Skip to main content Skip to main navigation menu Skip to site footer
Type: Article
Published: 2022-05-09
Page range: 92-112
Abstract views: 1029
PDF downloaded: 50

Description of a model tardigrade Paramacrobiotus metropolitanus sp. nov. (Eutardigrada) from Japan with a summary of its life history, reproduction and genomics

Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Japan.
Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Japan.
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan.
Tardigrada DNA barcoding Eutardigrada integrative taxonomy Macrobiotidae Parachela tardigrades

Abstract

The genus Paramacrobiotus was erected in 2009 from the genus Macrobiotus, and 43 Paramacrobiotus species have been described to date. Although the first genome sequence in the genus was reported for the TYO strain of Paramacrobiotus sp., which is a dioecious species and has five bivalent chromosomes, its precise taxonomic identification remained undetermined. Here, we report its morphology, confirming the presence of a microplacoid, cuticular bulge on the inner side of legs I–III, and granulation on the inner side of legs IV under both light and electron microscopy, and smooth areoles on the egg shell, indicating that it differs from other described species. In addition, the previously described karyotype 2n=10 of this strain is clearly distinct from other species of the genus Paramacrobiotus, supporting the hypothesis that the strain represents a new species. Molecular analyses for the small and large ribosomal subunit (18S rDNA, 28S rDNA), the internal transcribed spacer 2 (ITS-2) and cytochrome C oxidase subunit I (COI) were also performed. The TYO strain is most similar in the analysed nuclear markers to Paramacrobiotus experimentalis Kaczmarek, Mioduchowska, Poprawa & Roszkowska, 2020 and Paramacrobiotus sp. strain MG.002 (p-distances in 18S rDNA: 0.53%, 28S rDNA: 0.98–1.12%, and ITS-2: 9.9%), which corroborates with the overall morphological similarity between these taxa. Despite the close relationship between the TYO strain and P. experimentalis, the genetic species delimitation based on molecular analysis indicates that the TYO strain indeed is a distinct species. Therefore, this tardigrade is described here as Paramacrobiotus metropolitanus sp. nov.

 

