical Pathology and Public Health, Universidade Federal de Goiás, Goiânia City, 74605-050, Goiás State, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte City, 31270-901, Minas Gerais State, Brazil
| | - Alice Ferreira-Silva
- Agricultural Sciences Center, Department of Phytotechnics and Environmental Sciences, Universidade Federal da Paraíba, Areia City, 58397-000, Paraíba State, Brazil
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Molnár A, Knapp DG, Lovas M, Tóth G, Boldizsár I, Váczy KZ, Kovács GM. Untargeted metabolomic analyses support the main phylogenetic groups of the common plant-associated Alternaria fungi isolated from grapevine (Vitis vinifera). Sci Rep 2023; 13:19298. [PMID: 37935846 PMCID: PMC10630412 DOI: 10.1038/s41598-023-46020-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Alternaria, a cosmopolitan fungal genus is a dominant member of the grapevine (Vitis vinifera) microbiome. Several Alternaria species are known to produce a variety of secondary metabolites, which are particularly relevant to plant protection and food safety in field crops. According to previous findings, the majority of Alternaria species inhabiting grapevine belong to Alternaria sect. Alternaria. However, the phylogenetic diversity and secondary metabolite production of the distinct Alternaria species has remained unclear. In this study, our aim was to examine the genetic and metabolic diversity of endophytic Alternaria isolates associated with the above-ground tissues of the grapevine. Altogether, 270 Alternaria isolates were collected from asymptomatic leaves and grape clusters of different grapevine varieties in the Eger wine region of Hungary. After analyses of the nuclear ribosomal DNA internal transcribed spacer (ITS) and RNA polymerase second largest subunit (rpb2) sequences, 170 isolates were chosen for further analyses. Sequences of the Alternaria major allergen gene (Alt a 1), endopolygalacturonase (endoPG), OPA10-2, and KOG1058 were also included in the phylogenetic analyses. Identification of secondary metabolites and metabolite profiling of the isolates were performed using high-performance liquid chromatography (HPLC)-high-resolution tandem mass spectrometry (HR-MS/MS). The multilocus phylogeny results revealed two distinct groups in grapevine, namely A. alternata and the A. arborescens species complex (AASC). Eight main metabolites were identified in all collected Alternaria isolates, regardless of their affiliation to the species and lineages. Multivariate analyses of untargeted metabolites found no clear separations; however, a partial least squares-discriminant analysis model was able to successfully discriminate between the metabolic datasets from isolates belonging to the AASC and A. alternata. By conducting univariate analysis based on the discriminant ability of the metabolites, we also identified several features exhibiting large and significant variation between A. alternata and the AASC. The separation of these groups may suggest functional differences, which may also play a role in the functioning of the plant microbiome.
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Affiliation(s)
- Anna Molnár
- Centre for Research and Development, Eszterházy Károly Catholic University, Leányka utca 6, Eger, 3300, Hungary.
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary.
| | - Dániel G Knapp
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Department of Forestry and Wood Technology, Linnaeus University, Växjö, Sweden
| | - Miklós Lovas
- Centre for Research and Development, Eszterházy Károly Catholic University, Leányka utca 6, Eger, 3300, Hungary
- Hevesy György PhD School of Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gergő Tóth
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre U. 9, Budapest, 1092, Hungary
| | - Imre Boldizsár
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Department of Pharmacognosy, Semmelweis University, Üllői út 26, Budapest, 1085, Hungary
| | - Kálmán Zoltán Váczy
- Centre for Research and Development, Eszterházy Károly Catholic University, Leányka utca 6, Eger, 3300, Hungary
| | - Gábor M Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Plant Protection Institute, Centre for Agricultural Research, Budapest, 1525, Hungary
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8
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An X, Han S, Ren X, Sichone J, Fan Z, Wu X, Zhang Y, Wang H, Cai W, Sun F. Succession of Fungal Community during Outdoor Deterioration of Round Bamboo. J Fungi (Basel) 2023; 9:691. [PMID: 37367627 DOI: 10.3390/jof9060691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Bamboo's mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community's richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.
