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.

Summary Bacteria control major nutrient cycles and directly influence plant, animal, and human health. However, we know relatively little about the forces shaping their large-scale ecological ranges. Here, we reveal patterns in the distribution of individual bacterial taxa at multiple levels of phylogenetic resolution within and between Earth’s major habitat types. Our analyses suggest that while macro-scale habitats structure bacterial distribution to some degree, abundant bacteria (i.e., detectable using 16S rRNA gene sequencing methods) are confined to single assemblages. Additionally, we show that the most cosmopolitan taxa are also the most abundant in individual assemblages. These results add to the growing body of data that support that the diversity of the overall bacterial metagenome is tremendous. The mechanisms governing microbial distribution remain poorly understood, but our analyses provide a framework with which to test the importance of macro-ecological environmental gradients, relative abundance, neutral processes and the ecological strategies of individual taxa in structuring microbial communities.

Our paper describes the ecological controls on algal-mat diatom communities in the dynamic stream ecosystems of the McMurdo Dry Valleys in Antarctica. Dry Valley diatom communities are relatively diverse, and nearly ½ of the taxa found in these mats are considered endemic. Diatom community composition was examined in 5 streams in Taylor Valley during a 15-y cooling period that included a discrete flood event. Two hydrologic variables, total annual discharge and historical variation in discharge, gave the most parsimonious model of among-stream and interannual variation in diatom communities. Algal-mat biomass and chlorophyll a concentrations decreased after the flood, which occurred during the 2001/2002 summer season. Most algal-mat diatom communities recovered quickly after the flood. However, Green Creek, a relatively high-flow stream with low historical variation in discharge, appears to have experienced a persistent diatom community shift toward increased relative abundance of small, generalist species. Diatom relative biovolume, a proxy for the size of diatoms within a sample, was negatively correlated with stream flow, such that higher-discharge streams contained greater relative abundances of smaller diatoms than lower-flow streams. Therefore, diatom size may play a role in determining the distribution of a species in these streams and may be useful for monitoring environmental changes. Our study demonstrates the importance of understanding factors affecting ecosystem resilience, especially in polar regions, which are experiencing rapid climate changes.

Abstract. Global change drivers influence ecological processes at multiple scales and manifest across most of Earth as changes in biodiversity, biogeochemical cycles, infectious disease incidence, and ecohydrology. Small-scale investigations provide compelling evidence of specific effects of global change on local systems, but are of limited use in modeling complex ecological processes at continental-to-global scales. Long-term observations distributed across a diversity of habitat types are needed to improve the ability to forecast ecological change at large spatial and temporal scales. This special issue introduces the Terrestrial Observation System (TOS) of the National Ecological Observatory Network (NEON), a long-term, continental-scale ecological research platform designed to deliver these large-scale datasets. The TOS measures biodiversity of key biota (soil microbes, insects, plants, small mammals), ecosystem productivity and biogeochemistry, infectious disease dynamics, phenology, and population dynamics. The articles in this special issue describe the scientific rationale for the sampling designs of the TOS, including an overview of protocols, locations, and frequencies of measurements. The science designs are a culmination of design requirements scoped by NEON and the National Science Foundation, best available practices put forth by the scientific community, input from technical working groups, and consideration of logistical and financial constraints by NEON staff. Within each site, measurements have been collocated to the extent possible to optimize linkages among different sampling elements. Integrated analyses of terrestrial observations with sensor-based, imagery, and remote-sensing data collected by other NEON subsystems can facilitate scaling of measured parameters to larger spatial and temporal scales. NEON is designed to collect data for 30 years, and make these data freely available on a public data portal (data.neonscience.org). Samples and specimens will be archived and available to the scientific community upon request. The open access approach to the Observatory will provide users with the resources necessary to map, understand, and predict the effects of global change drivers on ecological processes at a continental scale.