Changes to soil quality indicators following conversion to organic vegetable production (OF0401)

This is the final report of Defra project OF0401. The attached report document starts with an Executive Summary, from which this text is extracted. The aim of this 1 year study was to examine how key functional indicators of soil quality are affected by contrasting organic and conventional management regimes. In particular, the project investigated the impact of contrasting fertility building regimes on soil quality, focussing on the initial 5-year period following conversion from conventional to organic production. Five 0.8 ha areas at HRI-Wellesbourne were selected for study. These were: two organic vegetable rotations supporting contrasting fertility building regimes, an organic arable rotation, a grass-clover ley, and a conventionally managed cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. The conventional area was adjacent. A range of chemical, biological and physical attributes were determined. There were differences between the organic and conventional management regimes in most chemical, biological and physical soil quality parameters. Contrasting organic management regimes had different effects on soil quality. Relative to organic vegetable and conventional arable management, the organic arable management rotation enhanced amounts of light fraction organic matter and labile N, with beneficial implications for long term nutrient retention and soil organic matter development. There was little difference in chemical quality between the organic vegetable and the conventional arable areas. There was evidence that organic management promoted a microbial community that was distinct in composition and functional attributes to that in conventional soil. Relative to conventional management, areas under organic management had greatly increased inoculum of arbuscular mycorrhizal fungi, a larger proportion of 'active' relative to 'resting' biomass within the microbiota, increased metabolic diversity and a distinct microbial community metabolism. However, there was evidence that the productivity of newly converted organic systems could be limited by low inoculum and diversity of arbuscular mycorrhizal fungi inherited following conventional management. The clearest effect on soil structure was with regard to the detrimental effects of vegetable production rather than to any benefit associated with organic management. Wheeling lines caused compaction that resulted in poor growth of subsequent cereal crops. However, it is likely that increased levels of organic matter may result in a soil better able to cope with damaging operations. There were differences in the susceptibility of the chemical and biological quality parameters to change. These differences provide possibilities to use selected parameters as early indicators of the effects of management on soil quality. Furthermore, the results highlight the need, when investigating soil quality, to consider a wide variety of 'quality' analyses. Limited data sets, focussing on traditional measures of soil quality (e.g. total SOM and biomass-N), could lead to unsound conclusions regarding the effects of management on other functional aspects of soil quality. There are opportunities to conduct further statistical analysis of our comprehensive data set in order to develop an index suitable for quantifying soil quality in organic systems. Such an index would be of generic value to rate soil quality in diverse agricultural systems. Further work is needed to determine the applicability and conclusions of our study to other soil types and organic management regimes. The work has highlighted fundamental shifts in microbial community structure and functioning following conversion from conventional to organic management. There is a need to characterise and quantify these changes. This will provide new groups of 'indicator' organisms which could be suitable for assessing changes to soil quality, and could also provide opportunities to manage soil microbial communities to improve the sustainability of organic and conventional farming

Arbuscular mycorrhizal fungi in organic systems

Arbuscular mycorrhizal fungi (AMF) are potential contributors to plant nutrition and pathogen suppression in low input agricultural systems, although individual species of AMF vary widely in their functional attributes. Recent studies at HRI and elsewhere have suggested that in some agricultural systems inoculum of AMF is substantially lower under conventional management relative to that under organic management. Further studies have suggested that conventional management selects AMF communities with limited benefits to their plant hosts relative to those in organic systems. There is a need to investigate the generality of these findings, and their implications for the productivity of organic systems, particularly during the period following conversion to organic management. The current project was designed to pull together existing understanding of the role, and potential role, of AMF in organic systems, and to identify sites and develop methods for use in a subsequent research programme. The project had three objectives: 01 To deliver a literature review covering current knowledge of the role of AMF in conventional and organic agricultural systems. The review considered the ways in which management influences the structure and functioning of AMF communities, including their contributions under conventional and organic management, and recommendations for future research needs. 02 To establish the extent of differences in AMF inoculum between organic and conventional systems, covering a range of management practices. Paired organic and conventional fields at 12 sites from across England were selected to investigate the relationships between management, AMF communities and soil chemistry. Organic and conventionally managed soils showed no significant difference in soil chemical properties (Organic C, total N, total P, extractable P, K, Mg). However, organically managed soils had greater AMF spore numbers and root colonisation potential, and therefore higher AMF inoculum potential, than conventionally managed soil. The relative difference in AMF spore numbers between organic and conventionally managed fields increased with time since conversion. Differences in AMF inoculum potential between organic and conventionally managed fields, and between farm sites, could not be related to differences in soil chemistry. 03 To develop a method suitable for characterising AM fungus communities in soil libraries, based on 18S rRNA terminal restriction fragment length polymorphism (T-RFLP) T-RFLP was shown to provide a rapid semi-quantitative method for analysis of AMF community diversity. However it was clear that primers currently used to amplify AMF are selective and do not allow diversity of the whole AMF community to be determined. Additionally these primers amplify contaminant fungi which need to be removed from the T-RFLP profile prior to analysis. However, contaminant diversity was shown to be low. The project has identified sites and techniques which could be valuable in future research to study the role of AMF under organic management. The study has also highlighted a number of key areas in which further research is needed in order to harness AMF to improve sustainability and productivity of organic and other agricultural systems. In particular, there is a need to determine the extent to which AMF diversity varies between organic and conventional management, the rate and mechanisms by which AMF diversity increases following conversion to organic production, the relationships between AMF diversity and crop nutrition/ pathogen control, and the soil factors controlling the effectiveness of AMF inoculum

