Plant Ecology and Evolution 152(3): 499-506, doi: 10.5091/plecevo.2019.1621
Unexplored diversity of microscopic myxomycetes: evidence from environmental DNA
expand article infoOleg N. Shchepin‡, Martin Schnittler§, Nikki H.A. Dagamac§, Dmitry V. Leontyev|, Yuri K. Novozhilov‡
‡ Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov Str. 2, 197376 St. Petersburg, Russia§ Institute of Botany and Landscape Ecology, University of Greifswald, Soldmannstr. 15, 17487 Greifswald, Germany| Department of Botany, H.S. Skovoroda Kharkiv National Pedagogical University, Valentynivska Str. 2, 61168 Kharkiv, Ukraine

Corresponding author: Oleg Shchepin ( ledum_laconicum@mail.ru )

© Oleg N. Shchepin, Martin Schnittler, Nikki H.A. Dagamac, Dmitry V. Leontyev, Yuri K. Novozhilov.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Shchepin ON, Schnittler M, Dagamac NH.A, Leontyev DV, Novozhilov YK (2019) Unexplored diversity of microscopic myxomycetes: evidence from environmental DNA. Plant Ecology and Evolution 152(3): 499-506. https://doi.org/10.5091/plecevo.2019.1621
Open Access
Abstract

Background and aims – Recent studies showed the position of two slime mould species with microscopic sporocarps, Echinosteliopsis oligospora and Echinostelium bisporum, within the class Myxomycetes. These minute species are seldom seen in studies based on detection of sporocarps and can easily be confused with protosteloid amoebozoans.

Methods – We searched all published ePCR data sets that targeted myxomycete 18S rDNA for the presence of environmental sequences similar to E. oligospora and Echinosteliales in traditional circumscription, and performed phylogenetic analyses that included short environmental sequences and full-length 18S rDNA sequences representing all the major groups of myxomycetes.

Key results – We report 19 unique sequences which are closely related to E. bisporum or E. oligospora based on sequence similarity (73.1–95.2% similarity) and which form well-supported monophyletic clades with these species in phylogenetic analyses. They may represent new species that are not yet described. Our phylogeny based on full-length 18S rDNA sequences further confirms the position of E. bisporum and E. oligospora within myxomycetes and the paraphyly of the order Echinosteliales in its traditional circumscription.

Conclusions – Our results show that ePCR-based studies can reveal myxomycete taxa that often escape detection by traditional approaches, including potentially new species, and thus provide valuable new data on diversity and ecology of myxomycetes. As such, strategies for studying myxomycetes biodiversity should be revised, focusing also on molecular detection techniques in addition to the sporocarp-based ones.

Keywords
18S rDNA, Echinosteliales, Echinosteliopsis, Echinostelium, hidden diversity, slime moulds, SSU

