Relevant Publications

Consortium Publications

  • Del Campo, J., Carlos-Oliveira, M., Čepička, I., Hehenberger, E., Horák, A., Karnkowska, A., Kolísko, M., Lara, E., Lukeš J., Pánek, T., Piwosz, K., Richter, D., Škaloud, P., Sutak, R., Tachezy, J., Hampl, V. (2024). The protist cultural renaissance. Trends in Microbiology, in press.

Metabarcoding

  • Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C, Bowler C, Lukeš J, Horák A. Extreme Diversity of Diplonemid Eukaryotes in the Ocean. Curr Biol. 2016 Nov 21;26(22):3060-3065. doi: 10.1016/j.cub.2016.09.031
  • del Campo, J., Kolisko, M., Boscaro, V., Santoferrara, L. F., Nenarokov, S., Massana, R., Guillou, L., Simpson, A. G. B., Berney, C., de Vargas, C., Brown, M. W., Keeling, P. J., & Wegener Parfrey, L. (2018). EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology, 16(9), e2005849. https://doi.org/10.1371/journal.pbio.2005849
  • Metz S, Singer D, Domaizon I, Unrein F, Lara E. Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches. Environ Microbiol. 2019 Oct;21(10):3885-3895. doi: 10.1111/1462-2920.14738
  • Flegontova O., Flegontov P., Castaňeda Londoňo P., Walczowski W., Śantić D., Edgcomb V., Lukeš J., Horák A. (2020) Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans Environmental Microbiology 22: 4014–4031. doi: 10.1111/1462-2920.15190
  • Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Lukeš J., Horák A. (2018) Neobodonids are dominant kinetoplastids in the global ocean Environmental Microbiology 20: 878-889. doi:  10.1111/1462-2920.14034
  • Lukešová S, Karlicki M, Tomečková Hadariová L, Szabová J, Karnkowska A, Hampl V. Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. Environ Microbiol Rep. 2020 Feb;12(1):78-91. doi: 10.1111/1758-2229.12817
  • Singer D, Seppey CVW, Lentendu G, Dunthorn M, Bass D, Belbahri L, Blandenier Q, Debroas D, de Groot GA, de Vargas C, Domaizon I, Duckert C, Izaguirre I, Koenig I, Mataloni G, Schiaffino MR, Mitchell EAD, Geisen S, Lara E. Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environ Int. 2021 Jan;146:106262. doi: 10.1016/j.envint.2020.106262
  • del Campo, J., Heger, T. J., Rodríguez-Martínez, R., Worden, A. Z., Richards, T. A., Massana, R., Keeling, P. J., del Campo, J., Heger, T. J., Rodríguez-Martínez, R., Worden, A. Z., Richards, T. A., Massana, R., & Keeling, P. J. (2019). Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework. Frontiers in Microbiology, 10(OCT), 1–15. https://doi.org/10.3389/fmicb.2019.02373
  • Piwosz, K., Całkiewicz, J., Gołębiewski, M., and Creer, S. (2018) Diversity and community composition of pico- and nanoplanktonic protists in the Vistula River estuary (Gulf of Gdańsk, Baltic Sea). Estuar Coast Shelf Sci 207: 242-249
  • Pánek T, Táborský P, Pachiadaki MG, Hroudová M, Vlček Č, Edgcomb VP, Čepička I. Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage. Front Microbiol. 2015 Nov 18;6:1288. doi: 10.3389/fmicb.2015.01288
  • Kolisko M, Flegontova O, Karnkowska A, Lax G, Maritz JM, Pánek T, Táborský P, Carlton JM, Čepička I, Horák A, Lukeš J, Simpson AGB, Tai V. EukRef-excavates: seven curated SSU ribosomal RNA gene databases. Database (Oxford). 2020 Nov 20;2020:baaa080. doi: 10.1093/database/baaa080
  • Łukomska-Kowalczyk M, Karnkowska A, Krupska M, Milanowski R, Zakryś B. DNA barcoding in autotrophic euglenids: evaluation of COI and 18s rDNA. J Phycol. 2016 Dec;52(6):951-960. doi: 10.1111/jpy.12439
  • Piwosz K, Shabarova T, Pernthaler J, Posch T, Šimek K, Porcal P, Salcher MM. Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations. mSphere. 2020 Mar 4;5(2):e00052-20. doi: 10.1128/mSphere.00052-20

