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We implemented a spatial application of a previously evaluated model of soil GHG emissions, ECOSSE, in the United Kingdom to examine the impacts to 2050 of land-use transitions from existing land use, rotational cropland, permanent grassland or woodland, to six bioenergy crops; three ‘first-generation’ energy crops: oilseed rape, wheat and sugar beet, and three ‘second-generation’ energy crops: Miscanthus, short rotation coppice willow (SRC) and short rotation forestry poplar (SRF). Conversion of rotational crops to Miscanthus, SRC and SRF and conversion of permanent grass to SRF show beneficial changes in soil GHG balance over a significant area. Conversion of permanent grass to Miscanthus, permanent grass to SRF and forest to SRF shows detrimental changes in soil GHG balance over a significant area. Conversion of permanent grass to wheat, oilseed rape, sugar beet and SRC and all conversions from forest show large detrimental changes in soil GHG balance over most of the United Kingdom, largely due to moving from uncultivated soil to regular cultivation. Differences in net GHG emissions between climate scenarios to 2050 were not significant. Overall, SRF offers the greatest beneficial impact on soil GHG balance. These results provide one criterion for selection of bioenergy crops and do not consider GHG emission increases/decreases resulting from displaced food production, bio-physical factors (e.g. the energy density of the crop) and socio-economic factors (e.g. expenditure on harvesting equipment). Given that the soil GHG balance is dominated by change in soil organic carbon (SOC) with the difference among Miscanthus, SRC and SRF largely determined by yield, a target for management of perennial energy crops is to achieve the best possible yield using the most appropriate energy crop and cultivar for the local situation.

We implemented a spatial application of a previously evaluated model of soil GHG emissions, ECOSSE, in the United Kingdom to examine the impacts to 2050 of land-use transitions from existing land use, rotational cropland, permanent grassland or woodland, to six bioenergy crops; three ‘first-generation’ energy crops: oilseed rape, wheat and sugar beet, and three ‘second-generation’ energy crops: Miscanthus, short rotation coppice willow (SRC) and short rotation forestry poplar (SRF). Conversion of rotational crops to Miscanthus, SRC and SRF and conversion of permanent grass to SRF show beneficial changes in soil GHG balance over a significant area. Conversion of permanent grass to Miscanthus, permanent grass to SRF and forest to SRF shows detrimental changes in soil GHG balance over a significant area. Conversion of permanent grass to wheat, oilseed rape, sugar beet and SRC and all conversions from forest show large detrimental changes in soil GHG balance over most of the United Kingdom, largely due to moving from uncultivated soil to regular cultivation. Differences in net GHG emissions between climate scenarios to 2050 were not significant. Overall, SRF offers the greatest beneficial impact on soil GHG balance. These results provide one criterion for selection of bioenergy crops and do not consider GHG emission increases/decreases resulting from displaced food production, bio-physical factors (e.g. the energy density of the crop) and socio-economic factors (e.g. expenditure on harvesting equipment). Given that the soil GHG balance is dominated by change in soil organic carbon (SOC) with the difference among Miscanthus, SRC and SRF largely determined by yield, a target for management of perennial energy crops is to achieve the best possible yield using the most appropriate energy crop and cultivar for the local situation.

Soil C sequestration in croplands is deemed to be one of the most promising greenhouse gas mitigation options for agriculture. We have used crop-level yields, modeled heterotrophic respiration (Rh) and land use data to estimate spatio-temporal changes in regional scale net primary productivity (NPP), plant C inputs, and net biome productivity (NBP) in northern Japan's arable croplands and grasslands for the period of 1959–2011. We compared the changes in C stocks derived from estimated NBP and using repeated inventory datasets for each individual land use type from 2005 to 2011. For the entire study region of 2193 ha, overall annual plant C inputs to the soil constituted 37% of total region NPP. Plant C inputs in upland areas (excluding bush/fallow) could be predicted by climate variables. Overall NBP for all land use types increased from − 1.26 Mg C ha− 1 yr− 1 in 1959–0.26 Mg C ha− 1 yr− 1 in 2011. However, upland and paddy fields showed a decreased in NBP over the period of 1959–2011, under the current C input scenario. From 1988, an increase in agricultural abandonment (bush/fallow) and grassland cover caused a slow increase in the regional C pools. The comparison of carbon budgets using the NBP estimation method and the soil inventory method indicated no significant difference between the two methods. Our results showed C loss in upland crops, paddy fields and sites that underwent land use change from paddy field to upland sites. We also show C gain in grassland from 2005 to 2011. An underestimation of NBP or an overestimation of repeated C inventories cannot be excluded, but either method may be suitable for tracking absolute changes in soil C, considering the uncertainty associated with these methods.

