INTRODUCTION TO THE PROTAMOEBA

The most obvious feature of these taxa is the pseudopod, a cytoplasmic extension of the naked cell. With the pseudopd, they are able to move about over a substrate and capture food particles (bacteria, eukaryotes, or detritus). The protamebans are amoeboid organisms that produce lobose (text with tooltip) Lobose (adj.) usually refers to the rounded shape of certain pseudopods. (rather than filose) pseudopodia (text with tooltip) A pseudopod (pseudopodium, sing; pseudopodia, pl) is an extension of a naked cell (no wall, pellicle, etc.) that is ephemeral and used for feeding or locomotion. , and the phylum has three main groups of amoebae depending on the overall form of the lobopod. The pseudopodia may be tubular (Figure 1), or spatuate (Figures 2 and 3). They may also produce subpseudopodia (pseudopodia on pseudopodia; Figure 4) and blunt with many subpseudopodia, sometimes branched (Figure 6). Cells may be monopodial (those that elaborate only one pseudopodium at a time) or polypodial (those that elaborate more than one pseudopodium at a time). Typically, the cytoplasm is distinctly partitioned between external, non-granular ectoplasm and an internal, granular endoplasm.

Lobosea, a group treated as a class in this system, forms tubular pseudopodia and includes the common Amoeba (Figure 1) and many other naked, lobose taxa. Amoeba, a polypodial taxon, extends pseudopodia in any direction from the main part of the cell. Usually, one pseudopodium becomes dominant for a time and the cell flows into it. When the cell encounters food (this could be bacteria, other protists, or small animals in the case of large cells like Amoeba), more than one of the pseudopodia embrace the food item and engulf it forming a food vacuole. Some of the loboseans produce tests from which the pseudopodia emerge through a single hole. The tests may be organic (e.g. Arcella, Figure 6) or a layer of cemented sand grains and sediment particles (e.g. Difflugia, Figure 6). Such testate (text with tooltip) A test is an external covering that is secreted or constructed by secretions from the cell. I distinguish it from a cell wall in that a test is not appressed to the plasmalemma. In fact, sometimes the cell can leave the test entirely. forms are among the most obvious amoebae in freshwater ponds and lakes, particularly from areas with much aquatic vegetation.

Discosea has cells that are strongly dorsoventrally flattened and typically produces one broad pseudopodium at the leading edge of the cell. The cells may have various types of coverings such as glycostyles (separate organic structures that cover and emerge from the cell surface), scales, and a glycocalyx of amorphous organic material (Cavalier-Smith et al. 2004). Thecamoeba (Figure 2), a relatively large (30-350μm long) and common genus in freshwater, soil, and marine environments, has an obvious glycocalyx with dorsal ridges on the cell. It travels by a broad spatulate pseudopodium. Typically these taxa are solitary feeders, but Dykova et al. (2008) report isolating and culturing a Thecamoeba for a marine fish that had a symbiotic Labyrinthula living inside of it. Mayorella (3), also a cell with discoid pseudopodia, also has small, blunt, finger-like subpseudopodia on the main pseudopod (see Figure 3).

Variosa includes a collection of taxa that may not be related. Indeed, some of them are very different from other members of this phylum. For example, Acanthamoeba (Figure 4) produces subpseudopodia, some of which are drawn into pointed, almost filopodial shapes. Furthermore, Acanthamoeba produces cysts. This genus is particularly interesting in that it is a very common member of almost all habitats with a film of water, and though typically bacterivorous, they will consume almost anything organic. In this way, they are important adventitious pathogens of humans where they may inhabit the cornea of the eye or make their way through the olfacory lobes to infect the central nervous system.

FIGURE 1. Amoeba in a stained preparation shows the tubular pseudopodia and large nucleus. Image from The Systematic Biology Biodiversity Archive	FIGURE 2. Thecamoeba usually makes a broad spatulate pseudopodium and wrinkles on the dorsal surface of the cell. Image from http://microscope.mbl.edu/baypaul/microscope/images/	FIGURE 3. Mayorella is flattened in contact with a substrate. Usually with finger-like subpsueudopodia. Image from http://microscope.mbl.edu/baypaul/microscope/images/
FIGURE 4. Acanthamoeba can make thin pseudopodia (not filopodia or actinopods) that are flexible and blunt. This genus, most often found as a common amoeba in water and soil, is a trophozoite that can be an adventitious pathogen growing in the cornea of the human eye or in the central nervous system. Image from http://www.dpd.cdc.gov/dpdx/	FIGURE 5. Arcella is an amoeba that produces an organic test. Note the tubular pseudopodia emerging from the margin of the test which is much wider than high. Image from http://microscope.mbl.edu/baypaul/microscope/images/	FIGURE 6. Difflugia is similar to Arcella but makes a test that is covered with silt, sand, and other ambient mineral structures. The test is much higher than wide. This species has horns on the top of the test. Image from http://www.pref.shiga.jp/biwako/plankton/gazou3/043_mini.jpg

SYSTEMATICS OF THE PROTAMOEBA

As it is defined, the Phylum Protamoeba (a group also referred to as Lobosa) is a modification of Cavalier-Smith (2003), Cavalier-Smith et al. (2004), and Kudryavtsev et al. (2005) and roughly is derived from the Rhizopoda of Margulis and Schwartz (1988 and 1998) and Schuster (1990). Margulis and Schwartz (1988 and 1998) claim that the rhizopods never had flagella and are not related to the phyla that possess flagella. Earlier systems separated the testate amoebae from other lobose forms (e.g. Bovee 1985). Such early systems took the approach that the amoeboid taxa were part of a large large phylum called Sarcomastigophora within the superclass Rhizopodea, a taxon which also includes the forams and slime molds (e.g. Kudo 1966, Grell 1973, Jeon 1973, and Sleigh et al. 1984).

This phylum has support (see Figure 7), but the monophyly of the phylum has been called into question. Adl et al. (2005 and 2012), Smirnov et al. (2004 and 2005), Pawlowski and Burki (2009), Fiore-Donno et al. (2011), and Lahr et al. (2011) call into question the monophyly of Lobosea + Discosea. Many of the analyses still have weak support, especially at the bases of the trees. Furthermore, almost all analyses have been done using SSU genes. Until there is good genomic analysis, we are reluctant to make a significant change.

The greatest problem with this phylum is nomenclatural. Many names have been proposed since 1995 (e.g. Rhizopoda, Tubulinea, Amoebozoa, and Lobosa) and are used in the current literature, a lamentation by many authors (e.g. Pawlowski 2008, Pawlowski and Burki 2009). We have chosen to use Protamoeba because it has a full diagnosis (Cavalier-Smith et al. 2004) at the beginning of the period of nomencaltural inflation.

FIGURE 7. A cladogram showing the relationships between classes of the Protamoeba (taxa in the shaded box). The topology is supported by Cavalier-Smith et al. (2004) and Kudryavtsev et al. (2005).