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Shifts in microbial communities driven by anthropogenic nitrogen (N) addition have broad-scale ecological consequences. However, responses of microbial groups to exogenous N supply vary considerably across studies, hindering efforts to predict community changes. We used meta-analytical techniques to explore how amoA gene abundances of ammonia-oxidizing archaea (AOA) and bacteria (AOB) respond to N addition, and found that N addition increased AOA and AOB abundances by an average of 27% and 326%, respectively. Responses of AOB varied by study type, ecosystem, fertilizer type, and soil pH, and were strongest in unmanaged wildland soils and soils fertilized with inorganic N sources. Increases in nitrification potential with N addition significantly correlated with only AOB. Our analyses suggest that elevated N supply enhances soil nitrification potential by increasing AOB populations, and that this effect may be most pronounced in unmanaged wildland soils.

Soil organic matter (SOM) decomposition has the potential to radically affect carbon dioxide concentrations in the atmosphere. Priming, the increased decomposition of SOM after the addition of a labile carbon (C) source, may be an important regulator of SOM dynamics, yet little is known about the mechanisms of the priming effect. Two hypotheses generated in the last decade have suggested that priming is caused by either the nutrient conditions in soil or the response of the microbial community to labile C addition. We used a three million year substrate age gradient, with associated changes in nutrient availability and microbial communities, to test these two hypotheses. We added 13C labeled glucose to soil in quantities similar to increases in root exudation that can be expected in a high carbon dioxide environment, and traced the effect of C addition on soil C, the microbial community, and soil nutrient pools and fluxes. We observed positive priming, negative priming, and no net priming depending on substrate age. Priming was most positive at the youngest sites with the smallest nitrogen (N) pools, and most negative at the site with the most available N. In contrast, we found no significant relationships between priming and phosphorus availability. Though components of the microbial community size and structure (measured by phospholipid fatty acid analysis) changed as a result of C addition, soil N availability was a better explanatory mechanism of priming effects than microbial community dynamics. Our results suggest close linkages between C and N cycles regulate the magnitude and direction of priming. If general, the stability of SOM in temperate ecosystems is likely to be governed by soil N status.

Emerging research is challenging existing paradigms of nitrogen (N) cycling in arid and semiarid ecosystems that experience distinct seasonal patterns in precipitation. We measured equal or greater potential nitrification rates in the dry season than the wet season in chemically and physically distinct soils along a three million year substrate age gradient in Arizona. These surprising and counterintuitive results are supported by recently published work in California Mediterranean grasslands. Considered together, these studies call attention to the need to measure process rates during the dry, non-growing season of xeric ecosystems. Several mechanisms may be responsible for these patterns, but we highlight the importance of understanding the contribution of archaeal ammonia oxidizers to nitrification in these seasonally dry ecosystems.

Most organic carbon (C) in soils eventually turns into CO2 after passing through microbial metabolic pathways, while providing cells with energy and biosynthetic precursors. Therefore, detailed insight into these metabolic processes may help elucidate mechanisms of soil C cycling processes. Here, we describe a modeling approach to quantify the C flux through metabolic pathways by adding 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose as metabolic tracers to intact soil microbial communities. The model calculates, assuming steady-state conditions and glucose as the only substrate, the reaction rates through glycolysis, Krebs cycle, pentose phosphate pathway, anaplerotic activity through pyruvate carboxylase, and various biosynthesis reactions. The model assumes a known and constant microbial proportional precursor demand, estimated from literature data. The model is parameterized with experimentally determined ratios of 13CO2 production from pyruvate and glucose isotopologue pairs. Model sensitivity analysis shows that metabolic flux patterns are especially responsive to changes in experimentally determined 13CO2 ratios from pyruvate and glucose. Calculated fluxes are far less sensitive to assumptions concerning microbial chemical and community composition. The calculated metabolic flux pattern for a young volcanic soil indicates significant pentose phosphate pathway activity in excess of pentose precursor demand and significant anaplerotic activity. These C flux patterns can be used to calculate C use efficiency, energy production and consumption for growth and maintenance purposes, substrate consumption, nitrogen demand, oxygen consumption, and microbial C isotope composition. The metabolic labeling and modeling methods may improve our ability to study the biochemistry and ecophysiology of intact and undisturbed soil microbial communities.

