SUMMARY: Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85 :183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity.

Although recent work has shown that both deterministic and stochastic processes are important in structuring microbial communities, the factors that affect the relative contributions of niche and neutral processes are poorly understood. The macrobiological literature indicates that ecological disturbances can influence assembly processes. Thus, we sampled bacterial communities at 4 and 16 weeks following a wildfire and used null deviation analysis to examine the role that time since disturbance has in community assembly. Fire dramatically altered bacterial community structure and diversity as well as soil chemistry for both time-points. Community structure shifted between 4 and 16 weeks for both burned and unburned communities. Community assembly in burned sites 4 weeks after fire was significantly more stochastic than in unburned sites. After 16 weeks, however, burned communities were significantly less stochastic than unburned communities. Thus, we propose a three-phase model featuring shifts in the relative importance of niche and neutral processes as a function of time since disturbance. Because neutral processes are characterized by a decoupling between environmental parameters and community structure, we hypothesize that a better understanding of community assembly may be important in determining where and when detailed studies of community composition are valuable for predicting ecosystem function.

Significance: In drylands worldwide, where plant cover is sparse, large amounts of the ground surface are covered by specialized organisms that form biological soil crusts (biocrusts). Biocrusts fix carbon and nitrogen, stabilize soils, and influence hydrology. Extensive physical disturbance from livestock/human trampling and off-road vehicles is known to destroy biocrusts and alter ecosystem function. More recent work also indicates that climate change can affect biocrust communities. Contrary to our expectations, experimental climate change and physical disturbance had strikingly similar impacts on biocrust communities, with both promoting a shift to degraded, early successional states. These results herald ecological state transitions in drylands as temperatures rise, calling for management strategies that consider risks from both physical disturbances and climate change.

Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.

The mountain pine beetle (MPB; Dendroctonus ponderosae) is native to western North America, attacks most trees of the genus Pinus, and periodically erupts in epidemics. The current epidemic of the MPB is an order of magnitude larger than any previously recorded, reaching trees at higher elevation and latitude than ever before. Here we show that after 2 decades of air-temperature increases in the Colorado Front Range, the MPB flight season begins more than 1 month earlier than and is approximately twice as long as the historically reported season. We also report, for the first time, that the life cycle in some broods has increased from one to two generations per year. Because MPBs do not diapause and their development is controlled by temperature, they are responding to climate change through faster development. The expansion of the MPB into previously inhospitable environments, combined with the measured ability to increase reproductive output in such locations, indicates that the MPB is tracking climate change, exacerbating the current epidemic.