1
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Song WL, Yan SZ, Chen SL. Morphological and phylogenetic analyses reveal four species of myxomycetes new to China. Arch Microbiol 2024; 206:364. [PMID: 39080072 DOI: 10.1007/s00203-024-04083-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 07/09/2024] [Accepted: 07/14/2024] [Indexed: 08/15/2024]
Abstract
Four species of myxomycetes (Arcyria pseudodenudata, Diderma europaeum, Lycogala irregulare, and Trichia armillata) new to China were observed via light microscope and scanning electron microscope, and detailed descriptions and illustrations are provided, along with comparisons with related species. Among them, A. pseudodenudata was discovered for the first time outside of the type locality, D. europaeum was discovered for the first time outside of Europe, and L. irregulare and T. armillata were reported again after being named. Phylogenetic analyses based on nuclear 18S rDNA and elongation factor-1 alpha sequences or nuclear 18S rDNA and cytochrome oxidase subunit I sequences was performed to provide a molecular basis for morphological identification. These specimens were deposited in the Herbarium of Fungi of Nanjing Normal University.
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Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China.
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2
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Song WL, Li M, Wang ZQ, Chen SL. Taxonomy and phylogeny of three species in Perichaena sensu lato (Myxomycetes = Myxogastria) from China. Eur J Protistol 2024; 95:126105. [PMID: 38908307 DOI: 10.1016/j.ejop.2024.126105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
After Gulielmina was erected and Ophiotheca was resurrected based on some species originally included in Perichaena (Trichiaceae, Trichiales, Myxomyxetes), some specimens from the Herbarium of Fungi of Nanjing Normal University previously identified as Perichaena species were reexamined from morphological and two-gene (nuclear 18S rDNA and elongation factor-1 alpha) phylogenetic perspectives. In this study, two new myxomycete species, Gulielmina subreticulospora and Ophiotheca dictyospora, are described. Gulielmina subreticulospora shows the following character combination: branched plasmodiocarps, single peridium with circular protrusions in the inner surface, capillitium (2.4-)2.8-3.0(-3.4) μm in diameter, spores (7.4-)8.0-8.5(-9.0) μm in diameter and sub-reticulated. Ophiotheca dictyospora shows the following character combination: sessile sporocarps to short plasmodiocarps, single peridium with a densely irregular network and protrusions in the inner surface, capillitium (2.7-)3.5-5.0(-7.1) μm in diameter, uneven, decorated with spines of uneven size, spores (7.7-)8.2-8.6(-9.4) μm in diameter including obviously complete cristate reticulation with serrated edges, with deep and clear grids. Both new taxa were compared with related species and their genetic isolation was statistically tested. Moreover, a comprehensive morphological description and a detailed figure plate are provided for Perichaena verrucifera, and its phylogenetic position is determined.
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Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Min Li
- College of Food Science and Pharmaceutical Engineering, Zaozhuang University, Zaozhuang 277160, Shandong Province, China
| | - Zi-Qi Wang
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province, China.
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3
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Zhang Z, Zhai C, Li Y, Stephenson SL, Liu P. Slime molds (Myxomycetes) causing a "disease" in crop plants and cultivated mushrooms. FRONTIERS IN PLANT SCIENCE 2024; 15:1411231. [PMID: 38916031 PMCID: PMC11194395 DOI: 10.3389/fpls.2024.1411231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/23/2024] [Indexed: 06/26/2024]
Abstract
Myxomycetes (plasmodial slime molds) are eukaryotic protist predators that are associated with wood, leaf litter, and soil in forests, where they feed on bacteria, protozoans, and (to a more limited extent) fungi. The health of crop plants is essential because they represent a primary food source for humans. However, when myxomycetes produce numerous fruiting bodies on the stems and leaves of crop plants, which is herein referred to as a myxomycete colonization, this has the potential of interfering with plant photosynthesis, transpiration and respiration by blocking out light and covering stomata. Myxomycetes are not pathogens, but their occurrence on plants can be mistakenly interpreted as some type of infection. However, this phenomenon has been largely ignored. This paper provides a comprehensive overview of the taxonomic and economic diversity of the organisms involved in myxomycete colonization. In addition, the various types of myxomycete colonization reported in the literature are described and discussed, a number of images provided, and cultural and chemical prevention and control measures are summarized. The latter should be of significant relevance for local production of crops and plant protective stations. While myxomycetes are not pathogens of crop plants, some species can seriously impact commercially grown mushrooms. Reports of myxomycetes affecting mushrooms are also described in this paper.
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Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chao Zhai
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
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4
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Henderson TC, Garcia-Gimeno L, Beasley CE, Fry NW, Bess J, Brown MW. High above the rest: standing behaviors in the amoebae of Sappinia and Thecamoeba. Eur J Protistol 2024; 94:126082. [PMID: 38703601 DOI: 10.1016/j.ejop.2024.126082] [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: 12/08/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Many terrestrial microbes have evolved cell behaviors that help them rise above their substrate, often to facilitate dispersal. One example of these behaviors is found in the amoebae of Sappinia pedata, which actively lift most of their cell mass above the substrate, known as standing. This standing behavior was first described in S. pedata in the 1890s from horse dung isolates but never molecularly characterized from dung. Our study expands this understanding, revealing the first molecularly confirmed S. pedata from herbivore dung in Mississippi, USA, and describing a new species, Sappinia dangeardi n. sp., with larger trophozoite cells. Additionally, we isolated another standing amoeba, Thecamoeba homeri n. sp., from soil, exhibiting a previously unreported "doughnut shape" transient behavior. In S. dangeardi n. sp., we discovered that standing is likely triggered by substrate drying, and that actin filaments actively localize in the "stalk" to support the standing cells, as observed through confocal microscopy. While the purpose of standing behaviors has not been investigated, we hypothesize it is energetically expensive and therefore a significant evolutionary strategy in these organisms. Overall, this study emphasizes behavioral adaptations to terrestrial environments within Amoebozoa, stressing the importance of diverse laboratory conditions that replicate natural habitats.
