VERMAMOEBA VERMIFORMIS (updated July 2021)
Among the various groups of small free-living amoebae, forms that have been classified as being members of the genus Hartmannella, or might be closely related to Hartmannella, are numerous. The first description of amoebae classified as Hartmannella (specifically a form designated Hartmannella hyalina ) was made by Dangeard, (1900). Subsequently, a number of other simple limax amoebae(*) have often been characterized as members of Hartmannella. Thus Alexeieff (1912), Volkonsky (1931) and Singh (1952), and others, described a variety of forms under names attributed to the genus. Various revisions were made which excluded some taxa, but the genus remained a grab-bag of small amoebae. Page (1967) reconsidered these small limax amoebae and concluded that they represented several genera. The amoebae now classified within Naegleria, Acanthamoeba and Valkampfia were all originally thought to be species within Hartmannella.
Molecular information has greatly facilitated our understanding of the phylogenetic relationships of the small limax amoebae. Phylogenetic analyses continue, and genomic data is likely to become increasingly important in revealing subtle relationships between forms that are difficult to separate morphologically. Among the molecular findings of this millennium has been the observation that one of the most commonly encountered species of “Hartmannella” was not in fact closely related, genetically, to other forms classified with the genus. Smirnov et al. (2005) reexamined the classification of the naked amoebae and showed that the species Hartmanella vermiformis did not group with other members of the genus. In a subsequent reclassification of the naked lobose amoebae (Smirnov et al. 2011), the genus Vermamoeba (Vermamoeba Cavalier-Smith and Smirnov gen. n.) was proposed, encompassing the isolates that had previously been placed within “Hartmannella” vermiformis. Under this model, Vermamoeba would no longer be considered part of the Family Hartmannellidae.
This reclassification of Vermamoeba (formerly Hartmannella) vermiformis is very significant because isolates of this taxon have been identified as important vectors of pathogenic bacteria such as Legionella. They also appear to be among the most common amoebae identified in environmental surveys that use ribosomal RNA to identify microbial components of an ecosystem. In fact they occur more frequently in such surveys than do members of Acanthamoeba. (Note: there are technical issues with the use of rRNA for the indirect study of environmental samples without culturing that may lead to an underestimation of the frequency of Acanthamoeba in a sample, compared to Vermamoeba. The number of cloned rRNA gene sequences in environmental studies do not have a 1:1 correspondence with numbers of sequences that are deposited in the databases from cultured samples).
MOLECULAR STUDIES ON HARTMANNELLA/VERMAMOEBA
The first 18S rRNA sequence from Vermamoeba (=Hartmannella) vermiformis was provided by Gunderson, Goss and Sogin (1994). Peter Weekers, working in the Byers/Fuerst lab, quickly provided the first population study (Weeker, Gast, Fuerst and Byers, 1994), which showed that isolates of V. (=Hartmannella) vermiformis were very similar genetically for the 18S rRNA gene, showing greater than 99.5% sequence similarity, while differing from Acanthamoeba by almost 20%.
Unlike the situation in Acanthamoeba, in V. vermiformis almost all of the phylogenetically useful information has been obtained using only the 18S rRNA gene. Over 80% of sequences in the DNA databases that are labeled as V. vermiformis or H. vermiformis are from the nuclear 18S rRNA. The only mitochondrial 16S-like rRNA sequences are from the complete DNA sequence of the mitochondrial genomes of ATCC 50236 and isolate strain BCP-EM3VF21-1.
Nevertheless, considerable information has been gathered about variation in V. vermiformis using the nuclear 18S rRNA. One difference that contrasts study of the 18S rRNA gene in Acanthamoeba and that in V. vermiformis concerns the structure of the gene in Vermamoeba. Unlike Acanthamoeba, Vermamoeba does not possess any obvious hypervariable segments. Consequently, the degree of divergence in Vermamoeba (which is less than 1% for most pairwise comparisons) cannot be considered to reflect the same evolutionary time axis as an equivalent <1% divergence of 18S rRNA gene sequence between isolates of Acanthamoeba. Equal values are expected to represent greater divergence times for Vermamoeba than for Acanthamoeba, possibly much greater times. Nevertheless, studies using the 18S rRNA gene have produced significant information about the structure of the global population of V. vermiformis.
DNA DATABASE INFORMATION ON V. VERMIFORMIS
Since the initial sequences were obtained by the Byers/Fuerst and the Sogin labs in 1994, more than 930 800 full or partial sequences of the 18S rRNA gene have been deposited in the DNA databases. Details are provided on the accompanying page. Information concerning genetic variation and geographic distribution of allelic types within V. vermiformis is provided on a second page. While the bulk of the DNA sequences come from cultured isolates, the remainder (~375) were obtained as taxonomically unidentified sequences from environmental surveys of uncultured eukaryotic microorganisms. The increasing importance to our knowledge of Vermamoeba that derives from studies of uncultured eukaryotes will be discussed elsewhere on this site .
SEQUENCES FROM OTHER MEMBERS OF “HARTMANNELLA“
A small number of additional 18S rRNA gene sequences from taxa which have been classified into the genus Hartmannella have been deposited in the DNA databases. These mostly represent “species” that have remained within the classical definition of Hartmannella. However, some may represent forms that could be considered to be putative members of other (possibly undescribed) genera. The sequences of the 18S rRNA genes from these isolates share sequence similarity of less than 85% with the sequences attributed to V. vermiformis.
Specifically, at least 4 sequences exist that have been obtained from isolates that group with the sequence of “H.” cantabrigiensis, and are likely to be members of the Amebozoan genus Copromyxa. They show less than 80% sequence similarity with the sequences of V. vermiformis.
At least two sequences have been obtained that are assigned to the taxa “H.” abertawensis. These isolates appear to belong to the genus Nolandella. These isolates show less than 85% sequence similarity to sequences of V. vermiformis.
As a result of these last two groups being reclassified, we may be in a position that no current 18S rRNA gene sequence can be attributed to an organism that is identified unambiguously with the genus Hartmannella.
(*) – the term “limax” amoebae is used as a broad reference to small naked free-living amoebae. (“limax” is a reference to the general shape of the organism as resembling a slug, alluding to the slug genus Limax). In the original sense, “limax amoebae” includes forms now in a genetically heterogenous group including Echinamoeba, Naegleria, Acanthamoeba, Hartmanella, Vermamoeba and other genera.