Microlife: Identification and Classification

  1. Guides for identification
  2. Recent changes to names
  3. Higher level classification
  4. References

Guides for identification

Since the organisms here are direct from natural sources, they have been identified based only on individual features visible through the microscope. The descriptions on the main pages are meant to give the basic reasoning behind each identification. They mainly rely on the following books, though these are not a complete list:

  1. “Taxonomic Keys to the Common Animals of the North Central States” (1967) by Eddy & Hodson
  2. “How to Know the Protozoa” 2nd ed. (1978) by Jahn, Bovee, and Jahn
  3. “How to Know the Freshwater Algae” 3rd ed. (1978) by Prescott
  4. “British and Other Freshwater Ciliated Protozoa” parts I, II (1982-1983) by Curds, Gates, and Roberts
  5. “Aquatic Invertebrates of Alberta” (1991) by Clifford
  6. “Das Leben im Wassertropfen” 9te Auf. (2002) by Streble & Krauter
  7. “Freshwater Algae: Identification and Use as Bioindicators” (2010) by Bellinger & Sigee

The information on-line at the Protist Information Server and NIES has also been helpful, and for ciliates, Foissner and Berger (1996) give a useful key with some details. I have done my best to be accurate, but even so, note I have had to assume some are more common types, and might have overlooked some key features.

Recent changes to names

Classification continues to change as our understanding improves. Some genera from the above sources have been divided into two or more new ones, usually because some species have turned out to be closer relatives of ones in other groups. I have tried to adopt the following changes:

Melosira → Orthoseira, Ellerbeckia, Paralia, Melosira, Aulacoseira e.g. in Round et al. (1990)
Vorticella → Pseudovorticella, Vorticella Foissner & Schiffmann (1975)
Difflugia → Difflugia, Netzelia Ogden (1979), Gomaa et al. (2017)
Platyias → Platyias, Plationus Segers et al. (1993)
Stylonychia → Stylonychia, Tetmemena Eigner (1999), Bernhard et al. (2001)
Phacus → Phacus, Monomorphina Marin et al. (2003)
Euglena → Discoplastis, Lepocinclis in part, Euglenaformis, Euglena, Euglenaria e.g. in Ciugulea & Triemer (2010), Karnkowska et al. (2014)
Holosticha → Biholosticha, Holosticha, Caudiholosticha, Anteholosticha Berger (2003), Li et al. (2009)
Pediastrum → Stauridium, Monactinus, Pseudopediastrum, Pediastrum, Parapediastrum Buchheim et al. (2005)
Ceratium → Ceratium, Tripos Gómez et al. (2010), Gómez (2013)
Chaetophora → Chaetophoropsis, Chaetophora Liu et al. (2019)

In other cases it turns out a previous separation is not well supported, and will probably need further revision before it reflects real relationships. Based on the following reviews, I have left together or united the following genera:

Thecamoeba ← Thecamoeba, Striamoeba Page (1977)
Notholca ← Notholca, Argonotholca Hollowday & Hussey (1989)
Euplotes ← Euplotes, Euplotoides, Euplotopsis, Moneuplotes Petroni et al. (2002), Shao et al. (2010)
Dendrosoma ← Dendrosoma, Baikalodendron, Baikalophrya, Lernaeophrya Dovgal (2002)
Ulva ← Ulva, Enteromorpha Hayden et al. (2003)
Cryptomonas ← Cryptomonas, Chilomonas Hoef-Emden & Melkonian (2003)
Hydra ← Hydra, Chlorohydra, Pelmatohydra Hemmrich et al. (2007)

A few genera are listed under several different names. As a rule the oldest valid one has priority, so for instance Chroodactylon supersedes Asterocystis or “Astrocystis”. Anthophysa is an exception, though; it was originally Anthophysis but the ICBN, which covers Ochrophyta, has ruled it a conserved orthography.

Higher level classification

For the over-all classification I have followed the six-kingdom system by Thomas Cavalier-Smith, who has played a major part in developing our current understanding of large-scale relationships, and in my opinion does the best job presenting them in a framework that is useful for discussing the groups in question.

