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Thomas G, Kay WT, Fones HN. Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere. BMC Biol 2024; 22:168. [PMID: 39113027 PMCID: PMC11304629 DOI: 10.1186/s12915-024-01967-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/01/2024] [Indexed: 08/11/2024] Open
Abstract
Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.
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Affiliation(s)
| | - William T Kay
- Department of Plant Sciences, University of Oxford, Oxford, UK
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2
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [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: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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3
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Gruppuso L, Receveur JP, Fenoglio S, Bona F, Benbow ME. Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways. MICROBIAL ECOLOGY 2023; 86:1499-1512. [PMID: 36646914 PMCID: PMC10497695 DOI: 10.1007/s00248-023-02169-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: 06/20/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.
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Affiliation(s)
- L Gruppuso
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy.
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy.
| | - J P Receveur
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - S Fenoglio
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - F Bona
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - M E Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
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Luo K, Zhao G, Chen M, Tian X. Effects of maize resistance and leaf chemical substances on the structure of phyllosphere fungal communities. FRONTIERS IN PLANT SCIENCE 2023; 14:1241055. [PMID: 37645458 PMCID: PMC10461017 DOI: 10.3389/fpls.2023.1241055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
It is well known that plant genotype can regulate phyllosphere fungi at the species level. However, little is known about how plant varieties shape the fungal communities in the phyllosphere. In this study, four types of maize varieties with various levels of resistances to Exserohilum turcicum were subjected to high-throughput sequencing to reveal the properties that influences the composition of phyllosphere fungal communities. The dominant fungi genera for all four maize varieties were Alternaria at different relative abundances, followed by Nigrospora. Hierarchical clustering analysis, non-metric multidimensional scaling and similarity analysis confirmed that the fungal communities in the phyllosphere of the four varieties were significantly different and clustered into the respective maize variety they inhabited. The findings from Redundancy Analysis (RDA) indicated that both maize resistance and leaf chemical constituents, including nitrogen, phosphorus, tannins, and flavonoids, were the major drivers in determining the composition of phyllosphere fungal communities. Among these factors, maize resistance was found to be the most influential, followed by phosphorus. The co-occurrence network of the fungal communities in the phyllosphere of highly resistant variety had higher complexity, integrity and stability compared to others maize varieties. In a conclusion, maize variety resistance and leaf chemical constituents play a major role in shaping the phyllosphere fungal community. The work proposes a link between the assembled fungal communities within the phyllosphere with maize variety that is resistant to pathogenic fungi infection.
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Affiliation(s)
- Kun Luo
- Hunan Agricultural University, Changsha, Hunan, China
| | - Gonghua Zhao
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mengfei Chen
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xueliang Tian
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
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Zhu C, Lin Y, Wang Z, Luo W, Zhang Y, Chu C. Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem. Front Microbiol 2023; 14:1147285. [PMID: 37007520 PMCID: PMC10064055 DOI: 10.3389/fmicb.2023.1147285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant–epiphyte and plant–endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant–endophyte network, plant–epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.
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Affiliation(s)
- Chunchao Zhu
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
- *Correspondence: Chunchao Zhu,
| | | | - Zihui Wang
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Yonghua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
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Nageen Y, Wang X, Pecoraro L. Seasonal variation of airborne fungal diversity and community structure in urban outdoor environments in Tianjin, China. Front Microbiol 2023; 13:1043224. [PMID: 36699604 PMCID: PMC9869124 DOI: 10.3389/fmicb.2022.1043224] [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: 09/13/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Airborne fungi are ubiquitous in human living environments and may be a source of respiratory problems, allergies, and other health issues. A 12 months study was performed to investigate the diversity, concentration and community structure of culturable airborne fungi in different outdoor environments of Tianjin City, using an HAS-100B air sampler. A total of 1,015 fungal strains belonging to 175 species and 82 genera of Ascomycota 92.5%, Basidiomycota 7%, and Mucoromycota 0.3% were isolated and identified using morphological and molecular analysis. The most abundant fungal genera were Alternaria 35%, Cladosporium 18%, Penicillium 5.6%, Talaromyces 3.9%, Didymella 3%, and Aspergillus 2.8%, while the most frequently occurring species were A. alternata (24.7%), C. cladosporioides (11%), A. tenuissima (5.3%), P. oxalicum (4.53%), and T. funiculosus (2.66%). The fungal concentration ranged from 0 to 340 CFU/m3 during the whole study. Environmental factors, including temperature, relative humidity, wind speed, and air pressure exerted a varying effect on the presence and concentration of different fungal taxa. The four analyzed seasons showed significantly different airborne fungal communities, which were more strongly influenced by air temperature and relative humidity in spring and summer, whereas wind speed and air pressure had a stronger effect in autumn and winter. Fungal communities from green and busy sites did not show significant differences over the four analyzed seasons, which may be due to the effect of the surrounding environments characterized by high human activities on the air of the relatively small parks present in Tianjin. The present study provided valuable information on the seasonal dynamics and the environmental factors shaping the diversity and concentration of the analyzed outdoor airborne fungal communities, which can be of help for air quality monitoring, microbial contamination control, and health risk assessment in urban environments.
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Gouka L, Raaijmakers JM, Cordovez V. Ecology and functional potential of phyllosphere yeasts. TRENDS IN PLANT SCIENCE 2022; 27:1109-1123. [PMID: 35842340 DOI: 10.1016/j.tplants.2022.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/20/2022] [Accepted: 06/14/2022] [Indexed: 05/20/2023]
Abstract
The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans, both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts.
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Affiliation(s)
- Linda Gouka
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
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Martínez‐Arias C, Witzell J, Solla A, Martin JA, Rodríguez‐Calcerrada J. Beneficial and pathogenic plant-microbe interactions during flooding stress. PLANT, CELL & ENVIRONMENT 2022; 45:2875-2897. [PMID: 35864739 PMCID: PMC9543564 DOI: 10.1111/pce.14403] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 05/29/2023]
Abstract
The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.
