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Huang L, Fu Y, Liu Y, Chen Y, Wang T, Wang M, Lin X, Feng Y. Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172231. [PMID: 38608902 DOI: 10.1016/j.scitotenv.2024.172231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.
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Affiliation(s)
- Lukuan Huang
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingyi Fu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yaru Liu
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yijie Chen
- IDEO Play Lab, CA 91006, United States of America
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, China
| | - Xianyong Lin
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Feng
- Key Laboratory of Environment Remediation and Ecological Health of Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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Pushpavathi D, Krishnamurthy YL. Study on endolichenic fungal assemblage in Parmotrema and Heterodermia lichens of Shivamoga, Karnataka. Mol Biol Rep 2024; 51:549. [PMID: 38642168 DOI: 10.1007/s11033-024-09497-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Lichen is a symbiotic association of algae and fungi, recognized as a self-sustaining ecosystem that constitutes an indeterminant number of bacteria, actinomycetes, fungi, and protozoa. We evaluated the endolichenic fungal assemblage given the dearth of knowledge on endolichenic fungi (ELFs), particularly from part of the Central Western Ghats, Karnataka, and conducted a phylogenetic analysis of xylariaceous fungi, the most diversified group of fungi using ITS and ITS+Tub2 gene set. RESULTS Out of 17 lichen thalli collected from 5 ecoregions, 42 morphospecies recovered, belong to the class Sordariomycetes, Eurotiomycetes, Dothideomycetes, Leotiomycetes, Saccharomycetes. About 19 and 13 ELF genera have been reported from Parmotrema and Heterodermia thallus. Among the ecoregions EC2 showing highest species diversity (Parmotrema (1-D) = 0.9382, (H) = 2.865, Fisher-α = 8.429, Heterodermia (1-D) = 0.8038, H = 1.894, F-α = 4.57) followed the EC3 and EC1. Xylariales are the predominant colonizer reported from at least one thallus from four ecoregions. The morphotypes ELFX04, ELFX05, ELFX08 and ELFX13 show the highest BLAST similarity (> 99%) with Xylaria psidii, X. feejeensis, X. berteri and Hypoxylon fragiforme respectively. Species delimitation and phylogenetic position reveal the closest relation of Xylariaceous ELFs with plant endophytes. CONCLUSIONS The observation highlights that the deciduous forest harness a high number of endolichenic fungi, a dominant portion of these fungi are non-sporulating and still exist as cryptic. Overall, 8 ELF species recognized based on phylogenetic analysis, including the two newly reported fungi ELFX03 and ELFX06 which are suspected to be new species based on the present evidence. The study proved, that the lichen being rich source to establish fungal diversity and finding new species. Successful amplification of most phylogenetic markers like RPB2, building of comprehensive taxonomic databases and application of multi-omics data are further needed to understand the complex nature of lichen-fungal symbiosis.
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Affiliation(s)
- D Pushpavathi
- Department of PG Studies and Research in Applied Botany, Kuvempu University, Jnanasahyadri, Shankaraghatta, Karnataka, 577451, India
| | - Y L Krishnamurthy
- Department of PG Studies and Research in Applied Botany, Kuvempu University, Jnanasahyadri, Shankaraghatta, Karnataka, 577451, India.
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Yang J, Woo JJ, Oh SY, Kim W, Hur JS. Fungal community inside lichen: a curious case of sparse diversity and high modularity. ENVIRONMENTAL MICROBIOME 2023; 18:73. [PMID: 37789449 PMCID: PMC10548754 DOI: 10.1186/s40793-023-00531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Lichens represent not only the mutualism of fungal and photosynthetic partners but also are composed of microbial consortium harboring diverse fungi known as endolichenic fungi. While endolichenic fungi are known to exert a remarkable influence on lichen ecology through their crucial roles in nutrient cycling, bioprospecting and biodiversity, the enigmatic community structures of these fungal inhabitants remain shrouded in mystery, awaiting further exploration and discovery. To address knowledge gap, we conducted metabarcoding on two lichens using 18S gene amplification, Dirinara applanta and Parmotrema tinctorum, and compared their microbial communities to those found in the pine bark to which the lichens were attached. Our hypothesis was that the endolichenic communities would exhibit distinct diversity patterns, community structures, network structures, and specialist composition compared to the surrounding epiphytic community. RESULTS Our investigation has shed light on the clear demarcation between the endolichenic and epiphytic fungal communities, as they exhibit markedly different characteristics that set them apart from each other. This research demonstrated that the endolichenic communities are less diverse as compared to the epiphytic communities. Through community similarity analysis, we observed that two endolichenic communities are more similar to each other in terms of community composition than with the adjacent epiphytic communities. Moreover, we unveiled a striking contrast in the network structures between the endolichenic and epiphytic communities, as the former displayed a more modular and less nested features that is evocative of a potent host-filtration mechanism. CONCLUSIONS Through our investigation, we have discovered that lichens harbor less intricate and interconnected fungal communities compared to the neighboring epiphytic environment. These observations provide valuable insights into the metagenomic architecture of lichens and offer a tantalizing glimpse into the unique mycobiome.
