Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

1THIS revision of the classification of eukaryotes updates that of the International Society of Protistologists (Adl et al. 2012). Since then, there has been a massive increase in DNA sequence information of phylogenetic relevance from environmental samples. We now have a much better sense of the undescribed biodiversity in our environment (De Vargas et al. 2015; Pawlowski et al. 2012). While significant, it still remains a partial estimation as several continents and soils in general are poorly sampled, and the deeper ocean is hard to reach. These new data clarified phylogenetic relationships and the new information is incorporated in this revision.

2We assembled the classification according to the principles outlined elsewhere, and we refer the reader to the introductions of both Adl et al. 2005 and 2012 for background information, and to Adl et al. 2007 for a discussion. Briefly, we adopted a hierarchical system without formal rank designations. The hierarchy is represented by indented paragraphs. The nomenclatural priority is given to the oldest name (and its authority) that correctly assembled genera or higher groups together into a clade, except where its composition was substantially modified. In these cases, we have used a newer term and its appropriate authorship. In cases where ranks were created to include a single lower rank, the higher ranks were eliminated as superfluous. In this scheme, monotypic taxa are represented by the genus only. Nested clades represent monophyletic lineages as best we know and para‐ or polyphyletic groups are so indicated.

3This system of hierarchical nameless ranks, that ignores endings of clade names, has proved its utility in providing name stability as we reconstructed a new phylogenetic classification during the past 20 years. Clade names in this system do not change when their rank or composition changes, and it is only the authority for the name that changes when each clade description is adjusted (Cantino, 1998 Pleijel and Rouse, 2003). Where a new term is introduced in this classification, it is identified with “Adl et al. 2019” as the authority, or by the submitting author (e.g. Mann in Adl et al., 2019), and they are to be cited as emended in this publication. The descriptions provided are not intended to substitute for formal diagnoses. They are provided primarily for the student and general users to identify common morphological features, such as synapomorphies and apomorphies, within monophyletic lineages.

4There are two novel components in this revision. First, we have provided trophic assignments for most taxa. This will prove useful in interpreting communities from environmental samples. Second, we informally suggest a phylum rank and classes in most clades to provide a point of reference in the classification hierarchy for the nonspecialist. This became possible, as there has been some stability at this level in the molecular phylogenetic reconstructions. It should be obvious that genera grouped into a clade then represent a family, and families into an order.

5This committee of the Society has had the responsibility of arbitrating nomenclature for protists in general. Historically, the task was simpler as most groups fell under one or the other of the two Codes of Nomenclature (algae and some other protists under the “International Code of Nomenclature for algae, fungi, and plants”, and protozoa under the “International Code of Zoological Nomenclature”), and few were described under both Codes. The Society was represented on the relevant committees. Notwithstanding that both Codes are incompatible, some have proposed to provide parallel classifications in each Code, while others proposed to adopt a modern unified code of nomenclature. Since the rearrangement of the classification along monophyletic lineages during the 1990s, many clades now include a mixture of taxa from both Codes. Several taxa, such as diatoms, are described in parallel under both Codes with different names. This situation created and perpetuates anomalies, such as the recent redescription of the dictyostellid amoebae with the botanical Code (Sheikh et al. 2018) for genera that are unarguably in Amoebozoa governed by the Zoological Code. Issues such as these have been thoroughly discussed in the past (Adl et al. 2007; Lahr et al. 2012). It has been the responsibility of this committee to discuss and arbitrate published phylogenetic hypotheses, proposals for new names and name changes. Underlying these discussions are principles of nomenclatural priority in the spirit of the codes of nomenclature.

6A classification is unlike a phylogenetic tree in a publication, where the discovery of new clades, branches, or robust nodes ultimately leads to proposing new names. Newly named clades and nodes have their utility in phylogenetic analysis and discussion, but do not need to be formalized in the classification immediately. An overwhelming number of spent names have thus accumulated, with an increasing frequency over the past four decades, most of which are no longer—or never were—in common use. Many of these names were ephemeral, as their monophyly did not stand the test of (time) statistical analysis. The proliferation of these names reflects a methodological error practiced by some. That is to formalize names prematurely and try to reorganize classifications single‐handedly. As we argued before (Adl et al. 2012), this must be done with care, respecting nomenclatural priority, published as a proposal or a phylogenetic hypothesis first, to be verified by the community, and only eventually considered for change in the classification. The task of refereeing and classifying falls on Society committees representing communities of professionals. The very formal and slow process of voting to conserve or reject names through the tradition of the botanical code takes years as it has to proceed through committees and then approved by vote on the floor of the congress at 6‐year intervals. That is, however, too slow for the pace of changes today given the rate at which new information is becoming available.

7In contrast to a phylogenetic tree, a classification system belongs to a community of users, and it is generated through discussions of the available evidence, for pragmatic purposes of teaching, curation, organizing data, archiving and communicating with a common language. It is a commonly agreed point of reference. It is not to be reimagined or re‐done at will by one individual. The Linnaean system that we have inherited has detailed codes of nomenclature that guide and regulate how living organisms are named, names changed and classified. The elaborate rules arise from disputes and mistakes made in the past, in part out of respect for each other's work. Instead of providing a long list of rejected and invalid names, we can specify that those not selected in this classification were considered nomina ambigua, nomina perplexa, nomina dubia, nomina nuda or did not have nomenclatural priority and are declared nomina rejicienda.

