Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology.

Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information: The online version contains supplementary material available at 10.1007/s10533-024-01122-6.

Challenges of accounting nitrous oxide emissions from agricultural crop residues.

Crop residues are important inputs of carbon (C) and nitrogen (N) to soils and thus directly and indirectly affect nitrous oxide (N2 O) emissions. As the current inventory methodology considers N inputs by crop residues as the sole determining factor for N2 O emissions, it fails to consider other underlying factors and processes. There is compelling evidence that emissions vary greatly between residues with different biochemical and physical characteristics, with the concentrations of mineralizable N and decomposable C in the residue biomass both enhancing the soil N2 O production potential. High concentrations of these components are associated with immature residues (e.g., cover crops, grass, legumes, and vegetables) as opposed to mature residues (e.g., straw). A more accurate estimation of the short-term (months) effects of the crop residues on N2 O could involve distinguishing mature and immature crop residues with distinctly different emission factors. The medium-term (years) and long-term (decades) effects relate to the effects of residue management on soil N fertility and soil physical and chemical properties, considering that these are affected by local climatic and soil conditions as well as land use and management. More targeted mitigation efforts for N2 O emissions, after addition of crop residues to the soil, are urgently needed and require an improved methodology for emission accounting. This work needs to be underpinned by research to (1) develop and validate N2 O emission factors for mature and immature crop residues, (2) assess emissions from belowground residues of terminated crops, (3) improve activity data on management of different residue types, in particular immature residues, and (4) evaluate long-term effects of residue addition on N2 O emissions.

A global dataset for the production and usage of cereal residues in the period 1997-2021.

Crop residue management plays an important role in determining agricultural greenhouse gas emissions and related changes in soil carbon stocks. However, no publicly-available global dataset currently exists for how crop residues are managed. Here we present such a dataset, covering the period 1997-2021, on a 0.5° resolution grid. For each grid cell we estimate the total production of residues from cereal crops, and determine the fraction of residues (i) used for livestock feed/bedding, (ii) burnt on the field, (iii) used for other off-field purposes (e.g. domestic fuel, construction or industry), and (iv) left on the field. This dataset is the first of its kind, and can be used for multiple purposes, such as global crop modelling, including the calculation of greenhouse gas inventories, estimating crop-residue availability for biofuel production or modelling livestock feed availability.

Long term impact of residue management on soil organic carbon stocks and nitrous oxide emissions from European croplands.

Application of crop residues to agricultural fields is a significant source of the greenhouse gas nitrous oxide (N2O) and an essential factor affecting the soil organic carbon (SOC) balance. Here we present a biogeochemical modelling study assessing the impact of crop residue management on soil C stocks and N2O fluxes for EU-27 using available information on soils, management and climate and by testing various scenarios of residue management. Three biogeochemical models, i.e. CERES-EGC, LandscapeDNDC and LandscapeDNDC-MeTrx, were used in an ensemble approach on a grid of 0.25° × 0.25° spatial resolution for calculating EU-27 wide inventories of changes in SOC stocks and N2O emissions due to residue management for the years 2000-2100 using different climate change projections (RCP4.5 and RCP8.5). Our results show, that climate change poses a threat to cropping systems in Europe, resulting in potential yield declines, increased N2O emissions and loss of SOC. This highlights the need for adapting crop management to mitigate climate change impacts, e.g. by improved residue management. For a scenario with 100% residues retention and reduced tillage we calculated that in average SOC stocks may increase over 50-100 years by 19-23% under RCP8.5 and RCP4.5. However, complete retention of crop residues also resulted in an increase of soil N2O emissions by 17-30%, so that climate benefits due to increases in SOC stocks were eventually compensated by increased N2O emissions. The long-term EFN2O for residue N incorporation was 1.18% and, thus slightly higher as the 1% value used by IPCC. We conclude that residue management can be an important strategy for mitigating climate change impacts on SOC stocks, though it requires as well improvements in N management for N2O mitigation.

Environmental and economic trade-offs of using composted or stockpiled manure as partial substitute for synthetic fertilizer.

Manure generated from livestock production could represent an important source of plant nutrients in substitution of synthetic fertilizer. To evaluate the sustainability of partially substituting synthetic fertilizer with soil organic amendments (OAs) in horticulture, an economic and greenhouse gas (GHG) budget was developed. The boundary for analysis included manure processing (stockpiling vs. composting) and transport and spreading of manure and compost (feedlot and chicken) in intensively cultivated horticultural fields. The OA field application rates were calculated based on the nitrogen supplied by OAs. The GHG budget based on directly measured emissions indicates that the application of composted manure, in combination with reduced fertilizer rate, was always superior to stockpiled manures. Compost treatments showed from 9 to 90% less GHG emissions than stockpiled manure treatments. However, higher costs associated with the purchase and transport of composted manure (three times higher) generated a greater economic burden compared with stockpiled manure and synthetic fertilizer application. The plant nutrient replacement value of the OAs was considered only for the first year of application, and if long-term nutrient release from OAs is taken into account, additional savings are possible. Because the income from soil carbon sequestration initiatives in response to OA application is unlikely to bridge this financial gap, particularly in the short term, this study proposes that future policy should develop methodologies for avoided GHG emissions from OA application. The combined income from soil carbon sequestration and potentially avoided GHG initiatives could incentivize farmers to adopt OAs as a substitute for synthetic fertilizers, thereby promoting more sustainable farming practices.

Important constraints on soil organic carbon formation efficiency in subtropical and tropical grasslands.

More than 10% of Australia's 49 M ha of grassland is considered degraded, prompting widespread interest in the management of these ecosystems to increase soil carbon (C) sequestration-with an emphasis on long-lived C storage. We know that management practices that increase plant biomass also increase C inputs to the soil, but we lack a quantitative understanding of the fate of soil C inputs into different soil organic carbon (SOC) fractions that have fundamentally different formation pathways and persistence in the soil. Our understanding of the factors that constrain SOC formation in these fractions is also limited, particularly within tropical climates. We used isotopically labelled residue (13 C) to determine the fate of residue C inputs into short-lived particulate organic matter (POM) and more persistent mineral-associated organic matter (MAOM) across a broad climatic gradient (ΔMAT 10°C) with varying soil properties. Climate was the primary driver of aboveground residue mass loss which corresponded to higher residue-derived POM formation. In contrast, MAOM formation efficiency was constrained by soil properties. The differential controls on POM and MAOM formation highlight that a targeted approach to grassland restoration is required; we must identify priority regions for improved grazing management in soils that have a relatively high silt+clay content and cation exchange capacity, with a low C saturation in the silt+clay fraction to deliver long-term SOC sequestration.

Climate impacts on global agriculture emerge earlier in new generation of climate and crop models.

Potential climate-related impacts on future crop yield are a major societal concern. Previous projections of the Agricultural Model Intercomparison and Improvement Project's Global Gridded Crop Model Intercomparison based on the Coupled Model Intercomparison Project Phase 5 identified substantial climate impacts on all major crops, but associated uncertainties were substantial. Here we report new twenty-first-century projections using ensembles of latest-generation crop and climate models. Results suggest markedly more pessimistic yield responses for maize, soybean and rice compared to the original ensemble. Mean end-of-century maize productivity is shifted from +5% to -6% (SSP126) and from +1% to -24% (SSP585)-explained by warmer climate projections and improved crop model sensitivities. In contrast, wheat shows stronger gains (+9% shifted to +18%, SSP585), linked to higher CO2 concentrations and expanded high-latitude gains. The 'emergence' of climate impacts consistently occurs earlier in the new projections-before 2040 for several main producing regions. While future yield estimates remain uncertain, these results suggest that major breadbasket regions will face distinct anthropogenic climatic risks sooner than previously anticipated.

Global Research Alliance N2 O chamber methodology guidelines: Considerations for automated flux measurement.