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Affiliation(s)
- Jiho Yang
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-ro, Suncheon, 57922, South Korea
- Department of Biology, Sunchon National University, 255 Jungang-ro, Suncheon, 57922, South Korea
| | - Jung-Jae Woo
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-ro, Suncheon, 57922, South Korea
- Department of Biology, Sunchon National University, 255 Jungang-ro, Suncheon, 57922, South Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, 20 Changwondaehak-ro, Changwon, 51140, South Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-ro, Suncheon, 57922, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, 255 Jungang-ro, Suncheon, 57922, South Korea.
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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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Miral A, Jargeat P, Mambu L, Rouaud I, Tranchimand S, Tomasi S. Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation methods. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:856-872. [PMID: 35860838 PMCID: PMC9796121 DOI: 10.1111/1758-2229.13105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/06/2022] [Accepted: 04/22/2022] [Indexed: 05/13/2023]
Abstract
Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture-dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non-studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture-dependent techniques.
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Affiliation(s)
- Alice Miral
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)‐UMR 6226RennesFrance
| | - Patricia Jargeat
- UMR 5174 UPS‐CNRS‐IRD Laboratoire Evolution et Diversité Biologique, EDBUniversité Toulouse‐3, Bât 4R1ToulouseFrance
| | - Lengo Mambu
- EA 7500 Laboratoire PEIRENE, Faculté de PharmacieUniversité de LimogesLimoges CedexFrance
| | - Isabelle Rouaud
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)‐UMR 6226RennesFrance
| | - Sylvain Tranchimand
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)‐UMR 6226Université de RennesRennesFrance
| | - Sophie Tomasi
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)‐UMR 6226RennesFrance
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Yang JH, Oh SY, Kim W, Hur JS. Endolichenic Fungal Community Analysis by Pure Culture Isolation and Metabarcoding: A Case Study of Parmotrema tinctorum. MYCOBIOLOGY 2022; 50:55-65. [PMID: 35291596 PMCID: PMC8890557 DOI: 10.1080/12298093.2022.2040112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 05/31/2023]
Abstract
Lichen is a symbiotic mutualism of mycobiont and photobiont that harbors diverse organisms including endolichenic fungi (ELF). Despite the taxonomic and ecological significance of ELF, no comparative investigation of an ELF community involving isolation of a pure culture and high-throughput sequencing has been conducted. Thus, we analyzed the ELF community in Parmotrema tinctorum by culture and metabarcoding. Alpha diversity of the ELF community was notably greater in metabarcoding than in culture-based analysis. Taxonomic proportions of the ELF community estimated by metabarcoding and by culture analyses showed remarkable differences: Sordariomycetes was the most dominant fungal class in culture-based analysis, while Dothideomycetes was the most abundant in metabarcoding analysis. Thirty-seven operational taxonomic units (OTUs) were commonly observed by culture- and metabarcoding-based analyses but relative abundances differed: most of common OTUs were underrepresented in metabarcoding. The ELF community differed in lichen segments and thalli in metabarcoding analysis. Dissimilarity of ELF community intra lichen thallus increased with thallus segment distance; inter-thallus ELF community dissimilarity was significantly greater than intra-thallus ELF community dissimilarity. Finally, we tested how many fungal sequence reads would be needed to ELF diversity with relationship assays between numbers of lichen segments and saturation patterns of OTU richness and sample coverage. At least 6000 sequence reads per lichen thallus were sufficient for prediction of overall ELF community diversity and 50,000 reads per thallus were enough to observe rare taxa of ELF.
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Affiliation(s)
- Ji Ho Yang
- Department of Biology, Sunchon National University, Suncheon, Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Korea
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Sun X, Li JL, He C, Li XC, Guo LD. Specific network and phylosymbiosis pattern in endophyte community of coastal halophytes. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2021.101088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lücking R, Leavitt SD, Hawksworth DL. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00477-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractLichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.
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Li T, Wu S, Yang W, Selosse MA, Gao J. How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics. FRONTIERS IN PLANT SCIENCE 2021; 12:647114. [PMID: 34025695 PMCID: PMC8138319 DOI: 10.3389/fpls.2021.647114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/13/2021] [Indexed: 05/04/2023]
Abstract
Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.
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Affiliation(s)
- Taiqiang Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Shimao Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Wenke Yang
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Marc-André Selosse
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
- Institut de Systématique, Évolution, Biodiversité, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Jiangyun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
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Siddique AB, Biella P, Unterseher M, Albrectsen BR. Mycobiomes of Young Beech Trees Are Distinguished by Organ Rather Than by Habitat, and Community Analyses Suggest Competitive Interactions Among Twig Fungi. Front Microbiol 2021; 12:646302. [PMID: 33936005 PMCID: PMC8086555 DOI: 10.3389/fmicb.2021.646302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
Beech trees (Fagus sylvatica) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52%) and Basidiomycota (26%) taxa. Significant correlations between richness and diversity indices were observed (p < 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.
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Affiliation(s)
- Abu Bakar Siddique
- Department of Ecology and Environmental Sciences, Faculty of Science and Technology, Umeå University, Umeå, Sweden
| | - Paolo Biella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Vaz ABM, Fonseca PLC, Silva FF, Quintanilha-Peixoto G, Sampedro I, Siles JA, Carmo A, Kato RB, Azevedo V, Badotti F, Ocampo JA, Rosa CA, Góes-Neto A. Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs. PeerJ 2020; 8:e10487. [PMID: 33344092 PMCID: PMC7719295 DOI: 10.7717/peerj.10487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/12/2020] [Indexed: 11/20/2022] Open
Abstract
The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
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Affiliation(s)
- Aline Bruna M Vaz
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paula Luize C Fonseca
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe F Silva
- Graduate Program of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Quintanilha-Peixoto
- Graduate Program of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Inmaculada Sampedro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, C.S.I.C., Granada, Spain
| | - Jose A Siles
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, C.S.I.C., Granada, Spain
| | - Anderson Carmo
- Department of Genetics, Ecology, and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo B Kato
- Graduate Program of Bioinformatics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juan A Ocampo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, C.S.I.C., Granada, Spain
| | - Carlos A Rosa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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12
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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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Huang YL. Effect of Host, Environment and Fungal Growth on Fungal Leaf Endophyte Communities in Taiwan. J Fungi (Basel) 2020; 6:jof6040244. [PMID: 33114080 PMCID: PMC7712724 DOI: 10.3390/jof6040244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/14/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022] Open
Abstract
Fungal endophytes inhabit plant tissues without causing disease symptoms. They are highly diverse and distributed globally in all plants that have been investigated. Host, geographic, and environmental effects on endophyte communities have been reported in several studies, but the direct effect of fungal growth rate on endophyte composition has not been tested. To understand the relationship between foliar endophyte composition and fungal growth and to examine the effect of host, elevation, and climatic factors on the foliar endophyte communities, this study examined the foliar endophyte communities of representative gymnosperms and Rhododendron spp. across different elevations of Hehuanshan and Taipingshan forests in Taiwan. The isolation frequency and diversity of foliar endophytes were higher at low elevations than at high elevations. The foliar endophyte community structure differed as a function of host family and forest vegetation type. Elevation, mean annual temperature, and precipitation were significantly correlated with the community structure. Fungal growth rate was correlated with the endophyte abundance, which indicates that fast-growing fungi might have a competitive advantage when coexisting with other fungi in a plant host.
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Affiliation(s)
- Yu-Ling Huang
- Department of Biology, National Museum of Natural Science, Taichung 40453, Taiwan
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15
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Mark K, Laanisto L, Bueno CG, Niinemets Ü, Keller C, Scheidegger C. Contrasting co-occurrence patterns of photobiont and cystobasidiomycete yeast associated with common epiphytic lichen species. THE NEW PHYTOLOGIST 2020; 227:1362-1375. [PMID: 32034954 DOI: 10.1111/nph.16475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The popular dual definition of lichen symbiosis is under question with recent findings of additional microbial partners living within the lichen body. Here we compare the distribution and co-occurrence patterns of lichen photobiont and recently described secondary fungus (Cyphobasidiales yeast) to evaluate their dependency on lichen host fungus (mycobiont). We sequenced the nuclear internal transcribed spacer (ITS) strands for mycobiont, photobiont, and yeast from six widespread northern hemisphere epiphytic lichen species collected from 25 sites in Switzerland and Estonia. Interaction network analyses and multivariate analyses were conducted on operational taxonomic units based on ITS sequence data. Our study demonstrates the frequent presence of cystobasidiomycete yeasts in studied lichens and shows that they are much less mycobiont-specific than the photobionts. Individuals of different lichen species growing on the same tree trunk consistently hosted the same or closely related mycobiont-specific Trebouxia lineage over geographic distances while the cystobasidiomycete yeasts were unevenly distributed over the study area - contrasting communities were found between Estonia and Switzerland. These results contradict previous findings of high mycobiont species specificity of Cyphobasidiales yeast at large geographic scales. Our results suggest that the yeast might not be as intimately associated with the symbiosis as is the photobiont.
