Elizabeth M. Baggs

Nitrous oxide emissions from soils: how well do we understand the processes and their controls?

Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N2O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant–microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant–microbe interactions in the rhizosphere, may provide a key to better understand the variability of N2O fluxes at the soil–atmosphere interface. Moreover, recent insights into the regulation of the reduction of N2O to dinitrogen (N2) have increased our understanding of N2O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N2O (and N2) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N2O emissions to changes in environmental conditions, land management and land use.

Mitigating release of the potent greenhouse gas N2O from the nitrogen cycle – could enzymic regulation hold the key?

When faced with a shortage of oxygen, many bacterial species use nitrate to support respiration via the process of denitrification. This takes place extensively in nitrogen-rich soils and generates the gaseous products nitric oxide (NO), nitrous oxide (N(2)O) and dinitrogen (N(2)). The denitrifying bacteria protect themselves from the endogenous cytotoxic NO produced by converting it to N(2)O, which can be released into the atmosphere. However, N(2)O is a potent greenhouse gas and hence the activity of the enzyme that breaks down N(2)O has a crucial role in restricting its atmospheric levels. Here, we review the current understanding of the process by which N(2)O is produced and destroyed and discuss the potential for feeding this into new approaches for combating N(2)O release.

Biological sources and sinks of nitrous oxide and strategies to mitigate emissions

Nitrous oxide (N2O) is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. Global emissions continue to rise. More than two-thirds of these emissions arise from bacterial and fungal denitrification and nitrification processes in soils, largely as a result of the application of nitrogenous fertilizers. This article summarizes the outcomes of an interdisciplinary meeting, ‘Nitrous oxide (N2O) the forgotten greenhouse gas’, held at the Kavli Royal Society International Centre, from 23 to 24 May 2011. It provides an introduction and background to the nature of the problem, and summarizes the conclusions reached regarding the biological sources and sinks of N2O in oceans, soils and wastewaters, and discusses the genetic regulation and molecular details of the enzymes responsible. Techniques for providing global and local N2O budgets are discussed. The findings of the meeting are drawn together in a review of strategies for mitigating N2O emissions, under three headings, namely: (i) managing soil chemistry and microbiology, (ii) engineering crop plants to fix nitrogen, and (iii) sustainable agricultural intensification.

Biochemical cycling in the rhizosphere having an impact on global change

Changes in chemical properties in soil around plant roots influence many microbial processes, including those having an impact on greenhouse gas emissions. To potentially mitigate these emissions according to the Kyoto protocol, knowledge about how and where these gases are produced and consumed in soils is required. In this review, we focus on the greenhouse gases nitrous oxide and methane, which are produced by nitrifying and denitrifying prokaryotes and methanogenic archaea, respectively. After describing the microbial processes involved in production and consumption of nitrous oxide and methane and how they can be affected in the rhizosphere, we give an overview of nitrous oxide and methane emissions from the rhizosphere and soils and sediments with plants. We also discuss strategies to mitigate emissions from the rhizosphere and consider possibilities for carbon sequestration.

Production of NO, N2O and N2 by extracted soil bacteria, regulation by NO2− and O2 concentrations

The oxygen control of denitrification and its emission of NO/N2O/N2 was investigated by incubation of Nycodenz-extracted soil bacteria in an incubation robot which monitors O2, NO, N2O and N2 concentrations (in He+O2 atmosphere). Two consecutive incubations were undertaken to determine (1) the regulation of denitrification by O2 and NO2(-) during respiratory O2 depletion and (2) the effects of re-exposure to O2 of cultures with fully expressed denitrification proteome. Early denitrification was only detected (as NO and N2O) at <or=80 microM O2 in treatments with NO2(-), and the rates were three orders of magnitude lower than the rates observed after oxygen depletion (with N2 as the primary product). When re-exposed to O2, the cultures continued to denitrify (8-55% of the rates during the foregoing anoxic phase), but its main product was N2O. The N2O reductase activity recovered as oxygen was being depleted. The results suggest that expression of the denitrifying proteome may result in significant subsequent aerobic denitrification, and this has profound implications for the understanding and modelling of denitrification and N2O emission. Short anoxic spells caused by transient flooding during rainfall, could lead to subsequent unbalanced aerobic denitrification, in which N2O is a major end product.

