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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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Item Open 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, AlistairLotus 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.Item Open 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, WEarthworms’ 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.Item Open 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, HongbinThis 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.Item Open 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, SIn 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.Item Open 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, SNumerous 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.Item Open 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-ZhengLand 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.Item Open 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, OEven 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.Item Open 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, NROptimizing 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.Item Open 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, H; Feng, H; Liu, Y; Lai, C-Y; Zhuge, Y; Zhang, Q; Tang, C; Di, Hong; Jia, Z; Gubry-Rangin, C; Li, Y; Xu, JGrassland 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.Item Open Access Phosphorus applications adjusted to optimal crop yields can help sustain global phosphorus reserves(Springer Nature, 2024-04) McDowell, Richard; Pletnyakov, P; Haygarth, PMWith 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.Item Open 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, CThe 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.Item Open 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, L; Dickie, IA; Wakelin, SAThe 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.Publication Open Access Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil(Frontiers, 2024-01-01) Shah, AS; Hsu, PC; Chisholm, C; Podolyan, Andriy; Cameron, Keith; Luo, J; Stenger, R; Carrick, S; Hu, W; Ferguson, SA; Wei, W; Shen, J; Zhang, L; Liu, H; Zhao, T; Wei, W; Ding, W; Pan, H; Liu, Y; Li, B; Du, J; Di, HongIntroduction: 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.Publication Open Access Learning by doing is more memorable: Soil judging as an educative tool(2022-07-31) Smith, Carol; Carrick, S; Nelson, J; Mazzetto, J; Penny, V; Butel, JSoil scientists are increasingly working in a multidisciplinary world where they interact with professionals from different disciplines and diverse end user groups. The ability to communicate, and to be an effective team player are just as important skills as the ability to apply practical field skills and describe soil profiles. The kinaesthetic approach embodied in soil judging allows the student to also connect with pedological theory; and it is a pedagogically aligned style of learning. At Lincoln University we first adopted innovative, experiential learning in the form of soil judging in 2016 to address these issues, and have worked collaboratively with Manaaki Whenua Landcare Research to develop this programme. Soil judging in New Zealand is in its infancy compared to other countries, but the undergraduate student soil science society and academic staff have been enthusiastic in practicing soil description skills and land use interpretation, participating in soil judging contests in New Zealand and Australia. Students report that they have become more confident in soil description and that it has stimulated their interest in learning about soil science. We designed a micro credential to recognize the academic work of the students. Several soil judging graduates have secured employment as pedologists at Crown Research Institutes or as soil resource specialists in local / regional government organisations. Soil judging may also be an effective recruitment pipeline into the discipline: offering those students with a practical and kinaesthetic aptitude who perform well at soil judging an insight into the academic side of the soil science discipline. We posit that soil judging competitions are an effective framework for students to acquire a valuable range of practical, field-based skills for a professional career in soil science or allied enterprises.Item Open Access Irrigation scheduling needs to consider both plant‐available water and soil aeration requirements(Wiley on behalf of Soil Science Society of America, 2024-05-29) Pragg, B; Deepagoda, Chamindu; Cameron, Keith; Di, Hong; Clough, Timothy; Carrick, SGlobal food production relying on irrigated agriculture accounts for >70% of the global freshwater withdrawal. A thorough understanding of soil–water characteristics (SWCs) and critical soil–water values in the soil and subsoil is important for effective management