8Another proposed classification of prokaryotes and eukaryotes was published recently (Ruggiero et al. 2015). This effort may be reasonable in their classification of the prokaryotes, but the eukaryote section does not pass standards of modern biology. Specifically, it is their refusal to use monophyly as a guiding principle, but to argue to retain “ancestral (paraphyletic) taxa when it seemed beneficial to do so” instead, even where monophyletic clades are already established. Their insistence on using a hodge‐podge of names that do not have nomenclatural priority, and that poorly describe the taxa included, further reduces its usefulness.

9The super‐groups utilized since 2005 (Adl et al. 2005; Simpson and Roger 2004) are revised as follows (Fig. 1):

10Eukaryotes now form two Domains called Amorphea and Diaphoretickes, with several additional clades that do not group into a third Domain.In the Amorphea, the Opisthokonta, Breviatea and Apusomonadida now form a robust clade, as noted earlier (Adl et al. 2012), called Obazoa. Within the Opisthokonta, the Holozoa and Nucletmycea(/Holomycota) are robust clades with improved resolution of the basal sister lineages. In the Holozoa, the sponges and the other animals group together as the Metazoa (Porifera, Placozoa, Ctenophora, Cnidaria, Bilateria). In addition, a sister clade to the Amorphea comprising several genera was recently described as CRuMs (Brown et al. 2018).There are two sister clades in Opisthokonta, the Holozoa and the Nucletmycea (/Holomycota). They share several characters, including synthesis of extracellular chitin in an exoskeleton, cyst/spore wall or cell wall of filamentous growth and hyphae; the extracellular digestion of substrates with osmotrophic absorption of nutrients; and other cell biosynthetic and metabolic pathways. Genera at the base of each clade are amoeboid and phagotrophic.The Archaeplastida, Sar and several other clades remain a monophyletic clade under Diaphoretickes. The clade Cryptista comprising the cryptomonads, kathablepharids and Palpitomonas is well recognized and robust, although placement of its node within the Diaphoretickes remains problematic. In some but not all analyses, the clade appears inside the Archaeplastida. This position has always occurred from time to time in some phylogenies with weak support, but there is now stronger support for this association. We are not committed to their inclusion within the Archaeplastida but do note its likelihood. The inclusion of the Cryptista in the Archaeplastida would expand that group without affecting its defining criteria. Questioning the single origin of a plastid within the Archaeplastida is a rare minority opinion. Yet, the possibility of more than one plastid origin must not be ruled‐out until the cryptomonads are robustly positioned.The new robust support for the Cryptista clade is accompanied by a similarly robust support for a clade comprising the Centroplasthelida and Haptophyta as the Haptista within the Diaphoretickes.Nodes at the base of the Alveolata are better resolved with additional genera. The placeholder name Protalveolata is no longer required.The Excavata comprise three clades: the Metamonada, the Discoba, and the Malawimonada. Their mutual relationships, as well as their relationships to other clades of eukaryotes, remain uncertain. We have dropped the supergroup Excavata in favour of the informal Excavates when referring to the “Discoba, Metamonada, Malawimonada”, as Incertae sedis in eukaryotes. The Excavates and several clades and genera fall outside of the two principal domains, but do not cluster together into a third domain.

11Eukaryotes now form two Domains called Amorphea and Diaphoretickes, with several additional clades that do not group into a third Domain.

12In the Amorphea, the Opisthokonta, Breviatea and Apusomonadida now form a robust clade, as noted earlier (Adl et al. 2012), called Obazoa. Within the Opisthokonta, the Holozoa and Nucletmycea(/Holomycota) are robust clades with improved resolution of the basal sister lineages. In the Holozoa, the sponges and the other animals group together as the Metazoa (Porifera, Placozoa, Ctenophora, Cnidaria, Bilateria). In addition, a sister clade to the Amorphea comprising several genera was recently described as CRuMs (Brown et al. 2018).

13There are two sister clades in Opisthokonta, the Holozoa and the Nucletmycea (/Holomycota). They share several characters, including synthesis of extracellular chitin in an exoskeleton, cyst/spore wall or cell wall of filamentous growth and hyphae; the extracellular digestion of substrates with osmotrophic absorption of nutrients; and other cell biosynthetic and metabolic pathways. Genera at the base of each clade are amoeboid and phagotrophic.

14The Archaeplastida, Sar and several other clades remain a monophyletic clade under Diaphoretickes. The clade Cryptista comprising the cryptomonads, kathablepharids and Palpitomonas is well recognized and robust, although placement of its node within the Diaphoretickes remains problematic. In some but not all analyses, the clade appears inside the Archaeplastida. This position has always occurred from time to time in some phylogenies with weak support, but there is now stronger support for this association. We are not committed to their inclusion within the Archaeplastida but do note its likelihood. The inclusion of the Cryptista in the Archaeplastida would expand that group without affecting its defining criteria. Questioning the single origin of a plastid within the Archaeplastida is a rare minority opinion. Yet, the possibility of more than one plastid origin must not be ruled‐out until the cryptomonads are robustly positioned.

