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Microbial Eukaryotic Biodiversity and Biogeography


Biodiversity and biogeographic research in Neotropical forests is also dominated by studies on plants and animals. And our view of the functioning and conservation of these ecosystems is likewise dominated by these macro-organisms. This macrobial focus is primarily due to them being more familiar and readily observable to us. With the advent of high-throughput sequencing (HTS) platforms, though, we are now in a better position to expand this view to include a broader microbial perspective.


We normally think about Neotropical forests communities as teaming with a hyper diverse number of animals and plants, and with species assemblies changing drastically among communities because of extreme levels of endemism. By contrast, we do not know if the less familiar and not readily observable microbial eukaryotic species that inhabit these same ecosystems exhibit similar patterns of biodiversity and biogeography. Although they comprise the bulk of the genetic and metabolic diversity found in eukaryotes, microbial eukaryotes arguably represent the least explored biological aspect of Neotropical forests.


The Microbial Diversity research group aims to explore this microbial eukaryotic diversity in Neotropical rainforest soils. First, though, we have worked on providing a more concrete conceptual background to evaluate HTS by comparing how the resulting short reads compare to previous longer Sanger sequencing reads from distance-based (Dunthorn et al. 2012) and phylogenetic-based (Dunthorn et al. 2014) perspectives. We also developed Swarm, a new clustering algorithm (Mahé et al. 2014). For the forests, we have sampled soils for the past two years in La Selva Biological Station, Costa Rica; Barro Colorado Island, Panama; and Tiputini Biodiversity Station, Ecuador. We are now in the process of sequencing DNA from 600 samples using universal SSU-rDNA V4 primers and Illumina MiSeq.


Putative Asexuality in Microbial Eukaryotes


Our theoretical understanding, and empirical observations, of the maintenance and distribution of meiotic sex within eukaryotes is dominated by research on plants and animals. While there is a cost to sex, almost all macro-organisms are known to be sexual, allowing them to survive changing environments and the eliminate harmful mutations, as well as other evolutionary pressures. If macrobial theory applies to all eukaryotes, most microbial eukaryotes (= protist) should be sexual. This is indeed the case, although the majority of individuals within any population are the result of cell division.


The Microbial Diversity research group is investigating two cases of putative asexuality in the aveolates: Colpodea cilitates, and the dinoflagellate Symbiodinium. Colpodeans form a clade of about 200 described species, and are often found in soils. As the colpodeans are ancient (up to 900 million years old), and the one known sexual species is derived (implying a loss and regain of a complex character), they may be secretively sexual (Dunthorn & Katz 2010). Symbiodinium are ecologically important as symbionts of corals and other marine organisms. We are using a meiotic-gene-inventory approach to evaluate secretive sexuality of these microbial eukaryotes. The presence of these genes suggest that their protein products are being used to construct meiotic machinery during sex, otherwise they would have been lost or inactivated.


To provide a background to what is expected, we first evaluated meiotic genes in four known sexual ciliates using published genomes (Chi et al. 2014, a). We then evaluated these same genes in the published genomes of Symbiodinium, were we found the same suite of meiotic genes, providing evidence that Symbiodinium is secretively sexual (Chi et al. 2014, b). For the colpodeans, we are now using Illumina to sequence the genomes of three species: Bursaria truncatella, the one sexual species; Colpoda magna, commonly found in soils; and Sorogena stoianovitchae, which has a slime-mold like multicellular stage.