Ecology, Biogeography

  • Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C, Bowler C, Lukeš J, Horák A. Extreme Diversity of Diplonemid Eukaryotes in the Ocean. Curr Biol. 2016 Nov 21;26(22):3060-3065. doi: 10.1016/j.cub.2016.09.031
  • Singer D, Mitchell EAD, Payne RJ, Blandenier Q, Duckert C, Fernández LD, Fournier B, Hernández CE, Granath G, Rydin H, Bragazza L, Koronatova NG, Goia I, Harris LI, Kajukało K, Kosakyan A, Lamentowicz M, Kosykh NP, Vellak K, Lara E. Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists. Mol Ecol. 2019 Jun;28(12):3089-3100. doi: 10.1111/mec.15117
  • Prokopchuk, G., Korytář, T., Juricová, V. Majstorović, J., Horák, A., Šimek, K., Lukeš, J. 2022. Trophic flexibility of marine diplonemids – switching from osmotrophy to bacterivory. ISME J. https://doi.org/10.1038/s41396-022-01192-0
  • Malych R, Stopka P, Mach J, Kotabová E, Prášil O, Sutak R. Flow cytometry-based study of model marine microalgal consortia revealed an ecological advantage of siderophore utilization by the dinoflagellate Amphidinium carterae. Comput Struct Biotechnol J. 2021 Dec 20;20:287-295. doi: 10.1016/j.csbj.2021.12.023
  • Kotabova E, Malych R, Pierella Karlusich JJ, Kazamia E, Eichner M, Mach J, Lesuisse E, Bowler C, Prášil O, Sutak R. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability. mSystems. 2021 Feb 9;6(1):e00738-20. doi: 10.1128/mSystems.00738-20
  • Flegontova O., Flegontov P., Castaňeda Londoňo P., Walczowski W., Śantić D., Edgcomb V., Lukeš J., Horák A. (2020) Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans Environmental Microbiology 22: 4014–4031. doi: 10.1111/1462-2920.15190
  • Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Lukeš J., Horák A. (2018) Neobodonids are dominant kinetoplastids in the global ocean Environmental Microbiology 20: 878-889. doi:  10.1111/1462-2920.14034
  • Janouškovec J., Horák A., Barott K., Rohwer F., Keeling P. (2012) Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. Current Biology 22: R518–R519. doi: 10.1016/j.cub.2012.04.047
  • Janouškovec J., Horák A., Barott K., Rohwer F., Keeling P. (2013) Environmental distribution of coral-associated relatives of apicomplexan parasites. ISME journal 7: 444-447. doi: 10.1038/ismej.2012.129
  • Singer, D., Kosakyan, A., Seppey, C.V.W., Pillonel, A., Fernandez, L.D., Fontaneto, D., Mitchell, E.A.D., Lara, E., 2018. Environmental filtering and phylogenetic clustering correlate with the distribution patterns of cryptic protist species. Ecology 99, 904-914. 
  • Škaloud, P., Škaloudová, M., Doskočilová, P., Kim, J.I., Shin, W., Dvořák, P., 2019. Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte. Mol Ecol 28:,1084-1095