In order to study controls on metabolic processes in soils, we determined the dynamics of 13 CO2 production from two position-specific 13 C-labeled pyruvate isotopologues in the presence and absence of glucose, succinate, pine, and legume leaf litter, and under anaerobic conditions. We also compared 13 CO2 production in soils along a semiarid substrate age gradient in Arizona. We observed that the C from the carboxyl group (C1) of pyruvate was lost as CO2 much faster than its other C atoms (C2,3). Addition of glucose, pine and legume leaf litter reduced the ratio between 13 CO2 production from 1- 13 C pyruvate and 2,3- 13 C pyruvate (C1/C2,3 ratio), whereas anaerobic conditions increased this ratio. Young volcanic soils exhibited a lower C1/C2,3 ratio than older volcanic soils. We interpret a low C1/C2,3 ratio as an indication of increased Krebs cycle activity in response to carbon inputs, while the higher ratio implies a reduced Krebs cycle activity in response to anaerobic conditions. Succinate, a gluconeogenic substrate, reduced 13 CO2 production from pyruvate to near zero, likely reflecting increased carbohydrate biosynthesis from Krebs cycle intermediates. The difference in 13 CO2 production rate from pyruvate isotopologues disappeared 4e5 days after pyruvate addition, indicating that C positions were scrambled by ongoing soil microbial transformations. This work demonstrates that metabolic tracers such as pyruvate can be used to determine qualitative aspects of C flux patterns through metabolic pathways of soil microbial communities. Understanding the controls over metabolic processes in soil may improve our understanding of soil C cycling processes.

Soil microbial organisms are central to carbon (C) and nitrogen (N) transformations in soils, yet not much is known about the stable isotope composition of these essential regulators of element cycles. We investigated the relationship between C and N availability and stable C and N isotope composition of soil microbial biomass across a three million year old semiarid substrate age gradient in northern Arizona. The δ15N of soil microbial biomass was on average 7.2‰ higher than that of soil total N for all substrate ages and 1.6‰ higher than that of extractable N, but not significantly different for the youngest and oldest sites. Microbial 15N enrichment relative to soil extractable and total N was low at the youngest site, increased to a maximum after 55,000 years, and then decreased slightly with age. The degree of 15N enrichment of microbial biomass correlated negatively with the C:N mass ratio of the soil extractable pool. The δ13C signature of soil microbial biomass was 1.4‰ and 4.6‰ enriched relative to that of soil total and extractable pools respectively and showed significant differences between sites. However, microbial 13C enrichment was unrelated to measures of C and N availability. Our results confirm that 15N, but not 13C enrichment of soil microbial biomass reflects changes in C and N availability and N processing during long-term ecosystem development.

We report the first simultaneous measurements of δ 15 N and δ 13 C of DNA extracted from surface soils. The isotopic composition of DNA differed significantly among nine different soils. The δ 13 C and δ 15 N of DNA was correlated with δ 13 C and δ 15 N of soil, respectively, suggesting that the isotopic composition of DNA is strongly influenced by the isotopic composition of soil organic matter. However, in all samples DNA was enriched in 13 C relative to soil, indicating microorganisms fractionated C during assimilation or preferentially used 13 C enriched substrates. Enrichment of DNA in 15 N relative to soil was not consistently observed, but there were significant differences between δ 15 N of DNA and δ 15 N of soil for three different sites, suggesting microorganisms are fractionating N or preferentially using N substrates at different rates across these contrasting ecosystems. There was a strong linear correlation between δ 15 N of DNA and δ 15 N of the microbial biomass, which indicated DNA was depleted in 15 N relative to the microbial biomass by approximately 3.4‰. Our results show that accurate and precise isotopic measurements of C and N in DNA extracted from the soil are feasible, and that these analyses may provide powerful tools for elucidating C and N cycling processes through soil microorganisms.

Stable isotope analysis is a powerful tool in the study of soil organic matter formation. It is often observed that more decomposed soil organic matter is 13 C, and especially 15 N-enriched relative to fresh litter and recent organic matter. We investigated whether this shift in isotope composition relates to the isotope composition of the microbial biomass, an important source for soil organic matter. We developed a new approach to determine the natural abundance C and N isotope composition of the microbial biomass across a broad range of soil types, vegetation, and climates. We found consistently that the soil microbial biomass was 15 N-enriched relative to the total (3.2 %) and extractable N pools (3.7 %), and 13 C-enriched relative to the extractable C pool (2.5 %). The microbial biomass was also 13 C-enriched relative to total C for soils that exhibited a C3-plant signature (1.6 %), but 13 C-depleted for soils with a C4 signature (� 1.1 %). The latter was probably associated with an increase of annual C3 forbs in C4 grasslands after an extreme drought. These findings are in agreement with the proposed contribution of microbial products to the stabilized soil organic matter and may help explain the shift in isotope composition during soil organic matter formation. r 2006 Elsevier Ltd. All rights reserved.