References

  1. Arakawa, K., Yoshida, Y. & Tomita, M. (2016) Genome sequencing of a single tardigrade Hypsibius dujardini individual. Scientific Data, 3, 160063. https://doi.org/10.1038/sdata.2016.63
    Bertolani, R., Guidetti, R., Marchioro, T., Altiero, T., Rebecchi, L. & Cesari, M. (2014) Phylogeny of Eutardigrada: New molecular data and their morphological support lead to the identification of new evolutionary lineages. Molecular Phylogenetics and Evolution, 76, 110–126. https://doi.org/10.1016/j.ympev.2014.03.006
    Binda, M.G. & Pilato, G. (2001) Macrobiotus savai and Macrobiotus humilis, two new species of tardigrades from Sri Lanka. Bollettino Accademia Gioenia Science Naturali, Catania, 34, 101–111.
    Biserov, V.I. (1998) Tardigrades of the Caucasus with a taxonomic analysis of the genus Ramazzottius (Parachela: Hypsibiidae). Zoologischer Anzeiger, 236, 139–159.
    Claps, M.C. & Rossi, G.C. (1997) Tardigrados de Uruguay, com descripcion de dos nuevas especies (Echiniscidae, Macrobiotidae). Iheringia Série Zoologia, 83, 17–22.
    Dastych, H., Hohberg, K. & Dabert, J. (2014) Phylogenetic position of the enigmatic clawless eutardigrade genus Apodibius Dastych, 1983 (Tardigrada), based on 18S and 28S rRNA sequence data from its type species A. confusus. Molecular Phylogenetics and Evolution, 70, 70–75. https://doi.org/10.1016/j.ympev.2013.09.012
    Degma, P., Bertolani, R. & Guidetti, R. (2021) Actual checklist of Tardigrada species (2009-2021, 40th Edition: 15-07-2021).
    http://doi.org/10.25431/11380_1178608
    Folmer, O., Black, M., Hoeh, W., Lutz, R. & Vrijenhoek, R. (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–299.
    Gąsiorek, P., Stec, D., Morek, W. & Michalczyk, Ł. (2017) An integrative redescription of Echiniscus testudo (Doyère, 1840), the nominal taxon for the class Heterotardigrada (Ecdysozoa: Panarthropoda: Tardigrada). Zoologischer Anzeiger, 270, 107–122. https://doi.org/10.1016/j.jcz.2017.09.006
    Guidetti, R., Gandolfi, A., Rossi, V. & Bertolani, R. (2005) Phylogenetic analysis of Macrobiotidae (Eutardigrada, Parachela): a combined morphological and molecular approach. Zoologica Scripta, 34, 3, 235–244. https://doi.org/10.1111/j.1463-6409.2005.00193.x
    Guidetti, R., Schill, R.O., Bertolani, R., Dandekar, T. & Wolf, M. (2009) New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov. Journal of Zoological Systematics and Evolutionary Research, 47 (4), 315–321.
    http://doi.org/10.1111/j.1439-0469.2009.00526.x
    Guidetti, R., Cesari, M., Bertolani, R., Altiero, T. & Rebecchi, L. (2019) High diversity in species, reproductive modes and distribution within the Paramacrobiotus richtersi complex (Eutardigrada, Macrobiotidae). Zoological letters, 5 (1), 1–28. https://doi.org/10.1186/s40851-018-0113-z
    Guil, N. & Giribet, G. (2011) A comprehensive molecular phylogeny of tardigrades—adding genes and taxa to a poorly resolved phylum-level phylogeny. Cladistics, 28, 1, 21–49. https://doi.org/10.1111/j.1096-0031.2011.00364.x
    Hara, Y., Shibahara, R., Kondo, K., Abe, W. & Kunieda T. (2021) Parallel evolution of trehalose production machinery in anhydrobiotic animals via recurrent gene loss and horizontal transfer. Open Biology, 11, 7. https://doi.org/10.1098/rsob.200413
    Kaczmarek. Ł., Michalczyk, Ł. & Diduszko, D. (2005) Some tardigrades from Siberia (Russia, Baikal region) with a description of Macrobiotus garynahi sp. nov. (Eutardigrada: Macrobiotidae: richtersi group). Zootaxa, 1053, 35–45. http://doi.org/10.11646/zootaxa.1053.1.3
    Kaczmarek. Ł., Cytan, J., Zawierucha, K., Diduszko, D. & Michalczyk, Ł. (2014) Tardigrades from Peru (South America), with descriptions of three new species of Parachela. Zootaxa, 3790 (2), 357–379. https://doi.org/10.11646/zootaxa.3790.2.5
    Kaczmarek, Ł. & Michalczyk, Ł. (2017) The Macrobiotus hufelandi group (Tardigrada) revisited. Zootaxa, 4363 (1), 101–113. https://doi.org/10.11646/zootaxa.4363.1.4
    Kaczmarek, Ł., Gawlak, M., Bartels, P.J., Nelson D.R. & Roszkowska, M. (2017) Revision of the genus Paramacrobiotus Guidetti et al., 2009 with the description of a new species, re-descriptions and a key. Annals Zoology, 67 (4), 627–656. https://doi.org/10.3161/00034541ANZ2017.67.4.001
    Kaczmarek. Ł., Roszkowska, M., Poprawa, I., Janelt, K., Kmita, H., Gawlak, M., Fiałkowska, E. & Mioduchowska, M. (2020a) Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis. Molecular Phylogenetics and Evolution, 145, 106730. https://doi.org/10.1016/j.ympev.2019.106730
