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Ángel-García C, Rodríguez-Arevalo KA, Murcia Riaño N, Martínez-Caballero LN, Ceballos-Aguirre G, Jaramillo Laverde A, Martínez MF. Molecular Identification and Fungal Diversity Associated with Diseases in Hass Avocado Fruit Grown in Cauca, Colombia. Pathogens 2023; 12:1418. [PMID: 38133301 PMCID: PMC10745791 DOI: 10.3390/pathogens12121418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 12/23/2023] Open
Abstract
Hass avocado fruit diseases are one of the main marketing constraints in Colombia. To identify and reveal the diversity of fungi associated with diseases in fruits and peduncles, symptomatic samples were collected from 67 farms in the 9 main Hass avocado-producing municipalities of the department of Cauca located in southwestern Colombia. A total of 237 monosporic isolates were obtained that were subjected to DNA extraction, amplification of the ITS region, sequencing and functional diversity analysis based on Hill numbers by municipality and altitude. The results indicated that the genera Pseudocercospora, Diaporthe, Colletotrichum, Neofusiococcum, Lasiodiplodia and Pestatoliopsis were associated with fruit diseases. The genus with the highest number of effective species was Colletotrichum. The ITS region revealed 100% identity of the species Pseudocercospora norchiensis, which was the first report of this pathogen in the crop. There was a greater richness and diversity of associated species in the three municipalities, revealing that the higher the altitude was, the lower the richness and diversity of fungi associated with fruit diseases. These results will provide a better understanding of the identification and diversity of pathogenic microorganisms present in avocado production systems in this region of Colombia.
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Affiliation(s)
| | | | | | | | | | | | - Mauricio Fernando Martínez
- Colombian Agricultural Research Corporation—AGROSAVIA, Palmira Research Center, Palmira 763533, Colombia; (C.Á.-G.); (K.A.R.-A.); (N.M.R.); (L.N.M.-C.); (G.C.-A.); (A.J.L.)
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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Migheli Q, Vloutoglou I, Gobbi A, Maiorano A, Pautasso M, Reignault PL. Pest categorisation of Pestalotiopsis microspora. EFSA J 2023; 21:e8493. [PMID: 38130321 PMCID: PMC10733803 DOI: 10.2903/j.efsa.2023.8493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Following an EFSA commodity risk assessment of bonsai plants (Pinus parviflora grafted on Pinus thunbergii) imported from China, the EFSA Plant Health Panel performed a pest categorisation of Pestalotiopsis microspora, a clearly defined plant pathogenic fungus of the family Pestalotiopsidaceae. The pathogen was reported on a wide range of monocotyledonous, dicotyledonous and gymnosperms, either cultivated or wild plant species, causing various symptoms such as leaf spot, leaf blight, scabby canker, fruit spot, pre- and post-harvest fruit rot and root rot. In addition, the fungus was reported as an endophyte on a wide range of asymptomatic plant species. This pest categorisation focuses on the hosts that are relevant for the EU and for which there is robust evidence that the pathogen was formally identified by a combination of morphology, pathogenicity and multilocus sequencing analyses. Pestalotiopsis microspora was reported in Africa, North, Central and South America, Asia and Oceania. In the EU, it was reported in the Netherlands. There is a key uncertainty on the geographical distribution of P. microspora worldwide and in the EU, because of the endophytic nature of the fungus, the lack of surveys, and because in the past, when molecular tools were not fully developed, the pathogen might have been misidentified as other Pestalotiopsis species or other members of the Pestalodiopsidaceae family based on morphology and pathogenicity tests. Pestalotiopsis microspora is not included in Commission Implementing Regulation (EU) 2019/2072. Plants for planting, fresh fruits, bark and wood of host plants as well as soil and other growing media associated with plant debris are the main pathways for the entry of the pathogen into the EU. Host availability and climate suitability in parts of the EU are favourable for the establishment and spread of the pathogen. The introduction and spread of the pathogen into the EU are expected to have an economic and environmental impact where susceptible hosts are grown. Phytosanitary measures are available to prevent the introduction and spread of the pathogen into the EU. Unless the restricted distribution in the EU is disproven, Pestalotiopsis microspora satisfies all the criteria that are within the remit of EFSA to assess for this species to be regarded as potential Union quarantine pest.
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Pereira DS, Hilário S, Gonçalves MFM, Phillips AJL. Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex. Microorganisms 2023; 11:2717. [PMID: 38004729 PMCID: PMC10673533 DOI: 10.3390/microorganisms11112717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.
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Affiliation(s)
- Diana S. Pereira
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
| | - Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Porto, Portugal;
- Faculty of Sciences, Biology Department, University of Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Micael F. M. Gonçalves
- Faculty of Sciences, Biology Department, University of Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
- Centre for Environmental and Marine Studies, Department of Biology, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Alan J. L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal;
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Gibson E, Zimmerman NB. Urban biogeography of fungal endophytes across San Francisco. PeerJ 2023; 11:e15454. [PMID: 37547726 PMCID: PMC10399560 DOI: 10.7717/peerj.15454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/03/2023] [Indexed: 08/08/2023] Open
Abstract
In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.
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Affiliation(s)
- Emma Gibson
- Department of Biology, University of San Francisco, San Francisco, CA, United States of America
| | - Naupaka B. Zimmerman
- Department of Biology, University of San Francisco, San Francisco, CA, United States of America
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Soares J, Karlsen-Ayala E, Salvador-Montoya C, Gazis R. Two novel endophytic Tolypocladium species identified from native pines in south Florida. Fungal Syst Evol 2023; 11:51-61. [PMID: 38532936 PMCID: PMC10964049 DOI: 10.3114/fuse.2023.11.04] [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: 11/12/2022] [Accepted: 03/01/2023] [Indexed: 03/28/2024] Open
Abstract
This study investigated the incidence and diversity of Tolypocladium within trunks of south Florida slash pines (Pinus densa). Thirty-five isolates were recovered from trunk tissue including living phloem, cambium, and sapwood. Two novel species of Tolypocladium (T. subtropicale and T. trecense) are described here based on morphological and molecular analysis of concatenated LSU, ITS, tef-1, tub, and RPB1 sequences. Our findings expand our understanding of the distribution, diversity, and ecology of this genus and confirm that it is widely spread as an endophyte across ecosystems and hosts. Strains collected in this survey will be used in future bioassays to determine their potential ecological roles as mycoparasites or entomopathogens. Citation: Soares JM, Karlsen-Ayala E, Salvador-Montoya CA, Gazis R (2023). Two novel endophytic Tolypocladium species identified from native pines in south Florida. Fungal Systematics and Evolution 11: 51-61. doi: 10.3114/fuse.2023.11.04.
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Affiliation(s)
- J.M. Soares
- Tropical Research and Education Center, Department of Plant Pathology, University of Florida, Homestead, FL 33031, USA
- USDA-ARS, Sugarcane Field Station, Canal Point, FL 33438, USA
| | - E. Karlsen-Ayala
- Tropical Research and Education Center, Department of Plant Pathology, University of Florida, Homestead, FL 33031, USA
- Southwest Research and Education Center, Department of Soil and Water Sciences, University of Florida, Immokalee, FL 34142, USA
| | - C.A. Salvador-Montoya
- Tropical Research and Education Center, Department of Plant Pathology, University of Florida, Homestead, FL 33031, USA
| | - R. Gazis
- Tropical Research and Education Center, Department of Plant Pathology, University of Florida, Homestead, FL 33031, USA
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Feng L, Zhang Y, Chen W, Mao B. Colletotrichum siamense Strain LVY 9 Causing Spot Anthracnose on Winterberry Holly in China. Microorganisms 2023; 11:microorganisms11040976. [PMID: 37110399 PMCID: PMC10146105 DOI: 10.3390/microorganisms11040976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Winterberry holly (Ilex verticillata) is an economically valuable landscaping ornamental plant. Serious outbreaks have been reported, in its leaf tips curl upward, irregular black brown spots appear on leaves, and extensive defoliation is commonly observed. The incidence in Hangzhou was estimated at 50% and resulted in large economic losses for growers in 2018. Samples were collected from the main cultivation area in Zhejiang Province. In total, 11 fungal isolates were obtained from diseased leaves through a single-spore purification method, and isolate LVY 9 exhibited strong pathogenicity. Based on morphology and molecular phylogenetic analyses based on multilocus sequence typing of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), internal transcribed spacer (ITS) regions, actin (ACT), calmodulin (CAL), and chitin synthase (CHS-1) genes, we identified the pathogen as Colletotrichum siamense, causative agent of anthracnose of winterberry holly.
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Affiliation(s)
- Lin Feng
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yahui Zhang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weiliang Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Bizeng Mao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
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Dutta R, K. J, Nadig SM, Manjunathagowda DC, Gurav VS, Singh M. Anthracnose of Onion ( Allium cepa L.): A Twister Disease. Pathogens 2022; 11:pathogens11080884. [PMID: 36015005 PMCID: PMC9415854 DOI: 10.3390/pathogens11080884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/20/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The onion (Allium cepa L.) is a lucrative and high-value vegetable–spice crop in India, but it is sensitive to several of diseases caused by fungi, bacteria, viruses, and nematodes, of which a fungal disease, anthracnose, caused by Colletotrichum spp., is a major issue for both onion producers and researchers since it severely affects the bulb production. Twister disease is currently one of the most common problems in onion production, particularly in humid regions, and it reduces productivity while also lowering the value and profitability. Twister disease is visualised by white or pale-yellow water-soaked oval depressed lesions on leaf blades, which are the first symptoms. Lesions expand as the disease advances, and numerous black-coloured, slightly elevated structures/fruiting bodies appear in the middle area, arranged in concentric rings. Curling, twisting, chlorosis of the leaves, and aberrant extension of the neck or pseudo-stem occurs, followed by rotting of the bulb. In an unmanaged crop, an excess gibberellin production by Colletotrichum gloeosporioides and Gibberella moniliformis is suspected to induce twisting and aberrant neck elongation, which will ruin onion productivity. It is difficult and environmentally unfriendly to control these infections. Since, to the best of our knowledge, this is the first review on onion anthracnose, we tried to consolidate information. This review updates our knowledge of the pathogen, including the disease cycle, infection pathways, and disease management techniques. As a result, growers will be benefit from the application of cultural, biological, and chemical measures and the use of resistant varieties.
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Affiliation(s)
- Ram Dutta
- ICAR-Directorate of Onion and Garlic Research, Pune 410505, MH, India
- Correspondence: (R.D.); (J.K.)
| | - Jayalakshmi K.
- ICAR-Directorate of Onion and Garlic Research, Pune 410505, MH, India
- Correspondence: (R.D.); (J.K.)
| | - Sharath M. Nadig
- ICAR-Directorate of Onion and Garlic Research, Pune 410505, MH, India
| | - Dalasanuru Chandregowda Manjunathagowda
- ICAR-Directorate of Onion and Garlic Research, Pune 410505, MH, India
- ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru 530068, KA, India
| | - Vishal S. Gurav
- ICAR-Directorate of Onion and Garlic Research, Pune 410505, MH, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Pune 410505, MH, India
- Plant Sciences, Agricultural Scientists Recruitment Board, DARE, Ministry of Agriculture and Farmers Welfare, Government of India, Krishi Anusandhan Bhavan-I, Pusa 110012, ND, India
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Gupta C, Salgotra RK, Damm U, Rajeshkumar KC. Phylogeny and pathogenicity of Colletotrichum lindemuthianum causing anthracnose of Phaseolus vulgaris cv. Bhaderwah-Rajmash from northern Himalayas, India. 3 Biotech 2022; 12:169. [PMID: 35845112 PMCID: PMC9279525 DOI: 10.1007/s13205-022-03216-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
With an annual loss of up to 100%, anthracnose caused by Colletotrichum is one of the most devastating diseases of common beans (Phaseolus vulgaris L.). Due to few distinctive morphological characters, Colletotrichum species are frequently misidentified. In India, several Colletotrichum species have been reported as pathogens of Phaseolus species, but none had previously been validated by means of molecular tools. In this study, we studied Colletotrichum strains from common beans cv. Bhaderwah-Rajmash from the northern Himalayas of India based on both morphological and DNA sequence data of six loci, namely ITS, gapdh, chs-1, his3, act, tub2. The strains were identified as C. lindemuthianum that belongs to the C. orbiculare species complex. Representative C. lindemuthianum strains tested on Phaseolus vulgaris cv. Bhaderwah-Rajmash were pathogenic and exhibited variation in symptomology and disease progression. By identifying the causal agent, we provided substantial information to develop the best control strategies for anthracnose of Phaseolus vulgaris from the northern Himalayas of India. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03216-0.
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Phylogenetic Analysis of Trichoderma Species Associated with Green Mold Disease on Mushrooms and Two New Pathogens on Ganoderma sichuanense. J Fungi (Basel) 2022; 8:jof8070704. [PMID: 35887460 PMCID: PMC9318549 DOI: 10.3390/jof8070704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
Edible and medicinal mushrooms are extensively cultivated and commercially consumed around the world. However, green mold disease (causal agent, Trichoderma spp.) has resulted in severe crop losses on mushroom farms worldwide in recent years and has become an obstacle to the development of the Ganoderma industry in China. In this study, a new species and a new fungal pathogen on Ganoderma sichuanense fruitbodies were identified based on the morphological characteristics and phylogenetic analysis of two genes, the translation elongation factor 1-α (TEF1) and the second-largest subunit of RNA polymerase II (RPB2) genes. The new species, Trichoderma ganodermatigerum sp. nov., belongs to the Harzianum clade, and the new fungal pathogen was identified as Trichoderma koningiopsis. Furthermore, in order to better understand the interaction between Trichoderma and mushrooms, as well as the potential biocontrol value of pathogenic Trichoderma, we summarized the Trichoderma species and their mushroom hosts as best as possible, and the phylogenetic relationships within mushroom pathogenic Trichoderma species were discussed.
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Carl S, Mohr S, Sahm R, Baschien C. Laboratory conditions can change the complexity and composition of the natural aquatic mycobiome on Alnus glutinosa leaf litter. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Hilário S, Santos L, Phillips AJL, Alves A. Caveats of the internal transcribed spacer region as a barcode to resolve species boundaries in Diaporthe. Fungal Biol 2021; 126:54-74. [PMID: 34930559 DOI: 10.1016/j.funbio.2021.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/13/2021] [Accepted: 10/25/2021] [Indexed: 01/03/2023]
Abstract
Species in Diaporthe are largely reported as important plant pathogens. Identification of species in this genus has been complemented by morphological and molecular features. However, one important factor delaying this process is the struggle to formulate robust species concepts to create adequate international phytosanitary measures. Regardless of the wide use of the internal transcribed spacer (ITS) rDNA region, established as the primary DNA barcode for fungi, the tendency for intraspecific variation has been reported, misleading interpretation of phylogenetic analyses. Therefore, the present study aimed to illustrate, using specific examples, how the ITS region may be problematic for species delimitation. We showed that the ITS region is highly variable, with strains of Diaporthe malorum and Diaporthe novem falling into more than one clade, which if analyzed on their own, would be likely recognized as distinct taxa. Divergent ITS paralogs were also proven to coexist within the genome of D. novem. We also suggest that ITS may have escaped from concerted evolution or has undergone a duplication event. Furthermore, this study reports for the first time the existence of a putative hybrid in the genus Diaporthe. Our findings offer new clues towards the intraspecific and intragenomic variation in the ITS region, raising questions about its value for barcoding, i.e., identifying species in the genus Diaporthe. Therefore, we recommend that the ITS region be analyzed cautiously and always compared for congruence prior to description of novel taxa.
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Affiliation(s)
- Sandra Hilário
- CESAM, Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Liliana Santos
- CESAM, Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Alan J L Phillips
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Artur Alves
- CESAM, Departamento de Biologia, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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Santos TTD, Pes AMO, Morais PBDE. A diverse and partially cellulolytic fungal community contributes to the diet of three species of the aquatic insect Phylloicus (Trichoptera: Calamoceratidae) in Amazonian streams. AN ACAD BRAS CIENC 2021; 93:e20210598. [PMID: 34852068 DOI: 10.1590/0001-3765202120210598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/09/2021] [Indexed: 11/21/2022] Open
Abstract
Investigations on the fungal community associated with the digestive tract (DT) of insects have provided insights into the diversity of associated microorganisms and their potential roles in the interaction with their hosts. However, most studies have focused on terrestrial insects, with few studies focusing on aquatic insects in Neotropical regions. We studied fungal taxa associated with the DT of larval stages of the aquatic shredders Phylloicus amazonas, P. elektoros and P. fenestratus in the Brazilian Amazon Forest. Filamentous fungi were isolated, purified and screened for cellulolytic activity. A total of 33 fungal taxa was identified through the combination of classical and molecular taxonomy. The genus Penicillium was the most frequent in DT of Phylloicus spp. (18.75%). The occurrence of fungal taxa among hosts was quite variable, with more than half of the associated fungi being exclusive of each host species. A significant portion of the fungal community associated with each host presented cellulolytic activity (± 50%). It was concluded that the fungal community associated with Phylloicus spp. larvae consist mainly of fungal taxa from food items, which come from riparian vegetation (whose plant species are variable) or are indigenous of the aquatic ecosystems, which is the habitat of these larvae.
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Affiliation(s)
- Taides T Dos Santos
- Universidade Federal do Oeste da Bahia, Centro Multidisciplinar de Luís Eduardo Magalhães, Rua Itabuna, 1278, 47850-000 Luís Eduardo Magalhães, BA, Brazil
| | - Ana Maria O Pes
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Av. André Araújo, 2936, 69067-375 Manaus, AM, Brazil
| | - Paula B DE Morais
- Universidade Federal do Tocantins, Laboratório de Microbiologia Ambiental e Biotecnologia, Campus Universitário de Palmas, Av. NS 15, ALCNO 14, s/n, Bloco II, 77001-090 Palmas, TO, Brazil
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Du Y, Shi N, Ruan H, Chen F. Three Mycogone Species, Including a New Species, Cause Wet Bubble Disease of Agaricus bisporus in China. PLANT DISEASE 2021; 105:3967-3977. [PMID: 34261355 DOI: 10.1094/pdis-03-21-0651-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
White button mushroom, Agaricus bisporus (Lange) Imbach, is the most extensively cultivated and edible mushroom worldwide. The production of A. bisporus is commonly affected by wet bubble disease (WBD), imposing a significant economic burden in China. Although studies have shown that this disease is caused by fungi of the Mycogone genus, the pathogen has not been fully characterized. In this study, 802 samples of diseased fruiting bodies of A. bisporus were collected from nine major mushroom-cultivating provinces in China, yielding a total of 586 Mycogone isolates. The morphologic characteristics of these isolates were observed and compared, and multilocus phylogenetic analyses (internal transcribed spacer [ITS], ACT, TEF1-α, TUB, RPB2, and large ribosomal subunit [LSU]) were performed on the selected representative isolates. Three Mycogone species were identified: a new species, M. xinjiangensis; M. perniciosa; and M. rosea. Mycogone rosea was the first ever reported in China. Furthermore, M. rosea was found to be the most prevalent species (54.95% of all isolates) in all the sampled areas, except in Hubei and Xinjiang, followed by M. perniciosa (39.93%) and M. xinjiangensis (5.12%). Pathogenicity tests on the fruiting body and mushroom bed substantiated Koch's postulates by the development of mildly different symptoms after inoculation with each species. This study, therefore, enhances our knowledge of the species associated with WBD in A. bisporus and provides useful insights for preventing WBD and allied diseases.
