Muscarella, M. | Search bioRxiv

bioRxiv2019

Dormancy dampens the microbial distance-decay relationship

Much of Earths biodiversity has the capacity to engage in dormancy whereby individuals enter a reversible state of reduced metabolic activity. By increasing resilience to unfavorable conditions, dormancy leads to the accumulation of \"seed banks\" that should diminish the influence of environmental filtering, while allowing passive dispersers to colonize new habitats. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biodiversity and biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) using 16S rRNA sequencing to characterize the total (DNA) and the active (RNA) bacterial communities in a regional survey of 49 forested ponds. As expected, the total community harbored greater diversity and exhibited weaker DDRs than the active portion of the community. These empirical observations were robust to different measures of community similarity and random resampling tests. Furthermore, findings from the field survey were reproduced by models that included aspects of dormancy along with the geographical coordinates and environmental characteristics of our study system. In addition to maintaining local diversity, our results support recent theoretical predictions that dormancy shapes geographical patterns of biodiversity.

microbiology↗

bioRxiv2019

Moving microbes: the dynamics of transient microbial residence on human skin

The human skin microbiome interacts intimately with human health, yet the drivers of skin microbiome composition and diversity are not well-understood. The composition of the skin microbiome has been characterized as both highly variable and relatively stable, depending on the time scale under consideration, and it is not clear what role contact with environmental sources of microbes plays in this variability. We experimentally mimicked human skin contact with two common environmental sources of microorganisms -- soils and plant leaves -- and characterized the dynamics of microbial acquisition and persistence on skin on very short time scales. Repeatable changes in skin community composition following encounters with environmental sources were observed, and these trajectories largely depend on donor community biomass distributions. Changes in composition persisted for at least 24 hours and through a soap and water wash following exposures to relatively high biomass soil communities. In contrast, exposures to lower biomass leaf communities were undetectable after a 24 hour period. Absolute abundances of bacterial taxa in source communities predicted transmission probabilities and residence times, independent of phylogenetic considerations. Our results suggest that variability in the composition of the skin microbiome can be driven by transient encounters with common environmental sources, and that these relatively transient effects can persist when the source is of sufficient biomass.\n\nImportanceHumans come into contact with environmental sources of microbes, such as soil or plants, constantly. Those microbial exposures have been linked to health through training and modulation of the immune system. While much is known about the human skin microbiome, the short term dynamics after a contact event, such as touching soil, have not been well characterized. In this study, we examine what happens after such a contact event, describing trends in microbial transmission to and persistence on the skin. Additionally, we use computational sampling model simulations to interrogate null expectations for these kinds of experiments. This work has broad implications for infection control strategies and therapeutic techniques that rely on modification of the microbiome, such as probiotics and faecal transplantation.

microbiology↗