Applying landscape genetics to the microbial world

Abstract

Landscape genetics, which explicitly quantifies landscape effects on gene flow and adaptation, has largely focused on macroorganisms, with little attention given to microorganisms. This is despite overwhelming evidence that microorganisms exhibit spatial genetic structuring in relation to environmental variables. The increasing accessibility of genomic data has opened up the opportunity for landscape genetics to embrace the world of microorganisms, which may be thought of as 'the invisible regulators' of the macroecological world. Recent developments in bioinformatics and increased data accessibility have accelerated our ability to identify microbial taxa and characterize their genetic diversity. However, the influence of the landscape matrix and dynamic environmental factors on microorganism genetic dispersal and adaptation has been little explored. Also, because many microorganisms coinhabit or codisperse with macroorganisms, landscape genomic approaches may improve insights into how micro-and macroorganisms reciprocally interact to create spatial genetic structure. Conducting landscape genetic analyses on microorganisms requires that we accommodate shifts in spatial and temporal scales, presenting new conceptual and methodological challenges not yet explored in 'macro'-landscape genetics. We argue that there is much value to be gained for microbial ecologists from embracing landscape genetic approaches. We provide a case for integrating landscape genetic methods into microecological studies and discuss specific considerations associated with the novel challenges this brings. We anticipate that microorganism landscape genetic studies will provide new insights into both micro-and macroecological processes and expand our knowledge of species' distributions, adaptive mechanisms and species' interactions in changing environments.

An inter-island comparison of Darwin’s finches reveals the impact of habitat, host phylogeny, and island on the gut microbiome

“…The divergence in finch gut microbiome communities we observe across islands highlights the role of dispersal limitation in determining microbial community structure within wild host species (reviewed in [16]). Previous work has shown that geographic distance increased the distance between gut microbiomes in mammalian species, tested in 17 species across the Americas [15].…”

“…The geographic distance provided additional explanatory power compared to the sole interpretation based on phylogenetic distance. Notably, environmental drivers of microbial community composition are increasingly being found with the emergence of novel genomic and spatial analyses [16].…”

Population structure and adaptation of a bacterial pathogen in California grapevines

“…The heterogeneous space or 'landscape' affects microevolutionary dynamics at various scales, leaving genomic signatures that may be identified (Biek and Real, 2010). To date, in this emerging field, Dudaniec and Tesson (2016) noted that little attention has been paid to the linkage between microorganism dispersal and environmental factors, despite evidence of non-random distributions and patterns of isolation by distance (IBD) within populations (Martiny et al, 2006). Because of their high dispersal abilities (Taylor et al, 2006), microbes were long thought to display little genetic biogeographic differentiation.…”

Microbiota acquisition and transmission in Drosophila flies

“… 10 For example, it is often expected that vertically transmitted microorganisms are more likely to have beneficial effects on their hosts than horizontally transmitted ones. 11 , 12 Studying how insects acquire microbial symbionts will therefore better our understanding of the spatiotemporal dynamics of microorganisms among hosts and resource patches 13 and our understanding of the evolution of symbiotic associations. 4 …”