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Affiliation(s)
- Yixin Du
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, Fujian, 350013, China
| | - Niuniu Shi
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, Fujian, 350013, China
| | - Hongchun Ruan
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, Fujian, 350013, China
| | - Furu Chen
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350013, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Fuzhou, Fujian, 350013, China
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14
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Arnold AE, Harrington AH, Huang YL, U'Ren JM, Massimo NC, Knight-Connoni V, Inderbitzin P. Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov., three new species of endophytes with distinctive morphology and functional traits. Int J Syst Evol Microbiol 2021; 71. [PMID: 34731078 DOI: 10.1099/ijsem.0.005003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A growing interest in fungi that occur within symptom-less plants and lichens (endophytes) has uncovered previously uncharacterized species in diverse biomes worldwide. In many temperate and boreal forests, endophytic Coniochaeta (Sacc.) Cooke (Coniochaetaceae, Coniochaetales, Sordariomycetes, Ascomycota) are commonly isolated on standard media, but rarely are characterized. We examined 26 isolates of Coniochaeta housed at the Gilbertson Mycological Herbarium. The isolates were collected from healthy photosynthetic tissues of conifers, angiosperms, mosses and lichens in Canada, Sweden and the United States. Their barcode sequences (nuclear ribosomal internal transcribed spacer and 5.8S; ITS rDNA) were ≤97% similar to any documented species available through GenBank. Phylogenetic analyses based on two loci (ITS rDNA and translation elongation factor 1-alpha) indicated that two isolates represented Coniochaeta cymbiformispora, broadening the ecological niche and geographic range of a species known previously from burned soil in Japan. The remaining 24 endophytes represented three previously undescribed species that we characterize here: Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov. Each has a wide host range, including lichens, bryophytes and vascular plants. C. elegans sp. nov. and C. nivea sp. nov. have wide geographic ranges. C. montana sp. nov. occurs in the Madrean biome of Arizona (USA), where it is sympatric with the other species described here. All three species display protease, chitinase and cellulase activity in vitro. Overall, this study provides insight into the ecological and evolutionary diversity of Coniochaeta and suggests that these strains may be amenable for studies of traits relevant to a horizontally transmitted, symbiotic lifestyle.
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Affiliation(s)
- A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Alison H Harrington
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Yu-Ling Huang
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan, ROC
| | - Jana M U'Ren
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
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15
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Vieto S, Escudero-Leyva E, Avendaño R, Rechnitzer N, Barrantes-Madrigal MD, Conejo-Barboza G, Herrera-Sancho OA, Chaverri P, Chavarría M. Biodeterioration and cellulolytic activity by fungi isolated from a nineteenth-century painting at the National Theatre of Costa Rica. Fungal Biol 2021; 126:101-112. [DOI: 10.1016/j.funbio.2021.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 12/23/2022]
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16
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Reynolds NK, Jusino MA, Stajich JE, Smith ME. Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples. Mol Ecol Resour 2021; 22:1065-1085. [PMID: 34695878 DOI: 10.1111/1755-0998.13540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.
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Affiliation(s)
- Nicole K Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Michelle A Jusino
- Center for Forest Mycology Research, USDA Forest Service, Northern Research Station, Madison, Wisconsin, USA
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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17
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Ndinga-Muniania C, Mueller RC, Kuske CR, Porras-Alfaro A. Seasonal variation and potential roles of dark septate fungi in an arid grassland. Mycologia 2021; 113:1181-1198. [PMID: 34686124 DOI: 10.1080/00275514.2021.1965852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
High temperatures and extended drought in temperate and tropical arid ecosystems promote the colonization of diverse microenvironments by dark septate fungi (DSF). These fungi contribute to soil nutrient cycling, soil stabilization, and plant survival, but the roles of individual DSF species, their distributions, and their community diversity are poorly understood. The objective of this study was to evaluate the distribution, seasonal variation, and potential roles of DSF on plant growth. We collected biocrust (lichen-, moss-, and cyanobacterium-dominated biocrusts) soils at different depths and rhizosphere soils from two grasses, Bromus tectorum and Pleuraphis jamesii, in an arid grassland near Moab, Utah, USA. Seasonal variation of DSF was evaluated using culture-based approaches and compared with fungal community profiles from next-generation sequencing (NGS). Culturing showed that DSF were 30% more abundant in biocrusts compared with the focal rhizospheres. The abundance of DSF varied seasonally in belowground samples (rhizosphere and below-biocrust), with a significant increase during the summer months. Pleosporales was the dominant order (35%) in both biocrust and rhizosphere soils out of 817 isolated fungi. Dominant DSF genera in culture included Alternaria, Preussia, Cladosporium, Phoma, and an unknown Pleosporales. Similar results were observed in biocrust and rhizosphere soils NGS. Further, seed germination experiments using dominant taxa were conducted to determine their potential roles on germination and seedling growth using maize as a model plant. Cladosporium and unknown Pleosporales isolates showed plant growth-promoting ability. The variation in abundance of DSF, their differential occurrence in different microenvironments, and their ability to grow in a xerotolerant medium reflect adaptations to summer environmental conditions and to changes in the abundance of organic matter, as well as a potential increase in plant investment in these fungi when heat and drought stresses are more severe.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, 55108, Minnesota
| | - Rebecca C Mueller
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana 59717
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Andrea Porras-Alfaro
- Department of Biological Sciences and Institute for Environmental Studies, Western Illinois University, Macomb, Illinois 61455.,Division of Environmental Biology, National Science Foundation, Alexandria, Virginia 22314
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18
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Fang K, Zhou J, Chen L, Li YX, Yang AL, Dong XF, Zhang HB. Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections. PLoS Pathog 2021; 17:e1009769. [PMID: 34265026 PMCID: PMC8315517 DOI: 10.1371/journal.ppat.1009769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/27/2021] [Accepted: 06/29/2021] [Indexed: 01/04/2023] Open
Abstract
The virulence evolution of multiple infections of parasites from the same species has been modeled widely in evolution theory. However, experimental studies on this topic remain scarce, particularly regarding multiple infections by different parasite species. Here, we characterized the virulence and community dynamics of fungal pathogens on the invasive plant Ageratina adenophora to verify the predictions made by the model. We observed that A. adenophora was highly susceptible to diverse foliar pathogens with mixed vertical and horizontal transmission within leaf spots. The transmission mode mainly determined the pathogen community structure at the leaf spot level. Over time, the pathogen community within a leaf spot showed decreased Shannon diversity; moreover, the vertically transmitted pathogens exhibited decreased virulence to the host A. adenophora, but the horizontally transmitted pathogens exhibited increased virulence to the host. Our results demonstrate that the predictions of classical models for the virulence evolution of multiple infections are still valid in a complex realistic environment and highlight the impact of transmission mode on disease epidemics of foliar fungal pathogens. We also propose that seedborne fungi play an important role in structuring the foliar pathogen community from multiple infections within a leaf spot. A growing number of examples indicate that many plant diseases are caused by multiple taxa of microbes. Therefore, how virulence evolves in the context of multiple infections by different species with both vertical and horizontal transmission modes represents an important area of pathogen ecology and evolution, but there is a lack of experimental study. Here, we employ a naturally occurring host-parasite system, the invasive plant Ageratina adenophora and its foliar pathogens, to verify that theoretical predictions of classical models for virulence evolution are still valid in a complex realistic environment, i.e., the transmission mode determines the dynamics of the virulence and pathogen community under multiple infections. Moreover, we propose that seedborne fungi are important in structuring the foliar pathogen community consisting of multiple infections within a leaf spot. Our findings provide valuable information for understanding how multiple infections affect the key components, i.e., the virulence evolution and pathogen community dynamics, of host-pathogen interactions in the field.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yu-Xuan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Ai-Ling Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- * E-mail:
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19
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Hilário S, Gonçalves MFM, Alves A. Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex. J Fungi (Basel) 2021; 7:507. [PMID: 34202282 PMCID: PMC8307253 DOI: 10.3390/jof7070507] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/11/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe. However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe.
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Affiliation(s)
| | | | - Artur Alves
- Centre for Environmental and Marine Studies (CESAM), Department of Biology, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal; (S.H.); (M.F.M.G.)
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20
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Høyer AK, Hodkinson TR. Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens. J Fungi (Basel) 2021; 7:jof7060466. [PMID: 34207673 PMCID: PMC8226481 DOI: 10.3390/jof7060466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.
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21
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Giusti A, Ricci E, Gasperetti L, Galgani M, Polidori L, Verdigi F, Narducci R, Armani A. Building of an Internal Transcribed Spacer (ITS) Gene Dataset to Support the Italian Health Service in Mushroom Identification. Foods 2021; 10:foods10061193. [PMID: 34070525 PMCID: PMC8227961 DOI: 10.3390/foods10061193] [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: 04/12/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 01/26/2023] Open
Abstract
This study aims at building an ITS gene dataset to support the Italian Health Service in mushroom identification. The target species were selected among those mostly involved in regional (Tuscany) poisoning cases. For each target species, all the ITS sequences already deposited in GenBank and BOLD databases were retrieved and accurately assessed for quality and reliability by a systematic filtering process. Wild specimens of target species were also collected to produce reference ITS sequences. These were used partly to set up and partly to validate the dataset by BLAST analysis. Overall, 7270 sequences were found in the two databases. After filtering, 1293 sequences (17.8%) were discarded, with a final retrieval of 5977 sequences. Ninety-seven ITS reference sequences were obtained from 76 collected mushroom specimens: 15 of them, obtained from 10 species with no sequences available after the filtering, were used to build the dataset, with a final taxonomic coverage of 96.7%. The other 82 sequences (66 species) were used for the dataset validation. In most of the cases (n = 71; 86.6%) they matched with identity values ≥ 97–100% with the corresponding species. The dataset was able to identify the species involved in regional poisoning incidents. As some of these species are also involved in poisonings at the national level, the dataset may be used for supporting the National Health Service throughout the Italian territory. Moreover, it can support the official control activities aimed at detecting frauds in commercial mushroom-based products and safeguarding consumers.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.G.); (A.A.)
- Correspondence: ; Tel.: +39-0502210204
| | - Enrica Ricci
- Experimental Zooprophylactic Institute of Lazio and Tuscany M. Aleandri, UOT Toscana Nord, SS Abetone e Brennero 4, 56124 Pisa, Italy; (E.R.); (L.G.)
| | - Laura Gasperetti
- Experimental Zooprophylactic Institute of Lazio and Tuscany M. Aleandri, UOT Toscana Nord, SS Abetone e Brennero 4, 56124 Pisa, Italy; (E.R.); (L.G.)
| | - Marta Galgani
- FishLab, Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.G.); (A.A.)
| | - Luca Polidori
- Tuscany Mycological Groups Association, via Turi, 8 Santa Croce sull’Arno, 56124 Pisa, Italy; (L.P.); (R.N.)
| | - Francesco Verdigi
- North West Tuscany LHA (Mycological Inspectorate), via A. Cocchi, 7/9, 56124 Pisa, Italy;
| | - Roberto Narducci
- Tuscany Mycological Groups Association, via Turi, 8 Santa Croce sull’Arno, 56124 Pisa, Italy; (L.P.); (R.N.)
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy; (M.G.); (A.A.)
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22
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O'Keeffe KR, Halliday FW, Jones CD, Carbone I, Mitchell CE. Parasites, niche modification and the host microbiome: A field survey of multiple parasites. Mol Ecol 2021; 30:2404-2416. [PMID: 33740826 DOI: 10.1111/mec.15892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 01/04/2023]
Abstract
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity and composition of the fungal microbiome associate with natural infection by fungal parasites with different feeding strategies. A parasite's feeding strategy affects both parasite requirements of the host environment and parasite impacts on the host environment. We hypothesized that parasites that more strongly modify niches available within a host will be associated with greater changes in microbiome diversity and composition. Parasites with a feeding strategy that creates necrotic tissue to extract resources (necrotrophs) may not only have different niche requirements, but also act as particularly strong niche modifiers. Barcoded amplicon sequencing of the fungal ITS region revealed that leaf segments symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments symptomatic of other parasite feeding strategies. Our results motivate future experimental work to test how the relationship between the microbiome and parasite infection is impacted by parasite feeding strategy and highlight the potential importance of parasite traits.
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Affiliation(s)
- Kayleigh R O'Keeffe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Fletcher W Halliday
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Charles E Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Environment, Ecology and Energy Program, University of North Carolina, Chapel Hill, NC, USA
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23
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Hilário S, Santos L, Alves A. Diaporthe amygdali, a species complex or a complex species? Fungal Biol 2021; 125:505-518. [PMID: 34140147 DOI: 10.1016/j.funbio.2021.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/25/2021] [Indexed: 11/29/2022]
Abstract
Delimitation of species boundaries within the fungal genus Diaporthe has been challenging, but the analyses of combined multilocus DNA sequences has become an important tool to infer phylogenetic relationships and to circumscribe species. However, analyses of congruence between individual gene genealogies and the application of the genealogical concordance principle have been somehow overlooked. We noted that a group of species including D. amygdali, D. garethjonesii, D. sterilis, D. kadsurae, D. ternstroemia, D. ovoicicola, D. fusicola, D. chongqingensis and D. mediterranea, commonly known as D. amygdali complex, occupy a monophyletic clade in Diaporthe phylogenies but the limits of all species within the complex are not entirely clear. To assess the boundaries of species within this complex we employed the Genealogical Concordance Phylogenetic Species Recognition principle (GCPSR) and coalescence-based models: General Mixed Yule-Coalescent (GMYC) and Poisson Tree Processes (PTP). The incongruence detected between individual gene phylogenies, as well as the results of coalescent methods do not support the recognition of lineages within the complex as distinct species. Moreover, results support the absence of reproductive isolation and barriers to gene flow in this complex, thus providing further evidence that the D. amygdali species complex constitutes a single species. This study highlights the relevance of the application of the GCPSR principle, showing that concatenation analysis of multilocus DNA sequences, although being a powerful tool, might lead to an erroneous definition of species limits. Additionally, it further shows that coalescent methods are useful tools to assist in a more robust delimitation of species boundaries in the genus Diaporthe.
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Affiliation(s)
- Sandra Hilário
- Departamento de Biologia, CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Liliana Santos
- Departamento de Biologia, CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Artur Alves
- Departamento de Biologia, CESAM (Centro de Estudos do Ambiente e do Mar), Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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24
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Seas C, Chaverri P. Response of psychrophilic plant endosymbionts to experimental temperature increase. ROYAL SOCIETY OPEN SCIENCE 2020; 7:201405. [PMID: 33489283 PMCID: PMC7813268 DOI: 10.1098/rsos.201405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Countless uncertainties remain regarding the effects of global warming on biodiversity, including the ability of organisms to adapt and how that will affect obligate symbiotic relationships. The present study aimed to determine the consequences of temperature increase in the adaptation of plant endosymbionts (endophytes) that grow better at low temperatures (psychrophilic). We isolated fungal endophytes from a high-elevation (paramo) endemic plant, Chusquea subtessellata. Initial growth curves were constructed at different temperatures (4-25°C). Next, experiments were carried out in which only the psychrophilic isolates were subjected to repeated increments in temperature. After the experiments, the final growth curves showed significantly slower growth than the initial curves, and some isolates even ceased to grow. While most studies suggest that the distribution of microorganisms will expand as temperatures increase because most of these organisms grow better at 25°C, the results from our experiments demonstrate that psychrophilic fungi were negatively affected by temperature increases. These outcomes raise questions concerning the potential adaptation of beneficial endosymbiotic fungi in the already threatened high-elevation ecosystems. Assessing the consequences of global warming at all trophic levels is urgent because many species on Earth depend on their microbial symbionts for survival.
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Affiliation(s)
- Carolina Seas
- Vicerrectoría de Investigación, Laboratorio de Ecología Urbana, Universidad Estatal a Distancia (UNED), 2050 San José, Costa Rica
- Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Escuela de Posgrado, Turrialba, Costa Rica
| | - Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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25
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Vohník M. Ericoid mycorrhizal symbiosis: theoretical background and methods for its comprehensive investigation. MYCORRHIZA 2020; 30:671-695. [PMID: 33043410 PMCID: PMC7548138 DOI: 10.1007/s00572-020-00989-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/14/2020] [Indexed: 05/20/2023]
Abstract
Despite decades of intensive research (especially from 1970s to 1990s), the ericoid mycorrhizal (ErM) hair root is still largely terra incognita and this simplified guide is intended to revive and promote the study of its mycobiota. Basic theoretical knowledge on the ErM symbiosis is summarized, followed by practical advices on Ericaceae root sample collection and handling, microscopic observations and photo-documentation of root fungal colonization, mycobiont isolation, maintenance and identification and resynthesis experiments with ericoid plants. The necessity of a proper selection of the root material and its surface sterilization prior to mycobiont isolation is stressed, together with the need of including suitable control treatments in inoculation experiments. The culture-dependent approach employing plating of single short (~ 2 mm) hair root segments on nutrient media is substantiated as a useful tool for characterization of Ericaceae root-associated fungal communities; it targets living mycelium and provides metabolically active cultures that can be used in physiological experiments and taxonomic studies, thus providing essential reference material for culture-independent approaches. On the other hand, it is stressed that not every mycobiont isolated from an ericoid hair root necessarily represent an ErM fungus. Likewise, not every intracellular hyphal coil formed in the Ericaceae rhizodermis necessarily represents the ErM symbiosis. Taxonomy of the most important ericoid mycobionts is updated, mutualism in the ErM symbiosis is briefly discussed from the mycobiont perspective, and some interesting lines of possible future research are highlighted.
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Affiliation(s)
- Martin Vohník
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, 252 43, Czech Republic.
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Araújo KS, Brito VN, Veloso TGR, de Leite TS, Alves JL, da Hora Junior BT, Moreno HLA, Pereira OL, Mizubuti ESG, de Queiroz MV. Diversity and distribution of endophytic fungi in different tissues of Hevea brasiliensis native to the Brazilian Amazon forest. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01613-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Sphaeropsis sapinea and fungal endophyte diversity in twigs of Scots pine (Pinus sylvestris) in Germany. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01617-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractSphaeropsis sapinea is the causal fungal agent of Diplodia tip blight disease of Scots pine (Pinus sylvestris) and other coniferous trees of relevance to forestry in Germany. In this study, the distribution and occurrence of S. sapinea and accompanying endophytic fungi in twigs of healthy and diseased Scots pine was investigated on a spatial and temporal scale. Sampling of 26,000 twig segments from trees in 105 temperate coniferous forest stands in Germany resulted in isolation of 33,000 endophytic fungi consisting of 103 species identified based on morphological and ITS-DNA sequence analyses. Approximately 98% of the sample was represented by fungi in the Ascomycota, with only two species (Peniophora pini and Coprinellus sp.) belonging to the Basidiomycota. Four species were detected in a frequency greater than 10% (Sphaeropsis sapinea, Sydowia polyspora, Microsphaeropsis olivacea, and Truncatella conorum-piceae) from the collective sample. A typical inhabitant of Scots pine twigs Desmazierella acicola was isolated and additionally typical hardwood colonizers like Biscogniauxia spp. were detected. S. sapinea, an endophytic plant pathogen with saprobic capabilities, was isolated from more than 80% of the studied pine trees, but the majority of trees sampled showed no symptoms of Diplodia tip blight. No invasive, pathogenic quarantine fungi for Germany were isolated from healthy or diseased Scots pines. Advantages and disadvantages of isolation-based endophyte studies over studies using direct DNA-isolation are discussed. Knowledge of the fungal endophyte communities in twigs of Scots pine allowed for identification S. sapinea and other potential pathogens of pines and other forest trees that may possibly contribute to increased disease under repeated periods of drought and heat stress in the future.
