Department of Soil and Physical Sciences

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The Department of Soil and Physical Sciences has responsibility for the delivery of all undergraduate and postgraduate soil-related subjects, and many physical science subjects.

The range of research being undertaken is extensive but in recent years has increasingly focused on environmental issues, especially soil's role and influence on water and air quality.

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Recent Submissions

  • ItemOpen Access
    Transcriptional activity of ammonia oxidisers in response to soil temperature, moisture and nitrogen amendment
    (Frontiers Media S.A., 2025-01-15) Chisholm, Chris; Di, Hong; Cameron, Keith; Podolyan, Andriy; Shen, Jupei; Zhang, Limei; Sirisena, Kosala; Che, Xueying
    The contrasting response of AOA, AOB, and comammox Nitrospira amoA transcript abundance to temperature, moisture, and nitrogen was investigated using soil microcosms. The moisture, temperature, and nitrogen treatments were selected to represent conditions typically found in a New Zealand (NZ) dairy farm. AOB dominated all synthetic urine treated soils. Peak AOB amoA transcript abundance was positively correlated with estimated soil ammonia availability. While AOB gDNA abundance and nitrification rate trends were similar. AOA were strongly influenced by soil temperature. At 20◦C, AOA amoA peak transcript abundance averaged over 1 order of magnitude higher than at 8 ◦C. Within the AOA community a member of the Nitrosocosmicus clade was positively correlated with ammonium and estimated ammonia concentrations. The presence and relative increase of an AOA community member in a high nitrogen environment poses an interesting contrast to current scientific opinion in NZ. Comammox Nitrospira abundance showed no correlation with soil moisture. This suggests that previously found associations are more complex than originally thought. Further research is required to determine the drivers of comammox Nitrospira abundance in a high moisture environment. Overall, these results indicate that AOB are the main drivers of nitrification in New Zealand dairy farm soils.
  • ItemOpen Access
    Assessing cadmium uptake in New Zealand agricultural systems
    (Fertilizer and Lime Research Centre, 2018) Cavanagh, Jo-Anne E; Yi, Zicheng; Gray, Colin; Young, Sandra; Smith, Stefan; Jeyakumar, Paramsothy; Munir, K; Wakelin, Steve; Lehto, Niklas; Robinson, Brett; Anderson, Chris; Currie, LD; Christensen, CL
    Soil cadmium (Cd) concentration is the primary indicator through which fertiliser-derived Cd is currently managed under the New Zealand Cadmium Management Strategy (MAF 2011). However, there is a lack of New Zealand-specific data on the soil Cd concentrations that may actually pose a risk for New Zealand agricultural systems and how these risks might be managed. This paper presents an overview of the results from a two-year study on cadmium uptake into food crops (wheat, potato, onion and leafy greens), effects on soil rhizobia-clover symbiosis and uptake into lambs grazed on crops with a range of Cd concentrations. Specifically, this includes the results of field surveys of these crops in their primary commercial growing regions across New Zealand and field trials to assess the influence of lime and compost addition on plant Cd; studies to assess the toxicity of Cd to clover in the presence and absence of rhizobia, and the influence Cd on plant nitrogen content, and investigation of the accumulation in the livers of lambs grazed on ryegrass, lucerne, plantain and chicory. The implications for managing the risk associated with fertiliser-derived Cd are discussed.