Nitrous oxide (N2 O) emissions are highly episodic in response to nitrogen additions and changes in soil moisture. Automated gas sampling provides the necessary high temporal frequency to capture these emission events in real time, ensuring the development of accurate N2 O inventories and effective mitigation strategies to reduce global warming. This paper outlines the design and operational considerations of automated chamber systems including chamber design and deployment, frequency of gas sampling, and options in terms of the analysis of gas samples. The basic hardware and software requirements for automated chambers are described, including the major challenges and obstacles in their implementation and operation in a wide range of environments. Detailed descriptions are provided of automated systems that have been deployed to assess the impacts of agronomy on the emissions of N2 O and other significant greenhouse gases. This information will assist researchers across the world in the successful deployment and operation of automated N2 O chamber systems.

Effect of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on N-turnover, the N2O reductase-gene nosZ and N2O:N2 partitioning from agricultural soils.

Nitrification inhibitors (NIs) have been shown to reduce emissions of the greenhouse gas nitrous oxide (N2O) from agricultural soils. However, their N2O reduction efficacy varies widely across different agro-ecosystems, and underlying mechanisms remain poorly understood. To investigate effects of the NI 3,4-dimethylpyrazole-phosphate (DMPP) on N-turnover from a pasture and a horticultural soil, we combined the quantification of N2 and N2O emissions with 15N tracing analysis and the quantification of the N2O-reductase gene (nosZ) in a soil microcosm study. Nitrogen fertilization suppressed nosZ abundance in both soils, showing that high nitrate availability and the preferential reduction of nitrate over N2O is responsible for large pulses of N2O after the fertilization of agricultural soils. DMPP attenuated this effect only in the horticultural soil, reducing nitrification while increasing nosZ abundance. DMPP reduced N2O emissions from the horticultural soil by >50% but did not affect overall N2 + N2O losses, demonstrating the shift in the N2O:N2 ratio towards N2 as a key mechanism of N2O mitigation by NIs. Under non-limiting NO3- availability, the efficacy of NIs to mitigate N2O emissions therefore depends on their ability to reduce the suppression of the N2O reductase by high NO3- concentrations in the soil, enabling complete denitrification to N2.

Mobile continuous-flow isotope-ratio mass spectrometer system for automated measurements of N2 and N2O fluxes in fertilized cropping systems.

The use of synthetic N fertilizers has grown exponentially over the last century, with severe environmental consequences. Most of the reactive N will ultimately be removed by denitrification, but estimates of denitrification are highly uncertain due to methodical constraints of existing methods. Here we present a novel, mobile isotope ratio mass spectrometer system (Field-IRMS) for in-situ quantification of N2 and N2O fluxes from fertilized cropping systems. The system was tested in a sugarcane field continuously monitoring N2 and N2O fluxes for 7 days following fertilization using a fully automated measuring cycle. The detection limit of the Field-IRMS proved to be highly sensitive for N2 (54 g ha-1 day-1) and N2O (0.25 g ha-1 day-1) emissions. The main product of denitrification was N2 with total denitrification losses of up to 1.3 kg N ha-1 day-1. These losses demonstrate sugarcane systems in Australia are a hotspot for denitrification where high emissions of N2O and N2 can be expected. The new Field-IRMS allows for the direct and highly sensitive detection of N2 and N2O fluxes in real time at a high temporal resolution, which will help to improve our quantitative understanding of denitrification in fertilized cropping systems.

Effect of urbanization on soil methane and nitrous oxide fluxes in subtropical Australia.

Increasing population densities and urban sprawl are causing rapid land use change from natural and agricultural ecosystems into smaller, urban residential properties. However, there is still great uncertainty about the effect that urbanization will have on biogeochemical C and N cycles and associated greenhouse gas (GHG) budgets. We aimed to evaluate how typical urbanization related land use change in subtropical Australia affects soil GHG exchange (N2 O and CH4 ) and the associated global warming potential (GWP). Fluxes were measured from three land uses: native forest, a long-term pasture, and a turf grass lawn continuously over two years using a high-resolution automated chamber system. The fertilized turf grass had the highest N2 O emissions, dominated by high fluxes >100 g N2 O-N day-1 immediately following establishment though decreased to just 0.6 kg N2 O-N ha-1 in the second year. Only minor fluxes occurred in the forest and pasture, with the high aeration of the sandy topsoil limiting N2 O emissions while promoting substantial CH4 uptake. Native forest was consistently the strongest CH4 sink (-2.9 kg CH4 -C ha-1  year-1 ), while the pasture became a short-term CH4 source after heavy rainfall when the soil reached saturation. On a two-year average, land use change from native forest to turf grass increased the non-CO2 GWP from a net annual GHG sink of -83 CO2 -e ha-1  year-1 to a source of 245 kg CO2 -e ha-1  year-1 . This study highlights that urbanization can substantially alter soil GHG exchange by altering plant soil water use and by increasing bulk density and inorganic N availability. However, on well-drained subtropical soils, the impact of urbanization on inter-annual non-CO2 GWP of turf grass was low compared to urbanized ecosystems in temperate climates.

