Dimensions US-China: Global Patterns of Biodiversity in the Ancient Ciliate Paramecium

Arizona State University, Scottsdale AZ

Investigators

Abstract

Do microbes exhibit patterns of biogeographic distribution similar to those of multicellular species? One idea is the 'everything is everywhere' hypothesis, which postulates high levels of migration scattering microbial species throughout the globe. Alternatively, environmental factors could be subdividing lineages into locally adapted taxa. This study focuses on a charismatic but poorly studied genus, the ciliate Paramecium, which originated prior to the appearance of vertebrates. These creatures are animal-like in many ways, such as having separate germline and somatic genomes and carrying a bacterial microbiome. Unlike animals, however, all species in this groups are similar in morphology, which simplifies many analyses. The population-genomic studies will reveal the extent to which intra- and interspecific variation is shaped by the population subdivision and migration. The researchers will explore the role of the microbiome in driving phylogenetic and geographic divergence. The study will examine if morphologically cryptic species are also similar in ecological/physiological traits. The combined efforts of two major ciliate labs, one in the US and one in China, will yield a public database of global molecular diversity. Graduate students and postdoctoral fellows will be trained by this research. Overall, this study will provide a wide-ranging exploration of speciation and adaptation in microbes of broad interest to the research community. An understanding of the distribution of biodiversity and its relevance requires information on key population-genetic parameters such as the power of random genetic drift and migration. Combined, these can constrain the development of local adaptations. This study will acquire whole-genome sequences in a worldwide survey of genetic variation within and among populations of 30 Paramecium species and their endocytobionts. Methods from molecular population genetics will yield estimates of global effective population sizes and migration rates for all such species. The temporal and geographic distributions of species will be revealed, and the existence of cryptic species complexes formally established. Classical methods from microbial physiology will estimate key parameters of basal metabolic requirements, growth, and cell size across gradients of temperature and resource availability. This work will be done on a wide range of geographic isolates of all species to determine whether local adaptation has occurred, or if such patterns are consistent with phenotypic-plasticity responses. Study of genotypes with and without endocytobionts will clarify whether such bacteria impose net metabolic losses or gains for their host cells. The resultant data will be organized into web portals to provide users with accessible assemblies and annotations of the genomes of all species, along with the survey of within-species variants found at all genetic loci. Sequenced strains will be cryopreserved in a viable state for use by future researchers. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.