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Rassbach J, Hilsberg N, Haensch VG, Dörner S, Gressler J, Sonnabend R, Semm C, Voigt K, Hertweck C, Gressler M. Non-canonical two-step biosynthesis of anti-oomycete indole alkaloids in Kickxellales. Fungal Biol Biotechnol 2023; 10:19. [PMID: 37670394 PMCID: PMC10478498 DOI: 10.1186/s40694-023-00166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/06/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Fungi are prolific producers of bioactive small molecules of pharmaceutical or agricultural interest. The secondary metabolism of higher fungi (Dikarya) has been well-investigated which led to > 39,000 described compounds. However, natural product researchers scarcely drew attention to early-diverging fungi (Mucoro- and Zoopagomycota) as they are considered to rarely produce secondary metabolites. Indeed, only 15 compounds have as yet been isolated from the entire phylum of the Zoopagomycota. RESULTS Here, we showcase eight species of the order Kickxellales (phylum Zoopagomycota) as potent producers of the indole-3-acetic acid (IAA)-derived compounds lindolins A and B. The compounds are produced both under laboratory conditions and in the natural soil habitat suggesting a specialized ecological function. Indeed, lindolin A is a selective agent against plant-pathogenic oomycetes such as Phytophthora sp. Lindolin biosynthesis was reconstituted in vitro and relies on the activity of two enzymes of dissimilar evolutionary origin: Whilst the IAA-CoA ligase LinA has evolved from fungal 4-coumaryl-CoA synthetases, the subsequently acting IAA-CoA:anthranilate N-indole-3-acetyltransferase LinB is a unique enzyme across all kingdoms of life. CONCLUSIONS This is the first report on bioactive secondary metabolites in the subphylum Kickxellomycotina and the first evidence for a non-clustered, two-step biosynthetic route of secondary metabolites in early-diverging fungi. Thus, the generally accepted "gene cluster hypothesis" for natural products needs to be reconsidered for early diverging fungi.
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Affiliation(s)
- Johannes Rassbach
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Nathalie Hilsberg
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Veit G Haensch
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Sebastian Dörner
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Julia Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Robin Sonnabend
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Caroline Semm
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Kerstin Voigt
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Markus Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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Reynolds NK, Stajich JE, Benny GL, Barry K, Mondo S, LaButti K, Lipzen A, Daum C, Grigoriev IV, Ho HM, Crous PW, Spatafora JW, Smith ME. Mycoparasites, Gut Dwellers, and Saprotrophs: Phylogenomic Reconstructions and Comparative Analyses of Kickxellomycotina Fungi. Genome Biol Evol 2023; 15:evac185. [PMID: 36617272 PMCID: PMC9866270 DOI: 10.1093/gbe/evac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023] Open
Abstract
Improved sequencing technologies have profoundly altered global views of fungal diversity and evolution. High-throughput sequencing methods are critical for studying fungi due to the cryptic, symbiotic nature of many species, particularly those that are difficult to culture. However, the low coverage genome sequencing (LCGS) approach to phylogenomic inference has not been widely applied to fungi. Here we analyzed 171 Kickxellomycotina fungi using LCGS methods to obtain hundreds of marker genes for robust phylogenomic reconstruction. Additionally, we mined our LCGS data for a set of nine rDNA and protein coding genes to enable analyses across species for which no LCGS data were obtained. The main goals of this study were to: 1) evaluate the quality and utility of LCGS data for both phylogenetic reconstruction and functional annotation, 2) test relationships among clades of Kickxellomycotina, and 3) perform comparative functional analyses between clades to gain insight into putative trophic modes. In opposition to previous studies, our nine-gene analyses support two clades of arthropod gut dwelling species and suggest a possible single evolutionary event leading to this symbiotic lifestyle. Furthermore, we resolve the mycoparasitic Dimargaritales as the earliest diverging clade in the subphylum and find four major clades of Coemansia species. Finally, functional analyses illustrate clear variation in predicted carbohydrate active enzymes and secondary metabolites (SM) based on ecology, that is biotroph versus saprotroph. Saprotrophic Kickxellales broadly lack many known pectinase families compared with saprotrophic Mucoromycota and are depauperate for SM but have similar numbers of predicted chitinases as mycoparasitic.
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Affiliation(s)
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California–Riverside
| | | | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Chris Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
- Department of Plant and Microbial Biology, University of California Berkeley
| | - Hsiao-Man Ho
- Department of Science Education, University of Education, 134, Section 2, Heping E. Road, National Taipei, Taipei 106, Taiwan
| | - Pedro W Crous
- Department of Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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Ri T, Suyama M, Takashima Y, Seto K, Degawa Y. A new genus Unguispora in Kickxellales shows an intermediate lifestyle between saprobic and gut-inhabiting fungi. Mycologia 2022; 114:934-946. [PMID: 36166197 DOI: 10.1080/00275514.2022.2111052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Kickxellomycotina encompasses two fungal groups: a saprobic group in excrement and soil and an arthropod gut-inhabiting group. The evolutionary transition between these two lifestyles is unclear due to the lack of knowledge on intermediate forms and lifestyles. Here, we describe a new species, Unguispora rhaphidophoridarum, that was isolated from the excrement of cave crickets (Rhaphidophoridae) in Japan. This species has a novel lifestyle that is intermediate between the saprobic and gut-inhabiting groups. The new genus Unguispora is a member of the Kickxellales and characterized by the sterile appendages born on the sporocladium and by the claw-like ornamentation of the sporangiole. Phylogenetic analysis based on 18S and 28S nuclear ribosomal DNA showed that this fungus is distinct from all known kickxellalean genera and is sister to Linderina. The sporangiospore of the new species germinated only in anaerobiosis and grew in a yeast-like form. The yeast-like cells, defined as "secondary spores," germinated into hyphae in aerobiosis. In the alimentary tract of cave crickets, the sporangiola are attached to the proventriculus (foregut) by the claw-like ornamentation and multiplicate in the same yeast-like form as under culture. We introduce a new term, "amphibious fungi," to describe fungi that have two life stages, one outside and the other inside the host gut, like U. rhaphidophoridarum. The discovery of an amphibious fungus in Kickxellales, which was formerly considered to be only saprobic, suggests that Kickxellomycotina has evolved in association with the animal gut.