  • PublicationOpen Access
    A transdisciplinary approach to understanding the connections between soil and people, through food production: A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University
    (Lincoln University, 2024) Gillespie, Julie
    There is a disconnect between soil, food, and people, that is being exacerbated as our populations become increasingly urban-based. This presents a ‘wicked’ challenge for soil and food security that soil science alone is unable to address. Resolving this issue requires understanding the extent and nature of the current (dis)connections, providing an opportunity to extend beyond the disciplinary boundaries of soil science. This research aims to develop an understanding of the (dis)connections between soil and people through the conduit of food in a place-based context by operating at the interface of mātauraka Māori (Māori knowledge) and soil science. This thesis provides two soil-centred examples of TDR in an Aotearoa New Zealand context, applying the He Awa Whiria (braided rivers) epistemological framework to guide the weaving of knowledges. To develop insight into how soil science and mātauraka Māori can be woven together and gain an understanding of historical connections between soil, food, and people, a case study guided by the questions of Mana Whenua regarding their past horticultural land use at Pōhatu (Flea Bay), Te Pātaka o Rākaihautū (Banks Peninsula), is undertaken. In this study, mātauraka Māori identified likely māra (garden) sites in the bay with oral histories identifying features such as gravel additions to the soil to improve drainage and retain warmth. Analysis of soil horizons modified with rounded beach gravels identified phytoliths with a morphotype consistent with kūmara leaves. Undertaking this study has demonstrated the importance of relationships when weaving knowledges, and the benefits of recognising equal value of the knowledges involved. Building on the results and learnings from the Pōhatu case study, a TDR methodology is applied to develop the place-based Food-Landscape Networks (FLN) framework, placing soil at its centre. The FLN framework applies a holistic approach to understanding the reciprocal connections between soil, food, and people in contemporary local food production systems. To assess the suitability of the FLN framework for understanding connections between soil, food, and people, it has been applied to three food-landscapes in Waitaha (Canterbury). Applying the framework makes visible the (dis)connections between soil, food, and people in three food-landscapes with the primary disconnection being people and soil across all three food-landscapes, as well as identifying where interdisciplinary collaboration is needed. This thesis enhances understanding and demonstrates the importance of engaging with mātauraka Māori as a knowledge of equal value to soil science for addressing complex, soil-centred environmental challenges facing Aotearoa New Zealand. The application of the transdisciplinary FLN framework illustrates the complexity of understanding the reciprocal connections between soil and people, highlighting the limitations of soil science in understanding and addressing this disconnect alone. This signals the need for interdisciplinary approaches, nested within TDR, for consumer disconnects to be addressed. The co-production of knowledge by weaving knowledges together to assess and understand these connections provides an opportunity to connect, and reconnect, people with where food comes from to work towards soil and food security.
  • ItemOpen Access
    Enhancing switchgrass growth with biochar derived from mushroom residue: A study on regulating physicochemical properties of acidic phosphogypsum
    (John Wiley & Sons Ltd., 2025-01) Xiang, Yangzhou; Mao, Yanting; Liu, Ying; Luo, Yang; Xue, Jianming; He, Ji; Shurpali, Narasinha J; Bhattarai, Hem Raj; Deepagoda, Chamindu; Yao, Bin; Siddique, Kadambot HM; Li, Yuan
    Acidity limits plant growth, particularly when the growing medium has a pH below 5, a challenge that is particularly relevant for certain plants like switchgrass Panicum virgatum. Although adding biochar to the growing medium has been shown to improve plant growth by modulating acidity, its specific impact on switchgrass remains largely uninvestigated. Thus, we conducted a pot experiment to assess how different biochar application rates (0%, 1%, 2.5%, 5%, 10%, and 20% w/w), derived from mushroom residue through muffle furnace pyrolysis at 350°C for 2 h, affect the physicochemical attributes of phosphogypsum and subsequent switchgrass growth. Our findings revealed that adding biochar to phosphogypsum significantly alleviated acidity and enhanced moisture, organic matter, total nitrogen, total phosphorus, total potassium, available phosphorus, and available potassium contents. Notably, the 10% biochar treatment had the most positive impacts on germination rates, while the 5% treatment had the greatest improvements in shoot length, tiller number, and total weight compared to the control. Structural equation modeling illustrated that biochar indirectly contributed to switchgrass health by altering the physicochemical properties of phosphogypsum, with pH as the pivotal regulator. Our study demonstrated the potential of mushroom residue biochar as an effective amendment for acidic substrates/matrix (e.g., soil), offering a promising strategy to improve physicochemical conditions and stimulate plant growth.
  • ItemOpen Access
    Research at the interface between Indigenous knowledge and soil science; weaving knowledges to understand horticultural land use in Aotearoa New Zealand
    (Copernicus GmbH, 2024-12-09) Gillespie, Julie; Payne, Matiu; Payne, Dione; Edwards, Sarah; Jolly, Dyanna; Smith, Carol; Cavanagh, Jo-Anne
    Addressing the complex challenges of soil and food security at international and local scales requires moving beyond the boundaries of individual disciplines and knowledge systems. The value of transdisciplinary research approaches is increasingly recognised, including those that value and incorporate Indigenous knowledge systems and holders. Using a case study at Pōhatu, Aotearoa New Zealand, this paper demonstrates the value of a transdisciplinary approach to explore past Māori food landscapes and contribute to contemporary Māori soil health and food sovereignty aspirations. Engaging at the interface between soil science and Indigenous knowledge (mātauraka Māori) in an Aotearoa New Zealand context, we provide an example and guide for weaving knowledges in a transdisciplinary context. Here, mātauraka Māori, including waiata (songs) and ingoa wāhi (place names), provided the map of where to look and why, and soil analysis yielded insight into past cultivation, soil modification and fertilisation practices. Both knowledges were needed to interpret the findings and support Māori to re-establish traditional horticultural practices. Furthermore, the paper extends the current literature on the numerous conceptual frameworks developed to support and guide transdisciplinary research by providing an example of how to do this type of research in an on-the-ground application.