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Affiliation(s)
- Tristan C Henderson
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Lucia Garcia-Gimeno
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Charles E Beasley
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Nicholas W Fry
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jayden Bess
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA.
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5
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Song WL, Chen SL. Arcyria similaris: A new myxomycete species from China. Mycologia 2024; 116:409-417. [PMID: 38442243 DOI: 10.1080/00275514.2024.2312077] [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: 10/12/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024]
Abstract
A new myxomycete species, Arcyria similaris, was reported herein. The specimens were found and collected in the field on dead bark from Jingangtai National Geopark in Henan Province of China. This species has distinct and unique morphological characteristics, including dark grayish olive sporothecae that fade to smoke gray with age, shallow saucer-shaped cups with marked reticulations and thick papillae on the inner surface, a netted capillitium with many bulges, uniformly marked with low, dense, and irregular reticulations, and spores (8.0-)9.3-10.1(-10.9) μm in diameter, marked with sparse small warts and grouped prominent warts. Apart from a comprehensive morphological study, partial sequences of the nuclear 18S rDNA and elongation factor-1 alpha (EF-1α) genes were also provided in this study. This new species was described and illustrated morphologically. The specimens are deposited in the Herbarium of Fungi of Nanjing Normal University (HFNNU).
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Affiliation(s)
- Wen-Long Song
- School of Life Sciences, Nanjing Normal University, No.1 Wenyuan Road Qixia District, Nanjing 210023, Jiangsu Province, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, No.1 Wenyuan Road Qixia District, Nanjing 210023, Jiangsu Province, China
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6
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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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7
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Rao G, Yan SZ, Song WL, Lin D, Chen YJ, Chen SL. Distribution, assembly, and interactions of soil microorganisms in the bright coniferous forest area of China's cold temperate zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165429. [PMID: 37437627 DOI: 10.1016/j.scitotenv.2023.165429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
The bright coniferous forest area in the cold temperate zone of China is a terrestrial ecosystem primarily dominated by low mountain Larix gmelinii trees. Limited information is available regarding the assembly mechanisms and interactions of microbial communities in the soil in this region. This study employed high-throughput techniques to obtain DNA from myxomycetes, bacteria, and fungi in the soil, evaluated their diversity in conjunction with environmental factors, associated them with the assembly process, and explored the potential interaction relationships between these microorganisms. The findings of our study showed that environmental factors had a more significant influence on the α and β diversity of bacteria compared to myxomycetes and fungi. Microbial communities were influenced by environmental selection and geographical diffusion, although environmental selection appeared to have a more significant impact than geographical diffusion. Our study suggested that different microorganisms exhibited unique evolutionary patterns and may have different assembly modes within phylogenetic groups. Myxomycetes and fungi exhibited a similar assembly process that was mainly influenced by stochastic dispersal limitation and drift. In contrast, bacteria's assembly process was primarily influenced by stochastic drift and deterministic homogeneous selection. The community of myxomycetes and fungi is greatly influenced by spatial distribution and random events, while bacteria have a relatively stable population composition in specific regions and may also be subject to environmental constraints. Finally, this study revealed that Humicolopsis cephalosporioides, a fungus that exclusively resided in cold environments, may play a critical role as a keystone species in maintaining molecular ecological networks and was considered a core member of the microbiome.
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Affiliation(s)
- Gu Rao
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Shu-Zhen Yan
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Wen-Long Song
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Di Lin
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Ya-Jing Chen
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Shuang-Lin Chen
- School of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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8
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Li S, Qi B, Peng X, Wang W, Wang W, Liu P, Liu B, Peng Z, Wang Q, Li Y. Genome size and GC content of myxomycetes. Eur J Protistol 2023; 90:125991. [PMID: 37331249 DOI: 10.1016/j.ejop.2023.125991] [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: 01/04/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/20/2023]
Abstract
More than 1272 myxomycetes species have been described, accounting for more than half of all Amoebozoa species. However, the genome size of only three myxomycetes species has been reported. Therefore, we used flow cytometry to present an extensive survey and a phylogeny-based analysis of genome size and GC content evolution in 144 myxomycetes species. The genome size of myxomycetes ranged from 18.7 Mb to 470.3 Mb, and the GC content ranged from 38.7% to 70.1%. Bright-spored clade showed larger genome sizes and more intra-order genome size variations than the dark-spored clade. GC content and genome size were positively correlated in both bright-spored and dark-spored clades, and spore size was positively correlated with genome size and GC content in the bright-spored clade. We provided the first genome size data set in Myxomycetes, and our results will provide helpful information for future Myxomycetes studies, such as genome sequencing.
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Affiliation(s)
- Shu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Xueyan Peng
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Wan Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Pu Liu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Zhanwu Peng
- Information Center, Jilin Agricultural University, Changchun, China.
| | - Qi Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China
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9
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Yajima Y. Dehydration and self-cell cleaning by a single cell drives the formation of fruiting body of Lamproderma columbinum (Myxomycetes). Mycologia 2023; 115:236-254. [PMID: 36877890 DOI: 10.1080/00275514.2023.2170146] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The noncellular complex structures of fruiting body produced by a multinucleate large plasmodium are the distinct character of Myxomycetes. Although the fruiting body distinguishes myxomycetes from other amoeboid single-cell organisms, it is unclear how such complex structures arise out of a single cell. The present study investigated the detailed process of fruiting body formation in Lamproderma columbinum, the type species of the genus Lamproderma, at the cellular level. A single cell excretes cellular waste and excess water during the formation of the fruiting body by controlling its shape, secreted materials, and organelle distribution. These excretion phenomena lead to the morphology of the mature fruiting body. The results of this study suggest that the structures of the L. columbinum fruiting body are involved not merely in spore dispersal but also in the process of dehydration and self-cell cleaning of the single cell for the next generation.
