Paramsothy Jeyakumar

Reliable extraction of high-quality DNA from ruminant faecal samples is essential for microbiome profiling, pathogen surveillance, and nutritional studies relevant to pastoral livestock systems. Faecal material from grazing sheep presents particular challenges due to high plant fibre content and the presence of PCR inhibitors. This study compares the performance of commercial soil and stool-specific DNA extraction kits for sheep faecal samples. Faecal samples were collected from eight adult Romney ewes grazing research pastures in New Zealand and processed in parallel using a stool and a soil-specific kit. DNA concentration and purity were assessed by NanoDrop spectrophotometry. The soil DNA kit yielded significantly higher DNA concentrations than the stool DNA kit (mean ± SD: 140.2 ± 65.1 ng µL−1 vs. 74.5 ± 36.4 ng µL−1; Wilcoxon signed-rank test, p = 0.0006), while purity ratios (A260/280 and A260/230) did not differ significantly between kits and met recommended thresholds for downstream sequencing. These results demonstrate that soil DNA extraction kits can provide superior DNA yields from sheep faecal samples without compromising purity, supporting their use in high-throughput ovine microbiome studies. These findings provide practical guidance for microbiome laboratories working with fibre-rich faecal matrices and support broader application of soil-oriented extraction protocols in ruminant microbiome research.

Soil and ruminant gut microbiomes are linked within grazing pastoral systems, yet the strength and direction of these connections under different pasture management systems remain poorly understood. This study characterised bacterial communities in soil and faeces from cattle and sheep grazing standard and diverse pastures managed under contemporary and regenerative practices using 16 S rRNA gene sequencing. Shared bacterial taxa between soil and gut were identified, and their dominance patterns and soil–gut diversity relationships were evaluated using Spearman correlations and Procrustes analyses. Several taxa, including Prevotella copri , Faecalibacterium prausnitzii , Akkermansia muciniphila , Bacteroides uniformis , Clostridium perfringens and Fibrobacter succinogenes were commonly shared between soil and gut but were usually more prevalent in the gut, indicating predominant host‑associated dominance. Soil exhibited significantly greater bacterial alpha diversity than the gut across all treatments, and neither pasture diversity nor management significantly affected soil–gut alpha diversity differences or the contributions of shared taxa. Correlations between soil and gut alpha diversity were weak and non-significant, and correlations for beta diversity between soil and gut varied through time and among treatments without reaching significance. These findings indicate that, although soil–gut microbial connectivity exists, gut communities are primarily shaped by host-related ecological processes and internal filtering, with soil acting mainly as a diverse reservoir and sink for gut-derived taxa. This highlights that host-driven gut microbiomes primarily shape the soil–gut microbiome link, limiting the strong direct influence of pasture diversity or management.

Pasture systems strongly influence microbiome diversity in both soils and grazing ruminants, and their interactions through interconnected microbial exchange pathways. In temperate regions, grazed pasture systems are predominantly composed of perennial ryegrass-white clover, representing standard systems under contemporary management. However, sustainable alternatives such as regenerative agriculture, which emphasise diverse pasture species, are gaining attention. Diverse pastures, due to their varied root structures and nutritional composition, exert more pronounced effects on soil and ruminant microbiomes than standard swards. This review synthesises current knowledge on soil and ruminant gut microbiome responses to diverse pasture systems. Diverse swards enhance soil organic carbon and microbial abundance, while their varied nutrient profiles and bioactive compounds, together with ingested soil microbes during grazing, contribute to a more diverse and stable gut microbiome, potentially strengthening soil–gut microbial interactions. However, few omics-based studies have explored microbiome responses to pasture management, and none have simultaneously investigated soil and ruminant gut microbiomes under regenerative management. This review highlights these gaps and proposes future research directions, including integrated multi-omics approaches, to advance understanding of soil–gut microbiome dynamics, interactions, and functional roles within pasture-based agroecosystems.

