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Stüer‐Patowsky K, Lilje O, Wurzbacher C. Quantification of the dark fungal taxon Cryptomycota using qPCR. Environ Microbiol Rep 2024; 16:e13257. [PMID: 38615691 PMCID: PMC11016352 DOI: 10.1111/1758-2229.13257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/20/2024] [Indexed: 04/16/2024]
Abstract
Fungi are present in a wide variety of natural environments, and in the last years, various studies have shown that they are quite abundant in aquatic ecosystems. In addition, a whole new highly diverse phylum, the Cryptomycota, was discovered. Nevertheless, research on aquatic fungi and a detailed evaluation of their functions and distribution are still sparse. One of the main reasons is a limitation in reliable identification and quantification methods. To bridge part of the research gap, this study aims to implement a quantitative PCR method to detect and quantify the newly discovered phylum. We developed and validated a Cryptomycota-specific qPCR primer pair targeting the 5.8S region that detects the majority of Cryptomycota, but Microsporidia. The resulting amplicon is 102 bp long. We used different environmental samples to evaluate the primer pair, various fungal sequences as negative control and positive control sequences. Obtained amplicons were sequenced using Illumina, and the obtained ASVs were all classified as Cryptomycota. The qPCR method works reliably and specifically for the quantification of Cryptomycota in environmental samples.
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Affiliation(s)
- Katrin Stüer‐Patowsky
- Chair of Urban Water Systems EngineeringTechnical University of MunichGarchingGermany
| | - Osu Lilje
- School of Life and Environmental SciencesThe University of SydneyCamperdownNew South WalesAustralia
| | - Christian Wurzbacher
- Chair of Urban Water Systems EngineeringTechnical University of MunichGarchingGermany
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2
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Sadek A, Taminiau B, Daube G, Sapountzis P, Chaucheyras-Durand F, Castex M, Coucheney F, Drider D. Impact of Dietary Regime and Seasonality on Hindgut's Mycobiota Diversity in Dairy Cows. Microorganisms 2023; 12:84. [PMID: 38257911 PMCID: PMC10820462 DOI: 10.3390/microorganisms12010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3-5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity.
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Affiliation(s)
- Ali Sadek
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Bernard Taminiau
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Panagiotis Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Mathieu Castex
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Françoise Coucheney
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
| | - Djamel Drider
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
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Radek R, Wurzbacher C, Strassert JFH. New nephridiophagid genera (Fungi, Chytridiomycota) in a mallow beetle and an earwig. MycoKeys 2023; 100:245-260. [PMID: 38162290 PMCID: PMC10757303 DOI: 10.3897/mycokeys.100.111298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/27/2023] [Indexed: 01/03/2024] Open
Abstract
Nephridiophagids are unicellular fungi (Chytridiomycota) that infect the Malpighian tubules of insects. Most species have been found in cockroach hosts and belong to the genus Nephridiophaga. Three additional genera have been described from beetles and an earwig. Here, we characterise morphologically and molecular phylogenetically the nephridiophagids of the European earwig Forficulaauricularia and the mallow beetle Podagricamalvae. Their morphology and life cycle stages resemble those of other nephridiophagids, but their rRNA gene sequences support the existence of two additional genera. Whereas the earwig nephridiophagid (Nephridiochytriumforficulaegen. nov. et sp. nov.) forms a sister lineage of the Nephridiophaga cluster, the mallow beetle nephridiophagid (Malpighivincopodagricaegen. nov. et sp. nov.) represents the earliest divergent lineage within the nephridiophagids, being sister to all other species. Our results corroborate the hypothesis that different insect groups harbour distinct nephridiophagid lineages.
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Affiliation(s)
- Renate Radek
- Evolutionary Biology, Institute of Biology, Free University of Berlin, 14195 Berlin, GermanyFree University of BerlinBerlinGermany
| | - Christian Wurzbacher
- Chair of Urban Water Systems, Engineering, Technical University of Munich, 85748 Garching, GermanyTechnical University of MunichMünchenGermany
| | - Jürgen F. H. Strassert
- Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, GermanyEvolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
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Lu J, Zhang X, Zhang X, Wang L, Zhao R, Liu XY, Liu X, Zhuang W, Chen L, Cai L, Wang J. Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments. Mol Ecol 2023; 32:6330-6344. [PMID: 35593386 DOI: 10.1111/mec.16534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/24/2022] [Accepted: 05/12/2022] [Indexed: 10/18/2022]
Abstract
High-throughput sequencing has substantially improved our understanding of fungal diversity. However, the short read (<500 bp) length of current second-generation sequencing approaches provides limited taxonomic and phylogenetic resolution for species discrimination. Longer sequences containing more information are highly desired to provide greater taxonomic resolution. Here, we amplified full-length rRNA operons (~5.5 kb) and established a corresponding fungal rRNA operon database for ONT sequences (FRODO), which contains ONT sequences representing eight phyla, 41 classes, 109 orders, 256 families, 524 genera and 1116 species. We also benchmarked the optimal method for sequence classification and determined that the RDP classifier based on our FRODO database was capable of improving the classification of ONT reads, with an average of 98%-99% reads correctly classified at the genus or species level. We investigated the applicability of our approach in three representative mycobiomes, namely, the soil, marine and human gut mycobiomes, and found that the gut contains the largest number of unknown species (over 90%), followed by the marine (42%) and soil (33.8%) mycobiomes. We also observed a distinct difference in the composition of the marine and soil mycobiomes, with the highest richness and diversity detected in soils. Overall, our study provides a systematic approach for mycobiome studies and revealed that the previous methods might have underestimated the diversity of mycobiome species. Future application of this method will lead to a better understanding of the taxonomic and functional diversity of fungi in environmental and health-related mycobiomes.
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Affiliation(s)
- Jingjing Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xudong Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linqi Wang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ruilin Zhao
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Yong Liu
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xinzhan Liu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenying Zhuang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lei Cai
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Seto K, Simmons DR, Quandt CA, Frenken T, Dirks AC, Clemons RA, McKindles KM, McKay RML, James TY. A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. mBio 2023; 14:e0131323. [PMID: 37486265 PMCID: PMC10470594 DOI: 10.1128/mbio.01313-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, protists, and micro-invertebrates, combined with subsequent long-read sequencing of the ribosomal DNA locus (rDNA). We successfully obtained rDNA sequences of 127 parasitic fungal cells, which clustered into 71 phylogenetic lineages belonging to seven phylum-level clades of EDF: Blastocladiomycota, Chytridiomycota, Aphelidiomycota, Rozellomycota, and three unknown phylum-level clades. Most of our single cells yielded novel sequences distinguished from both described taxa and existing metabarcoding data, indicating an expansive and hidden diversity of parasitic taxa of EDF. We also revealed an unexpected diversity of endobiotic Olpidium-like chytrids and hyper-parasitic lineages. Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota.
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Affiliation(s)
- Kensuke Seto
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - D. Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Cluster Nature and Society, HAS University of Applied Sciences, 's-Hertogenbosch, the Netherlands
| | - Alden C. Dirks
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rebecca A. Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Katelyn M. McKindles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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Tripodi P. Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad ( Diplotaxis spp.) Species. Genes (Basel) 2023; 14:1594. [PMID: 37628645 PMCID: PMC10454437 DOI: 10.3390/genes14081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.