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Affiliation(s)
- Clara Martínez‐Arias
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Johanna Witzell
- Department of Forestry and Wood TechnologyLinnaeus UniversityVäxjöSweden
| | - Alejandro Solla
- Faculty of Forestry, Institute for Dehesa Research (INDEHESA)Universidad de ExtremaduraPlasenciaSpain
| | - Juan Antonio Martin
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
| | - Jesús Rodríguez‐Calcerrada
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio NaturalUniversidad Politécnica de MadridMadridSpain
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Moharram AM, Zohri ANA, Hesham AEL, Abdel-Raheam HEF, Al-Ameen Maher M, Al-Bedak OAH. Production of cold-active pectinases by three novel Cladosporium species isolated from Egypt and application of the most active enzyme. Sci Rep 2022; 12:15599. [PMID: 36114347 PMCID: PMC9481535 DOI: 10.1038/s41598-022-19807-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/05/2022] [Indexed: 11/08/2022] Open
Abstract
Cladosporium parasphaerospermum, Cladosporium chlamydosporigenum, and Cladosporium compactisporum have all been discovered and characterized as new Cladosporium species. The three new species seemed to generate cold-active pectinases with high activity at pH 6.0 and 10 °C, pH 6.0 and 15 °C, and pH 5.0 and 15 °C, respectively, with the most active being C. parasphaerospermum pectinase. In submerged fermentation (SmF), C. parasphaerospermum produced the most cold-active pectinase with the highest activity and specific activity (28.84 U/mL and 3797 U/mg) after 8 days. C. parasphaerospermum cold-active pectinase was isolated using DEAE-Cellulose anion exchange resin and a Sephadex G 100 gel filtration column. The enzyme was purified 214.4-fold and 406.4-fold greater than the fermentation medium using DEAE-cellulose and Sephadex G 100, respectively. At pH 7.0 and 10 °C, pure pectinase had the highest activity (6684 U/mg), with Km and Vmax determined to be 26.625 mg/mL and 312.5 U/min, respectively. At 5 mM/mL, EDTA, MgCl2, and SDS inhibited the activity of pure pectinase by 99.21, 96.03, and 94.45%, respectively. The addition of 10 U/mL pure pectinase enhanced the yield of apple, orange, apricot, and peach juice by 17, 20, 13, and 24%, respectively, and improved the clarity and colour of orange juice by 194 and 339%, respectively. We can now add cold-active pectinase production to the long list of Cladosporium species that have been identified. We also report three new species that can be used in biotechnological solutions as active microbial pectinase producers. Although further research is needed, these distinct species might be used to decompose difficult and resistant pertinacious wastes as well as clear fruit juices.
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Affiliation(s)
- Ahmad Mohamed Moharram
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, 71511, Egypt
- Assiut University Mycological Centre, Assiut University, Assiut, 71511, Egypt
| | - Abdel-Naser Ahmed Zohri
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, 71511, Egypt
| | - Abd El-Latif Hesham
- Department of Genetics, Faculty of Agriculture, Beni-Suef University, Beni-Suef, Egypt.
| | | | - Mohamed Al-Ameen Maher
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, 71511, Egypt
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Suman A, Govindasamy V, Ramakrishnan B, Aswini K, SaiPrasad J, Sharma P, Pathak D, Annapurna K. Microbial Community and Function-Based Synthetic Bioinoculants: A Perspective for Sustainable Agriculture. Front Microbiol 2022; 12:805498. [PMID: 35360654 PMCID: PMC8963471 DOI: 10.3389/fmicb.2021.805498] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/29/2021] [Indexed: 11/29/2022] Open
Abstract
Interactions among the plant microbiome and its host are dynamic, both spatially and temporally, leading to beneficial or pathogenic relationships in the rhizosphere, phyllosphere, and endosphere. These interactions range from cellular to molecular and genomic levels, exemplified by many complementing and coevolutionary relationships. The host plants acquire many metabolic and developmental traits such as alteration in their exudation pattern, acquisition of systemic tolerance, and coordination of signaling metabolites to interact with the microbial partners including bacteria, fungi, archaea, protists, and viruses. The microbiome responds by gaining or losing its traits to various molecular signals from the host plants and the environment. Such adaptive traits in the host and microbial partners make way for their coexistence, living together on, around, or inside the plants. The beneficial plant microbiome interactions have been exploited using traditional culturable approaches by isolating microbes with target functions, clearly contributing toward the host plants' growth, fitness, and stress resilience. The new knowledge gained on the unculturable members of the plant microbiome using metagenome research has clearly indicated the predominance of particular phyla/genera with presumptive functions. Practically, the culturable approach gives beneficial microbes in hand for direct use, whereas the unculturable approach gives the perfect theoretical information about the taxonomy and metabolic potential of well-colonized major microbial groups associated with the plants. To capitalize on such beneficial, endemic, and functionally diverse microbiome, the strategic approach of concomitant use of culture-dependent and culture-independent techniques would help in designing novel "biologicals" for various crops. The designed biologicals (or bioinoculants) should ensure the community's persistence due to their genomic and functional abilities. Here, we discuss the current paradigm on plant-microbiome-induced adaptive functions for the host and the strategies for synthesizing novel bioinoculants based on functions or phylum predominance of microbial communities using culturable and unculturable approaches. The effective crop-specific inclusive microbial community bioinoculants may lead to reduction in the cost of cultivation and improvement in soil and plant health for sustainable agriculture.
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Affiliation(s)
- Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
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12
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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Katsoula A, Vasileiadis S, Karamanoli K, Vokou D, Karpouzas DG. Factors Structuring the Epiphytic Archaeal and Fungal Communities in a Semi-arid Mediterranean Ecosystem. MICROBIAL ECOLOGY 2021; 82:638-651. [PMID: 33594547 DOI: 10.1007/s00248-021-01712-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
The phyllosphere microbiome exerts a strong effect on plants' productivity, and its composition is determined by various factors. To date, most phyllosphere studies have focused on bacteria, while fungi and especially archaea have been overlooked. We studied the effects of plant host and season on the abundance and diversity of the epiphytic archaeal and fungal communities in a typical semi-arid Mediterranean ecosystem. We collected leaves in two largely contrasting seasons (summer and winter) from eight perennial species of varying attributes which could be grouped into the following: (i) high-canopy, evergreen sclerophyllοus shrubs with leathery leaves, and low-canopy, either semi-deciduous shrubs or non-woody perennials with non-leathery leaves, and (ii) aromatic and non-aromatic plants. We determined the abundance of epiphytic Crenarchaea, total fungi, Alternaria and Cladosporium (main airborne fungi) via q-PCR and the structure of the epiphytic archaeal and fungal communities via amplicon sequencing. We observed a strong seasonal effect with all microbial groups examined showing higher abundance in summer. Plant host and season were equally important determinants of the composition of the fungal community consisted mostly of Ascomycota, with Hypocreales dominating in winter and Capnodiales and Pleosporales in summer. In contrast, the archaeal community showed plant host driven patterns dominated by the Soil Crenarchaeotic Group (SCG) and Aenigmarchaeota. Plant habit and aromatic nature exhibited filtering effects only on the epiphytic fungal communities. Our study provides a first in-depth analysis of the key determinants shaping the phyllosphere archaeal and fungal communities of a semi-arid Mediterranean ecosystem.
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Affiliation(s)
- A Katsoula
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - S Vasileiadis
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece
| | - K Karamanoli
- School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - D Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - D G Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Viopolis, 41500, Larissa, Greece.
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Faticov M, Abdelfattah A, Roslin T, Vacher C, Hambäck P, Blanchet FG, Lindahl BD, Tack AJM. Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak. THE NEW PHYTOLOGIST 2021; 231:1770-1783. [PMID: 33960441 DOI: 10.1111/nph.17434] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/15/2021] [Indexed: 05/13/2023]
Abstract
Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multifactorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak Quercus robur across one growing season. Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially at the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming × genotype interactions on species richness and community composition. Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.