of irrigated water. A critical soil–water “window” for plants is generally taken as the plant-available water window without considering diffusion-dominated soil aeration as a co-requisite. This study examined SWC curves in vadose soil profiles (up to 1.5-m depth) in eight pasture soils. The soil moisture measurements were made over matric potentials ranging from −1 to −1500 kPa using tension table and pressure plate apparatus. The van Genuchten model was used to parameterize the measured SWC curve, while the Millington-Quirk model was used to derive soil–gas diffusivity from measured soil physical properties. We defined critical soil–water windows considering the threshold values for both plant-available water and soil–gas diffusivity to ensure water and aeration corequisites for plant growth. The results clearly distinguished depth-dependent regimes of gravitational, plant-available, and unavailable water in selected profiles and their responses to soil structural changes across the depth. In some of the observed soil profiles, only 30%–60% of the plant-available water window was able to be utilized by plants because the remainder existed under soil conditions where soil aeration was inadequate for plant growth, emphasizing the importance of considering both the plant's water and aeration requirements during irrigation scheduling. Further, the infiltration profiles in two selected soils under simulated irrigation highlighted the importance of a priori knowledge of the soil structure in deeper soil layers for scheduling irrigation.Publication Open Access Bioavailable iron concentrations regulate phytoplankton growth and bloom formation in low-nutrient lakes(Elsevier, 2023-12-01) Dengg, M; Stirling, CH; Safi, K; Lehto, Niklas; Wood, SA; Seyitmuhhamedov, K; Reid, MR; Verburg, PThe growth of phytoplankton in lakes is thought to be primarily controlled by macronutrient concentrations, but the availability of trace metal micronutrients, such as iron (Fe), are increasingly recognised as important regulators of lake primary production. This study evaluates the role of Fe in regulating phytoplankton growth in lakes of different nutrient status in New Zealand. The results of this unique year-long study, combining highly sensitive trace metal concentration analysis of waters and particulates with advanced trace metal bioavailability and speciation modelling, constrains thresholds for bioavailable Fe and colloidal Fe of 0.8 nmol·L¯¹and 30 nmol·L¯¹, respectively, below which phytoplankton growth-limitation occurs. These thresholds specifically control diatom bloom formation and termination in lakes, thereby exerting a strong influence on freshwater carbon sequestration, given the dominance of diatoms in lake bloom assemblages. Importantly, potentially toxic cyanobacteria thrived only after events of bottom water anoxia, when additional dissolved Fe in concentrations ≥4 nmol·L¯¹ was released into the water column. These new thresholds for bioavailable and colloidal Fe offer the potential to manage micronutrient levels in lakes for the purpose of regulating algal bloom formation and carbon sequestration, while at the same time, suppressing the formation of harmful cyanobacterial blooms.Publication Open Access Temporal changes in Cd sorption and plant bioavailability in compost-amended soils(MDPI, 2023-12) Al Mamun, S; Lehto, Niklas; Cavanagh, J; McDowell, Richard; Kellermann, L; Robinson, BHThe application of Cd-contaminated phosphate fertiliser has enriched concentrations of this non-essential element in many agricultural soils. Consequently, concentrations of the metal in some agricultural products exceed the Maximum Limit in foods. Composts can reduce the transfer of Cd from soil to plants; however, it is unclear how long this beneficial effect endures. We aimed to determine temporal changes of phytoavailable Cd in two market garden soils (an Allophanic Orthic Granular Soil and a Recent Silt Loam). Soils were amended with either municipal green waste compost or sawdust and animal waste compost at a rate of 2.5% w/w under three incubation regimes: at 19 °C, at 30 °C, and at 30 °C with additional N added as urea at 0.6 g urea/kg soil added over 1 year. Each replicate was sampled after 1, 5, 9, 13, 21, 31, and 49 weeks, and phytoavailable Cd was estimated through 0.05 M Ca(NO₃)₂ extraction. Seed potato (Solanum tuberosum), ‘Nadine’ variety, was grown in the Pukekohe Allophanic Orthic Granular Soil, freshly amended with municipal compost and the same soil aged for one year. The concentration of Cd in all samples was analysed using an ICP-OES (Inductively Coupled Plasma-Optical Emission Spectrometer). The C concentration in the soil—compost mixtures decreased over the year, with the greatest decreases occurring in the soils incubated at 30 °C with added N. Unexpectedly, the concentration of Ca(NO₃)₂-extractable Cd in the compost-amended soils did