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Cross-Amplification in Strigiformes: A New STR Panel for Forensic Purposes. Genes (Basel) 2021; 12:genes12111721. [PMID: 34828327 PMCID: PMC8625634 DOI: 10.3390/genes12111721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 11/25/2022] Open
Abstract
Strigiformes are affected by a substantial decline mainly caused by habitat loss and destruction, poaching, and trapping. Moreover, the increasing trend in bird trade and the growing interest in wild-caught rather than captive-bred birds are expected to encourage illegal trade. The biomolecular investigation represents a valuable tool to track illegal trade and to explore the genetic variability to preserving biodiversity. Microsatellite loci (STRs) are the most used markers to study genetic variability. Despite the availability of species-specific microsatellite loci in Strigiformes, a unique panel permitting the description of the genetic variability across species has not been identified yet. We tested 32 highly polymorphic microsatellite markers to evaluate the reliability of a unique microsatellite panel in different species of Strigiformes and its use for conservation and forensic purposes. We included in the study 84 individuals belonging to 28 parental groups and 11 species of Strigiformes. After screening polymorphic microsatellite loci, the description of genetic variability, and the kinship assessment, we characterized a final panel of 12 microsatellite loci able to identify individuals in 9 Strigiformes species. This STR panel might support the authorities in the forensic investigation for suspected smugglers and false parental claims; moreover, it can be useful to evaluate relatedness among individuals in captive-bred populations and to implement research projects finalized to the description of the genetic variability in wild populations.
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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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Metagenomes, metatranscriptomes and microbiomes of naturally decomposing deadwood. Sci Data 2021; 8:198. [PMID: 34344895 PMCID: PMC8333335 DOI: 10.1038/s41597-021-00987-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2021] [Indexed: 12/22/2022] Open
Abstract
Deadwood represents significant carbon (C) stock in a temperate forests. Its decomposition and C mobilization is accomplished by decomposer microorganisms – fungi and bacteria – who also supply the foodweb of commensalist microbes. Due to the ecosystem-level importance of deadwood habitat as a C and nutrient stock with significant nitrogen fixation, the deadwood microbiome composition and function are critical to understanding the microbial processes related to its decomposition. We present a comprehensive suite of data packages obtained through environmental DNA and RNA sequencing from natural deadwood. Data provide a complex picture of the composition and function of microbiome on decomposing trunks of European beech (Fagus sylvatica L.) in a natural forest. Packages include deadwood metagenomes, metatranscriptomes, sequences of total RNA, bacterial genomes resolved from metagenomic data and the 16S rRNA gene and ITS2 metabarcoding markers to characterize the bacterial and fungal communities. This project will be of use to microbiologists, environmental biologists and biogeochemists interested in the microbial processes associated with the transformation of recalcitrant plant biomass. Measurement(s) | metagenomic data • metatranscriptomic data • microbiome • RNA-seq of total RNA | Technology Type(s) | DNA sequencing • RNA-seq of total RNA • amplicon sequencing • RNA sequencing | Factor Type(s) | time of decomposition | Sample Characteristic - Organism | Fungi • Bacteria | Sample Characteristic - Environment | wood | Sample Characteristic - Location | Narodni prirodni rezervace Zofinsky prales |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14821752
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Voss C, Fiore-Donno AM, Guerreiro MA, Peršoh D, Bonkowski M. Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage. FEMS Microbiol Ecol 2019; 95:5565044. [DOI: 10.1093/femsec/fiz142] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
ABSTRACTForest litter harbors complex networks of microorganisms whose major components are bacteria, fungi and protists. Protists, being highly selective consumers of bacteria and fungi could influence decomposition processes by shifting competitive microbial interactions. We investigated the eukaryotic diversity from 18 samples of one-year beech (Fagus sylvatica) leaf litter by RNA-based high-throughput sequencing of the small-subunit ribosomal RNA gene. By applying a metatranscriptomics approach, we avoided biases inherent to PCR-based methods, and could therefore focus on elusive protistan groups. We obtained 14 589 eukaryotic assembled sequences (contigs) representing 2223 unique taxa. Fungi dominated the eukaryotic assemblage, followed by an equal proportion of protists and plants. Among protists, the phylum Amoebozoa clearly dominated, representing more than twice the proportion of Alveolata (mostly ciliates) and Rhizaria (mostly Cercozoa), which are often retrieved as the dominant protistan groups in soils, revealing potential primer biases. By assigning functional traits to protists, we could assess that the proportion of free-living and heterotrophs was much higher than that of parasites and autotrophs, opening the way to a better understanding of the role played by the protistan communities and how biodiversity interacts with decomposition processes.