The effect of organic management on soil quality indicators

This report was presented at the UK Organic Research 2002 Conference. A range of physical, biological and chemical parameters were measured in organic soil that had been managed in different ways and in a conventional control. Factors were identified that could be used to construct an index of soil quality

Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes

Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used 37 in agriculture and poses an environmental concern because of its susceptibility to leach 38 from soil to water. We investigated the effect of soil depth on mecoprop-p 39 biodegradation and its relationship with the number and diversity of tfdA related genes, 40 which are the most widely known genes involved in degradation of the 41 phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT50) was 42 approximately 12 days in soil sampled from <30 cm depth, and increased progressively 43 with soil depth, reaching over 84 days at 70-80 cm. In sub-soil there was a lag period of 44 between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in 45 top-soil samples prior to the onset of degradation. The maximum degradation rate was 46 the same in top-soil and sub-soil samples. Although diverse tfdAα and tfdA genes were 47 present prior to mecoprop-p degradation, real time PCR revealed that degradation was 48 associated with proliferation of tfdA genes. The number of tfdA genes and the most 49 probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p 50 addition were below the limit of quantification and detection respectively. Melting 51 curves from the real time PCR analysis showed that prior to mecoprop-p degradation 52 both class I and class III tfdA genes were present in top- and sub-soil samples. However 53 at all soil depths only tfdA class III genes proliferated during degradation. Denaturing 54 gradient gel electrophoresis confirmed that class III tfdA genes were associated with 55 mecoprop-p degradation. Degradation was not associated with the induction of novel 56 tfdA genes in top- or sub-soil samples, and there were no apparent differences in tfdA 57 gene diversity with soil depth prior to or following degradation

Contrasting arbuscular mycorrhizal communities colonizing different host plants show a similar response to a soil phosphorus concentration gradient

High soil phosphorus (P) concentration is frequently shown to reduce root colonization by arbuscular mycorrhizal (AM) fungi, but the influence of P on the diversity of colonizing AM fungi is uncertain. We used terminal restriction fragment length polymorphism (T-RFLP) of 18S rDNA and cloning to assess diversity of AM fungi colonizing maize (Zea mays), soybean (Glycene max) and field violet (Viola arvensis) at three time points in one season along a P gradient of 10–280 mg l−1 in the field. Percentage AM colonization changed between sampling time points but was not reduced by high soil P except in maize. There was no significant difference in AM diversity between sampling time points. Diversity was reduced at concentrations of P > 25 mg l−1, particularly in maize and soybean. Both cloning and T-RFLP indicated differences between AM communities in the different host species. Host species was more important than soil P in determining the AM community, except at the highest P concentration. Our results show that the impact of soil P on the diversity of AM fungi colonizing plants was broadly similar, despite the fact that different plants contained different communities. However, subtle differences in the response of the AM community in each host were evident

An empirical model approach for assessing soil organic carbon stock changes following biomass crop establishment in Britain

Land-use change (LUC) is a major influence on soil organic carbon (SOC) stocks and the global carbon cycle. LUC from conventional agricultural to biomass crops has increased in Britain but there is limited understanding of the effects on SOC stocks. Results from paired plot studies investigating site-specific effects document both increasing and decreasing SOC stocks over time. Such variation demonstrates the sensitivity of SOC to many factors including environmental conditions. Using a chronosequence of 93 biomass crop sites in England and Wales, mainly of 1–14 y age, empirical models were developed of SOC trajectory following LUC from arable and grassland to short rotation coppice (SRC) willow and Miscanthus production. SOC stocks were calculated for each site using a fixed sampling depth of 30 cm and changes were estimated by comparing with typical pre-conversion SOC stocks. Most LUCs had no demonstrable net effect on SOC stocks. An estimated net SOC loss of 45.2 ± 24.1 tonnes per hectare (±95% confidence intervals) occurred after 14 y following LUC from grassland to SRC willow. Soil texture and climate data for each site were included in multivariable models to assess the influence of different environmental conditions on SOC trajectory. In most cases the addition of explanatory variables improved the model fit. These models may provide some preliminary estimates of more region-specific changes in SOC following LUC. However, the model fit did not improve sufficiently as to provide a basis for adopting a more targeted LUC strategy for lignocellulosic biomass crop production

Spatiotemporal variations of soil reactive nitrogen oxide fluxes across the anthropogenic landscape

