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Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proc Natl Acad Sci U S A 2024; 121:e2316284121. [PMID: 38442176 PMCID: PMC10945790 DOI: 10.1073/pnas.2316284121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/24/2024] [Indexed: 03/07/2024] Open
Abstract
Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are, and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungus Metarhizium robertsii during experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome-but no other-was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis, we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment between M. robertsii and another congeneric insect pathogen, Metarhizium guizhouense. Hence, horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The accessory chromosome that was transferred contains genes that may be involved in its preferential horizontal transfer or support its establishment. These genes encode putative histones and histone-modifying enzymes, as well as putative virulence factors. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.
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Affiliation(s)
- Michael Habig
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel24118, Germany
- Max Planck Institute for Evolutionary Biology, Plön24306, Germany
| | - Anna V. Grasse
- Institute of Science and Technology Austria (ISTA), Klosterneuburg3400, Austria
| | - Judith Müller
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel24118, Germany
- Max Planck Institute for Evolutionary Biology, Plön24306, Germany
| | - Eva H. Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel24118, Germany
- Max Planck Institute for Evolutionary Biology, Plön24306, Germany
| | - Hanna Leitner
- Institute of Science and Technology Austria (ISTA), Klosterneuburg3400, Austria
| | - Sylvia Cremer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg3400, Austria
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2
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Bian C, Kusuya Y, Sklenář F, D’hooge E, Yaguchi T, Ban S, Visagie C, Houbraken J, Takahashi H, Hubka V. Reducing the number of accepted species in Aspergillus series Nigri. Stud Mycol 2022; 102:95-132. [PMID: 36760462 PMCID: PMC9903907 DOI: 10.3114/sim.2022.102.03] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. Citation: Bian C, Kusuya Y, Sklenář F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022). Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology 102: 95-132. doi: 10.3114/sim.2022.102.03.
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Affiliation(s)
- C. Bian
- Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Y. Kusuya
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Biological Resource Center, National Institute of Technology and Evaluation, Kisarazu, Japan
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - E. D’hooge
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - S. Ban
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - C.M. Visagie
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - H. Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Molecular Chirality Research Center, Chiba University, Chiba, Japan;, Plant Molecular Science Center, Chiba University, Chiba, Japan,*Corresponding authors: H. Takahashi, ; V. Hubka,
| | - V. Hubka
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;,*Corresponding authors: H. Takahashi, ; V. Hubka,
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Quintanilha-Peixoto G, Marone MP, Raya FT, José J, Oliveira A, Fonseca PLC, Tomé LMR, Bortolini DE, Kato RB, Araújo DS, De-Paula RB, Cuesta-Astroz Y, Duarte EAA, Badotti F, de Carvalho Azevedo VA, Brenig B, Soares ACF, Carazzolle MF, Pereira GAG, Aguiar ERGR, Góes-Neto A. Phylogenomics and gene selection in Aspergillus welwitschiae: Possible implications in the pathogenicity in Agave sisalana. Genomics 2022; 114:110517. [PMID: 36306958 DOI: 10.1016/j.ygeno.2022.110517] [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: 07/12/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/04/2022]
Abstract
Aspergillus welwitschiae causes bole rot disease in sisal (Agave sisalana and related species) which affects the production of natural fibers in Brazil, the main worldwide producer of sisal fibers. This fungus is a saprotroph with a broad host range. Previous research established A. welwitschiae as the only causative agent of bole rot in the field, but little is known about the evolution of this species and its strains. In this work, we performed a comparative genomics analysis of 40 Aspergillus strains. We show the conflicting molecular identity of this species, with one sisal-infecting strain sharing its last common ancestor with Aspergillus niger, having diverged only 833 thousand years ago. Furthermore, our analysis of positive selection reveals sites under selection in genes coding for siderophore transporters, Sodium‑calcium exchangers, and Phosphatidylethanolamine-binding proteins (PEBPs). Herein, we discuss the possible impacts of these gene functions on the pathogenicity in sisal.