  • PublicationOpen Access
    Impact of managed aquifer recharge on nitrate concentration changes in an alluvial aquifer : A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Water Resource Management at Lincoln University
    (Lincoln University, 2024) Teixeira, Sidinei
    Nitrate leaching poses significant challenges to agricultural environments, endangering water quality, human health, and ecosystems. Managed Aquifer Recharge (MAR) is a technology aimed at improving water quality in contaminated aquifers by dilution with high quality recharging water. This study investigates the effectiveness of MAR techniques, specifically infiltration basins and streambed channel modifications, in mitigating rising nitrate levels in the alluvial aquifers of the Hekeao/Hinds Plains (HHP), New Zealand. The research addresses four key objectives: identifying water sources contributing to groundwater recharge, evaluating biochemical processes affecting groundwater chemistry, comparing nitrate fluxes under different irrigation practices, and assessing MAR's impact on groundwater nitrate concentrations. Using chemical analyses, including isotopic signatures and major ion concentrations, alongside multivariate statistical techniques such as Bayesian mixing models, this study quantifies multiple recharge sources and their impact on nitrate pollution. The findings reveal that land surface recharge contributes 60% of groundwater recharge, with the remainder coming from water race recharge, and river recharge, collectively termed unmanaged aquifer recharge (UMAR). Oxidizing groundwater conditions were found to impede denitrification, significantly influencing groundwater chemistry and limiting natural nitrate attenuation. Areas irrigated with groundwater showed nitrate levels comparable to those irrigated with low-solute water, indicating additional influencing factors beyond irrigation water quality. Even with high-quality water inputs from abundant rain and low-solute irrigation, persistent soil solutes inevitably leach into groundwater. MAR demonstrated significant potential for nitrate dilution as far as 3 km down-gradient from the infiltration basin, with the dilution effect decreasing with distance. In one area, MAR contributed up to 52% of groundwater recharge, effectively decreasing nitrate concentrations from 26.6-30.9 mg NO3/L (start of MAR scheme operation in 2016) to 7-12 mg NO3/L (monitoring 2022). However, in areas without substantial MAR influence, the volume of MAR-influenced water was insufficient to dilute extensive nitrate plumes to below 50 mg NO3/L. This research contributes a transferable methodology for quantifying pollutant inputs in catchments with isotopically similar but chemically diverse sources. It precisely quantifies MAR's role in nitrate dilution, enhancing our understanding of sustainable groundwater management practices. The findings underscore the potential of MAR techniques as viable solutions for mitigating nitrate pollution while highlighting the need for comprehensive management strategies in alluvial aquifers. Given the oxidizing conditions that impede denitrification, effective management practices, including optimized MAR implementation, remain crucial for mitigating nitrate contamination. Keywords: Managed aquifer recharge, unmanaged aquifer recharge, heterogeneous alluvial aquifer, nitrate pollution mitigation, Bayesian mixing model, multivariate statistical techniques, stable water isotope, irrigation, groundwater chemistry, land surface recharge, Hekeao/Hinds Plains.