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Affiliation(s)
- Maria Faticov
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, A-8010, Austria
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, PO Box 7044, Uppsala, SE-756 51, Sweden
| | | | - Peter Hambäck
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - F Guillaume Blanchet
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département de Mathématique, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC, J1H 5N4, Canada
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, PO Box 7014, Uppsala, SE-750 07, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
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15
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Višňovská D, Pyszko P, Šigut M, Kostovčík M, Kolařík M, Kotásková N, Drozd P. Caterpillar gut and host plant phylloplane mycobiomes differ: a new perspective on fungal involvement in insect guts. FEMS Microbiol Ecol 2021; 96:5855491. [PMID: 32520323 DOI: 10.1093/femsec/fiaa116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Compared with the highly diverse microbiota of leaves, herbivorous insects exhibit impoverished gut microbial communities. Research to date has focused on the bacterial component of these gut microbiomes, neglecting the fungal component. As caterpillar gut bacterial microbiomes are derived strongly from their diet, we hypothesized that their mycobiomes would reflect the host leaf mycobiomes. Using the ITS2 rDNA and V5-V6 16S rRNA gene regions for DNA metabarcoding of caterpillar gut and host leaf sample pairs we compared their mycobiome genus diversity and compositions and identified genera associated with caterpillar guts. Leaves and caterpillar guts harbored different mycobiomes with quite low qualitative similarity (Jaccard index = 38.03%). The fungal genera most significantly associated with the caterpillar gut included Penicillium, Mucor and unidentified Saccharomycetales, whereas leaf-associated genera included Holtermanniella, Gibberella (teleomorph of Fusarium) and Seimatosporium. Although caterpillar gut and leaf mycobiomes had similar genus richness overall, this indicator was not correlated for individual duplets. Moreover, as more samples entered the analysis, mycobiome richness increased more rapidly in caterpillar guts than in leaves. The results suggest that the mycobiota of the caterpillar gut differs from that of their feeding substrate; further, the mycobiomes appear to be richer than the well-studied bacterial microbiotas.
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Affiliation(s)
- Denisa Višňovská
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Pyszko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Martin Šigut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Martin Kostovčík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, 128 44 Prague, Czech Republic
- BIOCEV, Institute of Microbiology, Academy of Sciences of the Czech Republic, Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Nela Kotásková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Pavel Drozd
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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16
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Casanova Navarro HM, Félix CR, Paulino GVB, Almeida JH, Valente P, Landell MF. Richness and biotechnological potential of the yeast community associated with the bromeliad phylloplane in the Brazilian Neotropical Forest. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01631-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Yao H, Sun X, He C, Li XC, Guo LD. Host identity is more important in structuring bacterial epiphytes than endophytes in a tropical mangrove forest. FEMS Microbiol Ecol 2020; 96:5800982. [PMID: 32149339 DOI: 10.1093/femsec/fiaa038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 03/05/2020] [Indexed: 01/24/2023] Open
Abstract
Interactions between plants and microbes are involved in biodiversity maintenance, community stability and ecosystem functioning. However, differences in the community and network structures between phyllosphere epiphytic and endophytic bacteria have rarely been investigated. Here, we examined phyllosphere epiphytic and endophytic bacterial communities of six mangrove species using Illumina MiSeq sequencing of the 16S rRNA gene. The results revealed that the community structure of epiphytic and endophytic bacteria was different. Plant identity significantly affected the diversity and community structure of both epiphytic and endophytic bacteria, with a greater effect on the community structure of the former than the latter. Network analysis showed that both plant-epiphytic and plant-endophytic bacterial network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the epiphytic bacterial network was more highly specialized and modular but less connected and more strongly anti-nested than the endophytic bacterial network. This study reveals that the phyllosphere epiphytic and endophytic bacterial community structures differ and plant identity has a greater effect on the epiphytic than on the endophytic bacteria, which may provide a comprehensive insight into the role of plant identity in driving the phyllosphere epiphytic and endophytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Hui Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Becker R, Ulrich K, Behrendt U, Kube M, Ulrich A. Analyzing Ash Leaf-Colonizing Fungal Communities for Their Biological Control of Hymenoscyphus fraxineus. Front Microbiol 2020; 11:590944. [PMID: 33193255 PMCID: PMC7649789 DOI: 10.3389/fmicb.2020.590944] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/02/2020] [Indexed: 01/17/2023] Open
Abstract
The invasive ascomycete Hymenoscyphus fraxineus has been threatening Fraxinus excelsior populations throughout Europe for over two decades. Since the infection and first colonization by the pathogen occurs in leaves, leaf-colonizing microorganisms have been discussed as a barrier and as possible biocontrol agents against the disease. To identify fungal groups with health-supporting potential, we compared the fungal microbiota of compound leaves from susceptible and tolerant ash trees in four ash stands with high H. fraxineus exposure. The fungal communities were analyzed both culture-independently by ITS2 amplicon sequencing and by the taxonomic classification of 1,704 isolates using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) or sequencing of the entire ITS region. The fungal community structure did not show significant differences depending on the health status. However, for several OTUs and a MALDI group, a significantly higher abundance was found in tolerant ash trees. Thus, the yeast Papiliotrema flavescens was significantly increased and accounted for 12.3% of the mycobiome of tolerant ashes (OTU0003), and it had also a distinctly higher abundance among the isolates. The filamentous ascomycete Sarocladium strictum was increased 24-fold among the isolates of tolerant trees, but its abundance was comparably low. An in vitro screening for the growth inhibition of the pathogen via cocultivation resulted in 28 yeast-like isolates and 79 filamentous fungi with antagonistic activity. A statistical cocultivation test on two H. fraxineus strains confirmed six of the yeast-like isolates that suppressed H. fraxineus significantly, from 39-50%, two of them through a fungicidal effect. The highest inhibition rates among the yeasts were found for three isolates belonging to Aureobasidium pullulans and P. flavescens. The cocultivation test of the filamentous isolates revealed higher effects compared to the yeasts. Four isolates showed significant inhibition of both H. fraxineus strains with a rate of 72-100%, and five further isolates inhibited only one H. fraxineus strain significantly. The most effective isolates were members of the genus Cladosporium. During the next step, in planta tests will be necessary to verify the efficacy of the antagonistic isolates and to assess their suitability as biocontrol agents.