    Kaczmarek, Ł., Mioduchowska, M., Kačarević, U., Kubska, K., Parnikoza, I., Gołdyn, B. & Roszkowska, M. (2020b) New records of Antarctic Tardigrada with comments on interpopulation variability of the Paramacrobiotus fairbanksi Schill, Förster, Dandekar and Wolf, 2010. Diversity, 12, 108. https://doi.org/10.3390/d12030108
    Katoh, K., Misawa, K., Kuma, K. & Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059–66. https://doi.org/10.1093/nar/gkf436
    Katoh, K. & Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9, 286–98. https://doi.org/10.1093/bib/bbn013
    Kiehl, E., Dastych, H., D’Haese, J. & Greven, H. (2007) The 18S rDNA sequences support polyphyly of the Hypsibiidae (Eutardigrada). Journal of Limnology, 66 (1s), 21–25. https://doi.org/10.4081/jlimnol.2007.s1.21
    Kosztyła, P., Stec, D., Morek, W., Gąsiorek, P., Zawierucha, K., Michno, K., Ufir, K., Małek, D., Hlebowicz, K., Laska, A., Dudziak, M., Frohme, M., Prokop, Z.M., Kaczmarek, Ł. & Michalczyk, Ł. (2016) Experimental taxonomy confirms the environmental stability of morphometric traits in a taxonomically challenging group of microinvertebrates. Zoological Journal of the Linnean Society, 178, 765–775. https://doi.org/10.1111/ zoj.12409
    Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870–1874. https://doi.org/10.1093/molbev/msw054
    Mackness, B.S. (2003) A review of nematophagy by terrestrial tardigrades with new observations on some Australian species. Proceedings of the Royal Society of Victoria, 115, 1–5.
    Marley, N.J., McInnes, S.J. & Sands, C.J. (2011) Phylum Tardigrada: a re-evaluation of the Parachela. Zootaxa, 2819, 51–64. https://doi.org/10.11646/zootaxa.2819.1.2
    Marley, N.J., Kaczmarek, Ł., Gawlak, M., Bartels, P.J., Nelson, D.R., Roszkowska, M., Stec, D. & Degma, P. (2018) A clarification for the subgenera of Paramacrobiotus Guidetti, Schill, Bertolani, Dandekar and Wolf, 2009, with respect to the International Code of Zoological Nomenclature. Zootaxa, 4407, 130–134. https://doi.org/10.11646/zootaxa.4407.1.9
    Michalczyk, Ł. & Kaczmarek, Ł. (2013) The Tardigrada Register: a comprehensive online data repository for tardigrade taxonomy. Journal of Limnology, 72(S1), 175–181. https://doi.org/10.4081/jlimnol.2013.s1.e22
    Mironov, S.V., Dabert, J. & Dabert, M. (2012) A new feather mite species of the genus Proctophyllodes Robin, 1877 (Astigmata: Proctophyllodidae) from the long-tailed tit Aegithalos caudatus (Passeriformes: Aegithalidae): morphological description with DNA barcode data. Zootaxa, 3253: 54–61. https://doi.org/10.11646/zootaxa.3253.1.2
    Morek, W., Stec, D., Gąsiorek, P., Schill, R.O., Kaczmarek, Ł. & Michalczyk, Ł. (2016) An experimental test of eutardigrade preparation methods for light microscopy. Zoological Journal of the Linnean Society, 178(4): 785-793. https://doi.org/10.1111/zoj.12457
    Morek, W. & Michalczyk, Ł. (2020) First extensive multilocus phylogeny of the genus Milnesium (Tardigrada) reveals no congruence between genetic markers and morphological traits. Zoological Journal of the Linnean Society, 188 (3), 681–693. https://doi.org/10.1093/zoolinnean/zlz040
    Pilato, G. (2000) Macrobiotus centesimus, new species of eutardigrade from the South America. Bollettino dell’Acca- demia Gioenia di Scienze Naturali, 33 (358), 97–101.
    Pilato, G. & Binda M.G. (1990) Notizie sui tardigradi muscicoli di Bali (Indonesia). Animalia, 17, 209–218.
    Pilato, G., Claxton, S. & Binda, M.G. (1989) Tardigrades from Australia. III. Echiniscus marcusi and Macrobiotus peteri, new species of tardigrades from New South Wales. Animalia, 16, 43–48.
    Pilato, G., Binda, M.G., Napolitano, A. & Moncada E. (2001) Notes on South American tardigrades with the description of two new species: Pseudechiniscus spinerectus and Macrobiotus danielae. Tropical Zoology, 14, 2, 223–231. https://doi.org/10.1080/03946975.2001.10531154
    Pilato, G., Binda, M.G. & Lisi, O. (2006) Eutardigrada from New Zealand, with descriptions of two new species. New Zealand Journal of Zoology, 33, 1, 49–63. https://doi.org/10.1080/03014223.2006.9518430
    Pilato, G., Kiosya, Y., Lisi, O. & G. Sabella. (2012) New records of Eutardigrada from Belarus with the description of three new species. Zootaxa, 3179: 39–60. https://doi.org/10.11646/zootaxa.3179.1.2
