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Shchepin ON, López Villalba Á, Inoue M, Prikhodko IS, Erastova DA, Okun MV, Woyzichovski J, Yajima Y, Gmoshinskiy VI, Moreno G, Novozhilov YK, Schnittler M. DNA barcodes reliably differentiate between nivicolous species of Diderma (Myxomycetes, Amoebozoa) and reveal regional differences within Eurasia. Protist 2024; 175:126023. [PMID: 38368650 DOI: 10.1016/j.protis.2024.126023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/03/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
The nivicolous species of the genus Diderma are challenging to identify, and there are several competing views on their delimitation. We analyzed 102 accessions of nivicolous Diderma spp. that were sequenced for two or three unlinked genes to determine which of the current taxonomic treatments is better supported by molecular species delimitation methods. The results of a haplotype web analysis, Bayesian species delimitation under a multispecies coalescent model, and phylogenetic analyses on concatenated alignments support a splitting approach that distinguishes six taxa: Diderma alpinum, D. europaeum, D. kamchaticum, D. meyerae, D. microcarpum and D. niveum. The first two approaches also support the separation of Diderma alpinum into two species with allopatric distribution. An extended dataset of 800 specimens (mainly from Europe) that were barcoded with 18S rDNA revealed only barcode variants similar to those in the species characterized by the first data set, and showed an uneven distribution of these species in the Northern Hemisphere: Diderma microcarpum and D. alpinum were the only species found in all seven intensively sampled mountain regions. Partial 18S rDNA sequences serving as DNA barcodes provided clear signatures that allowed for unambiguous identification of the nivicolous Diderma spp., including two putative species in D. alpinum.
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Affiliation(s)
- Oleg N Shchepin
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany; Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia.
| | - Ángela López Villalba
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Maho Inoue
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Ilya S Prikhodko
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Daria A Erastova
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Mikhail V Okun
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Jan Woyzichovski
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
| | - Yuka Yajima
- Department of Science and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, 0508585 Muroran, Japan
| | - Vladimir I Gmoshinskiy
- Department of Mycology and Algology, Faculty of Biology, Moscow State University, Leninskie Gory 1/12, Moscow 119992, Russia
| | - Gabriel Moreno
- Departamento Ciencias de la Vida (Botanica), Universidad de Alcala, Alcala de Henares, Madrid 28805, Spain
| | - Yuri K Novozhilov
- Komarov Botanical Institute of the Russian Academy of Sciences, Laboratory of Systematics and Geography of Fungi, Prof. Popov Street 2, 197376 St. Petersburg, Russia
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany
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Shchepin O, Novozhilov Y, Woyzichovski J, Bog M, Prikhodko I, Fedorova N, Gmoshinskiy V, Borg Dahl M, Dagamac NHA, Yajima Y, Schnittler M. Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing. Mol Ecol 2021; 31:372-390. [PMID: 34676941 DOI: 10.1111/mec.16239] [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: 06/14/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023]
Abstract
Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1-3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.
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Affiliation(s)
- Oleg Shchepin
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Jan Woyzichovski
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Manuela Bog
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Ilya Prikhodko
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Nadezhda Fedorova
- Laboratory of Systematics and Geography of Fungi, Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia.,Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir Gmoshinskiy
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Polistovsky National Nature Reserve, Pskov Region, Russia
| | - Mathilde Borg Dahl
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Nikki H A Dagamac
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany.,Department of Biological Sciences and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Yuka Yajima
- Muroran Institute of Technology, Muroran, Japan
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
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Nguyen LTT, Sanchez-Mahecha O, Almadrones-Reyes KJ, Redeña-Santos JC, Dagamac NHA. Occurrence of leaf litter inhabiting myxomycetes from lowland forest patches of Northern and Central Vietnam. Trop Ecol 2020. [DOI: 10.1007/s42965-020-00059-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractDuring the last years, much of the diversity studies of myxomycetes (plasmodial slime molds) have been concentrated mostly in the Southern region of Vietnam. Moreover, information on leaf litter inhabiting myxomycetes for the country is still in scarcity. Hence, this study aims to assess the occurrence and distribution of leaf litter inhabiting myxomycetes in different forest types in the subtropical northern and coastal tropical monsoon central part of the country. Samples of aerial and ground leaf litter that were used to prepare moist chamber cultures in the laboratory were collected in (1) Ba Vi National Park, Ha Noi, (2) Ho Nui Coc, Thai Nguyen, and (3) coastal forest patches in Da Nang. A total of 24 species belonging to 10 genera, wherein the majority of these myxomycete species appeared abundantly (11 species) is reported for this study. Based on species richness, Ha Noi harbored the highest number of myxomycete species. Leaf litter inhabiting myxomycete communities between aerial and ground substrates shared a high level of similarity based on their species composition and relative abundance. Highest level of similarity of leaf litter inhabiting myxomycete asssemblages is also reported between Ha Noi and Da Nang (CC = 0.78, PS = 0.56). This research study is the first step in understanding the complex myxomycete ecology of leaf inhabiting myxomycetes and would help filling now the large gap in one of the unexplored tropical areas of the world.