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Affiliation(s)
- Xiaojiao An
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuaibo Han
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xin Ren
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - John Sichone
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiwei Fan
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinxing Wu
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Wei Cai
- Anji Zhujing Bamboo Technology Co., Ltd., Huzhou 313300, China
| | - Fangli Sun
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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9
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Langa-Lomba N, Grimplet J, Sánchez-Hernández E, Martín-Ramos P, Casanova-Gascón J, Julián-Lagunas C, González-García V. Metagenomic Study of Fungal Microbial Communities in Two PDO Somontano Vineyards (Huesca, Spain): Effects of Age, Plant Genotype, and Initial Phytosanitary Status on the Priming and Selection of their Associated Microorganisms. PLANTS (BASEL, SWITZERLAND) 2023; 12:2251. [PMID: 37375877 DOI: 10.3390/plants12122251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The study of microbial communities associated with different plants of agronomic interest has allowed, in recent years, to answer a number of questions related to the role and influence of certain microbes in key aspects of their autoecology, such as improving the adaptability of the plant host to different abiotic or biotic stresses. In this study, we present the results of the characterization, through both high-throughput sequencing and classical microbiological methods, of the fungal microbial communities associated with grapevine plants in two vineyards of different ages and plant genotypes located in the same biogeographical unit. The study is configured as an approximation to the empirical demonstration of the concept of "microbial priming" by analyzing the alpha- and beta-diversity present in plants from two plots subjected to the same bioclimatic regime to detect differences in the structure and taxonomic composition of the populations. The results were compared with the inventories of fungal diversity obtained by culture-dependent methods to establish, where appropriate, correlations between both microbial communities. Metagenomic data showed a differential enrichment of the microbial communities in the two vineyards studied, including the populations of plant pathogens. This is tentatively explained due to factors such as the different time of exposure to microbial infection, different plant genotype, and different starting phytosanitary situation. Thus, results suggest that each plant genotype recruits differential fungal communities and presents different profiles of associated potential microbial antagonists or communities of pathogenic species.
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Affiliation(s)
- Natalia Langa-Lomba
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón (IUCA), EPS, University of Zaragoza, Carretera de Cuarte s/n, 22071 Huesca, Spain
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Jerome Grimplet
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50059 Zaragoza, Spain
- Departamento de Ciencia Vegetal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Eva Sánchez-Hernández
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - Pablo Martín-Ramos
- Department of Agricultural and Forestry Engineering, ETSIIAA, Universidad de Valladolid, Avenida de Madrid 44, 34004 Palencia, Spain
| | - José Casanova-Gascón
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), EPS, University of Zaragoza, Carretera de Cuarte s/n, 22071 Huesca, Spain
| | - Carmen Julián-Lagunas
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50059 Zaragoza, Spain
| | - Vicente González-García
- Departamento de Sistemas Agrícolas, Forestales y Medio Ambiente, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), 50059 Zaragoza, Spain
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10
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Vaccination of Elms against Dutch Elm Disease—Are the Associated Epiphytes and Endophytes Affected? J Fungi (Basel) 2023; 9:jof9030297. [PMID: 36983465 PMCID: PMC10057572 DOI: 10.3390/jof9030297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Dutch elm disease (DED) is causing extensive mortality of ecologically and culturally valuable elm trees (Ulmus spp.). Treatment of elms with the biological vaccine Dutch Trig® has been found to provide effective protection against DED by stimulating the defensive mechanisms of the trees. We hypothesized that the same mechanisms could also affect non-target organisms associated with elms. We explored the possible effects of vaccination on epiphytes (mainly lichens) and fungal endophytes living in the bark and young xylem of treated elms. Epiphyte cover percentage was assessed visually using a grid placed on the trunks, and a culture-based approach was used to study endophytes. Epiphyte cover was lower on the trunks of vaccinated trees as compared with unvaccinated trees, but the difference was not statistically significant. The presence of slow-growing and uncommon endophytes seemed to be reduced in continuously vaccinated elms; however, the highest endophyte diversity was found in elms four years after cessation of the vaccination treatments. Our findings suggest that although vaccination may shape epiphyte and endophyte communities in elms, its impacts are not straightforward. More detailed studies are, therefore, needed to inform the sustainable application of the vaccine as a part of the integrated management of DED.