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Affiliation(s)
- Tomohiko Ri
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-Kogen, Ueda, Nagano 386-2204, Japan
| | - Mai Suyama
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-Kogen, Ueda, Nagano 386-2204, Japan
| | - Yusuke Takashima
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-Kogen, Ueda, Nagano 386-2204, Japan
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya, Yokohama 240-8051, Japan
| | - Yousuke Degawa
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadaira-Kogen, Ueda, Nagano 386-2204, Japan
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The first record of the coprophilous Coemansia erecta in South America. MYCOTAXON 2022. [DOI: 10.5248/137.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
During a survey of the coprophilous zygosporic fungal diversity in the State of Pernambuco, Brazil, Coemansia erecta was recovered from dung of Cavia porcellus (guinea pig). This is the first record of this species in South America. Images and a description of the Brazilian
specimen are presented and discussed. An identification key for species of Coemansia from South America is provided.
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Reynolds NK, Jusino MA, Stajich JE, Smith ME. Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples. Mol Ecol Resour 2021; 22:1065-1085. [PMID: 34695878 DOI: 10.1111/1755-0998.13540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.
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Affiliation(s)
- Nicole K Reynolds
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Michelle A Jusino
- Center for Forest Mycology Research, USDA Forest Service, Northern Research Station, Madison, Wisconsin, USA
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
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Where are the basal fungi? Current status on diversity, ecology, evolution, and taxonomy. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00642-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chuang SC, Ho HM, Reynolds N, Smith ME, Benny GL, Chien CY, Tsai JL. Preliminary phylogeny of Coemansia (Kickxellales), with descriptions of four new species from Taiwan. Mycologia 2018; 109:815-831. [PMID: 29336682 DOI: 10.1080/00275514.2017.1401892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Four new species of Coemansia from Taiwan are described. Three produce spirally twisted sporangiophores, and these new taxa increase the number of species in the Coemansia spiralis complex from three to six. Each new taxon is morphologically unique. Coemansia biformis, sp. nov., has two different asexual reproductive types on the same thallus; one is straight and the other has a spiral fertile region. Coemansia helicoidea, sp. nov., has stoloniferous sporangiophores with a helicoid fertile region. Coemansia pennisetoides, sp. nov., has a sporangiophore with a fertile region that resembles the inflorescence of the plant genus Pennisetum. Coemansia umbellata, sp. nov., has an umbellate sporangiophore branching pattern and a spirally twisted fertile region on the lowest branches. A dichotomous key was provided to identify the 23 accepted Coemansia species. Phylogenetic analysis based on a combined data set of D1-D2 domains of nuc 28S ribosomal RNA (rDNA) and partial nuc 18S rDNA identifies several independent evolutionary lineages within Coemansia and suggests that Spirodactylon aureum and Kickxella alabastrina may be nested within the genus Coemansia. Sequences of nuc rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS] barcode) are also used to support the description of these new species of Coemansia.
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Affiliation(s)
- Shu-Cheng Chuang
- a Ph.D. Program in Microbial Genomics , National Chung Hsing University and Academia Sinica , No. 250, Kuo-Kuang Road, Taichung , 40227 , Taiwan
| | - Hsiao-Man Ho
- b Department of Science Education , National Taipei University of Education , No. 134, Section 2, He-Ping E. Road, Taipei , 10671 , Taiwan
| | - Nicole Reynolds
- c Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Matthew E Smith
- c Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Gerald L Benny
- c Department of Plant Pathology , 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville , Florida 32611-0680
| | - Chiu-Yuan Chien
- d Department of Life Science , National Normal University , No. 162, Sect. 1, He-Ping E. Road, Taipei , 10610 , Taiwan
| | - Ju-Lin Tsai
- b Department of Science Education , National Taipei University of Education , No. 134, Section 2, He-Ping E. Road, Taipei , 10671 , Taiwan
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Chuang SC, Ho HM, Benny GL, Lee CF. Two new Ramicandelaber species from Taiwan. Mycologia 2017; 105:320-34. [DOI: 10.3852/11-219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shu-Cheng Chuang
- Department of Science Education, National Taipei University of Education, No. 134, Sect. 2, He-Ping E. Road, Taipei, 10671, Taiwan
| | - Hsiao-Man Ho
- Department of Science Education, National Taipei University of Education, No. 134, Sect. 2, He-Ping E. Road, Taipei, 10671, Taiwan
| | - Gerald L. Benny
- Department of Plant Pathology, 1453 Fifield Hall, P.O. Box 110680, University of Florida, Gainesville, Florida 32611-0680
| | - Ching-Fu Lee
- Department of Applied Science, National Hsinchu University of Education, Hsinchu, 30014, Taiwan
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Benny GL, Smith ME, Kirk PM, Tretter ED, White MM. Challenges and Future Perspectives in the Systematics of Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina. BIOLOGY OF MICROFUNGI 2016. [DOI: 10.1007/978-3-319-29137-6_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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