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Janik P, Ronikier M, Ronikier A. New protocol for successful isolation and amplification of DNA from exiguous fractions of specimens: a tool to overcome the basic obstacle in molecular analyses of myxomycetes. PeerJ 2020; 8:e8406. [PMID: 32002333 PMCID: PMC6984339 DOI: 10.7717/peerj.8406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/16/2019] [Indexed: 11/23/2022] Open
Abstract
Herbarium collections provide an essential basis for a wide array of biological research and, with development of DNA-based methods, they have become an invaluable material for genetic analyses. Yet, the use of such material is hindered by technical limitations related to DNA degradation and to quantity of biological material. The latter is inherent for some biological groups, as best exemplified by myxomycetes which form minute sporophores. It is estimated that ca. two-thirds of myxomycete taxa are represented by extremely scanty material. As DNA isolation methods applied so far in myxomycete studies require destructive sampling of many sporophores, a large part of described diversity of the group remains unavailable for phylogenetic studies or barcoding. Here, we tested several procedures of DNA isolation and amplification to seek for an efficient and possibly non-destructive method of sampling. Tests were based on herbarium specimens of 19 species representing different taxonomic orders. We assayed several variants of isolation based on silica gel membrane columns, and a newly designed procedure using highly reduced amount of biological material (small portion of spores), based on fine disruption of spores and direct PCR. While the most frequently used column-based method led to PCR success in 89.5% of samples when a large amount of material was used, its performance dropped to 52% when based on single sporophores. Single sporophores provided amplicons in 89.5% of samples when using a kit dedicated to low-amount DNA samples. Our new procedure appeared the most effective (94.7%) while it used only a small fraction of spores, being nearly non-destructive; it was also the most cost-effective. We thus demonstrate that combination of adequate handling of spore micro-disruption coupled with application of direct PCR can be an efficient way to circumvent technical limitations for genetic studies in myxomycetes and thus can substantially improve taxon sampling for phylogeny and barcoding. Additionally, this approach gives a unique possibility to apply both molecular and morphological assays to the same structure (sporophore), which then can be further stored as documentation.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Michał Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
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Hosokawa A, Reid CR, Latty T. Slimes in the city: The diversity of myxomycetes from inner-city and semi-urban parks in Sydney, Australia. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bernardo JLM, Arioder LJQ, Almadrones-Reyes KJ, Dagamac NHA. Myxomycete communities occurring in fragmented forest patches in two municipalities of Laguna, Philippines. COMMUNITY ECOL 2018. [DOI: 10.1556/168.2018.19.3.10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- J. L. M. Bernardo
- Advanced Educational Program, Thai Nguyen University of Agriculture and Forestry, Quyết Thắng, Thái Nguyên, Vietnam
| | - L. J. Q. Arioder
- Advanced Educational Program, Thai Nguyen University of Agriculture and Forestry, Quyết Thắng, Thái Nguyên, Vietnam
| | - K. J. Almadrones-Reyes
- Advanced Educational Program, Thai Nguyen University of Agriculture and Forestry, Quyết Thắng, Thái Nguyên, Vietnam
| | - N. H. A. Dagamac
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstrasse 15, D-17487 Greifswald, Germany
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