An overview giving classes for most algae and protozoans appears in “Unravelling the Algae” (2007) eds. Brodie and Lewis. However, the kingdoms Chromista and Protozoa were also substantially changed in Cavalier-Smith (2010), removing one of the main differences remaining from the phylogeny determined by other authors.

For ciliates I have followed the classes and orders from “The Ciliated Protozoa” 3rd ed. (2008) by Lynn, together with updates by Vďačný et al. (2011) for Litostomatea and Gao et al. (2016) for some other classes. For the Amoebozoa I have followed the classification from Smirnov et al. (2011).

For animals many groups are been more or less stable, given in detail in for instance “Synopsis and Classification of Living Organisms” (1982) ed. Parker. The main exceptions are pseudocoelomate lines, which probably belong to a few larger groups. I have adopted Gnathifera as one that seems fairly well established.

The references listed below give some further details and adjustments. Most of these require subscriptions to access, but the links marked with asterisks should be freely available.

References

General

  1. Eddy, Hodson (1967). Taxonomic Keys to the Common Animals of the North Central States. Burgess Publishing Company.
  2. Jahn, Bovee, Jahn (1978). How to Know the Protozoa. (2nd ed.) WCB/McGraw-Hill.
  3. Prescott (1978). How to Know the Freshwater Algae. (3rd ed.) WCB/McGraw-Hill.
  4. Parker ed. (1982). Synopsis and Classification of Living Organisms. McGraw-Hill, New York.
  5. Bold & Wynne (1985). Introduction to the Algae. (2nd ed.) Benjamin Cummings.
  6. Streble & Krauter (2002). Das Leben im Wassertropfen: Mikroflora und Mikrofauna des Süßwassers. (9te Auf.) Kosmos-Verlags.
  7. Brodie, Lewis eds. (2007). Unravelling the algae: the past, present, and future of algal systematics. CRC Press.
  8. Bellinger & Sigee (2010). Freshwater Algae: Identification and Use as Bioindicators. Wiley-Blackwell.

Names & Etymology

  1. Ehrenberg (1830). Organisation, Systematik und geographisches Verhältniss der Infusionsthierchen. Zwei Vorträge, in der Akademie der Wissenschaften zu Berlin gehalten in den Jahren 1828 und 1830. Druckerei der Königlichen Akademie der Wissenschaften. [BHL*]
  2. Baird (1850). The Natural History of the British Entomostraca. The Ray Society. [BHL*]
  3. Lewis & Short (1879). A Latin Dictionary. Clarendon Press. [Perseus*]
  4. Hunter ed. (1881). The Encyclopædic Dictionary.
  5. Liddell, Scott, Jones (1940). A Greek-English Lexicon. Clarendon Press. [Perseus*]
  6. Brown (1956). Composition of Scientific Words. [archive.org*]
  7. Greuter, Barrie, Burdet, Chaloner, Demoulin, Hawksworth, Jørgensen, Nicholson, Silva, Trehane, McNeill (1994). International Code of Botanical Nomenclature (Tokyo Code). Koeltz Scientific Books. [BGBM*]
  8. Potts (1997). Etymology of the Genus Name Nostoc (Cyanobacteria). International Journal of Systematic and Evolutionary Microbiology 47: 584. [IJSEM*]

Bacteria & Plants

  1. Drew & Ross (1965). Some Generic Names in the Bangiophycidae. Taxon 14(3): 93-99. [JSTOR]
  2. Hayden, Blomster, Maggs, Silva, Stanhope, Waaland (2003). Linnaeus was right all along: Ulva and Enteromorpha are not distinct genera. European Journal of Phycology 38(3): 277-284. [Taylor & Francis*]
  3. Buchheim, Buchheim, Carlson, Braband, Hepperte, Krienitz, Wolf, Hegewald (2005). Phylogeny of the Hydrodictyaceae (Chlorophyceae): Inferences from rDNA Data. Journal of Phycology 41(5): 1039-1054. [Wiley]
  4. Liu, Xiong, Liu, Liu, Hu (2019). Molecular phylogeny and taxonomy of the genus Chaetophora (Chlorophyceae, Chlorophyta), including descriptions of Chaetophoropsis aershanensis gen. et sp. nov. Journal of Phycology 55(1): 74-83. [Wiley]
  5. Strunecký, Ivanova, Mareš (2023). An updated classification of cyanobacterial orders and families based on phylogenetic and polypasic analysis. Journal of Phycology 59(1): 12-51. [Wiley]

Chromista

  1. Round, Crawford, Mann (1990). The Diatoms: biology & morphology of the genera. Cambridge University Press, Cambridge.
  2. Hoef-Emden & Melkonian (2003). Revision of the genus Cryptomonas (Cryptophyceae): a Combination of Molecular Phylogeny and Morphology Provides Insights into a Long-Hidden Dimorphism. Protist 154: 371-409. [Elsevier]
  3. Cavalier-Smith (2010). Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. Biology Letters 6: 342-345. [NCBI*] [Eur PMC*]
  4. Gómez, Moreira, López-Garcia (2010). Neoceratium gen. nov., a New Genus for All Marine Species Currently Assigned to Ceratium (Dinophyceae). Protist 161(1): 35-54. [Aquaparadox*]
  5. Cavalier-Smith & Scoble (2013). Phylogeny of Heterokonta: Incisomonas marina, a uniciliate gliding opalozoan related to Solenicola (Nanomonadea), and evidence that Actinophryida evolved from raphidophytes. European Journal of Protistology 49(3): 328-353. [Elsevier]
  6. Gómez (2013). Reinstatement of the dinoflagellate genus Tripos to replace Neoceratium, marine species of Ceratium (Dinophyceae, Alveolata). CICIMAR Oceánides 28(1): 1-22. [CO*]
  7. Cavalier-Smith, Chao, Lewis (2015). Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista. Molecular Phylogenetics and Evolution 93: 331-362. [Elsevier*]

Ciliates

  1. Curds (1982). British and Other Freshwater Ciliated Protozoa. Part I: Ciliophora: Kinetophragmophora. Cambridge University Press, Cambridge.
  2. Curds, Gates, Roberts (1983). British and Other Freshwater Ciliated Protozoa. Part II: Ciliophora: Oligohymenophora and Polyhymenophora. Cambridge University Press, Cambridge.
  3. Foissner & Berger (1996). A user-friendly guide to the ciliates (Protozoa, Ciliophora) commonly used by hydrobiologists as bioindicators in rivers, lakes, and waste waters, with notes on their ecology. Freshwater Biology 35: 375-482. [Foissner*]
  4. Dovgal (2002). Evolution, phylogeny and classification of Suctorea (Ciliophora). Protistology 2(4): 194-270. [Protistology*]
  5. Foissner, Kusuoka, Shimano (2008). Morphology and Gene Sequence of Levicoleps biwae n. gen., n. sp. (Ciliophora, Prostomatida), a Proposed Endemic from the Ancient Lake Biwa, Japan. Journal of Eukaryotic Microbiology 55(3): 185-200. [NCBI*] [Eur PMC*] [Foissner*]
  6. Lynn (2008). The Ciliated Protozoa: Characterization, Classification, and Guide to the Literature. (3rd ed.) Springer. [Springer]
  7. Vďačný, Bourland, Orsi, Epstein, Foissner (2011). Phylogeny and classification of the Litostomatea (Protista, Ciliophora), with emphasis on free-living taxa and the 18S rRNA gene. Molecular Phylogenetics and Evolution 59: 510-522. [Foissner*]
  8. Gao, Warren, Zhang, Gong, Miao, Sun, Xu, Huang, Yi, Song (2016). The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata). Scientific Reports 6(1): 1-14. [NCBI*] [Eur PMC*] [Nature*]

Spirotrichea

  1. Eigner (1999). Comparison of Divisional Morphogenesis in Four Morphologically Different Clones of the Genus Gonostomum and Update of the Natural Hypotrich System (Ciliophora, Hypotrichida). European Journal of Protistology 35(1): 34-48. [Elsevier]
  2. Bernhard, Stechmann, Foissner, Ammermann, Hehn, Schlegel (2001). Phylogenetic Relationships within the Class Spirotrichea (Ciliophora) Inferred from Small Subunit rRNA Gene Sequences. Molecular Phylogenetics and Evolution 21(1): 86-92. [Foissner*]
  3. Petroni, Dini, Verni, Rosati (2002). A Molecular Approach to the Tangled Intrageneric Relationships Underlying Phylogeny in Euplotes (Ciliophora, Spirotrichea). Molecular Phylogenetics and Evolution 22: 118-130. [Elsevier]
  4. Berger (2003). Redefinition of Holosticha Wrzesniowski, 1877 (Ciliophora, Hypotricha). European Journal of Protistology 39(4): 373-379. [Elsevier]
  5. Li, Song, Shin, Warren, Al-Rasheid, Al-Khedhairy, Al-Arifi (2009). Reconsideration of the phylogenetic positions of three stichotrichous genera Holosticha, Anteholosticha and Pseudokeronopsis (Spirotrichea: Ciliophora) inferred from complete SSU rRNA gene sequences. Progress in Natural Science 19: 769-773. [Elsevier*]
  6. Shao, Ma, Gao, Al-Rasheid, Song (2010). Reevaluation of cortical developmental patterns in Euplotes (s.l.), including a morphogenetic redescription of E. charon (Protozoa, Ciliophora, Euplotida). Chinese Journal of Oceanology and Limnology 28(3): 593-602. [Springer]
  7. Bourland (2015). Morphology, ontogenesis and molecular characterization of Atractos contortus Vörösváry, 1950 and Stichotricha aculeata Wrzesniowskiego, 1866 (Ciliophora, Stichotrichida) with consideration of their systematic positions. European Journal of Protistology 51(5): 351-373. [Elsevier]

Protozoa

  1. Page (1977). The genus Thecamoeba (Protozoa, Gymnamoebia) Species distinctions, locomotive morphology, and protozoan prey. Journal of Natural History 11(1): 25-63. [Taylor & Francis]
  2. Ogden (1979). Siliceous Structures Secreted by Members of the Subclass Lobosia (Rhizopodea: Protozoa). Bulletin of the British Museum (Natural History) Zoology [BHL*]
  3. Marin, Palm, Klingberg, Melkonian (2003). Phylogeny and Taxonomic Revision of Plastid-Containing Euglenophytes based on SSU rDNA Sequence Comparisons and Synapomorphic Signatures in the SSU rRNA Secondary Structure. Protist 154(1): 99-145. [Elsevier]
  4. Ciugulea & Triemer (2010). A color atlas of photosynthetic euglenoids. East Lansing: Michigan State University Press.
  5. Smirnov, Chao, Nassonova, Cavalier-Smith (2011). A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa). Protist 162(4): 545-570. [Elsevier]
  6. Karnkowska, Bennett, Watza, Kim, Zakryś, Triemer (2014). Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon-rich Analyses of Five Genes. Journal of Eukaryotic Microbiology. [Wiley]
  7. Cavalier-Smith (2016). Higher classification and phylogeny of Euglenozoa. European Journal of Protistology 56: 250-276. [Elsevier*]
  8. Gomaa, Lahr, Todorov, Li, Lara (2017). A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences. European Journal of Protistology 59: 99-107. [Elsevier]

Animals

  1. Ruebush (1941). A Key to the American Freshwater Turbellarian Genera, Exclusive of the Tricladida. Transactions of the American Microscopical Society 60(1): 29-40. [JSTOR]
  2. Donner (1965). Ordnung Bdelloidea (Rotatoria, Rädertiere). Akademie-Verlag, Berlin.
  3. Hollowday & Hussey (1989). A re-appraisal of two members of the genus Notholca from the Andes, with a note on the fine structure of the lorica of N. foliacea (Ehrenberg). Hydrobiologia 186-187: 319-324. [Springer]
  4. Clifford (1991). Aquatic Invertebrates of Alberta. University of Alberta Press.
  5. Segers, Murugan, Dumont (1993). On the taxonomy of the Brachionidae: description of Plationus n. gen. (Rotifera, Monogononta). Hydrobiologia 268(1): 1-8. [Springer]
  6. Kristensen & Funch (2000). Micrognathozoa: a new class with complicated jaws like those of Rotifera and Gnathostomulida. Journal of Morphology 246:1-49. [Wiley]
  7. Hemmrich, Anokhin, Zacharias, Bosch (2007). Molecular phylogenetics in Hydra, a classical model in evolutionary developmental biology. Molecular Phylogenetics and Evolution 44: 281-290. [Elsevier]