Soil-atmosphere exchange of nitrous oxide and methane in New Zealand terrestrial ecosystems and their mitigation options: a review

The two non-CO₂ greenhouse gases (GHGs) nitrous oxide (N₂O) and methane (CH₄) comprise 54.8% of total New Zealand emissions. Nitrous oxide is mainly generated from mineral N originating from animal dung and urine, applied fertiliser N, biologically fixed N₂, and mineralisation of soil organic N. Even though about 96% of the anthropogenic CH₄ emitted in New Zealand is from ruminant animals (methanogenesis), methane uptake by aerobic soils (methanotrophy) can significantly contribute to the removal of CH₄ from the atmpsphere, as the global estimates confirm. Both the net uptake of CH₄ by soils and N₂O emissions from soils are strongly influenced by changes in land use and land management. Quantitative information on the fluxes of these two non-CO₂ GHGs is required for a range of land-use and land-management ecosystems to determine their contribution to the national emissions inventory, and for assessing the potential of mitigation options. Here we report soil N₂O fluxes and CH₄ uptake for a range of land-use and land-management systems collated from published and unpublished New Zealand studies. Nitrous oxide emissions are highest in dairy-grazed pastures (10–12 kg N₂O–N ha^?1 year^{? 1}), intermediate in sheep-grazed pastures, (4–6 kg N₂O–N ha^?1 year^?1), and lowest in forest, shrubland and ungrazed pasture soils (1–2 kg N₂O–N ha^?1 year^?1). N deposited in the form of animal urine and dung, and N applied as fertiliser, are the principal sources of N₂O production. Generally, N₂O emissions from grazed pasture soils are high when the soil water-filled pore-space is above field capacity, and net CH₄ uptake is low or absent. Although nitrification inhibitors have shown some promise in reducing N₂O emissions from grazed pasture systems, their efficacy as an integral part of farm management has yet to be tested. Methane uptake was highest for a New Zealand Beech forest soil (10–11 kg CH₄ ha^?1 year^?1), intermediate in some pine forest soils (4–6 kg CH₄ ha^?1 year^?1), and lowest in most pasture (<1 kg CH₄ ha^?1 year^?1) and cropped soils (1.5 kg CH₄ ha^?1 year^?1). Afforestation /reforestation of pastures results in increases in soil CH₄ uptake, largely as a result of increases in soil aeration status and changes in the population and activities of methanotrophs. Soil CH₄ uptake is also seasonally dependent, being about two to three times higher in a dry summer and autumn than in a wet winter. There are no practical ways yet available to reduce CH₄ emissions from agricultural systems. The mitigation options to reduce gaseous emissions are discussed and future research needs identified.     

Estimating seasonal and annual carbon inputs,and root decomposition rates in a temperate pasture following field 14C pulse-labelling

Using a ¹⁴C pulse-labelling technique, we studied the seasonal changes in assimilation and partitioning of photoassimilated C in the plant–root–soil components of a temperate pasture. Pasture and soil samples were taken after 4-h, and 35-day chase periods, to examine these seasonal ¹⁴C fluxes. Total C and ¹⁴C were determined in the shoot, root and soil system. The amounts of C translocated annually to roots and soil were also estimated from the seasonal ¹⁴C distribution and pasture growth. The in situ field decomposition of newly formed roots during different seasons, also using ¹⁴C-labelling, was studied for one year in undisturbed rhizosphere soil. The ¹⁴C-labelled roots were sampled five times and decomposition rates were calculated assuming first-order decomposition.Annual pasture production at the site was 16 020 kg DM ha^–1, and pasture growth varied with season being highest (75–79 kg ha^–1 d^–1) in spring and lowest (18–20 kg ha^–1 d^–1) in winter. The above- and below-ground partitioning of ¹⁴C also varied with the season. The respiratory ¹⁴C–CO₂ losses, calculated as the difference between the total amounts of ¹⁴C recovered in the soil-plant system at 4 h and 35 days, were high (66–70%) during the summer, autumn and winter season, and low (37–39%) during the spring and late-spring season. Pasture plants partitioned more C below-ground during spring compared with summer, autumn and winter seasons. Overall, at this high fertility dairy pasture site, 18 220 kg C/ha was respired, 6490 kg remained above-ground in the shoot, and 6820 kg was translocated to roots and 1320 kg to soil. Root decomposition rate constant (k) differed widely with the season and were the highest for the autumn roots. The half-life was highest (111 days) for autumn roots and lowest (64 days) for spring roots. About one-third of the root label measured in the spring season disappeared in the first 5 weeks after the initial 35 Day of allocation period. The late spring, summer, late summer and winter roots had intermediate half-lives (88–94 days). These results indicate that seasonal changes in root growth and decomposition should be accounted for to give a better quantification of root turnover.     