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Hilje-Rodríguez I, Albertazzi FJ, Rivera-Coto G, Molina-Bravo R. A multiplex qPCR TaqMan-assay to detect fungal antagonism between Trichoderma atroviride (Hypocreaceae) and Botrytis cinerea (Sclerotiniaceae) in blackberry fruits using a de novo tef1-α- and an IGS-sequence based probes. BIOTECHNOLOGY REPORTS 2020; 27:e00447. [PMID: 32528864 PMCID: PMC7276392 DOI: 10.1016/j.btre.2020.e00447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/07/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Quantitative polymerase chain reactions specifically detect Trichoderma atroviride. The method uses a probe based on the tef-1α for the detection. The method simultaneously detects T. atroviride and Botrytis cinerea in blackberries.
The aim of this study was to design a Trichoderma atroviride-specific qPCR oligo set, evaluate its specificity, and standardize a methodology that quantifies antagonism against Botrytis cinerea in blackberry fruits (Rubus adenotrichos Schltdl.). Primers and probe were designed based on the nuclear translation elongation factor 1-alpha (tef1-α) of T. atroviride. A commercial IGS-based oligo set was used to quantify B. cinerea. The specificity of the designed oligo set, along with ITS-based oligo sets, was assessed using other Trichoderma species and B. cinerea. Multiplex qPCR assays were performed using DNA from B. cinerea, T. atroviride, and blackberries inoculated with these fungi. Assays with the tef1-α oligo set showed high sensitivity and reproducibility. In inoculated fruits, T. atroviride and B. cinerea were quantified simultaneously, including in symptomless tissues. This work standardized a qPCR methodology that specifically targets a T. atroviride isolate. This newly-designed qPCR oligo set could be useful in future biological control programs.
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Affiliation(s)
- Irena Hilje-Rodríguez
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
- Corresponding author.
| | - Federico J. Albertazzi
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Apartado Postal 11501-2060, San José, Costa Rica
| | - German Rivera-Coto
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
| | - Ramón Molina-Bravo
- Escuela de Ciencias Agrarias, Universidad Nacional, Apartado Postal 86-3000, Heredia, Costa Rica
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Chen L, Zhou J, Zeng T, Miao YF, Mei L, Yao GB, Fang K, Dong XF, Sha T, Yang MZ, Li T, Zhao ZW, Zhang HB. Quantifying the sharing of foliar fungal pathogens by the invasive plant Ageratina adenophora and its neighbours. THE NEW PHYTOLOGIST 2020; 227:1493-1504. [PMID: 32343409 DOI: 10.1111/nph.16624] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/15/2020] [Indexed: 05/26/2023]
Abstract
Local pathogens can accumulate as asymptomatic endophytes, making it difficult to detect the impacts of invasive species as propagators of disease in the invaded range. We used the invasive plant Ageratina adenophora to assess such accumulation. We intensively collected foliar fungal endophytes and leaf spot pathogens of A. adenophora and co-occurring neighbours and performed an inoculation experiment to evaluate their pathogenicity and host range. Ageratina adenophora harboured diverse necrotrophic pathogens; its communities of endophytes and leaf spot pathogens were different in composition and shared only a small number of fungal species. In the pathogen communities of local plant hosts, 21% of the operational taxonomic units (OTUs), representing 50% of strains, also occurred as leaf spot pathogens and/or endophytes of A. adenophora. The local pathogen community was more similar to the endophytes than to the pathogens of A. adenophora. The inoculation experiment showed that local pathogens could infect A. adenophora leaves asymptomatically and that local plant hosts were susceptible to both A. adenophora endophytes and pathogens. Ageratina adenophora is a highly competent host for local pathogens, and its asymptomatic latent pathogens are fungi primarily shared with local neighbours. This poses challenges for understanding the long-term ecological consequences of plant invasion.
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Affiliation(s)
- Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Tian Zeng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Yi-Fang Miao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Liang Mei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Guang-Bo Yao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Tao Sha
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Ming-Zhi Yang
- School of Life Science, Yunnan University, Kunming, 650091, China
| | - Tao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Zhi-Wei Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
- School of Life Science, Yunnan University, Kunming, 650091, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
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Carro-Huerga G, Compant S, Gorfer M, Cardoza RE, Schmoll M, Gutiérrez S, Casquero PA. Colonization of Vitis vinifera L. by the Endophyte Trichoderma sp. Strain T154: Biocontrol Activity Against Phaeoacremonium minimum. FRONTIERS IN PLANT SCIENCE 2020; 11:1170. [PMID: 32849725 PMCID: PMC7417607 DOI: 10.3389/fpls.2020.01170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/20/2020] [Indexed: 05/26/2023]
Abstract
Trichoderma strains used in biological control products usually exhibit high efficiency in the control of plant diseases. However, their behavior under field conditions is difficult to predict. In addition, the potential of indigenous strains has been poorly assayed as well as their possible behavior as endophytes. Hence, niche colonization is a key feature for an effective protection. In this study, we aimed to: (i) explore the possibility of using a new Trichoderma strain isolated from vine to control pathogens, (ii) study the in planta interaction with the pathogen Phaeoacremonium minimum W. Gams, Crous, M.J. Wingf. & L. Mugnai (formerly Phaeoacremonium aleophilum), a pioneer fungus involved in Grapevine Trunk Diseases (GTDs) such as esca. For this purpose, fluorescently tagged Trichoderma sp. T154 and a P. minimum strain were used for scanning electron microscopy and confocal scanning laser microscopy analyses. Data showed that the Trichoderma strain is able to colonize plants up to 12 weeks post inoculation and is located in xylem, fibers, as well as in parenchymatic tissues inside the wood. The beneficial fungus reduced colonization of the esca-related pathogen colonizing the same niches. The main observed mechanism involved in biocontrol of Trichoderma against the esca pathogen was spore adhesion, niche exclusion and only few typical hypha coiling was found between Trichoderma and the pathogen. These results suggest that the Trichoderma strain has potential for reducing the colonization of Phaeoacremonium minimum and thus, an inoculation of this biological control agent can protect the plant by limiting the development of GTD, and the strain can behave as an endophyte.
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Affiliation(s)
- Guzmán Carro-Huerga
- Research Group of Engineering and Sustainable Agriculture, Natural Resources Institute, Universidad de León, León, Spain
| | - Stéphane Compant
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Markus Gorfer
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Rosa E. Cardoza
- Research Group of Engineering and Sustainable Agriculture, Natural Resources Institute, Universidad de León, León, Spain
- Area of Microbiology, University School of Agricultural Engineers, Universidad de León, Ponferrada, Spain
| | - Monika Schmoll
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Santiago Gutiérrez
- Research Group of Engineering and Sustainable Agriculture, Natural Resources Institute, Universidad de León, León, Spain
- Area of Microbiology, University School of Agricultural Engineers, Universidad de León, Ponferrada, Spain
| | - Pedro A. Casquero
- Research Group of Engineering and Sustainable Agriculture, Natural Resources Institute, Universidad de León, León, Spain
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Biodiversity of Trichoderma from grassland and forest ecosystems in Northern Xinjiang, China. 3 Biotech 2020; 10:362. [PMID: 32821644 PMCID: PMC7392985 DOI: 10.1007/s13205-020-02301-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Trichoderma spp., a cosmopolitan fungal genus, has remarkable economic value in industry and agriculture. The resources of Trichoderma spp. in the grassland and forest ecosystems of northern Xinjiang were explored in this study. A total of 634 soil samples was collected, and 312 strains assigned to 23 species of Trichoderma spp. were identified. T. harzianum was the dominant species with 28.2% from all isolates. The principal components analysis indicated that ecosystem was the most dominant impact factor among longitude, latitude, altitude and ecosystems for the species diversities of Trichoderma spp. with the decreasing trend from the north to the south of northern Xinjiang (e.g., from Altay, followed by Yili, Changji, Bayingolin and finally Urumqi). Overall, Trichoderma spp. were more frequently encountered in forest ecosystems (coniferous forest and coniferous and broadleaf mixed forest) than in grassland ecosystems (desert steppe and temperate steppe). Frequency of Trichoderma spp. was significantly decreased along with increased altitude and only a few strains were isolated from altitudes above 3000 m. The results provided essential information on Trichoderma occurrence and distribution, which should benefit the application of Trichoderma in agriculture.
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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Khodadadi F, González JB, Martin PL, Giroux E, Bilodeau GJ, Peter KA, Doyle VP, Aćimović SG. Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov. Sci Rep 2020; 10:11043. [PMID: 32632221 PMCID: PMC7338416 DOI: 10.1038/s41598-020-66761-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 05/27/2020] [Indexed: 11/21/2022] Open
Abstract
Apple bitter rot caused by Colletotrichum species is a growing problem worldwide. Colletotrichum spp. are economically important but taxonomically un-resolved. Identification of Colletotrichum spp. is critical due to potential species-level differences in pathogenicity-related characteristics. A 400-isolate collection from New York apple orchards were morphologically assorted to two groups, C. acutatum species complex (CASC) and C. gloeosporioides species complex (CGSC). A sub-sample of 44 representative isolates, spanning the geographical distribution and apple varieties, were assigned to species based on multi-locus phylogenetic analyses of nrITS, GAPDH and TUB2 for CASC, and ITS, GAPDH, CAL, ACT, TUB2, APN2, ApMat and GS genes for CGSC. The dominant species was C. fioriniae, followed by C. chrysophilum and a novel species, C. noveboracense, described in this study. This study represents the first report of C. chrysophilum and C. noveboracense as pathogens of apple. We assessed the enzyme activity and fungicide sensitivity for isolates identified in New York. All isolates showed amylolytic, cellulolytic and lipolytic, but not proteolytic activity. C. chrysophilum showed the highest cellulase and the lowest lipase activity, while C. noveboracense had the highest amylase activity. Fungicide assays showed that C. fioriniae was sensitive to benzovindiflupyr and thiabendazole, while C. chrysophilum and C. noveboracense were sensitive to fludioxonil, pyraclostrobin and difenoconazole. All species were pathogenic on apple fruit with varying lesion sizes. Our findings of differing pathogenicity-related characteristics among the three species demonstrate the importance of accurate species identification for any downstream investigations of Colletotrichum spp. in major apple growing regions.