  • PublicationRestricted
    Characterisation of the hydraulic properties of soil columns via tension infiltrometer and dye tracer patterns: A dissertation submitted in partial fulfilment of the requirements for the degree of Master of Natural Resources Management and Ecological Engineering
    (Lincoln University, 2007) Hanzl, Markus
    Water is a renewable resource, which is naturally recycled in the hydrological cycle. Surface waters have a short residence time in the hydrological cycle, while ground waters have a long residence time. This recycling renews water resources and provides a continuous supply. Nowadays, water management is becoming more and more important, especially the modification of irrigation schemes. An effective irrigation management which is similar to "drainage control" will avoid a high water outflow from an irrigated area and therefore the nutrient losses in the outflow water can be negligible. This is absolutely important because nutrients, for example nitrates and phosphorus, can lead to problems in the drinking water supply of a region with intensive irrigation.Therefore, it is essential to know as much as possible of the soil hydraulic properties and to convert this knowledge into management practices for the efficient use of water and soil resources. Tension infiltrometers have become a valuable tool for field determination of soil hydraulic properties. To estimate necessary input parameters for the Hydros-ID model (which simulates the one-dimensional movement of water and solutes through the unsaturated zone), measurements were obtained in three lysimeters (D, E, F) of: tension infiltration rates, soil water content and suction using time domain reflectometry (TDR) probes and tensiometers, installed at fixed depths. Infiltration experiments were performed under 40 mm and 0 mm suctions. Hydros was used to estimate the soil hydraulic conductivitiy K(h) at the corresponding suction values (h in cm). Water retention data measured on replicate soil cores from the 3 lysimeters and K(h) data were fitted with the Mualem-van Genuchten (MvG) equation to estimate the lysimeters' water retention curves. The resulting curves showed significant differences from the measured ones from the laboratory tension table tests. Further, dye experiments were performed to identify the flow types of the lysimeters. To stain the flow pathways, the lysimeter surfaces were flooded with a dye solution of 10 litres Brilliant Blue FCF with a concentration of 10 g/1. After a few days, the lysimeters were excavated and brought into the lab for the vertical and horizontal profile analysis. Images were taken using a digital camera (Nikon Coolpix 8800) under daylight conditions. Photographs of the soil profiles were processed by image analysis to distinguish between stained and unstained areas and to classify the stained areas into classes of dye concentrations. The flow profiles showed a logical sequence, with macropore flow along cracks for the coarser lysimeters E and F, and homogeneous matrix flow for the finer structured lysimeter D
  • PublicationOpen Access
    Earth science field trips in the age of Covid-19: A case study of the SOSC223 virtual field trip : A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Applied Science at Lincoln University
    (Lincoln University, 2024) Hall, Louisa
    Undergraduate earth science education emphasises the role of field trips in student learning and development. Thus, when the Covid-19 pandemic caused teaching to shift online, many educators developed replacement virtual field trips (VFTs) to deliver the field components of their courses. Such was the case with SOSC223, a second-year geomorphology course at Lincoln University, where the 2021 Covid-19 lockdown saw us replace the scheduled field trips with a VFT to the same locations. In this thesis, I investigate instructor and student experiences developing and learning from the SOSC223 VFT in order to evaluate what may have been lost or gained through the rapid shift from a traditional field trip (TFT) to virtual. I conducted semi-structured interviews with students and staff involved with the VFT and analysed the interview data for themes relating to 1) student and instructors’ perceptions of the VFT, 2) the strengths and weaknesses of the trip, and 3) how the VFT compared to a TFT. Thematic analysis of participants’ interview transcripts revealed different overall attitudes between the students and instructors. Instructors' reflections heavily featured the limitations and frustrations of developing the trip during lockdown. They felt the VFT was an adequate resource given the circumstance yet nevertheless saw potential benefits to VFTs as a whole. Students were apprehensive at the outset of the VFT but appreciated having the computerised replacement to the TFTs. Although most would have preferred attending a TFT, they felt the VFT benefitted their learning given the circumstances. The weaknesses of the VFT included its lack of easy interpersonal interaction, its reliance on technology like fast computers and stable internet, and the resourcing requirements to integrate multimedia and scaffold the content of the trip. Despite these challenges, the flexibility and repeatability of the VFT benefitted all participants, and the trip demonstrated clear potential for well-designed interactive multimedia to facilitate students' visual connection to place and ability to visualise complex processes. The SOSC223 VFT differed from TFTs in the logistical constraints and affordances of each and how the mode of delivery impacted students' social and physical immersion within the learning experience. Through conducting this research, it became clear that VFTs can add value to course design when thoroughly resourced and thoughtfully integrated. Whether they are used to augment or replace TFTs or incorporated into a course as standalone activities, VFTs should be designed in a way that builds on their flexibility and repeatability, minimises the impact of their lack of sociality, and builds visual connection through well-resourced, well-integrated multimedia.
