Fluxes of N2O,CH4 and CO2 on afforested boreal agricultural soils

After drainage of natural boreal peatlands, the decomposition of organic matter increases and peat soil may turn into a net source of CO₂ and N₂O, whereas CH₄ emission is known to decrease. Afforestation is a potential mitigation strategy to reduce greenhouse gas emission from organic agricultural soils. A static chamber technique was used to evaluate the fluxes of CH₄, N₂O and CO₂ from three boreal organic agricultural soils in western Finland, afforested 1, 6 or 23 years before this study. The mean emissions of CH₄ and N₂O during the growing seasons did not correlate with the age of the tree stand. All sites were sources of N₂O. The highest daily N₂O emission during the growing season, measured in the oldest site, was as high as 29 mg N₂O m^–2d^–1. In general, organic agricultural soils are sinks for methane. Here, the oldest site acted as a small sink for methane, whereas the two youngest afforested organic soils were sources for methane with maximum emission rates (up to 154 mg m^–2d^–1) similar to those reported for minerogenous natural peatlands. Soil respiration rates decreased with the age of the forest. The high soil respiration in the younger sites, probably resulted from the high biomass production of herbs, could create soil anaerobiosis and increase methane production. Our results show that afforestation of agricultural peat soils does not abruptly terminate the N₂O emissions during the first two decades, and afforestation can even enhance methane emission for a few years. The carbon accumulation in the developing tree stand can partly compensate the carbon loss from soil.     

Fluxes of CH4 and N2O in aspen stands grown under ambient and twice-ambient CO2

The objectives of this study were: (1) to quantify the effects of plant species' loss from designed calcareous grassland communities at a field site in northwestern Switzerland on the size and composition of earthworm communities, and (2) to evaluate how exposure of plant communities to elevated atmospheric CO2 might alter the effects of plant species' loss on earthworm communities. We non-destructively censused earthworm communities in each of 24 1.2 m2 experimental plots in autumn 1996 when soils were wet and earthworms were active. Each plot contained an experimental plant community with 31, 12 or 5 native plant species (eight plots each). Half of the plots in each species treatment were exposed to ambient CO2 concentrations (350 μL CO2 L-1) and half to elevated CO2 (600 μL CO2 L-1) using screen-aided CO2 control. The study was conducted in the fourth year after community establishment and the third year of CO2 treatment as part of a long-term study on the interactive effects of plant species' loss and elevated CO2 on grassland communities. The size (density and biomass) of earthworm communities declined linearly when the number of plant species in the community was reduced from 31 to 5 species (e.g. 32 ± 1 g m-2 to 23 ± 2 g m-2) due mainly to a decline in the endogeic worm species Allolobophora rosea which was the most abundant of nine earthworm species observed (nearly half of all worms in each plot). However, no changes in the relative contribution of individual species or the three main earthworm ecological groups (anecics, endogeics, epigeics) to the entire earthworm community were observed with declining number of plant species. The responses of earthworm communities to plant species'; loss appear to reflect changes in community fine root biomass in the topsoil (e.g. declining worm biomass with declining fine root biomass) observed in parallel studies conducted at this site. Further the results of this study demonstrate that a loss of plant species from these calcareous grassland communities may also alter the age structure of earthworm communities, but not significantly influence their diversity or composition. Our data also indicate that rising atmospheric CO2 may not greatly impact the size and composition of worm communities or alter the effects of plant species' loss on earthworm communities. Therefore, the disappearance of plant species from these native grasslands, as a result of ever increasing human activities, may be expected to lead to reductions in the size of earthworm communities and the ecosystem services they provide. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge

Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.     