Genomics, Transcriptomics

  • Rotterová J, Salomaki E, Pánek T, Bourland W, Žihala D, Táborský P, Edgcomb VP, Beinart RA, Kolísko M, Čepička I. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Curr Biol. 2020 Jun 8;30(11):2037-2050.e6. doi: 10.1016/j.cub.2020.03.064
  • Žárský V, Klimeš V, Pačes J, Vlček Č, Hradilová M, Beneš V, Nývltová E, Hrdý I, Pyrih J, Mach J, Barlow L, Stairs CW, Eme L, Hall N, Eliáš M, Dacks JB, Roger A, Tachezy J. The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba. Mol Biol Evol. 2021 May 19;38(6):2240-2259. doi: 10.1093/molbev/msab020
  • Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol. 2016 May 23;26(10):1274-84. doi: 10.1016/j.cub.2016.03.053
  • Woo Y., Ansari H., Otto T.D., Klinger C., Kolísko M., Michálek J., Saxena A., Shanmugam D., Tayyrov A., Veluchamy A., Ali S., Bernal A., Del C., Cihlář J., Flegontov P., Gornik S., Hajdušková E., Horák A., Janouškovec J., Katris N., Mast F., Miranda-Saavedra D., Mourier T., Naeem R., Nair M., Panigrahi A., Rawlings N., Regelado E., Ramaprasad A., Samad N., Tomčala A., Wilkes J., Neafsey D., Doerig C., Bowler C., Keeling P., Roos D., Dacks J., Templeton T., Waller R., Lukeš J., Oborník M., Pain A. (2015) “Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites ” eLife 4: e06974. doi: 10.7554/eLife.06974
  • Škodová-Sveráková I., Záhonová K., Juricová V., Danchenko M., Moos M., Baráth P., Prokopchuk G., Butenko A., Lukáčová V., Kohútová L., Bučková B., Horák A., Faktorová D., Horváth A., Šimek P., Lukeš J. (2021) Highly flexible metabolism of the marine euglenozoan protist /Diplonema papillatum/. BMC Biology 19: 251. doi: 10.1186/s12915-021-01186-y
  • Treitli SC, Peña-Diaz P, Hałakuc P, Karnkowska A, Hampl V. High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis. Microb Genom. 2021 Dec;7(12):000745. doi: 10.1099/mgen.0.000745
  • Soukal P, Hrdá Š, Karnkowska A, Milanowski R, Szabová J, Hradilová M, Strnad H, Vlček Č, Čepička I, Hampl V. Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Sci Rep. 2021 Jun 22;11(1):13070. doi: 10.1038/s41598-021-92174-3
  • Albanaz ATS, Gerasimov ES, Shaw JJ, Sádlová J, Lukeš J, Volf P, Opperdoes FR, Kostygov AY, Butenko A, Yurchenko V. Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping Pathogenicity. Genes (Basel). 2021 Mar 20;12(3):444. doi: 10.3390/genes12030444
  • Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Lukeš J, Yurchenko V, Kolesnikov A. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res. 2021 Apr 6;49(6):3354-3370. doi: 10.1093/nar/gkab114
  • Kayama M, Maciszewski K, Yabuki A, Miyashita H, Karnkowska A, Kamikawa R (2020). Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis. Front Plant Sci, doi: 10.3389/fpls.2020.602455
  • Bakuła Z, Gromadka R, Gawor J, Siedlecki P, Pomorski J, Maciszewski K, Gromadka A, Karnkowska A, Jagielski T (2020) Sequencing and analysis of the complete organellar genomes of Prototheca wickerhamii. Frontiers in Plant Science:  doi: 10.3389/fpls.2020.01296
  • Han KY, Maciszewski K, Graf L, Yang JH, Andersen RA, Karnkowska A, Yoon HS. Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization. J Phycol. 2019 Oct;55(5):1166-1180. doi: 10.1111/jpy.12904
  • Opperdoes FR, Butenko A, Zakharova A, Gerasimov ES, Zimmer SL, Lukeš J, Yurchenko V. The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions. Pathogens. 2021 Jan 14;10(1):68. doi: 10.3390/pathogens10010068
  • Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Čepička I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nat Ecol Evol. 2017 Apr 1;1(4):0092. doi: 10.1038/s41559-017-0092
  • Hehenberger E, Tikhonenkov DV, Kolisko M, Del Campo J, Esaulov AS, Mylnikov AP, Keeling PJ. Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals. Curr Biol. 2017 Jul 10;27(13):2043-2050.e6. doi: 10.1016/j.cub.2017.06.006
  • Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol. 2017 Aug;1(8):1160-1167. doi: 10.1038/s41559-017-0237-0. Epub 2017 Jul 21
  • Mathur V, Kolísko M, Hehenberger E, Irwin NAT, Leander BS, Kristmundsson Á, Freeman MA, Keeling PJ. Multiple Independent Origins of Apicomplexan-Like Parasites. Curr Biol. 2019 Sep 9;29(17):2936-2941.e5. doi: 10.1016/j.cub.2019.07.019
  • Salas-Leiva DE, Tromer EC, Curtis BA, Jerlström-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavallée L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun. 2021 Oct 14;12(1):6003. doi: 10.1038/s41467-021-26077-2. Erratum in: Nat Commun. 2021 Dec 16;12(1):7350