  • ItemOpen Access
    The effects of soil acidity and aluminium on the root systems and shoot growth of Lotus pedunculatus and Lupinus polyphyllus
    (Multidisciplinary Digital Publishing Institute (MDPI), 2024-08) Bell, LE; Moir, James; Black, Alistair
    Lotus pedunculatus (lotus) and Lupinus polyphyllus (Russell lupin) persist in the upland grasslands of New Zealand, where soil acidity and associated aluminium (Al) toxicity impede conventional pasture legumes. This experiment investigated the response of lotus and Russell lupin to soil acidity and Al. The species were sown in 20 cm tall 1.2 L pots of acidic upland soil. A mass of 4.5 or 6.7 g lime (CaCO₃)/L was added to either the top or bottom or both soil horizons (0–9 cm and 9–18 cm), resulting in six treatments across six randomised blocks in a glasshouse. The soil pH was 4.4, 4.9, and 5.4; the exchangeable Al concentrations were 24, 2.5, and 1.5 mg/kg for 0, 4.5, and 6.7 g lime/L. At 16 weeks post-sowing, the plants were divided into shoots and roots at 0–9 cm and 9–18 cm. Root morphology, shoot and root dry matter (DM), shoot nitrogen (N), and nodulation were measured. The total plant DM and shoot-to-root DM ratio were higher, and the shoot %N was lower for the lotus plants than the Russell lupin plants for the various lime rates (13.2 vs. 2.9 g plant‾¹, 5.6 vs. 1.6, and 2.4 vs. 3.3%, p < 0.05). No response to lime in terms of total DM or total root morphology parameters was exhibited in either species (p > 0.05). Root morphology adjustments in response to acidity between soil horizons were not observed. The results indicated that lotus and Russell lupin are tolerant to high soil acidity (pH 4.4–5.4) and exchangeable Al (1.5–24 mg kg‾¹), highlighting their considerable adaptation to grasslands with acidic soils.
  • ItemOpen Access
    Elucidating the role of earthworms on the fate of fertilizer N with synthetic and organic fertilizer application
    (Elsevier B.V., 2024-12) Hao, R; Wu, Y; Di, Hong; Chen, Y; Chen, W; Hu, R; Tan, W
    Earthworms’ activities not only increase soil nitrogen (N) uptake by crops but also lead to N losses to environment. However, it remains unclear whether earthworms’ impact on the fate of fertilizer N differs based on the type of fertilizer application. Therefore, the present pot experiment examined the transformation and fate of two types of ¹⁵N-labeled fertilizer (synthetic fertilizer urea and organic fertilizer compost applied at rate of 400 mg N/pot) with and without earthworms (Amynthas corticis) in a soil-lettuce system over three seasons of cultivation. Results showed that earthworms increased the fresh biomass of lettuce in all three seasons, regardless of the type of fertilizer used. However, the effect of earthworms on fertilizer N uptake varied depending on the type of fertilizer. With earthworms present, lettuce took up an additional 20.97 mg/pot of synthetic fertilizer N in the first season, which sharply decreased to 2.72 mg/pot and 4.63 mg/pot in the second and third seasons, respectively. In contrast, the uptake of organic fertilizer N by lettuce increased by 10.08–11.24 mg/pot throughout the entire experiment when earthworms were present. The presence of earthworms increased the percentage of synthetic fertilizer N lost to the environment by 0.8 %, due to increased N leaching, N₂O emission, NH₃ volatilization, etc. In contrast, earthworms decreased the percentage of organic fertilizer N lost to the environment by 1.9 %, primarily through reduced NH₃ volatilization, etc. This study underscores the pivotal role of earthworms in modulating fertilizer N dynamics, with organic fertilizer offering superior ecosystem services compared to synthetic fertilizer. Given that only one earthworm species was studied and nearly half of the organic fertilizer remained in the soil, future long-term experiments incorporating diverse earthworm species and changes in the soil's native N pool are essential to fully understand the role of earthworms in agro-ecosystem N cycling.