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Affiliation(s)
- Fatemeh Khodadadi
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Hudson Valley Research Laboratory, Highland, NY, USA
| | - Jonathan B González
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Ithaca, NY, USA
| | - Phillip L Martin
- Pennsylvania State University, Department of Plant Pathology and Environmental Microbiology, Fruit Research and Extension Center, Biglerville, PA, USA
| | - Emily Giroux
- Pathogen Identification Research Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Guillaume J Bilodeau
- Pathogen Identification Research Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Kari A Peter
- Pennsylvania State University, Department of Plant Pathology and Environmental Microbiology, Fruit Research and Extension Center, Biglerville, PA, USA
| | - Vinson P Doyle
- Louisiana State University AgCenter, Department of Plant Pathology and Crop Physiology, Baton Rouge, Louisiana, USA
| | - Srđan G Aćimović
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Hudson Valley Research Laboratory, Highland, NY, USA.
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Calvillo-Medina RP, Gunde-Cimerman N, Escudero-Leyva E, Barba-Escoto L, Fernández-Tellez EI, Medina-Tellez AA, Bautista-de Lucio V, Ramos-López MÁ, Campos-Guillén J. Richness and metallo-tolerance of cultivable fungi recovered from three high altitude glaciers from Citlaltépetl and Iztaccíhuatl volcanoes (Mexico). Extremophiles 2020; 24:625-636. [PMID: 32535716 DOI: 10.1007/s00792-020-01182-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/29/2020] [Indexed: 11/26/2022]
Abstract
In Mexico little is known about high-altitude glacial psychrotolerant or psychrophilic fungal species, with most glacial fungi isolated from polar environments or Alpine glaciers. It has been documented that some of these species may play an important role in bioremediation of contaminated environments with heavy metals. In the present study, 75 fungi were isolated from glaciers in Citlaltépetl (5675 masl) and Iztaccíhuatl (5286 masl) volcanoes. Combining morphological characteristics and molecular methods, based on ITS rDNA, 38 fungi were partially identified to genus level, 35 belonging to Ascomycota and three to Mucoromycota. The most abundant genera were Cladosporium, followed by Alternaria and Sordariomycetes order. All isolated fungi were psychrotolerant, pigmented and resistant to different concentrations of Cr(III) and Pb(II), while none tolerated Hg(II). Fungi most tolerant to Cr(III) and Pb(II) belong to the genera Stemphylium, Cladosporium and Penicillium and to a lesser extent Aureobasidium and Sordariomycetes. To our knowledge, this is the first report on cultivable mycobiota richness and their Cr and Pb tolerance. The results open new research possibilities about fungal diversity and heavy metals myco-remediation. Extremophilic fungal communities should be further investigated before global warming causes permanent changes and we miss the opportunity to describe these sites in Mexico.
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Affiliation(s)
| | - Nina Gunde-Cimerman
- Molecular Genetics and Biology of Microorganisms, Dept. Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Efraín Escudero-Leyva
- Centro de Investigaciones en Productos Naturales (CIPRONA) Y Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), Centro Nacional de Computación Avanzada (CNCA), CeNAT-CONARE, San José, Costa Rica
| | - Luis Barba-Escoto
- International Maize and Wheat Improvement Center (CIMMYT), Sustainable Intensification Program, Texcoco, Mexico
| | | | | | - Victor Bautista-de Lucio
- Laboratorio de Microbiología Y Proteómica, Instituto de Oftalmología "Fundación de Asistencia Privada Conde de Valenciana", Mexico City, Mexico
| | | | - Juan Campos-Guillén
- Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro, Qro, Mexico
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Menolli N, Sánchez-García M. Brazilian fungal diversity represented by DNA markers generated over 20 years. Braz J Microbiol 2020; 51:729-749. [PMID: 31828716 PMCID: PMC7203393 DOI: 10.1007/s42770-019-00206-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/01/2019] [Indexed: 10/25/2022] Open
Abstract
Molecular techniques using fungal DNA barcoding (ITS) and other markers have been key to identifying the biodiversity of different geographic areas, mainly in megadiverse countries. Here, we provide an overview of the fungal diversity in Brazil based on DNA markers of phylogenetic importance generated since 1996. We retrieved fungal sequences of ITS, LSU, SSU, tef1-α, β-tubulin, rpb1, rpb2, actin, chitin synthase, and ATP6 from GenBank using different field keywords that indicated their origin in Brazil. A total of 19,440 sequences were recovered. ITS is the most representative marker (11,209 sequences), with 70.1% belonging to Ascomycota, 18.6% Basidiomycota, 10.2% unidentified, 1.1% Mucoromycota, two sequences of Olpidium bornovanus (Fungi incertae sedis), one sequence of Blastocladiomycota (Allomyces arbusculus), and one sequence of Chytridiomycota (Batrachochytrium dendrobatidis). Considering the sequences of all selected markers, only the phyla Cryptomycota and Entorrhizomycota were not represented. Based on ITS, using a cutoff of 98%, all sequences comprise 3047 OTUs, with the majority being Ascomycota (2088 OTUs) and Basidiomycota (681 OTUs). Previous numbers based mainly on morphological and bibliographical data revealed 5264 fungal species from Brazil, with a predominance of Basidiomycota (2741 spp.) and Ascomycota (1881 spp.). The unidentified ITS sequences not assigned to a higher taxonomic level represent 1.61% of all ITS sequences sampled and correspond to 38 unknown class-level lineages (75% cutoff). A maximum likelihood phylogeny based on LSU illustrates the fungal classes occurring in Brazil.
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Affiliation(s)
- Nelson Menolli
- Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo, Rua Pedro Vicente 625, São Paulo, SP, 01109-010, Brazil.
- Núcleo de Pesquisa em Micologia, Instituto de Botânica, Av. Miguel Stefano 3687, Água Funda, São Paulo, SP, 04301-012, Brazil.
| | - Marisol Sánchez-García
- Biology Department, Clark University, Worcester, MA, 01610, USA
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75005, Sweden
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36
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Hung N, Hsiao CH, Yang CS, Lin HC, Yeh LK, Fan YC, Sun PL. Colletotrichum keratitis: A rare yet important fungal infection of human eyes. Mycoses 2020; 63:407-415. [PMID: 32022938 DOI: 10.1111/myc.13058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND Colletotrichum is a rare cause of human infection. Previous reports about Colletotrichum keratitis were limited, and most diagnoses from past reports were based on morphological distinction, which could have led to underestimation of the prevalence of Colletotrichum species. OBJECTIVE We reported phylogenetic analysis, clinical feature and treatment outcome of molecularly diagnosed Colletotrichum keratitis in our hospital. PATIENTS/METHODS We recruited 65 patients with culture-proven filamentous fungal keratitis between January 1, 2015 and December 30, 2018. Through molecular sequencing including internal transcribed spacer (ITS) and multi-locus phylogenetic analysis of fungal DNA, seven patients were verified as infected with Colletotrichum species, and their medical records were reviewed to determine the clinical characteristics. RESULTS Six of seven patients had predisposing factors including trauma (5) and immunosuppressive status (1). Six isolates were initially misidentified as other fungi through morphological identification. ITS sequencing identified the isolates belonged to two species complex (SC): C. truncatum and C. gloeosporioides; multi-locus phylogenetic analysis enabled species identification including C. tropicale (3), C. fructicola (2), C. truncatum (1) and C. fusiforme (1). Five patients with C. gloeosporioides SC responded well to medical treatment and two patients with C truncatum SC underwent evisceration because of either no visual potential or intractable pain. CONCLUSIONS The molecular approach provides accurate diagnosis and raises epidemiological awareness of Colletotrichum keratitis. Through multi-locus phylogenetic analysis, we report the human infections caused by C. tropicale, C. fructicola and C. fusiforme. We also highlight the different clinical outcomes between C. gloeosporioides SC and C. truncatum SC.
