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Guide to the Methods of Study and Identification of Soil Gymnamoebae

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Guide to the Methods of Study and Identification of Soil Gymnamoebae Protistology 3 (3), 148190 (2004) Protistology Guide to the methods of study and identification of soil gymnamoebae Alexey V. Smirnov1 and Susan Brown2 1 Department of Invertebrate Zoology, Faculty of Biology and Soil Sciences, St.Petersburg State University, Russia 2 CEH Dorset, Dorchester, UK Summary The present guide is an attempt to build a “bridge” between the general textbooks on protozoa and the guides to amoebae intended for specialists. We try to outline the subset of freshwater amoebae species that may be found in the soil and list them in the text. The extended introduction section provides detailed descriptions of the methods and shortcomings of amoeba investigation and gives one some ideas on the peculiarities, biology and ecology of soil amoebae. Special section guides the reader through the identification process to prevent him from potential errors. From our experience, dichotomous keys to amoebae are rather artificial and difficult in use, so this guide is based on a classification system of amoeba morphotypes, i.e. on the classification of the generalized shapes of the locomotive form of an amoeba. It allows easy and fast initial classification of an amoeba into one of 16 groups of species containing from two to twentyfive species. The section dedicated to each morphotype contains the sample plate of photographs and the list of relevant literature for further identification of species of the chosen morphotype. Key words: gymnamoebae, amoeba, systematics, identification, methods, guide Foreword morphological and ultrastructural data) requires establishment of cultures and both light (LM) and Amoeboid protists are among the most common electron (EM) microscopy examination, and is highly and abundant microbes in all types of soil habitats. They dependent on the carefulness and experience of the can be isolated easily using relatively simple methods investigator. Many species are poorly or insufficiently and most soil samples yield dozens of amoeba species. described and correct identification of such amoebae However, identification of most species is a difficult and requires detailed analysis of the literature, including challenging task and, in many cases, cannot be older reports. Consequently, amoebae remain beyond conclusive. Identification of amoebae (based on the scope of attention of most soil biologists. © 2004 by Russia, Protistology Protistology · 149 There are several comprehensive keys to marine, common set of methods and which require similar freshwater and soil amoebae, by Bovee and Sawyer approaches to their observation and study. These are (1979), Bovee (1985) and Page (1976a, 1983, 1988, the lobose gymnamoebae (class Lobosea, subclass 1991). They are intended principally for researchers Gymnamoebia), and the class Heterolobosea, which who are already familiar with amoeboid protists and includes the schizopirenids and acrasids, in accordance with LM and EM methods. Usage of these keys by a with the classification scheme of Page (1987). We also beginner results in numerous errors and misidentifications. include the order Himatismenida – a group of lobose On the other hand, textbooks on protozoa do not contain amoebae of unclear systematic affinity that are very sufficiently detailed information on amoeboid protists common in soils and frequently isolated together with to enable a reader to become familiar with this group. gymnamoebae. All other naked amoeboid protists are The section dedicated to Gymnamoebia published in beyond the scope of this guide, although the reader may the new Illustrated Guide to the Protozoa (Rogerson find them occasionally in his soil samples. and Patterson, 2000) is a very useful source of data and amoebae images, but it does not represent a detailed 1.2. SYSTEMATICS OF NAKED AMOEBAE key for the practical identification of species. There is an urgent need for an “intermediate” guide, and the There is a general consensus that the term “amo present text is an attempt to build a “bridge” between eba” embodies a type of organisation of the cell rather the textbooks on protozoa and the guides to amoebae than a solid taxon or monophyletic group of organisms by E.C. Bovee, T.K. Sawyer and F.C. Page. (e.g. Schaeffer, 1926; Page, 1987). Attempts to Soil amoebae have never been made the subject of construct morphologybased systematics of amoebae separate guide or key. F.C. Page reasonably considers using LM data (Schaeffer, 1926; Jahn and Bovee, 1965; most of them to form a subset of the freshwater amoebae Bovee and Jahn, 1965; 1966; Jahn et al., 1974; Page, fauna (Page, 1976a, 1988, 1991). In this publication 1976a) lead to the conclusion that morphology presents we try to