  • ItemOpen Access
    Spatio-temporal analysis of net anthropogenic phosphorus inputs (NAPIs) and their impacts in Ningxia Hui Autonomous Region using Monte Carlo simulations and sensitivity analysis
    (MDPI AG, 2024-11) Ma, Hua; Liu, Xiaotong; Lei, Qiuliang; Luo, Jiafa; Di, Hong; Du, Xinzhong; Zhao, Ying; Zhang, Xuejun; Liu, Hongbin
    This study employed the Net Anthropogenic Phosphorus Inputs (NAPI) model to assess the impact of human activities on phosphorus input in a watershed, analyzing county-level statistical data and NAPI model parameters from 1991 to 2020. The Monte Carlo method was used for a quantitative analysis of the model parameters’ effects on each NAPI component and the overall simulation results. The sensitivity index method identified each component’s sensitive parameters. The study found that the lowest NAPI value was 454 kg/(km²·a) in 1991 and the highest was 1336 kg/(km²·a) in 2003. NAPI in Ningxia showed an overall upward trend from 1991 to 1999, a slight decrease from 1999 to 2003, and a slight increase from 2003 to 2020, with fertilizer being the main contributing factor, accounting for 77.4% of the total input. On a spatial scale, NAPI in Ningxia was significantly correlated with land use patterns, showing higher values in the northern and southern regions compared to the central part. The NAPI values derived from Monte Carlo simulations with appropriate parameters ranged from −24.83% to 31.49%. The study highlighted the net food and feed imports component as having the highest uncertainty, impacting simulation results within a range of −23.89% to 53.98%. It was observed that the larger a component’s proportion in the NAPI model, the more sensitive its parameters, with the phosphorus fertilizer (Pfer) component’s parameters being notably more sensitive than those of the food/feed phosphorus input and the non-food phosphorus input (Pnf) components. These findings can inform phosphorus pollution control policies in Northwest China, while the selection of sensitive parameters provides a useful reference for future NAPI research in other regions.
  • ItemOpen Access
    Sulfur-doped binary layered metal oxides incorporated on pomegranate peel-derived activated carbon for removal of heavy metal ions
    (Multidisciplinary Digital Publishing Institute (MDPI), 2022-12) Jume, BH; Valizadeh Dana, N; Rastin, M; Parandi, E; Darajeh, N; Rezania, S
    In this study, a novel biomass adsorbent based on activated carbon incorporated with sulfur-based binary metal oxides layered nanoparticles (SML-AC), including sulfur (S₂), manganese (Mn), and tin (Sn) oxide synthesized via the solvothermal method. The newly synthesized SML-AC was studied using FTIR, FESEM, EDX, and BET to determine its functional groups, surface morphology, and elemental composition. Hence, the BET was performed with an appropriate specific surface area for raw AC (356 m²·g‾¹) and modified AC-SML (195 m²·g‾¹). To prepare water samples for ICP-OES analysis, the suggested nanocomposite was used as an efficient adsorbent to remove lead (Pb²⁺), cadmium (Cd²⁺), chromium (Cr³⁺), and vanadium (V⁵⁺) from oil-rich regions. As the chemical structure of metal ions is influenced by solution pH, this parameter was considered experimentally, and pH 4, dosage 50 mg, and time 120 min were found to be the best with high capacity for all adsorbates. At different experimental conditions, the AC-SML provided a satisfactory adsorption capacity of 37.03–90.09 mg·g⁻¹ for Cd²⁺, Pb²⁺, Cr3³⁺, and V⁵⁺ ions. The adsorption experiment was explored, and the method was fitted with the Langmuir model (R² = 0.99) as compared to the Freundlich model (R² = 0.91). The kinetic models and free energy (<0.45 KJ·mol‾¹) parameters demonstrated that the adsorption rate is limited with pseudo-second order (R² = 0.99) under the physical adsorption mechanism, respectively. Finally, the study demonstrated that the AC-SML nanocomposite is recyclable at least five times in the continuous adsorption–desorption of metal ions.
  • ItemOpen Access
    Nitrate as an alternative electron acceptor destabilizes the mineral associated organic carbon in moisturized deep soil depths
    (Frontiers Media, 2023-02-08) Song, W; Hu, C; Luo, Y; Clough, Timothy; Wrage-Mönnig, N; Ge, T; Luo, J; Zhou, S; Qin, S
    Numerous studies have investigated the effects of nitrogen (N) addition on soil organic carbon (SOC) decomposition. However, most studies have focused on the shallow top soils <0.2 m (surface soil), with a few studies also examining the deeper soil depths of 0.5–1.0 m (subsoil). Studies investigating the effects of N addition on SOC decomposition in soil >1.0 m deep (deep soil) are rare. Here, we investigated the effects and the underlying mechanisms of nitrate addition on SOC stability in soil depths deeper than 1.0 m. The results showed that nitrate addition promoted deep soil respiration if the stoichiometric mole ratio of nitrate to O₂ exceeded the threshold of 6:1, at which nitrate can be used as an alternative acceptor to O₂ for microbial respiration. In addition, the mole ratio of the produced CO₂ to N₂O was 2.57:1, which is close to the theoretical ratio of 2:1 expected when nitrate is used as an electron acceptor for microbial respiration. These results demonstrated that nitrate, as an alternative acceptor to O₂, promoted microbial carbon decomposition in deep soil. Furthermore, our results showed that nitrate addition increased the abundance of SOC decomposers and the expressions of their functional genes, and concurrently decreased MAOC, and the ratio of MAOC/SOC decreased from 20% before incubation to 4% at the end of incubation. Thus, nitrate can destabilize the MAOC in deep soils by stimulating microbial utilization of MAOC. Our results imply a new mechanism on how above-ground anthropogenic N inputs affect MAOC stability in deep soil. Mitigation of nitrate leaching is expected to benefit the conservation of MAOC in deep soil depths.