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Affiliation(s)
- Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Michael Kube
- Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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19
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Farysia magdalena sp. nov. and description of the anamorph of Anthracocystis heteropogonicola from the Americas. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01610-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Kucharska K, Wachowska U, Czaplicki S. Wheat phyllosphere yeasts degrade propiconazole. BMC Microbiol 2020; 20:242. [PMID: 32758148 PMCID: PMC7409705 DOI: 10.1186/s12866-020-01885-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/29/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yeasts, which are ubiquitous in agroecosystems, are known to degrade various xenobiotics. The aim of this study was to analyze the effect of fungicides on the abundance of natural yeast communities colonizing winter wheat leaves, to evaluate the sensitivity of yeast isolates to fungicides in vivo, and to select yeasts that degrade propiconazole. RESULTS Fungicides applied during the growing season generally did not affect the counts of endophytic yeasts colonizing wheat leaves. Propiconazole and a commercial mixture of flusilazole and carbendazim decreased the counts of epiphytic yeasts, but the size of the yeast community was restored after 10 days. Epoxiconazole and a commercial mixture of fluoxastrobin and prothioconazole clearly stimulated epiphyte growth. The predominant species isolated from leaves were Aureobasidium pullulans and Rhodotorula glutinis. In the disk diffusion test, 14 out of 75 yeast isolates were not sensitive to any of the tested fungicides. After 48 h of incubation in an aqueous solution of propiconazole, the Rhodotorula glutinis Rg 55 isolate degraded the fungicide in 75%. Isolates Rh. glutinis Rg 92 and Rg 55 minimized the phytotoxic effects of propiconazole under greenhouse conditions. The first isolate contributed to an increase in the dry matter content of wheat seedlings, whereas the other reduced the severity of chlorosis. CONCLUSION Not sensitivity of many yeast colonizing wheat leaves on the fungicides and the potential of isolate Rhodotorula glutinis Rg 55 to degrade of propiconazole was established. Yeast may partially eliminate the ecologically negative effect of fungicides.
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Affiliation(s)
- Katarzyna Kucharska
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Environmental Management and Agriculture, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Urszula Wachowska
- Department of Entomology, Phytopathology and Molecular Diagnostics, Faculty of Environmental Management and Agriculture, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Sylwester Czaplicki
- Department of Food Plant Chemistry and Processing, Faculty of Food Sciences, University of Warmia and Mazury in Olsztyn, pl. Cieszyński 1, 10-726 Olsztyn, Poland
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21
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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22
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Haelewaters D, Toome-Heller M, Albu S, Aime MC. Red yeasts from leaf surfaces and other habitats: three new species and a new combination of Symmetrospora ( Pucciniomycotina, Cystobasidiomycetes). Fungal Syst Evol 2019; 5:187-196. [PMID: 32467923 PMCID: PMC7250012 DOI: 10.3114/fuse.2020.05.12] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Our understanding of the systematics of red yeasts has greatly improved with the availability of sequence data and it is now clear that the majority of these fungi belong to three different classes of Pucciniomycotina (Basidiomycota): Agaricostilbomycetes, Cystobasidiomycetes, and Microbotryomycetes. Despite improvements in phylogenetic placement, the taxonomy of these fungi has long been in need of revision and still has not been entirely resolved, partly due to missing taxa. In the present study, we present data of culture-based environmental yeast isolation, revealing several undescribed species of Symmetrospora, which was recently introduced to accommodate six species previously placed in the asexual genera Sporobolomyces and Rhodotorula in the gracilis/marina clade of Cystobasidiomycetes. Based on molecular phylogenetic analyses of three rDNA loci, morphology, and biochemical studies, we formally describe the following new species: Symmetrospora clarorosea sp. nov. from leaf surfaces in Portugal and the USA; S. pseudomarina sp. nov. from leaf surfaces in Brazil, and the USA and decaying wood in the USA; and S. suhii sp. nov. from a beetle gut in the USA, leaf surfaces in Brazil and marine water in the Taiwan and Thailand. Finally, we propose a new combination for Sporobolomyces oryzicola based on our molecular phylogenetic data, Symmetrospora oryzicola comb. nov.
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Affiliation(s)
- D Haelewaters
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - M Toome-Heller
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.,Current address: Plant Health and Environment Laboratory, Ministry for Primary Industries, 231 Morrin Road, Auckland 1072, New Zealand
| | - S Albu
- Department of Plant Pathology and Crop Physiology, Louisiana State University, 302 Life Science Building, Baton Rouge, LA 70803, USA.,Plant Pest Diagnostics Branch, California Department of Food & Agriculture, Sacramento, CA 95832, USA
| | - M C Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.,Department of Plant Pathology and Crop Physiology, Louisiana State University, 302 Life Science Building, Baton Rouge, LA 70803, USA
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23
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Kachalkin AV, Turchetti B, Inácio J, Carvalho C, Mašínová T, Pontes A, Röhl O, Glushakova AM, Akulov A, Baldrian P, Begerow D, Buzzini P, Sampaio JP, Yurkov AM. Rare and undersampled dimorphic basidiomycetes. Mycol Prog 2019. [DOI: 10.1007/s11557-019-01491-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Yao H, Sun X, He C, Maitra P, Li XC, Guo LD. Phyllosphere epiphytic and endophytic fungal community and network structures differ in a tropical mangrove ecosystem. MICROBIOME 2019; 7:57. [PMID: 30967154 PMCID: PMC6456958 DOI: 10.1186/s40168-019-0671-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/22/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Revealing the relationship between plants and fungi is very important in understanding biodiversity maintenance, community stability, and ecosystem functioning. However, differences in the community and network structures of phyllosphere epiphytic and endophytic fungi are currently poorly documented. In this study, we examined epiphytic and endophytic fungal communities associated with the leaves of six mangrove species using Illumina MiSeq sequencing of internal transcribed spacer 2 (ITS2) sequences. RESULTS A total of 635 operational taxonomic units (OTUs) of endophytic and epiphytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Tremellomycetes. Plant identity had a significant effect on the OTU richness of endophytic fungi, but not on epiphytic fungi. The community composition of epiphytic and endophytic fungi was significantly different, and plant identity had a greater effect on endophytic fungi than on epiphytic fungi. Network analysis showed that both epiphytic and endophytic network structures were characterized by significantly highly specialized and modular but lowly connected and anti-nested properties. Furthermore, the endophytic network had higher levels of specialization and modularity but lower connectance and stronger anti-nestedness than the epiphytic network. CONCLUSIONS This study reveals that the phyllosphere epiphytic and endophytic fungal communities differ, and plant identity has a greater effect on the endophytic fungi than on epiphytic fungi. These findings demonstrate the role of host plant identity in driving phyllosphere epiphytic and endophytic community structure.