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Affiliation(s)
- Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), 84098 Pontecagnano Faiano, Italy
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Nakanishi H, Seto K, Takeuchi N, Kagami M. Novel parasitic chytrids infecting snow algae in an alpine snow ecosystem in Japan. Front Microbiol 2023; 14:1201230. [PMID: 37408638 PMCID: PMC10318532 DOI: 10.3389/fmicb.2023.1201230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Microbial communities are important components of glacier and snowpack ecosystems that influence biogeochemical cycles and snow/ice melt. Recent environmental DNA surveys have revealed that chytrids dominate the fungal communities in polar and alpine snowpacks. These could be parasitic chytrids that infect snow algae as observed microscopically. However, the diversity and phylogenetic position of parasitic chytrids has not been identified due to difficulties in establishing their culture and subsequent DNA sequencing. In this study, we aimed to identify the phylogenetic positions of chytrids infecting the snow algae, Chloromonas spp., bloomed on snowpacks in Japan. Methods By linking a microscopically picked single fungal sporangium on a snow algal cell to a subsequent sequence of ribosomal marker genes, we identified three novel lineages with distinct morphologies. Results All the three lineages belonged to Mesochytriales, located within "Snow Clade 1", a novel clade consisting of uncultured chytrids from snow-covered environments worldwide. Additionally, putative resting spores of chytrids attached to snow algal cells were observed. Discussion This suggests that chytrids may survive as resting stage in soil after snowmelt. Our study highlights the potential importance of parasitic chytrids that infect snow algal communities.
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Affiliation(s)
- Hiroaki Nakanishi
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Maiko Kagami
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
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Ohta A, Nishi K, Hirota K, Matsuo Y. Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution. Sci Rep 2023; 13:9785. [PMID: 37328565 PMCID: PMC10275880 DOI: 10.1038/s41598-023-37016-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023] Open
Abstract
The study of microbiota has been revolutionized by the development of DNA metabarcoding. This sequence-based approach enables the direct detection of microorganisms without the need for culture and isolation, which significantly reduces analysis time and offers more comprehensive taxonomic profiles across broad phylogenetic lineages. While there has been an accumulating number of researches on bacteria, molecular phylogenetic analysis of fungi still remains challenging due to the lack of standardized tools and the incompleteness of reference databases limiting the accurate and precise identification of fungal taxa. Here, we present a DNA metabarcoding workflow for characterizing fungal microbiota with high taxonomic resolution. This method involves amplifying longer stretches of ribosomal RNA operons and sequencing them using nanopore long-read sequencing technology. The resulting reads were error-polished to generate consensus sequences with 99.5-100% accuracy, which were then aligned against reference genome assemblies. The efficacy of this method was explored using a polymicrobial mock community and patient-derived specimens, demonstrating the marked potential of long-read sequencing combined with consensus calling for accurate taxonomic classification. Our approach offers a powerful tool for the rapid identification of pathogenic fungi and has the promise to significantly improve our understanding of the role of fungi in health and disease.
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Affiliation(s)
- Atsufumi Ohta
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Kenichiro Nishi
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
- Department of Anesthesiology and Intensive Care, Osaka Red Cross Hospital, Osaka, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan.
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Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K. How, not if, is the question mycologists should be asking about DNA-based typification. MycoKeys 2023; 96:143-157. [PMID: 37214179 PMCID: PMC10194844 DOI: 10.3897/mycokeys.96.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/28/2023] [Indexed: 05/24/2023] Open
Abstract
Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community - that the current situation is satisfactory and that no change is needed to "the code" - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.
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Affiliation(s)
- R. Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
- College of Science, King Saud University, 1145 Riyadh, Saudi Arabia
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Sergei Põlme
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Viacheslav Spirin
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
| | - Sten Svantesson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
- Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Martin Hartmann
- Botany Unit (Mycology), Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014, Helsinki, Finland
| | - Charlotte Lennartsdotter
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Pauline Belford
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Maryia Khomich
- Interaction Design and Software Engineering, Chalmers University of Technology, Lindholmsplatsen 1, 417 56 Göteborg, Sweden
| | - Alice Retter
- Department of Clinical Science, University of Bergen, Box 7804, 5020 Bergen, Norway
| | - Natàlia Corcoll
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Daniela Gómez Martinez
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Tobias Jansson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Masoomeh Ghobad-Nejhad
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Duong Vu
- Department of Biotechnology, Iranian Research Organization for Science and Technology, PO Box 3353-5111, Tehran 3353136846, Iran
| | | | - Erik Kristiansson
- Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Kessy Abarenkov
- Mycology and Microbiology Center, University of Tartu, Liivi 2, 50409 Tartu, Estonia
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10
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Šašić Zorić L, Janjušević L, Djisalov M, Knežić T, Vunduk J, Milenković I, Gadjanski I. Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production. Biology (Basel) 2023; 12. [PMID: 36829575 DOI: 10.3390/biology12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.
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11
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Vass M, Eriksson K, Carlsson-Graner U, Wikner J, Andersson A. Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host-parasite interactions. FEMS Microbiol Ecol 2022; 98:fiac120. [PMID: 36202390 PMCID: PMC9621394 DOI: 10.1093/femsec/fiac120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
Our knowledge of aquatic fungal communities, their assembly, distributions and ecological roles in marine ecosystems is scarce. Hence, we aimed to investigate fungal metacommunities of coastal habitats in a subarctic zone (northern Baltic Sea, Sweden). Using a novel joint species distribution model and network approach, we quantified the importance of biotic associations contributing to the assembly of mycoplankton, further, detected potential biotic interactions between fungi-algae pairs, respectively. Our long-read metabarcoding approach identified 493 fungal taxa, of which a dominant fraction (44.4%) was assigned as early-diverging fungi (i.e. Cryptomycota and Chytridiomycota). Alpha diversity of mycoplankton declined and community compositions changed along inlet-bay-offshore transects. The distributions of most fungi were rather influenced by environmental factors than by spatial drivers, and the influence of biotic associations was pronounced when environmental filtering was weak. We found great number of co-occurrences (120) among the dominant fungal groups, and the 25 associations between fungal and algal OTUs suggested potential host-parasite and/or saprotroph links, supporting a Cryptomycota-based mycoloop pathway. We emphasize that the contribution of biotic associations to mycoplankton assembly are important to consider in future studies as it helps to improve predictions of species distributions in aquatic ecosystems.
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Affiliation(s)
- Máté Vass
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Karolina Eriksson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Ulla Carlsson-Graner
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
| | - Johan Wikner
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
- Sweden Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden
- Sweden Umeå Marine Sciences Centre, Umeå University, SE-905 71, Hörnefors, Sweden
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12
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Van den Wyngaert S, Ganzert L, Seto K, Rojas-Jimenez K, Agha R, Berger SA, Woodhouse J, Padisak J, Wurzbacher C, Kagami M, Grossart HP. Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits. ISME J 2022; 16:2242-2254. [PMID: 35764676 PMCID: PMC9381765 DOI: 10.1038/s41396-022-01267-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022]
Abstract
Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.