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Affiliation(s)
- Kristiina Mark
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Lauri Laanisto
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu, 51006, Estonia
- Estonian Academy of Sciences, Kohtu 6, Tallinn, 10130, Estonia
| | - Christine Keller
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
| | - Christoph Scheidegger
- Department of Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
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16
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Rajulu MBG, Thirunavukkarasu N, Kumar SS, Kaur T, Reddy MS, Suryanarayanan TS. Endolichenic fungal diversity associated with some lichens of the Western Ghats. PLANTA MEDICA 2020; 86:960-966. [PMID: 31766071 DOI: 10.1055/a-1045-1989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A total of 389 strains of fungi belonging to 38 species were isolated from 10 lichen species of the Western Ghats, southern India. All the lichens screened, irrespective of their growth forms or location, harboured endolichenic fungi. Most of the fungi belonged to the Ascomycotina. Chaetomium sp. 1, Hypoxylon investiens, Nemania bipapillata, Nodulisporium sp., Paecilomyces sp., and Sporormiella intermedia were the most common ones and were present in 5 or more lichen species. Of the 28 sporulating fungi, 7 belonged to Xylariales, and their total colonization frequency in all the lichens was also high. This observation further substantiates the high ecological amplitude of Xylariales, possibly due to overlapping ecological niches and their ability to inhibit co-occurring endolichenic fungi.
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Affiliation(s)
| | | | - Subramanya Shravan Kumar
- Divecha Centre for Climate Change & Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Tanveer Kaur
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Mondem Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
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17
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Diversity and Distribution Patterns of Endolichenic Fungi in Jeju Island, South Korea. SUSTAINABILITY 2020. [DOI: 10.3390/su12093769] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lichens are symbiotic organisms containing diverse microorganisms. Endolichenic fungi (ELF) are one of the inhabitants living in lichen thalli, and have potential ecological and industrial applications due to their various secondary metabolites. As the function of endophytic fungi on the plant ecology and ecosystem sustainability, ELF may have an influence on the lichen diversity and the ecosystem, functioning similarly to the influence of endophytic fungi on plant ecology and ecosystem sustainability, which suggests the importance of understanding the diversity and community pattern of ELF. In this study, we investigated the diversity and the factors influencing the community structure of ELF in Jeju Island, South Korea by analyzing 619 fungal isolates from 79 lichen samples in Jeju Island. A total of 112 ELF species was identified and the most common species belonged to Xylariales in Sordariomycetes. The richness and community structure of ELF were significantly influenced by the host taxonomy, together with the photobiont types and environmental factors. Our results suggest that various lichen species in more diverse environments need to be analyzed to expand our knowledge of the diversity and ecology of ELF.
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Cañón ERP, de Albuquerque MP, Alves RP, Pereira AB, Victoria FDC. Morphological and Molecular Characterization of Three Endolichenic Isolates of Xylaria (Xylariaceae), from Cladonia curta Ahti & Marcelli (Cladoniaceae). PLANTS (BASEL, SWITZERLAND) 2019; 8:E399. [PMID: 31597306 PMCID: PMC6843379 DOI: 10.3390/plants8100399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 11/17/2022]
Abstract
Endophyte biology is a branch of science that contributes to the understanding of the diversity and ecology of microorganisms that live inside plants, fungi, and lichen. Considering that the diversity of endolichenic fungi is little explored, and its phylogenetic relationship with other lifestyles (endophytism and saprotrophism) is still to be explored in detail, this paper presents data on axenic cultures and phylogenetic relationships of three endolichenic fungi, isolated in laboratory. Cladonia curta Ahti & Marcelli, a species of lichen described in Brazil, is distributed at three sites in the Southeast of the country, in mesophilous forests and the Cerrado. Initial hyphal growth of Xylaria spp. on C. curta podetia started four days after inoculation and continued for the next 13 days until the hyphae completely covered the podetia. Stromata formation and differentiation was observed, occurring approximately after one year of isolation and consecutive subculture of lineages. Phylogenetic analyses indicate lineages of endolichenic fungi in the genus Xylaria, even as the morphological characteristics of the colonies and anamorphous stromata confirm this classification. Our preliminary results provide evidence that these endolichenic fungi are closely related to endophytic fungi, suggesting that the associations are not purely incidental. Further studies, especially phylogenetic analyses using robust multi-locus datasets, are needed to accept or reject the hypothesis that endolichenic fungi isolated from Xylaria spp. and X. berteri are conspecific.
