Population genetics: the next stop for microbial ecologists?

Abstract

Microbes play key roles in the functioning of the biosphere. Still, our knowledge about their total diversity is very limited. In particular, we lack a clear understanding of the evolutionary dynamics occurring within their populations (i.e. among members of the same biological species). Unlike animals and plants, microbes normally have huge population sizes, high reproductive rates and the potential for unrestricted dispersal. As a consequence, the knowledge of population genetics acquired from studying animals and plants cannot be applied without extensive testing to microbes. Next generation molecular tools, like High Throughput Sequencing (e.g. 454 and Illumina) coupled to Single Cell Genomics, now allow investigating microbial populations at a very fine scale. Such techniques have the potential to shed light on several ecological and evolutionary processes occurring within microbial populations that so far have remained hidden. Furthermore, they may facilitate the identification of microbial species. Eventually, we may find an answer to the question of whether microbes and multicellular organisms follow the same or different rules in their population diversification patterns.

Airborne Microalgae: Insights, Opportunities, and Challenges

“…Genetic characterization can be performed on cultures, single cells, or environmental samples. A step forward is the use of high-throughput sequencing to rapidly assess microalgal diversity of even very rare community members directly from environmental samples ( 125 ). For instance, the v4/v9 regions of the 18S ribosomal DNA are often used in water and soil ( 126 , 127 ) and in aerosol (bacteria and lichens [ 128 ]) samples to assess taxonomic composition and diversity in protists.…”

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

“…Furthermore, FGMT provided insight on how microbial communities structure in space and time, suggesting the existence of cosmopolitan and endemic taxa (Hughes Martiny et al, 2006). FGMT have been used in the limited number of studies that focused in microbial population genetics (Logares, 2011) revealing, for example, large effective population sizes (Snoke et al, 2006) and important amounts of intra-species genetic diversity (Logares et al, 2009). The link between taxonomic identity and metabolic function is another area where FGMT have contributed significantly.…”

Decoding populations in the ocean microbiome

“…Even though microbial population genetics and genomics are growing fields [ 51 , 79 , 80 ], our understanding of mutation , selection , gene flow , and genetic drift is still predominantly based on the study of animals and plants. Comprehending how these processes operate in marine microbes is crucial, as microbes differ from multicellular organisms in at least three fundamental aspects: dispersal , reproductive rates , and population size [ 81 , 82 ]. Even though the dispersal rate of most microbes, including those in marine environments, is still largely unknown, indirect evidence points to high dispersal rates [ 81 , 83 ] that could be substantially higher than in multicellular organisms.…”