Response of methanotrophic communities to afforestation and reforestation in New Zealand

Methanotrophs use methane (CH₄) as a carbon source. They are particularly active in temperate forest soils. However, the rate of change of CH₄ oxidation in soil with afforestation or reforestation is poorly understood. Here, soil CH₄ oxidation was examined in New Zealand volcanic soils under regenerating native forests following burning, and in a mature native forest. Results were compared with data for pasture to pine land-use change at nearby sites. We show that following soil disturbance, as little as 47 years may be needed for development of a stable methanotrophic community similar to that in the undisturbed native forest soil. Corresponding soil CH₄-oxidation rates in the regenerating forest soil have the potential to reach those of the mature forest, but climo-edaphic fators appear limiting. The observed changes in CH₄-oxidation rate were directly linked to a prior shift in methanotrophic communities, which suggests microbial control of the terrestrial CH₄ flux and identifies the need to account for this response to afforestation and reforestation in global prediction of CH₄ emission.     

FREM1 Mutations Cause Bifid Nose, Renal Agenesis, and Anorectal Malformations Syndrome

An autosomal-recessive syndrome of bifid nose and anorectal and renal anomalies (BNAR) was previously reported in a consanguineous Egyptian sibship. Here, we report the results of linkage analysis, on this family and on two other families with a similar phenotype, which identified a shared region of homozygosity on chromosome 9p22.2-p23. Candidate-gene analysis revealed homozygous frameshift and missense mutations in FREM1, which encodes an extracellular matrix component of basement membranes. In situ hybridization experiments demonstrated gene expression of Frem1 in the midline of E11.5 mouse embryos, in agreement with the observed cleft nose phenotype of our patients. FREM1 is part of a ternary complex that includes FRAS1 and FREM2, and mutations of the latter two genes have been reported to cause Fraser syndrome in mice and humans. The phenotypic variability previously reported for different Frem1 mouse mutants suggests that the apparently distinct phenotype of BNAR in humans may represent a previously unrecognized variant of Fraser syndrome.     

Effect of nitrogen and phosphorus fertilization on the composition of rhizobacterial communities of two Chilean Andisol pastures

The effect of nitrogen (N) and phosphorus (P) fertilization on composition of rhizobacterial communities of volcanic soils (Andisols) from southern Chile at molecular level is poorly understood. This paper investigates the composition of rhizobacterial communities of two Andisols under pasture after 1- and 6-year applications of N (urea) and P (triple superphosphate). Soil samples were collected from two previously established sites and the composition of rhizobacterial communities was determined by denaturing gradient gel electrophoresis (PCR–DGGE). The difference in the composition and diversity between rhizobacterial communities was assessed by nonmetric multidimensional scaling (MDS) analysis and the Shannon–Wiener index. In Site 1 (fertilized for 1 year), PCR–DGGE targeting 16S rRNA genes and MDS analysis showed that moderate N application (270 kg N ha^?1 year^?1) without P significantly changed the composition of rhizobacterial communities. However, no significant community changes were observed with P (240 kg P ha^?1 year^?1) and N–P application (270 kg N ha^?1 year^?1 plus 240 kg P ha^?1 year^?1). In Site 2 (fertilized for 6 years with P; 400 kg P ha^?1 year^?1), PCR–DGGE targeting rpoB, nifH, amoA and alkaline phosphatase genes and MDS analysis showed changes in rhizobacterial communities only at the highest rate of N application (600 kg N ha^?1 year^?1). Quantitative PCR targeting 16S rRNA genes also showed higher abundance of bacteria at higher N application. In samples from both sites, the Shannon–Wiener index did not show significant difference in the diversity of rhizobacterial communities. The changes observed in rhizobacterial communities coincide in N fertilized pastures with lower soil pH and higher pasture yields. This study indicates that N–P application affects the soil bacterial populations at molecular level and needs to be considered when developing fertilizer practices for Chilean pastoral Andisols.     