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Affiliation(s)
- Silke Van den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhütte 2, 16775, Stechlin, Germany. .,Department of Biology, University of Turku, Vesilinnantie 5, 20014, Turku, Finland.
| | - Lars Ganzert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhütte 2, 16775, Stechlin, Germany.,GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473, Potsdam, Germany.,Marbio, UiT- The Arctic University of Norway, Sykehusveien 23, 9019, Tromsø, Norway
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, Tokiwadai 79-7, Hodogayaku, Yokohama, Kanagawa, 240-8501, Japan.,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | | | - Ramsy Agha
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - Stella A Berger
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhütte 2, 16775, Stechlin, Germany
| | - Jason Woodhouse
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhütte 2, 16775, Stechlin, Germany
| | - Judit Padisak
- Research Group of Limnology, Centre of Natural Sciences, University of Pannonia, Egyetem u. 10, 8200, Veszprém, Hungary
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748, Garching, Germany
| | - Maiko Kagami
- Faculty of Environment and Information Sciences, Yokohama National University, Tokiwadai 79-7, Hodogayaku, Yokohama, Kanagawa, 240-8501, Japan.
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Zur alten Fischerhütte 2, 16775, Stechlin, Germany. .,Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469, Potsdam, Germany.
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13
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Rosenblad MA, Larsson E, Walker A, Thongklang N, Wurzbacher C, Nilsson RH. Evidence for further non-coding RNA genes in the fungal rDNA region. MycoKeys 2022; 90:203-213. [PMID: 36760425 PMCID: PMC9849065 DOI: 10.3897/mycokeys.90.84866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/14/2022] [Indexed: 11/12/2022] Open
Abstract
Non-coding RNA (ncRNA) genes play important, but incompletely understood, roles in various cellular processes, notably translation and gene regulation. A recent report on the detection of the ncRNA Signal Recognition Particle gene in the nuclear ribosomal internal transcribed spacer region of several species of three genera of ectomycorrhizal basidiomycetes prompted a more thorough bioinformatics search for additional ncRNA genes in the full fungal ribosomal operon. This study reports on the detection of three ncRNA genes hitherto not known from the fungal ribosomal region: nuclear RNase P RNA, RNase MRP RNA, and a possible snoRNA U14 in a total of five species of Auricularia and Inocybe. We verified their presence through resequencing of independent specimens. Two completed Auricularia genomes were found to lack these ncRNAs elsewhere than in the ribosomal operon, suggesting that these are functional genes. It seems clear that ncRNA genes play a larger role in fungal ribosomal genetics than hitherto thought.
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Affiliation(s)
- Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, National Infrastructure of Bioinformatics (NBIS), Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Ellen Larsson
- Department of Chemistry and Molecular Biology, National Infrastructure of Bioinformatics (NBIS), Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Arttapon Walker
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden
| | - Naritsada Thongklang
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden
| | - Christian Wurzbacher
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - R. Henrik Nilsson
- Department of Chemistry and Molecular Biology, National Infrastructure of Bioinformatics (NBIS), Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
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14
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Runnel K, Abarenkov K, Copoț O, Mikryukov V, Kõljalg U, Saar I, Tedersoo L. DNA barcoding of fungal specimens using PacBio long-read high-throughput sequencing. Mol Ecol Resour 2022; 22:2871-2879. [PMID: 35666173 DOI: 10.1111/1755-0998.13663] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
Molecular methods are increasingly used to identify species that lack conspicuous macro- or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long-read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intra-individual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogs, which can provide crucial information for species delimitation and population-level studies.
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Affiliation(s)
- Kadri Runnel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Kessy Abarenkov
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,Natural History Museum, University of Tartu, Tartu, Estonia
| | - Ovidiu Copoț
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Vladimir Mikryukov
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Natural History Museum, University of Tartu, Tartu, Estonia
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
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15
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M Sandin M, Romac S, Not F. Intra-genomic rRNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing. Environ Microbiol 2022; 24:2979-2993. [PMID: 35621046 PMCID: PMC9545545 DOI: 10.1111/1462-2920.16081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/01/2022]
Abstract
Ribosomal RNA (rRNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large-scale exploration of environmental microbial diversity through metabarcoding approaches have been focused mainly on the V4 and V9 regions of the 18S rRNA gene. The accurate interpretation of such environmental surveys is hampered by technical (e.g., PCR and sequencing errors) and biological biases (e.g., intra-genomic variability). Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra-genomic variability of Nassellaria and Spumellaria is generally low, yet some Spumellaria specimens showed two different copies of the V4 with <97% similarity. From the different sequencing methods, Illumina showed the highest number of contaminations (i.e., environmental DNA, cross-contamination, tag-jumping), revealed by its high sequencing depth; and MinION showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results highlight the requirement for a careful interpretation of Illumina based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full-length rDNA environmental metabarcoding surveys.
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Affiliation(s)
- Miguel M Sandin
- Sorbonne University, CNRS - UMR7144 - Ecology of Marine Plankton Group - Station Biologique de Roscoff, Roscoff, France.,Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, Uppsala, Sweden
| | - Sarah Romac
- Sorbonne University, CNRS - UMR7144 - Ecology of Marine Plankton Group - Station Biologique de Roscoff, Roscoff, France
| | - Fabrice Not
- Sorbonne University, CNRS - UMR7144 - Ecology of Marine Plankton Group - Station Biologique de Roscoff, Roscoff, France
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16
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Seto K, Nakada T, Tanabe Y, Yoshida M, Kagami M. Aphelidium parallelum, sp. nov., a new aphelid parasitic on selenastracean green algae. Mycologia 2022; 114:544-555. [PMID: 35605094 DOI: 10.1080/00275514.2022.2039487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Aphelids (phylum Aphelida = Aphelidiomycota) are intracellular parasitoids of algae and represent one of the early-diverging or sister lineages of the kingdom Fungi. Although aphelids are a small group comprising four genera and 17 species, molecular phylogenetic analyses revealed that numerous environmental DNA sequences represent undescribed lineages, indicating their hidden diversity. Here, we investigated a novel aphelid strain, KS114, that parasitizes selenastracean green algae. KS114 exhibited a life cycle typical of aphelids and produced posteriorly uniflagellate zoospores that resembled those of Aphelidium chlorococcorum f. majus in possessing a single apical filopodium but could be distinguished by ultrastructure features. In KS114, the kinetosome and nonflagellated centriole were aligned in parallel, a unique characteristic among the known aphelids. Kinetid-associated structures, such as fibrillar root and microtubules, were not found in the zoospores of KS114. In the molecular phylogeny of nuc 18S rDNA sequences, KS114 clustered with two environmental sequences and was distinct from all other sequenced species. Based on these results, we describe this aphelid as a new species, Aphelidium parallelum.http://www.zoobank.org/urn:lsid:zoobank.org:act:3CB658DB-1F12-41EF-A57D-2CBFCDE6A49A.