Changes in nutrient inputs due to aboveground herbivory may influence the litter and soil microbial community responsible for processes such as decomposition. The mesophyll-feeding scale insect (Matsucoccus acalyptus) found near Sunset Crater National Monument in northern Arizona, USA significantly increases pinon (Pinus edulis) needle litter nitrogen (N) and phosphorus (P) concentrations by 50%, as well as litter inputs to soil by 21%. Because increases in needle litter quality and quantity of this magnitude should affect the microbial communities responsible for decomposition, we tested the hypothesis that insect herbivory causes a shift in soil microbial and litter microarthropod function. Four major findings result from this research: (1) Despite increases in needle inputs due to herbivory, soil carbon (C) was 56% lower beneath scale-susceptible trees than beneath resistant trees; however, soil moisture, N, and pH were similar among treatments. (2) Microbial biomass was 80% lower in soils beneath scale-susceptible trees when compared to resistant trees in the dry season, while microbial enzyme activities were lower beneath susceptible trees in the wet season. (3) Bacterial community-level physiological profiles differed significantly between susceptible and resistant trees during the dry season but not during the wet season. (4) There was a 40% increase in Oribatida and 23% increase in Prostigmata in susceptible needle litter relative to resistant litter. Despite these changes, the magnitude of microbial biomass, activity, and community structure response to herbivory was lower than expected and appears to take a long time to develop. These results suggest that herbivores impact soils in subtle, but important ways; we suggest that while litter chemistry may strongly mediate soil fertility and microbial communities in mesic ecosystems, the influence is lower than expected in this primary succession xeric ecosystem where season mediates differences in microbial populations. Understanding how insect herbivores alter the distribution of susceptible and resistant trees and their associated decomposer communities in arid environments may lead to better prediction of how these ecosystems respond to climatic change.

Nitrogen-fixing tree species have been shown to improve site fertility and increase N transformation rates, but the influence of N-fixing plants on the soil microbial community as a whole is largely unknown. We used patterns of individual carbon-source utilization and enzyme activities to assess the relative effects of N-fixing red alder on the soil microbial community in three adjacent stands (pure conifer, mixed alder-conifer, and pure alder) of a highly productive coastal Oregon forest where the density of red alder has been experimentally manipulated for over 65 years. Two major patterns were revealed: (1) bacterial and fungal carbon-source utilization patterns in soil from pure conifer stands were significantly different from both pure alder soils and mixed conifer-alder soils, while there was no difference in substrate utilization patterns between soils from the mixed alder-conifer and pure alder stands; and (2) the activities of nine extracellular enzymes involved in ligno-cellulose degradation and the mineralization of organic nitrogen, phosphate, and sulfate compounds were all significantly greater in pure alder soils compared to either pure conifer or mixed conifer-alder soils. Our results show that, in addition to an overall increase in soil fertility, microbial biomass, and microbial activity, the presence of N-fixing red alder significantly alters the physiological profile of the microbial community-even in an ecosystem already of high N status.

We investigated the influence of fumigation conditions of the chloroform fumigation‐ extraction method on the release of extractable carbon (C) and nitrogen (N) from organic and mineral soil horizons of 11 mature forests. Soil samples were fumigated with chloroform vapor for 1, 3, 5, or 10 d at two different water contents: field moist or field capacity (233 kPa matric potential). We found that for approximately half our soils, 0.5 M K2SO4-extractable N and C reached a maximum after 1 d of fumigation. The effect of soil wetting on C and N flushes from O horizons was variable but in mineral soils, increasing the soil water content generally resulted in more extractable C and N following fumigation. For the majority of soils assessed, increasing the soil water content did not change the fumigation time necessary to generate the maximum C or N flush. Observed changes in the C/N ratios of the fumigation flush with changes in fumigation time and the sensitivity of this C/N ratio to changes in soil water content suggest that different fumigation conditions may result in different organic pools being extracted. These effects appear to be extremely soil specific. We recommend that the effects of fumigation time and water content be evaluated before the C and N flushes from the fumigation extraction method are used to assess differences in microbial C and N among contrasting forest soils. q 2002 Elsevier Science Ltd. All rights reserved.