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Affiliation(s)
- Yuka Yajima
- Department of Science and Informatics, Muroran Institute of Technology, Mizumoto-cho 27-1, 0508585, Muroran, Japan
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10
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Leontyev D, Buttgereit M, Kochergina A, Shchepin O, Schnittler M. Two independent genetic markers support separation of the myxomycete Lycogala epidendrum into numerous biological species. Mycologia 2023; 115:32-43. [PMID: 36399690 DOI: 10.1080/00275514.2022.2133526] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lycogala epidendrum is one of the most widely known myxomycete species and the first-ever discovered representative of this group. Using 687 original DNA sequences from 330 herbarium specimens from Europe, Asia, North and Central America, and Australia, we constructed the first detailed phylogenies of the genus Lycogala, based on two independently inherited genetic markers, the ribosome small subunit 18S rRNA nuclear gene (18S rDNA) and the mitochondrial cytochrome oxidase subunit I gene (COI). In both phylogenies, L. epidendrum appeared to be a polyphyletic group, represented by numerous clades. The four other recognized species of the genus (L. confusum, L. conicum, L. exiguum, and L. flavofuscum) are scattered between branches corresponding to L. epidendrum. A barcode gap analysis revealed 60 18S rDNA phylogroups of L. epidendrum, which are distant from each other not less than from other species of the genus Lycogala. For 18 of these phylogroups with both 18S rDNA and COI sequences available, recombination patterns were analyzed to test for reproductive isolation. In contrast to the results of a simulation assuming panmixis, no crossing between ribosomal and mitochondrial phylogroups was found, thus allowing the conclusion that all tested phylogroups represent biospecies. More than one third (39.6%) of the studied specimens share a single 18S rDNA phylogroup, which we consider to be L. epidendrum s. str. This group displays the broadest geographic distribution and the highest intraspecific genetic variability. Nearly all (93.3%) of the remaining non-singleton 18S rDNA phylogroups are restricted to certain continents or even regions. At the same time, various reproductively isolated phylogroups occur sympatric at a given location.
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Affiliation(s)
- Dmytro Leontyev
- Department of Botany, H.S. Skovoroda Kharkiv National Pedagogical University, Valentynivska 2, Kharkiv 61168, Ukraine.,Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, Greifswald D-17487, Germany
| | - Marina Buttgereit
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, Greifswald D-17487, Germany
| | | | - Oleg Shchepin
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, Greifswald D-17487, Germany
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, Greifswald D-17487, Germany
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11
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Novozhilov YK, Prikhodko IS, Fedorova NA, Shchepin ON, Gmoshinskiy VI, Schnittler M. <i>Lamproderma vietnamense</i>: a new species of myxomycetes with reticulate spores from Phia Oắc - Phia Đén National Park (northern Vietnam) supported by molecular phylogeny and morphological analysis. MYCOSCIENCE 2022; 63:149-155. [PMID: 37090470 PMCID: PMC10043568 DOI: 10.47371/mycosci.2022.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/29/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022]
Abstract
A new species of Lamproderma (Myxomycetes), described herein as L. vietnamense, was recovered in the field on ground litter from mountain subtropical forests (Phia Oắc - Phia Đén National Park) of northern Vietnam. Morphological details were examined by light and scanning electron microscopy. The species is characterized by a distinct and unique combination of morphological features, including a bright blue, shiny and very thin membranous peridium, a small dome-shaped columella, rigid, straight, branched, brown capillitial threads which gradually become pale at the periphery and finally colorless at the tips and small-meshed, banded-reticulate spores with 9-12 meshes across the spore diameter and solid walls without perforations 0.3-0.5 µm high. The stability of the taxonomic characters of L. vietnamense is supported by two well-developed collections found in 2018 and 2019. Partial sequences of three molecular markers (SSU, EF1α, COI) for both collections are identical. A two-gene phylogeny of the first two markers displays the two known accessions as a well-separated entity and indicates affinity of the new species with L. columbinum (the type taxon of the genus), L. violaceum, and several nivicolous Lamproderma species.
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Affiliation(s)
| | | | | | - Oleg N. Shchepin
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences
| | | | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University Greifswald
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12
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New insights on the evolutionary relationships between the major lineages of Amoebozoa. Sci Rep 2022; 12:11173. [PMID: 35778543 PMCID: PMC9249873 DOI: 10.1038/s41598-022-15372-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
The supergroup Amoebozoa unites a wide diversity of amoeboid organisms and encompasses enigmatic lineages that have been recalcitrant to modern phylogenetics. Deep divergences, taxonomic placement of some key taxa and character evolution in the group largely remain poorly elucidated or controversial. We surveyed available Amoebozoa genomes and transcriptomes to mine conserved putative single copy genes, which were used to enrich gene sampling and generate the largest supermatrix in the group to date; encompassing 824 genes, including gene sequences not previously analyzed. We recovered a well-resolved and supported tree of Amoebozoa, revealing novel deep level relationships and resolving placement of enigmatic lineages congruent with morphological data. In our analysis the deepest branching group is Tubulinea. A recent proposed major clade Tevosa, uniting Evosea and Tubulinea, is not supported. Based on the new phylogenetic tree, paleoecological and paleontological data as well as data on the biology of presently living amoebozoans, we hypothesize that the evolution of Amoebozoa probably was driven by adaptive responses to a changing environment, where successful survival and predation resulted from a capacity to disrupt and graze on microbial mats-a dominant ecosystem of the mid-Proterozoic period of the Earth history.
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13
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Lado C, Treviño-Zevallos I, García-Martín JM, Wrigley de Basanta D. Diachea mitchellii: A new myxomycete species from high elevation forests in the tropical Andes of Peru. Mycologia 2022; 114:798-811. [PMID: 35695815 DOI: 10.1080/00275514.2022.2072140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A new species of the genus Diachea (order Physarales, Myxomycetes, Amoebozoa) is described from Peru. Relevant details on spore germination, as well as morphological and phylogenetic data, are provided. At first glance, the new species shares some morphological similarities with both D. leucopodia, type of the genus, and D. koazei, but it strikingly differs from all other species of its genus by combining a short dark stalk, with a reticulate columella, and clustered spores. Moreover, it seems to be the only species of Diachea exclusively associated with Polylepis tropical forests at elevations above 3500 m. Apart from a comprehensive morphological study of 31 specimens, we here provide phylogenetic evidence to confirm the inclusion of this species in the genus Diachea. Specifically, our phylogenetic analyses of the nuclear 18S rDNA (18S), mitochondrial 17S rDNA (17S), and elongation factor-1 alpha (EF-1α) genes show that the new species is related to D. leucopodia and D. bulbillosa. The remarkably different morphological characters distinguishing the new Diachea from all other species of its genus, along with its particular ecological preferences and geographic distribution, indicate that it is a distinct entity deserving recognition as an independent species.