Loss of N2O reductase activity as an explanation for poor growth of Pseudomonas aeruginosa on N2O

N2O uptake activity of cells and N2O reductase activity of the soluble fraction from denitrifying bacteria were assayed. Pseudomonas aeruginosa strains PAO1 and P1 lost most of their N2O uptake activity and the ability to grow well on N2O within 2 to 5 h after exposure to N2O. Extensive loss of N2O reductase activity accompanied the nearly complete loss of N2O uptake activity under N2O. Paracoccus denitrificans retained much, but not all, of both activities and the ability to grow vigorously on N2O. The pattern with P. aeruginosa strain P2 resembled that for PAO1 and P1 except that loss of the activities proceeded at a slower rate and growth could continue for up to 12 h after exposure to N2O. The inability of a number of P. aeruginosa strains to grow well on N2O is therefore a direct consequence of the nearly complete loss of N2O reductase activity. Turnover-dependent inactivation of N2O reductase and its reactivation under reducing conditions occurred in vitro for the enzyme from P. aeruginosa and Paracoccus denitrificans. These events may be significant in determining the activity level of N2O reductase in denitrifying bacteria during N2O respiration.     

Novel Reassortant Highly Pathogenic H5N2 Avian Influenza Viruses in Poultry in China

There has been multiple evidence that domestic poultry may act as a vessel for the generation of novel influenza A viruses. In this study, we have analyzed the evolution and pathogenicity of 4 H5N2 avian influenza viruses isolated from apparently healthy poultry from H5N1 virus endemic areas in China. Phylogenetic analysis revealed that two of these viruses, A/duck/Eastern China/1111/2011 (DK/EC/1111/11) and A/goose/Eastern China/1112/2011 (GS/EC/1112/11) were derived from reassortment events in which clade 2.3.4 highly pathogenic avian influenza (HPAI) H5N1 viruses acquired novel neuraminidase and nonstructural protein genes. Another two isolates, A/chicken/Hebei/1102/2010 (CK/HB/1102/10) and A/duck/Hebei/0908/2009 (DK/HB/0908/09), possess hemagglutinin (HA) gene belong to clade 7 H5 viruses and other genes from endemic H9N2 viruses, or from viruses of various subtypes of the natural gene pool. All of these H5N2 isolates bear characteristic sequences of HPAI virus at the cleavage site of HA, and animal experiments indicated that all of these viruses but DK/HB/0908/09 is highly pathogenic to chickens. In particular, DK/EC/1111/11 and GS/EC/1112/11 are also highly pathogenic to ducks and moderately pathogenic to mice. All of these 4 viruses were able to replicate in domestic ducks and mice without prior adaptation. The emergence of these novel H5N2 viruses adds more evidence for the active evolution of H5 viruses in Asia. The maintenance of the highly pathogenic phenotype of some of these viruses even after reassortment with a new NA subtypes, their ability to replicate and transmit in domestic poultry, and the pathogenicity in the mammalian mouse model, highlight the potential threat posed by these viruses to both veterinary and public health.     

The Impact of Nitrogen Placement and Tillage on NO, N2O, CH4 and CO2 Fluxes from a Clay Loam Soil

To evaluate the impact of N placement depth and no-till (NT) practice on the emissions of NO, N₂O, CH₄ and CO₂ from soils, we conducted two N placement experiments in a long-term tillage experiment site in northeastern Colorado in 2004. Trace gas flux measurements were made 2–3 times per week, in zero-N fertilizer plots that were cropped continuously to corn (Zea mays L.) under conventional-till (CT) and NT. Three N placement depths, replicated four times (5, 10 and 15 cm in Exp. 1 and 0, 5 and 10 cm in Exp. 2, respectively) were used. Liquid urea–ammonium nitrate (UAN, 224 kg N ha⁻¹) was injected to the desired depth in the CT- or NT-soils in each experiment. Mean flux rates of NO, N₂O, CH₄ and CO₂ ranged from 3.9 to 5.2 μg N m⁻² h⁻¹, 60.5 to 92.4 μg N m⁻² h⁻¹, −0.8 to 0.5 μg C m⁻² h⁻¹, and 42.1 to 81.7 mg C m⁻² h⁻¹ in both experiments, respectively. Deep N placement (10 and 15 cm) resulted in lower NO and N₂O emissions compared with shallow N placement (0 and 5 cm) while CH₄ and CO₂ emissions were not affected by N placement in either experiment. Compared with N placement at 5 cm, for instance, averaged N₂O emissions from N placement at 10 cm were reduced by more than 50% in both experiments. Generally, NT decreased NO emission and CH₄ oxidation but increased N₂O emissions compared with CT irrespective of N placement depths. Total net global warming potential (GWP) for N₂O, CH₄ and CO₂ was reduced by deep N placement only in Exp. 1 but was increased by NT in both experiments. The study results suggest that deep N placement (e.g., 10 cm) will be an effective option for reducing N oxide emissions and GWP from both fertilized CT- and NT-soils.     

