Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil.

Introduction: Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study. Methods: The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing. Results and Discussion: The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations.

The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha-1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.

S-map parameters for APSIM.

Agroecosystem models have become an important tool for impact assessment studies, and their results are often used for management and policy decisions. Soil information is a key input for these models, yet site-specific soil property data are often not available, and soil databases are increasingly being used to provide input parameters. For New Zealand, the digital spatial soil information system S-map provides geospatial data on a range of soil characteristics, including estimates of soil water properties. We describe a protocol for how properties from S-map can be used as input parameters for the APSIM (Agricultural Production Systems sIMulator) framework. Finally, we investigate how changes in the physical description of soil layers, and soil organic matter pools, affect the various outputs of APSIM.•This paper presents a description of how information from S-map, a digital soil map of New Zealand, can be used for building a soil description for APSIM.•A sensitivity analysis shows the effect of soil layering and the set-up setup, size, and distribution of SOM pools on model outputs, including plant growth and N leaching.

Irrigation increases forage production of newly established lucerne but enhances net ecosystem carbon losses.

In New Zealand, dairy farming faces increasing scrutiny for its environmental impacts, including those on soil carbon (C) stocks; hence, alternative management practices are required. One such practice is usage of deep-rooting forage, such as lucerne (Medicago sativa L.). We measured the C and water exchange of two neighbouring lucerne fields on stony, well-drained soil for 3 years, following conversion from grassland. One field received irrigation and effluent; the other received neither. Net CO2 exchange and evaporation were measured by eddy covariance, drainage and leaching with lysimeters, and water inputs with rain gauges. Biomass removal from harvesting and grazing was recorded by direct sampling. In the conversion year, irrigated lucerne was C-neutral despite two harvests and losses from the conversion process. In the 2nd and 3rd years combined, the biomass-C removal exceeded net CO2 uptake, causing net losses of 450 g C m-2 and 210 g C m-2 for irrigated and non-irrigated lucerne, respectively. Leaching losses accounted for 1 to 9 % of annual net C uptake from the atmosphere. The ratio of ecosystem respiration to gross photosynthetic productivity (GPP) increased from <0.7 in spring to ≈ 1 in autumn. Consequently, the net C balance for both lucerne crops showed gains in the first two growth periods of each year and losses in the subsequent two to four growth periods. Irrigation made no difference to the photosynthetic water-use efficiency at field scale (GPP/evaporation), but enhanced production water-use efficiency (biomass/water input). Irrigation increased both the absolute amount of drainage and the fraction of water inputs lost by drainage. In one year, significant summer drainage occurred for the irrigated lucerne. To prevent that, soil-water content should be kept well below field capacity but above the crop's water-stress level. Such practice would likely also help retain soil carbon.

Leaching of from stony soils after effluent application.

Irrigation of dairy shed effluent (DSE) onto land is an integral part of New Zealand's farming practice. The use of inappropriate soils can result in contamination of ground waters with microbes and nutrients. A gap in our knowledge is the ability of stony soils to safely treat DSE. Replicates of four stony soils were collected from the Canterbury region of New Zealand as intact soil lysimeters 460 mm in diameter and up to 750 mm deep. The soils had either stones to the surface or 300 to 600 mm fines over stones. To determine breakthrough characteristics, a pulse of DSE (25 mm depth) spiked with bromide (2000 mg L) was applied to the soil cores followed by continuous artificial rainfall, for one pore volume, at 5 mm h. Leachate aliquots were analyzed for , bromide, and NH-N. The lysimeters were then subjected to hoof pugging using a mechanical hoof, and the leaching characteristics of the soil were determined again. breakthrough curves revealed that the potential for to leach through the soils was high for Selwyn very stony soil and low for other soils analyzed. After pugging, leaching of increased in Mackenzie soil with stones to the surface. For most other soil cores, concentrations in soil leachates were low. In soils where stones are close to the surface, especially where the soil matrix is sandy, we anticipate that shallow groundwater is vulnerable to microbial contamination under some land management practices.