Soil C sequestration in croplands is deemed to be one of the most promising greenhouse gas mitigation options for agriculture. We have used crop-level yields, modeled heterotrophic respiration (Rh) and land use data to estimate spatio-temporal changes in regional scale net primary productivity (NPP), plant C inputs, and net biome productivity (NBP) in northern Japan's arable croplands and grasslands for the period of 1959–2011. We compared the changes in C stocks derived from estimated NBP and using repeated inventory datasets for each individual land use type from 2005 to 2011. For the entire study region of 2193 ha, overall annual plant C inputs to the soil constituted 37% of total region NPP. Plant C inputs in upland areas (excluding bush/fallow) could be predicted by climate variables. Overall NBP for all land use types increased from − 1.26 Mg C ha− 1 yr− 1 in 1959–0.26 Mg C ha− 1 yr− 1 in 2011. However, upland and paddy fields showed a decreased in NBP over the period of 1959–2011, under the current C input scenario. From 1988, an increase in agricultural abandonment (bush/fallow) and grassland cover caused a slow increase in the regional C pools. The comparison of carbon budgets using the NBP estimation method and the soil inventory method indicated no significant difference between the two methods. Our results showed C loss in upland crops, paddy fields and sites that underwent land use change from paddy field to upland sites. We also show C gain in grassland from 2005 to 2011. An underestimation of NBP or an overestimation of repeated C inventories cannot be excluded, but either method may be suitable for tracking absolute changes in soil C, considering the uncertainty associated with these methods.

Soil C sequestration in croplands is deemed to be one of the most promising greenhouse gas mitigation options for agriculture. We have used crop-level yields, modeled heterotrophic respiration (Rh) and land use data to estimate spatio-temporal changes in regional scale net primary productivity (NPP), plant C inputs, and net biome productivity (NBP) in northern Japan's arable croplands and grasslands for the period of 1959–2011. We compared the changes in C stocks derived from estimated NBP and using repeated inventory datasets for each individual land use type from 2005 to 2011. For the entire study region of 2193 ha, overall annual plant C inputs to the soil constituted 37% of total region NPP. Plant C inputs in upland areas (excluding bush/fallow) could be predicted by climate variables. Overall NBP for all land use types increased from − 1.26 Mg C ha− 1 yr− 1 in 1959–0.26 Mg C ha− 1 yr− 1 in 2011. However, upland and paddy fields showed a decreased in NBP over the period of 1959–2011, under the current C input scenario. From 1988, an increase in agricultural abandonment (bush/fallow) and grassland cover caused a slow increase in the regional C pools. The comparison of carbon budgets using the NBP estimation method and the soil inventory method indicated no significant difference between the two methods. Our results showed C loss in upland crops, paddy fields and sites that underwent land use change from paddy field to upland sites. We also show C gain in grassland from 2005 to 2011. An underestimation of NBP or an overestimation of repeated C inventories cannot be excluded, but either method may be suitable for tracking absolute changes in soil C, considering the uncertainty associated with these methods.

Understanding and predicting the effects of land-use change to short rotation forestry (SRF) on soil C is an important requirement for fully assessing the C mitigation potential of SRF as a bioenergy crop. There is little current knowledge of SRF in the UK and in particular a lack of consistent measured datasets on the direct impacts of land use change on soil C stocks. The ECOSSE model was developed to simulate soil C dynamics and greenhouse gas (GHG) emissions in mineral and organic soils. The ECOSSE model has already been applied spatially to simulate land-use change impacts on soil C and GHG emissions. However, it has not been extensively evaluated under SRF. Eleven sites comprising 29 transitions in Britain, representing land-use change from non-woodland land uses to SRF, were selected to evaluate the performance of ECOSSE in predicting soil C and soil C change in SRF plantations. The modelled C under SRF showed a strong correlation with the soil C measurements at both 0-30 cm (R = 0.93) and 0-100 cm soil depth (R = 0.82). As for the SRF plots, the soil C at the reference sites have been accurately simulated by the model. The extremely high correlation for the reference fields (R ≥ 0.99) shows a good performance of the model spin-up. The statistical analysis of the model performance to simulate soil C and soil C changes after land-use change to SRF highlighted the absence of significant error between modelled and measured values as well as the absence of significant bias in the model. Overall, this evaluation reinforces previous studies on the ability of ECOSSE to simulate soil C and emphasize its accuracy to simulate soil C under SRF plantations.

Understanding and predicting the effects of land-use change to short rotation forestry (SRF) on soil C is an important requirement for fully assessing the C mitigation potential of SRF as a bioenergy crop. There is little current knowledge of SRF in the UK and in particular a lack of consistent measured datasets on the direct impacts of land use change on soil C stocks. The ECOSSE model was developed to simulate soil C dynamics and greenhouse gas (GHG) emissions in mineral and organic soils. The ECOSSE model has already been applied spatially to simulate land-use change impacts on soil C and GHG emissions. However, it has not been extensively evaluated under SRF. Eleven sites comprising 29 transitions in Britain, representing land-use change from non-woodland land uses to SRF, were selected to evaluate the performance of ECOSSE in predicting soil C and soil C change in SRF plantations. The modelled C under SRF showed a strong correlation with the soil C measurements at both 0-30 cm (R = 0.93) and 0-100 cm soil depth (R = 0.82). As for the SRF plots, the soil C at the reference sites have been accurately simulated by the model. The extremely high correlation for the reference fields (R ≥ 0.99) shows a good performance of the model spin-up. The statistical analysis of the model performance to simulate soil C and soil C changes after land-use change to SRF highlighted the absence of significant error between modelled and measured values as well as the absence of significant bias in the model. Overall, this evaluation reinforces previous studies on the ability of ECOSSE to simulate soil C and emphasize its accuracy to simulate soil C under SRF plantations.