15The new robust support for the Cryptista clade is accompanied by a similarly robust support for a clade comprising the Centroplasthelida and Haptophyta as the Haptista within the Diaphoretickes.

16Nodes at the base of the Alveolata are better resolved with additional genera. The placeholder name Protalveolata is no longer required.

17The Excavata comprise three clades: the Metamonada, the Discoba, and the Malawimonada. Their mutual relationships, as well as their relationships to other clades of eukaryotes, remain uncertain. We have dropped the supergroup Excavata in favour of the informal Excavates when referring to the “Discoba, Metamonada, Malawimonada”, as Incertae sedis in eukaryotes. The Excavates and several clades and genera fall outside of the two principal domains, but do not cluster together into a third domain.

18This classification will serve as a primary starting reference for the taxonomic framework developed by UniEuk (unieuk.org; Berney et al. 2017), the Society supported, consensus‐driven, community‐based and expert‐driven international initiative to maintain a universal taxonomy for, at least, microbial eukaryotes. A specific aim of the UniEuk project is to apply one taxonomic framework to all genetic data in the International Nucleotide Sequence Database Collaboration (INSDC) repositories, which includes DDBJ (ddbj.nig.ac.jp), GenBank (ncbi.nlm.nih.gov) and ENA (ebi.ac.uk/ena) databases. The system's broad use and preservation will be ensured by a direct implementation of the UniEuk taxonomic framework into the ENA (European Nucleotide Archive) at EMBL‐EBI ( http://www.ebi.ac.uk/ena). The project will capture our collective knowledge on eukaryotic diversity, evolution, and ecology via three main modules (EukRef, EukBank and EukMap). EukRef (eukref.org; del Campo et al. 2018) uses a standardized, open‐source bioinformatics pipeline to generate homogenous, high‐quality curation of sequences (primarily 18S rDNA) available in INSDC databases. EukRef is fully operational; outputs include (on a lineage‐by‐lineage basis) taxonomically curated sequences, sequence alignments, phylogenetic trees and metadata. EukBank is a public repository of (primarily V4 18S rDNA) high‐throughput metabarcoding data sets, centralized at ENA, with standardized protocols for submitting data sets and metadata. EukMap (eukmap.unieuk.org) is an editable, user‐friendly representation of the UniEuk taxonomy in the form of a publicly navigable tree, where each node/taxon is associated with contextual data (taxonomic and ecological information, links to representative images, etc.). It will be operational by 2019 and will allow registered community members to directly interact with and inform the taxonomic framework, and to flag taxonomy issues requiring revision. As a whole, the UniEuk system will represent a community hub to centralize, standardize, and promote global knowledge on eukaryotic diversity, taxonomy and ecology.

19Several terms were clarified to correct misuse of terminology in publications. In 2005, these were: eukaryote, prokaryote, algae, zoosporic fungi, protozoa, zooplankton, phytoplankton, cyst, spore and cilium. In 2012, they were related to the cytoskeleton and motility: lobopodia, lamellipodia, filopodia, granuloreticulopodia, reticulopodia, axopodia, centriole, centrosome, microtubular organizing centre (MTOC), basal body, kinetosome, kinetid and mastigont. In this revision, they pertain to trophic functional groups.

20In addition to descriptions of morphology that accompany specimen, which is critical for understanding cell function and interpreting phylogenetic trees, improved descriptions of site and food preferences are required for an ecological interpretation of the role in the community and ecosystem. Often species lack sufficient description of the collection site or feeding habit.

21To compare environmental DNA data sets, adequate metadata is necessary to select appropriate samples for comparison. The same issue exists when trying to re‐isolate a species or to verify the type specimen. Therefore, it is important that the environment and habitat is sufficiently described. Merely stating marine, terrestrial or soil is grossly inadequate. The soil, for example, is heterogeneous horizontally at the sub‐millimetre to regional scales. It is also stratified through the profile, and across the diameter of each ped. Whether a soil or aquatic sample, solution chemistry and site physical parameters contribute to define the niche space.

22Because we care about nomenclature and the exact meaning of words and of names of things, especially species and their groupings into nodes and stems on phylogenetic trees, it is equally important to care for how we describe sampling sites and feeding habits. There are two parts to describing the feeding habit: what is eaten and how it is eaten.

23Species that release enzymes extracellularly to digest substrates in their habitat, are generally called saprotrophic or lysotrophic, and contribute to the decomposition of organic matter. One incredible resource is FunGuild (Nguyen et al. 2016, ( https://github.com/UMNFuN/FUNGuild) to determine substrate utilization for saprotrophic fungi. Probably all eukaryotes are capable of osmotrophy, the acquisition of soluble nutrients through the cell membrane. For example, plants obtain their carbon for photosynthesis from the air, as well as some oxygen—however, they rely on osmotrophy through the roots to obtain all the other elements they need. Osmotrophy occurs through the ciliary pit, by pinocytosis, by diffusion, and by various membrane transport proteins. Some species have no alternative form of acquiring energy, are very poor at decomposing substrates and are strict osmotrophs relying on dissolved nutrients. Detritus eaters ingest particles derived from cells and tissues, decomposing organic matter, starch granules, plant or animal debris, or wood (microchip) fragments.

24Species that eat other species are called consumers, and there are a variety of terms to describe the functional groups. Some acquire suspended particles in the solution and accumulate the particles by filtration into an oral region or cytostome (not filter‐feeders, as they do not feed on filters). The size of particles filtered out of the liquid depend on the current generated, and the structure of the feeding apparatus (Fenchel 1986), and it is a good idea to specify what size prey are ingested. The remaining consumers fall into two categories, the grazers and predators. Grazers, like a cow in a field of grasses, browse and ingest from surfaces covered with potential food items (e.g. an amoeba on a lawn of bacteria, or on soil particle surfaces). Predators pursue scarce prey according to optimal foraging theory, typically handle one prey at a time, and it is mathematically distinct (e.g. a Jakoba ingesting one bacterium). Species gather bacteria by filtration prior to phagocytosis, or directly by phagocytosis; it is best to specify “bacteria by filtration” or “bacteria by phagocytosis”. A popular term bacterivore has the unintended implication of voraciously devouring (voracitas L.) which is a false description of how many bacteria eaters acquire their prey, and an incomplete description. Use it, but be aware that some readers and reviewers will be more discriminating. In contrast, the more appropriate term –trophy (trophe Gr.), to eat for food and nourishment, sounds more awkward in English. For species that ingest unicellular protists by phagotrophy, the correct term is cytotrophy. Bacterium (Ehrenberg 1838) has been the word used to refer to a prokaryotic cell, while cell (Dutrochet 1824; Schleiden 1838; Schwann 1839) has been used since to refer to a eukaryotic cell. Mixotrophy refers to photosynthetic species that also ingest food by phagocytosis, and heterotrophs that retain prey plastids and symbionts.

25There are two distinct mechanisms to feed on algal filaments (cellulosic cell wall) or fungal hyphae (chitinous cell wall). One mechanism is to slurp the filaments like noodles and ingest them, and the other is to penetrate through the cell wall. Those that puncture through phagocytose cytoplasm, and some species even penetrate inside to ingest cytoplasm along the tube or in the spore. It is best to distinguish between the cell wall material to digest and the mechanism of ingestion. Thus, we have mycotrophy or phycotrophy, by either swallowing (devoratis L.) or by penetrating (penetrando L.).

26In microbial food webs, there are also consumers of consumers, typically by predation, that are equivalent above‐ground or in aquatic systems to carnivores (meat eaters), or other functional groups. Although 2° consumers, 3° consumers, and so on exist in microbial food webs, it is hardly correct to refer to carnivores in food webs where there is no meat.

27Another poorly crafted term one encounters, albeit rarely, is eukaryovory. Although there are famous examples of eukaryovory (Saint‐Exupéry 1943), eukaryotes eating eukaryotes can include parasitism, as intracellular or extracellular parasites, on hosts that are protists or multicellular, with various grades of host specificity, and it is a poor substitute for cytotrophy.

28We have summarized the higher level classification of eukaryotes in Table 1, with an estimate of the known number of genera, and providing informal phylum and class designations to help orient the student and users along the hierarchy, or nodes on a phylogenetic tree. The revised classification of eukaryotes is presented in Table 2, and genera that have not been studied enough to place in the classification are listed in Table 3 as incertae sedis Eukarya. Table 4 provides recommended primers for analysing DNA from environmental samples, noting that the choice of primers and depth of sequencing are important sources of variation between studies. Appendix S1 provides additional supporting literature that we considered important to understand the changes. Appendix S2 provides more detail about the trophic functional assignments across protists, by noting exceptions at the genus level. Appendix S3 provides a standardized guide to East Asian users for the new terminology.

29Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes by Sina M. Adl, David Bass, Christopher E. Lane, Julius Lukeš, Conrad L. Schoch, Alexey Smirnov, Sabine Agatha, Cedric Berney, Matthew W. Brown, Fabien Burki, Paco Cárdenas, Ivan Čepička, Ludmila Chistyakova, Javier del Campo, Micah Dunthorn, Bente Edvardsen, Yana Eglit, Laure Guillou, Vladimír Hampl, Aaron A. Heiss, Mona Hoppenrath, Timothy Y. James, Anna Karnkowska, Sergey Karpov, Eunsoo Kim, Martin Kolisko, Alexander Kudryavtsev, Daniel J. G. Lahr, Enrique Lara, Line Le Gall, Denis H. Lynn, David G. Mann, Ramon Massana i Molera, Edward A. D. Mitchell, Christine Morrow, Jong Soo Park, Jan W. Pawlowski, Martha J. Powell, Daniel J. Richter, Sonja Rueckert, Lora Shadwick, Satoshi Shimano, Frederick W. Spiegel, Guifré Torruella i Cortes, Noha Youssef, Vasily Zlatogursky, Qianqian Zhang.

30Appendix S1. Supplementary references.

31Appendix S2. Functional group assignments.

32Appendix S3. Translation guide for East Asian users.

33Berney, C., Geisen, S., Van Wichelen, J., Nitsche, F., Vanormelingen, P., Bonkowski, M. & Bass, D. 2015. Expansion of the “reticulosphere”: diversity of novel branching and network‐forming amoebae helps to define Variosea (Amoebozoa). Protist, 166, 271–295.

