Characteristics of a nitrogen-fixing methanotroph,Methylocystis T-1

A methane-oxidizing bacterium capable of nitrogen fixation was isolated from soil taken from an area which leaked methane gas. Strain T-1 was a catalase and oxidase-positive, gram-negative straight rod-shaped strictly aerobic bacterium which formed lipid cysts and type II intracytoplasmic membranes. The organism was a microaerophilic nitrogen-fixing methanotroph. Strain T-1 is considered to be classified intoMethylocystis. The organism evolved hydrogen gas when grown in the nitrogen-free medium of atmospheric oxygen concentrations of 1.5% or more. Below this level, however, hydrogen gas was not evolved. In addition to methanol, formaldehyde and formate, ethanol, acetate and hydrogen gas served as oxidizable substrates for the acetylene reduction test. H₂-stimulated nitrogenase activity was limited in a very narrow range of oxygen concentration and not detected at 2% O₂. With acetate as the substrate, however, about an 80% of the maximum acetylene reduction activity was detected at 2% O₂. These results suggest that strain T-1 is capable of recycling the hydrogen gas evolved during nitrogen fixation under low partial pressures of O₂.     

NO Gas Loss from Biologically Crusted Soils in Canyonlands National Park,Utah

In this study, we examined N gas loss as nitric oxide (NO) from N-fixing biologically crusted soils in Canyonlands National Park, Utah. We hypothesized that NO gas loss would increase with increasing N fixation potential of the biologically crusted soil. NO fluxes were measured from biologically crusted soils with three levels of N fixation potential (Scytonema-Nostoc-Collema spp. (dark)>Scytonema-Nostoc-Microcoleus spp. (medium)>Microcoleus spp. (light)) from soil cores and field chambers. In both cores and field chambers there was a significant effect of crust type on NO fluxes, but this was highly dependent on season. NO fluxes from field chambers increased with increasing N fixation potential of the biologically crusted soils (dark>medium>light) in the summer months, with no differences in the spring and autumn. Soil chlorophyllasis Type a content (an index of N fixation potential), percent N, and temperature explained 40% of the variability in NO fluxes from our field sites. Estimates of annual NO loss from dark and light crusts was 0.04-0.16 and 0.02-0.11-N/ha/year. Overall, NO gas loss accounts for approximately 3-7% of the N inputs via N fixation in dark and light biologically crusted soils. Land use practices have drastically altered biological soil crusts communities over the past century. Livestock grazing and intensive recreational use of public lands has resulted in a large scale conversion of dark cyanolichen crusts to light cyanobacterial crusts. As a result, changes in biologically crusted soils in arid and semi-arid regions of the western US may subsequently impact regional NO loss.     

Conservation in soil of h(2) liberated from n(2) fixation by hup nodules

Pigeon peas (Cajanus cajan) were grown in large soil columns (90-cm length by 30-cm diameter) and inoculated with four different strains of cowpea rhizobia, which varied with respect to hydrogen uptake activity (Hup). Despite the profuse liberation of H(2) from Hup nodules in vitro, H(2) gas was not detected in any of the soil columns. When H(2) was injected into the columns, the rates of consumption were highest in the treatments (including control) containing Hup nodules (218 and 177 nmol . h . cm) and lowest in the Hup treatments (158, 92, and 64 nmoles . h . cm). In situ H(2) uptake rates in small soil cores at fixed distances from the nodules decreased exponentially with distance from the nodule (R = 0.99). This decrease in H(2) consumption was associated with a similar decrease in numbers of H(2)-oxidizing chemolithotrophic bacteria as determined by the most-probable-number method. On the basis of two equations derived separately upon diffusive theory (Fix's Law) and kinetic theory (Michaelis-Menten), the empirically derived rate constants and coefficients indicated that all of the H(2) emitted from Hup nodules would be consumed by H(2)-oxidizing bacteria within a 3- to 4.5-cm radius of the nodule surface. It is concluded that H(2) is not lost from the soil-plant ecosystem during N(2) fixation in C. cajan but is conserved by H(2)-oxidizing bacteria.     

