A Deep Hidden Diversity of Dictyostelia

Characterization of the bacterial microbiomes of social amoebae and exploration of the roles of host and environment on microbiome composition

“…In this study, we cultured amoebae with only their natural soil substrate as a bacterial food source, but it is unknown how culturing social amoebae in the laboratory affects the amoeba microbiome. Furthermore, many species of social amoeba are not easily cultured in the laboratory (Baldauf et al ., 2018), and it is possible that culturable amoebae have different microbiomes than unculturable amoebae. It is also possible that unculturable amoebae carry culturable bacteria that become part of the microbiomes of other amoebae after cultivation.…”

“…Prior to sending samples for next‐generation sequencing, a subset of extracted DNA from the amoeba samples was amplified with PCR using dictyostelid specific primers (18S‐D307F, 18S‐D862R Baldauf et al ., 2018) and sent to Eurofins Genomics (Louisville, KY, USA) for Sanger sequencing. Sequences were cleaned with the program Geneious v10 (https://itol.embl.de/) and used to confirm amoeba species identity with the NCBI Blast database.…”

“…Social amoebae are a 600 million year‐old monophyletic group of amoebae found ubiquitously in soil of all latitudes (Cavender and Raper, 1965; Fiz‐Palacios et al ., 2013). Like other amoebae, they are phagocytic predators of bacteria (Baldauf et al ., 2018). However, they have a unique life cycle that consists of a unicellular trophic stage when food is abundant followed by aggregation into a multicellular slug when starved.…”

Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids

“…When food is depleted, the amoeba can aggregate and together differentiate into a multicellular slug-like organism that eventually transforms into a multicellular fruiting body. So far, more than 150 species have been discovered and described (Baldauf et al, 2018). Of the known dictyostelids, Dictyostelium discoideum is the only well-studied species and is used as a model microorganism for various biological processes, including autophagy (Calvo-Garrido et al, 2010;Mesquita et al, 2017), phagocytosis (Vogel et al, 1980;Bozzaro and Eichinger, 2011), cell signaling (Devreotes, 1989), and chemotaxis (Gerisch, 1982;King and Insall, 2009).…”

“…Of the known dictyostelids, Dictyostelium discoideum is the only well-studied species and is used as a model microorganism for various biological processes, including autophagy (Calvo-Garrido et al, 2010;Mesquita et al, 2017), phagocytosis (Vogel et al, 1980;Bozzaro and Eichinger, 2011), cell signaling (Devreotes, 1989), and chemotaxis (Gerisch, 1982;King and Insall, 2009). The first species was described in the 1800s; since then, they have been continuously discovered especially from nutrient-rich habitats, which were believed to have large species diversity (Baldauf et al, 2018). However, more recently, soil samples from poor habitats have also shown a large diversity of dictyostelids (Landolt et al, 2006).…”