Rapid PCR-based method for detection and differentiation of Didymiaceae and Physaraceae (myxomycetes) in environmental samples

Kamono, Akiko; Fukui, Manabu

doi:10.1016/j.mimet.2006.05.003

Cited by 27 publications

(11 citation statements)

References 20 publications

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“…Sawyer, not included in this study) thus deserving a better determination for future use. Also, Hyperamoeba SSU rRNA gene sequences have been deposited in GenBank, and confuse the BLAST results when identifying environmental sequences (Kamono and Fukui 2006; Kamono et al 2009a, b; Win Ko Ko et al 2009). To avoid taxonomic and phylogenetic confusion, clarifying the nomenclature of the two taxa for which EST projects are in progress— H. dachnaya , which has been often mis‐spelled as “ dachnya ,” and Hyperamoeba sp.…”

Section: New Names Given To Hyperamoeba Species and Strains Asterismentioning

confidence: 99%

“…To better allocate the Physarida‐related hyperamoebae, a second dataset was made for a SSU rRNA fragment obtained for 10 genera and 95 nominal species of Physarida (Kamono and Fukui 2006; Kamono et al 2009b), along with the truncated Physarida sequences used in the previous alignment, totalling 147 strains. From the 242 short fragments published by Kamono and Fukui (2006) and Kamono et al (2009b), only unique or nearly unique (≤98% similarity) sequences were selected for each taxon. All sequences were manually aligned using BioEdit software version 7.0.5.3 (Hall 1999).…”

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confidence: 99%

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

Fiore-Donno

Kamono

Chao

et al. 2010

J Eukaryotic Microbiology

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The genus Hyperamoeba Alexeieff, 1923 was established to accommodate an aerobic amoeba exhibiting three life stages-amoeba, 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 approximately 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.

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Section: New Names Given To Hyperamoeba Species and Strains Asterismentioning

confidence: 99%

mentioning

confidence: 99%

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

Fiore-Donno

Kamono

Chao

et al. 2010

J Eukaryotic Microbiology

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“…However, the few studies of this type carried out thus far are rather preliminary. Kamono and Fukui (2006) used a short SSU fragment (~460 bp) to investigate the presence of members of Physarales in soil. Later, this same method was applied to samples of leaf litter and decaying wood collected from a forest in northern Thailand (Ko Ko et al 2009), where five species not recorded as field collections were revealed.…”

Section: Beyond Morphologymentioning

confidence: 99%

From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos (1969) monograph

Stephenson

2011

Fungal Diversity

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Myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Because they produce aerial spore-bearing structures that resemble those of certain fungi and also typically occur in some of the same types of ecological situations as fungi, myxomycetes have been traditionally studied by mycologists, and this continued to be the case for the greater part of the twentieth century. However, there is now abundant molecular data to confirm that they are amoebozoans and not fungi. Efforts are currently underway to develop the first molecular phylogeny for myxomycetes, and several recent studies have used molecular techniques to detect the presence of these organisms in nature by means of direct environmental sampling.

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“…To better allocate the Physarida-related hyperamoebae, a second dataset was made for a SSU rRNA fragment obtained for 10 genera and 95 nominal species of Physarida (Kamono and Fukui 2006;Kamono et al 2009b), along with the truncated Physarida sequences used in the previous alignment, totalling 147 strains. From the 242 short fragments published by Kamono and Fukui (2006) and Kamono et al (2009b), only unique or nearly unique ( 98% similarity) sequences were selected for each taxon. All sequences were manually aligned using BioEdit software version 7.0.5.3 (Hall 1999).…”

Section: Methodsmentioning

confidence: 99%

“…Sawyer, not included in this study) thus deserving a better determination for future use. Also, Hyperamoeba SSU rRNA gene sequences have been deposited in GenBank, and confuse the BLAST results when identifying environmental sequences (Kamono and Fukui 2006;Kamono et al 2009a, b;Win Ko Ko et al 2009). To avoid taxonomic and phylogenetic confusion, clarifying the nomenclature of the two taxa for which EST projects are in progress-H. dachnaya, which has been often mis-spelled as ''dachnya,'' and Hyperamoeba sp.…”

mentioning

confidence: 99%

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

Fiore‐Donno¹,

Kamono²,

Chao³

et al. 2017

Preprint

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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.

show abstract

Rapid PCR-based method for detection and differentiation of Didymiaceae and Physaraceae (myxomycetes) in environmental samples

Cited by 27 publications

References 20 publications

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

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

From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos (1969) monograph

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

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