Systems approaches have great potential for application in predictive ecology. In this paper, we present a range of examples, where systems approaches are being developed and applied at a range of scales in the field of global change and biogeochemical cycling. Systems approaches range from Bayesian calibration techniques at plot scale, through data assimilation methods at regional to continental scales, to multi-disciplinary numerical model applications at country to global scales. We provide examples from a range of studies and show how these approaches are being used to address current topics in global change and biogeochemical research, such as the interaction between carbon and nitrogen cycles, terrestrial carbon feedbacks to climate change and the attribution of observed global changes to various drivers of change. We examine how transferable the methods and techniques might be to other areas of ecosystem science and ecology

Systems approaches have great potential for application in predictive ecology. In this paper, we present a range of examples, where systems approaches are being developed and applied at a range of scales in the field of global change and biogeochemical cycling. Systems approaches range from Bayesian calibration techniques at plot scale, through data assimilation methods at regional to continental scales, to multi-disciplinary numerical model applications at country to global scales. We provide examples from a range of studies and show how these approaches are being used to address current topics in global change and biogeochemical research, such as the interaction between carbon and nitrogen cycles, terrestrial carbon feedbacks to climate change and the attribution of observed global changes to various drivers of change. We examine how transferable the methods and techniques might be to other areas of ecosystem science and ecology

1. The application of population genetic analysis and molecular ecological approaches allows us to examine the invasion of species in the wild. In particular, we can gain an insight into the role of dispersal, a key determinant of the invasion and population dynamics of important pest species. Since the 1980s, severe outbreaks of the winter moth, Operophtera brumata (Linnaeus), have caused extensive damage to heather moorlands in the Orkney Isles. The population genetic structure of O. brumata in Orkney was examined in order to establish whether the widely dispersed outbreaking populations are connected. 2. Amplified fragment length polymorphism (AFLP) analysis showed a high level of genetic diversity within subpopulations. This is consistent with an initial mass colonisation event and/or continuing dispersal between populations of O. brumata in Orkney. 3. Genetic differentiation among populations is low, and although some weak isolation by distance is detectable, no effect of isolation as a result of a sea barrier was found. High gene flow between populations is consistent with the low genetic differentiation observed, although there is evidence to suggest that the populations are not panmictic. 4. Given the limited dispersal of adults, the present results suggest that larvae may disperse over considerable distances by ballooning on strong winds across the Orkney Isles.

1. The application of population genetic analysis and molecular ecological approaches allows us to examine the invasion of species in the wild. In particular, we can gain an insight into the role of dispersal, a key determinant of the invasion and population dynamics of important pest species. Since the 1980s, severe outbreaks of the winter moth, Operophtera brumata (Linnaeus), have caused extensive damage to heather moorlands in the Orkney Isles. The population genetic structure of O. brumata in Orkney was examined in order to establish whether the widely dispersed outbreaking populations are connected. 2. Amplified fragment length polymorphism (AFLP) analysis showed a high level of genetic diversity within subpopulations. This is consistent with an initial mass colonisation event and/or continuing dispersal between populations of O. brumata in Orkney. 3. Genetic differentiation among populations is low, and although some weak isolation by distance is detectable, no effect of isolation as a result of a sea barrier was found. High gene flow between populations is consistent with the low genetic differentiation observed, although there is evidence to suggest that the populations are not panmictic. 4. Given the limited dispersal of adults, the present results suggest that larvae may disperse over considerable distances by ballooning on strong winds across the Orkney Isles.

Landscape heterogeneity can be instrumental in determining local disease risk, pathogen persistence and spread. This is because different landscape features such as habitat type determine the abundance and spatial distributions of hosts and pathogen vectors. Therefore, disease prevalence and distribution are intrinsically linked to the hosts and vectors that utilise the different habitats. Here, we develop a simplified reaction diffusion model of the louping-ill virus and red grouse (Lagopus lagopus scoticus) system to investigate the occurrence of a tick-borne pathogen and the effect of host movement and landscape structure. Ticks (Ixodes ricinus), the virus-vector, are dispersed by a virally incompetent tick host, red deer (Cervus elephus), between different habitats, whilst the virus infects only red grouse. We investigated how deer movement between different habitats (forest and moorland) affected tick distribution and hence prevalence of infected ticks and grouse and hence, the effect of habitat size ratio and fragmentation on infection. When habitat type has a role in the survival of the pathogen vector, we demonstrated that habitat fragmentation can have a considerable effect on infection. These results highlight the importance of landscape heterogeneity and the proximity and size of adjacent habitats when predicting disease risk in a particular location. In addition, this model could be useful for other pathogen systems with generalist vectors and may inform policy on possible disease management strategies that incorporate host movements.