34Brown, M. W., Sharpe, S. C., Silberman, J. D., Heiss, A. A., Lang, B. F., Simpson, A. G. B. & Roger, A. J. 2013. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc. R. Soc. Lond. B, 280:1769.

35Cavalier‐Smith, T., Chao, E., E., & Lewis, R. 2016. 187‐Gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep‐branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. Mol. Phylogenet. Evol., 99: 275–296.

36Hamann, E., Gruber‐Vodicka, H., Kleiner, M., Tegetmeyer, H. E., Riedel, D., Littmann, S., Chen, J., Milucka, J., Viehweger, B., Becker, K. W., Dong, X., Stairs, C. W., Hinrichs, K.‐U., Brown, M. W., Roger, A. J. & Strous, M. 2016. Environmental Breviatea harbor mutualistic Acrobacter epibionts. Nature, 534:254–258.

37Heiss, A. A., Lee, W. J., Ishida, K. & Simpson, A. G. B. 2015. Cultivation and characterisation of new species of apusomonads (the sister group to opisthokonts), including close relatives of Thecamonas (Chelonemonas n. gen.). J. Eukaryot. Microbiol., 62:637‐649.

38Kang, 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., Kudryavstev, A., Lahr, D. J., & Brown, M. W. 2017. Between a pod and a hard test: the deep evolution of amoebae. Mol Biol Evol msx162. https://doi.org/10.1093/molbev/msx162.

39Pánek, T, Zadrobílková, Walker, G., Brown, M. W., Gentekaki, E., Hroudrová, M., Kang, S. Roger, A. J., Tice, A. K., Vlček, Č., & Čepička, I. 2016. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Molec. Phylogen. Evol., 98:41‐51.

40Schaap, P., Winckler, T., Nelson, M., Alvarez‐Curto, E., Elgie, B., Hagiwara, H., Cavender, J., Milano‐Curto, A., Rozen, D. E., Dingermann, T., Mutzel, R. & Baldauf, S. 2006. Molecular phylogeny and evolution of morphology in the social amoebas. Science, 314: 661‐663.

41Spiegel, F. W., Shadwick, L. L., Ndiritu, G. G., Brown, M. W., Aguilar, M., & Shadwick, J. D. L. 2017. Protosteloid Amoeboazoa (Protosteliids, Protosporangiida, Cavostellida, Schizoplasmodiida, Fractoviteliida, and sporcarpic members of Vanellida, Centramoebida, and Pellitida). In: Archibald, J. M.,Simpson, A. G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e‐book) https://doi.org/10.1007/978-3-319-32669-6_12-1

42Sheikh, S., MatsThulin Cavender, J.C., Escalante, R., Kawakami, S.I., Lado, C., Landolt, J.C., Nanjundiah, V., Queller, D.C., Strassmann, J.E., Spiegel, F.W., Stephenson, S.L., Vadell, S.M., & Baldauf, S.L. 2018. A new classification of the dictyostelids. Protist 169: 1‐28.

43Wilkinson, D. M. & Mitchell, E. A. D. 2010. Testate amoebae and nutrient cycling with particular reference to soils. Geomicrobiol J., 27(6):520‐533. https://doi.org/10.1080/01490451 003702925.

44Walker, G., Zadrobílková, E., Čepička., I. (2017) Archamoebae In: Archibald, J. M.,Simpson, A. G. B., & Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e‐book) https://doi.org/10.1007/978-3-319-28149-0_11

45Berney, C., Geisen, S., Van Wichelen, J., Nitsche, F., Vanormelingen, P., Bonkowski, M. & Bass, D. 2015. Expansion of the “reticulosphere”: diversity of novel branching and network‐forming amoebae helps to define Variosea (Amoebozoa). Protist, 166, 271–295.

46Cavalier‐Smith, T., Chao, E., E., & Lewis, R. 2016. 187‐Gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep‐branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution. Mol. Phylogenet. Evol., 99: 275–296.

47Kang, 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., Kudryavstev, A., Lahr, D. J. & Brown, M. W. 2017. Between a pod and a hard test: the deep evolution of amoebae. Mol Biol Evol msx162. https://doi.org/10.1093/molbev/msx162.

48Pánek, T, Zadrobílková, Walker, G., Brown, M. W., Gentekaki, E., Hroudrová, M., Kang, S. Roger, A. J., Tice, A. K., Vlček, Č., & Čepička, I. 2016. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Molec. Phylogenet. Evol., 98:41‐51.

49Schaap, P., Winckler, T., Nelson, M., Alvarez‐Curto, E., Elgie, B., Hagiwara, H., Cavender, J., Milano‐Curto, A., Rozen, D. E., Dingermann, T., Mutzel, R. & Baldauf, S. 2006. Molecular phylogeny and evolution of morphology in the social amoebas. Science, 314: 661‐663.