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11
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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12
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Investigating plant-microbe interactions within the root. Arch Microbiol 2022; 204:639. [PMID: 36136275 DOI: 10.1007/s00203-022-03257-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/15/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022]
Abstract
A diverse lineage of microorganisms inhabits plant roots and interacts with plants in various ways. Further, these microbes communicate and interact with each other within the root microbial community. These symbioses add an array of influences, such as plant growth promotion or indirect protection to the host plant. Omics technology and genetic manipulation have been applied to unravel these interactions. Recent studies probed plants' control over microbes. However, the activity of the root microbial community under host influence has not been elucidated enough. In this mini-review, we discussed the recent advances and limits of omics technology and genetics for dissecting the activity of the root-associated microbial community. These materials may help us formulate the correct experimental plans to capture the entire molecular mechanisms of the plant-microbe interaction.
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13
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Qu JZ, Liu F, Pan XX, Liao CM, Li T, Zhang HB, Yang MZ. Coordinative Changes in Metabolites in Grape Cells Exposed to Endophytic Fungi and Their Extracts. Molecules 2022; 27:molecules27175566. [PMID: 36080331 PMCID: PMC9458220 DOI: 10.3390/molecules27175566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Endophytes and their elicitors can all be utilized in regulating crop biochemical qualities. However, living endophytes and their derived elicitors are always applied separately; little is known about the similarities and differences of their effects. To increase the efficiency of this system when applied in practice, the present work profiled simultaneously the metabolomes in grape cells exposed to endophytic fungi (EF) and their corresponding fungal extracts (CFE). As expected, grape cells exposed separately to different fungi, or to different fungi derived extracts, each exhibited different modifications of metabolite patterns. The metabolic profiles of certain EF- and CFE-exposed grape cells were also differently influenced to certain degrees, owing to the presence of differentially responding metabolites (DRMs). However, the detected majority proportions of coordinately responding metabolites (CRMs) in both the EF- and the CFE-exposed grape cells, as well as the significantly influenced metabolites (SIMs) which are specific to certain fungal strains, clearly indicate coordinative changes in metabolites in grape cells exposed to EF and CFEs. The coordinative changes in metabolites in EF- and CFE-treated grape cells appeared to be fungal strain-dependent. Notably, several of those fungal strain-specific CRMs and DRMs are metabolites and belong to amino acids, lipids, organic acids, phenolic acids, flavonoids, and others, which are major contributors to the biochemistry and sensory qualities of grapes and wines. This research clarifies the detailed responses of metabolites in grape cells exposed to EF and CFEs. It also demonstrates how endophytes can be selectively used in the form of extracts to produce functions as CRMs of the living fungus with increased eco-safety, or separately applied to the living microbes or elicitors to emphasize those effects related to their specifically initiated SIMs and DRMs.
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Affiliation(s)
- Jin-Zhuo Qu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
- School of Life Science, Yunnan University, Kunming 650504, China
| | - Fang Liu
- School of Life Science, Yunnan University, Kunming 650504, China
| | - Xiao-Xia Pan
- School of Chemistry and Environment, Yunnan Minzu University, Kunming 650504, China
| | - Chang-Mei Liao
- School of Life Science, Yunnan University, Kunming 650504, China
| | - Tong Li
- School of Life Science, Yunnan University, Kunming 650504, China
| | - Han-Bo Zhang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Ming-Zhi Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
- Correspondence:
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14
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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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15
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Wei RT, Chen N, Ding YT, Wang L, Gao FF, Zhang L, Liu YH, Li H, Wang H. Diversity and Dynamics of Epidermal Microbes During Grape Development of Cabernet Sauvignon (Vitis vinifera L.) in the Ecological Viticulture Model in Wuhai, China. Front Microbiol 2022; 13:935647. [PMID: 35847061 PMCID: PMC9280189 DOI: 10.3389/fmicb.2022.935647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/24/2022] [Indexed: 01/10/2023] Open
Abstract
Grapevine-related microorganisms affect the health and yield of grapes, the metabolic pathways of the fermentation process, and the regional characteristics of wine. However, the diversity of epidermal microorganisms during the development of berries under the ecological viticulture model has not been described in detail. In this study, high-throughput amplicon sequencing technology was used to perform ITS and 16S sequencing of Cabernet Sauvignon epidermal microbes at different developmental stages in the Wuhai region to investigate the succession of epidermal microbes and their response to developmental stages and vineyard weather. The results showed that the diversity of fungi and bacteria decreased during development. Epidermal microorganisms recruited members according to their developmental stages, but retained the core taxa, such as the fungi genera Alternaria, Jattaea, and Jattaea and the bacteria genera Brevundimonas, Sphingomonas, Acinetobacter, and Pseudomonas. In addition, the microbial diversity was associated with specific meteorological parameters, implying that there was a connection between the environmental conditions of the vineyard and the microbial distribution pattern such as the fungus genus Filobasidium was positively correlated with relative humidity and negatively correlated with average high temperature, average low temperature, and average ground temperature; the bacterium genus Lactobacillus was positively correlated with sunlight time, and negatively correlated with relative humidity. In conclusion, this study can help vineyard managers understand the microbial consortia associated with particular diseases, and also the dynamics of infection processes in order to take preventive actions, especially at the most critical moments.