Diverse catalytic activities in the alphabeta-hydrolase family of enzymes: activation of H2O, HCN, H2O2, and O2

The article describes the observation of novel catalytic activities in the alphabeta-hydrolase superfamily apparently unrelated to ester hydrolysis and unexpected biochemical observations relating to the structure and function of the serine catalytic triad in these enzymes. One common feature of these novel activities is the activation of a small diatomic molecule, but via diverse chemistry. Possible mechanisms of catalysis are discussed.     

Highly Diverse Endophytic and Soil Fusarium oxysporum Populations Associated with Field-Grown Tomato Plants

The diversity and genetic differentiation of populations of Fusarium oxysporum associated with tomato fields, both endophytes obtained from tomato plants and isolates obtained from soil surrounding the sampled plants, were investigated. A total of 609 isolates of F. oxysporum were obtained, 295 isolates from a total of 32 asymptomatic tomato plants in two fields and 314 isolates from eight soil cores sampled from the area surrounding the plants. Included in this total were 112 isolates from the stems of all 32 plants, a niche that has not been previously included in F. oxysporum population genetics studies. Isolates were characterized using the DNA sequence of the translation elongation factor 1α gene. A diverse population of 26 sequence types was found, although two sequence types represented nearly two-thirds of the isolates studied. The sequence types were placed in different phylogenetic clades within F. oxysporum, and endophytic isolates were not monophyletic. Multiple sequence types were found in all plants, with an average of 4.2 per plant. The population compositions differed between the two fields but not between soil samples within each field. A certain degree of differentiation was observed between populations associated with different tomato cultivars, suggesting that the host genotype may affect the composition of plant-associated F. oxysporum populations. No clear patterns of genetic differentiation were observed between endophyte populations and soil populations, suggesting a lack of specialization of endophytic isolates.     

Construction of an Acid-Tolerant Rhizobium leguminosarum Biovar Trifolii Strain with Enhanced Capacity for Nitrogen Fixation

Strain ANU1173 is an acid-tolerant Rhizobium leguminosarum biovar trifolii strain that is able to nodulate subterranean clover plants growing in agar culture at pH 4.4 At pH 6.5, its symbiotic effectiveness in association with Trifolium subterraneum cv. Mt. Barker was 80% relative to that of strain ANU794, a Sm^r derivative of the commercial inoculant R. leguminosarum bv. trifolii TA1. Strain ANU1173 contained four indigenous megaplasmids, the smallest of these being the symbiotic (Sym) plasmid. The critical pH requirement for growth of strain ANU1173 in laboratory media was shown not to be associated with this plasmid. When the Sym plasmid of strain ANU1173(pSym-1173) was mobilized into a Nod^- strain of R. leguminosarum bv. viciae, the plasmid conferred to the transconjugant a level of symbiotic effectiveness in association with T. subterraneum that was similar to that observed with ANU1173. The symbiotic effectiveness of strain ANU1173 was improved by first curing pSym-1173 (generating strain ANU1184) and replacing it with another R. leguminosarum bv. trifolii Sym plasmid, pBR1AN. Subterranean clover plants inoculated with strain ANU1184 (pBR1AN) exhibited a 35 or 53% increase in acetylene reduction activity and a 20 or 17% increase in dry weight when grown at pH 6.5 and pH 4.4, respectively, compared with plants inoculated with strain ANU1173 and grown under the same pH conditions. It was further shown that pBR1AN was stably maintained in strain ANU1184 under free-living and symbiotic conditions. These results indicate that it is possible to construct an acid-tolerant strain of R. leguminosarum bv. trifolii with an enhanced capacity for nitrogen fixation.     