References

  • Aguilar M., Fiore-Donno A.M., Lado C., Cavalier-Smith T. (2013) Using environmental niche models to test the ‘everything is everywhere’ hypothesis for Badhamia. The ISME Journal 8: 737–745. https://doi.org/10.1038/ismej.2013.183
  • Alexopoulos C. (1960) Gross morphology of the plasmodium and its significance in the relationships among the myxomycetes. Mycologia 52(1): 1–20. https://doi.org/10.2307/3756246
  • Borg Dahl M., Brejnrod A.D., Unterseher M., Hoppe T., Feng Y., Novozhilov Y.K., Sørensen S.J., Schnittler M. (2018a) Genetic barcoding of dark-spored myxomycetes (Amoebozoa) – identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies. Molecular Ecology Resources 18(2): 306–318. https://doi.org/10.1111/1755-0998.12725
  • Borg Dahl M., Shchepin O.N., Schunk C., Menzel A., Novozhilov Y.K., Schnittler M. (2018b) A four year survey reveals a coherent pattern between distribution of fruit bodies and soil amoebae populations for nivicolous myxomycetes. Scientific Reports 8(1): 11662. https://doi.org/10.1038/s41598-018-30131-3
  • Clissmann F., Fiore-Donno A.M., Hoppe B., Krüger D., Kahl T., Unterseher M., Schnittler M. (2015) First insight into dead wood protistean diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime moulds) in decaying beech logs. FEMS Microbiology Ecology 91(6): fiv50. https://doi.org/10.1093/femsec/fiv050
  • Dagamac N.H.A., Rojas C., Novozhilov Y.K., Moreno G.H., Schlueter R., Schnittler M. (2017) Speciation in progress? A phylogeographic study among populations of Hemitrichia serpula (Myxomycetes). PLoS ONE 12(4): e0174825. https://doi.org/10.1371/journal.pone.0174825
  • Feng Y., Schnittler M. (2015) Sex or no sex? Independent marker genes and group I introns reveal the existence of three sexual but reproductively isolated biospecies in Trichia varia (Myxomycetes). Organisms Diversity & Evolution 15(4): 631–650. https://doi.org/10.1007/s13127-015-0230-x
  • Feng Y., Klahr A., Janik P., Ronikier A., Hoppe T., Novozhilov Y.K., Schnittler M. (2016) What an intron may tell: several sexual biospecies coexist in Meriderma spp. (Myxomycetes). Protist 167(3): 234–253. https://doi.org/10.1016/j.protis.2016.03.003
  • Fiore-Donno A.M., Haskins E.F., Pawlowski J., Cavalier-Smith T. (2009) Semimorula liquescens is a modified echinostelid myxomycete (Mycetozoa). Mycologia 101(6): 773–776. https://doi.org/10.3852/08-075
  • Fiore-Donno A.M., Weinert J., Wubet T., Bonkowski M. (2016) Metacommunity analysis of amoeboid protists in grassland soils. Scientific Reports 6: 19068. https://doi.org/10.1038/srep19068
  • Fiore-Donno A.M., Tice A.K., Brown M.W. (2018) A non-flagellated member of the Myxogastria and expansion of the Echinosteliida. Journal of Eukaryotic Microbiology https://doi.org/10.1111/jeu.12694
  • Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., von Haeseler A., Jermiin L.S. (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods 14(6): 587–589. https://doi.org/10.1038/nmeth.4285
  • Kamono A., Kojima H., Matsumoto J., Kawamura K., Fukui M. (2009a) Airborne myxomycete spores: detection using molecular techniques. Naturwissenschaften 96(1): 147–151. https://doi.org/10.1007/s00114-008-0454-0
  • Kamono A., Matsumoto J., Kojima H., Fukui M. (2009b) Characterization of myxomycete communities in soil by reverse transcription polymerase chain reaction (RT-PCR)-based method. Soil Biology and Biochemistry 41(6): 1324–1330. https://doi.org/10.1016/j.soilbio.2009.04.001
  • Kamono A., Meyer M., Cavalier-Smith T., Fukui M., Fiore-Donno A.M. (2013) Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis. FEMS Microbiology Ecology 84(1): 98–109. https://doi.org/10.1111/1574-6941.12042
  • Kang S., Tice A.K., Spiegel F.W., Silberman J.D., Pánek T., Čepička I., Kostka M., Kosakyan A., Alcântara D.M., Roger A.J., Shadwick L.L., Smirnov A., KudryavstevA., Lahr D.J.G., Brown M.W. (2017) Between a pod and a hard test: The deep evolution of amoebae. Molecular Biology and Evolution 34(9): 2258–2270. https://doi.org/10.1093/molbev/msx162