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Affiliation(s)
- Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, 240-8501, Kanagawa, Japan
| | - Takashi Nakada
- Faculty of Environment and Information Sciences, Yokohama National University, 240-8501, Kanagawa, Japan
| | - Yuuhiko Tanabe
- Algae Biomass and Energy System R&D Center, University of Tsukuba, 305-8572, Ibaraki, Japan.,Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, 305-8506, Ibaraki, Japan
| | - Masaki Yoshida
- Algae Biomass and Energy System R&D Center, University of Tsukuba, 305-8572, Ibaraki, Japan
| | - Maiko Kagami
- Faculty of Environment and Information Sciences, Yokohama National University, 240-8501, Kanagawa, Japan
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17
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Paloi S, Luangsa-ard JJ, Mhuantong W, Stadler M, Kobmoo N. Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Pomerantz A, Sahlin K, Vasiljevic N, Seah A, Lim M, Humble E, Kennedy S, Krehenwinkel H, Winter S, Ogden R, Prost S. Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Nat Protoc. [DOI: 10.1038/s41596-022-00682-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
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19
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Stewart JE, Miller ST, Zink FA, Caballero JI, Tembrock LR. Genetic and Phenotypic Characterization of the Fungal Pathogen Cytospora plurivora from Western Colorado Peach Orchards and the Development of a ddPCR Assay for Detection and Quantification. Phytopathology 2022; 112:917-928. [PMID: 34554008 DOI: 10.1094/phyto-05-21-0210-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cytospora canker is one of the most important diseases affecting peach production in Colorado, yet previous efforts to characterize Cytospora species diversity in Colorado have relied exclusively on morphological traits. Recently, several new Cytospora species were described from peach orchards within the United States using molecular and morphological data, prompting the need to reexamine Cytospora spp. present on peach trees in Colorado. A total of 137 isolates of Cytospora spp. were collected from eight orchards in western Colorado. Isolates were sequenced at the internal transcribed spacer region and elongation factor 1-α and assessed with reference sequences in phylogenetic analyses. All isolates from western Colorado peach trees resolved with the newly described Cytospora plurivora. In addition to molecular characterization, temperature growth and virulence assays were conducted to assess phenotypic variation among the isolates from western Colorado. Variation across isolates was found both in growth at different temperatures and in virulence. Ancestral state reconstruction analyses resolved the most virulent (and most often collected) haplotypes together in a well-supported clade from which a single monophyletic origin of high virulence can be inferred. Finally, a droplet digital PCR assay was developed for use in ongoing and future studies to detect and quantify C. plurivora from field and laboratory samples.
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Affiliation(s)
- Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
| | - Stephan T Miller
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
| | - Frida A Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
| | | | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
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20
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Ilicic D, Grossart HP. Basal Parasitic Fungi in Marine Food Webs-A Mystery Yet to Unravel. J Fungi (Basel) 2022; 8:114. [PMID: 35205868 PMCID: PMC8874645 DOI: 10.3390/jof8020114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 02/01/2023] Open
Abstract
Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.
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Affiliation(s)
- Doris Ilicic
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany;
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany;
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469 Potsdam, Germany
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21
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Svantesson S, Kõljalg U, Wurzbacher C, Saar I, Larsson KH, Larsson E. Polyozellus vs. Pseudotomentella: generic delimitation with a multi-gene dataset. Fungal Syst Evol 2022; 8:143-154. [PMID: 35005578 PMCID: PMC8687065 DOI: 10.3114/fuse.2021.08.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/26/2021] [Indexed: 11/07/2022] Open
Abstract
Polyozellus and Pseudotomentella are two genera of closely related, ectomycorrhizal fungi in the order Thelephorales; the former stipitate and the latter corticioid. Both are widespread in the Northern Hemisphere and many species from both genera seem to be restricted to old growth forest. This study aimed to: a) identify genetic regions useful in inferring the phylogenetic relationship between Polyozellus and Pseudotomentella, b) infer this relationship with the regions identified and c) make any taxonomic changes warranted by the result. RPB2, mtSSU and nearly full-length portions of nrLSU and nrSSU were found to be comparatively easy to sequence and provide a strong phylogenetic signal. A STACEY species tree of these three regions revealed that Polyozellus makes Pseudotomentella paraphyletic. As a result, nearly all species currently placed in Pseudotomentella were recombined to Polyozellus. Pseudotomentella larsenii was found to be closer to Tomentellopsis than Polyozellus, but its placement needs further study and it was hence not recombined.
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Affiliation(s)
- S Svantesson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden.,Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, Victoria 3004, Australia
| | - U Kõljalg
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - C Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden.,Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, 85748 Garching, Germany
| | - I Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - K-H Larsson
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden.,Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway
| | - E Larsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
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22
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Bandini D, Oertel B, Eberhardt U. More smooth-spored species of Inocybe (Agaricales, Basidiomycota): type studies and 12 new species from Europe. persoonia. [DOI: 10.3767/persoonia.2022.48.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Twelve new species of Inocybe (I. adorabilis, I. comis, I. demetris, I. filiana, I. galactica, I. morganae, I. othini, I. ovilla, I. proteica, I. somae, I. suryana and I. venerabilis) are described from Europe on the basis of detailed morphological and molecular investigation. A portrait of the recently described I. ianthinopes is given. All species are smooth-spored and some pruinose only in the apical part of the stipe, and some on entire length. The new species are compared to 24 type specimens (17 characterized by at least partial ITS sequence data), all of which are described and revised here. Epitypes were selected for two species, I. hirtella and I. sindonia. Based on our studies, we confirm that I. kuehneri and I. sindonia on one hand, and I. subalbidodisca and I. ochroalba on the other, are synonyms and furthermore suggest that I. abietis is synonymous with I. catalaunica, I. exilis with I. rufobrunnea, I. hirtellarum with I. mycenoides, I. lapidicola with I. deianae, I. ochraceolutea with I. sindonia, I. stangliana with I. pelargonium, I. subrubens with I. subhirtella and I. sulfovirescens with I. langei. All of the new species are supported by phylogenetic analyses. Among the 16 previously described species accepted here, 10 are represented by types in the phylogenetic analyses and five by own collections corresponding to the type. Two species, I. eutheloides (remaining doubtful) and I. pallidolutea are only treated morphologically. In summary, we describe as new or verify the taxonomic status and provide or corroborate morphological concepts for 37 smooth-spored species of Inocybe.
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Zang L, Liu Y, Song X, Cai L, Liu K, Luo T, Zhang R. Unique T4-like phages in high-altitude lakes above 4500 m on the Tibetan Plateau. Sci Total Environ 2021; 801:149649. [PMID: 34428653 DOI: 10.1016/j.scitotenv.2021.149649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Viruses are the most abundant biological entities in the biosphere; however, little is known about viral ecology in high altitude lakes. Here, we characterized viruses from 13 lakes, nine of which located ≥4500 m above sea level, on the Tibetan Plateau, the highest plateau on Earth. The abundance of virus-like particle (VLP) in Tibetan lakes ranged from 4.8 ± 0.2 × 105 VLPs mL-1 to 6.0 ± 0.2 × 107 VLPs mL-1 and the virus-to-bacterium ratio was in the lower range of values reported for other lakes. The viral population size was positively correlated with turbidity and negatively correlated with particulate organic carbon concentration. Highly diverse VLP morphologies, including large (~300 nm) morphotypes, were observed. Phylogenetic analysis of T4-like bacteriophages based on major capsid gene (g23) identified a novel viral group, which were detected in abundance in hyposaline and mesosaline Tibetan lakes. Adaptation to lake evolution, water source (glacier-fed or non-glacier-fed) and environmental conditions (e.g., salinity, phosphorus concentration and productivity) are likely responsible for the variation in T4-like myovirus community composition in contrasting Tibetan lakes. This first investigation of viruses in high-altitude alpine lakes above 4500 m could contribute to our understanding of viral ecology in global alpine lakes.
