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1 Academic CV: Alexey V. Smirnov ________________________________________________________________________ Personal Details Smirnov Alexey Valerievich Date of birth: 16.01.1970 PhD, associate professor, head of the Nationality: Russia Laboratory of Invertebrate Zoology e-mail: [email protected] Department of Invertebrate Zoology, [email protected] Faculty of Biology & Soil Sciences, St. Petersburg State University, tel: +7 812 7742364 Universitetskaja nab. 7/9, 199034, mob: +7 921 7473372 St.Petersburg, Russia. fax: +7 812 3289703 Education and 23.10.1997: PhD in zoology, St.Petersburg State University Qualifications 1993-1997: Postgraduate, St. Petersburg State University 17.06.1993: Diploma, St.Petersburg State university 1987-1993: Graduate student, St.Petersburg State University 1992: Diploma, International course "The Baltic Sea Environment" 1986: Qualification certificate, 4th grade “Computer operator and software developer” Career Summary, Papers in refereed journals: 47 01.11.2004 Book chapters: 7 Web-pages: 3 Abstracts and proceedings: 13 Research grants and fellowships: 22 Personal awards: 3 Presentations and invited talks: 29 _______________________________________________________________________ Primary Scientific Interests • Systematics, biodiversity, ultrastructure and phylogeny of amoeboid protists and related groups • Species problem and genome organization in gymnamoebae, molecular tools for distinction and identification of amoebae • Type collections and materials on amoebae, development of guides and keys to amoeboid organisms, new ways and tools to document and deposit data on amoebae species • Organization of the protozoan communities; development and evolution of the global-scale and local-scale microbial diversity • Microstructure of the natural habitats, microgradients and microbiogeocoenoses • Bioinformatics; web-based and electronic presentation of scientific data; creation of user- friendly interfaces to the databases and collection; promotion and popularization of biodiversity knowledge Ongoing Research Projects • “Encyclopedia of amoebae” – an ultimate guide to naked amoeboid protists • Molecular systematics of amoeboid protists • Cryptic freshwater amoebae species in marine environment and the species flow as a functional component of microbial ecosystem • "The construction of the microbial communities", or why and how does the observed pattern of microbial diversity form and evolve _______________________________________________________________________ 2 Career History Permanent Positions: 01.02.2009 – current: Head of the Laboratory of Protistology and experimental zoology, Department of Invertebrate Zoology, Faculty of Biology & Soil Sciences, St. Petersburg State University, Russia 01.01.2005 – current: Associate Professor, Department of Invertebrate Zoology, Faculty of Biology & Soil Sciences, St. Petersburg State University, Russia 01.12.1997 - 31.12.2004: Assistant Professor, Department of Invertebrate Zoology, Faculty of Biology & Soil Sciences, St. Petersburg State University, Russia Visiting Appointments and Secondments: 01.07.2009 – 25.07.2009: Visiting scientist, Marine Biological Laboratory, University of Copenhagen, Denmark 01.06.2007 – 31.07.2007: Visiting scientist, Station Zoologie Exp. Gen. University of Geneva, Switzerland 09.04.2005 – 31.08.2005: Visiting scientist, Department of Zoology, University of Oxford, UK 01.10.2003 - 30.04.2004: Assistant Professor (visiting), Marine Biological Laboratory, University of Copenhagen, Denmark 01.12.2002 - 15.02.2003: Visiting scientist, Station Zoologie Exp. Gen. University of Geneva, Switzerland 01.05.2002 - 15.07.2002: Visiting scientist, Centre of Ecology and Hydrobiology, Windermere, UK 01.02.2002 - 31.05.2002: Visiting scientist, Department of Zoology, University of Oxford, UK 01.03.2001 – 31.05.2001: Visiting scientist, Station Zoologie Exp. Gen. University of Geneva, Switzerland 01.04.2000 - 31.12.2000: Assistant Professor (postdoc), Marine Biological Laboratory, University of Copenhagen, Denmark 01.09.1999 - 15.10.1999: Visiting scientist, Institute of Freshwater Ecology, UK 30.12.1997 – 01.08.1998: Visiting Scientist, Spezielle Zoologie, TU Dresden 01.10.1994 – 29.02.1995: Research training, Marine Biological Laboratory, University of Copenhagen, Denmark ________________________________________________________________________ Membership Since 1993: member of St. Petersburg Naturalists Society Since 1992: member of Russian Society of Protozoologists ________________________________________________________________________ Teaching Departmental Duties: Length of Number of Title Course Students Lecture Courses Systematic zoology: Rhizopoda 36 4-5 (Masters) Ecology of Protozoa 36 4-5 (Masters) Light microscopy and microphotography 36 4-5 (Masters) Basic zoology: Rhizopoda 36 7-9 (Bachelors) Selected chapters on Rhizopods 16 12-20 (Bachelors) Tutorials/Seminars Basic courses in invertebrate zoology 264 24-28 (Bachelors) Summer courses in invertebrate zooology 256 25-30 (Bachelors) TOTAL 670 3 Research Supervision: Other Teaching: Number of successful students since 1994: 10 2001:"Methods of electron microscopy", Number of unsuccessful students since 1994: 0 invited course. Spezielle Zoologie, TU Dresden, Germany (joint with Prof. R. Entzeroth), for bachelors. Duration: 64h. ________________________________________________________________________ Editorial Editorial board: Protistology (Russia) ISSN 1680-0826 Boards of reviwers: European Journal of Protistology Journal of Eukaryotic Microbiology Research Publications: (i)Papers in Refereed Journals 1. Nassonova E, Smirnov A, Fahrni J, Pawlowski J. 2010. Barcoding Amoebae: Comparison of SSU, ITS and COI Genes as Tools for Molecular Identification of Naked Lobose Amoebae. Protist 161 : 102-115 2. Smirnov A, Nassonova E, Fahrni J, Pawlowski J. 2009. Rhizamoeba neglecta n. sp. (Amoebozoa, Tubulinea) from the bottom sediments of freshwater Lake Leshevoe (Valamo Island, North-Western Russia), with notes on the phylogeny of the order Leptomyxida. Eur J Protistol. 45: 251-259 3. Smirnov AV, Nassonova ES, Cavalier-Smith T. 2008. Correct identification of species makes the amoebozoan rRNA tree congruent with morphology for the order Leptomyxida Page 1987; with description of Acramoeba dendroida n. g., n. sp., originally misidentified as ‘Gephyramoeba sp.’ Europ. J. Protistol. 44 : 35-44 4. Adl S, Leander B, Simpson AG, Archibald J, Anderson OR, Bass D, Bowser S, Brugerole G, Farmer M, Karpov S, Kolisko M, Lane K, Lodge D, Mann D, Meisterfield R, Mendoza L, Moestrup O, Mozley-Standrisge S, Smirnov A, Spiegel F. 2007. Diversity, Nomenclature, and Taxonomy of Protists. Syst. Biol. 56:1-6 5. Michel R, Wylezich C, Hauröder B and Smirnov A (2007) Phylogenetic position and notes on the ultrastructure of Sappinia diploidea (Thecamoebidae). Protistology 4: 319-325 6. Smirnov AV (2007) Cryptic freshwater amoeba species in the bottom sediments of Nivå Bay (Øresund, Baltic Sea). Europ. J. Protistol. 43: 87-94 7. Smirnov AV, Nassonova ES, Chao E and Cavalier-Smith T (2007). Phylogeny, evolution and taxonomy of vannellid amoebae. Protist 158, 295-324 8. Kudryavtsev AA, Smirnov AV (2006) Cochliopodium gallicum n. sp. (Himatismenida), an amoeba bearing unique scales, from cyanobacterial mats in the Camargue (France). Europ J Protistol 42: 3-7 9. Smirnov AV (2005) Rate of amoebae dispersion in a model ecosystem. Protistology 4: 145- 148. 4 10. Adl SM, SimpsonGB, Farmer M, Andersen RA, Anderson OR, Barta JR, Bowser S, Brugerolle G, Fensome RA, Frederico S, James T, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA, Lodge J, Lynn DH, Mann Dg, MsCourt RM, Mendoza L, Moestrup O, Mozley- Standbridge SE, Nerad TA, Shearer CA, Smirnov AV, Spiegel FW and Tyalor MJR (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Euk Microbiol 52: 399-451 11. Smirnov AV, Kudryavtsev AA (2005) Pellitidae n. fam. (Lobosea, Gymnamoebia) – a new family, accommodating two amoebae with an unusual cell coat and an original mode of locomotion, Pellita catalonica n.g., n.sp. and Pellita digitata comb. nov. Europ J Protistol 41: 257-267 12. Smirnov AV, Nassonova ES, Berney C, Fahrni J, Bolivar I, and Pawlowski J (2005) Molecular Phylogeny and Classification of the Lobose Amoebae. Protist 156: 129-142 13. Nassonova ES and Smirnov AV (2005) Synaptonemal complexes as evidence for meiosis in the life cycle of the monomorphic diplokaryotic microsporidium Paranosema grylli. Europ. J. Protistol. 