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Affiliation(s)
- Ehidy Rocio Peña Cañón
- Grupo de Investigación Biología para la Conservación, Departamento de Biología, Universidad Pedagógica y Tecnológica de Colombia, Avenida Central del Norte 39-115, 150003 Tunja, Colombia.
| | - Margeli Pereira de Albuquerque
- Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha, 1847, 97300-000 São Gabriel CEP, Brazil.
| | - Rodrigo Paidano Alves
- Max Planck Institute for Chemistry, Andre Araujo Avenue, 2936, 69067-375 Manaus, Brazil.
| | - Antonio Batista Pereira
- Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha, 1847, 97300-000 São Gabriel CEP, Brazil.
| | - Filipe de Carvalho Victoria
- Núcleo de Estudos da Vegetação Antártica (NEVA), Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha, 1847, 97300-000 São Gabriel CEP, Brazil.
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19
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Lendemer JC, Keepers KG, Tripp EA, Pogoda CS, McCain CM, Kane NC. A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens. AMERICAN JOURNAL OF BOTANY 2019; 106:1090-1095. [PMID: 31397894 DOI: 10.1002/ajb2.1339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.
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Affiliation(s)
- James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Christy M McCain
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
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20
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Habitat quality and disturbance drive lichen species richness in a temperate biodiversity hotspot. Oecologia 2019; 190:445-457. [DOI: 10.1007/s00442-019-04413-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 04/30/2019] [Indexed: 01/14/2023]
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21
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Furmanek Ł, Czarnota P, Seaward M. Antifungal activity of lichen compounds against dermatophytes: a review. J Appl Microbiol 2019; 127:308-325. [DOI: 10.1111/jam.14209] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/31/2018] [Accepted: 01/14/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Ł. Furmanek
- Department of Agroecology University of Rzeszów Rzeszów Poland
| | - P. Czarnota
- Department of Agroecology University of Rzeszów Rzeszów Poland
| | - M.R.D. Seaward
- School of Archaeological & Forensic Sciences University of Bradford Bradford UK
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22
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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: 100] [Impact Index Per Article: 20.0] [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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Bennett AE, Evans DM, Powell JR. Potentials and pitfalls in the analysis of bipartite networks to understand plant–microbe interactions in changing environments. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13223] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alison E. Bennett
- Evolution, Ecology, and Organismal Biology The Ohio State University Columbus Ohio
| | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University Penrith New South Wales Australia
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24
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Strong specificity and network modularity at a very fine phylogenetic scale in the lichen genus Peltigera. Oecologia 2018; 187:767-782. [PMID: 29761320 DOI: 10.1007/s00442-018-4159-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 05/03/2018] [Indexed: 10/16/2022]
Abstract
Identifying the drivers and evolutionary consequences of species interactions is a major goal of community ecology. Network-based analyses can provide mathematical tools to detect non-random patterns of interactions, and potentially help predicting the consequences of such patterns on evolutionary dynamics of symbiotic systems. Here, we characterize the structure of a lichen network at a very fine phylogenetic scale, by identifying the photosynthetic partners (i.e., cyanobacteria of the genus Nostoc) of lichenized fungi belonging to a monophyletic section of a single genus (i.e., section Polydactylon of the genus Peltigera), worldwide. Even at such a fine phylogenetic scale, we found that interactions were highly modular and anti-nested, indicating strong preferences in interactions. When considering local Peltigera communities, i.e., datasets at small spatial scales with only a slightly broader phylogenetic range, interactions remained modular but were asymmetric, with generalist Nostoc partners interacting with specialized Peltigera species. This asymmetry was not detected with our global spatial scale dataset. We discuss these results in the light of lichen community assembly, and explore how such interaction patterns may influence coevolution in lichens and the evolutionary stability of the mutualism in general.