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Affiliation(s)
- Lin Zang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Science, Beijing 100101, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China; University of Chinese Academy of Science, Beijing 100101, China.
| | - Xuanying Song
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Tingwei Luo
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China.
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Bandini D, Oertel B, Eberhardt U. A fresh outlook on the smooth-spored species of Inocybe: type studies and 18 new species. Mycol Prog 2021; 20:1019-114. [DOI: 10.1007/s11557-021-01712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractOn the basis of detailed morphological and molecular investigation, eighteen new species of Inocybe (I. alberichiana, I. beatifica, I. bellidiana, I. clandestina, I. drenthensis, I. dryadiana, I. gaiana, I. ghibliana, I. grusiana, I. knautiana, I. lampetiana, I. oetziana, I. orionis, I. plurabellae, I. rivierana, I. scolopacis, I. sitibunda and I. tiburtina) are described. All of them are smooth-spored, and most of them are pruinose only in the apical part of the stipe. The new species are compared to 40 type specimens, all of which are described here and for several of which (partial) ITS sequences have been generated. For eight species, epi-, lecto- or neotypes were selected, among these are I. geophylla, I. glabripes and I. tigrina. Based on these studies, we suggest twelve synonymies, i.e. that I. clarkii is synonymous with I. sindonia, I. conformata with I. cincinnata, I. elegans with I. griseolilacina, I. fuscidula with I. glabripes, I. griseotarda with I. psammobrunnea, I. obscurella with I. obscuroides, I. obscuromellea with I. semifulva, I. patibilis and I. tigrinella with I. tigrina, I. petroselinolens with I. tenuicystidiata and I. rubidofracta with I. pseudorubens and I. subporospora is synonymized with I. tjallingiorum. All of the new species are supported by phylogenetic analyses. Among the previously described species accepted here, sixteen are represented by types in the phylogenetic analyses and ten by own collections morphologically corresponding to the type. In summary, we here verify or provide morphological concepts associated with molecular data for 44 smooth-spored species of Inocybe.
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Vasconcelos S, Nunes GL, Dias MC, Lorena J, Oliveira RRM, Lima TGL, Pires ES, Valadares RBS, Alves R, Watanabe MTC, Zappi DC, Hiura AL, Pastore M, Vasconcelos LV, Mota NFO, Viana PL, Gil ASB, Simões AO, Imperatriz‐Fonseca VL, Harley RM, Giulietti AM, Oliveira G. Unraveling the plant diversity of the Amazonian canga through DNA barcoding. Ecol Evol 2021; 11:13348-13362. [PMID: 34646474 PMCID: PMC8495817 DOI: 10.1002/ece3.8057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 01/04/2023] Open
Abstract
The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.
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Affiliation(s)
| | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Renato R. M. Oliveira
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Daniela C. Zappi
- Instituto Tecnológico ValeBelémBrazil
- Instituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | | | - Mayara Pastore
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Liziane V. Vasconcelos
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em EcologiaUniversidade Federal do ParáBelémBrazil
| | - Nara F. O. Mota
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Pedro L. Viana
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André S. B. Gil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André O. Simões
- Departamento de Biologia VegetalUniversidade Estadual de CampinasCampinasBrazil
| | | | | | - Ana M. Giulietti
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em BotânicaUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
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Srivathsan A, Lee L, Katoh K, Hartop E, Kutty SN, Wong J, Yeo D, Meier R. ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biol 2021; 19:217. [PMID: 34587965 PMCID: PMC8479912 DOI: 10.1186/s12915-021-01141-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via "innovation through subtraction" and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. RESULTS We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells ("R10.3") which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. CONCLUSIONS We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle ("Flongle") while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Leshon Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kazutaka Katoh
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
| | - Emily Hartop
- Zoology Department, Stockholms Universitet, Stockholm, Sweden
- Station Linné, Öland, Sweden
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Johnathan Wong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Darren Yeo
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany.
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Paloi S, Mhuantong W, Luangsa-ard JJ, Kobmoo N. Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species. J Fungi (Basel) 2021; 7:767. [PMID: 34575804 PMCID: PMC8467230 DOI: 10.3390/jof7090767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1-D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification.
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Affiliation(s)
| | | | | | - Noppol Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development Agency (NSTDA), 113 Thailand Science Park, Phahonuyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (W.M.); (J.J.L.)
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Ghobad-Nejhad M, Langer E, Nakasone K, Diederich P, Nilsson RH, Rajchenberg M, Ginns J. Digging Up the Roots: Taxonomic and Phylogenetic Disentanglements in Corticiaceae s.s. (Corticiales, Basidiomycota) and Evolution of Nutritional Modes. Front Microbiol 2021; 12:704802. [PMID: 34512580 PMCID: PMC8425454 DOI: 10.3389/fmicb.2021.704802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Corticiaceae is one of the traditional families of the Agaricomycetes and served for a long time as a convenient placement for basidiomycetes with a resupinate, corticioid form of fruiting body. Molecular studies have helped to assign many corticioid fungi to diverse families and orders; however, Corticiaceae still lacks a phylogenetic characterization and modern circumscription. Here, we provide the first comprehensive phylogenetic and taxonomic revision of the family Corticiaceae based on extensive type studies and sequences of nLSU, ITS, IGS, nSSU, and mtSSU regions. Our analyses support the recognition of ten monophyletic genera in the Corticiaceae, and show that nutritional mode is not a robust basis for generic delimitations in the family. The genus Mycobernardia and the species Corticium thailandicum, Erythricium vernum, and Marchandiomyces allantosporus are described as new to science, and five new combinations are proposed. Moreover, ancestral character state reconstruction revealed that saprotrophy is the plesiomorphic nutritional mode in the Corticiaceae, while several transitions have occurred to diverse nutritional modes in this family. Identification keys are provided to the genera in Corticiaceae s.s. as well as to the species in Corticium, Erythricium, Laetisaria, and Marchandiomyces.
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Affiliation(s)
- Masoomeh Ghobad-Nejhad
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Ewald Langer
- Department of Ecology, FB 10 (Mathematics and Natural Sciences), University Kassel, Kassel, Germany
| | - Karen Nakasone
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, WI, United States
| | - Paul Diederich
- Musée national d'histoire naturelle, Luxembourg, Luxembourg
| | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Mario Rajchenberg
- Centro de Investigación y Extensión Forestal Andino Patagónico, National Research Council of Argentina (CONICET), Esquel, Argentina
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Abstract
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Sten Anslan
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
- Braunschweig University of Technology, Zoological Institute, Braunschweig, Germany
| | - Benjamin Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Porter TM, Hajibabaei M. Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC Bioinformatics 2021; 22:256. [PMID: 34011275 PMCID: PMC8136176 DOI: 10.1186/s12859-021-04180-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/10/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. RESULTS Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. CONCLUSIONS Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.
