Publications

<em>Escherichia coli</em> cells were forced to mineralize or assimilate nitrogen <em>in vitro</em> by manipulating substrate carbon and nitrogen availability. When grown on an organic nitrogen source, <em>E. coli</em> cells released NH₄⁺ and were enriched in ¹⁵N relative to the nitrogen source (1.6–3.1‰). However, when cells were grown on an inorganic nitrogen source, the biomass was depleted (6.1–9.1‰) relative to the source. By measuring ¹⁵N enrichment of microorganisms relative to nitrogen pools, ecosystem ecologists may be able to determine if microorganisms are assimilating or mineralizing nitrogen.

Organic carbon (C) and nitrogen (N) are essential for heterotrophic soil microorganisms, and their bioavailability strongly influences ecosystem C and N cycling. We show here that the natural ¹⁵N abundance of the soil microbial biomass is affected by both the availability of C and N and ecosystem N processing. Microbial ¹⁵N enrichment correlated negatively with the C : N ratio of the soil soluble fraction and positively with net N mineralization for ecosystems spanning semiarid, temperate and tropical climates, grassland and forests, and over four million years of ecosystem development. In addition, during soil incubation, large increases in microbial ¹⁵N enrichment corresponded to high net N mineralization rates. These results support the idea that the N isotope composition of an organism is determined by the balance between N assimilation and dissimilation. Thus, ¹⁵N enrichment of the soil microbial biomass integrates the effects of C and N availability on microbial metabolism and ecosystem processes.

Ponderosa pine (<em>Pinus ponderosa</em>) forests of the southwestern United States are a mosaic of stands where undisturbed forests are carbon sinks, and stands recovering from wildfires may be sources of carbon to the atmosphere for decades after the fire. However, the relative magnitude of these sinks and sources has never been directly measured in this region, limiting our understanding of the role of fire in regional and US carbon budgets. We used the eddy covariance technique to measure the CO₂ exchange of two forest sites, one burned by fire in 1996, and an unburned forest. The fire was a high-intensity stand-replacing burn that killed all trees. Ten years after the fire, the burned site was still a source of CO₂ to the atmosphere [109±6 (SEM) g C m⁻² yr⁻¹], whereas the unburned site was a sink (−164±23 g C m⁻² yr⁻¹). The fire reduced total carbon storage and shifted ecosystem carbon allocation from the forest floor and living biomass to necromass. Annual ecosystem respiration was lower at the burned site (480±5 g C m⁻² yr⁻¹) than at the unburned site (710±54 g C m⁻² yr⁻¹), but the difference in gross primary production was even larger (372±13 g C m⁻² yr⁻¹ at the burned site and 858±37 g C m⁻² yr⁻¹at the unburned site). Water availability controlled carbon flux in the warm season at both sites, and the burned site was a source of carbon in all months, even during the summer, when wet and warm conditions favored respiration more than photosynthesis. Our study shows that carbon losses following stand-replacing fires in ponderosa pine forests can persist for decades due to slow recovery of the gross primary production. Because fire exclusion is becoming increasingly difficult in dry western forests, a large US forest carbon sink could shift to a decadal-scale carbon source.

<div> Organisms acquire some elements from the environment with ease.  Diffusion alone often provides enough carbon dioxide, oxygen and water.  But getting other elements requires more effort, spurring unique evolutionary adaptations: instead of taking up nutrients from the soil, some plants in acidic bogs trap insects to obtain nitrogen and phosphorus 1; geophagy — or eating dirt — may sometimes be important for acquiring iron by primates 2; plants and microorganisms secrete compounds that liberate phosphorus from unavailable forms in soil 3; and many bacteria secrete metal-scavenging compounds called siderophores to capture iron and copper 4,5.  Evidence has mounted that molybdenum is also specifically targeted 6. On page 243 of this issue, Bellenger and colleagues 7 confirm this, showing that siderophores produced by the nitrogen-fixing bacterium Azotobacter vinelandiibind with molybdenum and vanadium in the laboratory, promoting uptake of these metals.</div>

Management of forests for carbon uptake is an important tool in the effort to slow the increase in atmospheric CO₂ and global warming. However, some current policies governing forest carbon credits actually promote avoidable CO₂ release and punish actions that would increase long-term carbon storage. In fire-prone forests, management that reduces the risk of catastrophic carbon release resulting from stand-replacing wild-fire is considered to be a CO₂ source, according to current accounting practices, even though such management may actually increase long-term carbon storage. Examining four of the largest wildfires in the US in 2002, we found that, for forest land that experienced catastrophic stand-replacing fire, prior thinning would have reduced CO₂ release from live tree biomass by as much as 98%. Altering carbon accounting practices for forests that have historically experienced frequent, low-severity fire could provide an incentive for forest managers to reduce the risk of catastrophic fire and associated large carbon release events.