Fluxes of CO2, CH4 and N2O from a Welsh peatland following simulation of water table draw-down: Potential feedback to climatic change

A potential effect of climatic change was simulated by manipulating the water table height within intact peat monoliths. The treatment decreased methane flux (maximum –80%) and increased both carbon dioxide flux (maximum 146%) and nitrous oxide flux maximum 936%). Returning the water table height to its original level caused both nitrous oxide and carbon dioxide flux to rapidly return to control levels. However, methane flux remained at its experimentally induced low levels.     

Steady-state nitrogen isotope effects of N2 and N2O production in Paracoccus denitrificans

Nitrogen stable-isotope compositions (delta15N) can help track denitrification and N2O production in the environment, as can knowledge of the isotopic discrimination, or isotope effect, inherent to denitrification. However, the isotope effects associated with denitrification as a function of dissolved-oxygen concentration and their influence on the isotopic composition of N2O are not known. We developed a simple steady-state reactor to allow the measurement of denitrification isotope effects in Paracoccus denitrificans. With [dO2] between 0 and 1.2 microM, the N stable-isotope effects of NO3- and N2O reduction were constant at 28.6 per thousand +/- 1.9 per thousand and 12.9 per thousand +/- 2.6 per thousand, respectively (mean +/- standard error, n = 5). This estimate of the isotope effect of N2O reduction is the first in an axenic denitrifying culture and places the delta15N of denitrification-produced N2O midway between those of the nitrogenous oxide substrates and the product N2 in steady-state systems. Application of both isotope effects to N2O cycling studies is discussed.     

Mechanistic studies of O2-resistant N2-fixation in N2-fixing Escherichia coli

Escherichia coli carrying the entire nif gene cluster from Klebsiella pneumoniae on a multicopy plasmid becomes more O2-resistant in a N-free medium as a result of the integration of the nif gene cluster into the chromosome and the loss of the plasmid (H.Iwahashi and J.Someya, Biochem. Biophys. Res. Comm. 1990, 168: 288–294). Our purpose is to characterize the physiological reason why the strain became O2-resistant by measuring the levels of nif proteins in cells under microaerobic conditions. The O2-resistant strain had a higher amount of NifH and a lower amount of NifL under microaerobic conditions (compared to that under anaerobic conditions), while the parent strain showed the opposite characteristics. Thus, the biochemical mechanism of the O2-resistant strain is attributed to the strain's ability to synthesize and maintain a high amount of NifH and a low amount of NifL under microaerobic conditions. © Rapid Science Ltd. 1998     

N Kinetic Analysis of N(2)O Production by Nitrosomonas europaea: an Examination of Nitrifier Denitrification

A series of N isotope tracer experiments showed that Nitrosomonas europaea produces nitrous oxide only under oxygen-limiting conditions and that the labeled N from nitrite, but not nitrate, is incorporated into nitrous oxide, indicating the presence of the "denitrifying enzyme" nitrite reductase. A kinetic analysis of the m/z 44, 45, and 46 nitrous oxide produced by washed cell suspensions of N. europaea when incubated with 4 mM ammonium (99% N) and 0.4 mM nitrite (99% N) was performed. No labeled nitrite was reduced to ammonium. All labeled material added was accounted for as either nitrite or nitrous oxide. The hypothesis that nitrous oxide is produced directly from nitrification was rejected since (i) it does not allow for the large amounts of double-labeled (m/z 46) nitrous oxide observed; (ii) the observed patterns of m/z 44, 45, and 46 nitrous oxide were completely consistent with a kinetic analysis based on denitrification as the sole mechanism of nitrous oxide production but not with a kinetic analysis based on both mechanisms; (iii) the asymptotic ratio of m/z 45 to m/z 46 nitrous oxide was consistent with denitrification kinetics but inconsistent with nitrification kinetics, which predicted no limit to m/z 45 production. It is concluded that N. europaea is a denitrifier which, under conditions of oxygen stress, uses nitrite as a terminal electron acceptor and produces nitrous oxide.     