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Affiliation(s)
- T M Porter
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ON, Canada.
| | - M Hajibabaei
- Department of Integrative Biology and Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
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Ogden R, Vasiljevic N, Prost S. Nanopore sequencing in non-human forensic genetics. Emerg Top Life Sci 2021:ETLS20200287. [PMID: 34002773 DOI: 10.1042/ETLS20200287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/28/2022]
Abstract
The past decade has seen a rapid expansion of non-human forensic genetics coinciding with the development of 2nd and 3rd generation DNA sequencing technologies. Nanopore sequencing is one such technology that offers massively parallel sequencing at a fraction of the capital cost of other sequencing platforms. The application of nanopore sequencing to species identification has already been widely demonstrated in biomonitoring studies and has significant potential for non-human forensic casework, particularly in the area of wildlife forensics. This review examines nanopore sequencing technology and assesses its potential applications, advantages and drawbacks for use in non-human forensics, alongside other next-generation sequencing platforms and as a possible replacement to Sanger sequencing. We assess the specific challenges of sequence error rate and the standardisation of consensus sequence production, before discussing recent progress in the validation of nanopore sequencing for use in forensic casework. We conclude that nanopore sequencing may be able to play a considerable role in the future of non-human forensic genetics, especially for applications to wildlife law enforcement within emerging forensic laboratories.
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Simmons DR, Longcore JE, James TY. Polyrhizophydium stewartii, the first known rhizomycelial genus and species in the Rhizophydiales, is closely related to Batrachochytrium. Mycologia 2021; 113:684-690. [PMID: 33847227 DOI: 10.1080/00275514.2021.1885206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Molecular and ultrastructural investigations of the Chytridiomycota during the last 20 years have led to the separation of new orders, including the Rhizophydiales. Most species in this order are morphologically similar, possessing monocentric, eucarpic, spherical thalli. Here, based on analysis of nuc 18S and 28S rDNA, we add the new genus and species Polyrhizophydium stewartii to the order. This saprobe of moribund aquatic plant leaves is the first known rhizomycelial species in the order. In our molecular phylogeny, P. stewartii groups with the amphibian pathogens Batrachochytriuim dendrobatidis and B. salamandrivorans, making it of particular interest to investigators studying evolutionary pathways associated with host-switching and morphological adaptation.
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Affiliation(s)
- D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-1085
| | - Joyce E Longcore
- School of Biology and Ecology, University of Maine, Orono, Maine 04469-5722
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-1085
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Mešić A, Haelewaters D, Tkalčec Z, Liu J, Kušan I, Aime MC, Pošta A. Inocybe brijunica sp. nov., a New Ectomycorrhizal Fungus from Mediterranean Croatia Revealed by Morphology and Multilocus Phylogenetic Analysis. J Fungi (Basel) 2021; 7:199. [PMID: 33801963 PMCID: PMC8000951 DOI: 10.3390/jof7030199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/09/2023] Open
Abstract
A new ectomycorrhizal species was discovered during the first survey of fungal diversity at Brijuni National Park (Croatia), which consists of 14 islands and islets. The National Park is located in the Mediterranean Biogeographical Region, a prominent climate change hot-spot. Inocybe brijunica sp. nov., from sect. Hysterices (Agaricales, Inocybaceae), is described based on morphology and multilocus phylogenetic data. The holotype collection was found at the edge between grassland and Quercus ilex forest with a few planted Pinus pinea trees, on Veli Brijun Island, the largest island of the archipelago. It is easily recognized by a conspicuous orange to orange-red-brown membranaceous surface layer located at or just above the basal part of the stipe. Other distinctive features of I. brijunica are the medium brown, radially fibrillose to rimose pileus; pale to medium brown stipe with fugacious cortina; relatively small, amygdaliform to phaseoliform, and smooth basidiospores, measuring ca. 6.5-9 × 4-5.5 µm; thick-walled, utriform, lageniform or fusiform pleurocystidia (lamprocystidia) with crystals and mostly not yellowing in alkaline solutions; cheilocystidia of two types (lamprocystidia and leptocystidia); and the presence of abundant caulocystidia only in the upper 2-3 mm of the stipe. Phylogenetic reconstruction of a concatenated dataset of the internal transcribed spacer region (ITS), the nuclear 28S rRNA gene (nrLSU), and the second largest subunit of RNA polymerase II (rpb2) resolved I. brijunica and I. glabripes as sister species.
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Affiliation(s)
- Armin Mešić
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
| | - Danny Haelewaters
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA; (J.L.); (M.C.A.)
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Zdenko Tkalčec
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
| | - Jingyu Liu
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA; (J.L.); (M.C.A.)
| | - Ivana Kušan
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA; (J.L.); (M.C.A.)
| | - Ana Pošta
- Laboratory for Biological Diversity, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia; (A.M.); (Z.T.); (I.K.); (A.P.)
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Choudhary P, Singh BN, Chakdar H, Saxena AK. DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance. World J Microbiol Biotechnol 2021; 37:54. [PMID: 33604719 DOI: 10.1007/s11274-021-03019-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.
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Affiliation(s)
- Prassan Choudhary
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Bansh Narayan Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
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Romero-Zambrano GL, Bermúdez-Puga SA, Sánchez-Yumbo AF, Yánez-Galarza JK, Ortega-Andrade HM, Naranjo-Briceño L. Amphibian chytridiomycosis, a lethal pandemic disease caused by the killer fungus Batrachochytrium dendrobatidis: New approaches to host defense mechanisms and techniques for detection and monitoring. RB 2021. [DOI: 10.21931/rb/2021.06.01.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Chytridiomycosis is a catastrophic disease currently decimating worldwide amphibian populations, caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. Massive species decline to extinction catalyzes radical changes in ecosystems globally, including the largest continuous rainforest ecosystem on Earth, the Amazon rainforest. Innovative research that aims to propose feasible mechanisms of mitigation and the origins of the disease is vital, including studies addressing climatic effects on the expansion of chytridiomycosis. Thus, this publication aims to provide a comprehensive review of: i) the current technologies used for B. dendrobatidis detection and monitoring, and ii) the known Neotropical amphibian's skin microbiota with anti-fungal properties against B. dendrobatidis. Several immunologic and DNA-based methods are discussed to understand the emerging fungal pathogens and their effects on the biosphere, which can help to mitigate the devastating ecological impacts of mass amphibian morbidity. The establishment of rapid and highly accurate B. dendrobatidis detection techniques and methods for monitoring amphibian's cutaneous microbiome is crucial in the fight against chytridiomycosis.
