Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

Abstract

BackgroundAcanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses.ResultsHere we show using a phylogenomic approach that the Acanthamoebidae is a fully supported monophyletic group within Amoebozoa with both ML and Bayesian analyses. We also expand the known range of morphological and life cycle diversity found in the Acanthamoebidae by demonstrating that the amoebozoans “Protostelium” arachisporum, Dracoamoeba jormungandri n. g. n. sp., and Vacuolamoeba acanthoformis n.g. n.sp., belong within the group. We also found that “Protostelium” pyriformis is clearly a species of Acanthamoeba making it the first reported sporocarpic member of the genus, that is, an amoeba that individually forms a walled, dormant propagule elevated by a non-cellular stalk. Our phylogenetic analyses recover a fully supported Acanthamoebidae composed of five genera. Two of these genera (Acanthamoeba and Luapeleameoba) have members that are sporocarpic.ConclusionsOur results provide high statistical support for an Acanthamoebidae that is composed of five distinct genera. This study increases the known morphological diversity of this group and shows that species of Acanthamoeba can include spore-bearing stages. This further illustrates the widespread nature of spore-bearing stages across the tree of Amoebozoa.ReviewersThis article was reviewed by Drs. Eugene Koonin, Purificacion Lopez-Garcia and Sandra Baldauf. Sandra Baldauf was nominated by Purificacion Lopez-Garcia, an Editorial Board member.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0171-0) contains supplementary material, which is available to authorized users.

Variation in the SSUrDNA of the Genus Protostelium Leads to a New Phylogenetic Understanding of the Genus and of the Species Concept for Protostelium mycophaga (Protosteliida, Amoebozoa)

“…Both are now considered to be in the group Centramoebida with P. pyriformis moved to Acanthamoeba pyriformis and P. arachisporum to Luapeleamoeba arachisporum (Tice et al. ). Spiegel et al.…”

“…Two other nominal members of the genus, P. pyriformis and P. arachisporum, have had their affinity to the genus Protostelium called into question (Best 1984;Spiegel 1990;Spiegel et al 1994). Both are now considered to be in the group Centramoebida with P. pyriformis moved to Acanthamoeba pyriformis and P. arachisporum to Luapeleamoeba arachisporum (Tice et al 2016). Spiegel et al (1994) emended the description of the genus Protostelium to include only those organisms with nonflagellate amoebae that are typically uninucleate, containing orange pigmented lipid droplets, lamellate pseudopodia with fine, acutely pointed subpseudopodia ( Fig.…”

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

“…() and Tekle and Wood () for an isolate that is a distinct genus named Dracoamoeba (see Tice et al. ). To date, no molecular data on a true Stereomyxa are available and thus it remains incertae sedis . …”

An efficient single-cell transcriptomics workflow to assess protist diversity and lifestyle

“…Because of this improvement and since we expect that many protists are harder to lyse than the mammalian cells used to optimized Smart-seq2, we suggest that freeze-thaw cycles should be used when generating protist transcriptomes from single-cell input. Because our experience is that the freeze-thaw cycles can be necessary to get a successful cDNA library [14], we have used freeze-thaw in all of our modifications of the Smart-seq2 protocol.…”

“…Also for cells with low RNA content, there can be a problem with unspecific amplification due to changed balance between the concentration of oligos and mRNA of the cell [13]. The potential problem with lysis is addressed by using freeze-thaw cycles in -80 °C chilled isopropanol, which previously have been reported as a successful lysis procedure [14,15]. Besides the improved lysis we already know can be crucial, we test modifications of Smart-seq2 that could make the protocol more cost-efficient or reduce the generation of artifacts during cDNA synthesis.…”