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Affiliation(s)
- Hui Yao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Xiang Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Pulak Maitra
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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25
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Screening of Fusarium sp. for xylan and cellulose hydrolyzing enzymes and perspectives for the saccharification of delignified sugarcane bagasse. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Šibanc N, Zalar P, Schroers HJ, Zajc J, Pontes A, Sampaio JP, Maček I. Occultifur mephitis f.a., sp. nov. and other yeast species from hypoxic and elevated CO 2 mofette environments. Int J Syst Evol Microbiol 2018; 68:2285-2298. [DOI: 10.1099/ijsem.0.002824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Nataša Šibanc
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Polona Zalar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Hans-Josef Schroers
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova 17, 1000 Ljubljana, Slovenia
| | - Janja Zajc
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Ana Pontes
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, UCIBIO-REQUIMTE, 2829-516 Caparica, Portugal
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, UCIBIO-REQUIMTE, 2829-516 Caparica, Portugal
| | - Irena Maček
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies (FAMNIT), University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
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27
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de Vega C, Albaladejo RG, Guzmán B, Steenhuisen SL, Johnson SD, Herrera CM, Lachance MA. Flowers as a reservoir of yeast diversity: description of Wickerhamiella nectarea f.a. sp. nov., and Wickerhamiella natalensis f.a. sp. nov. from South African flowers and pollinators, and transfer of related Candida species to the genus Wickerhamiella as new combinations. FEMS Yeast Res 2018; 17:3966713. [PMID: 28810705 DOI: 10.1093/femsyr/fox054] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/13/2017] [Indexed: 11/14/2022] Open
Abstract
Flowers offer favourable microenvironments for yeast growth, and are increasingly recognised as a rich source of novel yeast species. Independent surveys of yeasts associated with flowers and pollinators in South Africa led to the discovery of 38 strains of two new species. Physiological profiles and analysis of the internal transcribed spacer and the D1/D2 domains of the large subunit rRNA gene showed that they represent two novel species that belong to the Wickerhamiella clade. We describe the species as Wickerhamiella nectarea f.a. sp. nov. (type strain EBDCdVSA11-1T, CBS 14162T, NRRL Y-63791T) and W. natalensis f.a. sp. nov. (type strain EBDCdVSA7-1T, CBS 14161T, NRRL Y-63790T). We extend the known range of flower-associated Wickerhamiella species to South Africa and discuss the ecology and phylogenetic relationships of the clade in relation to its host species and biogeography. Examination of growth characteristics supports that the Wickerhamiella clade exhibits a high degree of evolutionary lability, and that specialisation to different niches may occur rapidly. We review the current status of floral yeast biodiversity and nectar as a reservoir of species diversity, and the importance of pollinators and biogeography. In addition, 18 species formerly assigned to the genus Candida are reassigned formally to the genus Wickerhamiella.
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Affiliation(s)
- Clara de Vega
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida de Américo Vespucio s/n, 41092 Sevilla, Spain
| | - Rafael G Albaladejo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, C/ Profesor García González 2, 41012 Sevilla, Spain
| | - Beatriz Guzmán
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Sandy-Lynn Steenhuisen
- Department of Biological Sciences, University of Cape Town, P/Bag, Rondebosch 7701, South Africa
| | - Steven D Johnson
- School of Life Sciences, University of KwaZulu-Natal, P/ Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
| | - Carlos M Herrera
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avenida de Américo Vespucio s/n, 41092 Sevilla, Spain
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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Nutaratat P, Monprasit A, Srisuk N. High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits. 3 Biotech 2017; 7:305. [PMID: 28948133 DOI: 10.1007/s13205-017-0937-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/04/2017] [Indexed: 11/24/2022] Open
Abstract
Enterobacter sp. DMKU-RP206 was isolated from rice leaves in Thailand and identified by the 16S rRNA gene and multilocus sequence (gyrB, rpoB, atpD, and infB genes) analysis. The bacterium was assessed on plant growth-promoting traits including indole-3-acetic acid (IAA) production. Phosphate solubilization, ammonia production, and antagonism to fungal plant pathogens, as well as siderophore production, were shown by this bacterium. However, only IAA production was focused on. The production of IAA by Enterobacter sp. DMKU-RP206 was optimized by statistical methods. A Box-Behnken design was used for the investigation of interactions among the basic influencing factors and for the optimization of IAA production. The results showed that l-tryptophan had a significant importance in terms of IAA production. Enterobacter sp. DMKU-RP206 produced a higher amount of IAA than previously reported for the genus Enterobacter. 0.85% of lactose as a carbon source, 1.3% of yeast extract as a nitrogen source, 1.1% of l-tryptophan as a precursor, 0.4% of NaCl, an initial pH of 5.8, an incubation temperature at 30 °C, and a shaking speed of 200 rpm were found to be the optimum conditions for IAA production. In addition, IAA production was performed to scale up IAA production, and the highest amount, 5561.7 mg l-1, was obtained. This study reported a 13.4-fold improvement in IAA production by Enterobacter sp. DMKU-RP206.
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Affiliation(s)
- Pumin Nutaratat
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900 Thailand
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok, 10900 Thailand
| | - Apitchaya Monprasit
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900 Thailand
| | - Nantana Srisuk
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900 Thailand
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok, 10900 Thailand
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The isolation and characterization of resident yeasts from the phylloplane of Arabidopsis thaliana. Sci Rep 2016; 6:39403. [PMID: 28004784 PMCID: PMC5177952 DOI: 10.1038/srep39403] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/23/2016] [Indexed: 11/08/2022] Open
Abstract
The genetic model plant Arabidopsis thaliana (arabidopsis) has been instrumental to recent advances in our understanding of the molecular function of the plant immune system. However, this work has not yet included plant associated and phytopathogenic yeasts largely due to a lack of yeast species known to interact with arabidopsis. The plant phylloplane is a significant habitat for neutral-residents, plant-growth and health-promoting species, and latent-pathogenic species. However, yeast phylloplane residents of arabidopsis remain underexplored. To address this, resident yeasts from the phyllosphere of wild arabidopsis collected in field conditions have been isolated and characterized. A total of 95 yeast strains representing 23 species in 9 genera were discovered, including potentially psychrophilic and pathogenic strains. Physiological characterization revealed thermotolerance profiles, sensitivity to the arabidopsis phytoalexin camalexin, the production of indolic compounds, and the ability to activate auxin responses in planta. These results indicate a rich diversity of yeasts present in the arabidopsis phylloplane and have created culture resources and information useful in the development of model systems for arabidopsis-yeast interactions.
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Batool F, Rehman Y, Hasnain S. Phylloplane associated plant bacteria of commercially superior wheat varieties exhibit superior plant growth promoting abilities. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1256842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Characterization of basidiomycetous yeasts in hypersaline soils of the Urmia Lake National Park, Iran. Extremophiles 2016; 20:915-928. [DOI: 10.1007/s00792-016-0883-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
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Laforest-Lapointe I, Messier C, Kembel SW. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species. PeerJ 2016; 4:e2367. [PMID: 27635335 PMCID: PMC5012278 DOI: 10.7717/peerj.2367] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/25/2016] [Indexed: 11/20/2022] Open
Abstract
Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual samples from consistent positions within the tree canopy from multiple individuals per species can be used to accurately quantify variation in phyllosphere bacterial community structure. However, the considerable amount of intra-individual variation within a tree canopy ask for a better understanding of how changes in leaf characteristics and local abiotic conditions drive spatial variation in the phyllosphere microbiome.