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Affiliation(s)
- Ru-teng Wei
- College of Enology, Northwest A&F University, Xianyang, China
| | - Ning Chen
- College of Enology, Northwest A&F University, Xianyang, China
| | - Yin-ting Ding
- College of Enology, Northwest A&F University, Xianyang, China
| | - Lin Wang
- College of Enology, Northwest A&F University, Xianyang, China
| | - Fei-fei Gao
- College of Enology, Northwest A&F University, Xianyang, China
| | - Liang Zhang
- College of Enology, Northwest A&F University, Xianyang, China
| | - Yi-hui Liu
- College of Enology, Northwest A&F University, Xianyang, China
| | - Hua Li
- College of Enology, Northwest A&F University, Xianyang, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang, China
- China Wine Industry Technology Institute, Zhongguancun Innovation Center, Yinchuan, China
- *Correspondence: Hua Li,
| | - Hua Wang
- College of Enology, Northwest A&F University, Xianyang, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang, China
- China Wine Industry Technology Institute, Zhongguancun Innovation Center, Yinchuan, China
- Hua Wang,
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16
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Gramaje D, Eichmeier A, Spetik M, Carbone MJ, Bujanda R, Vallance J, Rey P. Exploring the Temporal Dynamics of the Fungal Microbiome in Rootstocks, the Lesser-Known Half of the Grapevine Crop. J Fungi (Basel) 2022; 8:jof8050421. [PMID: 35628677 PMCID: PMC9144578 DOI: 10.3390/jof8050421] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/03/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alpha-diversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.
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Affiliation(s)
- David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain;
- Correspondence:
| | - Aleš Eichmeier
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (A.E.); (M.S.)
| | - Milan Spetik
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valticka 334, 69144 Lednice, Czech Republic; (A.E.); (M.S.)
| | - María Julia Carbone
- Departamento de Protección Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay;
| | - Rebeca Bujanda
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas, Universidad de la Rioja, Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain;
| | - Jessica Vallance
- Bordeaux Sciences Agro, INRAE, ISVV, SAVE, 33140 Villenave d’Ornon, France; (J.V.); (P.R.)
- Université de Bordeaux, Bordeaux Sciences Agro, UMR 1065 SAVE, 33175 Gradignan, France
| | - Patrice Rey
- Bordeaux Sciences Agro, INRAE, ISVV, SAVE, 33140 Villenave d’Ornon, France; (J.V.); (P.R.)