Phylogenomics

  • Tice AK, Žihala D, Pánek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A, Shen XX, Strassert JFH, Kolísko M, Brown MW. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biol. 2021 Aug 6;19(8):e3001365. doi: 10.1371/journal.pbio.3001365
  • Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3859-64. doi: 10.1073/pnas.0807880106
  • Janouškovec J., Horák A., Oborník M., Lukeš J., Keeling P. (2010) A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proceedings of the National Academy of Sciences of the United States of America 107: 10949–10954. DOI: 10.1073/pnas.1003335107
  • Kostygov AY, Karnkowska A, Votýpka J, Tashyreva D, Maciszewski K, Yurchenko V, Lukeš J. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol. 2021 Mar;11(3):200407. doi: 10.1098/rsob.200407
  • Butenko A, Hammond M, Field MC, Ginger ML, Yurchenko V, Lukeš J. Reductionist Pathways for Parasitism in Euglenozoans? Expanded Datasets Provide New Insights. Trends Parasitol. 2021 Feb;37(2):100-116. doi: 10.1016/j.pt.2020.10.001
  • Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol. 2020 Mar 2;18(1):23. doi: 10.1186/s12915-020-0754-1.
  • Ševčíková T., Horák A., Klimeš V., Zbránková V., Demir-Hilton E., Sudek S., Jenkins J., Schmutz J., Přibyl P., Vlček Č., Lang B., Oborník M., Worden A., Eliáš M. (2015) Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Scientific Reports 5: 10134. doi: 10.1038/srep10134
  • Gentekaki E, Kolisko M, Gong Y, Lynn D. Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic. Mol Phylogenet Evol. 2017 Jan;106:1-5. doi: 10.1016/j.ympev.2016.09.016
  • Salomaki ED, Eme L, Brown MW, Kolisko M. Releasing uncurated datasets is essential for reproducible phylogenomics. Nat Ecol Evol. 2020 Nov;4(11):1435-1437. doi: 10.1038/s41559-020-01296-w
  • Heiss AA, Kolisko M, Ekelund F, Brown MW, Roger AJ, Simpson AGB. Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. R Soc Open Sci. 2018 Apr 4;5(4):171707. doi: 10.1098/rsos.171707
  • Lynn DH, Kolisko M, Bourland W. Phylogenomic Analysis of Nassula variabilis n. sp., Furgasonia blochmanni, and Pseudomicrothorax dubius Confirms a Nassophorean Clade. Protist. 2018 Apr;169(2):180-189. doi: 10.1016/j.protis.2018.02.002
  • Lynn DH, Kolisko M. Molecules illuminate morphology: phylogenomics confirms convergent evolution among ‘oligotrichous’ ciliates. Int J Syst Evol Microbiol. 2017 Sep;67(9):3676-3682. doi: 10.1099/ijsem.0.002060

Single-cell

  • Treitli SC, Kolisko M, Husník F, Keeling PJ, Hampl V. Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19675-19684. doi: 10.1073/pnas.1910793116
  • Beinart RA, Rotterová J, Čepička I, Gast RJ, Edgcomb VP. The genome of an endosymbiotic methanogen is very similar to those of its free-living relatives. Environ Microbiol. 2018 Jul;20(7):2538-2551. doi: 10.1111/1462-2920.14279
  • Gawryluk, R. M. R., del Campo, J., Okamoto, N., Strassert, J. F. H., Lukeš, J., Richards, T. A., Worden, A. Z., Santoro, A. E., & Keeling, P. J. (2016). Morphological Identification and Single-Cell Genomics of Marine Diplonemids. Current Biology, 26(22), 3053–3059. ttps://doi.org/10.1016/j.cub.2016.09.013
  • Strassert JFH, Karnkowska A, Hehenberger E, Del Campo J, Kolisko M, Okamoto N, Burki F, Janouškovec J, Poirier C, Leonard G, Hallam SJ, Richards TA, Worden AZ, Santoro AE, Keeling PJ. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME J. 2018 Jan;12(1):304-308. doi: 10.1038/ismej.2017.167
  • Záhonová K, Lax G, Sinha SD, Leonard G, Richards TA, Lukeš J, Wideman JG. Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans. BMC Biol. 2021 May 17;19(1):103. doi: 10.1186/s12915-021-01035-y
  • ​​Salomaki ED, Terpis KX, Rueckert S, Kotyk M, Varadínová ZK, Čepička I, Lane CE, Kolisko M. Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans. BMC Biol. 2021 Apr 16;19(1):77. doi: 10.1186/s12915-021-01007-2
  • Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogenet Evol. 2021 Jun;159:107088. doi: 10.1016/j.ympev.2021.107088