N2O and CO2 emissions following repeated application of organic and mineral N fertiliser from a vegetable crop rotation.

Accounting for nitrogen (N) release from organic amendments (OA) can reduce the use of synthetic N-fertiliser, sustain crop production, and potentially reduce soil borne greenhouse gases (GHG) emissions. However, it is difficult to assess the GHG mitigation potential for OA as a substitute of N-fertiliser over the long term due to only part of the organic N added to soil is being released in the first year after application. High-resolution nitrous oxide (N2O) and carbon dioxide (CO2) emissions monitored from a horticultural crop rotation over 2.5 years from conventional urea application rates were compared to treatments receiving an annual application of raw and composted chicken manure combined with conventional and reduced N-fertiliser rates. The repeated application of composted manure did not increase annual N2O emissions while the application of raw manure resulted in N2O emissions up to 35.2 times higher than the zero N fertiliser treatment and up to 4.7 times higher than conventional N-fertiliser rate due to an increase in C and N availability following the repeated application of raw OA. The main factor driving N2O emissions was the incorporation of organic material accompanied by high soil moisture while the application of synthetic N-fertiliser induced only short-term N2O emission pulse. The average annual N2O emission factor calculated accounting for the total N applied including OA was equal to 0.27 ±â€¯0.17%, 3.7 times lower than the IPCC default value. Accounting for the estimated N release from OA only enabled a more realistic N2O emission factor to be defined for organically amended field that was equal to 0.48 ±â€¯0.3%. This study demonstrated that accounting for the N released from repeated application of composted rather than raw manure can be a viable pathway to reduce N2O emissions and maintain soil fertility.

Nitrification inhibitors can increase post-harvest nitrous oxide emissions in an intensive vegetable production system.

To investigate the effect of nitrification inhibitors (NIs) 3,4-dimethylpyrazole phosphate (DMPP) and 3-methylpyrazole 1,2,4-triazole (3MP + TZ), on N2O emissions and yield from a typical vegetable rotation in sub-tropical Australia we monitored soil N2O fluxes continuously over an entire year using an automated greenhouse gas measurement system. The temporal variation of N2O fluxes showed only low emissions over the vegetable cropping phases, but significantly higher emissions were observed post-harvest accounting for 50-70% of the annual emissions. NIs reduced N2O emissions by 20-60% over the vegetable cropping phases; however, this mitigation was offset by elevated N2O emissions from the NIs treatments over the post-harvest fallow period. Annual N2O emissions from the conventional fertiliser, the DMPP treatment, and the 3MP + TZ treatment were 1.3, 1.1 and 1.6 (sem = 0.2) kg-N ha-1 year-1, respectively. This study highlights that the use of NIs in vegetable systems can lead to elevated N2O emissions by storing N in the soil profile that is available to soil microbes during the decomposition of the vegetable residues. Hence the use of NIs in vegetable systems has to be treated carefully and fertiliser rates need to be adjusted to avoid an oversupply of N during the post-harvest phase.

An improved (15) N tracer approach to study denitrification and nitrogen turnover in soil incubations.