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Affiliation(s)
- Carlos Lado
- Department of Mycology, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, 28014, Spain
| | | | - Joaquina María García-Martín
- Department of Mycology, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, 28014, Spain
| | - Diana Wrigley de Basanta
- Department of Mycology, Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, 28014, Spain
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14
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Rong P, Wang JL, Angelova A, Almsherqi ZA, Deng Y. Plasmalogenic Lipid Analogs as Platelet-Activating Factor Antagonists: A Potential Novel Class of Anti-inflammatory Compounds. Front Cell Dev Biol 2022; 10:859421. [PMID: 35493091 PMCID: PMC9048793 DOI: 10.3389/fcell.2022.859421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/24/2022] [Indexed: 12/31/2022] Open
Abstract
Plasmalogens and Platelet-Activating Factor (PAF) are both bioactive ether phospholipids. Whereas plasmalogens are recognized for their important antioxidant function and modulatory role in cell membrane structure and dynamics, PAF is a potent pro-inflammatory lipid mediator known to have messenger functions in cell signaling and inflammatory response. The relationship between these two types of lipids has been rarely studied in terms of their metabolic interconversion and reciprocal modulation of the pro-inflammation/anti-inflammation balance. The vinyl-ether bonded plasmalogen lipid can be the lipid sources for the precursor of the biosynthesis of ether-bonded PAF. In this opinion paper, we suggest a potential role of plasmalogenic analogs of PAF as modulators and PAF antagonists (anti-PAF). We discuss that the metabolic interconversion of these two lipid kinds may be explored towards the development of efficient preventive and relief strategies against PAF-mediated pro-inflammation. We propose that plasmalogen analogs, acting as anti-PAF, may be considered as a new class of bioactive anti-inflammatory drugs. Despite of the scarcity of available experimental data, the competition between PAF and its natural plasmalogenic analogs for binding to the PAF receptor (PAF-R) can be proposed as a mechanistic model and potential therapeutic perspective against multiple inflammatory diseases (e.g., cardiovascular and neurodegenerative disorders, diabetes, cancers, and various manifestations in coronavirus infections such as COVID-19).
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Affiliation(s)
- Pu Rong
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jie-Li Wang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Angelina Angelova
- CNRS, Institut Galien Paris-Saclay, Université Paris-Saclay, Châtenay-Malabry, France
| | - Zakaria A. Almsherqi
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- *Correspondence: Zakaria A. Almsherqi, ; Yuru Deng,
| | - Yuru Deng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
- *Correspondence: Zakaria A. Almsherqi, ; Yuru Deng,
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15
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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: 7] [Impact Index Per Article: 2.3] [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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16
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Janik P, Szczepaniak M, Lado C, Ronikier A. Didymium pseudonivicola: A new myxomycete from the austral Andes emerges from broad-scale morphological and molecular analyses of D. nivicola collections. Mycologia 2021; 113:1327-1342. [PMID: 34533412 DOI: 10.1080/00275514.2021.1961068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A new nivicolous myxomycete is described as a result of a comprehensive study of Didymium nivicola collections from the entire range of its occurrence. Statistical analysis of 12 morphological characters, phylogenetic analyses of nuc 18S rDNA and elongation factor 1-alpha gene (EF1A), and a delimitation method (automatic barcode gap diversity) have been applied to corroborate the identity of the new species. A preliminary morphological analysis of D. nivicola revealed high variability of South American populations where four types of spore ornamentation were noted. However, results of molecular study and statistical analysis of morphological characters did not support recognition of these four forms but the distinction of two morphotypes. Consequently, two species have been recognized: D. nivicola and the newly proposed D. pseudonivicola. The new species can be distinguished from D. nivicola by distinctly larger and mostly plasmodiocarpic sporophores, which are scattered to gregarious, paler spores, and by the paler, more delicate and more elastic capillitium. Spore ornamentation of D. pseudonivicola is uniform and can be described as distinctly spiny (pilate under scanning electron microscope [SEM]), whereas those of D. nivicola is more variable, where spines (pilae under SEM) are delicate, distinct, or conspicuous. Additionally, whereas D. nivicola is a species distributed worldwide, D. pseudonivicola occurs only in the austral Andes of Argentina and Chile.
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Affiliation(s)
- Paulina Janik
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Magdalena Szczepaniak
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Carlos Lado
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28014, Spain
| | - Anna Ronikier
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
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17
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A Phylogenetic Approach to Structural Variation in Organization of Nuclear Group I Introns and Their Ribozymes. Noncoding RNA 2021; 7:ncrna7030043. [PMID: 34449660 PMCID: PMC8395846 DOI: 10.3390/ncrna7030043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 01/22/2023] Open
Abstract
Nuclear group I introns are restricted to the ribosomal DNA locus where they interrupt genes for small subunit and large subunit ribosomal RNAs at conserved sites in some eukaryotic microorganisms. Here, the myxomycete protists are a frequent source of nuclear group I introns due to their unique life strategy and a billion years of separate evolution. The ribosomal DNA of the myxomycete Mucilago crustacea was investigated and found to contain seven group I introns, including a direct repeat-containing intron at insertion site S1389 in the small subunit ribosomal RNA gene. We collected, analyzed, and compared 72 S1389 group IC1 introns representing diverse myxomycete taxa. The consensus secondary structure revealed a conserved ribozyme core, but with surprising sequence variations in the guanosine binding site in segment P7. Some S1389 introns harbored large extension sequences in the peripheral region of segment P9 containing direct repeat arrays. These repeats contained up to 52 copies of a putative internal guide sequence motif. Other S1389 introns harbored homing endonuclease genes in segment P1 encoding His-Cys proteins. Homing endonuclease genes were further interrupted by small spliceosomal introns that have to be removed in order to generate the open reading frames. Phylogenetic analyses of S1389 intron and host gene indicated both vertical and horizontal intron transfer during evolution, and revealed sporadic appearances of direct repeats, homing endonuclease genes, and guanosine binding site variants among the myxomycete taxa.
