High Diversity of Testate Amoebae (Amoebozoa, Arcellinida) Detected by HTS Analyses in a New England Fen using Newly‐designed Taxon‐specific Primers

Testate (shell-building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida-specific primers for the SSU-rDNA gene to assess the community composition on the molecular level in two sample sets from a New England fen: 1) 36 cm horizontal transects and vertical cores; and 2) 26 m horizontal transects fractioned into four size classes (2-10 microm, 10-35 microm, 35-100 microm, 100-300 microm). Analyses of these data show: 1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; 2) communities characterized by DNA (i.e. active + quiescent) are distinct from those characterized by RNA (i.e. active, indicator of biomass); 3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and 4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting possible life history stages. Together these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.