Soybean genotypic differences in sensitivity of symbiotic nitrogen fixation to soil dehydration

Nitrogen fixation activity by soybean (Glycine max (L.) Merr.) nodules has been shown to be especially sensitive to soil dehydration. Specifically, nitrogen fixation rates have been found to decrease in response to soil dehydration preceding alterations in plant gas exchange rates. The objective of this research was to investigate possible genetic variation in the sensitivity of soybean cultivars for nitrogen fixation rates in response to soil drying. Field tests showed substantial variation among cultivars with Jackson and CNS showing the least sensitivity in nitrogen accumulation to soil drying. Glasshouse experiments confirmed a large divergence among cultivars in the nitrogen fixation response to drought. Nitrogen fixation in Jackson was again found to be tolerant of soil drying, but the other five cultivars tested, including CNS, were found to be intolerant. Experiments with CNS which induced localized soil drying around the nodules did not result in decreases in nitrogen fixation rates, but rather nitrogen fixation responded to drying of the entire rooting volume. The osmotic potential of nodules was found to decrease markedly upon soil drying. However, the decrease in nodule osmotic potential occurred after significant decreases in nitrogen fixation rates had already been observed. Overall, the results of this study indicate that important genetic variations for sensitivity of nitrogen fixation to soil drying exist in soybean, and that the variation may be useful in physiology and breeding studies.     

The effect of water-logging on fixation of nitrogen by soil incubated with straw

Summary When straw was incubated with a calcareous soil under water-logged conditions nitrogen fixation occurred if the gas above the incubation contained oxygen: no detectable fixation occurred if oxygen was excluded. Moist soil failed to fix nitrogen when incubated with straw in either the presence or absence of oxygen.     

Hydrogen oxidation and nitrogen fixation in rhizobia,with special attention focused on strain ORS 571

In this survey we describe the influence of hydrogen oxidation on the physiology ofRhizobium ORS 571. The presence of hydrogen is required for the synthesis of hydrogenase. Carbon substrates do not repress the synthesis of hydrogenase. The respiratory system contains cytrochromes of theb- andc-type. Cytochromea ₆₀₀ is present after growth at high oxygen tensions. The nature of the terminal oxidases functioning at low oxygen tensions has not been established yet. → H⁺/O values with endogenous substrates are between 6 and 7. The results show the presence of two phosphorylation sites: site 1 (ATP/2e=1.0) and site 2(ATP/2e=1.33). By measuring molar growth yields it has been demonstrated that carbon-limited, nitrogen-fixing cultures obtain additional ATP from hydrogen oxidation, and that site 2 of oxidative phosphorylation is passed during hydrogen oxidation. A method is described to calculate ATP/N₂ values (the total amount of ATP used by nitrogenase during the fixation of 1 mol N₂) and H₂/N₂ ratios (mol hydrogen formed per mol N₂ fixed) in aerobic organisms. ForRhizobium ORS 571 the ATP/N₂ value is about 40 and the H₂/N₂ ratio is between 5 and 7.5. Cells obtained from oxygen-limited nitrogen-fixing cultures contain 30–40% poly-β-hydroxybutyrate, which explains the high molar growth yields found. Hydrogen has not been detected in the effluent gas of these cultures, which may point to reoxidation of the hydrogen formed at nitrogen fixation. Calculations show that the effect of hydrogen reoxidation on the efficiency of nitrogen fixation (g N fixed × mol⁻¹ substrate converted) is not very large and that the actual H₂/N₂ ratio is of much more importance. After addition of hydrogen to succinate-limited, ammonia-assimilating cultures, an initial increase of the Y_succinate value (g dry wt × mol⁻¹ succinate) is followed by a gradual decrease. This is accompanied by a large decrease of the value, and an increased permeability of the cytoplasmic membrane to protons. The results may be explained by a transition of the culture from an energy-limited state to a carbon-limited state.     