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18
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Zhao FY, Liu SY, Stephenson SL, Hsiang T, Qi B, Li Z. Morphological and molecular characterization of the new aethaloid species Didymium yulii. Mycologia 2021; 113:926-937. [PMID: 34236946 DOI: 10.1080/00275514.2021.1922224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Five specimens, initially presumed to be Fuligo septica or Mucilago crustacea, were collected from Jilin Province and the Inner Mongolia Autonomous Region in China, but all five turned out to represent a new aethaloid species, Didymium yulii. This new species is characterized by pseudocapillitia without capillitia and an aethalioid fruiting body, features that are morphologically distinct from those of any other species of Didymium. To assess the phylogenetic relationships between D. yulii and other members of Didymium and in the Didymiaceae, sequences from two nonoverlapping targeted portions of nuc 18S rDNA (~450 bp and ~1050 bp) and translation elongation factor 1-alpha (tef1) were obtained and analyzed. The results indicate that D. yulii forms a single clade separate from other species of Didymium and the clade that contains M. crustacea, which strongly supports the identification of the five specimens as a new species.
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Affiliation(s)
- Feng-Yun Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, Jilin Province, People's Republic of China.,College of Life Sciences, Baicheng Normal University, Baicheng 137000, Jilin Province, People's Republic of China
| | - Shu-Yan Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, Jilin Province, People's Republic of China.,College of Plant Protection, Jilin Agricultural University, Changchun 130118, Jilin Province, People's Republic of China
| | - Steven L Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Tom Hsiang
- Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Bao Qi
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, Jilin Province, People's Republic of China
| | - Zhuang Li
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong Province, People's Republic of China
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19
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Wang W, Wang W, Wei S, Huang W, Qi B, Wang Q, Li Y. Design of potentially universal SSU primers in myxomycetes using next-generation sequencing. J Microbiol Methods 2021; 184:106203. [PMID: 33722637 DOI: 10.1016/j.mimet.2021.106203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 11/18/2022]
Abstract
Unlike fungi, which have a universally accepted barcode marker, universal primers still lack in myxomycetes. Typically, DNA barcode primers were designed based on comparing existing myxomycetes sequences and targeting the conserved regions. However, the extreme genetic diversity within major myxomycetes groups and the frequent occurrence of group I introns have made the development of universal DNA barcode a severe challenge. The emergence of next-generation sequencing provides an opportunity to address this problem. We sequenced the mixed genomic DNA of 81 myxomycetes and extracted the SSU gene's reads using next-generation sequencing. After alignment and assembly, we designed a set of SSU primers that matched all potential SNPs, avoided all known group I intron insertion sites, and were highly conserved between major myxomycetes orders. This set of SSU primers has the potential to become one of the universal primer combinations. Due to the high genetic divergence caused by long and complicated evolutionary histories, the lack of universal barcode primers is common in protists. Our research provides a new method to solve this problem.
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Affiliation(s)
- Wan Wang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Shuwei Wei
- Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Wei Huang
- Key Laboratory of Applied Statistics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
| | - Qi Wang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
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20
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Strelow D, de Haan M, Bonkowski M, Fiore-Donno AM. New insights into the phylogeny of the dark-spored Myxomycetes (Amoebozoa: Conosa: Myxogastria: Fuscisporidia) and polyphyly of the genus Stemonitis. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1733128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Daniel Strelow
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
| | - Myriam de Haan
- Research Department, Meise Botanic Garden, Nieuwelaan 38, Meise, 1860, Belgium
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
- Research Department, Meise Botanic Garden, Nieuwelaan 38, Meise, 1860, Belgium
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
- Research Department, Meise Botanic Garden, Nieuwelaan 38, Meise, 1860, Belgium
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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21
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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: 5] [Impact Index Per Article: 1.3] [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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22
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Cainelli R, Haan M, Meyer M, Bonkowski M, Fiore‐Donno AM. Phylogeny of Physarida (Amoebozoa, Myxogastria) Based on the Small‐Subunit Ribosomal RNA Gene, Redefinition of
Physarum pusillum
s. str. and Reinstatement of
P. gravidum
Morgan. J Eukaryot Microbiol 2020; 67:327-336. [DOI: 10.1111/jeu.12783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 12/10/2019] [Accepted: 01/02/2020] [Indexed: 01/16/2023]
Affiliation(s)
| | - Myriam Haan
- Research Department Meise Botanic Garden Nieuwelaan 38 1860 Meise Belgium
| | | | - Michael Bonkowski
- Terrestrial Ecology Institute of Zoology University of Cologne Zülpicher Str. 47b 50674 Cologne Germany
- Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - Anna Maria Fiore‐Donno
- Terrestrial Ecology Institute of Zoology University of Cologne Zülpicher Str. 47b 50674 Cologne Germany
- Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
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23
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Dai D, Okorley BA, Li Y, Zhang B. Life Cycles of Myxogastria Stemonitopsis typhina and Stemonitis fusca on Agar Culture. J Eukaryot Microbiol 2020; 67:66-75. [PMID: 31408563 PMCID: PMC6973090 DOI: 10.1111/jeu.12754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/29/2019] [Accepted: 08/05/2019] [Indexed: 01/25/2023]
Abstract
Myxogastria is a group of protozoa characterized by cellular uninucleate amoeboflagellates (myxamoebae and flagellated swarm cell), acellular multinucleate plasmodia, and stationary spore-bearing sporocarps. The Stemonitales is a large order in the Myxogastria and contains approximately 230 species, but only 13 species have their completed life cycles observed so far. Here, we described the life cycles of two species in Stemonitales, Stemonitopsis typhina and Stemonitis fusca by culturing in water agar medium and observing the morphogenesis of their spore germination, plasmodium, and sporocarp development. The spore-to-spore life cycles of Ste. typhina and S. fusca were completed in approximately 67 and 12 d, respectively. Both species possessed an aphanoplasmodium. However, the spores of Ste. typhina and S. fusca germinated by the V-shape split and pore methods, respectively. Unlike S. fusca with an evanescent peridium, Ste. typhina produced a shiny persistent peridium which was continuous with the membrane surrounding its stalk. The information will contribute to a better understanding of their taxonomy and phylogeny.