Forest ecosystems assimilate more CO₂ from the atmosphere and store more carbon in woody biomass than most nonforest ecosystems, indicating strong potential for afforestation to serve as a carbon management tool. However, converting grasslands to forests could affect ecosystem–atmosphere exchanges of other greenhouse gases, such as nitrous oxide and methane (CH₄), effects that are rarely considered. Here, we show that afforestation on a well-aerated grassland in Siberia reduces soil CH₄ uptake by a factor of 3 after 35 years of tree growth. The decline in CH₄ oxidation was observed both in the field and in laboratory incubation studies under controlled environmental conditions, suggesting that not only physical but also biological factors are responsible for the observed effect. Using incubation experiments with ¹³CH₄ and tracking ¹³C incorporation into bacterial phospholipid fatty acid (PLFA), we found that, at low CH₄ concentrations, most of the ¹³C was incorporated into only two PLFAs, 18 : 1ω7 and 16 : 0. High CH₄ concentration increased total ¹³C incorporation and the number of PLFA peaks that became labeled, suggesting that the microbial assemblage oxidizing CH₄ shifts with ambient CH₄ concentration. Forests and grasslands exhibited similar labeling profiles for the high-affinity methanotrophs, suggesting that largely the same general groups of methanotrophs were active in both ecosystems. Both PLFA concentration and labeling patterns indicate a threefold decline in the biomass of active methanotrophs due to afforestation, but little change in the methanotroph community. Because the grassland consumed CH₄ at a rate five times higher than forest soils under laboratory conditions, we concluded that not only biomass but also cell-specific activity was higher in grassland than in afforested plots. While the decline in biomass of active methanotrophs can be explained by site preparation (plowing), inorganic N (especially NH₄⁺) could be responsible for the change in cell-specific activity. Overall, the negative effect of afforestation of upland grassland on soil CH₄ uptake can be largely explained by the reduction in biomass and to a lesser extent by reduced cell-specific activity of CH₄-oxidizing bacteria.

<div data-canvas-width="658.8216666666666">1. Ecological restoration often involves returning ecosystem structure to some predisturbance</div> <div data-canvas-width="679.9833333333332">reference state, but ecosystem function must also recover if restoration efforts are to be self-sustaining</div> <div data-canvas-width="680.0049999999998">over the long term. In the south-western United States, ponderosa pine forest structure was altered</div> <div data-canvas-width="679.9983333333332">by disruption of the fire regime following Euro-American settlement. Forest structure is now being</div> <div data-canvas-width="679.9983333333331">restored to presettlement conditions through the application of thinning and burning treatments.</div> <div data-canvas-width="663.6866666666666">However, the effects of these treatments on below-ground ecosystem processes remain unclear.</div> <div data-canvas-width="658.8149999999998">2. We conducted a water and nitrogen (N) addition experiment in adjacent restored and unrestored</div> <div data-canvas-width="366.61499999999995">ponderosa pine stands and compared soil CO2 efflux in response to these treatments over a 13-month</div> <div data-canvas-width="680.0016666666666">period. Our goals were to (i) quantify water and N limitation to below-ground carbon (C) cycling</div> <div data-canvas-width="680.0066666666665">in contemporary high-density ponderosa pine forests; and (ii) determine if restoration alleviates</div> <div data-canvas-width="170.73000000000002">water and N limitations.</div> <div data-canvas-width="158.11333333333332">3. Restoration thinning and burning increased soil CO2 efflux, along with surface soil watercontent, temperature and herbaceous fine root biomass, while total fine root biomass decreased asa result of restoration.</div> <div data-canvas-width="658.8283333333333">4. Water and N additions increased C flux from soils to a similar degree in both restored and</div> <div data-canvas-width="680.0166666666668">unrestored ponderosa pine stands, but the increase was relatively small when compared to that</div> <div data-canvas-width="180.79666666666665">stimulated by restoration.</div> <div data-canvas-width="476.5566666666667">5. Synthesis and applications.  An understanding of how ecosystem processes respond to treatments</div> <div data-canvas-width="680.0016666666667">designed to restore ecosystem structure is critical in ensuring the long-term success of restoration</div> <div data-canvas-width="680.0033333333333">efforts. Here we show that, although water and N stimulate C flux from soils in these semi-arid</div> <div data-canvas-width="679.9999999999999">forests, restoration treatments have a much greater effect on soil C balance than increased water and N availability by themselves. This suggests that increased quality of C inputs from a recovering</div> <div data-canvas-width="680.17">understorey herbaceous community is a key component of restoring ecosystem function (e.g.</div> <div data-canvas-width="460.53999999999996">below-ground C cycling) in south-western ponderosa pine forests.</div>