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Affiliation(s)
| | - Marina Püpke Marone
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Fábio Trigo Raya
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Juliana José
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | - Adriele Oliveira
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Dener Eduardo Bortolini
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, United States
| | - Ruth B De-Paula
- Department of Neurology, Baylor College of Medicine, Houston, United States
| | - Yesid Cuesta-Astroz
- Instituto Colombiano de Medicina Tropical, Universidad CES, Medellín, Colombia
| | - Elizabeth A A Duarte
- Centro Universitário Maria Milza, Cruz das Almas, Brazil; Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Fernanda Badotti
- Department of Chemistry, Federal Center of Technological Education of Minas Gerais, Belo Horizonte, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
| | - Marcelo Falsarella Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Seekles SJ, Punt M, Savelkoel N, Houbraken J, Wösten HAB, Ohm RA, Ram AFJ. Genome sequences of 24 Aspergillus niger sensu stricto strains to study strain diversity, heterokaryon compatibility, and sexual reproduction. G3 (BETHESDA, MD.) 2022; 12:jkac124. [PMID: 35608315 PMCID: PMC9258588 DOI: 10.1093/g3journal/jkac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/10/2022] [Indexed: 12/02/2022]
Abstract
Mating-type distribution within a phylogenetic tree, heterokaryon compatibility, and subsequent diploid formation were studied in 24 Aspergillus niger sensu stricto strains. The genomes of the 24 strains were sequenced and analyzed revealing an average of 6.1 ± 2.0 variants/kb between Aspergillus niger sensu stricto strains. The genome sequences were used together with available genome data to generate a phylogenetic tree revealing 3 distinct clades within Aspergillus niger sensu stricto. The phylogenetic tree revealed that both MAT1-1 and MAT1-2 mating types were present in each of the 3 clades. The phylogenetic differences were used to select for strains to analyze heterokaryon compatibility. Conidial color markers (fwnA and brnA) and auxotrophic markers (pyrG and nicB) were introduced via CRISPR/Cas9-based genome editing in a selection of strains. Twenty-three parasexual crosses using 11 different strains were performed. Only a single parasexual cross between genetically highly similar strains resulted in a successful formation of heterokaryotic mycelium and subsequent diploid formation, indicating widespread heterokaryon incompatibility as well as multiple active heterokaryon incompatibility systems between Aspergillus niger sensu stricto strains. The 2 vegetatively compatible strains were of 2 different mating types and a stable diploid was isolated from this heterokaryon. Sclerotium formation was induced on agar media containing Triton X-100; however, the sclerotia remained sterile and no ascospores were observed. Nevertheless, this is the first report of a diploid Aspergillus niger sensu stricto strain with 2 different mating types, which offers the unique possibility to screen for conditions that might lead to ascospore formation in A. niger.
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Affiliation(s)
- Sjoerd J Seekles
- TIFN, 6708 PW, Wageningen, the Netherlands
- Department Molecular Microbiology and Biotechnology, Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Maarten Punt
- TIFN, 6708 PW, Wageningen, the Netherlands
- Microbiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Niki Savelkoel
- Department Molecular Microbiology and Biotechnology, Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Jos Houbraken
- TIFN, 6708 PW, Wageningen, the Netherlands
- Applied & Industrial Mycology, Westerdijk Fungal Biodiversity Institute, 3584 CT, Utrecht, the Netherlands
| | - Han A B Wösten
- TIFN, 6708 PW, Wageningen, the Netherlands
- Microbiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Robin A Ohm
- TIFN, 6708 PW, Wageningen, the Netherlands
- Microbiology, Department of Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Arthur F J Ram
- TIFN, 6708 PW, Wageningen, the Netherlands
- Department Molecular Microbiology and Biotechnology, Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
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Development of sexual structures influences metabolomic and transcriptomic profiles in Aspergillus flavus. Fungal Biol 2022; 126:187-200. [DOI: 10.1016/j.funbio.2022.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/02/2023]
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Ellena V, Sauer M, Steiger MG. The fungal sexual revolution continues: discovery of sexual development in members of the genus Aspergillus and its consequences. Fungal Biol Biotechnol 2020; 7:17. [PMID: 33357234 PMCID: PMC7761153 DOI: 10.1186/s40694-020-00107-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/15/2020] [Indexed: 12/24/2022] Open
Abstract
Asexuality was considered to be a common feature of a large part of fungi, including those of the genus Aspergillus. However, recent advances and the available genomic and genetic engineering technologies allowed to gather more and more indications of a hidden sexuality in fungi previously considered asexual. In parallel, the acquired knowledge of the most suitable conditions for crossings was shown to be crucial to effectively promote sexual reproduction in the laboratory. These discoveries not only have consequences on our knowledge of the biological processes ongoing in nature, questioning if truly asexual fungal species exist, but they also have important implications on other research areas. For instance, the presence of sexuality in certain fungi can have effects on their pathogenicity or on shaping the ecosystem that they normally colonize. For these reasons, further investigations of the sexual potential of Aspergillus species, such as the industrially important A. niger, will be carried on.