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Affiliation(s)
- Dan Dai
- College of Plant ProtectionShenyang Agricultural UniversityShenyangLiaoning110866China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal FungiJilin Agricultural UniversityChangchunJilin130118China
| | - Benjamin A. Okorley
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal FungiJilin Agricultural UniversityChangchunJilin130118China
| | - Yu Li
- College of Plant ProtectionShenyang Agricultural UniversityShenyangLiaoning110866China
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal FungiJilin Agricultural UniversityChangchunJilin130118China
| | - Bo Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal FungiJilin Agricultural UniversityChangchunJilin130118China
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24
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Rikkinen J, Grimaldi DA, Schmidt AR. Morphological stasis in the first myxomycete from the Mesozoic, and the likely role of cryptobiosis. Sci Rep 2019; 9:19730. [PMID: 31874965 PMCID: PMC6930221 DOI: 10.1038/s41598-019-55622-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/30/2019] [Indexed: 01/03/2023] Open
Abstract
Myxomycetes constitute a group within the Amoebozoa well known for their motile plasmodia and morphologically complex fruiting bodies. One obstacle hindering studies of myxomycete evolution is that their fossils are exceedingly rare, so evolutionary analyses of this supposedly ancient lineage of amoebozoans are restricted to extant taxa. Molecular data have significantly advanced myxomycete systematics, but the evolutionary history of individual lineages and their ecological adaptations remain unknown. Here, we report exquisitely preserved myxomycete sporocarps in amber from Myanmar, ca. 100 million years old, one of the few fossil myxomycetes, and the only definitive Mesozoic one. Six densely-arranged stalked sporocarps were engulfed in tree resin while young, with almost the entire spore mass still inside the sporotheca. All morphological features are indistinguishable from those of the modern, cosmopolitan genus Stemonitis, demonstrating that sporocarp morphology has been static since at least the mid-Cretaceous. The ability of myxomycetes to develop into dormant stages, which can last years, may account for the phenotypic stasis between living Stemonitis species and this fossil one, similar to the situation found in other organisms that have cryptobiosis. We also interpret Stemonitis morphological stasis as evidence of strong environmental selection favouring the maintenance of adaptations that promote wind dispersal.
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Affiliation(s)
- Jouko Rikkinen
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Helsinki, Finland. .,Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, 00014, Helsinki, Finland.
| | - David A Grimaldi
- Division of Invertebrate Zoology, American Museum of Natural History, New York, 10024-5192, USA
| | - Alexander R Schmidt
- Department of Geobiology, University of Göttingen, Goldschmidtstraße 3, 37077, Göttingen, Germany.
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25
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Leontyev DV, Schnittler M, Stephenson SL, Novozhilov YK. Systematic revision of the Tubifera casparyi-T. dictyoderma complex: Resurrection of the genus Siphoptychium and introduction of the new genus Thecotubifera. Mycologia 2019; 111:981-997. [PMID: 31613722 DOI: 10.1080/00275514.2019.1660842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The genus Siphoptychium is resurrected on the basis of comparative morphology and phylogeny of partial nuc 18S rDNA (18S) and translation elongation factor 1-alpha (EF1A) nucleotide sequences. The genus is characterized by the firm upper surface of the pseudoaethalium, accreted but easily separable sporothecae, a tubular or fibrous columella, and spores with a reticulate ornamentation consisting of 7-9 meshes across the diameter. In addition to the currently known single species S. casparyi (= Tubifera casparyi), two new members of Siphoptychium are described: S. violaceum from coniferous forests of Europe, east Asia, and southeast Asia, and S. reticulatum from temperate and subarctic regions of North America and alpine regions of Europe. A second genus, Thecotubifera, is described to accommodate Tubifera dictyoderma. The fruiting body of this species is transitional between a pseudoaethalium and a true aethalium. It is covered by a contiguous membranous cortex formed by the fused tips of the sporothecae, a feature typical for aethalia. However, the inner portions of sporothecae remain discernible, a feature more typical for pseudoaethalia. Columellae of Th. dictyoderma are formed by perforated plates, and the spores have a reticulate ornamentation consisting of 2-5 meshes across the diameter. For Th. dictyoderma, we could confirm records only for tropical regions and Japan, whereas all studied European specimens, including those mentioned in current monographs, represent species of Siphoptychium.
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Affiliation(s)
- Dmitry V Leontyev
- Department of Botany, H.S. Skovoroda Kharkiv National Pedagogical University, Valentynivs'ka 2, Kharkiv 61168, Ukraine
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Soldmannstr. 15, Greifswald, Germany D-17487
| | - Steven L Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Yuri K Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov St. 2, 197376 St. Petersburg, Russia
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Evidence of Intra-individual SSU Polymorphisms in Dark-spored Myxomycetes (Amoebozoa). Protist 2019; 170:125681. [PMID: 31586669 DOI: 10.1016/j.protis.2019.125681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 11/24/2022]
Abstract
The nuclear small subunit rRNA gene (SSU or 18S) is a marker frequently used in phylogenetic and barcoding studies in Amoebozoa, including Myxomycetes. Despite its common usage and the confirmed existence of divergent copies of ribosomal genes in other protists, the potential presence of intra-individual SSU variability in Myxomycetes has never been studied before. Here we investigated the pattern of nucleotide polymorphism in the 5' end fragment of SSU by cloning and sequencing a total of 238 variants from eight specimens, each representing a species of the dark-spored orders Stemonitidales and Physarales. After excluding singletons, a relatively low SSU intra-individual variability was found but our data indicate that this might be a widely distributed phenomenon in Myxomycetes as all samples analyzed possessed various ribotypes. To determine if the occurrence of multiple SSU variants within a single specimen has a negative effect on the circumscription of species boundaries, we conducted phylogenetic analyses that revealed that clone variation may be detrimental for inferring phylogenetic relationships among some of the specimens analyzed. Despite that intra-individual variability should be assessed in additional taxa, our results indicate that special care should be taken for species identification when working with closely related species.