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Affiliation(s)
- Christian Voss
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Marco Alexandre Guerreiro
- Department of Geobotany, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitaetstr. 150, 44801 Bochum, Germany
| | - Derek Peršoh
- Department of Geobotany, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitaetstr. 150, 44801 Bochum, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
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Vlasenko AV, Novozhilov YK, Schnittler M, Vlasenko VA, Tomoshevich MA. Pattern of Substrate Preferences of Free Living Protists (Myxomycetes) on Decaying Wood. CONTEMP PROBL ECOL+ 2018. [DOI: 10.1134/s1995425518050104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Adamonytė G, Motiejūnaitė J, Iršėnaitė R. Crown fire and surface fire: effects on myxomycetes inhabiting pine plantations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:1431-1439. [PMID: 26953140 DOI: 10.1016/j.scitotenv.2016.02.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/22/2016] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
Myxomycetes are heterotrophic eukaryote organisms that have three life stages, none of which are known to be resistant to fire. The response of myxobiota to different severity of fire is not well known either. We examined myxomycetes in Pinus mugo plantations following a crown fire and in Pinus sylvestris plantations following a surface fire during the first three years after the wildfire event in forested coastal sand dunes in western Lithuania. Additionally, we investigated myxomycetes in corresponding unburned stands. All studied sites (unburned and burned) bore rather different myxomycete assemblages but the disparities of the species compositions between both burn types were more pronounced showing that fire severity had stronger impact on myxomycete species composition than the pre-fire stand type. Analysis of myxomycete assemblages (including the results from field collections, bark and litter cultures) showed that surface fire sites bore the highest number of post-fire species compared to crown fire and unburned sites. Dynamic annual changes in species composition were observed in all studied sites but only crown fire plots showed a clear chronosequence of post-fire myxomycete assemblages. Fire impact promoted establishment and/or sporulation of myxomycete species that are rare in similar unburned stands, or are usually confined to other types of forests and substrata. In addition, individual myxomycete species tended to switch substratum usage during the course of vegetation succession, with a final return to their usual substrata. This possibly signaled the end of early stage of post-fire succession.
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Affiliation(s)
- Gražina Adamonytė
- Nature Research Centre, Institute of Botany, Laboratory of Mycology, Žaliųjų Ežerų Str. 49, LT-08406, Vilnius, Lithuania.
| | - Jurga Motiejūnaitė
- Nature Research Centre, Institute of Botany, Laboratory of Mycology, Žaliųjų Ežerų Str. 49, LT-08406, Vilnius, Lithuania.
| | - Reda Iršėnaitė
- Nature Research Centre, Institute of Botany, Laboratory of Mycology, Žaliųjų Ežerų Str. 49, LT-08406, Vilnius, Lithuania.
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Baldrian P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol Rev 2016; 41:109-130. [DOI: 10.1093/femsre/fuw040] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2016] [Indexed: 12/13/2022] Open
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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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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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Xavier de Lima V, de Holanda Cavalcanti L. Ecology of lignicolous myxomycetes in Brazilian Atlantic rain forest. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1115-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yamashita S, Masuya H, Abe S, Masaki T, Okabe K. Relationship between the decomposition process of coarse woody debris and fungal community structure as detected by high-throughput sequencing in a deciduous broad-leaved forest in Japan. PLoS One 2015; 10:e0131510. [PMID: 26110605 PMCID: PMC4481346 DOI: 10.1371/journal.pone.0131510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/03/2015] [Indexed: 11/18/2022] Open
Abstract
We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process.
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Affiliation(s)
- Satoshi Yamashita
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Hayato Masuya
- Tohoku Research Center, Forestry and Forest Products Research Institute, Morioka, Iwate, Japan
| | - Shin Abe
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Takashi Masaki
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Kimiko Okabe
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
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