Soil compaction caused by uncontrolled machinery traffic is a major constraint to sustainable crop production. Controlled Traffic Farming (CTF), which restricts machinery movement to permanent lanes, has been practiced in New Zealand for more than a decade but has not been evaluated against Random Traffic Farming (RTF). This knowledge gap limits farmer awareness and adoption. This study hypothesized that CTF reduces soil compaction and improves soil physical properties compared with RTF. A one-year field experiment was conducted at Pukekohe, New Zealand, using annual ryegrass grown under CTF and RTF. Soil penetration resistance (PR), bulk density, total porosity, moisture content, and air-filled porosity were measured to a 40 cm depth. RTF increased soil PR relative to CTF across 10–40 cm. Bulk density was lower under CTF (0.96–1.03 g·cm⁻³) than RTF (1.11–1.30 g·cm⁻³), with improved total porosity (0.60–0.62 cm·cm⁻³) and aeration (12–23 cm·cm⁻³). CTF achieved a 5.7% higher bed-level yield. When scaled to the whole-field context, the productivity of tramlines contributed to 8% greater dry matter yield under CTF than RTF, indicating that the area allocated to tramlines did not negate the system-level productivity. This study provides the first New Zealand-specific empirical comparison of CTF and RTF to support adoption of CTF.

The Overseer model is widely used in New Zealand as a precision-agriculture-related tool for estimating nitrate (NO₃⁻) leaching losses in agricultural systems. This study evaluated the accuracy of the Overseer model in predicting nitrate (NO₃⁻) leaching through a two-year lysimeter experiment conducted at Woodhaven Gardens, New Zealand, under beetroot and pak choi cultivation. Seven distinct nitrogen (N) fertilizer treatments were applied to assess model performance. In year 1, Overseer overestimated NO₃⁻ leaching by an average of 45.2 kg N/ha (15.7%), and in year 2, the model overestimated by 35.2 kg N/ha (43.5%). A sensitivity analysis highlighted soil texture, impeded layer depth and crop residue incorporation as key drivers of leaching variability, underscoring the need for improved model calibration. Overseer performed reasonably well under lysimeter conditions, with a strong linear relationship (Pearson’s correlation coefficient r = 0.89, p < 0.0001) between measured and predicted values and explaining 77% of the variance (R² = 0.77) in the observed data. The model predicted a baseline leaching loss of 39.4 kg N/ha/year even when measured losses were zero. Overseer demonstrates moderate reliability in predicting NO₃⁻ leaching under vegetable cropping systems but exhibits notable limitations in handling crop-specific N dynamics, soil hydrology, and fertilizer timing.

The Overseer model is widely used in New Zealand for estimating nitrate (NO₃⁻) leaching losses in agricultural systems. This study evaluated the accuracy of the Over-seer model in simulating nitrate (NO₃⁻) leaching through a two-year lysimeter experi-ment conducted at Woodhaven Gardens, New Zealand, under beetroot and pak choi cultivation. Seven distinct nitrogen (N) fertiliser treatments were applied to assess model performance. In Year 1, Overseer overestimated NO₃⁻ leaching by an average of 45.2 kg N/ha (15.7%), due to underestimated crop uptake. Similarly, overestimations were observed in Year 2, with overprediction rates reaching up to 63.5%. Sensitivity analysis highlighted soil texture, impeded layer depth and crop residue incorporation as key drivers of leaching variability, underscoring the need for improved model cali-bration. Overseer performed reasonably well under lysimeter conditions, with a strong linear relationship (Pearson’s correlation coefficient r = 0.89, P < 0.0001) between measured and predicted values and explaining 77% of the variance (R²=0.77) in the observed data. The model predicted a baseline leaching loss of 39.4 kg N/ha/year even when measured losses were zero. Overseer demonstrates moderate reliability in simulating NO₃⁻ leaching under vegetable cropping systems but exhibits notable limi-tations in handling crop-specific N dynamics, soil hydrology, and fertiliser timing.