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Affiliation(s)
- Isabelle Laforest-Lapointe
- Centre d'étude de la forêt, Montreal, Canada; Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada
| | - Christian Messier
- Centre d'étude de la forêt, Montreal, Canada; Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada; ISFORT - Institut des Sciences de la Forêt Tempérée, Université du Québec en Outaouais, Ripon, Quebec, Canada
| | - Steven W Kembel
- Centre d'étude de la forêt, Montreal, Canada; Sciences Biologiques, Université du Québec à Montréal, Montreal, Quebec, Canada
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Nutaratat P, Srisuk N, Arunrattiyakorn P, Limtong S. Indole-3-acetic acid biosynthetic pathways in the basidiomycetous yeast Rhodosporidium paludigenum. Arch Microbiol 2016; 198:429-37. [DOI: 10.1007/s00203-016-1202-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 11/24/2022]
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Cystofilobasidium intermedium sp. nov. and Cystofilobasidium alribaticum f.a. sp. nov., isolated from Mediterranean forest soils. Int J Syst Evol Microbiol 2016; 66:1058-1062. [DOI: 10.1099/ijsem.0.000835] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Cappelletti M, Perazzolli M, Antonielli L, Nesler A, Torboli E, Bianchedi PL, Pindo M, Puopolo G, Pertot I. Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine. FRONTIERS IN PLANT SCIENCE 2016; 7:1053. [PMID: 27486468 PMCID: PMC4949236 DOI: 10.3389/fpls.2016.01053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/05/2016] [Indexed: 05/20/2023]
Abstract
Protein derivatives and carbohydrates can stimulate plant growth, increase stress tolerance, and activate plant defense mechanisms. However, these molecules can also act as a nutritional substrate for microbial communities living on the plant phyllosphere and possibly affect their biocontrol activity against pathogens. We investigated the mechanisms of action of a protein derivative (nutrient broth, NB) against grapevine downy mildew, specifically focusing on the effects of foliar treatments on plant defense stimulation and on the composition and biocontrol features of the phyllosphere microbial populations. NB reduced downy mildew symptoms and induced the expression of defense-related genes in greenhouse- and in vitro-grown plants, indicating the activation of grapevine resistance mechanisms. Furthermore, NB increased the number of culturable phyllosphere bacteria and altered the composition of bacterial and fungal populations on leaves of greenhouse-grown plants. Although, NB-induced changes on microbial populations were affected by the structure of indigenous communities originally residing on grapevine leaves, degrees of disease reduction and defense gene modulation were consistent among the experiments. Thus, modifications in the structure of phyllosphere populations caused by NB application could partially contribute to downy mildew control by competition for space or other biocontrol strategies. Particularly, changes in the abundance of phyllosphere microorganisms may provide a contribution to resistance induction, partially affecting the hormone-mediated signaling pathways involved. Modifying phyllosphere populations by increasing natural biocontrol agents with the application of selected nutritional factors can open new opportunities in terms of sustainable plant protection strategies.
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Affiliation(s)
- Martina Cappelletti
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
- Department of Agricultural and Environmental Sciences, University of UdineUdine, Italy
| | - Michele Perazzolli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
- *Correspondence: Michele Perazzolli
| | - Livio Antonielli
- Bioresources Unit, Department of Health and Environment, Austrian Institute of TechnologyTulln and der Donau, Austria
| | - Andrea Nesler
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Esmeralda Torboli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Pier L. Bianchedi
- Technology Transfer Center, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Massimo Pindo
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Gerardo Puopolo
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Ilaria Pertot
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
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Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment. Urban Ecosyst 2015. [DOI: 10.1007/s11252-015-0514-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Yurkov AM, Röhl O, Pontes A, Carvalho C, Maldonado C, Sampaio JP. Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands and scrub biome. FEMS Yeast Res 2015; 16:fov103. [PMID: 26568202 DOI: 10.1093/femsyr/fov103] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2015] [Indexed: 11/12/2022] Open
Abstract
Soil yeasts represent a poorly known fraction of the soil microbiome due to limited ecological surveys. Here, we provide the first comprehensive inventory of cultivable soil yeasts in a Mediterranean ecosystem, which is the leading biodiversity hotspot for vascular plants and vertebrates in Europe. We isolated and identified soil yeasts from forested sites of Serra da Arrábida Natural Park (Portugal), representing the Mediterranean forests, woodlands and scrub biome. Both cultivation experiments and the subsequent species richness estimations suggest the highest species richness values reported to date, resulting in a total of 57 and 80 yeast taxa, respectively. These values far exceed those reported for other forest soils in Europe. Furthermore, we assessed the response of yeast diversity to microclimatic environmental factors in biotopes composed of the same plant species but showing a gradual change from humid broadleaf forests to dry maquis. We observed that forest properties constrained by precipitation level had strong impact on yeast diversity and on community structure and lower precipitation resulted in an increased number of rare species and decreased evenness values. In conclusion, the structure of soil yeast communities mirrors the environmental factors that affect aboveground phytocenoses, aboveground biomass and plant projective cover.
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Affiliation(s)
- Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Brunswick, Germany
| | - Oliver Röhl
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Pontes
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cláudia Carvalho
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Cristina Maldonado
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Sapkota R, Knorr K, Jørgensen LN, O'Hanlon KA, Nicolaisen M. Host genotype is an important determinant of the cereal phyllosphere mycobiome. THE NEW PHYTOLOGIST 2015; 207:1134-44. [PMID: 25898906 DOI: 10.1111/nph.13418] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/16/2015] [Indexed: 05/10/2023]
Abstract
The phyllosphere mycobiome in cereals is an important determinant of crop health. However, an understanding of the factors shaping this community is lacking. Fungal diversity in leaves from a range of cultivars of winter wheat (Triticum aestivum), winter and spring barley (Hordeum vulgare) and a smaller number of samples from oat (Avena sativa), rye (Secale cereale) and triticale (Triticum × Secale) was studied using next-generation sequencing. The effects of host genotype, fungicide treatment and location on fungal communities were explored. In total, 635 251 fungal internal transcribed spacer (ITS) reads were obtained from 210 leaf samples. Visual disease assessments and relative read abundance of Zymoseptoria tritici and Ramularia collo-cygni were strongly positively related. Crop genotype at the species level explained 43% of the variance in the total dataset, followed by fungicide treatment (13%) and location (4%). Indicator species, including plant pathogens, responding to factors such as crop species, location and treatment were identified. Host genotype at both the species and cultivar level is important in shaping phyllosphere fungal communities, whereas fungicide treatment and location have minor effects. We found many host-specific fungal pathogens, but also a large diversity of fungi that were relatively insensitive to host genetic background, indicating that host-specific pathogens live in a 'sea' of nonspecific fungi.