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Affiliation(s)
- Valeria Ellena
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna, Austria. .,Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.
| | - Michael Sauer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna, Austria.,Institute of Microbiology and Microbial Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,CD Laboratory for Biotechnology of Glycerol, Muthgasse 18, Vienna, Austria
| | - Matthias G Steiger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 18, Vienna, Austria.,Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
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Covo S. Genomic Instability in Fungal Plant Pathogens. Genes (Basel) 2020; 11:E421. [PMID: 32295266 PMCID: PMC7230313 DOI: 10.3390/genes11040421] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/29/2020] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Fungi and fungal-like organisms (oomycetes) that cause diseases in plants have impacted human communities for centuries and probably from the dawn of agriculture. In modern agriculture, there is a constant race between new strategies to manage fungal plant pathogens and their ability to adapt. An important component in this race is fungal genetic diversity. Mechanisms such as sexual and parasexual recombination that contribute to the creation of novel allele combinations in fungal plant pathogens are briefly discussed in the first part of this review. Advances in genomics have enabled the investigation of chromosomal aberrations of agriculturally important fungal isolates at the nucleotide level. Some of these cases are summarized in the second part of this review; it is claimed that the effect of chromosomal aberrations on pathogenicity should be studied mechanistically. More data on the effect of gene copy number variations on phenotypes that are relevant to agriculture are especially needed. Genome rearrangements through translocations have shaped the genome of fungal plant pathogens by creating lineage-specific chromosome territories encoding for genes participating in plant diseases. Pathogenicity chromosomes are unique cases of such lineage-specific genetic elements, interestingly these chromosomes can be transferred horizontally and thus transforming a non-pathogenic strain to a pathogenic one. The third part of this review describes our attempts to reveal mutators in fungal plant pathogens by identifying fungi that lack important DNA repair genes or respond to DNA damage in an unconventional way. We found that a group of fungal plant pathogens lack conserved genes that are needed for an important Holliday junction resolution pathway. In addition, in Fusarium oxysporum, the rate-limiting step in dNTP production is not induced under DNA replication stress. This is very different from organisms from bacteria to humans. It remains to be seen if these mechanisms promote genetic instability in fungal plant pathogens.
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Affiliation(s)
- Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University, Rehovot 76100001, Israel
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Lei M, Liu J, Fang Y, Shao Y, Li L, Yu JH, Chen F. Effects of Different G-Protein α-Subunits on Growth, Development and Secondary Metabolism of Monascus ruber M7. Front Microbiol 2019; 10:1555. [PMID: 31354659 PMCID: PMC6632705 DOI: 10.3389/fmicb.2019.01555] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/21/2019] [Indexed: 11/13/2022] Open
Abstract
Strains of Monascus filamentous fungal species have been used to produce fermented foods in Asian countries, such as China, Japan, and The Korean Peninsula, for nearly 2,000 years. At present, their fermented products are widely used as food additives and nutraceutical supplements worldwide owing to their production of beneficial secondary metabolites. Heterotrimeric G-protein signaling pathways participate in regulating multiple biological processes in fungi. Previously, we identified three Monascus ruber M7 G-protein α subunits (Mga1–3) and demonstrated that Mga1 can regulate growth, reproduction and some secondary metabolites’ production. Here, we systematically analyzed and compared the roles of mga1–3 by combining single- and double-gene(s) knockouts and their transcriptomic data. First, mga2 and mga3 knock-out mutants and pairwise combinations of mga1–3 deletion strains were generated. Then the changes in growth, development and the main secondary metabolites, Monascus pigments and citrinin, in these mutants were systematically compared with M. ruber M7. Moreover, RNA-Seq analyses of these mutants were performed. All three Gα subunits worked together to regulate biological processes in M. ruber M7, with Mga1 playing a major role, while Mga2 and Mga3 playing supplemental roles. According to the existing literatures which we can find, gene knock-out mutants of the pairwise combination of mga1–3 and their transcriptome analysis are first reported in this study. The current results have clearly demonstrated the functional division of Mga1–3 in M. ruber M7, and could provide a deeper understanding of the effects of different Gα subunits on growth, development and secondary metabolism in other filamentous fungi.