  • ItemOpen Access
    Land use conversion to uplands significantly increased the risk of antibiotic resistance genes in estuary area
    (Elsevier BV, 2024-09) Shen, Jupei; Yu, Danting; Liu, Zikai; Di, Hong; He, Ji-Zheng
    Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10¯²-1.5 × 10¯¹ copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas.
  • ItemOpen Access
    Anthropogenic N input increases global warming potential by awakening the “sleeping” ancient C in deep critical zones
    (American Association for the Advancement of Science, 2023-02-10) Qin, S; Yuan, H; Hu, C; Li, X; Wang, Y; Zhang, Y; Dong, W; Clough, Timothy; Luo, J; Zhou, S; Wrage-Mönnig, N; Ma, L; Oenema, O
    Even a small net increase in soil organic carbon (SOC) mineralization will cause a substantial increase in the atmospheric CO₂ concentration. It is widely recognized that the SOC mineralization within deep critical zones (2 to 12 m depth) is slower and much less influenced by anthropogenic disturbance when compared to that of surface soil. Here, we showed that 20 years of nitrogen (N) fertilization enriched a deep critical zone with nitrate, almost doubling the SOC mineralization rate. This result was supported by corresponding increases in the expressions of functional genes typical of recalcitrant SOC degradation and enzyme activities. The CO₂ released and the SOC had a similar ¹⁴C age (6000 to 10,000 years before the present). Our results indicate that N fertilization of crops may enhance CO₂ emissions from deep critical zones to the atmosphere through a previously disregarded mechanism. This provides another reason for markedly improving N management in fertilized agricultural soils.
  • ItemOpen Access
    Nitrogen optimization coupled with alternate wetting and drying practice enhances rhizospheric nitrifier and denitrifier abundance and rice productivity
    (Frontiers Media, 2022-10-11) Abid, AA; Zhang, Q; Adil, MF; Batool, I; Abbas, M; Hassan, Z; Khan, AA; Castellano-Hinojosa, A; Zaidi, SHR; Di, Hong; Abdeslsalam, NR
    Optimizing nitrogen (N) fertilization without sacrificing grain yield is a major concern of rice production system because most of the applied N has been depleted from the soil and creating environmental consequences. Hence, limited information is available about nutrient management (NM) performance at a specific site under alternate wetting and drying (AWD) irrigation compared to conventional permanent flooding (PF). We aimed to inquire about the performance of NM practices compared to the farmer’s fertilizer practice (FFP) under PF and AWD on rhizospheric nitrifier and denitrifier abundance, rice yield, plant growth, and photosynthetic parameters. Two improved NM practices; nutrient management by pig manure (NMPM); 40% chemical N replaced by pig manure (organic N), and nutrient management by organic slow-release fertilizer (NMSR); 40% chemical N replaced by organic slow-release N were compared. The results showed an increased total grain yield (16.06%) during AWD compared to PF. Compared to conventional FFP, NMPM, and NMSR significantly increased the yields by 53.84 and 29.67%, respectively, during AWD. Meanwhile, PF prompted a yield increase of 45.07 and 28.75% for NMPM and NMSR, respectively, (p < 0.05) compared to FFP. Besides, a significant correlation was observed between grain yield and nitrogen content during AWD (R² = 0.58, p < 0.01), but no significant correlation was observed during PF. The NMPM contributed to photosynthetic attributes and the relative chlorophyll content under both watering events. Moreover, relatively higher abundances of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were observed during AWD, and the highest value was found after the late panicle stage. Our results suggest that the AWD–NMPM model is the best option to stimulate nitrifier and denitrifier gene abundance and promote rice production.