50Spiegel, F. W., Shadwick, L. L., Ndiritu, G. G., Brown, M. W., Aguilar, M. & Shadwick, J. D. L. 2017. Protosteloid Amoeboazoa (Protosteliids, Protosporangiida, Cavostellida, Schizoplasmodiida, Fractoviteliida, and sporcarpic members of Vanellida, Centramoebida, and Pellitida). In: Archibald, J. M.,Simpson, A. G. B., and Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e‐book) https://doi.org/10.1007/978-3-319-32669-6_12-1

51Sheikh, S., MatsThulin Cavender, J.C., Escalante, R., Kawakami, S.I., Lado, C., Landolt, J.C., Nanjundiah, V., Queller, D.C., Strassmann, J.E., Spiegel, F.W., Stephenson, S.L., Vadell, S.M. & Baldauf, S.L. 2018. A new classification of the dictyostelids. Protist 169: 1‐28.

52Smirnov, A., V., Brown, S., 2004. Guide to the methods of study and identification of soil gymnamoebae. Protistology 3, 148–190.

53Wilkinson, D. M. & Mitchell, E. A. D. 2010. Testate amoebae and nutrient cycling with particular reference to soils. Geomicrobiol J., 27(6):520‐533. https://doi.org/10.1080/01490451003702925.

54Walker, G., Zadrobílková, E. & Čepička., I. 2017 Archamoebae In: Archibald, J. M.,Simpson, A. G. B. & Slamovits, C., eds. Handbook of the Protists (Second Edition of the Handbook of Protoctista by Margulis et al.) Springer Reference Works (e‐book) https://doi.org/10.1007/978-3-319-28149-0_11

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328Trophic functional group assignments facilitate interpretation of community structure and food web assembly from DNA sequence information identification of “operational taxonomic unit” (OTU). Here we tried to provide details of trends in eating habits of non‐parasitic protists. Many genera have never been cultured so their feeding preferences are unknown. For definition of terms, please refer to the main text, page 6.

329Across protists, in most cases it is safe to assume that species within a genus are most likely to have the same trophic function, with rare exceptions. However, it is not the case in some taxa, where there can be considerable variation between species within a genus. That is the case, for example, in Dinoflagellata, Arcellinida, and Euglyphida.

330In the Amoebozoa, genera can be assumed to ingest bacteria by phagocytosis with the following exceptions: Amphizonella (Corycida) and Dermamoeba also ingest Cyanobacteria; the Euamoebida genera Amoeba, Cashia, Chaos, Polychaos, Trichamoeba and Deuteramoeba are also cytotrophic; amoebae of the genera Polychaos and Pseudothecamoeba ingest diatoms. Some species or genera have a preference for heterotrophic bacteria over of photosynthetic ones, or even discriminate against Cyanobacteria such as Copromyxa and Copromyxella. In Protosteliida, Protostelium spp. prefer yeasts but some will also eat bacteria, and several can eat coccoid green algae, except P. nocturnum which only eats bacteria; they can be cannibalistic in culture as can Cavosteliida and some Protosporangiidae. In Schizoplasmodiidae, all do best in culture on a mixture of yeast and bacteria, though some will survive on bacteria alone; when they eat yeasts, they puncture the cell wall and ingest only the protoplast. Multicilia (Holomastigida) is cytotrophic on other amoebae. Dictyostelia are primarily bacterivorous but they will eat yeasts in culture, and can also be cannibalistic in culture; zygotes are cannibalistic exclusively. Myxogastria ciliated stage is bacterivorous, their plasmodia are omnivorous and often cannibalistic when they first form. The Entamoebae are mostly commensal or parasitic and can eat bacteria by phagotrophy. A few strains of Sappinia and Acanthamoeba can be parasitic. Some Archamoebae, Tricholimax, Thecamoeba, Korotnevella, Gocevia, Paragocevia, Leptomyxa and Mayorella species are omnivores. There are some diatom specialists as in Difflugia and Phryganella. The ability to feed on yeast might be more widespread than reported. Similarly, in their habitat some soil amoebae probably ingest small Cercozoa such as Glissomonads. In the Arcellinida, at least species of Nebela and Cryptodifflugia are known to prey on nematodes. The tendency to cannibalism amongst some amoebae may be due to crowding in culture.

331In Arcellinida certain species of Cucurbitella, Difflugia, Heleopera, Hyalosphenia and Netzelia form symbiosis with Trebouxiophyta species and can be considered mixotrophic.

332Free‐living basal genera of Holozoa and Nucletmycea are amoeboid, phagotrophic on bacteria. Parasitic ones, including Microsporidia, are intracellular parasites. The Choanoflagellata feed on bacteria by filtration through the collar. The Fungi are saprotrophic on external substrate, obtaining their nutrient by osmotrophy through a chitinous cell wall. Lichenous fungi are capable of photosynthesis. Mycorrhizal fungi receive most or all of their organic molecules from the host plant. Many Fungi are parasitic (see table 2). For details of substrate preference the reader is referred to FUNGuild (Nguyen et al., 2016, https://github.com/UMNFuN/FUNGuild).