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Affiliation(s)
- Génesis L. Romero-Zambrano
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Stalin A. Bermúdez-Puga
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Alex F. Sánchez-Yumbo
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - Jomira K. Yánez-Galarza
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
| | - H. Mauricio Ortega-Andrade
- 2Biogeography and Spatial Ecology Research Group, Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150 3Herpetology Division, Instituto Nacional de Biodiversidad (INABIO), calle Rumipamba 341 y Av. de los Shyris, Quito, Ecuador
| | - Leopoldo Naranjo-Briceño
- Biotechnology Engineering Career. Faculty of Life Sciences. Universidad Regional Amazónica Ikiam, Tena, Ecuador 150150
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Sahlin K, Lim MCW, Prost S. NGSpeciesID: DNA barcode and amplicon consensus generation from long-read sequencing data. Ecol Evol 2021; 11:1392-1398. [PMID: 33598139 PMCID: PMC7863402 DOI: 10.1002/ece3.7146] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
Third-generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long-read sequences. This is not only advantageous for genome sequencing projects, but also advantageous for amplicon-based high-throughput sequencing experiments, such as DNA barcoding. However, the relatively high error rates associated with these technologies still pose challenges for generating high-quality consensus sequences. Here, we present NGSpeciesID, a program which can generate highly accurate consensus sequences from long-read amplicon sequencing technologies, including ONT and PacBio. The tool includes clustering of the reads to help filter out contaminants or reads with high error rates and employs polishing strategies specific to the appropriate sequencing platform. We show that NGSpeciesID produces consensus sequences with improved usability by minimizing preprocessing and software installation and scalability by enabling rapid processing of hundreds to thousands of samples, while maintaining similar consensus accuracy as current pipelines.
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Affiliation(s)
- Kristoffer Sahlin
- Department of MathematicsScience for Life LaboratoryStockholm UniversityStockholmSweden
| | - Marisa C. W. Lim
- Department of Population Health and ReproductionUniversity of CaliforniaDavisCAUSA
| | - Stefan Prost
- LOEWE‐Centre for Translational Biodiversity GenomicsSenckenbergFrankfurtGermany
- South African National Biodiversity InstituteNational Zoological GardenPretoriaSouth Africa
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D’Andreano S, Cuscó A, Francino O. Rapid and real-time identification of fungi up to species level with long amplicon nanopore sequencing from clinical samples. Biol Methods Protoc 2021; 6:bpaa026. [PMID: 33506108 PMCID: PMC7820110 DOI: 10.1093/biomethods/bpaa026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/02/2020] [Accepted: 12/18/2020] [Indexed: 12/21/2022] Open
Abstract
The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level and in real-time. We assess the applicability for taxonomic assignment of amplicons targeting a 3.5 Kb region (V3 18S-ITS1-5.8S-ITS2-28S D2) and a 6 Kb region (V1 18S-ITS1-5.8S-ITS2-28S D12) with the What's in my pot (WIMP) classifier. We used the ZymoBIOMICSTM mock community and different microbiological fungal cultures as positive controls. Long amplicon sequencing correctly identified Saccharomyces cerevisiae and Cryptococcus neoformans from the mock community and Malassezia pachydermatis, Microsporum canis and Aspergillus fumigatus from the microbiological cultures. Besides, we identified Rhodotorula graminis in a culture mislabelled as Candida spp. We applied the same approach to external otitis in dogs. Malassezia was the dominant fungal genus in dogs' ear skin, whereas Ma. pachydermatis was the main species in the healthy sample. Conversely, we identified a higher representation of Ma. globosa and Ma. sympodialis in otitis affected samples. We demonstrate the suitability of long ribosomal amplicons to characterize the fungal community of complex samples, either healthy or with clinical signs of infection.
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Affiliation(s)
- Sara D’Andreano
- SVGM, Servei Veterinari de Genètica
Molecular, Universitat Autònoma de Barcelona, 08193,
Bellaterra, Barcelona, Spain
- Vetgenomics, Edifici EUREKA, Parc de Recerca de la
UAB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Anna Cuscó
- Vetgenomics, Edifici EUREKA, Parc de Recerca de la
UAB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Olga Francino
- SVGM, Servei Veterinari de Genètica
Molecular, Universitat Autònoma de Barcelona, 08193,
Bellaterra, Barcelona, Spain
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Jeong J, Yun K, Mun S, Chung WH, Choi SY, Nam YD, Lim MY, Hong CP, Park C, Ahn YJ, Han K. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep 2021; 11:1727. [PMID: 33462291 PMCID: PMC7814050 DOI: 10.1038/s41598-020-80826-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
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Affiliation(s)
- Jinuk Jeong
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyeongeui Yun
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Song-Yi Choi
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Young-do Nam
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Chang Pyo Hong
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - ChanHyeok Park
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Yong Ju Ahn
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea.
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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Strassert JFH, Wurzbacher C, Hervé V, Antany T, Brune A, Radek R. Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota and a potential to switch between hosts. Sci Rep 2021; 11:396. [PMID: 33431987 DOI: 10.1038/s41598-020-79842-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores. Nephridiophagids are poor in morphological characteristics, and although they have been tentatively identified as early-branching fungi based on the SSU rRNA gene sequences of three species, their exact position within the fungal tree of live remained unclear. In this study, we describe two new species of nephridiophagids (Nephridiophaga postici and Nephridiophaga javanicae) from cockroaches. Using long-read sequencing of the nearly complete rDNA operon of numerous further species obtained from cockroaches and earwigs to improve the resolution of the phylogenetic analysis, we found a robust affiliation of nephridiophagids with the Chytridiomycota-a group of zoosporic fungi that comprises parasites of diverse host taxa, such as microphytes, plants, and amphibians. The presence of the same nephridiophagid species in two only distantly related cockroaches indicates that their host specificity is not as strict as generally assumed.
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Malarczyk DG, Panek J, Frąc M. Triplex Real-Time PCR Approach for the Detection of Crucial Fungal Berry Pathogens- Botrytis spp., Colletotrichum spp. and Verticillium spp. Int J Mol Sci 2020; 21:E8469. [PMID: 33187143 DOI: 10.3390/ijms21228469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/04/2020] [Accepted: 11/08/2020] [Indexed: 12/30/2022] Open
Abstract
Phytopathogens cause undeniably serious damage in agriculture by harming fruit cultivations and lowering harvest yields, which as a consequence substantially reduces food production efficiency. Fungi of the Botrytis, Colletotrichum and Verticillium genera are a main concern in berry production. However, no rapid detection method for detecting all of these pathogens simultaneously has been developed to date. Therefore, in this study, a multiplex real-time PCR assay for this purpose was established. Universal fungal primers for the D2 region of the large subunit ribosomal DNA and three multiplexable fluorogenic probes specific for the chosen fungi were designed and deployed. The triplex approach for the molecular detection of these fungi, which was developed in this study, allows for the rapid and effective detection of crucial berry pathogens, which contributes to a more rapid implementation of protective measures in plantations and a significant reduction in losses caused by fungal diseases.
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Gostinčar C. Towards Genomic Criteria for Delineating Fungal Species. J Fungi (Basel) 2020; 6:E246. [PMID: 33114441 DOI: 10.3390/jof6040246] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 02/06/2023] Open
Abstract
The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%—and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed—not as the only criterion—but as an additional tool in the versatile toolbox of fungal taxonomy.
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Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C, Edwards JE, Fliegerová K. Anaerobic Fungi: Past, Present, and Future. Front Microbiol 2020; 11:584893. [PMID: 33193229 PMCID: PMC7609409 DOI: 10.3389/fmicb.2020.584893] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/29/2020] [Indexed: 11/13/2022] Open
Abstract
Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.
