DNA barcoding as a tool for identification of plasmodia and sclerotia of myxomycetes (Myxogastria) appearing in moist chamber cultures

Abstract

Moist chamber culture experiments are one of the basic methods of detection of myxomycete diversity that is usually employed to complement field datasets based on fruit bodies (sporocarps). However, often a large fraction of plasmodia that appear in moist chamber cultures does not yield sporocarps that can be determined to species based on morphological traits. Instead, plasmodia convert to a dormant stage called sclerotium. Both structures essentially lack taxonomically valuable morphological characters, preventing assignment to a species. Here we report the results of application of DNA barcoding as a method of taxonomical identification of plasmodia and sclerotia that develop in moist chamber cultures. The first ca. 600 bp of 18S rRNA gene were successfully amplified for 38 sclerotium and 32 plasmodium samples. Comparison to a large collection of reference sequences and phylogenetic analysis allowed identifying sequences up to species (45), genus (15) or order (10) following several formal criteria. Additionally four partial EF1A gene sequences were obtained, demonstrating that single-copy nuclear genes can also be easily amplified from plasmodia and sclerotia. The outlined methodology could facilitate future studies of myxomycete diversity and ecology based on moist chamber cultures, effectively increasing diversity estimates.

Documenting the first records of myxomycetes on rice litter of Cotabato, Southern Mindanao, Philippines

“…Application of organic fetilizers has the potential to increase bacterivorous and other phagotrophic protists (Xiong et al 2017). Although at this point it would be difficult to conclude if farming practices directly affect the propensity of fructification of other species of myxomycetes, applying for example barcoding approach for species identification of plasmodia (Shchepin et al 2017) that appear in moist chambers or the more sophisticated eDNA analysis method (Shchepin et al 2019) for litter and soil samples would help disentangle these speculations.…”

Quick n’ Cheap – a simplified workflow to barcode plasmodial slime molds(Myxomycetes)

“…This makes it easy to collect spores immediately after a survey before the specimens are fully dried out and eventually shed spores, reducing the risk of cross-contamination between specimens. With some modifications, this protocol should as well work for plasmodia emerging from moist chamber cultures (Shchepin et al 2017).…”

Occurrence of leaf litter inhabiting myxomycetes from lowland forest patches of Northern and Central Vietnam

“…However, with the many modern molecular approach applied nowadays to many biodiversity studies in other organisms such as in birds (Quek et al 2018) or plants (Xu et al 2018), applying it to myxomycetes particularly in Vietnam will help disentangle the real hidden diversity of myxomycetes (Shchepin et al 2019). Similar with other studies that merges barcoding techniques (Feng and Schnittler 2017;Shchepin et al 2017;Schnittler et al 2017b) or species distribution modelling (Almadrones-Reyes and Dagamac 2018) with field surveys, it would be such a promising feat for myxomycete diversity in Vietnam to incorporate these modern ecological tools. Nonetheless, this research study is the first step in understanding the complex myxomycete ecology in particular the leaf inhabiting myxomycetes.…”