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Affiliation(s)
- Ning Hung
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Ching-Hsi Hsiao
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Sheng Yang
- Department of Dermatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan.,Research Laboratory of Medical Mycology, Department of Dermatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Hsin-Chiung Lin
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Lung-Kun Yeh
- Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yun-Chen Fan
- Research Laboratory of Medical Mycology, Department of Dermatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Pei-Lun Sun
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Dermatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan.,Research Laboratory of Medical Mycology, Department of Dermatology, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
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Fang K, Miao YF, Chen L, Zhou J, Yang ZP, Dong XF, Zhang HB. Tissue-Specific and Geographical Variation in Endophytic Fungi of Ageratina adenophora and Fungal Associations With the Environment. Front Microbiol 2019; 10:2919. [PMID: 31921082 PMCID: PMC6930192 DOI: 10.3389/fmicb.2019.02919] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022] Open
Abstract
To understand the distribution of the cultivable fungal community in plant tissues and the associations of these fungi with their surrounding environments during the geographical expansion of an invasive plant, Ageratina adenophora, we isolated the cultivable fungi from 72 plant tissues, 12 soils, and 12 air samples collected from six areas in Yunnan Province, China. A total of 4066 isolates were investigated, including 1641 endophytic fungi, 233 withered leaf fungi, 1255 fungi from air, and 937 fungi from soil. These fungi were divided into 458 and 201 operational taxonomic units (OTUs) with unique and 97% ITS gene sequence identity, respectively. Phylogenetic analysis showed that the fungi belonged to four phyla, including Ascomycota (94.20%), Basidiomycota (2.71%), Mortierellomycota (3.03%), and Mucoromycota (0.07%). The dominant genera of cultivable endophytic fungi were Colletotrichum (34.61%), Diaporthe (17.24%), Allophoma (8.03%), and Fusarium (4.44%). Colletotrichum and Diaporthe were primarily isolated from mature leaves, Allophoma from stems, and Fusarium from roots, indicating that the enrichment of endophytic fungi is tissue-specific and fungi rarely grew systemically within A. adenophora. In the surrounding environment, Alternaria (21.46%), Allophoma (19.31%), Xylaria (18.45%), and Didymella (18.03%) were dominant in the withered leaves, Cladosporium (22.86%), Trichoderma (14.27%), and Epicoccum (9.83%) were dominant in the canopy air, and Trichoderma (27.27%) and Mortierella (20.46%) were dominant in the rhizosphere soils. Further analysis revealed that the cultivable endophytic fungi changed across geographic areas and showed a certain degree of variation in different tissues of A. adenophora. The cultivable fungi in mature and withered leaves fluctuated more than those in roots and stems. We also found that some cultivable endophytic fungi might undergo tissue-to-tissue migration and that the stem could be a transport tissue by which airborne fungi infect roots. Finally, we provided evidence that the fungal community within A. adenophora was partially shared with the contiguous environment. The data suggested a frequent interaction between fungi associated with A. adenophora and those in surrounding environments, reflecting a compromise driven by both functional requirements for plant growth and local environmental conditions.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yi-Fang Miao
- Lu Cheng Center for Disease Control and Prevention, Changzhi, China
| | - Lin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jie Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Zhi-Ping Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Xing-Fan Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- School of Life Sciences, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
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38
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Deaver NR, Hesse C, Kuske CR, Porras-Alfaro A. Presence and distribution of insect-associated and entomopathogenic fungi in a temperate pine forest soil: An integrated approach. Fungal Biol 2019; 123:864-874. [PMID: 31733729 DOI: 10.1016/j.funbio.2019.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 01/26/2023]
Abstract
For decades entomopathogenic fungi have garnered interest as possible alternatives to chemical pesticides. However, their ecology outside of agroecosystems demands further study. We assessed the diversity and abundance of entomopathogenic and insect-associated fungi at a loblolly pine forest in North Carolina, USA using culture-dependent and next-generation sequencing libraries. Fungi were isolated using Galleriamellonella larvae, as well as from soil dilutions plated on a selective medium. Isolates were identified using Sanger sequencing of the ITS and LSU rRNA gene regions, and represented 36 OTUs including Metarhizium, Lecanicillium, and Paecilomyces. Additionally, we assessed the chitinolytic potential of isolates and found widespread, variable ability to degrade chitin within and between genera. Phylogenetic analyses resolved several isolates to genus, with some forming clades with other insect-associated taxa, as well as with fungi associated with plant tissues. Saprophytes were widely distributed in soil, while entomopathogens were less abundant and present primarily in the top two cm of the soil. The similarity between culture-dependent and next-generation sequencing results demonstrates that both methods can be used concurrently in this system to study the ecology of entomopathogenic fungi.
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Affiliation(s)
- Noland R Deaver
- Biological Sciences Department, Western Illinois University, 1 University Circle, Macomb, 61455 IL, USA
| | - Cedar Hesse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA; United States Department of Agriculture, 3420 NW Orchard Ave, Corvallis, 97330 OR, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, 87545 NM, USA
| | - Andrea Porras-Alfaro
- Biological Sciences Department, Western Illinois University, 1 University Circle, Macomb, 61455 IL, USA.
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39
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Hu J, Zhou Y, Chen K, Li J, Wei Y, Wang Y, Wu Y, Ryder MH, Yang H, Denton MD. Large‐scale
Trichoderma
diversity was associated with ecosystem, climate and geographic location. Environ Microbiol 2019; 22:1011-1024. [DOI: 10.1111/1462-2920.14798] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/29/2019] [Accepted: 09/05/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Jindong Hu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yi Zhou
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
- School of Agriculture, Food and Wine The University of Adelaide SA Australia
| | - Kai Chen
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Jishun Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yanli Wei
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yilian Wang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Yuanzheng Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Maarten H. Ryder
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
- School of Agriculture, Food and Wine The University of Adelaide SA Australia
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
| | - Matthew D. Denton
- China‐Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences) Shandong China
- Waite campus The University of Adelaide SA Australia
- School of Agriculture, Food and Wine The University of Adelaide SA Australia
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40
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Skaltsas DN, Badotti F, Vaz ABM, Silva FFD, Gazis R, Wurdack K, Castlebury L, Góes-Neto A, Chaverri P. Exploration of stem endophytic communities revealed developmental stage as one of the drivers of fungal endophytic community assemblages in two Amazonian hardwood genera. Sci Rep 2019; 9:12685. [PMID: 31481728 PMCID: PMC6722055 DOI: 10.1038/s41598-019-48943-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Many aspects of the dynamics of tropical fungal endophyte communities are poorly known, including the influence of host taxonomy, host life stage, host defence, and host geographical distance on community assembly and composition. Recent fungal endophyte research has focused on Hevea brasiliensis due to its global importance as the main source of natural rubber. However, almost no data exist on the fungal community harboured within other Hevea species or its sister genus Micrandra. In this study, we expanded sampling to include four additional Hevea spp. and two Micrandra spp., as well as two host developmental stages. Through culture-dependent and -independent (metagenomic) approaches, a total of 381 seedlings and 144 adults distributed across three remote areas within the Peruvian Amazon were sampled. Results from both sampling methodologies indicate that host developmental stage had a greater influence in community assemblage than host taxonomy or locality. Based on FunGuild ecological guild assignments, saprotrophic and mycotrophic endophytes were more frequent in adults, while plant pathogens were dominant in seedlings. Trichoderma was the most abundant genus recovered from adult trees while Diaporthe prevailed in seedlings. Potential explanations for that disparity of abundance are discussed in relation to plant physiological traits and community ecology hypotheses.
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Affiliation(s)
- Demetra N Skaltsas
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland, 20742, USA.
- U.S. Department of Agriculture, Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA.
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN, 37831, USA.
| | - Fernanda Badotti
- Centro Federal de Educação Tecnológica de Minas Gerais, Departamento de Química, 30421-169, Belo Horizonte, Minas Gerais, 30421-169, Brazil
| | - Aline Bruna Martins Vaz
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, 31270-901, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Felipe Ferreira da Silva
- Universidade Federal de Minas Gerais, Departamento de Microbiologia, 31270-901, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Romina Gazis
- University of Florida, Department of Plant Pathology, Tropical Research & Education Center, 18905 SW 280 Street, Homestead, Florida, 33031, USA
| | - Kenneth Wurdack
- Smithsonian Institution, Department of Botany, National Museum of Natural History, P.O. Box 37012, Washington, District of Columbia, 20013, USA
| | - Lisa Castlebury
- U.S. Department of Agriculture, Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland, 20705, USA
| | - Aristóteles Góes-Neto
- Centro Federal de Educação Tecnológica de Minas Gerais, Departamento de Química, 30421-169, Belo Horizonte, Minas Gerais, 30421-169, Brazil
| | - Priscila Chaverri
- University of Maryland, Department of Plant Science and Landscape Architecture, 2112 Plant Sciences Building, College Park, Maryland, 20742, USA
- Escuela de Biología, Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, San José, 11501, Costa Rica, USA
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41
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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42
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Sundaresan N, Sahu AK, Jagan EG, Pandi M. Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study. Fungal Biol 2019; 123:517-527. [PMID: 31196521 DOI: 10.1016/j.funbio.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 04/01/2019] [Accepted: 05/02/2019] [Indexed: 01/19/2023]
Abstract
Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Amit Kumar Sahu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
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Makiola A, Dickie IA, Holdaway RJ, Wood JR, Orwin KH, Lee CK, Glare TR. Biases in the metabarcoding of plant pathogens using rust fungi as a model system. Microbiologyopen 2018; 8:e00780. [PMID: 30585441 PMCID: PMC6612544 DOI: 10.1002/mbo3.780] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/24/2023] Open
Abstract
Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost-effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next-generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large-scale detection and quantification of rust fungi, but not for confirming the absence of species.
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Affiliation(s)
- Andreas Makiola
- Agroécologie, AgroSup Dijon, INRAUniversité Bourgogne, Université Bourgogne Franche‐ComtéDijonFrance,Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyNew Zealand
| | | | - Jamie R. Wood
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Kate H. Orwin
- Manaaki Whenua – Landcare ResearchLincolnNew Zealand
| | - Charles K. Lee
- Waikato DNA Sequencing Facility, School of ScienceUniversity of WaikatoHamiltonNew Zealand
| | - Travis R. Glare
- Bio‐Protection Research CentreLincoln UniversityLincolnNew Zealand
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Kaliane SA, Vanessa NB, Tomás GRV, Tiago DSL, Olinto LP, Eduardo SGM, Marisa VDQ. Diversity of culturable endophytic fungi of Hevea guianensis: A latex producer native tree from the Brazilian Amazon. ACTA ACUST UNITED AC 2018. [DOI: 10.5897/ajmr2018.8980] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Vaz ABM, Fonseca PLC, Badotti F, Skaltsas D, Tomé LMR, Silva AC, Cunha MC, Soares MA, Santos VL, Oliveira G, Chaverri P, Góes-Neto A. A multiscale study of fungal endophyte communities of the foliar endosphere of native rubber trees in Eastern Amazon. Sci Rep 2018; 8:16151. [PMID: 30385829 PMCID: PMC6212449 DOI: 10.1038/s41598-018-34619-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/17/2018] [Indexed: 12/18/2022] Open
Abstract
Hevea brasiliensis is a native hyperdiverse tree species in the Amazon basin with great economic importance since it produces the highest quality natural rubber. H. brasiliensis, in its natural habitat, may harbor fungal endophytes that help defend against phytopathogenic fungi. In this work, we investigated the fungal endophytic communities in two pristine areas in Eastern Amazon (Anavilhanas National Park - ANP and Caxiuanã National Forest - CNF) at different spatial scales: regional, local, individual (tree), and intra-individual (leaflet). Using a culture-based approach, 210 fungal endophytes were isolated from 240 sampling units and assigned to 46 distinct MOTUs based on sequencing of the nrITS DNA. The community compositions of the endophytomes are different at both regional and local scales, dominated by very few taxa and highly skewed toward rare taxa, with many endophytes infrequently isolated across hosts in sampled space. Colletotrichum sp. 1, a probably latent pathogen, was the most abundant endophytic putative species and was obtained from all individual host trees in both study areas. Although the second most abundant putative species differed between the two collection sites, Clonostachys sp. 1 and Trichoderma sp. 1, they are phylogenetically related (Hypocreales) mycoparasites. Thus, they probably exhibit the same ecological function in the foliar endosphere of rubber tree as antagonists of its fungal pathogens.