RATIONALE: Denitrification (the reduction of oxidized forms of inorganic nitrogen (N) to N2 O and N2 ) from upland soils is considered to be the least well-understood process in the global N cycle. The main reason for this lack of understanding is that the terminal product (N2 ) of denitrification is extremely difficult to measure against the large atmospheric background. METHODS: We describe a system that combines the (15) N-tracer technique with a 40-fold reduced N2 (2% v/v) atmosphere in a fully automated incubation setup for direct quantification of N2 and N2 O emissions. The δ(15) N values of the emitted N2 and N2 O were determined using a custom-built gas preparation unit that was connected to a DELTA V Plus isotope ratio mass spectrometer. The system was tested on a pasture soil from sub-tropical Australia under different soil moisture conditions and combined with (15) N tracing in extractable soil N pools to establish a full N balance. RESULTS: The method proved to be highly sensitive for detecting N2 (1.12 µg N h(-1)  kg(-1) dry soil (ds)) and N2 O (0.36 µg N h(-1)  kg(-1) ds) emissions. The main end product of denitrification in the investigated soil was N2 O for both water contents, with N2 accounting for only 3% to 13% of the total denitrification losses. Between 90 and 95% of the added (15) N fertiliser could be recovered in N gases and extractable soil N pools. CONCLUSIONS: The high and N2 O-dominated denitrification rates found in this study are pointing at both the high ecological and the agronomic importance of denitrification in subtropical pasture soils. The new system allows for a direct and highly sensitive detection of N2 and N2 O fluxes from soils and may help to significantly improve our mechanistic understanding of N cycling and denitrification in terrestrial agro-ecosystems. Copyright © 2016 John Wiley & Sons, Ltd.

Greenhouse gas emissions from sub-tropical agricultural soils after addition of organic by-products.

As the cost of mineral fertilisers increases globally, organic soil amendments (OAs) from agricultural sources are increasingly being used as substitutes for nitrogen. However, the impact of OAs on the production of greenhouse gases (CO2 and N2O) is not well understood. A 60-day laboratory incubation experiment was conducted to investigate the impacts of applying OAs (equivalent to 296 kg N ha(-1) on average) on N2O and CO2 emissions and soil properties of clay and sandy loam soils from sugar cane production. The experiment included 6 treatments, one being an un-amended (UN) control with addition of five OAs being raw mill mud (MM), composted mill mud (CM), high N compost (HC), rice husk biochar (RB), and raw mill mud plus rice husk biochar (MB). These OAs were incubated at 60, 75 and 90% water-filled pore space (WFPS) at 25°C with urea (equivalent to 200 kg N ha(-1)) added to the soils thirty days after the incubation commenced. Results showed WFPS did not influence CO2 emissions over the 60 days but the magnitude of emissions as a proportion of C applied was RB < CM < MB < HC < MM. Nitrous oxide emissions were significantly less in the clay soil compared to the sandy loam at all WFPS, and could be ranked RB < MB < MM < CM < UN < HC. These results led to linear models being developed to predict CO2 and N2O emissions as a function of the dry matter and C/N ratio of the OAs, WFPS, and the soil CEC. Application of RB reduced N2O emissions by as much as 42-64% depending on WFPS. The reductions in both CO2 and N2O emissions after application of RB were due to a reduced bioavailability of C and not immobilisation of N. These findings show that the effect of OAs on soil GHG emissions can vary substantially depending on their chemical properties. OAs with a high availability of labile C and N can lead to elevated emissions of CO2 and N2O, while rice husk biochar showed potential in reducing overall soil GHG emissions.

Modeling nitrous oxide emissions from irrigated agriculture: testing DayCent with high-frequency measurements.

A unique high temporal frequency data set from an irrigated cotton-wheat rotation was used to test the agroecosystem model DayCent to simulate daily N20 emissions from subtropical vertisols under different irrigation intensities. DayCent was able to simulate the effect of different irrigation intensities on N20 fluxes and yield, although it tended to overestimate seasonal fluxes during the cotton season. DayCent accurately predicted soil moisture dynamics and the timing and magnitude of high fluxes associated with fertilizer additions and irrigation events. At the daily scale we found a good correlation of predicted vs. measured N20 fluxes (r2 = 0.52), confirming that DayCent can be used to test agricultural practices for mitigating N20 emission from irrigated cropping systems. A 25-year scenario analysis indicated that N20 losses from irrigated cotton-wheat rotations on black vertisols in Australia can be substantially reduced by an optimized fertilizer and irrigation management system (i.e., frequent irrigation, avoidance of excessive fertilizer application), while sustaining maximum yield potentials.