Problems of the Acetylene Reduction Technique Applied to Water-Saturated Paddy Soils

The acetylene reduction assay for the measurement of N₂ fixation in a water-saturated paddy soil is limited by the slow diffusion of acetylene and ethylene. In laboratory incubation tests, vigorous shaking after the assay period is needed to release ethylene into the gas within the assay vials. Shaking prior to the incubation is also effective for dissolving acetylene in the water-saturated soil. However, a water-saturated soil depth of less than 10 mm during incubation is recommended. In field assays, some amounts of ethylene remain in the water-saturated soil phase of the acetylene reduction assay chamber, but stirring the water-saturated soil before sampling reduces the amount of ethylene remaining in soil. Evidence of a downward movement of acetylene and an upward movement of ethylene through rice plants was obtained. Because of the rapid transfer of acetylene to rice plant roots, an in situ acetylene reduction assay covering a rice hill is likely to detect nitrogen fixation in the proximity of roots where acetylene is easily accessible. Acetylene introduction to the water-saturated soil phase prior to assay did not greatly increase the acetylene reduction rate. Carbon dioxide enrichment in the assay chamber did not enhance nitrogen fixation in a paddy including rice and algae during a 1-day cycle.     

X-ray, ESR, and quantum mechanics studies unravel a spin well in the cofactor-less urate oxidase

Urate oxidase (EC 1.7.3.3 or UOX) catalyzes the conversion of uric acid using gaseous molecular oxygen to 5-hydroxyisourate and hydrogen peroxide in absence of any cofactor or transition metal. The catalytic mechanism was investigated using X-ray diffraction, electron spin resonance spectroscopy (ESR), and quantum mechanics calculations. The X-ray structure of the anaerobic enzyme-substrate complex gives credit to substrate activation before the dioxygen fixation in the peroxo hole, where incoming and outgoing reagents (dioxygen, water, and hydrogen peroxide molecules) are handled. ESR spectroscopy establishes the initial monoelectron activation of the substrate without the participation of dioxygen. In addition, both X-ray structure and quantum mechanic calculations promote a conserved base oxidative system as the main structural features in UOX that protonates/deprotonates and activate the substrate into the doublet state now able to satisfy the Wigner's spin selection rule for reaction with molecular oxygen in its triplet ground state.     

Rhizosphere soil nitrogenase (C2H2 reduction) as influenced by plant density in intermediate deep water rice

Summary Nitrogenase activity in the rhizosphere soil of intermediate deep water rice was investigated employing gas chromatographic acetylene reduction assay. A raise in the plant density decreased the rhizosphere nitrogenase. Moreover, nitrogen fixation in the rhizosphere soil varied among the three rice varieties under intermediate deep water situations. Results indicate that nitrogen fixation is affected by plant density and the rice variety.     

Conformational study of erythritol and threitol in the gas state by density functional theory calculations

Density functional theory calculations using the B3LYP functional and the 6-311++G(d,p) basis set were carried out on the isolated molecules of erythritol and L-threitol. For the meso isomer, a relatively large number of conformers have to be considered to describe the gas state structure. The lowest energy conformer is characterized by the establishment of a strong intramolecular H-bond between the two terminal hydroxyl groups, giving rise to a seven-membered ring and two additional weaker H-bonds between vicinal OH groups. In the case of L-threitol, two conformers are predominant in the gas state, and both are stabilized by the formation of a cyclic system of four intramolecular hydrogen bonds involving all OH groups. The conformational stability in both diastereomers is discussed in terms of the electronic energy and of the Gibbs energy. The weighted mean enthalpy of both diastereomers in the gas state at 298.15 K was obtained from the thermodynamic data and Boltzmann populations of the low-energy conformers.     