  • ItemOpen Access
    Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils
    (Springer Nature on behalf of Oxford University Press, 2021-12) Pan, Hong; Feng, Haojie; Liu, Yaowei; Lai, Chun-Yu; Zhuge, Yuping; Zhang, Qichun; Tang, Caixian; Di, Hong; Jia, Zhongjun; Gubry-Rangin, Cécile; Li, Yong; Xu, Jianming
    Grassland soils serve as a biological sink and source of the potent greenhouse gases (GHG) methane (CH₄) and nitrous oxide (N₂O). The underlying mechanisms responsible for those GHG emissions, specifically, the relationships between methane- and ammonia-oxidizing microorganisms in grazed grassland soils are still poorly understood. Here, we characterized the effects of grazing on in situ GHG emissions and elucidated the putative relations between the active microbes involving in methane oxidation and nitrification activity in grassland soils. Grazing significantly decreases CH₄ uptake while it increases N₂O emissions basing on 14-month in situ measurement. DNA-based stable isotope probing (SIP) incubation experiment shows that grazing decreases both methane oxidation and nitrification processes and decreases the diversity of active methanotrophs and nitrifiers, and subsequently weakens the putative competition between active methanotrophs and nitrifiers in grassland soils. These results constitute a major advance in our understanding of putative relationships between methane- and ammonia-oxidizing microorganisms and subsequent effects on nitrification and methane oxidation, which contribute to a better prediction and modeling of future balance of GHG emissions and active microbial communities in grazed grassland ecosystems.
  • ItemOpen Access
    Phosphorus applications adjusted to optimal crop yields can help sustain global phosphorus reserves
    (Springer Nature, 2024-04) McDowell, Richard; Pletnyakov, P; Haygarth, PM
    With the longevity of phosphorus reserves uncertain, distributing phosphorus to meet food production needs is a global challenge. Here we match plant-available soil Olsen phosphorus concentrations to thresholds for optimal productivity of improved grassland and 28 of the world’s most widely grown and valuable crops. We find more land (73%) below optimal production thresholds than above. We calculate that an initial capital application of 56,954 kt could boost soil Olsen phosphorus to their threshold concentrations and that 28,067 kt yr¯¹ (17,500 kt yr¯¹ to cropland) could maintain these thresholds. Without additional reserves becoming available, it would take 454 years at the current rate of application (20,500 kt yr¯¹) to exhaust estimated reserves (2020 value), compared with 531 years at our estimated maintenance rate and 469 years if phosphorus deficits were alleviated. More judicious use of phosphorus fertilizers to account for soil Olsen phosphorus can help achieve optimal production without accelerating the depletion of phosphorus reserves.
  • ItemOpen Access
    Real-time genomics for One Health
    (Springer, 2023-08-08) Urban, L; Perlas, A; Francino, O; Martí-Carreras, J; Muga, BA; Mwangi, JW; Boykin Okalebo, L; Stanton, J-AL; Black, Amanda; Waipara, N; Fontsere, C; Eccles, D; Urel, H; Reska, T; Morales, HE; Palmada-Flores, M; Marques-Bonet, T; Watsa, M; Libke, Z; Erkenswick, G; van Oosterhout, C
    The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself – from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.
  • ItemOpen Access
    Plant species identity and plant-induced changes in soil physicochemistry—but not plant phylogeny or functional traits - shape the assembly of the root-associated soil microbiome
    (Oxford University Press, 2023-11) Byers, Alexa; Condron, LM; O’Callaghan, M; Waller, Lauren; Dickie, IA; Wakelin, SA
    The root-associated soil microbiome contributes immensely to support plant health and performance against abiotic and biotic stressors. Understanding the processes that shape microbial assembly in root-associated soils is of interest in microbial ecology and plant health research. In this study, 37 plant species were grown in the same soil mixture for 10 months, whereupon the root-associated soil microbiome was assessed using amplicon sequencing. From this, the contribution of direct and indirect plant effects on microbial assembly was assessed. Plant species and plant-induced changes in soil physicochemistry were the most significant factors that accounted for bacterial and fungal community variation. Considering that all plants were grown in the same starting soil mixture, our results suggest that plants, in part, shape the assembly of their root-associated soil microbiome via their effects on soil physicochemistry. With the increase in phylogenetic ranking from plant species to class, we observed declines in the degree of community variation attributed to phylogenetic origin. That is, plant-microbe associations were unique to each plant species, but the phylogenetic associations between plant species were not important. We observed a large degree of residual variation (> 65%) not accounted for by any plant-related factors, which may be attributed to random community assembly.