Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.

The mountain pine beetle, Dendroctonus ponderosae , is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta , and their more recent host, hybrid P. contorta-Pinus banksiana . We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas , Rahnella , Serratia , and Burkholderia , and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.

Warming climate has increased access of native bark beetles to high-elevation pines that historically received only intermittent exposure to these tree-killing herbivores. Here we show that a dominant, relatively naïve, high-elevation species, whitebark pine, has inferior defenses against mountain pine beetle compared with its historical lower-elevation host, lodgepole pine. Lodgepole pines respond by exuding more resin and accumulating higher concentrations of toxic monoterpenes than whitebark pine, where they co-occur. Furthermore, the chemical composition of whitebark pine appears less able to inhibit the pheromonal communication beetles use to jointly overcome tree defenses. Despite whitebark pine’s inferior defenses, beetles were more likely to attack their historical host in mixed stands. This finding suggests there has been insufficient sustained contact for beetles to alter their complex behavioral mechanisms driving host preference. In no-choice assays, however, beetles readily entered and tunneled in both hosts equally, and in stands containing less lodgepole pine, attacks on whitebark pines increased. High-elevation trees in pure stands may thus be particularly vulnerable to temperature-driven range expansions. Predators and competitors were more attracted to volatiles from herbivores attacking their historical host, further increasing risk in less coevolved systems. Our results suggest cold temperatures provided a sufficient barrier against herbivores for high-elevation trees to allocate resources to other physiological processes besides defense. Changing climate may reduce the viability of that evolutionary strategy, and the life histories of high-elevation trees seem unlikely to foster rapid counter adaptation. Consequences extend from reduced food supplies for endangered grizzly bears to altered landscape and hydrological processes.