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Shchepin ON, Schnittler M, Erastova DA, Prikhodko IS, Borg Dahl M, Azarov DV, Chernyaeva EN, Novozhilov YK. Community of dark-spored myxomycetes in ground litter and soil of taiga forest (Nizhne-Svirskiy Reserve, Russia) revealed by DNA metabarcoding. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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28
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Fiore‐Donno AM, Tice AK, Brown MW. A Non‐Flagellated Member of the Myxogastria and Expansion of the Echinosteliida. J Eukaryot Microbiol 2018; 66:538-544. [DOI: 10.1111/jeu.12694] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Anna Maria Fiore‐Donno
- Department of Terrestrial Ecology Zoological Institute University of Cologne Zülpicher Str. 47b 50674 Cologne Germany
| | - Alexander K. Tice
- Department of Biological Sciences Mississippi State University Starkville Mississippi 39762 USA
| | - Matthew W. Brown
- Department of Biological Sciences Mississippi State University Starkville Mississippi 39762 USA
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29
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Dahl MB, Shchepin O, Schunk C, Menzel A, Novozhilov YK, Schnittler M. A four year survey reveals a coherent pattern between occurrence of fruit bodies and soil amoebae populations for nivicolous myxomycetes. Sci Rep 2018; 8:11662. [PMID: 30076328 PMCID: PMC6076320 DOI: 10.1038/s41598-018-30131-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Among soil-inhabiting protists, myxomycetes stand out by their macroscopic fructifications which have allowed studies on their ecology and distribution for more than two hundred years. One of the most distinct ecological guilds in myxomycetes are the nivicolous or "snowbank" myxomycete species, which produce fruit bodies at the edge of melting snowbanks in spring. Relationship between the occurrence of fructifications and myxamoebae remain unknown. In this study we used modern molecular techniques, by direct DNA amplification from soil extracts (NGS metabarcoding) to compare the distribution of soil-inhabiting myxamoebae found in 2016 with fructifications from the same sites collected over the course of four years (2013, 2015-17) along an elevational transect in the northern German Alps. A coherent community composition between fructification and soil myxamoebae, though with species-specific differences in relative abundance, was revealed. Although patterns varied among species, myxamoebae were found at both low and high elevations, whereas fruit bodies were mainly found at higher elevations, likely explained by the presence of a stable and long-lasting snow cover. In addition, a year to year comparison of fructification records support the hypothesis that the abundance of fructifications strongly depends on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany.
| | - Oleg Shchepin
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St, Petersburg, Russia
| | - Christian Schunk
- Ecoclimatology, Technical University of Munich, Freising, Germany
| | - Annette Menzel
- Ecoclimatology, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Yuri K Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St, Petersburg, Russia
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
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Morphological and molecular characterization of a new succulenticolous Physarum (Myxomycetes, Amoebozoa) with unique polygonal spores linked in chains. Eur J Protistol 2018; 63:13-25. [DOI: 10.1016/j.ejop.2017.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 11/21/2022]
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31
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Wrigley de Basanta D, Estrada-Torres A, García-Cunchillos I, Cano Echevarría A, Lado C. Didymium azorellae, a new myxomycete from cushion plants of cold arid areas of South America. Mycologia 2018. [DOI: 10.1080/00275514.2018.1426925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Arturo Estrada-Torres
- Centro Tlaxcala de Biología de la Conducta, Universidad Autónoma de Tlaxcala, km 1.5 carretera Tlaxcala-Puebla s/n, 90,062, AP 262 Tlaxcala, Mexico
| | | | - Asunción Cano Echevarría
- Laboratorio de Florística, Departamento de Dicotiledóneas, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Avda. Arenales 1256, Lima 11, Perú
| | - Carlos Lado
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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32
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Borg Dahl M, Brejnrod AD, Unterseher M, Hoppe T, Feng Y, Novozhilov Y, Sørensen SJ, Schnittler M. Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies. Mol Ecol Resour 2017; 18:306-318. [PMID: 29024429 DOI: 10.1111/1755-0998.12725] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 09/26/2017] [Accepted: 10/01/2017] [Indexed: 12/18/2022]
Abstract
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Asker D Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Thomas Hoppe
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yun Feng
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
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33
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Ronikier A, Lado C. Nivicolous Stemonitales from the Austral Andes: analysis of morphological variability, distribution and phenology as a first step toward testing the large-scale coherence of species and biogeographical properties. Mycologia 2017; 107:258-83. [DOI: 10.3852/14-164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Ronikier
- Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Carlos Lado
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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34
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Ronikier A, Lado C, Meyer M, de Basanta DW. Two new species of nivicolousLamproderma(Myxomycetes) from the mountains of Europe and America. Mycologia 2017; 102:718-28. [DOI: 10.3852/09-223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Ronikier
- Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Carlos Lado
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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35
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Novozhilov YK, Okun MV, Erastova DA, Shchepin ON, Zemlyanskaya IV, García-Carvajal E, Schnittler M. Description, culture and phylogenetic position of a new xerotolerant species of Physarum. Mycologia 2017; 105:1535-46. [DOI: 10.3852/12-284] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuri K. Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov St. 2, 197376 St Petersburg, Russia
| | - Mikhail V. Okun
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov St. 2, 197376 St Petersburg, Russia, and CIBIV (Center for Integrative Bioinformatics in Vienna), Max F. Perutz Laboratories (MFPL), University of Vienna, Medical University of Vienna, Campus Vienna Biocenter 5 (VBC5), A-1030, Vienna, Austria
| | | | - Oleg N. Shchepin
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov St. 2, 197376 St Petersburg, Russia
| | - Inna V. Zemlyanskaya
- Volgograd State Medicinal University, Pavshikh Boitzov Square 1, Volgograd 400066, Russia
| | | | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt University Greifswald, Grimmer Str. 88, D-17487 Greifswald, Germany