not increase over time and in some cases even decreased. This was confirmed through a pot experiment, which showed the Cd concentration in potato was reduced by 50% in both the freshly amended soil and the amended soil aged for one year. Cadmium immobilisation in soils might be due to both the sorption of Cd by organic matter and the occlusion of sorbed Cd by oxy-hydroxides of iron and aluminium. Over 49 weeks, soluble Cd does not increase as organic matter oxidises. The application of municipal compost to soil will reduce both plant Cd solubility and plant Cd uptake for at least one year in the soils tested.Publication Open Access Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs(Elsevier B.V., 2024-05-10) Chisholm, C; Di, Hong; Cameron, Keith; Podolyan, Andriy; Shen, J; Zhang, L; Sirisena, Kosala; Godsoe, WilliamThis study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1–6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.Publication Open Access Thermal adaptation of soil microbial functional responses: Insights from a geothermal gradient in Aotearoa New Zealand(2023) Alster, Charlotte; van de Laar, A; Arcus, V; Prentice, E; Bååth, E; Schipper, LNatural soil temperature gradients provide an excellent proxy to study how soil microbial communities, and their associated activities, will adapt to global warming. The rate at which soil microbes adapt to warming has important implications for biogeochemical cycling and predictions of soil carbon loss. In Aotearoa New Zealand, we take advantage of a decades long geothermal gradient, ranging from 15-42°C mean annual soil temperature, to investigate thermal adaptation of soil microbial respiration (with unlimited substrate), bacterial growth, and extracellular enzyme activities (β-glucosidase, acid phosphatase, and N-acetyl-β-ᴅ-glucosaminidase). We sampled soils from across this gradient and constructed temperature response curves for each soil sample in the lab by incubating them at six or more different temperatures. Using these temperature response curves, we then estimated rates of thermal adaptation for each microbial function and compared how different microbial processes adapt differentially. Despite major changes in microbial community diversity and composition along the gradient, we found only modest shifts in thermal adaptation of the microbial functional responses. The temperature response curves for soil microbial respiration and bacterial growth increased at a rate of approximately 0.2°C per 1°C increase in mean annual temperature. In contrast, we did not find a significant relationship between mean soil temperature and the temperature response of extracellular enzyme activity, suggesting that temperature responses are highly conserved across a variety of soil microbial functions. Nonetheless, it is important to consider how these changes in microbial rates may affect predictions of soil carbon loss with global warming.Publication Open Access Quantifying soil microbial thermal adaptation(2024-04) Alster, C; van de Laar, A; Goodrich, J; Arcus, V; Deslippe, J; Marshall, A; Schipper, LThermal adaptation of soil microbial respiration has the potential to greatly alter carbon cycle-climate feedbacks through acceleration or reduction of soil microbial respiration as the climate warms. However despite its importance, the relationship between warming and soil microbial activity remains poorly constrained. Part of this uncertainty stems from persistent methodological issues and difficulties isolating the interacting effects of changes in microbial community responses from changes in soil carbon availability. To address these challenges, we sampled nearly 50 soils from around New Zealand, including from a long-term geothermal gradient, with mean annual temperatures ranging from 11-35°C. For each of these soils we constructed temperature response curves of microbial respiration given unlimited substrate and estimated a temperature optima (Topt) and inflection point (Tinf). We found that thermal adaptation of microbial respiration occurred at a rate of 0.29°C ± 0.04 1SE for Topt and 0.27°C ± 0.05 1SE for Tinf per degree of warming, demonstrating that thermal adaptation is considerably offset from warming. These relatively small changes occurred despite large structural shifts in microbial community composition and diversity. We also quantitatively assessed how thermal adaptation may alter potential respiration rates under future warming scenarios by consolidating all of the temperature response curves. Depending on the specific mean and instantaneous soil temperatures, we found that thermal adaptation of microbial respiration could both limit and accelerate soil carbon losses. This work highlights the importance of considering the entire temperature response curve when making predictions about how thermal adaptation of soil microbial respiration will influence soil carbon losses.