Regenerative agricultural practices emphasize the use of diverse pasture species within sustainable agriculture production systems. The inclusion of a range of legume species in diverse pasture swards is likely to increase biological N fixation (BNF) across seasons, reducing the system’s reliance on synthetic N inputs. The present field study aims to quantify BNF in selected legume species within diverse pasture (combining 9 species) and standard pastures (ryegrass and clover combination) and assess their performance to identify the potential for improving N supply while maintaining year-round pasture quality. A year-round seasonal BNF was assessed by evaluating soil N status, nodulation patterns, plant composition, and conducting ¹⁵N natural abundance studies. The results revealed that the diverse pasture sward produced 5.4% more dry matter compared to the standard pasture, while soil mineral N (NO₃⁻, NH₄⁺) remained statistically similar between the two treatments. Nitrogen yield was 9.3% higher in the diverse pasture than in the standard pasture. ¹⁵N natural abundance analysis assessment revealed no substantial variation in BNF rates across treatments throughout the study. However, in contrast to standard pasture, the BNF rate in diverse pasture experienced a 3-fold increase from winter to summer, while the standard pasture exhibited a 1.5-fold increase. In both pasture systems, BNF increased with clover proportion up to 30%, indicating optimal fixation at moderate clover levels. The findings underscore the potential of diverse pastures when strategically managed to enhance seasonal BNF while sustaining pasture productivity.

Intensive vegetable farming emits high nitrous oxide (N₂O) due to traffic-induced compaction, highlighting the need for preventing nitrogen (N) losses through better traffic management. This study examined the effects of Controlled Traffic Farming (CTF) and Random Traffic Farming (RTF) on N₂O emissions using intact soil cores (diameter: 18.7 cm; depth: 25 cm) collected from a vegetable production system in Pukekohe, New Zealand. Soil cores from CTF beds, CTF tramlines, and RTF plots were analysed under fertilised (140 kg N/ha) and unfertilised conditions. N₂O fluxes were monitored over 58 days using gas chambers. The fertilised RTF system significantly (p < 0.05) increased N₂O emissions (5.4 kg N₂O–N/ha) compared to the unfertilised RTF system (1.53 kg N₂O–N/ha). The emission from fertilised RTF was 46% higher than the maximum N₂O emissions (3.7 kg N₂O–N/ha) reported under New Zealand pasture conditions. The fertilised CTF system showed a 31.6% reduction in N₂O emissions compared to fertilised RTF and did not differ significantly from unfertilised CTF. In general, CTF has demonstrated some resilience against fertiliser-induced N₂O emissions, indicating the need for further investigation into its role as a greenhouse gas mitigation strategy.

Purpose: Inconsistent yield responses to inorganic phosphorus (P) fertilisers in tropical rice paddy soils remain a challenge. This study investigated the contributions of applied P fertilisers to soluble soil P and P transformation mechanisms in P-added paddy soils. Methods: An incubation study was conducted on three rice-growing soils (Ultisol, Alfisol, and Entisol) in Sri Lanka with and without single superphosphate (SSP), triple superphosphate (TSP), and urea. Dissolved reactive phosphorus (DRP) was measured over 112 days of submergence. Thermodynamic modelling and chemical P fractionation were employed to assess soil P transformations. Results: Phosphorus-fertilised soils had significantly higher DRP concentrations (1.1–8.0 mg L⁻¹) compared to controls at 7 days after submergence but DRP declined beyond 21 days (0.024–0.300 mg L⁻¹). Single superphosphate increased DRP more than TSP, short-term. Urea did not affect DRP concentration. Ultisols exhibited the lowest DRP, while Alfisols maintained higher DRP than Ultisol which was near or above the critical concentration for rice (0.1 mg L⁻¹) after 28 days. In Entisol, only SSP maintained DRP above 0.1 mg L⁻¹. Modelling suggested Ca phosphates and Fe oxy(hydr)oxides dissolved during submergence. Released P may be resorbed by Fe/Al oxy(hydr)oxides and Ca minerals, with evidence of downward movement of dissolved P and its resorption onto Fe/Al and Ca minerals possibly due to saturation of P sorption sites in the topsoil layer. Conclusion: Low dissolved P in porewater may be linked to inherent soil characteristics, including low organic matter and high amorphous Fe and Al oxides.