Biofilm Formation Protects Escherichia coli against Killing by Caenorhabditis elegans and Myxococcus xanthus

Enteric bacteria, such as Escherichia coli, are exposed to a variety of stresses in the nonhost environment. The development of biofilms provides E. coli with resistance to environmental insults, such as desiccation and bleach. We found that biofilm formation, specifically production of the matrix components curli and cellulose, protected E. coli against killing by the soil-dwelling nematode Caenorhabditis elegans and the predatory bacterium Myxococcus xanthus. Additionally, matrix-encased bacteria at the air-biofilm interface exhibited ∼40-fold-increased survival after C. elegans and M. xanthus killing compared to the non-matrix-encased cells that populate the interior of the biofilm. To determine if nonhost Enterobacteriaceae reservoirs supported biofilm formation, we grew E. coli on media composed of pig dung or commonly contaminated foods, such as beef, chicken, and spinach. Each of these medium types provided a nutritional environment that supported matrix production and biofilm formation. Altogether, we showed that common, nonhost reservoirs of E. coli supported the formation of biofilms that subsequently protected E. coli against predation.     

Using the NZ–DNDC model to estimate agricultural N2O emissions in the Manawatu–Wanganui region

Nitrous oxide (N₂O) emissions are difficult to quantify at regional and national scales. There is considerable spatial and temporal variability in N₂O emissions from soil, partly because of variability in the underlying biogenic processes responsible for soil N₂O production. The process-based NZ–DNDC (New Zealand Denitrification-Decomposition) model was used, with georeferenced input data on soils, climate and land use, to map and predict net N₂O emissions from farming in the Manawatu–Wanganui region. The Manawatu–Wanganui region has a temperate, maritime climate and the major agricultural land use is pastoral grazing. We created databases of regional soil, climate and farm management information from various available data sources including national databases of climate, soil type and land use, and national agricultural production statistics. The error introduced by upscaling the model was assessed by comparing results using measured site data with the corresponding predictions using the regional approximations. We also examined the effect of climate conditions by rerunning the 2003 simulation using the climate data for the years ended June 1990 and 2004. The modelled net N₂O emissions for this region for the year ended June 2003 were 4.6?±?1.5 Gg N₂O–N per year. The total fertiliser and excretal N inputs for the region were approximately 224,140 tonnes, so the percentage emitted as N₂O was 2.0?±?0.7%. The modelled net N₂O emissions for the region for the year ended June 1990 were 3.8?±?2.1 Gg N₂O–N per year, indicating annual net N₂O emissions in the Manawatu–Wanganui region between 1990 and 2003 had increased by 0.8?±?0.6 Gg N₂O–N (an increase of about 20%). This change can be attributed to both changes in weather conditions and land use and farm management between 1990 and 2003.     

IL-13 is pivotal in the fibro-obliterative process of bronchiolitis obliterans syndrome

Acute allograft rejection is considered to be a predominately type 1 immune mediated response to the donor alloantigen. However, the type 2 immune mediated response has been implicated in multiple fibroproliferative diseases. Based on the fibro-obliterative lesion found during bronchiolitis obliterans syndrome (BOS), we hypothesized that the type 2 immune mediated response is involved in chronic lung allograft rejection. Specifically, whereas acute rejection is, in part, a type 1 immune response, chronic rejection is, in part, a type 2 immune response. We found the type 2 cytokine, IL-13, to be elevated and biologically active in human bronchoalveolar lavage fluid during BOS. Translational studies using a murine model of BOS demonstrated increased expression of IL-13 and its receptors that paralleled fibro-obliteration. In addition, in vivo neutralization of IL-13 reduced airway allograft matrix deposition and murine BOS, by a mechanism that was independent of IL-4. Furthermore, using IL-13Ralpha2(-/-) mice, we found increased fibro-obliteration. Moreover, anti-IL-13 therapy in combination with cyclosporin A had profound effects on reducing murine BOS. This supports the notion that IL-13 biological axis plays an important role during the pathogenesis of BOS independent of the IL-4 biological axis.     

Small molecule analogues of the immunomodulatory parasitic helminth product ES-62 have anti-allergy properties

ES-62, a glycoprotein secreted by the filarial nematode Acanthocheilonema viteae, exhibits anti-inflammatory properties by virtue of covalently attached phosphorylcholine moieties. Screening of a library of ES-62 phosphorylcholine-based small molecule analogues (SMAs) revealed that two compounds, termed 11a and 12b, mirrored the helminth product both in inhibiting mast cell degranulation and cytokine responses in vitro and in preventing ovalbumin-induced Th2-associated airway inflammation and eosinophil infiltration of the lungs in mice. Furthermore, the two SMAs inhibited neutrophil infiltration of the lungs when administered therapeutically. ES-62-SMAs 11a and 12b thus represent starting points for novel drug development for allergies such as asthma.