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Affiliation(s)
- Matthias Hess
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Shyam S. Paul
- Gut Microbiome Lab, ICAR-Directorate of Poultry Research, Indian Council of Agricultural Research, Hyderabad, India
| | - Anil K. Puniya
- Anaerobic Microbiology Lab, ICAR-National Dairy Research Institute, Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Claire Shaw
- Systems Microbiology & Natural Product Discovery Laboratory, Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Joan E. Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Kateřina Fliegerová
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Prague, Czechia
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Simmons DR, Bonds AE, Castillo BT, Clemons RA, Glasco AD, Myers JM, Thapa N, Letcher PM, Powell MJ, Longcore JE, James TY. The Collection of Zoosporic Eufungi at the University of Michigan (CZEUM): introducing a new repository of barcoded Chytridiomyceta and Blastocladiomycota cultures. IMA Fungus 2020; 11:20. [PMID: 33062585 PMCID: PMC7537106 DOI: 10.1186/s43008-020-00041-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/30/2020] [Indexed: 11/10/2022] Open
Abstract
We formed the Collection of Zoosporic Eufungi at the University of Michigan (CZEUM) in 2018 as a cryopreserved fungal collection consolidating the University of Maine Culture Collection (UMCC, or JEL), the University of Alabama Chytrid Culture Collection (UACCC), and additional zoosporic eufungal accessions. The CZEUM is established as a community resource containing 1045 cryopreserved cultures of Chytridiomycota, Monoblepharidomycota, and Blastocladiomycota, with 52 cultures being ex-type strains. We molecularly characterized 431 cultures by amplifying the majority of the rDNA operon in a single reaction, yielding an average fragment length of 4739 bp. We sequenced multiplexed samples with an Oxford Nanopore Technology MinION device and software, and demonstrate the method is accurate by producing sequences identical to published Sanger sequences. With these data, we generated a phylogeny of 882 zoosporic eufungi strains to produce the most comprehensive phylogeny of these taxa to date. The CZEUM is thus largely characterized by molecular data, which can guide instructors and researchers on future studies of these organisms. Cultures from the CZEUM can be purchased through an online portal.
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Affiliation(s)
- D Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Anne E Bonds
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Buck T Castillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Rebecca A Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Alex D Glasco
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Jillian M Myers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Natasha Thapa
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Peter M Letcher
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Martha J Powell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 USA
| | - Joyce E Longcore
- School of Biology & Ecology, University of Maine, Orono, ME 04469 USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
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Tedersoo L, Anslan S, Bahram M, Kõljalg U, Abarenkov K. Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00456-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sipiczki M. Metschnikowia pulcherrima and Related Pulcherrimin-Producing Yeasts: Fuzzy Species Boundaries and Complex Antimicrobial Antagonism. Microorganisms 2020; 8:E1029. [PMID: 32664630 PMCID: PMC7409158 DOI: 10.3390/microorganisms8071029] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/30/2022] Open
Abstract
Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large ascomycetous genus Metschnikowia frequently turn out to produce the characteristic maroon-red pulcherrimin when tested for pigment production and prove to exert antagonistic effects on many types of microorganisms. The determination of the exact taxonomic position of the strains is hampered by the shortage of distinctive morphological and physiological properties of the species of the clade and the lack of rDNA barcode gaps. The rDNA repeats of the type strains of the species are not homogenized and are assumed to evolve by a birth-and-death mechanism combined with reticulation. The taxonomic division is further hampered by the incomplete biological (reproductive) isolation of the species: certain type strains can be hybridized and genome sequencing revealed chimeric genome structures in certain strains that might have evolved from interspecies hybrids (alloploid genome duplication). Various mechanisms have been proposed for the antimicrobial antagonism. One is related to pulcherrimin production. The diffusible precursor of pulcherrimin, the pulcherriminic acid is secreted by the cells into the environment where it forms the insoluble pulcherrimin with the ferric ions. The lack of free iron caused by the immobilization of ferric ions inhibits the growth of many microorganisms. Recent results of research into the complexity of the taxonomic division of the pulcherrimin-producing Metschnikowia yeasts and the mechanism(s) underlying their antimicrobial antagonism are discussed in this review.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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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: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Seto K, Matsuzawa T, Kuno H, Kagami M. Morphology, Ultrastructure, and Molecular Phylogeny of Aphelidium collabens sp. nov. (Aphelida), a Parasitoid of a Green Alga Coccomyxa sp. Protist 2020; 171:125728. [PMID: 32544843 DOI: 10.1016/j.protis.2020.125728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
Abstract
Aphelids (Aphelida) are intracellular parasitoids of algae and represent one of the early diverging or sister lineages of the kingdom Fungi. Although Aphelida is a small group, molecular phylogenetic analyses revealed that many environmental sequences belong to Aphelida, suggesting that aphelids are distributed worldwide; however, the extent of their diversity is unclear. Here, we investigated a novel aphelid culture APH2 that parasitizes the green alga Coccomyxa sp. APH2 produced posteriorly uniflagellate zoospores, a defining character of the genus Aphelidium. The residual body of APH2 was spherical in the mature plasmodium, but became amorphous during zoospore formation and collapsed after zoospore discharge, which has not been described for other Aphelidium species. Zoospores of APH2 possessed a striated rhizoplast that extended anteriorly from the kinetosome to the posterior end of the nucleus, and a microtubular root arising from the side of the kinetosome and lying almost parallel to the rhizoplast, both of which are unique among aphelid taxa. A molecular phylogenetic analysis based on the 18S rDNA sequences placed APH2 as sister lineage to all other known aphelid sequences. Based on these results, we describe this aphelid as a new species, Aphelidium collabens.
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Affiliation(s)
- Kensuke Seto
- Graduate School of Environment and Information Sciences, Yokohama National University, Tokiwadai 79-7, Hodogaya, Yokohama 240-8501, Japan
| | - Toshihiro Matsuzawa
- Advanced Research and Innovation Center, DENSO CORPORATION, Komenoki-cho, Nisshin-Shi, Aichi 470-0111, Japan.
| | - Hitoshi Kuno
- Advanced Research and Innovation Center, DENSO CORPORATION, Komenoki-cho, Nisshin-Shi, Aichi 470-0111, Japan
| | - Maiko Kagami
- Graduate School of Environment and Information Sciences, Yokohama National University, Tokiwadai 79-7, Hodogaya, Yokohama 240-8501, Japan.
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Abstract
Species names are fundamental to managing biological information. The surge of interest in microbial diversity has resulted in an increase in the number of microbes that need to be identified and assigned a species name. This article provides an introduction to the principles of DNA-based identification of Archaea and Bacteria traditionally known as prokaryotes, and Fungi, the Oomycetes and other protists, collectively referred to as fungi. The prokaryotes and fungi are the most commonly studied microbes from plants, and we introduce the most relevant concepts of prokaryote and fungal taxonomy and nomenclature. We first explain how prokaryote and fungal species are defined, delimited, and named, and then summarize the criteria and methods used to identify prokaryote and fungal organisms to species.
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Affiliation(s)
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892
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50
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Abstract
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.
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