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Affiliation(s)
- Aline B M Vaz
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
- Faculdade de Minas (FAMINAS), Belo Horizonte, MG, 31744-007, Brazil
| | - Paula L C Fonseca
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Belo Horizonte, MG, 30480-000, Brazil
| | | | - Luiz M R Tomé
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Allefi C Silva
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Mayara C Cunha
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Marco A Soares
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | - Vera L Santos
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil
| | | | - Priscilla Chaverri
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Aristóteles Góes-Neto
- Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, 31270-901, Brazil.
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46
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Loyd AL, Barnes CW, Held BW, Schink MJ, Smith ME, Smith JA, Blanchette RA. Elucidating "lucidum": Distinguishing the diverse laccate Ganoderma species of the United States. PLoS One 2018; 13:e0199738. [PMID: 30020945 PMCID: PMC6051579 DOI: 10.1371/journal.pone.0199738] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/13/2018] [Indexed: 11/18/2022] Open
Abstract
Ganoderma is a large, diverse and globally-distributed genus in the Basidiomycota that includes species causing a white rot form of wood decay on a variety of tree species. For the past century, many studies of Ganoderma in North America and other regions of the world have used the name G. lucidum sensu lato for any laccate (shiny or varnished) Ganoderma species growing on hardwood trees or substrates. Molecular studies have established that G. lucidum sensu stricto (Curtis) Karst is native to Europe and some parts of China. To determine the species of the laccate Ganoderma that are present in the United States, we studied over 500 collections from recently collected samples and herbarium specimens from hardwoods, conifers, and monocots. A multilocus phylogeny using ITS, tef1α, rpb1 and rpb2 revealed three well-supported clades, similar to previously reported findings. From the U.S. collections, thirteen taxa representing twelve species were identified, including: G. curtisii, G. lucidum sensu stricto, G. martinicense, G. oregonense, G. polychromum, G. ravenelii, G. sessile, G. tsugae, G. tuberculosum, G. cf. weberianum, G. zonatum, and Tomophagus colossus (syn. G. colossus). The species G. meredithiae is synonymized with G. curtisii, and considered a physiological variant that specializes in decay of pines. The designation G. curtisii f.sp. meredithiae forma specialis nov. is proposed. Species such as G. curtisii and G. sessile, once considered as G. lucidum sensu lato, were found to be divergent from one another, and highly divergent from G. lucidum sensu stricto. Morphological characteristics such as context tissue color and features (e.g. melanoid bands), basidiospore shape and size, geographic location, and host preference were found to aid in species identification. Surprisingly, G. lucidum sensu stricto was found in the U.S., but only in geographically restricted areas of northern Utah and California. These collections appear to have resulted from the introduction of this species into the United States possibly from mushroom growers producing G. lucidum outdoors. Overall, this study clarifies the chaotic taxonomy of the laccate Ganoderma in the United States, and will help to remove ambiguities from future studies focusing on the North American species of laccate Ganoderma.
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Affiliation(s)
- A. L. Loyd
- University of Florida, School of Forest Resources and Conservation, Gainesville, FL, United States of America
- The F.A. Bartlett Tree Experts Company, Charlotte, NC, United States of America
- * E-mail:
| | - C. W. Barnes
- Departamento Nacional de Protection Vegetal, INAP, Quito, Ecuador
| | - B. W. Held
- University of Minnesota, Department of Plant Pathology, St. Paul, MN, United States of America
| | - M. J. Schink
- Independent Researcher, Port Crane, NY, United States of America
| | - M. E. Smith
- University of Florida, Department of Plant Pathology, Gainesville, FL, United States of America
| | - J. A. Smith
- University of Florida, School of Forest Resources and Conservation, Gainesville, FL, United States of America
| | - R. A. Blanchette
- University of Minnesota, Department of Plant Pathology, St. Paul, MN, United States of America
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Lücking R, Hawksworth DL. Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them. IMA Fungus 2018; 9:143-166. [PMID: 30018876 PMCID: PMC6048566 DOI: 10.5598/imafungus.2018.09.01.09] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 05/15/2018] [Indexed: 11/25/2022] Open
Abstract
There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6–8, 14195 Berlin, Germany
| | - David L. Hawksworth
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; and Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK; Jilin Agricultural University, Changchun, Jilin Province,130118 China
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48
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Mycobiota associated with insect galleries in walnut with thousand cankers disease reveals a potential natural enemy against Geosmithia morbida. Fungal Biol 2018; 122:241-253. [DOI: 10.1016/j.funbio.2018.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 01/22/2018] [Indexed: 12/30/2022]
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49
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Veloso JS, Câmara MPS, Lima WG, Michereff SJ, Doyle VP. Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil. Fungal Biol 2018; 122:677-691. [PMID: 29880203 DOI: 10.1016/j.funbio.2018.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 03/05/2018] [Accepted: 03/13/2018] [Indexed: 01/03/2023]
Abstract
Anthracnose is one of the most important plant diseases globally, occurring on a wide range of cultivated and wild host species. This study aimed to identify the Colletotrichum species associated with cashew anthracnose in Brazil, determine their phylogenetic relationships and geographical distribution, and provide some insight into the factors that may be influencing community composition. Colletotrichum isolates collected from symptomatic leaves, stems, inflorescences, and fruit of cultivated and wild cashew, across four Brazilian biomes, were identified as Colletotrichum chrysophilum, Colletotrichum fragariae, Colletotrichum fructicola, Colletotrichum gloeosporioides sensu stricto, Colletotrichum queenslandicum, Colletotrichum siamense and Colletotrichum tropicale. Colletotrichum siamense was the most dominant species. The greatest species richness was associated with cultivated cashew; leaves harbored more species than the other organs; the Atlantic Forest encompassed more species than the other biomes; and Pernambuco was the most species-rich location. However, accounting for the relative abundance of Colletotrichum species and differences in sample size across strata, the interpretation of which community is most diverse depends on how species are delimited. The present study provides valuable information about the Colletotrichum/cashew pathosystem, sheds light on the causal agents identification,and highlights the impact that species delimitation can have on ecological studies of fungi.
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Affiliation(s)
- Josiene S Veloso
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, Pernambuco, Brazil.
| | - Marcos P S Câmara
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, Pernambuco, Brazil.
| | - Waléria G Lima
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, Pernambuco, Brazil.
| | - Sami J Michereff
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, Pernambuco, Brazil.
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA, 70803, USA.
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50
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Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR, Labutti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora J, Grigoriev IV, Martin FM, Pujade-Renaud V. Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors. Front Microbiol 2018; 9:276. [PMID: 29551995 PMCID: PMC5840194 DOI: 10.3389/fmicb.2018.00276] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/07/2018] [Indexed: 12/26/2022] Open
Abstract
Corynespora cassiicola is an Ascomycetes fungus with a broad host range and diverse life styles. Mostly known as a necrotrophic plant pathogen, it has also been associated with rare cases of human infection. In the rubber tree, this fungus causes the Corynespora leaf fall (CLF) disease, which increasingly affects natural rubber production in Asia and Africa. It has also been found as an endophyte in South American rubber plantations where no CLF outbreak has yet occurred. The C. cassiicola species is genetically highly diverse, but no clear relationship has been evidenced between phylogenetic lineage and pathogenicity. Cassiicolin, a small glycosylated secreted protein effector, is thought to be involved in the necrotrophic interaction with the rubber tree but some virulent C. cassiicola isolates do not have a cassiicolin gene. This study set out to identify other putative effectors involved in CLF. The genome of a highly virulent C. cassiicola isolate from the rubber tree (CCP) was sequenced and assembled. In silico prediction revealed 2870 putative effectors, comprising CAZymes, lipases, peptidases, secreted proteins and enzymes associated with secondary metabolism. Comparison with the genomes of 44 other fungal species, focusing on effector content, revealed a striking proximity with phylogenetically unrelated species (Colletotrichum acutatum, Colletotrichum gloesporioides, Fusarium oxysporum, nectria hematococca, and Botrosphaeria dothidea) sharing life style plasticity and broad host range. Candidate effectors involved in the compatible interaction with the rubber tree were identified by transcriptomic analysis. Differentially expressed genes included 92 putative effectors, among which cassiicolin and two other secreted singleton proteins. Finally, the genomes of 35 C. cassiicola isolates representing the genetic diversity of the species were sequenced and assembled, and putative effectors identified. At the intraspecific level, effector-based classification was found to be highly consistent with the phylogenomic trees. Identification of lineage-specific effectors is a key step toward understanding C. cassiicola virulence and host specialization mechanisms.
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Affiliation(s)
- David Lopez
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
| | - Sébastien Ribeiro
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France.,CIRAD, UMR AGAP, Clermont-Ferrand, France.,AGAP, Université Montpellier, CIRAD, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
| | - Philippe Label
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
| | - Boris Fumanal
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
| | - Jean-Stéphane Venisse
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France
| | - Annegret Kohler
- Institut National de la Recherche Agronomique, UMR INRA-Université de Lorraine "Interaction Arbres/Microorganismes", Champenoux, France
| | | | - Kurt Labutti
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Kathleen Lail
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Diane Bauer
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Robin A Ohm
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States.,Department of Microbiology, Utrecht University, Utrecht, Netherlands
| | - Kerrie W Barry
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
| | - Joseph Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Francis M Martin
- Institut National de la Recherche Agronomique, UMR INRA-Université de Lorraine "Interaction Arbres/Microorganismes", Champenoux, France
| | - Valérie Pujade-Renaud
- Université Clermont Auvergne, Institut National de la Recherche Agronomique, UMR PIAF, Clermont-Ferrand, France.,CIRAD, UMR AGAP, Clermont-Ferrand, France.,AGAP, Université Montpellier, CIRAD, Institut National de la Recherche Agronomique, Montpellier SupAgro, Montpellier, France
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