    Roszkowska, M., Ostrowska, M., Stec, D., Janko, K. & Kaczmarek, Ł. (2017) Macrobiotus polypiformis sp. nov., a new tardigrade (Macrobiotidae; hufelandi group) from the Ecuadorian Pacifi c coast, with remarks on the claw abnormalities in eutardigrades. European Journal of Taxonomy, 327, 1–19. https://doi.org/10.5852/ejt.2017.327
    Rebecchi, L., Altiero, T. & Bertolani, R. (2002) Banding techniques on tardigrade chromosomes: the karyotype of Macrobiotus richtersi (Eutardigrada, Macrobiotidae). Chromosome Research, 10, 6, 437–443. https://doi.org/10.1023/A:1020949228862
    Ronquist, F. & Huelsenbeck, J.P. (2012) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–4. https://doi.org/10.1093/bioinformatics/btg180
    Ronquist, F., Teslenko, M., Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck JP. (2012) MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology, 61, 539–542. https://doi.org/10.1093/sysbio/sys029
    Schill, R.O. & Steinbrück, G. (2007) Identification and differentiation of Heterotardigrada and Eutardigrada species by riboprinting. Journal of Zoological Systematics and Evolutionary Research, 45 (3), 184–190. https://doi.org/10.1111/j.1439-0469.2007.00409.x
    Schill, R.O., Forster, F., Dandekar, T. & Wolf, N. (2010) Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada). Organisms Diversity & Evolution, 10 (4), 287–296. https://doi.org/10.1007/s13127-010-0025-z
    Stec, D., Roszkowska, M., Kaczmarek. Ł. & Michalczyk, Ł. (2018a) Paramacrobiotus lachowskae, a new species of Tardigrada from Colombia (Eutardigrada: Parachela: Macrobiotidae). New Zealand Journal of Zoology, 45 (1), 43–60. https://doi.org/10.1080/03014223.2017.1354896
    Stec, D., Arakawa, K. & Michalczyk, Ł. (2018b) An integrative description of Macrobiotus shonaicus sp. nov. (Tardigrada: Macrobiotidae) from Japan with notes on its phylogenetic position within the hufelandi group. PLoS One, 13 (2), e0192210. https://doi.org/10.1371/journal. pone.0192210
    Stec, D., Krzywański, Ł., Zawierucha, K. & Michalczyk, Ł. (2020a) Untangling systematics of the Paramacrobiotus areolatus species complex by an integrative redescription of the nominal species for the group, with multilocus phylogeny and species delineation within the genus Paramacrobiotus. Zoological Journal of the Linnean Society, 188 (3), 694–716. https://doi.org/10.1093/zoolinnean/zlz163
    Stec, D., Dudziak, M. & Michalczyk, Ł. (2020b) Integrative descriptions of two new Macrobiotidae species (Tardigrada: Eutardigrada: Macrobiotoidea) from French Guiana and Malaysian Borneo. Zoological Studies, 59, e23. https://doi.org/10.6620/zs.2020.59-23
    Stec, D., Vecchi, M., Calhim, S. & Michalczyk, Ł. (2021) New multilocus phylogeny reorganises the family Macrobiotidae (Eutardigrada) and unveils complex morphological evolution of the Macrobiotus hufelandi group. Molecular Phylogenetics & Evolution, 160: 106987. https://doi.org/10.1016/j.ympev.2020.106987
    Sugiura, K., Minato, H., Suzuki, A.C., Arakawa, K., Kunieda, T. & Matsumoto, M. (2019) Comparison of sexual reproductive behaviors in two species of Macrobiotidae (Tardigrada: Eutardigrada). Zoological Science, 36 (2), 120–127.
    https://doi.org/10.2108/zs180103
    Sugiura, K., Arakawa, K. & Matsumoto, M. (2020) Distribution of Macrobiotus shonaicus Stec, Arakawa & Michalczyk, 2018 (Tardigrada: Eutardigrada: Macrobiotidae) in Japan. Zootaxa, 4767 (1), 56–70. https://doi.org/10.11646/zootaxa.4767.1.2
    Sugiura, K. & Matsumoto, M. (2021) Spermatozoa morphology changes during reproduction and first observation of acrosomal contact in two dioecious species of Macrobiotidae (Tardigrada: Eutardigrada). Zygote, 29, 42–48.
    https://doi.org/10.1017/S0967199420000490
    Sugiura, K., Shiba, K., Inaba, K. & Matsumoto, M. (2022) Morphological differences in tardigrade spermatozoa induce variation in gamete motility. BMC Zoology, 7, 8. https://doi.org/10.1186/s40850-022-00109-w
    Suma, H.R., Prakash, S. & Eswarappa S.M. (2020) Naturally occurring fluorescence protects the eutardigrade Paramacrobiotus sp. from ultraviolet radiation. Biology Letters, 16, 10. https://doi.org/10.1098/rsbl.2020.0391
    Suzuki, A.C. (2017) Tardigrade Research in Japan. In: Morikawa, M. & Kajihara, H. (Eds.), Species Diversity of Animals in Japan. Springer Japan, Tokyo, pp. 267–84. https://doi.org/10.1007/978-4-431-56432-4_10
    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 (W1), W232–W235. https://doi.org/10.1093/nar/gkw256
    Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29, 2869–2876. https://doi.org/10.1093/bioinformatics/btt499