How do soil emissions of N2O, CH4 and CO2 from perennial bioenergy crops differ from arable annual crops?

It is important to demonstrate that replacing fossil fuel with bioenergy crops can reduce the national greenhouse gas (GHG) footprint. We compared field emissions of nitrous oxide (N2O), methane (CH4) and soil respiration rates from the C4 grass Miscanthus × giganteus and willow (salix) with emissions from annual arable crops grown for food production. The study was carried out in NE England on adjacent fields of willow, Miscanthus, wheat (Triticum aetivum) and oilseed rape (Brassica napus). N2O, CH4 fluxes and soil respiration rates were measured monthly using static chambers from June 2008 to November 2010. Net ecosystem exchange (NEE) of carbon dioxide (CO2) was measured by eddy covariance on Miscanthus from May 2008 and on willow from October 2009 until November 2010. The N2O fluxes were significantly smaller from the bioenergy crops than that of the annual crops. Average fluxes were 8 and 32 μg m−2 h−1 N2O‐N from wheat and oilseed rape, and 4 and 0.2 μg m−2 h−1 N2O‐N from Miscanthus and willow, respectively. Soil CH4 fluxes were negligible for all crops and soil respiration rates were similar for all crops. NEE of CO2 was larger for Miscanthus (−770 g C m−2 h−1) than willow (−602 g C m−2 h−1) in the growing season of 2010. N2O emissions from Miscanthus and willow were lower than for the wheat and oilseed rape which is most likely a result of regular fertilizer application and tillage in the annual arable cropping systems. Application of 15N‐labelled fertilizer to Miscanthus and oil seed rape resulted in a fertilizer‐induced increase in N2O emission in both crops. Denitrification rates (N2O + N2) were similar for soil under Miscanthus and oilseed rape. Thus, perennial bioenergy crops only emit less GHGs than annual crops when they receive no or very low rates of N fertilizer.

Partitioning the components of soil respiration: a research challenge

Little is known about the respiratory components of CO2 emitted from soils and attaining a reliable quantification of the contribution of root respiration remains one of the major challenges facing ecosystem research. Resolving this would provide major advances in our ability to predict ecosystem responses to climate change. The merits and technical and theoretical difficulties associated with different approaches adopted for partitioning respiration components are discussed here. The way forward is suggested to be the development of non-invasive regression analysis validated by stable isotope approaches to increase the sensitivity of model functions to include components of rhizosphere microbial activity, changing root biomass and the dynamics of a wide range of soil C pools.

Soil nitrate reducing processes drivers, mechanisms for spatial variation, and significance for nitrous oxide production

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate (NO3−) and production of the potent greenhouse gas, nitrous oxide (N2O). A number of factors are known to control these processes, including O2 concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N2O production from soils.

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

ABSTRACT Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles.

Nitrous oxide production in soil isolates of nitrate-ammonifying bacteria

Here we provide the first demonstration of the potential for N2 O production by soil-isolated nitrate-ammonifying bacteria under different C and N availabilities, building on characterizations informed from model strains. The potential for soil-isolated Bacillus sp. and Citrobacter sp. to reduce NO3 (-) , and produce NH4 (+) , NO2 (-) and N2 O was examined in batch and continuous (chemostat) cultures under different C-to-NO3 (-) ratios, NO3 (-) -limiting (5 mM) and NO3 (-) -sufficient (22 mM) conditions. C-to-NO3 (-) ratio had a major influence on the products of nitrate ammonification, with NO2 (-) , rather than NH4 (+) , being the major product at low C-to-NO3 (-) ratios in batch cultures. N2 O production was maximum and accompanied by high NO2 (-) production under C-limitation/NO3 -sufficiency conditions in chemostat cultures. In media with lower C-to-NO3 -N ratios (5- and 10-to-1) up to 2.7% or 5.0% of NO3 (-) was reduced to N2 O by Bacillus sp. and Citrobacter sp., respectively, but these reduction efficiencies were only 0.1% or 0.7% at higher C-to-NO3 (-) ratios (25- and 50-to-1). As the highest N2 O production did not occur under the same C-to-NO3 (-) conditions as highest NH4 (+) production we suggest that a re-evaluation may be necessary of the environmental conditions under which nitrate ammonification contributes to N2 O emission from soil.