We conducted laboratory studies to determine the effects of red alder ( Alnus rubra Bong.) on soil N transformations and N availability indices at two conifer forest sites of contrasting productivity. The inclusion of red alder in conifer forests significantly increased gross rates of N mineralization, N immobilization, nitrification and NO 3 − immobilization, and the effects of alder were generally similar for soils from low- and high-productivity sites. However, the addition of alder to the conifer stand at the high productivity site increased gross N mineralization and immobilization processes more than at the low productivity site. At both sites, gross N and NO 3 − production were enhanced by alder more than gross N immobilization processes, leading to higher rates of net N mineralization and nitrification. At the fertile site, most microbial N assimilation occurred from the NO 3 − pool, compared with less than half at the infertile site (none as NO 3 − in the less productive pure conifer stand). Heterotrophic nitrification (as indicated by a lack of C 2 H 2 inhibition) accounted for 65–72% of the gross nitrification in all stands that exhibited nitrification (no nitrification was detected in the pure conifer stand at the infertile site). The inclusion of red alder had no effect on the proportion of total nitrification that was heterotrophic, despite the lower soil pH in mixed alder-conifer stands compared to conifer stands. Gross rates of N mineralization correlated well with both autotrophic and heterotrophic nitrification across all soils. Gross N mineralization may be a good index of NH 4 + availability to autotrophic nitrifiers, as well as the quality of organic N as a substrate for heterotrophic nitrification. Most estimates of microbial biomass and activity, N availability and N transformation rates were significantly correlated with each other. In general, gross N transformations were better correlated with other indices of N availability and microbial activity than estimates of net N transformations. Similar N cycling rates and microbial biomass N pool sizes in pure alder and adjacent alder-conifer stands at the fertile site suggest that continued inputs of N via symbiotic N-fixation by red alder in coniferous forest stands can lead to the elimination of N-limitation to forest ecosystem production.

A comparative study of N dynamics in an annual grassland and a young mixed-conifer forest, that occur on the same soil great group in California, was made by adding small amounts of 15NH4+ to mineral soils within field microplots and following changes in 15N recoveries in soil and plant pools over 12–16 months. In annual grassland microplots, the aboveground plant biomass contained 5–6% of the added 15N at the end of the growing season. One month after 15N addition almost 70% of the added 15N was recovered in the soil organic matter (SOM) pool, which included surface litter and roots but not microbial biomass. Laboratory incubation of sterilized soil cores indicated that as much as half of the 15N recovered in the SOM pool may have been fixed abiotically. Nevertheless, substantial and rapid incorporation of 15N in the SOM pool indicates a high potential for N immobilization and a rapid turnover of the microbial biomass-N pool in this soil. Recovery of 15N in microbial biomass ranged from 9 to 15%; recovery in the soil solution was lower than in the microbial biomass, but showed a similar seasonal trend. Total 15N recovery ranged from 72 to 85% over the study period. In forest microplots (which excluded plants), recovery of added 15N was generally lower than in the grassland for all soil pools examined. Recovery of 15N in SOM and microbial pools showed reciprocal trends seasonally, suggesting that there was considerable movement of N between these pools in the forest soil. Total 15N recovery was only about 54% 6 months after 15N addition, indicating a high potential for rapid N loss from the surface soil of this forest. Substantially lower recovery of 15N in the forest soil cannot be attributed entirely to the exclusion of plant uptake because plant 15N recovery in the grassland was relatively low. The low 15N recovery in the forest soil might be due to the low capacity of this soil to immobilize N and protect immobilized N from being remineralized and lost from the soil via leaching or denitrification. In both ecosystems estimates of N flow from the mineral soil to decomposing surface residues (presumably via fungal translocation) was significant (0.29 and 0.02 g-N m−2 yr−1 for the grassland and forest, respectively) relative to the net internal dynamics of N within the surface detritus. Comparison of net changes in litter N and accumulation of 15N during decomposition suggests that N was mineralized from litter concurrently as N was immobilized from the mineral soil in both sites.

The direct extraction method for estimating microbial biomass-N, which involves chloroform fumigation and extraction without an incubation step, affords the opportunity to analyze soils for which the incubation step is problematic. We tested the direct extraction method on freshly sampled grassland and forest soils of California, which experience seasonal wetting and drying cycles and labile substrate inputs. Time-course profiles of extractable-N during fumigation varied among soils, with the forest samples achieving peak N-flush after only 1-day fumigation, while the grassland soils required 5–7 days. When dry grassland soil was wetted to different moisture contents before fumigation, direct extraction efficiency was positively related to soil moisture. Direct extraction efficiency appeared to vary seasonally in the forest soils. Comparisons of N-flushes from direct extraction and fumigation-incubation methods are equivocal because of differential microbial immobilization during incubation. Agreement between the two methods was best when a variable k N was used to convert the fumigation-incubation data to microbial biomass-N. Although the direct extraction procedure offers some promise for evaluating a labile fraction of the microbial biomass-N, which is difficult to evaluate in these soils by any current method, uncertainties remain regarding duration of fumigation, consistency of water content and conversion to biomass-N.