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25
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Dissanayake AJ, Purahong W, Wubet T, Hyde KD, Zhang W, Xu H, Zhang G, Fu C, Liu M, Xing Q, Li X, Yan J. Direct comparison of culture-dependent and culture-independent molecular approaches reveal the diversity of fungal endophytic communities in stems of grapevine (Vitis vinifera). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0399-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Epps MJ, Arnold AE. Quantifying beetle-macrofungal associations in a temperate biodiversity hot spot. Mycologia 2018; 110:269-285. [DOI: 10.1080/00275514.2018.1430439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mary Jane Epps
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona 85721
| | - A. Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona 85721
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Ertz D, Guzow-Krzemińska B, Thor G, Łubek A, Kukwa M. Photobiont switching causes changes in the reproduction strategy and phenotypic dimorphism in the Arthoniomycetes. Sci Rep 2018; 8:4952. [PMID: 29563606 PMCID: PMC5862901 DOI: 10.1038/s41598-018-23219-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/07/2018] [Indexed: 01/03/2023] Open
Abstract
Phylogenetic analyses using mtSSU and nuITS sequences of Buellia violaceofusca (previously placed in Lecanoromycetes), a sterile, sorediate lichen having a trebouxioid photobiont, surprisingly prove that the species is conspecific with Lecanographa amylacea (Arthoniomycetes), a fertile, esorediate species with a trentepohlioid photobiont. These results suggest that L. amylacea and B. violaceofusca are photomorphs of the same mycobiont species, which, depending on the photobiont type, changes the morphology and the reproduction strategy. This is the first example of a lichenized fungus that can select between Trebouxia (Trebouxiophyceae) and trentepohlioid (Ulvophyceae) photobionts. Trebouxia photobionts from the sorediate morphotype belong to at least three different phylogenetic clades, and the results suggest that Lecanographa amylacea can capture the photobiont of other lichens such as Chrysothrix candelaris to form the sorediate morphotype. Phylogenetic analyses based on rbcL DNA data suggest that the trentepohlioid photobiont of L. amylacea is closely related to Trentepohlia isolated from fruticose lichens. The flexibility in the photobiont choice enables L. amylacea to use a larger range of tree hosts. This strategy helps the lichen to withstand changes of environmental conditions, to widen its distribution range and to increase its population size, which is particularly important for the survival of this rare species.
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Affiliation(s)
- Damien Ertz
- Botanic Garden Meise, Department Research, Nieuwelaan 38, B-1860, Meise, Belgium. .,Fédération Wallonie-Bruxelles, Direction Générale de l'Enseignement non obligatoire et de la Recherche scientifique, Rue A. Lavallée 1, B-1080, Bruxelles, Belgium.
| | - Beata Guzow-Krzemińska
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308, Gdańsk, Poland
| | - Göran Thor
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, SE-750 07, Uppsala, Sweden
| | - Anna Łubek
- Institute of Biology, The Jan Kochanowski University in Kielce, Świętokrzyska 15A, PL-25-406, Kielce, Poland
| | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308, Gdańsk, Poland
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Apigo A, Oono R. Dimensions of Host Specificity in Foliar Fungal Endophytes. ENDOPHYTES OF FOREST TREES 2018. [DOI: 10.1007/978-3-319-89833-9_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Interactions between abundant fungal species influence the fungal community assemblage on limestone. PLoS One 2017; 12:e0188443. [PMID: 29211748 PMCID: PMC5718416 DOI: 10.1371/journal.pone.0188443] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/07/2017] [Indexed: 11/19/2022] Open
Abstract
The assembly of fungal communities on stone materials is mainly influenced by the differential bioreceptivity of such materials and environmental conditions. However, little is known about the role of fungal interactions in the colonization and establishment of fungal species. We analyzed the effects of intra- and interspecific interactions between 11 species of fungi in oligotrophic and copiotrophic media and on limestone coupons. In a previous study, these species were the most frequently isolated in the epilithic biofilms of limestone walls exposed to a subtropical climate. In the culture media, we found a greater frequency of intra- and interspecific inhibitory effects in the oligotrophic medium than in the copiotrophic medium. On the limestone coupons, all fungi were able to establish; however, the colonization success rate varied significantly. Cladosporium cladosporioides had a less extensive colonization in isolation (control) than in dual interactions (coexistence) with other species. Phoma eupyrena exhibited the highest colonization success rate and competitive dominance among all tested species. X-ray diffraction (XRD) and scanning electron microscope (SEM) analyses revealed that Pestalotiopsis maculans and Paraconiothyrium sp. produced calcium oxalate crystals during their growth on coupon surfaces, both in isolation and in dual interactions. Our results demonstrate that interactions between abundant fungal species influence the fungal colonization on substrates, the biomineralization and the fungal community assemblage growing in limestone biofilms.
