Invalidation of Hyperamoeba by Transferring its Species to Other Genera of Myxogastria

Abstract

ABSTRACT. The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stagesamoeba, flagellate, and cyst. As more species/strains were isolated, it became increasingly evident from small subunit (SSU) gene phylogenies and ultrastructure that Hyperamoeba is polyphyletic and its species occupy different positions within the class Myxogastria. To pinpoint Hyperamoeba strains within other myxogastrid genera we aligned numerous myxogastrid sequences: whole small subunit ribosomal (SSU or 18S rRNA) gene for 50 dark-spored (i.e. Stemonitida and Physarida) Myxogastria (including a new ''Hyperamoeba''/ Didymium sequence) and a $ 400-bp SSU fragment for 147 isolates assigned to 10 genera of the order Physarida. Phylogenetic analyses show unambiguously that the type species Hyperamoeba flagellata is a Physarum (Physarum flagellatum comb. nov.) as it nests among other Physarum species as robust sister to Physarum didermoides. Our trees also allow the following allocations: five Hyperamoeba strains to the genus Stemonitis; Hyperamoeba dachnaya, Pseudodidymium cryptomastigophorum, and three other Hyperamoeba strains to the genus Didymium; and two further Hyperamoeba strains to the family Physaridae. We therefore abandon the polyphyletic and redundant genus Hyperamoeba. We discuss the implications for the ecology and evolution of Myxogastria, whose amoeboflagellates are more widespread than previous inventories supposed, being now found in freshwater and even marine environments.

Phylogeny of Physarida (Amoebozoa, Myxogastria) Based on the Small‐Subunit Ribosomal RNA Gene, Redefinition of Physarum pusillum s. str. and Reinstatement of P. gravidum Morgan

“…G1a, previously identified as the now invalidated Hyperamoeba (Fiore‐Donno et al. 2010a); it was obtained from an amoeba isolated from a physiotherapy bath, and no sporophores were observed (Walochnik et al. ); and (iii) named P. roseum (Nandipati et al.…”

“…The partial sequence Physarum pusillum YY‐26614 (TNS) (Fiore‐Donno et al. 2010a; Kamono and Fukui ) matched the sequences of the subglobose form, but was not included in our alignment for being too short.…”

Metatranscriptomic census of active protists in soils

“…Thus, a strongly biased view of the protist community in soils is being depicted as only a subset of its diversity can be recovered (Jeon et al, 2008;Hong et al, 2009), whereas, on the other hand, some taxa within this subset will be overrepresented because of preferential PCR amplification (Berney et al, 2004;Medinger et al, 2010;Stoeck et al, 2014). Taxa of the common supergroup Amoebozoa as one of the dominant soil protists for instance, are notoriously underrepresented in molecular surveys because of long SSU rRNA sequences, frequent mismatches in primer regions and presence of introns (Berney et al, 2004;Fiore-Donno et al, 2010;Pawlowski et al, 2012). Ciliates on the contrary are highly overrepresented because of their shorter SSU rRNA sequences that ease amplification, and the presence of extremely high SSU rRNA gene copy numbers (Gong et al, 2013).…”

Environmental Free-Living Amoebae Can Predate on Diverse Antibiotic-Resistant Human Pathogens

“…Like Tetramitus , this amoebal genus has been isolated from environmental samples but remains poorly described and studied ( 35 , 45 , 46 ). Two amoebae were identified as Stemonitis (formerly Hyperamoeba ), amoebae that are close to slime molds and whose phylogeny has long been a source of debate ( 47 , 48 ). Also, but not displayed in the tree of Fig.…”