Treatment of Used Diesel Invert Drilling Mud to Remove Hydrocarbons,Fix Lead,and Leach Brine

A sample of used, highly saline diesel invert drilling mud (DIDM), artificially contaminated with lead, was tested for remediation using ICPET/ NRC's Solvent Extraction Soil Remediation (SESR) process. The work comprised investigation of the concurrent solvent extraction of diesel oil and fixation of lead by co-agglomeration of metal binding agents. Peat, soluble and insoluble phosphates, coal combustion fly ashes, and flue gas desulfurization scrubber sludge were tested as lead fixation agents. Virtually complete extraction of diesel oil was achieved in a five-step extraction process using toluene, trichloroethylene, or hexane as solvents. The effect of the metal fixation agents on solvent extraction efficiency was also investigated. After remediation to remove hydrocarbons and fix heavy metals, the DIDM sample remained saline. Successful leaching of brine from the dried agglomerates was accomplished by water percolation through a fixed bed of the dried, agglomerated soil. The cleaned DIDM was evaluated for resistance to acid leaching of lead using the U.S.-EPA's toxicity test method 1310A and Toxicity Characteristics Leaching Procedure method 1311. Long-term stability of the treated solids to acid leaching was tested using the U.S.EPA's multiple extraction procedure method 1320. Bioavailability of fixed lead to barley plants grown on synthetic soils prepared from remediated DIDM was determined by analyzing the roots and shoots for lead content. Acid phosphatase, peroxidase, and protein levels were determined in plant roots and soil leachates by biochemical analysis methods. These results were used to assess the effect of enzymes produced by plant root systems, or soil associated microorganisms, on the stability of fixed lead. The presence of fixation agents reduced the bioavailability of lead to the plants.     

N2Fixation Response to Drought in Common Bean (Phaseolus vulgarisL.)

Nitrogen fixation activity in common bean is generally thoughtto be low and sensitive to soil drying and, consequently, droughtcan have important negative effects on N accumulation and yieldpotential. The objectives of this research were to examine theresponse of N₂fixation to drought stress in common bean, andto test the hypothesis that drought sensitivity of N₂fixationin common bean is linked to ureide levels in the plants. Twoglasshouse experiments were conducted to compare the responsesof leaf transpiration and acetylene reduction activity (ARA)to soil water contents. ARA decrease during soil dehydrationwas found to lag behind the decline in transpiration. This indicatesthat ARA is relatively less sensitive to soil dehydration comparedto leaf gas exchange. Further, in comparing two cultivars therewas no consistent difference in the relative response of ARAand transpiration to soil drying. The ureide concentrationsmeasured in common bean plants were low, ranging from 0.1 to1.0 mmol l^-1in xylem sap exudates. Ureide concentrations inthe sap exudate varied significantly among the two genotypeseven though there was no difference in ARA response to drought.It was concluded that in common bean, the lower sensitivityof N₂fixation to drought compared to leaf gas exchange couldbe related to low ureide concentrations in petioles and xylemsap.Copyright 1998 Annals of Botany Company Phaseolus vulgaris,nitrogen fixation, drought stress, nodules, ureides.     

Hydrogen metabolism and energy costs of nitrogen fixation

Abstract The high energy costs of biological nitrogen fixation are partly caused by hydrogen production during the reduction of dinitrogen to ammonia. Some nitrogen-fixing organisms can recycle the evolved hydrogen via a membrane-bound uptake hydrogenase. The energetic aspects of hydrogen metabolism and nitrogen fixation are discussed.
Studies on both isolated nitrogenase proteins and nitrogen-fixing chemostat cultures show that energy limitation will result in a high hydrogen production by nitrogenase. In plant- Rhizobium symbiosis, the supply of oxygen or photosynthetate is the limiting factor for nitrogen fixation. In both cases, nitrogen fixation is energy-limited, and it is concluded that a large amount of hydrogen is produced during nitrogen fixation in these symbioses.
Hydrogen reoxidation yields less energy than the oxidation of endogenous substrates, and therefore expression of hydrogenase under oxygen-limited conditions is energetically unfavourable. Moreover, hydrogen reoxidation can never completely regain the energy invested during hydrogen production. The controversial reports of the effect of hydrogen reoxidation on the efficiency of nitrogen fixation are being discussed.
The determination of the energy costs of nitrogen fixation (expressed as the amount of ATP needed to fix 1 mol of N₂) using chemostat cultures is described. Calculations show that the nitrogenase-catalysed hydrogen production has more influence on the efficiency of nitrogen fixation than the absence or presence of a hydrogen uptake system.     