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Affiliation(s)
- Rumakanta Sapkota
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK4200, Slagelse, Denmark
| | - Kamilla Knorr
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK4200, Slagelse, Denmark
| | - Lise Nistrup Jørgensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK4200, Slagelse, Denmark
| | | | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, DK4200, Slagelse, Denmark
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Imazaki I, Kadota I. Molecular phylogeny and diversity of Fusarium endophytes isolated from tomato stems. FEMS Microbiol Ecol 2015; 91:fiv098. [PMID: 26298015 DOI: 10.1093/femsec/fiv098] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2015] [Indexed: 11/14/2022] Open
Abstract
Plant tissues are a known habitat for two types of Fusarium species: plant pathogens and endophytes. Here, we investigated the molecular phylogeny and diversity of endophytic fusaria, because endophytes are not as well studied as pathogens. A total of 543 Fusarium isolates were obtained from the inside of tomato stems cultivated in soils mainly obtained from agricultural fields. We then determined partial nucleotide sequences of the translation elongation factor-1 alpha (EF-1α) genes of the isolates. Among the isolates from tomato, 24 EF-1α gene sequence types (EFST) were found: nine were classified as being from the Fusarium oxysporum species complex and its sister taxa (FOSC, 332 isolates), seven from the F. fujikuroi species complex (FFSC, 75 isolates) and eight from the F. solani species complex (FSSC, 136 isolates). To determine more characteristic details of the tomato isolates, we isolated 180 fusaria directly from soils and found 95% of them were nested within the FOSC (82 isolates; five EFSTs), FFSC (21 isolates; six FESTs) and FSSC (68 isolates; 11 EFSTs). These results suggested that the dominant Fusarium endophytes within tomato stems were members of the same three species complexes, which were also the dominant fusaria in the soils.
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Affiliation(s)
- Iori Imazaki
- NARO Tohoku Agricultural Research Center, Morioka, Japan
| | - Ikuo Kadota
- NARO Tohoku Agricultural Research Center, Morioka, Japan
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Jindamorakot S, Am-In S, Kaewwichian R, Limtong S. Yamadazyma insecticola f.a., sp. nov. and Yamadazyma epiphylla f.a., sp. nov., two novel yeast species. Int J Syst Evol Microbiol 2015; 65:1290-1296. [DOI: 10.1099/ijs.0.000100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yeast strains representing two novel yeast species were isolated from frass of an unidentified insect (ST-78T) and the external surfaces of rice leaves (YE170T) collected in Thailand. The two strains were genetically, morphologically and phenotypically distinct from recognized species and were found to represent two novel species of the genus Yamadazyma although formation of ascospores was not observed. In terms of pairwise sequence similarity of the D1/D2 region of the large subunit rRNA gene, the closest relative of strain ST-78T was Candida lessepsii CBS 9941T but with 3.8 % nucleotide substitutions, while the closest relative of strain YE170T was strain ST-78T but with 4.3 % nucleotide substitutions. Analysis of the sequences of the internal transcribed spacer 1 and 2 (ITS1–2) regions revealed that strain ST-78 differed from C. lessepsii CBS 9941T by 8.8 % nucleotide substitutions and from strain YE170T by 9.4 % nucleotide substitutions. The result of pairwise sequence similarity of the D1/D2 and ITS1–2 regions together with phylogenetic analysis indicated that strains ST-78T and YE170T represented two novel species within the Yamadazyma clade. The names Yamadazyma insecticola f.a., sp. nov. (type strain ST-78T = BCC 8314T = NBRC 110421T = CBS 13382T; MycoBank no. MB810546) and Yamadazyma epiphylla f.a., sp. nov. (type strain YE170T = BCC 63466T = NBRC 110423T = CBS 13384T; MycoBank no. MB810547) are proposed for the two novel yeast species.
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Affiliation(s)
- Sasitorn Jindamorakot
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Somjit Am-In
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Rungluk Kaewwichian
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Savitree Limtong
- Center for Advanced Studies in Tropical Natural Resources, National Research University Kasetsart University, Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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Microbial Life on Green Biomass and Their Use for Production of Platform Chemicals. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Khunnamwong P, Surussawadee J, Jindamorakot S, Limtong S. W
ickerhamiella siamensis f.a., sp. nov., an endophytic and epiphytic yeast species isolated from sugar cane leaf. Int J Syst Evol Microbiol 2014; 64:3849-3855. [DOI: 10.1099/ijs.0.067702-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six strains representing a novel yeast species were isolated from tissue (DMKU-SE106T, DMKU-SE110, DMKU-SE112 and DMKU-SE132) and the external surface (DMKU-SP335 and DMKU-SP406) of sugar cane leaves collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 region of the LSU rRNA gene and the internal transcribed spacer (ITS) region, the six strains were found to represent a single novel species of the genus Wickerhamiella although the formation of ascospores was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and ITS region of the six strains differed from each other by 0–2 and 2–3 nt substitutions, respectively. The novel species was related most closely to Candida infanticola but with 4.5–4.6 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene and 6.6–7.1 % nucleotide substitutions in the ITS region. The name Wickerhamiella siamensis f.a., sp. nov. is proposed. The type strain is DMKU-SE106T ( = BCC 61185T = NBRC 109697T = CBS 13331T).
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Affiliation(s)
- Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Janjira Surussawadee
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sasitorn Jindamorakot
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani, Thailand
| | - Savitree Limtong
- Center for Advanced Studied in Tropical Natural Resources, National Research University Kasetsart University, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
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Abu-Ghosh S, Droby S, Korine C. Seasonal and plant-dependent variations in diversity, abundance and stress tolerance of epiphytic yeasts in desert habitats. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:373-382. [PMID: 24992536 DOI: 10.1111/1758-2229.12161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 03/01/2014] [Indexed: 06/03/2023]
Abstract
We studied the epiphytic yeast species of the plants of the Negev Desert and the Dead Sea region, Israel, which are considered one of the most extreme hyper-arid lands in the world. For this purpose, we developed isolation protocols; we performed morphological, cultural and molecular identification tests and compared yeast diversity between the locations and the plants. The composition of the yeast populations present in the study's plants underwent seasonal fluctuations, whereas differences in community compositions were significant within sites. The maximum number of species of yeast occurred in autumn and Cryptococcus spp. were predominant year round. The isolated yeast strains showed an unusual tolerance to extreme growth conditions, such as high temperatures (up to 72% viability at 50°C), lethal hydrogen peroxide and NaCl concentrations. These results suggest that epiphytic yeasts inhabit the plants of the Dead Sea region and the Negev Desert have a community structure that is unique to the plant species and have a high tolerance to the harsh conditions that enables them to adapt to an arid ecosystem.
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Affiliation(s)
- Said Abu-Ghosh
- Department of Postharvest Science, The Volcani Center, Agricultural Research Organization (ARO), Bet Dagan, 50250, Israel
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Surussawadee J, Khunnamwong P, Srisuk N, Limtong S. Papiliotrema siamense f.a., sp. nov., a yeast species isolated from plant leaves. Int J Syst Evol Microbiol 2014; 64:3058-3062. [PMID: 24925598 DOI: 10.1099/ijs.0.065607-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains representing a novel species were isolated from the external surface of a sugar cane leaf (DMKU-SP85(T)) and tissue of a rice leaf (DMKU-RE97) collected in Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, the two strains were determined to represent a novel species of the genus Papiliotrema although sexual reproduction was not observed. The sequences of the D1/D2 region of the LSU rRNA gene and ITS region of the two strains were identical, but differed from those of the type strain of Cryptococcus nemorosus by 0.6 % nucleotide substitutions (four nucleotide substitutions out of 597 nucleotides) in the D1/D2 region of the LSU rRNA gene and 1.8 % nucleotide substitutions (nine nucleotide substitutions out of 499 nucleotides) in the ITS region. The name Papiliotrema siamense f.a., sp. nov. is proposed. The type strain is DMKU-SP85(T)( = BCC 69499(T) = CBS 13330(T)).