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Fernández-Mendoza F, Fleischhacker A, Kopun T, Grube M, Muggia L. ITS1 metabarcoding highlights low specificity of lichen mycobiomes at a local scale. Mol Ecol 2017; 26:4811-4830. [PMID: 28771869 DOI: 10.1111/mec.14244] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 05/22/2017] [Accepted: 07/06/2017] [Indexed: 01/21/2023]
Abstract
As self-supporting and long-living symbiotic structures, lichens provide a habitat for many other organisms beside the traditionally considered lichen symbionts-the myco- and the photobionts. The lichen-inhabiting fungi either develop diagnostic phenotypes or occur asymptomatically. Because the degree of specificity towards the lichen host is poorly known, we studied the diversity of these fungi among neighbouring lichens on rocks in an alpine habitat. Using a sequencing metabarcoding approach, we show that lichen mycobiomes clearly reflect the overlap of multiple ecological sets of taxa, which differ in their trophic association with lichen thalli. The lack of specificity to the lichen mycobiome is further supported by the lack of community structure observed using clustering and ordination methods. The communities encountered across samples largely result from the subsampling of a shared species pool, in which we identify three major ecological components: (i) a generalist environmental pool, (ii) a lichenicolous/endolichenic pool and (iii) a pool of transient species. These taxa majorly belong to the fungal classes Dothideomycetes, Eurotiomycetes and Tremellomycetes with close relatives in adjacent ecological niches. We found no significant evidence that the phenotypically recognized lichenicolous fungi influence the occurrence of the other asymptomatic fungi in the host thalli. We claim that lichens work as suboptimal habitats or as a complex spore and mycelium bank, which modulate and allow the regeneration of local fungal communities. By performing an approach that minimizes ambiguities in the taxonomic assignments of fungi, we present how lichen mycobiomes are also suitable targets for improving bioinformatic analyses of fungal metabarcoding.
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Affiliation(s)
| | | | - Theodora Kopun
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Trieste, Italy
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Suryanarayanan TS, Thirunavukkarasu N. Endolichenic fungi: the lesser known fungal associates of lichens. Mycology 2017; 8:189-196. [PMID: 30123639 PMCID: PMC6059131 DOI: 10.1080/21501203.2017.1352048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
Lichens are the result of a stable mutualism between a fungal and a photosynthesising partner (alga or cyanobacterium). In addition to the fungal partner in this mutualism, lichens are associated with endolichenic fungi which reside inside their thalli. The endolichenic fungi appear to have evolved with the lichen and many of them are a source of novel metabolites vested with unique bioactivities. There is very little information on the biology of endolichenic fungi and their interactions with the other components of a lichen microbiome. There is an urgent need to understand these aspects of endolichenic fungi such that their ecology and economic potential are known more completely. The current knowledge on endolichenic fungi is reviewed here.
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Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, Morsy M, Eisen JA, Leach JE, Dangl JL. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol 2017; 15:e2001793. [PMID: 28350798 PMCID: PMC5370116 DOI: 10.1371/journal.pbio.2001793] [Citation(s) in RCA: 347] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems. Here, we identify priorities for research in this area: (1) develop model host-microbiome systems for crop plants and non-crop plants with associated microbial culture collections and reference genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the rules of synthetic, functionally programmable microbiome assembly, (4) determine functional mechanisms of plant-microbiome interactions, and (5) characterize and refine plant genotype-by-environment-by-microbiome-by-management interactions. Meeting these goals should accelerate our ability to design and implement effective agricultural microbiome manipulations and management strategies, which, in turn, will pay dividends for both the consumers and producers of the world food supply.