Ab initio conformational study of N-acetyl-L-proline-N',N'-dimethylamide: a model for polyproline

We report here the results on N-acetyl-l-proline-N',N'-dimethylamide (Ac-Pro-NMe2) as a model for polyproline at the HF/6-31+G(d) level with the conductor-like polarizable continuum model of self-consistent reaction field methods to figure out the conformational preference and cis-trans isomerization of polyproline in the gas phase, chloroform, methanol, and water. The second methyl substitution at the carboxyl amide end results in different backbone structures and their populations from those of N-acetyl-L-proline-N-methylamide (Ac-Pro-NHMe). In particular, all conformations with the C7 hydrogen bond between acetyl and amide ends, which is the most probable conformations of Ac-Pro-NHMe in the gas phase and in nonpolar solvents, disappeared for Ac-Pro-NMe2 even in the gas phase due to the lack of amide hydrogen. The dominant conformation for Ac-Pro-NMe2 is the polyproline II structure with the trans prolyl peptide bond in the gas phase and in solutions. In methanol, the population of the polyproline I structure with the cis prolyl peptide bond is calculated to be larger than that in water, which is consistent with experiments. It should be noted that Ac-Pro-NMe2 has higher rotational barriers for the cis-trans isomerization of the Ac-Pro peptide bond than Ac-Pro-NHMe in the gas phase and in solutions, which could be due to the lack of the intramolecular hydrogen bond between prolyl nitrogen and carboxyl N-H group for the transition state of Ac-Pro-NMe2. The rotational barriers for Ac-Pro-NMe2 are increased with the increase of solvent polarity, as seen for Ac-Pro-NHMe.     

Effect of hydrogen on soil bacterial community structure in two soils as determined by terminal restriction fragment length polymorphism

The metabolism of hydrogen evolved from HUP^? legume nodules can alter bacterial community structures in the rhizosphere. Our earlier experiments demonstrated increased hydrogen uptake and appearance of white spots within bacterial colonies in H₂-treated soil. We were also able to isolate hydrogen-oxidizing bacteria from soil samples exposed to hydrogen, but not from samples exposed to air. To further understand the effect of hydrogen metabolism on soil microbial communities, in this study 16S rRNA terminal restriction fragment (TRF) profiles of different soil samples exposed to hydrogen gas under laboratory, greenhouse, and field conditions were analyzed. Relationships between soil bacterial community structures from hydrogen-treated soil samples and controls, illustrated by UPGMA (unpaired group mathematical averages) dendrograms, indicated a significant contribution of hydrogen metabolism to the variation in bacterial community. The intensity variation of TRF peaks includes both hydrogen-utilizing bacteria, whose growth were stimulated by hydrogen exposure, and other bacterial species whose growth was inhibited. Comparison of TRF profiles between laboratory and greenhouse samples showed that T-RFLP is a useful technique in the detection of root-related effects on soil bacterial community structure.     

Temperature influence on the energy of nonspecific and specific interactions taking place between 4-aminophthalimide (4-AP) and homogeneous solvents.

Temperature induced spectral shifts of the 4-aminophthalimide (4-AP) emission spectra have been measured and compared to the predictions of the McRae solvent induced shift theory (J. Phys. Chem., 1957, 61, 562-572). Three moderately polar chloroalkanes selected as nonspecifically interacting media, and six hydrogen accepting or/and electron pair donating solvents have been used as the media in which the temperature influence on 4-AP-solvent interactions has been studied in the range of 180-320 K. Using the ab initio determined 4-AP ground state dipole moment and fitting appropriate expression originating from the mentioned theory to the shifts found in the chloroalkanes it has been possible to estimate the 4-AP excited state dipole moment, the probe excited state Onsager radius and its gas phase emission spectrum position. Using these values the thermochromic shifts of 4-AP emission spectra in hydrogen bond forming solvents have been predicted and compared to the experimental one. Temperature has been found to have different impact on the changes, upon excitation of the probe, in the mean values of the energies of different hydrogen bonds formed by 4-AP with solvents molecules.     