333In the Archaeplastida, ignoring the Embryophyta, all Chloroplastida are photosynthetic with chl a, b, with the exception of Helicosporidium (insect gut parasite), Polytomella, Polytoma, Prototheca which have 2° lost photosynthesis and are strictly osmotrophic. Among the Rhodophyceae, some Cyanidiales are facultative heterotrophs. Amongs the red algae certain species in several genera have lost photosynthesis and are parasites of other red algae. For example: Gracilariophila oryzoides, Harveyella mirabilis, Choreocolax polysiphoniae, Janczewskia gardneri, Faucheocolax attenuata, Bostrychiocolax australis, Dawsoniocolax bostrychiae, Coccotylus hartzii, Epulo multipedes (see Blouin and Lane, 2012, Table S1). Nearly all of the parasitic genera end with the term “colax” to indicate the lifestyle. Most parasites are sister species with the hosts, and many of these genera need to be merged with the genus of their hosts, as they were described separately. This is in progress but obviously correcting the taxonomy is a slow process.

334The Cryptista ingest bacteria prey by phagocytosis, and the photosynthetic ones are mixotrophic. In Haptophyta, Coccolithales are autotrophic, while genera without scales can be mixotrophic or heterotrophic on bacteria, with or without haptonema contributing to bacteria capture. The Centroplasthelida are typically cytotrophic.

335In the Apicomplexa, all species are historically treated as parasites. Recent observation suggest some may be endobionts as commensals or at least not as parasites, especially among some invertebrate hosts. However, there are no free‐living species known. The presence of a relic plastid genome in the Apicomplexa, and apicoplast in some, provides useful metabolic targets for drug treatment development. In contrast, both Dinoflagellata and Ciliophora provide a wide diversity of trophic functional groups.

336The Dinoflagellata functional assignments vary between closely related genera, and are shown in Appendix 2, Table 2.1.

337The Ciliophora are to be assumed to ingest bacteria by filtration except as noted below. Some genera of Karyorelictea (eg. Kentrophoridae) can be considered grazers as they live on sand surfaces covered in bacteria, and often harbour symbiotic bacteria. We discriminate between surface‐feeding and water‐column filtration feeding. Surface‐feeding ciliophores spend most of their time gathering food particles from surfaces rather than by swimming in a volume of water. Thus clearing rates are calculated by surface area rather than volume of liquid. Most ciliophores (with exceptions noted in table 2.2) ingest bacteria, and many also ingest small protists (labelled omnivorous), while others can ingest larger protists by predation. Many omnivores can also ingest some detritus if the cytostome permits. In Ciliophora one should not assume that a small cell or a small cytostome implies a bacteria diet. There are parasites, histophagous species, endocommensals, and epibionts. The Stichotrichida contain species that can ingest larger protists and even small ciliophores for example in some species of Oxytrichidae. The Litostomatea are redoubtable predatory cytotrophs, and some can ingest prey larger than themselves. Entodiniomorphida are often (or typically) commensals in rumen. Among the Colpodea a small number of genera are cytotrophic, for example Bursaria (and maybe other Bursariomorphida). In the Nassulida, Nassula is phycotrophic by swallowing and can ingest cyanobacteria filaments. In the Prorodontida several genera, eg. Coleps, are attracted to dead or wounded invertebrates to the leaking tissues. The Astomatia can be found as symbionts in Oligochaetae gut. Some Tetrahymenida genera are parasitic or histophagous. The Suctoria (Phyllopharyngea) use specialised tentacles to capture and manipulate prey, typically other ciliophores or small invertebrates; they are cytotrophic predators and 3° consumers as predators of invertebrates. The Rhynchodia (Phyllopharyngea) are parasites of bivalves. Among the Scuticociliatia the Philasterida contain cytotrophic genera, for example Uronema. See Appendix table 2.2 for more details.

338Also in the Alveolates, the colpodellids, Colponema, Acavomonas, and Oxyrrhis are cytotrophic predators, while the Perkinsidae are parasitic as trophozoites.

339Stramenopiles in the Ochrophyta are almost all photosynthetic. The Actinophryidae are cytotrophic. The Opalinata, Bicosoecida, and Placidida are phagotrophic on bacteria, with the exception of the Proteromonada and Blastocystis (osmotrophic) which are intestinal commensals or parasites. The Hyphochytriales and Peronosporomycetes are saprotrophs, but the latter contains numerous plant parasites. The Pirsoniales are parasites on diatoms.

340Rhizaria. The Cercomonadida, Paracercomonadida, and Glissomonadida can be assumed to be phagotrophic predators on bacteria, with the notable exception of the Viridiraptoridae which are phycotrophic (mycotrophy not known) by penetration. The Vampyrellida are mycotrophic or phycotrophic. The Euglyphida show some variation, although most are phagotrophic on bacteria. Observations indicate that the larger the cell the more likely it is to be cytotrophic; in fact the larger species cannot survive on bacteria alone. Many Hyalospheniidae need to prey at least partly on Euglyphida and use the scales to build their own test. Symbiosis occurs between Trebouxiophyta (photosynthetic) with several genera of Rhizaria. This implicates at least some species of Placocista (Euglyphida), Amphitrema and Archerella (Labyrinthulomycetes). Chlorarachnea are photosynthetic but some species are mixotrophic on bacteria. In the Endomyxa, the Phytomyxea are plant root parasites, while the Ascetosporea are parasites of invertebrates.

341The Foraminifera are primarily bacteria eaters, but can ingest detritus, other protists, and larger forms can prey on small invertebrates.

342Among the Discoba (Excavates) Heterolobosea graze bacteria by phagocytosis, except Stephanopogon and Creneis which are cytotrophic. Some strains of Naegleria fowleri can cause primary amoebic meningoencephalitis, penetrating through the nose. The Jakobida and Tsukubomonas are predatory on bacteria which are ingested by phagocytosis. The Diplonema are cytotrophic by phagocytosis and have an important role in aphotic marine waters; some species are parasitic or symbiotic with animals. Among the Euglenida (Discoba) the Aphagea (Rhabdomonas, Gyropaigne, Menoidium, Parmidium and Rhabdospira), Astasia and Distigma are osmotrophic; Euglenophyceae (except Rapaza) are photosynthetic with chl a, b in plastids, or secondarily osmotrophic, and Rapaza is cytotrophic; the Peranemids, Anisonemids, Pleotiids, and Petalomonadida are phagotrophic. Certain clades graze on bacteria by phagotrophy or are cytotrophic predators. Among the Kinetoplastea (Discoba) all except the Trypanosomatida are predatory phagotrophs on bacteria. The Trypanosomatida are animal blood and tissue parasites, except Phytomonas which lives in plant latex vessels, and all are transferred by insect vectors.

343The Metamonada (Fornicata, Parabasalia, and Preaxostyla Excavates) are predatory or grazers on bacteria, ingested by phagocytosis. The Preaxostyla are endosymbiont detritivores that phagocytose wood microchips, and acquire many nutrients by osmotrophy from syntrophic bacteria; some genera may also ingest bacteria by phagocytosis. Giardia (Diplomonadida) are osmotrophic gut parasites. Several genera have species that can be parasitic in humans and other animals.

344Human parasites. For protists that are human parasites, see Adl and Matheson (2019) in ASM‐Manual of Clinical Microbiology chapter 132 (Taxonomy and Classification of Human Eukaryotic Parasites), 12th edn.

345Definitions. We further provide descriptions and clarifications for symbisois, microbiome, holobiont, intra‐ cellular and extracellular locations, that relate to interactions between organisms.

346Symbiosis is a sustained relationship between at least two individuals (same or different species), living in direct contact or close enough one to the other, during part or the whole live cycle of the two partners. This interaction is transmitted either vertically (from one generation to the other) or horizontally (acquired de novo at each generation). Symbiosis is the antonym of transitory interactions (predatory). A symbiosis can be beneficial for both partners (mutualism) or at the other extreme, deleterious for one of these partners (parasite or parasitoid). In general, the larger species of this association is called the host, the smallest one is the symbiont. Examples of symbiosis: photosymbiosis (corals and Symbiodinium, kleptoplast), mycorrhizae, lichens, parasitism and hyperparasitism (parasite of parasite). Some specialist predators may also be considered as symbionts (example: Helcion living exclusively on laminarian). A virus is a parasitic symbiont.

347The microbiome is a microbial community living in, on or at the close vicinity of an individual. Examples: gut community, biosphere of phytoplanktonic cells, microbes living on the skin/cuticule of metazoan, in the rhizopshere, microbes living in specialized tissues, or part of the cell. Unicellular symbionts are part of the microbiome of their host.

348Holobiont. Ecoevolutionary concept considering an individual together with its microbiome as the true unit on which evolutionary processes will act.

349Intracellular (endocellular) versus extracellular. Intracellular symbionts are those where the parasite cytoplasm and nucleus enter inside the host and reside inside the host cell. In some extracellular symbionts, part of the cytoplasm (including the mitochondrion) may penetrate inside the host cell, but never the parasite nucleus. Endobionts penetrate the host tissue between cells, or inside a matrix, but do not reside inside host cells. Mycorrhizae are symbiotic endobionts.

350L = photosynthetic, M = mixotrophic (photosynthesis and phagotrophy), B = phagotrophic on bacteria, C = cytotrophic (phagotrophic on protists), H = heterotrophic. In general, few dinoflagellates nutritional strategy is really investigated, documented, and understood. For most of the taxa we can only indirectly judge and it is more or less a guess. Some genera are difficult to assign because some species are mixotrophic, and for other species we do not know whether they feed in addition to phototrophy. In Amphidinium s.s. for example we have pure heterotrophic but also photosynthetic and mixotrophic species. For these genera there is species level variation in trophic functions. Heterotrophic taxa are the species that have to feed on something, because they are not photosynthetic but we do not know what they feed on (only food bodies or vacuoles are visible but the content cannot be identified and the feeding process has not been recorded).

351All genera feed on bacteria by filtration (B) except where noted. Omnivorous genera (O) ingest small protists in addition to bacteria. Those that are labelled cytrophic (C) need to ingest protists for growth, in addition to bacteria that are co‐ingested. Many omnivores can occasionally ingest detritus (D). Those that feed on fungi (F) do so by digesting a small hole, while those that feed on other filaments (f) (Cyanobacteria and algae) do so by swallowing. Predators (P) are distinguished from those that obtain their food particles by filtration (the default state in ciliophores) or by grazing where noted. Histophagous genera (P*) are distinguished from parasites (X) and commensals (*). Osmotrophic (S) genera feed extensively, or exclusively, by pinocytosis and other membrane transport mechanisms.

352Protist names and common names for East Asian translations