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Affiliation(s)
- Posy E. Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Chinmay Soman
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
| | - Maggie R. Wagner
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Maren L. Friesen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| | - James Kremer
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Alison Bennett
- The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Mustafa Morsy
- College of Natural Sciences and Mathematics, University of West Alabama, Livingston, Alabama, United States of America
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, California, United States of America
| | - Jan E. Leach
- Bioagricultural Sciences and Pest Management, Colorado State University, Ft Collins, Colorado, United States of America
| | - Jeffery L. Dangl
- Howard Hughes Medical Institute, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Bonito G, Hameed K, Toome-Heller M, Healy R, Reid C, Liao HL, Aime MC, Schadt C, Vilgalys R. Atractiella rhizophila, sp. nov., an endorrhizal fungus isolated from thePopulusroot microbiome. Mycologia 2017; 109:18-26. [DOI: 10.1080/00275514.2016.1271689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824
| | - Khalid Hameed
- Biology Department, Duke University, Durham, North Carolina 27708
| | - Merje Toome-Heller
- Department of Plant Pathology, Ministry for Primary Industries, Auckland 1140, New Zealand
| | - Rosanne Healy
- Botany and Plant Pathology, University of Florida, Gainesville, Florida 32611
| | - Chantal Reid
- Biology Department, Duke University, Durham, North Carolina 27708
| | - Hui-Ling Liao
- Botany and Plant Pathology, University of Florida, Gainesville, Florida 32611
| | - M. Catherine Aime
- Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Christopher Schadt
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Rytas Vilgalys
- Biology Department, Duke University, Durham, North Carolina 27708
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Suryanarayanan TS, Govindarajulu MB, Rajamani T, Tripathi M, Joshi Y. Endolichenic fungi in lichens of Champawat district, Uttarakhand, northern India. Mycol Prog 2017. [DOI: 10.1007/s11557-016-1268-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Heilmann-Clausen J, Maruyama PK, Bruun HH, Dimitrov D, Laessøe T, Frøslev TG, Dalsgaard B. Citizen science data reveal ecological, historical and evolutionary factors shaping interactions between woody hosts and wood-inhabiting fungi. THE NEW PHYTOLOGIST 2016; 212:1072-1082. [PMID: 27659274 DOI: 10.1111/nph.14194] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/08/2016] [Indexed: 05/04/2023]
Abstract
Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and network modularity, that is, subcommunity structure, across woody hosts in Denmark, using a citizen science data set comprising > 80 000 records of > 1000 fungal species on 91 genera of woody plants. Fungal species richness was positively related to host size, wood pH, and the number of species in the host genus, with limited influence of host frequency and host history, that is, time since host establishment in the area. Modularity patterns were unaffected by host history, but largely reflected host phylogeny. Notably, fungal communities differed substantially between angiosperm and gymnosperm hosts. Host traits and evolutionary history appear to be more important than host frequency and recent history in structuring interactions between hosts and wood-inhabiting fungi. High wood acidity appears to act as a stress factor reducing fungal species richness, while large host size, providing increased niche diversity, enhances it. In some fungal groups that are known to interact with live host cells in the establishment phase, host selectivity is common, causing a modular community structure.
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Affiliation(s)
- Jacob Heilmann-Clausen
- Centre for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Pietro K Maruyama
- Centre for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas (UNICAMP), Cx. Postal 6109, Campinas, SP, CEP: 13083-862, Brazil
| | - Hans Henrik Bruun
- Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Dimitar Dimitrov
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, Oslo, NO-0318, Norway
| | - Thomas Laessøe
- Centre for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-2100, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Tobias Guldberg Frøslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-1350, Denmark
| | - Bo Dalsgaard
- Centre for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, DK-2100, Denmark
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Wang Y, Zheng Y, Wang X, Wei X, Wei J. Lichen-Associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude. Front Microbiol 2016; 7:1231. [PMID: 27547204 PMCID: PMC4975045 DOI: 10.3389/fmicb.2016.01231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/25/2016] [Indexed: 11/13/2022] Open
Abstract
Lichen-associated fungal species have already been investigated in almost all the main growth forms of lichens, however, whether or not they are homogeneous and constant within each lichen species are still inconclusive. Moreover, the related ecological factors to affect and structure the fungal composition have been poorly studied. In order to answer these questions, we took Hypogymnia hypotrypa as a model to study the relationship between the lichen-associated fungal composition and two ecological factors, i.e., site and altitude, using the method of IlluminaMiSeq sequencing. Four different sites and two levels of altitude were included in this study, and the effects of site and altitude on fungal community composition were assessed at three levels, i.e., operational taxonomic unit (OTU), class and phylum. The results showed that a total of 50 OTUs were identified and distributed in 4 phyla, 13 classes, and 20 orders. The lichen-associated fungal composition within H. hypotrypa were significantly affected by both site and altitude at OTU and class levels, while at the phylum level, it was only affected by altitude. While the lichen associated fungal communities were reported to be similar with endophytic fungi of the moss, our results indicated the opposite results in some degree. But whether there exist specific OTUs within this lichen species corresponding to different sites and altitudes is still open. More lichen species and ecological factors would be taken into the integrated analyses to address these knowledge gaps in the near future.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
| | - Yong Zheng
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
| | - Xinyu Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany - Chinese Academy of Sciences Kunming, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology - Chinese Academy of Sciences Beijing, China
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