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Affiliation(s)
- Ming Lei
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiao Liu
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yang Fang
- National Engineering Research Center for Natural Medicines, Chengdu, China
| | - Yanchun Shao
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Li
- College of Life Science, Yangtze University, Jingzhou, China
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin - Madison, Madison, WI, United States.,Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
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Ding X, Liu K, Lu Y, Gong G. Morphological, transcriptional, and metabolic analyses of osmotic-adapted mechanisms of the halophilic Aspergillus montevidensis ZYD4 under hypersaline conditions. Appl Microbiol Biotechnol 2019; 103:3829-3846. [PMID: 30859256 DOI: 10.1007/s00253-019-09705-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 11/30/2022]
Abstract
Halophilic fungi in hypersaline habitats require multiple cellular responses for high-salinity adaptation. However, the exact mechanisms behind these adaptation processes remain to be slightly known. The current study is aimed at elucidating the morphological, transcriptomic, and metabolomic changes of the halophilic fungus Aspergillus montevidensis ZYD4 under hypersaline conditions. Under these conditions, the fungus promoted conidia formation and suppressed cleistothecium development. Furthermore, the fungus differentially expressed genes (P < 0.0001) that controlled ion transport, amino acid transport and metabolism, soluble sugar accumulation, fatty acid β-oxidation, saturated fatty acid synthesis, electron transfer, and oxidative stress tolerance. Additionally, the hypersalinized mycelia widely accumulated metabolites, including amino acids, soluble sugars, saturated fatty acids, and other carbon- and nitrogen-containing compounds. The addition of metabolites-such as neohesperidin, biuret, aspartic acid, alanine, proline, and ornithine-significantly promoted the growth (P ≤ 0.05) and the morphological adaptations of A. montevidensis ZYD4 grown in hypersaline environments. Our study demonstrated that morphological shifts, ion equilibrium, carbon and nitrogen metabolism for solute accumulation, and energy production are vital to halophilic fungi so that they can build tolerance to high-salinity environments.
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Affiliation(s)
- Xiaowei Ding
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.,School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China
| | - Kaihui Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China. .,School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China.
| | - Yuxin Lu
- School of Biological Science and Engineering
- Shaanxi University of Technology, Hanzhong City, 723001, Shaanxi, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
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11
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Tran NT, Miles AK, Dietzgen RG, Dewdney MM, Zhang K, Rollins JA, Drenth A. Sexual Reproduction in the Citrus Black Spot Pathogen, Phyllosticta citricarpa. PHYTOPATHOLOGY 2017; 107:732-739. [PMID: 28387613 DOI: 10.1094/phyto-11-16-0419-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Citrus black spot (Phyllosticta citricarpa) causes fruit blemishes and premature fruit drop, resulting in significant economic losses in citrus growing areas with summer rainfall across the globe. The mating type locus of P. citricarpa has recently been characterized, revealing the heterothallic nature of this pathogen. However, insight into the occurrence of mating and the impact of completing the sexual cycle of P. citricarpa was lacking. To investigate the occurrence and impact of sexual reproduction, we developed a method to reliably, and for the first time, produce ascospores of P. citricarpa on culture media. To demonstrate meiosis during the mating process, we identified recombinant genotypes through multilocus genotyping of single ascospores. Because the process of fertilization was not well understood, we experimentally determined that fertilization of P. citricarpa occurs via spermatization. Our results demonstrate that P. citricarpa is heterothallic and requires isolates of different MAT idiomorphs to be in direct physical contact, or for spermatia to fulfill their role as male elements to fertilize the receptive organs, in order to initiate the mating process. The impact of mating on the epidemiology of citrus black spot in the field is discussed.