Volatile reactive nitrogen oxides (NO y ) are significant atmospheric pollutants, including NO x (nitric oxide [NO] + nitrogen dioxide [NO2]) and NO z (nitrous acid [HONO] + nitric acid [HNO3] + nitrogen trioxide [NO3] + ...). NO y species are products of nitrogen (N) cycle processes, particularly nitrification and denitrification. Biogenic sources, including soil, account for over 50% of natural NO y emissions to the atmosphere, yet emissions from soils are generally not included in atmospheric models as a result of a lack of mechanistic data. This work is a unique investigation of NO y fluxes on a landscape scale, taking a comprehensive set of land-use types, human influence, and seasonality into account to determine large-scale heterogeneity to provide a basis for future modeling and hypothesis generation. By coupling 16S rRNA amplicon sequencing and quantitative polymerase chain reaction, we have linked significant differences in functional potential and activity of nitrifying and denitrifying soil microbes to NO y emissions from soils. Further, we have identified soils subject to increased N deposition that are less microbially active despite increased available N, potentially as a result of poor soil health from anthropogenic pollution. Structural equation modeling suggests human influence on soils to be a more significant effector of soil NO y emissions than land-use type

Quantifying microplastic dispersion due to density effects

An experimental study was conducted on how polymer density affects the transport and fate of microplastics in aquatic flows. For the first time, polypropylene (PP), polyethylene (PE), polymethyl methacrylate (PMMA), polyetheretherketone (PEEK), and polyvinyl chloride (PVC) were chemically stained and tested using solute transport techniques and velocities found among rivers in the natural environment (0.016 – 0.361 m/s). The movement of 3D-polymers with densities ranging from 0.9 – 1.4 g/cm³ was quantified in a laboratory flume scaled to simulate open-channel flows in fluvial systems. Except for PP, in most conditions microplastics exhibited similar transport characteristics to solutes regardless of density and established solute transport models were successfully implemented to predict their transport and fate. Mass recoveries and ADE routing model demonstrated microplastic deposition and resuspension was associated with polymer density below critical velocity thresholds ≤ 0.1 m/s. When density becomes the dominant force at these slower velocities, concentrations of denser than water microplastics will be momentarily or permanently deposited in channel beds and microplastics follow the classical Shields sediment transport methodology. This data is the first to provide microplastic suspension and deposition thresholds based on river velocity and polymer density, making a key contribution to research predicting microplastic fate and organismal exposure

Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

Soil microbes play pivotal roles in global carbon cycling; however, the fundamental interactions between microbes and their infecting viruses remain unclear. This is exacerbated with soil depth, where the patterns of viral dispersal, ecology, and evolution are markedly underexplored. To investigate viral communities throughout the soil depth profile, we leveraged a publicly available metagenomic data set sampled from grassland soil in Northern California. In total, 10,196 non-redundant viral operational taxonomic units were recovered from soil between 20 cm and 115 cm below the surface. Viral prevalence was high throughout the soil depth profile, with viruses infecting dominant soil hosts, including Actinomycetia . Contrary to leading hypotheses, lysogeny did not dominate in the soil viral communities. Viral diversity was assessed at both the population level (i.e., macrodiversity) and strain level (i.e., microdiversity) to reveal diverse ecological and evolutionary patterns of virus-host interactions in surface and subsurface soils. Investigating viral microdiversity uncovered potential patterns of antagonistic co-evolution across both surface and subsurface soils. Furthermore, we have provided evidence for the potential of soil viruses to augment the remineralization of soil carbon. While we continue to yield a more comprehensive understanding of soil viral ecology, our work appeals to future researchers to further investigate subsurface viral communities. IMPORTANCE Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems

Functional differences in the microbial processing of recent assimilates under two contrasting perennial bioenergy plantations

Land use change driven alteration of microbial communities can have implications on belowground C cycling and storage, although our understanding of the interactions between plant C inputs and soil microbes is limited. Using phospholipid fatty acids (PLFA's) we profiled the microbial communities under two contrasting UK perennial bioenergy crops, Short Rotation Coppice (SRC) willow and Miscanthus Giganteus (miscanthus), and used 13C – pulse labelling to investigate how recent carbon (C) assimilates were transferred through plant tissues to soil microbes. Total PLFA's and fungal to bacterial (F:B) ratios were higher under SRC willow (Total PLFA = 47.70 ± 1.66 SE μg PLFA g−1 dry weight soil, F:B = 0.27 ± 0.01 SE) relative to miscanthus (Total PLFA = 30.89 ± 0.73 SE μg PLFA g−1 dry weight soil, F:B = 0.17 ± 0.00 SE). Functional differences in microbial communities were highlighted by contrasting processing of labelled C. SRC willow allocated 44% of total 13C detected into fungal PLFA relative to 9% under miscanthus and 380% more 13C was returned to the atmosphere in soil respiration from SRC willow soil compared to miscanthus. Our findings elucidate the roles that bacteria and fungi play in the turnover of recent plant derived C under these two perennial bioenergy crops, and provide important evidence on the impacts of land use change to bioenergy on microbial community composition