Warming-induced enhancement of soil N2O efflux linked to distinct response times of genes driving N2O production and consumption

Temperature responses of denitrifying microbes likely play a governing role in the production and consumption of N₂O. We investigated temperature effects on denitrifier communities and their potential to produce N₂O and N₂ by incubating grassland soils collected in multiple seasons at four temperatures with ¹⁵N-enriched NO₃ ^? for ~24 h. We quantified [N₂O] concentration across time, estimated its production and reduction to N₂, and quantified relative abundance of genes responsible for N₂O production (cnorB) and reduction (nosZ). In all seasons, net N₂O production was positively linked to incubation temperature, with highest estimates of net and gross N₂O production in late spring soils. N₂O dynamics were tightly coupled to changes in denitrifier community structure, which occurred on both seasonal and incubation time scales. We observed increases in nosZ abundance with increasing incubation temperature after 24 h, and relatively larger increases in cnorB abundance from winter to late June. The difference between incubation and in situ temperature was a robust predictor of cnorB:nosZ. These data provide convincing evidence that short-term increases in temperature can induce remarkably rapid changes in community structure that increase the potential for reduction of N₂O to N₂, and that seasonal adaptation of denitrifying communities is linked to seasonal changes in potential N₂O production, with warmer seasons linked to large increases in N₂O production potential. This work helps explain observations of high spatial and temporal variation in N₂O effluxes, and highlights the importance of temperature as an influence on denitrification enzyme kinetics, denitrifier physiology and community adaptations, and associated N₂O efflux and reduction.     

The Impact of Corn Stover Removal on N2O Emission and Soil Respiration: an Investigation with Automated Chambers

Corn stover removal, whether for silage, bedding, or bioenergy production, could have a variety of environmental consequences through its effect on soil processes, particularly N₂O production and soil respiration. Because these effects may be episodic in nature, weekly snapshots with static chambers may not provide a complete picture. We adapted commercially available automated soil respiration chambers by incorporating a portable N₂O analyzer, allowing us to measure both CO₂ and N₂O fluxes on an hourly basis through two growing seasons in a corn field in southern Minnesota, from spring 2010 to spring 2012. This site was part of a USDA multilocation research project for five growing seasons, 2008–2012, with three levels of stover removal: zero, full, and intermediate. Initially in spring 2010, two chambers were placed in each of the treatments, but following planting in 2011, the configuration was changed, with four chambers installed on zero removal plots and four on full removal plots. The cumulative data revealed no significant difference in N₂O emission as a function of stover removal. CO₂ loss from the full removal plots was slightly lower than that from the zero removal plots, but the difference between treatments was much smaller than the amount of C removed in the residue, implying loss of soil carbon from the full removal plots. This is consistent with soil sampling data, which showed that in five of six sampled blocks, the SOC change in the full removal treatments was negative relative to the zero removal plots. We conclude that (a) full stover removal may have little impact on N₂O production, and (b) while it will reduce soil CO₂ production, the reduction will not be commensurate with the decrease in fresh carbon inputs and, thus, will result in SOC loss.     

Recombination Is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China

In 2009 to 2010, there was a marked increase in the number of infections with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) in China. Through phylogenetic analysis, we show that viruses from this outbreak originated from a single recombination event, illustrating the potential importance of this process for disease emergence.     

Total denitrification and the ratio between N2O and N2 during the growth of spring barley

Summary Total denitrification (N₂O+N₂) and nitrous oxide emission were measured on intact soil cores using the acetylene inhibition technique.Total denitrification from the depth 0–8 cm during the growth period from April to August was 7 kg N/ha from plots supplied with 30 kg N/ha and 19 kg N/ha from plots supplied with 120 kg N/ha. The amounts of precipitation, plant growth, and N application were found to affect the denitrification rate. These factors also affected the ratio (N₂O+N₂)/N₂O, which varied from 1.0 to 7.2. Plant growth and precipitation increased the proportion of N₂ produced, whereas a high nitrate content increased the proportion of N₂O.