41: 175-181 14. Smirnov AV and Thar R (2004) Vertical distribution of Gymnamoebae (Rhizopoda, Lobosea) in the top layer of brackish-water sediments. Protist 155: 437-446 15. Smirnov AV and Goodkov AV (2004) Ultrastructure and geographic distribution of the genus Paradermamoeba (Gymnamoebia, Thecamoebidae). Europ. J. Protistol. 40: 113-118 16. Smirnov AV and Brown S (2004) Guide to the study and identification of soil amoebae. Protistology 3: 148-190 17. Brown S and Smirnov AV (2004) Diversity of gymnamoebae in grassland soil in southern Scotland. Protistology 3: 191-195 18. Kudryavtsev AA, Brown S, Smirnov AV (2004) Cochliopodium barki n. sp. (Rhizopoda, Himatismenida) re-isolated from soil 30 years after its initial description. Europ. J. Protistol. 40: 283-287 19. Fahrni JH, Bolivar I, Berney C, Nassonova E, Smirnov A, and Pawlowski J. (2003) Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes. Mol. Biol. Evol. 20: 1881-1886 20. Smirnov AV and Thar R (2003) Spatial distribution
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  • Two New Species of Ripella (Amoebozoa, Vannellida) and Unusual

    Two New Species of Ripella (Amoebozoa, Vannellida) and Unusual

    Available online at www.sciencedirect.com ScienceDirect European Journal of Protistology 61 (2017) 92–106 Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus a,∗ a,b Alexander Kudryavtsev , Anna Gladkikh a Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia b Irkutsk Antiplague Research Institute of Siberia and Far East, 664047 Irkutsk, Russia Received 3 June 2017; received in revised form 22 August 2017; accepted 8 September 2017 Available online 14 September 2017 Abstract Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa.
  • Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa

    Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa

    GBE Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa Paulo G. Hofstatter1,MatthewW.Brown2, and Daniel J.G. Lahr1,* 1Departamento de Zoologia, Instituto de Biociencias,^ Universidade de Sao~ Paulo, Brazil 2Department of Biological Sciences, Mississippi State University *Corresponding author: E-mail: [email protected]. Accepted: October 30, 2018 Data Deposition: Accession numbers are listed on a supplementary table 1, Supplementary Material online, already uploaded. Abstract Sex and reproduction are often treated as a single phenomenon in animals and plants, as in these organisms reproduction implies mixis and meiosis. In contrast, sex and reproduction are independent biological phenomena that may or may not be linked in the majority of other eukaryotes. Current evidence supports a eukaryotic ancestor bearing a mating type system and meiosis, which is a process exclusive to eukaryotes. Even though sex is ancestral, the literature regarding life cycles of amoeboid lineages depicts them as asexual organisms. Why would loss of sex be common in amoebae, if it is rarely lost, if ever, in plants and animals, as well as in fungi? One way to approach the question of meiosis in the “asexuals” is to evaluate the patterns of occurrence of genes for the proteins involved in syngamy and meiosis. We have applied a comparative genomic approach to study the occurrence of the machinery for plasmogamy, karyogamy, and meiosis in Amoebozoa, a major amoeboid supergroup. Our results support a putative occurrence of syngamy and meiotic processes in all major amoebozoan lineages. We conclude that most amoebozoans may perform mixis, recombination, and ploidy reduction through canonical meiotic processes.