Detection of a Reproducible,Single-Member Shift in Soil Bacterial Communities Exposed to Low Levels of Hydrogen

Soil is exposed to hydrogen when symbiotic rhizobia in legume root nodules cannot recycle the hydrogen that is generated during nitrogen fixation. The hydrogen emitted is most likely taken up by free-living soil bacteria that use hydrogen as an energy source, though the bacteria that do this in situ remain unclear. In this study, we investigated the effect of hydrogen exposure on the bacteria of two different soils in a microcosm setup designed to simulate hydrogen-emitting root nodules. Although the size and overall composition of the soil bacterial community did not significantly alter after hydrogen exposure, one ribotype increased in relative abundance within each soil. This single-ribotype shift was identified by generating multiple terminal restriction fragment length polymorphism (T-RFLP) profiles of 16S rRNA genes from each soil sample, with gene sequence confirmation to identify terminal restriction fragments. The increased abundance of a single ribotype after hydrogen exposure, within an otherwise similar community, was found in replicate samples taken from each microcosm and was reproducible across replicate experiments. Similarly, only one member of the soil bacterial community increased in abundance in response to hydrogen exposure in soil surrounding the root nodules of field-grown soybean (Glycine max). The ribotypes that increased after hydrogen exposure in each soil system tested were all from known hydrogen-oxidizing lineages within the order Actinomycetales. We suggest that soil actinomycetes are important utilizers of hydrogen at relevant concentrations in soil and could be key contributors to soil''s function as a sink in the global hydrogen cycle.Soil is the major sink in the global hydrogen cycle and accounts for approximately 75 to 80% of uptake from the atmosphere (7, 11). Soil is such a strong sink that the atmospheric mixing ratio of molecular hydrogen, H₂, is hemispherically asymmetric because of the greater landmass in the Northern Hemisphere (11). Many nitrogen-fixing bacteria that form symbiotic relationships with legume plants cannot recycle the H₂ that is generated during N₂ fixation (2, 13). Most of the H₂ emitted from legume root nodules is taken up by the surrounding soil, within a few centimeters of the nodule surface, and is not released to the atmosphere (20). Although the H₂ emitted by the rhizobial symbionts costs the legume approximately 5% of its daily photosynthate and “represents a significant investment by the plant” (9), there is growing evidence to suggest that soil exposed to H₂ is beneficial to plant growth, separate from the benefits derived from N₂ fixation (8, 10, 28). Previously, La Favre and Focht have hypothesized that “the hydrogen which is evolved during N₂ fixation represents an additional energy input into the plant-soil ecosystem… since metabolism of H₂ by chemolithotrophic bacteria results in an input of fixed carbon to the system” (20). A number of studies have found that when H₂ is taken up by soil, net CO₂ fixation occurs at the rate of 7 to 8 nmol CO₂ per g of soil per h (22, 34). For a legume fixing 200 kg of atmospheric N₂ per hectare, over 200,000 liters of H₂ could be released into the legume''s rhizosphere over the duration of the growing season and CO₂ fixation could result in an extra 25 kg of soil carbon fixed per hectare (9, 10, 28).Many bacteria isolated from soil are able to utilize H₂ as an energy source (2, 5-7, 21), and free-living bacteria are most likely responsible for the H₂ uptake observed by soil surrounding legume roots (22). Adding a bacterial energy source, such as H₂, could affect the microbial population size, as has been observed previously (34), but more specific shifts within the bacterial community may occur if just the microorganisms able to utilize the energy source multiply. Their activity could also have downstream consequences specifically on other members of the community. Most H₂-oxidizing cultures have required enrichment with concentrations of H₂ that are not environmentally relevant and therefore cannot be assumed to be carrying out H₂ oxidation at much lower, naturally occurring concentrations (5-7). Recent surveys of microbes present in soil samples, via their nucleic acids, have revealed many novel bacterial inhabitants that have been little studied and thus may also be contributing to the repertoire of bacterial soil processes, such as H₂ uptake (16). A recent study into the effect of H₂ on soil bacteria focused on a few groups of H₂-oxidizing, autotrophic bacteria and thus ignored many other H₂ utilizers potentially present in soil (34).There are now many ways of characterizing the entire microbial community in environmental samples, either via their entire genomic content, though metagenomic analysis of soil is difficult at present, or via analysis of the lineages present according to 16S rRNA gene sequences, or ribotypes (36). A recent study comparing high-throughput pyrosequencing of 16S rRNA genes and an easily accessible profiling method, known as terminal restriction fragment length polymorphism (T-RFLP), found the simpler profiles were appropriate for comparing the dominant ribotypes in multiple samples (24). Although T-RFLP profiles only provide a simplified snapshot of the dominant members in microbial communities, compared to the deeper analyses provided by microarrays or high-throughput sequencing technologies, T-RFLP profiling is a cost-effective, reproducible, and robust method of “fingerprinting” many soil samples rapidly and efficiently (14, 24, 25, 32).In this study, we chose to assess the dominant members of the soil bacterial community via T-RFLP profiles of ribotypes present in H₂-treated and control soils to avoid a narrow focus on well-studied H₂ oxidizers. We investigated the bacterial community structure in two different soils, utilizing a microcosm setup with concentrations of H₂ calculated to occur in the rhizosphere of N₂-fixing legumes, to determine whether common responses to H₂ exposure could be predicted from soils that differ by climate, edaphic characteristics, and starting communities. Soil in microcosms has previously been shown to have similar H₂ uptake properties to soil close to H₂-emitting legume nodules (9), but we also complemented our plant-free microcosm work with an examination of soil collected from the root systems of field-grown soybean (Glycine max (L.) Merr.).     

Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO).

Production and consumption processes in soils contribute to the global cycles of many trace gases (CH4, CO, OCS, H2, N2O, and NO) that are relevant for atmospheric chemistry and climate. Soil microbial processes contribute substantially to the budgets of atmospheric trace gases. The flux of trace gases between soil and atmosphere is usually the result of simultaneously operating production and consumption processes in soil: The relevant processes are not yet proven with absolute certainty, but the following are likely for trace gas consumption: H2 oxidation by abiontic soil enzymes; CO cooxidation by the ammonium monooxygenase of nitrifying bacteria; CH4 oxidation by unknown methanotrophic bacteria that utilize CH4 for growth; OCS hydrolysis by bacteria containing carbonic anhydrase; N2O reduction to N2 by denitrifying bacteria; NO consumption by either reduction to N2O in denitrifiers or oxidation to nitrate in heterotrophic bacteria. Wetland soils, in contrast to upland soils are generally anoxic and thus support the production of trace gases (H2, CO, CH4, N2O, and NO) by anaerobic bacteria such as fermenters, methanogens, acetogens, sulfate reducers, and denitrifiers. Methane is the dominant gaseous product of anaerobic degradation of organic matter and is released into the atmosphere, whereas the other trace gases are only intermediates, which are mostly cycled within the anoxic habitat. A significant percentage of the produced methane is oxidized by methanotrophic bacteria at anoxic-oxic interfaces such as the soil surface and the root surface of aquatic plants that serve as conduits for O2 transport into and CH4 transport out of the wetland soils. The dominant production processes in upland soils are different from those in wetland soils and include H2 production by biological N2 fixation, CO production by chemical decomposition of soil organic matter, and NO and N2O production by nitrification and denitrification. The processes responsible for CH4 production in upland soils are completely unclear, as are the OCS production processes in general. A problem for future research is the attribution of trace gas metabolic processes not only to functional groups of microorganisms but also to particular taxa. Thus, it is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level. However, different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature; or different rates and modes of NO and N2O production in different soils and under different conditions.