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Affiliation(s)
- Nga T Tran
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
| | - Andrew K Miles
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
| | - Ralf G Dietzgen
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
| | - Megan M Dewdney
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
| | - Ke Zhang
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
| | - Jeffrey A Rollins
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
| | - André Drenth
- First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville
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Paulussen C, Hallsworth JE, Álvarez‐Pérez S, Nierman WC, Hamill PG, Blain D, Rediers H, Lievens B. Ecology of aspergillosis: insights into the pathogenic potency of Aspergillus fumigatus and some other Aspergillus species. Microb Biotechnol 2017; 10:296-322. [PMID: 27273822 PMCID: PMC5328810 DOI: 10.1111/1751-7915.12367] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/08/2016] [Accepted: 04/18/2016] [Indexed: 01/26/2023] Open
Abstract
Fungi of the genus Aspergillus are widespread in the environment. Some Aspergillus species, most commonly Aspergillus fumigatus, may lead to a variety of allergic reactions and life-threatening systemic infections in humans. Invasive aspergillosis occurs primarily in patients with severe immunodeficiency, and has dramatically increased in recent years. There are several factors at play that contribute to aspergillosis, including both fungus and host-related factors such as strain virulence and host pulmonary structure/immune status, respectively. The environmental tenacity of Aspergilllus, its dominance in diverse microbial communities/habitats, and its ability to navigate the ecophysiological and biophysical challenges of host infection are attributable, in large part, to a robust stress-tolerance biology and exceptional capacity to generate cell-available energy. Aspects of its stress metabolism, ecology, interactions with diverse animal hosts, clinical presentations and treatment regimens have been well-studied over the past years. Here, we synthesize these findings in relation to the way in which some Aspergillus species have become successful opportunistic pathogens of human- and other animal hosts. We focus on the biophysical capabilities of Aspergillus pathogens, key aspects of their ecophysiology and the flexibility to undergo a sexual cycle or form cryptic species. Additionally, recent advances in diagnosis of the disease are discussed as well as implications in relation to questions that have yet to be resolved.
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Affiliation(s)
- Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - John E. Hallsworth
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Sergio Álvarez‐Pérez
- Faculty of Veterinary MedicineDepartment of Animal HealthUniversidad Complutense de MadridMadridE‐28040Spain
| | | | - Philip G. Hamill
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - David Blain
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen's University BelfastBelfastBT9 7BLUK
| | - Hans Rediers
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM)Department of Microbial and Molecular Systems (M2S)KU LeuvenCampus De NayerSint‐Katelijne‐WaverB‐2860Belgium
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13
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Kraemer SA, Boynton PJ. Evidence for microbial local adaptation in nature. Mol Ecol 2017; 26:1860-1876. [DOI: 10.1111/mec.13958] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Susanne A. Kraemer
- Ashworth Laboratories; University of Edinburgh; King's Buildings EH9 3FL Edinburgh UK
| | - Primrose J. Boynton
- Max Planck Institute for Evolutionary Biology; August-Thienemann-Str. 2 24306 Plön Germany
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Del-Prado R, Divakar PK, Lumbsch HT, Crespo AM. Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group. PLoS One 2016; 11:e0161031. [PMID: 27513649 PMCID: PMC4981466 DOI: 10.1371/journal.pone.0161031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/28/2016] [Indexed: 11/19/2022] Open
Abstract
Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum–Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny–maximum likelihood and Bayesian–genetic distances, automatic barcode gap discovery and coalescent-based methods–PTP, GMYC, spedeSTEM and *Beast–in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum–P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex–during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.
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Affiliation(s)
- Ruth Del-Prado
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
- * E-mail:
| | - Pradeep Kumar Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - H. Thorsten Lumbsch
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Ana M. Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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