Agarwal, A. | Search bioRxiv

bioRxiv2018

Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software

With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. We generated realistic simulated datasets for popular imaging modalities - 2D, astigmatic 3D, biplane 3D, and double helix 3D - and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.

biophysics↗

bioRxiv2018

Restoring ancestral microbiome aids beetle adaptation to new diets

Eukaryotic hosts often depend on microbes that enhance their fitness, and such relationships may be relatively easily maintained in a stable environment. What is the fate of these associations under rapid environmental change? For instance, if the host switches to a new diet and/or encounters a different microbial community, how does the host-microbiome relationship change? Are the changes adaptive, and how rapidly do they occur? We addressed these questions with the red flour beetle Tribolium castaneum, a generalist insect pest that both consumes and lives in stored grain flour. We found that beetle fitness is enhanced by flour-acquired microbes in the ancestral habitat (wheat flour), but not in novel suboptimal environments (e.g. corn flour) that have a different resident microbial community. Beetles that disperse to new habitats thus have low fitness and a dramatically altered microbiome. Enriching novel habitats with ancestral (wheat-derived) microbes increased beetle fitness, suggesting a viable adaptive strategy. Indeed, within a few generations of laboratory adaptation to two distinct novel habitats, we found that beetle populations gradually restored their ancestral microbiome. Importantly, evolved populations showed a microbe-dependent increase in fecundity and survival on the new diet. We suggest that such repeated, rapid restoration of host-microbe associations may allow generalists to successfully colonize new habitats and escape extinction despite sudden environmental changes.

evolutionary biology↗