- Université de Bordeaux, Bordeaux Sciences Agro, UMR 1065 SAVE, 33175 Gradignan, France
- Institut des Sciences Analytiques et de Physicochimie pour l‘Environnement et les Matériaux—UMR 5254, Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IBEAS Avenue de l’Université, 64013 Pau, France
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Špetík M, Balík J, Híc P, Hakalová E, Štůsková K, Frejlichová L, Tříska J, Eichmeier A. Lignans Extract from Knotwood of Norway Spruce—A Possible New Weapon against GTDs. J Fungi (Basel) 2022; 8:jof8040357. [PMID: 35448588 PMCID: PMC9025846 DOI: 10.3390/jof8040357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/10/2022] Open
Abstract
Grapevine trunk diseases (GTDs) pose a major threat to the wine industry worldwide. Currently, efficient biological methods or chemical compounds are not available for the treatment of infected grapevines. In the present study, we used an extract from the knotwood of spruce trees as a biological control against GTDs. Our in vitro trial was focused on the antifungal effects of the extract against the most common GTD pathogens—Cadophora luteo-olivacea, Dactylonectria torresensis, Diaporthe ampelina, Diaporthe bohemiae, Diplodia seriata, Eutypa lata, and Phaeoacremonium minimum. Our in vitro trial revealed a high antifungal effect of the extract against all tested fungi. The inhibition rates varied among the different species from 30% to 100% using 1 mg·mL−1 extract. Subsequently, the efficiency of the extract was supported by an in planta experiment. Commercial grafts of Vitis vinifera were treated with the extract and planted. The total genomic DNA of grapevines was extracted 10 days and 180 days after the treatment. The fungal microbial diversities of the treated/untreated plants were compared using high-throughput amplicon sequencing (HTAS). Treated plants showed 76.9% lower relative abundance of the genus Diaporthe and 70% lower relative abundance of the genus Phaeoacremonium 10 days after treatment. A similar scenario was observed for the genus Cadophora 180 days after treatment, where treated plants showed 76% lower relative abundance of this genus compared with untreated grapevines.
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Affiliation(s)
- Milan Špetík
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
| | - Josef Balík
- Department of Post-Harvest Technology of Horticultural Products, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
| | - Pavel Híc
- Department of Post-Harvest Technology of Horticultural Products, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
| | - Eliška Hakalová
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
| | - Kateřina Štůsková
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
| | - Lucie Frejlichová
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
| | - Jan Tříska
- Global Change Research Institute CAS, Bělidla 986/4a, 603 00 Brno, Czech Republic
| | - Aleš Eichmeier
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 691 44 Lednice na Moravě, Czech Republic
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18
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Wei Y, Lan G, Wu Z, Chen B, Quan F, Li M, Sun S, Du H. Phyllosphere fungal communities of rubber trees exhibited biogeographical patterns, but not bacteria. Environ Microbiol 2022; 24:3777-3790. [PMID: 35001480 DOI: 10.1111/1462-2920.15894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 11/28/2022]
Abstract
Phyllosphere microbiomes play an essential role in maintaining host health and productivity. Still, the diversity patterns and the drivers for the phyllosphere microbial community of the tropical cash crop Rubber tree (Hevea brasiliensis) - are poorly understood. We sampled the phyllosphere of field-grown rubber trees in South China. We examined the phyllosphere bacterial and fungal composition, diversity and main drivers of these microbes using the Illumina® sequencing and assembly. Fungal communities were distinctly different in different climatic regions (i.e. Xishuangbanna and Hainan Island) and climatic factors, especially mean annual temperature, and they were the main driving factors of foliar fungal communities, indicating fungal communities showed a geographical pattern. Significant differences of phyllosphere bacterial communities were detected in different habitats (i.e. endophytic and epiphytic). Most of the differences in taxa composition came from Firmicutes spp., which have been assigned as nitrogen-fixing bacteria. Since these bacteria cannot penetrate the cuticle like fungi, the abundant epiphytic Firmicutes spp. may supplement the deficiency of nitrogen acquisition. And the main factor influencing endophytic bacteria were internal factors, such as total nitrogen, total phosphorus and water content of leaves. External factors (i.e. climate) were the main driving force for epiphytic bacteria community assembly. Our work provides empirical evidence that the assembly of phyllosphere bacterial and fungal differed, which creates a precedent for preventing and controlling rubber tree diseases and pests and rubber tree yield improvement.
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Affiliation(s)
- Yaqing Wei
- College of Ecology and Environment, Hainan University, Haikou, 570228, China.,Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Bangqian Chen
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Fei Quan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Mingmei Li
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Shuqing Sun
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
| | - Haonan Du
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road, Haikou, Hainan, 571737, China.,Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, 571737, China
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Impact of Harvest on Switchgrass Leaf Microbial Communities. Genes (Basel) 2021; 13:genes13010022. [PMID: 35052362 PMCID: PMC8774549 DOI: 10.3390/genes13010022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022] Open
Abstract
Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.
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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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