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Affiliation(s)
- Janjira Surussawadee
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pannida Khunnamwong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Nantana Srisuk
- Center for Advanced Studies in Tropical Natural Resources, National Research University, Kasetsart University, Thailand.,Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Savitree Limtong
- Center for Advanced Studies in Tropical Natural Resources, National Research University, Kasetsart University, Thailand.,Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
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Introduction of Aureobasidium pullulans to the Phyllosphere of Organically Grown Strawberries with Focus on Its Establishment and Interactions with the Resident Microbiome. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3040704] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Ferreira AS, Sampaio A, Maduro AP, Silva I, Teles F, Martins MDL, Inácio J. Genotypic diversity of environmentalCryptococcus neoformansisolates from Northern Portugal. Mycoses 2013; 57:98-104. [DOI: 10.1111/myc.12106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 05/27/2013] [Accepted: 06/11/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Ana Sofia Ferreira
- Laboratório Nacional de Investigação Veterinária; Instituto Nacional de Investigação Agrária e Veterinária; Lisbon Portugal
- Microbiology Unit; Instituto de Higiene e Medicina Tropical; Universidade Nova de Lisboa; Lisbon Portugal
| | - Ana Sampaio
- Departamento de Biologia e Ambiente; Centro de Investigação e de Tecnologias Agroambientais e Biológicas (CITAB); Universidade de Trás-os-Montes e Alto Douro (UTAD); Vila Real Portugal
| | - Ana Paula Maduro
- Microbiology Unit; Instituto de Higiene e Medicina Tropical; Universidade Nova de Lisboa; Lisbon Portugal
| | - Inês Silva
- Microbiology Unit; Instituto de Higiene e Medicina Tropical; Universidade Nova de Lisboa; Lisbon Portugal
| | - Fernando Teles
- Microbiology Unit; Instituto de Higiene e Medicina Tropical; Universidade Nova de Lisboa; Lisbon Portugal
- Centre for Malaria and Tropical Diseases; Instituto de Higiene e Medicina Tropical; Universidade Nova de Lisboa; Lisbon Portugal
| | - Maria da Luz Martins
- Microbiology Unit; Instituto de Higiene e Medicina Tropical; Universidade Nova de Lisboa; Lisbon Portugal
- Faculdade de Ciências e Tecnologia; Departamento de Ciências da Vida; Centro de Recursos Microbiológicos; Universidade Nova de Lisboa; Lisbon Portugal
| | - João Inácio
- Laboratório Nacional de Investigação Veterinária; Instituto Nacional de Investigação Agrária e Veterinária; Lisbon Portugal
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Cordier T, Robin C, Capdevielle X, Desprez-Loustau ML, Vacher C. Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.12.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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49
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Cordier T, Robin C, Capdevielle X, Fabreguettes O, Desprez-Loustau ML, Vacher C. The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica) varies significantly along an elevation gradient. THE NEW PHYTOLOGIST 2012; 196:510-519. [PMID: 22934891 DOI: 10.1111/j.1469-8137.2012.04284.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
Little is known about the potential effect of climate warming on phyllosphere fungi, despite their important impact on the dynamics and diversity of plant communities. The structure of phyllosphere fungal assemblages along elevation gradients may provide information about this potential effect, because elevation gradients correspond to temperature gradients over short geographic distances. We thus investigated variations in the composition of fungal assemblages inhabiting the phyllosphere of European beech (Fagus sylvatica) at four sites over a gradient of 1000 m of elevation in the French Pyrénées Mountains, by using tag-encoded 454 pyrosequencing. Our results show that the composition of fungal assemblages varied significantly between elevation sites, in terms of both the relative abundance and the presence-absence of species, and that the variations in assemblage composition were well correlated with variations in the average temperatures. Our results therefore suggest that climate warming might alter both the incidence and the abundance of phyllosphere fungal species, including potential pathogens. For example, Mycosphaerella punctiformis, a causal agent of leaf spots, showed decreasing abundance with elevation and might therefore shift to higher elevations in response to warming.
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Affiliation(s)
- Tristan Cordier
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- University of Bordeaux, UMR1202 BIOGECO, F-33400, Talence, France
| | - Cécile Robin
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- University of Bordeaux, UMR1202 BIOGECO, F-33400, Talence, France
| | - Xavier Capdevielle
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- University of Bordeaux, UMR1202 BIOGECO, F-33400, Talence, France
| | - Olivier Fabreguettes
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- University of Bordeaux, UMR1202 BIOGECO, F-33400, Talence, France
| | - Marie-Laure Desprez-Loustau
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- University of Bordeaux, UMR1202 BIOGECO, F-33400, Talence, France
| | - Corinne Vacher
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- University of Bordeaux, UMR1202 BIOGECO, F-33400, Talence, France
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Peñuelas J, Rico L, Ogaya R, Jump AS, Terradas J. Summer season and long-term drought increase the richness of bacteria and fungi in the foliar phyllosphere of Quercus ilex in a mixed Mediterranean forest. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:565-575. [PMID: 22289059 DOI: 10.1111/j.1438-8677.2011.00532.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We explored the changes in richness, diversity and evenness of epiphytic (on the leaf surface) and endophytic (within leaf tissues) bacteria and fungi in the foliar phyllosphere of Quercus ilex, the dominant tree species of Mediterranean forests. Bacteria and fungi were assessed during ontogenic development of the leaves, from the wet spring to the dry summer season in control plots and in plots subjected to drought conditions mimicking those projected for future decades. Our aim was to monitor succession in microbiota during the colonisation of plant leaves and its response to climate change. Ontogeny and seasonality exerted a strong influence on richness and diversity of the microbial phyllosphere community, which decreased in summer in the whole leaf and increased in summer in the epiphytic phyllosphere. Drought precluded the decrease in whole leaf phyllosphere diversity and increased the rise in the epiphytic phyllosphere. Both whole leaf bacterial and fungal richness decreased with the decrease in physiological activity and productivity of the summer season in control trees. As expected, the richness of epiphytic bacteria and fungi increased in summer after increasing time of colonisation. Under summer dry conditions, there was a positive relationship between TRF (terminal restriction fragments) richness and drought, both for whole leaf and epiphytic phyllosphere, and especially for fungal communities. These results demonstrate that changes in climate are likely to significantly alter microbial abundance and composition of the phyllosphere. Given the diverse functions and large number of phyllospheric microbes, the potential functional implications of such community shifts warrant exploration.
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Affiliation(s)
- J Peñuelas
- Global Ecology Unit, Center for Ecological Research and Forestry Applications, Universitat Autònoma Barcelona, Bellaterra, Spain.
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