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.

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The finding that microbial communities are active under snow has changed the estimated global rates of biogeochemical processes beneath seasonal snow packs. We used microbiological and molecular techniques to elucidate the phylogenetic composition of undersnow microbial communities in Colorado, the United States. Here, we show that tundra soil microbial biomass reaches its annual peak under snow, and that fungi account for most of the biomass. Phylogenetic analysis of tundra soil fungi revealed a high diversity of fungi and three novel clades that constitute major new groups of fungi (divergent at the subphylum or class level). An abundance of previously unknown fungi that are active beneath the snow substantially broadens our understanding of both the diversity and biogeochemical functioning of fungi in cold environments.

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.

Most terrestrial carbon sequestration at mid-latitudes in the Northern Hemisphere occurs in seasonal, montane forest ecosystems. Winter respiratory carbon dioxide losses from these ecosystems are high, and over half of the carbon assimilated by photosynthesis in the summer can be lost the following winter. The amount of winter carbon dioxide loss is potentially susceptible to changes in the depth of the snowpack; a shallower snowpack has less insulation potential, causing colder soil temperatures and potentially lower soil respiration rates. Recent climate analyses have shown widespread declines in the winter snowpack of mountain ecosystems in the western USA and Europe that are coupled to positive temperature anomalies. Here we study the effect of changes in snow cover on soil carbon cycling within the context of natural climate variation. We use a six-year record of net ecosystem carbon dioxide exchange in a subalpine forest to show that years with a reduced winter snowpack are accompanied by significantly lower rates of soil respiration. Furthermore, we show that the cause of the high sensitivity of soil respiration rate to changes in snow depth is a unique soil microbial community that exhibits exponential growth and high rates of substrate utilization at the cold temperatures that exist beneath the snow. Our observations suggest that a warmer climate may change soil carbon sequestration rates in forest ecosystems owing to changes in the depth of the insulating snow cover.

Primary succession is a fundamental process in macroecosystems; however, if and how soil development influences microbial community structure is poorly understood. Thus, we investigated changes in the bacterial community along a chronosequence of three unvegetated, early successional soils ( approximately 20-year age gradient) from a receding glacier in southeastern Peru using molecular phylogenetic techniques. We found that evenness, phylogenetic diversity, and the number of phylotypes were lowest in the youngest soils, increased in the intermediate aged soils, and plateaued in the oldest soils. This increase in diversity was commensurate with an increase in the number of sequences related to common soil bacteria in the older soils, including members of the divisions Acidobacteria, Bacteroidetes, and Verrucomicrobia. Sequences related to the Comamonadaceae clade of the Betaproteobacteria were dominant in the youngest soil, decreased in abundance in the intermediate age soil, and were not detected in the oldest soil. These sequences are closely related to culturable heterotrophs from rock and ice environments, suggesting that they originated from organisms living within or below the glacier. Sequences related to a variety of nitrogen (N)-fixing clades within the Cyanobacteria were abundant along the chronosequence, comprising 6-40% of phylotypes along the age gradient. Although there was no obvious change in the overall abundance of cyanobacterial sequences along the chronosequence, there was a dramatic shift in the abundance of specific cyanobacterial phylotypes, with the intermediate aged soils containing the greatest diversity of these sequences. Most soil biogeochemical characteristics showed little change along this approximately 20-year soil age gradient; however, soil N pools significantly increased with soil age, perhaps as a result of the activity of the N-fixing Cyanobacteria. Our results suggest that, like macrobial communities, soil microbial communities are structured by substrate age, and that they, too, undergo predictable changes through time.

Past studies of plant-microbe interactions in the alpine nitrogen cycle have revealed a seasonal separation of N use, with plants absorbing N primarily during the summer months and microbes immobilizing N primarily during the autumn months. On the basis of these studies, it has been concluded that competition for N between plants and microbes is minimized along this seasonal gradient. In this study, we examined more deeply the links between microbial population dynamics and plant N availability in an alpine dry meadow. We conducted a year-round field study and performed experiments on isolated soil microorganisms. Based on previous work in this ecosystem, we hypothesized that microbial biomass would decline before the plant growing season and would release N that would become available to plants. Microbial biomass was highest when soils were cold, in autumn, winter, and early spring. During this time, N was immobilized in microbial biomass. After snow melt in spring, microbial biomass decreased. A peak in the soil protein concentration was seen at this time, followed by peaks in soil amino acid and ammonium concentrations in late June. Soil protease rates were initially high after snow melt, decreased to below detection limits by midsummer, and partially recovered by late summer. Proteolytic activity in soil was saturated early in the growing season and became protein limited later in the summer. We concluded that the key event controlling N availability to alpine plants occurs after snow melt, when protein is released from the winter microbial biomass. This protein pulse provides substrate for soil proteases, which supply plants with amino acids during the growing season. On average, microbial biomass was lower in the summer than at other times, although the biomass fluctuated widely during the summer. Within the summer months, maximum numbers of amino-acid-degrading microorganisms and the maximum amount of microbial biomass coincided with the peak in soil amino acids, when plants are most active. All bacterial strains isolated from this summer community had the ability to grow rapidly on low concentrations of amino acids and to degrade protein. This explains the previously observed result that the soil microbial biomass can compete strongly with plants for organic N, despite the seasonal offset of maximum plant and microbial N uptake.

Abstract. Experiments were conducted during 1993 at Niwot Ridge in the Colorado Front Range to determine if the insulating effect of winter snow cover allows soil microbial activity to significantly affect nitrogen inputs and outputs in alpine systems. Soil surface temperatures under seasonal snowpacks warmed from -14 OC in January to 0 OC by May 4th. Snowmelt began in mid-May and the sites were snow free by mid June. Heterotrophic microbial activity in snow-covered soils, measured as C02 production, was first identified on March 4, 1993. Net CO* flux increased from 55 mg COz-C m-' day-' in early March to greater than 824mg C02-C m-' day-' by the middle of May. Carbon dioxide production decreased in late May as soils became saturated during snowmelt. Soil inorganic N concentrations increased before snowmelt, peaking between 101 and 276 mg kg-' soil in May, and then decreasing as soils became saturated with melt water. Net N mineralization for the period of March 3 to May 4 ranged from 2.23 to 6.63 g N m-' , and were a proximately two orders of magnitude greater P than snowmelt inputs of 50.4 mg N m-2 for NH, and 97.2 mg N m-' for NO,. Both NO, and NH: concentrations remained at or below detection limits in surface water during snowmelt, indicating the only export of inorganic N from the system was through gaseous losses. Nitrous oxide production under snow was first observed in early April. Production increased as soils warmed, peaking at 75 p g N20-N m-2 day-' in soils saturated with melt water one week before the sites were snow free. These data suggest that microbial activity in snow-covered soils may play a key role in alpine N cycling before plants become active.