Oxidation of atmospheric methane in Northern European soils, comparison with other ecosystems, and uncertainties in the global terrestrial sink

This paper reports the range and statistical distribution of oxidation rates of atmospheric CH₄ in soils found in Northern Europe in an international study, and compares them with published data for various other ecosystems. It reassesses the size, and the uncertainty in, the global terrestrial CH₄ sink, and examines the effect of land‐use change and other factors on the oxidation rate. Only soils with a very high water table were sources of CH₄; all others were sinks. Oxidation rates varied from 1 to nearly 200 μg CH₄ m^?2 h^?1; annual rates for sites measured for ≥1 y were 0.1–9.1 kg CH₄ ha^?1 y^?1, with a log‐normal distribution (log‐mean ≈ 1.6 kg CH₄ ha^?1 y^?1). Conversion of natural soils to agriculture reduced oxidation rates by two‐thirds –‐ closely similar to results reported for other regions. N inputs also decreased oxidation rates. Full recovery of rates after these disturbances takes > 100 y. Soil bulk density, water content and gas diffusivity had major impacts on oxidation rates. Trends were similar to those derived from other published work. Increasing acidity reduced oxidation, partially but not wholly explained by poor diffusion through litter layers which did not themselves contribute to the oxidation. The effect of temperature was small, attributed to substrate limitation and low atmospheric concentration. Analysis of all available data for CH₄ oxidation rates in situ showed similar log‐normal distributions to those obtained for our results, with generally little difference between different natural ecosystems, or between short‐and longer‐term studies. The overall global terrestrial sink was estimated at 29 Tg CH₄ y^?1, close to the current IPCC assessment, but with a much wider uncertainty range (7 to > 100 Tg CH₄ y^?1). Little or no information is available for many major ecosystems; these should receive high priority in future research.     

NO and N2O transformations of diverse fungi in hypoxia: evidence for anaerobic respiration only in Fusarium strains

Fungal denitrification is claimed to produce non-negligible amounts of N₂O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with . Enzymatic reduction of (NIR) and NO (NOR) was assessed by correcting measured NO- and N₂O-kinetics for abiotic NO- and N₂O-production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N₂O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N₂O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N₂O as a response to an abiotic NO production from the medium.     

Genome-wide association and genomic prediction for host response to porcine reproductive and respiratory syndrome virus infection

Background

Host genetics has been shown to play a role in porcine reproductive and respiratory syndrome (PRRS), which is the most economically important disease in the swine industry. A region on Sus scrofa chromosome (SSC) 4 has been previously reported to have a strong association with serum viremia and weight gain in pigs experimentally infected with the PRRS virus (PRRSV). The objective here was to identify haplotypes associated with the favorable phenotype, investigate additional genomic regions associated with host response to PRRSV, and to determine the predictive ability of genomic estimated breeding values (GEBV) based on the SSC4 region and based on the rest of the genome. Phenotypic data and 60 K SNP genotypes from eight trials of ~200 pigs from different commercial crosses were used to address these objectives.

Results

Across the eight trials, heritability estimates were 0.44 and 0.29 for viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain to 42 days post infection (WG), respectively. Genomic regions associated with VL were identified on chromosomes 4, X, and 1. Genomic regions associated with WG were identified on chromosomes 4, 5, and 7. Apart from the SSC4 region, the regions associated with these two traits each explained less than 3% of the genetic variance. Due to the strong linkage disequilibrium in the SSC4 region, only 19 unique haplotypes were identified across all populations, of which four were associated with the favorable phenotype. Through cross-validation, accuracies of EBV based on the SSC4 region were high (0.55), while the rest of the genome had little predictive ability across populations (0.09).

Conclusions

Traits associated with response to PRRSV infection in growing pigs are largely controlled by genomic regions with relatively small effects, with the exception of SSC4. Accuracies of EBV based on the SSC4 region were high compared to the rest of the genome. These results show that selection for the SSC4 region could potentially reduce the effects of PRRS in growing pigs, ultimately reducing the economic impact of this disease.     

Excessive use of nitrogen in Chinese agriculture results in high N2O/(N2O+N2) product ratio of denitrification,primarily due to acidification of the soils

China is the world's largest producer and consumer of fertilizer N, and decades of overuse has caused nitrate leaching and possibly soil acidification. We hypothesized that this would enhance the soils' propensity to emit N₂O from denitrification by reducing the expression of the enzyme N₂O reductase. We investigated this by standardized oxic/anoxic incubations of soils from five long‐term fertilization experiments in different regions of China. After adjusting the nitrate concentration to 2 mM, we measured oxic respiration (R), potential denitrification (D), substrate‐induced denitrification, and the denitrification product stoichiometry (NO, N₂O, N₂). Soils with a history of high fertilizer N levels had high N₂O/(N₂O+N₂) ratios, but only in those field experiments where soil pH had been lowered by N fertilization. By comparing all soils, we found a strong negative correlation between pH and the N₂O/(N₂O+N₂) product ratio (r² = 0.759, P < 0.001). In contrast, the potential denitrification (D) was found to be a linear function of oxic respiration (R), and the ratio D/R was largely unaffected by soil pH. The immediate effect of liming acidified soils was lowered N₂O/(N₂O+N₂) ratios. The results provide evidence that soil pH has a marginal direct effect on potential denitrification, but that it is the master variable controlling the percentage of denitrified N emitted as N₂O. It has been known for long that low pH may result in high N₂O/(N₂O+N₂) product ratios of denitrification, but our documentation of a pervasive pH‐control of this ratio across soil types and management practices is new. The results are in good agreement with new understanding of how pH may interfere with the expression of N₂O reductase. We argue that the management of soil pH should be high on the agenda for mitigating N₂O emissions in the future, particularly for countries where ongoing intensification of plant production is likely to acidify the soils.     