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36
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de Basanta DW, Lado C, García-Martín JM, Estrada-Torres A. Didymium xerophilum, a new myxomycete from the tropical Andes. Mycologia 2017; 107:157-68. [DOI: 10.3852/14-058] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Arturo Estrada-Torres
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, km 10.5 carretera Texmelucan-Tlaxcala, Ixtacuixtla, 90122, Tlaxcala, México
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37
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Walker LM, Stephenson SL. The Species Problem in Myxomycetes Revisited. Protist 2016; 167:319-338. [DOI: 10.1016/j.protis.2016.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 05/12/2016] [Accepted: 05/27/2016] [Indexed: 11/27/2022]
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38
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Feng Y, Klahr A, Janik P, Ronikier A, Hoppe T, Novozhilov YK, Schnittler M. What an Intron May Tell: Several Sexual Biospecies Coexist in Meriderma spp. (Myxomycetes). Protist 2016; 167:234-53. [DOI: 10.1016/j.protis.2016.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 03/14/2016] [Accepted: 03/23/2016] [Indexed: 12/17/2022]
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39
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40
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Kretzschmar M, Kuhnt A, Bonkowski M, Fiore-Donno AM. Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa). J Eukaryot Microbiol 2016; 63:453-9. [DOI: 10.1111/jeu.12289] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/30/2015] [Accepted: 12/03/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Martin Kretzschmar
- Department of Terrestrial Ecology; Zoological Institute; University of Cologne; Zülpicher Str. 47b 50674 Cologne Germany
| | | | - Michael Bonkowski
- Department of Terrestrial Ecology; Zoological Institute; University of Cologne; Zülpicher Str. 47b 50674 Cologne Germany
| | - Anna Maria Fiore-Donno
- Department of Terrestrial Ecology; Zoological Institute; University of Cologne; Zülpicher Str. 47b 50674 Cologne Germany
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41
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Sex or no sex? Group I introns and independent marker genes reveal the existence of three sexual but reproductively isolated biospecies in Trichia varia (Myxomycetes). ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0230-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Clissmann F, Fiore-Donno AM, Hoppe B, Krüger D, Kahl T, Unterseher M, Schnittler M. First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs. FEMS Microbiol Ecol 2015; 91:fiv050. [DOI: 10.1093/femsec/fiv050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
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43
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The prospects and perspectives of the phylogenetic system of myxomycetes (Myxogastrea). UKRAINIAN BOTANICAL JOURNAL 2015. [DOI: 10.15407/ukrbotj72.02.147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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44
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Schnittler M, Erastova D, Shchepin O, Heinrich E, Novozhilov Y. Four years in the Caucasus – observations on the ecology of nivicolous myxomycetes. FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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45
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Hoppe T, Kutschera U. Species-specific cell mobility of bacteria-feeding myxamoebae in plasmodial slime molds. PLANT SIGNALING & BEHAVIOR 2015; 10:e1074368. [PMID: 26357877 PMCID: PMC4883942 DOI: 10.1080/15592324.2015.1074368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/15/2015] [Indexed: 05/25/2023]
Abstract
On decaying wood or litter in forests, plasmodial slime molds (myxomycetes) represent a large fraction of eukaryotic protists that feed on bacteria. In his seminal book Experimental Physiology of Plants (1865), Julius Sachs referred to the multinucleate plasmodium of myxomycetes, which were considered at that time as primitive plants (or fungi). Today it is well established that myxomycetes are members of the Amoebozoa (Protista). In this study we compare the mobility of myxamoebae of 3 European species, Lycogala epidendrum (order Liceales), Tubulifera arachnoidea, and Trichia decipiens (order Trichiales). Using agar plates, on which 3 separate bacterial species were cultivated as prey organisms (Methylobacterium mesophilicum, Escherichia coli, Agrobacterium tumefaciens), we document large differences in cell motility between the myxomycetes investigated. In addition, we show that the 3 species of myxamoebae can be distinguished based on their average cell size. These data shed light on the mode of co-occurrence via differential substrate utilization in these members of the Amoebozoa.
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Affiliation(s)
- Thomas Hoppe
- Institute of Botany and Landscape Ecology; University of Greifswald; Greifswald, Germany
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46
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Watson PM, Sorrell SC, Brown MW. Ptolemeba
n. gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba. J Eukaryot Microbiol 2014; 61:611-9. [DOI: 10.1111/jeu.12139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Pamela M. Watson
- Department of Biological Sciences; Mississippi State University; Mississippi State Mississippi 39762
| | - Stephanie C. Sorrell
- Department of Biological Sciences; Mississippi State University; Mississippi State Mississippi 39762
| | - Matthew W. Brown
- Department of Biological Sciences; Mississippi State University; Mississippi State Mississippi 39762
- Institute for Genomics, Biocomputing & Biotechnology; Mississippi State University; Mississippi State Mississippi 39762
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47
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Aguilar M, Fiore-Donno AM, Lado C, Cavalier-Smith T. Using environmental niche models to test the 'everything is everywhere' hypothesis for Badhamia. ISME JOURNAL 2013; 8:737-45. [PMID: 24132078 DOI: 10.1038/ismej.2013.183] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 11/09/2022]
Abstract
It is often discussed whether the biogeography of free-living protists is better explained by the 'everything is everywhere'(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of 'moderate endemicity' in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America.
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Affiliation(s)
- María Aguilar
- 1] Mycology Department, Real Jardín Botánico, CSIC, Madrid, Spain [2] Department of Cell Biology, Medical Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Carlos Lado
- Mycology Department, Real Jardín Botánico, CSIC, Madrid, Spain
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48
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49
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50
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Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences. Mycol Prog 2013. [DOI: 10.1007/s11557-013-0892-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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