  • Katoh K., Kuma K., Toh H., Miyata T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33(2): 511–518. https://doi.org/10.1093/nar/gki198
  • Katoh K., Rozewicki J., Yamada K.D. (2017) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics: bbx108. https://doi.org/10.1093/bib/bbx108
  • Ko T.W., Stephenson S.L., Jeewon R., Lumyong S., Hyde K.D. (2009) Molecular diversity of myxomycetes associated with decaying wood and forest floor leaf litter. Mycologia 101(5): 592–598. https://doi.org/10.3852/08-158
  • Lado C. (2005–2019) An on-line nomenclatural information system of Eumycetozoa. Available at http://eumycetozoa.com/ [accessed 2 Apr. 2019].
  • Lado C., Eliasson U. (2017) Taxonomy and systematics: current knowledge and approaches on the taxonomic treatment of Myxomycetes. In: Stephenson S.L., Rojas C. (eds) Myxomycetes. Biology, systematics, biogeography and ecology: 205–251. United Kingdom, Elsevier, Academic Press. https://doi.org/10.1016/B978-0-12-805089-7.00007-X
  • Leontyev D.V., Schnittler M., Stephenson S.L., Shadwick L.L., Novozhilov Y.K., Shchepin O.N. (2019) Towards a phylogenetic classification of the Myxomycetes. Phytotaxa 399(3): 209–238. https://doi.org/10.11646/phytotaxa.399.3.5
  • Minh B.Q., Nguyen M.A.T., Von Haeseler A. (2013) Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30(5): 1188–1195. https://doi.org/10.1093/molbev/mst024
  • Novozhilov Y.K., Okun M.V., Erastova D.A., Shchepin O.N., Zemlyanskaya I.V., García-Carvajal E., Schnittler M. (2013) Description, culture and phylogenetic position of a new xerotolerant species of Physarum. Mycologia 105(6): 1535–1546. https://doi.org/10.3852/12-284
  • Novozhilov Y.K., Rollins A.W., Schnittler M. (2017) Ecology and distribution of Myxomycetes. In: Stephenson S.L., Rojas C. (eds) Myxomycetes. Biology, systematics, biogeography and ecology: 83–105. United Kingdom, Elsevier, Academic Press. https://doi.org/10.1016/B978-0-12-805089-7.00008-1
  • Schnittler M., Novozhilov Y.K., Shadwick J.D.L., Spiegel F.W., García-Carvajal E., König P. (2015) What substrate cultures can reveal: Myxomycetes and myxomycete-like organisms from the Sultanate of Oman. Mycosphere 6(3): 356–384. https://doi.org/10.5943/mycosphere/6/3/11
  • Shchepin O.N., Novozhilov Y.K., Schnittler M. (2016) Disentangling the taxonomic structure of the Lepidoderma chailletii-carestianum species complex (Myxogastria, Amoebozoa): genetic and morphological aspects. Protistology 10(4): 117–129. https://doi.org/10.21685/1680-0826-2016-10-4-1
  • Shchepin O.N., Schnittler M, Erastova D.A., Prikhodko I.S., Borg Dahl M., Azarov D.V., Chernyaeva E.N., Novozhilov Y.K. (2019) Community of dark-spored myxomycetes in ground litter and soil of taiga forest (Nizhne-Svirskiy Reserve, Russia) revealed by DNA metabarcoding. Fungal Ecology 39: 80–93. https://doi.org/10.1016/j.funeco.2018.11.006
  • Stephenson S.L., Schnittler M., Novozhilov Y.K. (2008) Myxomycete diversity and distribution from the fossil record to the present. Biodiversity and Conservation 17(2): 285–301. https://doi.org/10.1007/s10531-007-9252-9
  • Suutari M., Majaneva M., Fewer D.P., Voirin B., Aiello A., Friedl T., Chiarello A.G., Blomster J. (2010) Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae). BMC Evolutionary Biology 10: 86. https://doi.org/10.1186/1471-2148-10-86
  • Talavera G., Castresana J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56(4): 564–577. https://doi.org/10.1080/10635150701472164
  • Trifinopoulos J., Nguyen L.T., von Haeseler A., Minh B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44: W232–W235. https://doi.org/10.1093/nar/gkw256
  • Vlasenko A.V., Filippova N.V., Vlasenko V.A. (2018) Echinostelium novozhilovii (Echinosteliaceae, Myxomycetes), a new species from Northern Asia. Phytotaxa 367(1): 91–96. https://doi.org/10.11646/phytotaxa.367.1.11