A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

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We conducted a 456—d laboratory incubation of an old—growth coniferous forest soil to aid in the elucidation of C controls on N cycling processes in forest soils. Gross rates of N mineralization, immobilization, and nitrification were measured by 15N isotope dilution, and net rates N mineralization and nitrification were calculated from changes in KCl—extractable inorganic N and NO3—@ON pool sizes, respectively. Changes in the availability of C were assessed by monitoring rates of CO2 evolution and the sizes of extractable organic C and microbial biomass pools. Net and gross rates of N mineralization (r2 = 0.038, P = .676) and nitrification (r2 = 0.403, P = .125) were not significantly correlated over the course of the incubation, suggesting that the factors controlling N consumptive and productive processes do not equally affect these processes. A significant increase in the NO3— pool size (net nitrification) only occurred after 140 d, when the NO3— pool size increased suddenly and massively. However, gross nitrification rates were substantial throughout the entire incubation and were poorly correlated with these changes in NO3— pool sizes. Concurrent decreases in the microbial biomass suggest that large increases in NO3— pool sizes after prolonged incubation of coniferous forest soil may arise from reductions in the rate of microbial immobilization of NO3—, rather than from one of the mechanisms proposed previously (e.g., sequestering of NH4+ by microbial heterotrophs, the deactivation of allelopathic compounds, or large increases in autotrophic nitrifier populations). Strong correlations were found between rates of CO2 evolution and gross N mineralization (r2 = 0.974, P < .0001) and immobilization (r2 = 0.980, P < .0001), but not between CO2 evolution and net N mineralization rates. Microbial growth efficiency, determined by combining estimates of gross N immobilization, CO2 evolution, and microbial biomass C and N pool sizes, declined exponentially over the incubation. These results suggest the utilization of lower quality substrates as C availability declined during incubation. Results from this research indicate the measurement of gross rates of N transformations in soil provides a powerful tool for assessing C and N cycling relationships in forests.

In Fennoscandian boreal forests, soil pH and N supply generally increase downhill as a result of water transport of base cations and N, respectively. Simultaneously, forest productivity increases, the understory changes from ericaceous dwarf shrubs to tall herbs; in the soil, fungi decrease whereas bacteria increase. The composition of the soil microbial community is mainly thought to be controlled by the pH and C-to-N ratio of the substrate. However, the latter also determines the N supply to plants, the plant community composition, and should also affect plant allocation of C below ground to roots and a major functional group of microbes, mycorrhizal fungi. We used phospholipid fatty acids (PLFAs) to analyze the potential importance of mycorrhizal fungi by comparing the microbial community composition in a tree-girdling experiment, where tree belowground C allocation was terminated, and in a long-term (34 years) N loading experiment, with the shifts across a natural pH and N supply gradient. Both tree girdling and N loading caused a decline of ca. 45% of the fungal biomarker PLFA 18:2omega6,9, suggesting a common mechanism, i.e., that N loading caused a decrease in the C supply to ectomycorrhizal fungi just as tree girdling did. The total abundance of bacterial PLFAs did not respond to tree girdling or to N loading, in which cases the pH (of the mor layer) did not change appreciably, but bacterial PLFAs increased considerably when pH increased across the natural gradient. Fungal biomass was high only in acid soil (pH < 4.1) with a high C-to-N ratio (>38). According to a principal component analysis, the soil C-to-N ratio was as good as predictor of microbial community structure as pH. Our study thus indicated the soil C-to-N ratio, and the response of trees to this ratio, as important factors that together with soil pH influence soil microbial community composition.

Organisms with the denitrification capacity are widely distributed and in high density in nature. It is not well understood why they are so successful. A survey of denitrifying enzyme content of various habitats is presented which indicates a role of carbon and oxygen, but not nitrate, in affecting denitrifier populations. It is suggested that organic carbon is more important than oxygen status in determining denitrifying enzyme content of habitats. In low oxygen environments, denitrifiers compete with organisms that dissimilate nitrate to ammonium, a process which conserves nitrogen. The energetic and kinetic parameters that affect this competition are evaluated. The latter is examined using Michaelis-Menten theoretical models by varying Vmax, Km, and So (substrate concentration) for the two competing populations. The outcome predicted by these models is presented and discussed in relation to previous data on population densities and Km values for representatives of these competing groups. These models suggest the conditions required to achieve changes in partitioning between the two fates of nitrate. These considerations are important if one is to be able to evaluate and successfully "manage" the fate of nitrate in any habitat.

The advent of molecular techniques has improved our understanding of the microbial communities responsible for denitrification and is beginning to address their role in controlling denitrification processes. There is a large diversity of bacteria, archaea, and fungi capable of denitrification, and their community composition is structured by long-term environmental drivers. The range of temperature and moisture conditions, substrate availability, competition, and disturbances have long-lasting legacies on denitrifier community structure. These communities may differ in physiology, environmental tolerances to pH and O2, growth rate, and enzyme kinetics. Although factors such as O2, pH, C availability, and NO3- pools affect instantaneous rates, these drivers act through the biotic community. This review summarizes the results of molecular investigations of denitrifier communities in natural environments and provides a framework for developing future research for addressing connections between denitrifier community structure and function.

To determine the long—term effect of alder on soil fertility, biogeochemical fluxes were measured and calculated for two pairs of adjacent, 55—yr—old stands dominated by conifers, primarily Douglas—fir (Pseudotsuga menziesii), and by conifers and nitrogen—fixing red alder (Alnus rubra). At a low—fertility site in the Wind River Experimental Forest in southwestern Washington, biomass of the alder—conifer stand (289 Mg/ha) exceeded that of the conifer stand (171 Mg/ha), and the aboveground net primary production (ANPP) of the alder—conifer stand (10.3 Mg.ha—1.yr—1) was more than twice that of the conifer stand (4.8 Mg.ha—1.yr—1). At a more fertile site in the Cascade Head Experimental Forest in western Oregon, both biomass and ANPP were higher than at Wind River, and biomass and ANPP were higher in the conifer stand (584 Mg/ha and 19.2 Mg.ha—1.yr—1) than in the alder—conifer stand (342 Mg/ha and 10.7 Mg.ha—1.yr—1). Nitrogen accretion in the alder—conifer stand at Wind River averaged 54 kg.ha—1.yr—1 for the 52 yr since stand establishment, with a current rate of N fixation of °75 kg.ha—1.yr—1. For the alder—conifer stand at Cascade Head, N accretion averaged 73 kg.ha—1.yr—1 for 55 yr, with a current N—fixation rate of 85 kg.ha—1.yr—1. The cycling of all nutrient appeared very malleable under the influence of alder. At Wind River, return of nutrients in fine litterfall in the alder—conifer stand ranged from 1.5 (P) to 7.9 (N) times those in the conifer stand; whereas at Cascade Head, these ratios ranged from 1.7 (S) to 4.2 (N). Nutrient—use efficiencies (kilograms of ANPP per kilogram of nutrient uptake) were generally lower for the alder—conifer stands at both sites. Denitrification appeared negligible (<0.3 kg.ha—1.yr—1) in all stands. Leaching of organic plus inorganic N ranged from °5 kg.ha—1.yr—1 for the conifer stand at Wind River, to 50 Kg.ha—1.yr—1 for the alder—conifer stand at Cascade Head.

Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a 13 C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:15 PLFA were more active in utilizing 13 C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:26,9 was the most highly labeled. These results demonstrate the effectiveness of using 13 C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved.