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The mxaF gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene's usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae) detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.

Soil warming has the potential to alter both soil and plant processes that affect carbon storage in forest ecosystems. We have quantified these effects in a large, long-term (7-y) soil-warming study in a deciduous forest in New England. Soil warming has resulted in carbon losses from the soil and stimulated carbon gains in the woody tissue of trees. The warming-enhanced decay of soil organic matter also released enough additional inorganic nitrogen into the soil solution to support the observed increases in plant carbon storage. Although soil warming has resulted in a cumulative net loss of carbon from a New England forest relative to a control area over the 7-y study, the annual net losses generally decreased over time as plant carbon storage increased. In the seventh year, warming-induced soil carbon losses were almost totally compensated for by plant carbon gains in response to warming. We attribute the plant gains primarily to warming-induced increases in nitrogen availability. This study underscores the importance of incorporating carbon—nitrogen interactions in atmosphere—ocean—land earth system models to accurately simulate land feedbacks to the climate system.

Methanotroph abundance was analyzed in control and long-term nitrogen-amended pine and hardwood soils using rRNA-targeted quantitative hybridization. Family-specific 16S rRNA and pmoA/amoA genes were analyzed via PCR-directed assays to elucidate methanotrophic bacteria inhabiting soils undergoing atmospheric methane consumption. Quantitative hybridizations suggested methanotrophs related to the family Methylocystaceae were one order of magnitude more abundant than Methyloccocaceae and more sensitive to nitrogen-addition in pine soils. 16S rRNA gene phylotypes related to known Methylocystaceae and acidophilic methanotrophs and pmoA/amoA gene sequences, including three related to the upland soil cluster Alphaproteobacteria (USCα) group, were detected across different treatments and soil depths. Our results suggest that methanotrophic members of the Methylocystaceae and Beijerinckiaceae may be the candidates for soil atmospheric methane consumption.

Reported in this paper are foliar chemistry, tree growth (above- and below-ground), soil chemistry, nitrogen cycling (net mineralization and nitrification) and soil $\\mathrm{N}_2\\mathrm{O}$ flux responses to the first 6 yr of chronic nitrogen amendments at the Harvard Forest (Massachusetts, USA). A 70-yr-old red pine (Pinus resinosa Ait.) stand and a 50-yr-old mixed hardwood stand received control, low nitrogen (50 kg$\\cdot$ ha$^{-1}\\cdot$ yr$^{-1})$, high nitrogen (150 kg$\\cdot$ ha$^{-1}\\cdot$ yr$^{-1})$, and low nitrogen plus sulfur treatments, with additions occurring in six equal doses over the growing season as NH$_4$NO$_3$ and Na$_2$SO$_4$. Foliar N concentrations increased up to 25% in the hardwood stand and 67% in the pines, and there was no apparent decrease of N retranslocation due to fertilization. Wood production increased in the hardwood stand in response to fertilization but decreased in the pine stand. Fine-root nitrogen concentrations increased with N additions, and fine roots were a significant sink for added nitrogen. Nitrate leaching losses increased continuously over the 6-yr period in the treated pine stands but remained insignificant in the hardwoods. Annual net N mineralization increased substantially in response to treatments in both stands but declined in the pine high-N plot by the end of year six. Net nitrification increased from 17% of net mineralization in 1988 to 51% in 1993 for the pine high-N plot. Only a slight increase in net nitrification was measured in the hardwood stand, and only in 1993. Extractable $\\mathrm{NH}_4$ was consistently higher in treated plots than in controls in both stands, where extractable $\\mathrm{NO}_3$ was higher than controls only in the treated pine plots. Soil extracts yielded $<$1.5 kg/ha of $\\mathrm{NO}_3$-N for all plots in the hardwood stand throughout the experiment. Effluxes of $\\mathrm{N}_2$O were consistently greater in the pine high-N plot than in the pine control plot, but there were no observed large-scale increases in $\\mathrm{N}_2\\mathrm{O}$ emissions immediately following fertilizer application. Calculated nitrogen budgets for the first 6 yr showed extremely high N retention (85-99%). Of the retained N, 50-83% appears to be in the long-term, recalcitrant soil pool. The relative importance of biotic and abiotic mechanisms of N incorporation into soils remains uncertain. Size, kinetics, and uptake capacity of this soil pool are critical and largely unknown factors determining ecosystem response to increased N loading and may be related to land-use history.

Tropical soils are important sources of nitrous oxide (N2O) and nitric oxide (NO) emissions from the Earths terrestrial ecosystems. Clearing of tropical rainforest for pasture has the potential to alter N2O and NO emissions from soils by altering moisture, nitrogen supply or other factors that control N oxide production. In this review we report annual rates of N2O and NO emissions from forest and pastures of different ages in the western Brazilian Amazon state of Rondônia and examine how forest clearing alters the major controls of N oxide production. Forests had annual N2O emissions of 1.7 to 4.3 kg N ha-1 y-1 and annual NO emissions of 1.4 kg N ha-1 y-1. Young pastures of 1-3 years old had higher N2O emissions than the original forest (3.1-5.1 kg N ha-1 y-1) but older pastures of 6 years or more had lower emissions (0.1 to 0.4 kg N ha-1 y-1). Both soil moisture and indices of soil N cycling were relatively poor predictors of N2O, NO and combined N2O + NO emissions. In forest, high N2O emissions occurred at soil moistures above 30 water-filled pore space, while NO emissions occurred at all measured soil moistures (18-43). In pastures, low N availability led to low N2O and NO emissions across the entire range of soil moistures. Based on these patterns and results of field fertilization experiments, we concluded that: (1) nitrification was the source of NO from forest soils, (2) denitrification was not a major source of N2O production from forest soils or was not limited by NO- supply, (3) denitrification was a major source of N2O production from pasture soils but only when NO3- was available, and (4) nitrification was not a major source of 3 NO production in pasture soils. Pulse wettings after prolonged dry periods increased N2O and NO3- emissions for only short periods and not enough to appreciably affect annual emission rates. We project that Basin-wide, the effect of clearing for pasture in the future will be a small reduction in total N2O emissions if the extensive pastures of the Amazon continue to be managed in a way similar to current practices. In the future, both N2Oand NO fluxes could increase if uses of pastures change to include greater use of N fertilizers or N-fixing crops. Predicting the consequences of these changes for N oxide production will require an understanding of how the processes of nitrification and denitrification interact with soil type and regional moisture regimes to control N2O and NO production from these new anthropogenic N sources.

To determine whether repeated, long-term NH 4 + fertilization alters the enzymatic function of the atmospheric CH 4 oxidizer community in soil, we examined CH 4 uptake kinetics in temperate pine and hardwood forest soils amended with 150 kg N ha −1 y −1 as NH 4NO 3 for more than a decade. The highest rates of atmospheric CH 4 consumption occurred in the upper 5 cm mineral soil of the control plots. In contrast to the results of several previous studies, surface organic soils in the control plots also exhibited high consumption rates. Fertilization decreased in situ CH 4 consumption in the pine and hardwood sites relative to the control plots by 86% and 49%, respectively. Fertilization increased net N mineralization and relative nitrification rates and decreased CH 4 uptake most dramatically in the organic horizon, which contributed substantially to the overall decrease in field flux rates. In all cases, CH 4 oxidation followed Michaelis–Menten kinetics, with apparent K m ( K m(app)) values typical of high-affinity soil CH 4 oxidizers. Both K m(app) and V max(app) were significantly lower in fertilized soils than in unfertilized soils. The physiology of the methane consumer community in the fertilized soils was distinct from short-term responses to NH 4 + addition. Whereas the immediate response to NH 4 + was an increase in K m(app), resulting from apparent enzymatic substrate competition, the long-term response to fertilization was a community-level shift to a lower K m(app), a possible adaptation to diminish the competitiveness of NH 4 + for enzyme active sites.

We are conducting a field study to determine the long-term response of belowground processes to elevated soil temperatures in a mixed deciduous forest. We established 18 experimental plots and randomly assigned them to one of three treatments in six blocks. The treatments are: (1) heated plots in which the soil temperature is raised 5@?C above ambient using buried heating cables; (2) disturbance control plots (cables but no heat); and (3) undisturbed control plots (no cables and no heat). In each plot we measured indexes of N availability, the concentration of N in soil solutions leaching below the rooting zone, and trace gas emissions (CO\"2, N\"2O, and CH\"4). In this paper we present results from the first 6 mo of this study. The daily average efflux of CO\"2 increased exponentially with increasing soil temperature and decreased linearly with increasing soil moisture. A linear regression of temperature and the natural logarithm of CO\"2 flux explained 92% of the variability. A linear regression of soil moisture and CO\"2 flux could explain only 44% of the variability. The relationship between soil temperature and CO\"2 flux is in good agreement with the Arrhenius equation. For these CO\"2 flux data, the activation energy was 63 kJ/mol and the Q\"1\"0 was 2.5. The daily average uptake of CH\"4 increased linearly with increasing soil temperatures and decreased linearly with increasing soil moisture. Linear regression could explain 46% of the variability in the relationship between temperature and CH\"4 uptake and 49% of the variability in the relationship between soil moisture and CH\"4 uptake. We predicted the annual CO\"2 flux from our study site in 1991 using two empirical relationships: the relationship between air temperature and soil temperature, and the relationship between soil temperature and CO\"2 flux. We estimate that the annual CO\"2-C flux in 1991 was 712 g/m^2 from unheated soil and 1250 g/m^2 from heated soil. By elevating the soil temperature 5@?C above ambient, we estimate that an additional carbon flux of 538 g@?m^-^2@?yr^-^1 was released from the soil as CO\"2.

Efforts to restore productivity of pastures often employ agricultural management regimes involving either tillage or no-tillage options combined with various combinations of fertilizer application, herbicide use and the planting of a cash crop prior to the planting of forage grasses. Here we report on the emissions of CO^sub 2^, N^sub 2^O and NO from the initial phases (first 6 months) of three treatments in central Rondônia. The treatments were (1) control; (2) conventional tillage followed by planting of forage grass (Brachiaria brizantha) and fertilizer additions; (3) no-tillage/herbicide treatment followed by two plantings, the first being a cash crop of rice followed by forage grass. In treatment 3, the rice was fertilized. Relative to the control, tillage increased CO^sub 2^ emission by 37% over the first 2 months, while the no-tillage/herbicide regime decreased CO^sub 2^ emissions by 7% over the same period. The cumulative N^sub 2^O emissions over the first 2 months from the tillage regime (0.94 kg N ha^sup -1^) were much higher than the N^sub 2^O releases from either the no-tillage/herbicide regime (0.64 kg N ha^sup -1^) or the control treatment (0.04 kg N ha^sup -1^). The highest levels of N^sub 2^O fluxes from both management regimes were observed following N fertilizations. The cumulative NO releases over the first 2 months were largest in the tillage treatment (0.98 kg N ha^sup -1^), intermediate in the no-tillage treatment (0.72 kg N ha^sup -1^), and smallest in the control treatment (0.12 kg N ha^sup -1^). For the first week following fertilization the percentage of fertilizer N lost as N^sub 2^O plus NO was 1.0% for the tillage treatment and 3.0% for the no-tillage treatment.[PUBLICATION ABSTRACT]

Losses of nitrogen (N) often follow severe disturbance of forest ecosystems. In tropical forests, losses of N associated with the disturbance of clearing may be particularly important because rates of soil N cycling are high and forest clearing now occurs on a large scale. We measured soil solution inorganic N concentrations and fluxes for 1 year in an intact forest in the Brazilian Amazon state of Rondônia and in an adjacent 3-ha forest plot that was cleared for pasture by cutting, burning and planting pasture grass and in established cattle pastures on the same soils that were 5 and 22 years old. The cleared forest had higher soil solution NO3-concentrations than the intact forest, but the difference between the cleared and control forests declined with time after the start of the first post-clearing rainy season. Established pastures had much lower solution NH4+and NO3-concentrations than forest or cleared forest. Estimated annual dissolved inorganic solution N fluxes to below 1 m during the first year after clearing were 2.5 kg ha-1 in forest and 24.4 kg ha-1 in newly cleared forest compared with only 0.5–1.2 kg ha-1 in established pastures. The solution fluxes from cleared forest during the first year after clearing were approximately 7 times greater than gaseous N oxide (N2O + NO) losses estimated for the same time. These results were consistent with the characterization of moist tropical forests on weathered soils as N-rich and likely to respond to disturbances that elevate soil N availability with increased loss to both soil solution and the atmosphere. These results also suggest that the relative increase in N oxide loss is substantially less than the increase solution inorganic N loss.

Previous studies of the effect of tropical forest conversion to cattle pasture on soil N dynamics showed that rates of net N mineralization and net nitrification were lower in pastures compared with the original forest. In this study, we sought to determine the generality of these patterns by examining soil inorganic N concentrations, net mineralization and nitrification rates in 6 forests and 11 pastures 3 years old or older on ultisols and oxisols that encompassed a wide variety of soil textures and spanned a 700-km geographical range in the southwestern Brazilian Amazon Basin state of Rondônia. We sampled each site during October-November and April-May. Forest soils had higher extractable NO3 --N and total inorganic N concentrations than pasture soils, but substantial NO3 --N occurred in both forest and pasture soils. Rates of net N mineralization and net nitrification were higher in forest soils. Greater concentrations of soil organic matter in finer textured soils were associated with greater rates of net N mineralization and net nitrification, but this relationship was true only under native forest vegetation; rates were uniformly low in pastures, regardless of soil type or texture. Net N mineralization and net nitrification rates per unit of total soil organic matter showed no pattern across the different forest sites, suggesting that controls of net N mineralization may be broadly similar across a wide range of soil types. Similar reductions in rates of net N transformations in pastures 3 years old or older across a range of textures on these soils suggest that changes to soil N cycling caused by deforestation for pasture may be Basin-wide in extent. Lower net N mineralization and net nitrification rates in established pastures suggest that annual N losses from largely deforested landscapes may be lower than losses from the original forest. Total ecosystem N losses since deforestation are likely to depend on the balance between lower N loss rates from established pastures and the magnitude and duration of N losses that occur in the years immediately following forest clearing.