outline this subset of amoebae more clearly. insufficient features for reliable species differentiation The present text has been designed to provide the reader and recognition. Use of other characteristics, like the with basic knowledge of the methods and shortcomings nuclear division patterns (Singh, 1955a; Singh et al., of amoeba investigation, together with some ideas on 1982) also generated more theoretical, rather than the peculiarities, biology and the ecology of soil practical, schemes. The implementation of EM amoebae, and to guide him though the identification techniques allowed resolution of ultrastructural details process so that he will be better able to understand the which, when combined with morphological and keys and other relevant literature. biological characteristics, lead to the development of a The greatest difficulty for beginners concerns the more elaborate system for gymnamoebae (Page, 1987), generic identification of amoebae and the use of and enabled species to be identified with a higher degree dichotomous keys, which are rather artificial in the case of confidence (Page, 1988, 1991). More recently, from of these organisms. To avoid this problem, this guide is the fruits of molecular biology research, it has been based on a classification system of amoeba morphotypes concluded that in some taxa even the resolution (Smirnov and Goodkov, 1999a) based on the shapes of provided by Page’s system is insufficient (e.g. De the locomotive form. We hope that this morphotype Jonckheere, 1998; Brown and De Jonckheere, 1999), system represents a more recognisable and clearer and nonmorphological data are required to distinguish structuring of amoebae diversity than a dichotomous isolates, especially among heteroloboseans. Other key. molecular studies have confirmed many of Page’s groupings of amoeboid taxa and cast doubt on others; 1. Introduction we now know for certain that gymnamoebae do not form a single, monophyletic group, as in trees based on 1.1. WHAT ARE “NAKED AMOEBAE”? THE SCOPE OF THIS both ribosomal DNA and actin sequence comparisons, GUIDE naked amoebae are divided between at least three large clades (as well as several independent lineages) that are Within the field of protozoan ecology naked not reflected in the higher levels of the morphology amoebae (or “gymnamoebae”) are generally considered based classification of amoebae (AmaralZettler et al., as a single “functional group”, despite the fact that they 2000; Bolivar et al., 2001; Peglar et al., 2003). However, are highly diverse and systematically heterogeneous. In most of the morphologically defined lower level taxa this guide we decided to restrict the terms “naked from Page’s system, like genera and even some families amoebae” (and “gymnamoebae”) to two groups of of amoebae, can be recognised as clusters in the protists that are isolated from the environment using a molecular trees (Fahrni et al., 2003). 150 · Alexey V. Smirnov and Susan Brown It is evident that a comprehensive, natural system Class Lobosea Carpenter 1861 of amoeboid protists is goal for the future. However, Subclass Gymnamoebia Haeckel 1866 Page’s system of gymnamoebae is still the most popular Order Euamoebida Lepsi 1960 and useful for practical studies. It is a “classification” 1. Family Amoebidae (Ehrenberg 1838) Page 1987 (an artificial system allowing the construction of keys Genera: Amoeba, Chaos, Polychaos, Parachaos, and species identification, but not promising to reflect Trichamoeba, Hydramoeba, Deuteramoeba the phylogenetic relationships between all included 2. Family Thecamoebidae (Schaeffer 1926) Smirnov taxa), designed for wide application across the field of and Goodkov 1994 protozoan research and both to facilitate the study of Genera: Thecamoeba, Sappinia, Dermamoeba, gymnamoebae morphological diversity and to diffe Paradermamoeba, Pseudothecamoeba, Parvamoeba, rentiate between species. Consequently, the classi Thecochaos fication of gymnamoebae used in this guide (listed 3. Family Hartmannellidae (Volkonsky 1931) Page below) is based on that of Page (1987). All freeliving 1974 genera, including marine, are listed here, as there is a Genera: Hartmannella, Saccamoeba, Cashia, Glae need for an uptodate checklist of taxa which includes seria, Nolandella “postPage” modifications and additions. 4. Family Paramoebidae (Poche 1913) Page 1987 The present checklist lists only “wellrecognised” Genera: Mayorella, Korotnevella, Paramoeba genera, which we define as follows: 5. Family Vexilliferidae (Page 1987) a) The genus was correctly established (or revised) Genera: Vexillifera, Pseudoparamoeba, Neopar with an appropriate diagnosis following the basic rules amoeba of taxonomical nomenclature listed in the current edition 6. Family Vannellidae (Bovee 1970) Page 1987 of the International Code of Zoological Nomenclature. Genera: Vannella, Platyamoeba,
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