Nitrous Oxide Production and Methane Oxidation by Different Ammonia-Oxidizing Bacteria

Ammonia-oxidizing bacteria (AOB) are thought to contribute significantly to N₂O production and methane oxidation in soils. Most of our knowledge derives from experiments with Nitrosomonas europaea, which appears to be of minor importance in most soils compared to Nitrosospira spp. We have conducted a comparative study of levels of aerobic N₂O production in six phylogenetically different Nitrosospira strains newly isolated from soils and in two N. europaea and Nitrosospira multiformis type strains. The fraction of oxidized ammonium released as N₂O during aerobic growth was remarkably constant (0.07 to 0.1%) for all the Nitrosospira strains, irrespective of the substrate supply (urea versus ammonium), the pH, or substrate limitation. N. europaea and Nitrosospira multiformis released similar fractions of N₂O when they were supplied with ample amounts of substrates, but the fractions rose sharply (to 1 to 5%) when they were restricted by a low pH or substrate limitation. Phosphate buffer (versus HEPES) doubled the N₂O release for all types of AOB. No detectable oxidation of atmospheric methane was detected. Calculations based on detection limits as well as data in the literature on CH₄ oxidation by AOB bacteria prove that none of the tested strains contribute significantly to the oxidation of atmospheric CH₄ in soils.     

Cortisol receptor expression differs in the brains of rainbow trout selected for divergent cortisol responses

In rainbow trout (Oncorhynchus mykiss), selection for divergent post-stress plasma cortisol levels has yielded low (LR)- and high (HR) responsive lines, differing in behavioural and physiological aspects of stress coping. For instance, LR fish display prolonged retention of a fear response and of previously learnt routines, compared to HR fish. This study aims at investigating putative central nervous system mechanisms controlling behaviour and memory retention. The stress hormone cortisol is known to affect several aspects of cognition, including memory retention. Cortisol acts through glucocorticoid receptors 1 and 2 (GR1 and 2) and a mineralcorticoid receptor (MR), all of which are abundantly expressed in the salmonid brain. We hypothesized that different expressions of MR and GRs in LR and HR trout brains could be involved in the observed differences in cognition. We quantified the mRNA expression of GR1, GR2 and MR in different brain regions of stressed and non-stressed LR and HR trout. The expression of MR was higher in LR than in HR fish in all brain parts investigated. This could be associated with reduced anxiety and enhanced memory retention in LR fish. MR and GR1 expression was also subject to negative regulation by stress in a site-specific manner.     

Microbial Biomass, Community Structure and Metal Tolerance of a Naturally Pb-Enriched Forest Soil

The effect of long-term elevated soil Pb levels on soil microbiota was studied at a forest site in Norway, where the soil has been severely contaminated with Pb since the last period of glaciation (several thousand years). Up to 10% Pb (total amount, w/w) has been found in the top layer. The microbial community was drastically affected, as judged from changes in the phospholipid fatty acid (PLFA) pattern. Specific PLFAs that were high in Pb-enriched soil were branched (especially br17:0 and br18:0), whereas PLFAs common in eukaryotic organisms such as fungi (18:2ω6,9 and 20:4) were low compared with levels at adjacent, uncontaminated sites. Congruent changes in the PLFA pattern were found upon analyzing the culturable part of the bacterial community. The high Pb concentrations in the soil resulted in increased tolerance to Pb of the bacterial community, measured using both thymidine incorporation and plate counts. Furthermore, changes in tolerance were correlated to changes in the community structure. The bacterial community of the most contaminated soils showed higher specific activity (thymidine and leucine incorporation rates) and higher culturability than that of control soils. Fungal colony forming units (CFUs) were 10 times lower in the most Pb-enriched soils, the species composition was widely different from that in control soils, and the isolated fungi had high Pb tolerance. The most commonly isolated fungus in Pb-enriched soils was Tolypocladium inflatum. Comparison of isolates from Pb-enriched soil and isolates from unpolluted soils showed that T. inflatum was intrinsically Pb-tolerant, and that the prolonged conditions with high Pb had not selected for any increased tolerance.     

Gastrointestinal and renal responses to water intake in the green-backed firecrown (Sephanoides sephanoides), a South American hummingbird

To maintain water balance, nectar-feeding vertebrates oscillate between meeting the challenges of avoiding overhydration and preventing dehydration. To understand how green-backed firecrowns (Sephanoides sephanoides) accomplish this, we examined the response of water-handling processes in the gastrointestinal tract (GIT) and kidney to different rates of water intake during the evening, night, and morning. Fractional water absorption in the GIT was independent of water intake rate (evening: 0.91 +/- 0.08; morning: 0.88 +/- 0.04). Consistent with this nonregulated water absorption, we found linear increases in water flux, fractional turnover of body water, and the rate of renal water loading as water intake rate increased during both the evening and morning. Despite these relationships, glomerular filtration rate (GFR) was insensitive to water loading (evening: 2.08 +/- 0.56 ml/h; morning: 1.84 +/- 0.68 ml/h) and less than the allometric expectation (2.92 ml/h). During the evening, fractional renal water reabsorption decreased linearly as the rate of water intake increased. At night, a period of natural fasting for hummingbirds, mean GFR was not different from zero (0.00 +/- 0.05 ml/h). These findings indicate that green-backed firecrowns eliminate excess ingested water by decreasing water reabsorption in the kidney; to conserve water, it appears that hummingbirds arrest whole kidney GFR, effectively preventing urinary water losses. After discounting evaporative water losses, our results show that hummingbirds rely principally on their renal system to resolve the osmoregulatory quandary posed by nectarivory.