In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity. This review examines how a growing knowledge of the vast range of animal–bacterial interactions, whether in shared ecosystems or intimate symbioses, is fundamentally altering our understanding of animal biology. Specifically, we highlight recent technological and intellectual advances that have changed our thinking about five questions: how have bacteria facilitated the origin and evolution of animals; how do animals and bacteria affect each other’s genomes; how does normal animal development depend on bacterial partners; how is homeostasis maintained between animals and their symbionts; and how can ecological approaches deepen our understanding of the multiple levels of animal–bacterial interaction. As answers to these fundamental questions emerge, all biologists will be challenged to broaden their appreciation of these interactions and to include investigations of the relationships between and among bacteria and their animal partners as we seek a better understanding of the natural world

The order and timing of species immigration during community assembly can affect species abundances at multiple spatial scales. Known as priority effects, these effects cause historical contingency in the structure and function of communities, resulting in alternative stable states, alternative transient states, or compositional cycles. The mechanisms of priority effects fall into two categories, niche preemption and niche modification, and the conditions for historical contingency by priority effects can be organized into two groups, those regarding regional species pool properties and those regarding local population dynamics. Specifically, two requirements must be satisfied for historical contingency to occur: The regional pool contains species that can together cause priority effects, and local dynamics are rapid enough for early-arriving species to preempt or modify niches before other species arrive. Organizing current knowledge this way reveals an outstanding key question: How are regional species pools that yield priority effects generated and maintained? 1

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.

Summary1. Plant-soil feedbacks is becoming an important concept for explaining vegetation dynamics, the invasiveness of introduced exotic species in new habitats and how terrestrial ecosystems respond to global land use and climate change. Using a new conceptual model, we show how critical alterations in plant-soil feedback interactions can change the assemblage of plant communities. We highlight recent advances, define terms and identify future challenges in this area of research and discuss how variations in strengths and directions of plant-soil feedbacks can explain succession, invasion, response to climate warming and diversity-productivity relationships. 2. While there has been a rapid increase in understanding the biological, chemical and physical mechanisms and their interdependencies underlying plant-soil feedback interactions, further progress is to be expected from applying new experimental techniques and technologies, linking empirical studies to modelling and field-based studies that can include plant-soil feedback interactions on longer time scales that also include long-term processes such as litter decomposition and mineralization. 3. Significant progress has also been made in analysing consequences of plant-soil feedbacks for biodiversity-functioning relationships, plant fitness and selection. 4. To further integrate plant-soil feedbacks into ecological theory, it will be important to determine where and how observed patterns may be generalized, and how they may influence evolution. 5. Synthesis. Gaining a greater understanding of plant-soil feedbacks and underlying mechanisms is improving our ability to predict consequences of these interactions for plant community composition and productivity under a variety of conditions. Future research will enable better prediction and mitigation of the consequences of human-induced global changes, improve efforts of restoration and conservation and promote sustainable provision of ecosystem services in a rapidly changing world.

Despite decades of research, it remains controversial whether ecological communities converge towards a common structure determined by environmental conditions irrespective of assembly history. Here, we show experimentally that the answer depends on the level of community organization considered. In a 9-year grassland experiment, we manipulated initial plant composition on abandoned arable land and subsequently allowed natural colonization. Initial compositional variation caused plant communities to remain divergent in species identities, even though these same communities converged strongly in species traits. This contrast between species divergence and trait convergence could not be explained by dispersal limitation or community neutrality alone. Our results show that the simultaneous operation of trait-based assembly rules and species-level priority effects drives community assembly, making it both deterministic and historically contingent, but at different levels of community organization.