How do wild microbes adapt to the environment?

• To understand the origin and diversification of microbial life, we use a combination of experiments, natural history, genetics, and population genomics. Bacteria thrive in extreme environments that require them to tolerate stresses ranging from toxic heavy metals in the environment to assault from host immune systems in symbiosis with host organisms. The genetic basis of bacterial adaptation to such diverse environments is largely undescribed in natural systems, yet this information is critical for understanding the generation and functional significance of bacterial diversity.
• Diversity persists if the genes or traits that underlie adaptation to one environment diminish fitness in another environment. This fitness tradeoff can promote niche specialization and prevent competitive exclusion. However, bacteria have modular, fluid genomes—adaptive genes are rapidly horizontally transmitted between strains. This can allow adaptive variants to assort across environmental gradients without the constraints that limit both allelic substitution and exploration of the adaptive landscape in macro-organisms. Whether trade-offs are critical to the generation and maintenance of microbial diversity remains a frontier in Evolutionary Biology.
• We aim to link the genomic, physiological, and ecological bases of local adaptation to heavy metal enriched serpentine soils in several clades of wild symbiotic Mesorhizobium bacteria. We have identified candidate genes for heavy metal adaptation in wild Mesorhizobium bacteria are leveraging association mapping and molecular genetic approaches to dissect the genetic basis of heavy metal adaptation. These Mesorhizobium symbiotically fixing nitrogen for native legume species and our system serves as an emerging bacterial model of adaptation that will lead to innovative strategies to incorporate metal-adapted soil microbiota in bioremediation of heavy metal contaminated soils.

How do microbial symbionts affect biological invasions? 

• Invasive species wreak havoc on ecosystems by displacing natives and by altering abiotic conditions. While much is known about the substantial harm invasive plants and animals inflict, we know little about the impacts of the invisible communities of microbial mutualists that co-invade with their hosts or how host-symbiont mutualisms are re-shaped at genomic and ecological levels during biological invasions.
• The legume-rhizobium symbiosis is an ecologically important model mutualism amenable to addressing these fundamental questions. Medicago polymorpha, a noxious legume weed and a relative of alfalfa, has co-invaded North America from Europe with its rhizobial partner, Ensifer medicae.
• These co-invading mutualists have experienced dramatically different population genomic consequences of invasion. While the plant shows substantial reductions in genomic diversity in the invaded range relative to populations in the native range, its symbiont has not experienced a similar bottleneck in genomic diversity during invasion. We find that robust cooperation between the partners is unaltered by the process of invasion, yet the partners show reduced genetic variance in mutualistic traits in the invaded range. Therefore, the mutualism functions similarly in the invaded and native range, but has a lower capacity for cooperation to evolve in the invaded range. We also find that low symbiont abundance in the soil is a key ecological attribute slowing the spread of this noxious weed and that the success of this weed not only depends upon symbiont nitrogen fixation, but also benefits from symbiont mediated protection from soil pathogens.

How do microbiome inocula impact the establishment of conifer seedlings during post-fire reforestation?

• As wildfires become more common and more intense in response to climate change, we must attempt to mitigate the effects of these devastating events on our landscape. After a wildfire, soil microbiota are critical for conifer re-establishment. Depending on the intensity of the fire, soil microbe communities can be greatly altered or diminished at a burned site. Inoculation presents a potential route for improvement of reforestation outcomes. However, predicting inoculum effects on host microbiome development and performance remains a challenge. 
• After testing how emergent properties of inoculum and established root microbiomes predict seedling performance for Grand Fir and a competing shrub in post-wildfire forest soil in the greenhouse. We find that, consistent with strong priority effects, inocula with contrasting wildfire histories conferred benefits, and established microbiomes that were distinct from those of a negative control, even though few of the inoculated taxa persisted after one year. Inocula with higher fungal diversity, and established root microbiomes with more mutualists and greater network complexity, were associated with higher seedling performance.
• We continue to investigate the impacts of post-burn microbiome inoculation through a project in collaboration with the Forest Service, using greenhouse experiments to mimic re-forestation conditions for Douglas fir, a commercially and ecologically important species in the Pacific Northwest.