Taxonomy, Diversity, Cultivation of New Lineage

  • Lahr DJG, Kosakyan A, Lara E, Mitchell EAD, Morais L, Porfirio-Sousa AL, Ribeiro GM, Tice AK, Pánek T, Kang S, Brown MW. Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic. Curr Biol. 2019 Mar 18;29(6):991-100
  • Stairs CW, Táborský P, Salomaki ED, Kolisko M, Pánek T, Eme L, Hradilová M, Vlček Č, Jerlström-Hultqvist J, Roger AJ, Čepička I. Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes. Curr Biol. 2021 Dec 20;31(24):5605-5612.e5. doi: 10.1016/j.cub.2021.10.010
  • Lukeš J, Tesařová M, Yurchenko V, Votýpka J. Characterization of a new cosmopolitan genus of trypanosomatid parasites, Obscuromonas gen. nov. (Blastocrithidiinae subfam. nov.). Eur J Protistol. 2021 Jun;79:125778. doi: 10.1016/j.ejop.2021.125778
  • Kostygov AY, Frolov AO, Malysheva MN, Ganyukova AI, Chistyakova LV, Tashyreva D, Tesařová M, Spodareva VV, Režnarová J, Macedo DH, Butenko A, d’Avila-Levy CM, Lukeš J, Yurchenko V. Vickermania gen. nov., trypanosomatids that use two joined flagella to resist midgut peristaltic flow within the fly host. BMC Biol. 2020 Dec 2;18(1):187. doi: 10.1186/s12915-020-00916-y
  • Králová J, Grybchuk-Ieremenko A, Votýpka J, Novotný V, Kment P, Lukeš J, Yurchenko V, Kostygov AY. Insect trypanosomatids in Papua New Guinea: high endemism and diversity. Int J Parasitol. 2019 Dec;49(13-14):1075-1086. doi: 10.1016/j.ijpara.2019.09.004
  • Prokopchuk G, Tashyreva D, Yabuki A, Horák A, Masařová P, Lukeš J. Morphological, Ultrastructural, Motility and Evolutionary Characterization of Two New Hemistasiidae Species. Protist. 2019 Jul;170(3):259-282. doi: 10.1016/j.protis.2019.04.001
  • Okamoto N, Gawryluk RMR, Del Campo J, Strassert JFH, Lukeš J, Richards TA, Worden AZ, Santoro AE, Keeling PJ. A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. & sp. J Eukaryot Microbiol. 2019 May;66(3):519-524. doi: 10.1111/jeu.12679
  • Jagielski T, Bakuła Z, Gawor J, Maciszewski K, Kusber W-H, Dyląg M, Nowakowska J, Gromadka R, Karnkowska A (2019)  Prototheca (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies. Algal Research, 43: 101639.
  • Łukomska-Kowalczyk M, Karnkowska A, Milanowski R, Łach Ł, Zakryś B. Delimiting species in the Phacus longicauda complex (Euglenida) through morphological and molecular analyses. J Phycol. 2015 Dec;51(6):1147-57. doi: 10.1111/jpy.12352
  • Karnkowska A, Bennett MS, Watza D, Kim JI, Zakryś B, Triemer RE. Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon-rich Analyses of Five Genes. J Eukaryot Microbiol. 2015 May-Jun;62(3):362-73. doi: 10.1111/jeu.12192

Metagenomics, Metatranscriptomics

  • Karlicki M, Antonowicz S, Karnkowska A. Tiara: Deep learning-based classification system for eukaryotic sequences. Bioinformatics. 2021 Sep 27;38(2):344–50. doi: 10.1093/bioinformatics/btab6725.
  • Durante IM, Butenko A, Rašková V, Charyyeva A, Svobodová M, Yurchenko V, Hashimi H, Lukeš J. Large-Scale Phylogenetic Analysis of Trypanosomatid Adenylate Cyclases Reveals Associations with Extracellular Lifestyle and Host-Pathogen Interplay. Genome Biol Evol. 2020 Dec 6;12(12):2403-2416. doi: 10.1093/gbe/evaa226
  • Nenarokova A, Záhonová K, Krasilnikova M, Gahura O, McCulloch R, Zíková A, Yurchenko V, Lukeš J. Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes. mBio. 2019 Jul 16;10(4):e01541-19. doi: 10.1128/mBio.01541-19

Soil Biology

  • Jassey VEJ, Walcker R, Kardol P, Geisen S, Heger T, Lamentowicz M, Hamard S, Lara E. Contribution of soil algae to the global carbon cycle. New Phytol. 2022 Feb 1. doi: 10.1111/nph.17950
  • Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev. 2018 May 1;42(3):293-323. doi: 10.1093/femsre/fuy006

FISH, CARD-FISH

  • Piwosz, K. (2019) Weekly dynamics of abundance and size structure of specific nanophytoplankton lineages in coastal waters (Baltic Sea). Limnol Oceanogr 64: 2172-2186.  https://doi.org/10.1002/lno.11177
  • Piwosz K, Kownacka J, Ameryk A, Zalewski M, Pernthaler J. Phenology of cryptomonads and the CRY1 lineage in a coastal brackish lagoon (Vistula Lagoon, Baltic Sea). J Phycol. 2016 Aug;52(4):626-37. doi: 10.1111/jpy.12424
  • Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol. 2021 Mar 4;12:640066. doi: 10.3389/fmicb.2021.640066
  • Piwosz K, Wiktor JM, Niemi A, Tatarek A, Michel C. Mesoscale distribution and functional diversity of picoeukaryotes in the first-year sea ice of the Canadian Arctic. ISME J. 2013 Aug;7(8):1461-71. doi: 10.1038/ismej.2013.39