Development and optimization of an Agro-BGC ecosystem model for C4 perennial grasses

Extrapolating simulations of bioenergy crop agro-ecosystems beyond data-rich sites requires biophysically accurate ecosystem models and careful estimation of model parameters not available in the literature. To increase biophysical accuracy we added C₄ perennial grass functionality and agricultural practices to the Biome-BGC (BioGeochemical Cycles) ecosystem model. This new model, Agro-BGC, includes enzyme-driven C₄ photosynthesis, individual live and dead leaf, stem, and root carbon and nitrogen pools, separate senescence and litter fall processes, fruit growth, optional annual seeding, flood irrigation, a growing degree day phenology with a killing frost option, and a disturbance handler that simulates nitrogen fertilization, harvest, fire, and incremental irrigation. To obtain spatially generalizable vegetation parameters we used a numerical method to optimize five unavailable parameters for Panicum virgatum (switchgrass) using biomass yield data from three sites: Mead, Nebraska, Rockspring, Pennsylvania, and Mandan, North Dakota. We then verified simulated switchgrass yields at three independent sites in Illinois (IL). Agro-BGC is more accurate than Biome-BGC in representing the physiology and dynamics of C₄ grass and management practices associated with agro-ecosystems. The simulated two-year average mature yields with single-site Rockspring optimization have Root Mean Square Errors (RMSE) of 70, 152, and 162 and biases of 43, −87, 156 g carbon m⁻² for Shabbona, Urbana, and Simpson IL, respectively. The simulated annual yields in June, August, October, December, and February have RMSEs of 114, 390, and 185 and biases of −19, −258, and 147 g carbon m⁻² for Shabbona, Urbana, and Simpson IL, respectively. These RMSE and bias values are all within the largest 90% confidence interval around respective IL site measurements. Twenty-four of twenty-six simulated annual yields with Rockspring optimization are within 95% confidence intervals of Illinois site measurements during the mature fourth and fifth years of growth. Ten of eleven simulated two-year average mature yields with Rockspring optimization are within 65% confidence intervals of Illinois site measurements and the eleventh is within the 95% confidence interval. Rockspring optimized Agro-BGC achieves accuracies comparable to those of two previously published models: Agricultural Land Management Alternatives with Numerical Assessment Criteria (ALMANAC) and Integrated Farm System Model (IFSM). Agro-BGC suffers from static vegetation parameters that can change seasonally and as plants age. Using mature plant data for optimization mitigates this deficiency. Our results suggest that a multi-site optimization scheme using mature plant data from more sites would be adequate for generating spatially generalizable vegetation parameters for simulating mature bioenergy crop agro-ecosystems with Agro-BGC.     

Bioreduction of nitrate in groundwater using a pilot-scale hydrogen-based membrane biofilm reactor

A long-term pilot-scale H₂-based membrane biofilm reactor (MBfR) was tested for removal of nitrate from actual groundwater. A key feature of this second-generation pilot MBfR is that it employed lower cost polyester hollow fibers and still achieved high loading rate. The steady-state maximum nitrate surface loading at which the effluent nitrate and nitrite concentrations were below the Maximum Contaminant Level (MCL) was at least 5.9 g·N·(m²·d)^?1, which corresponds to a maximum volumetric loading of at least 7.7 kg·N·(m³·d) ^?1. The steady-state maximum nitrate surface area loading was higher than the highest nitrate surface loading reported in the first-generation MBfRs using composite fibers (2.6 g·N·(m²·d)^?1). This work also evaluated the H₂-utilization efficiency in MBfR. The measured H₂ supply rate was only slightly higher than the stoichiometric H₂-utilization rate. Thus, H₂ utilization was controlled by diffusion and was close to 100% efficiency, as long as biofilm accumulated on the polyester-fiber surface and the fibers had no leaks.     

Beyond geomorphosites: trade-offs, optimization, and networking in heritage landscapes

This study uses Danxiashan, a world heritage site in Guangdong province, China, as a case study for planning a hypothetical geotourism network of heritage sites. This landscape has a multiplicity of values—its geoheritage cannot be separated from its ecological or cultural heritage. When designing a network of heritage sites for such a diversely valued landscape trade-offs must be made between differing and potentially conflicting objectives such as geotourism and geoconservation. To solve this multi-criteria decision problem, sites with potential value for people were designated as heritage sites, adapting the concept of geomorphosites—i.e., geomorphological heritage sites—to represent the intersection of anthropic values. In a GIS-based spatial decision support system heritage values for each site were weighted and ranked using the analytic hierarchy process and scenarios for alternative trail systems, and networks of tourism sites were generated by multi-criteria map overlay analysis and networking algorithms. The scenarios generated show how trade-offs can be made between oft-conflicting tourism and conservation objectives, how the design of parks can be optimized for multiple objectives, and how alternative design strategies can be explored. Such an approach could be used in scenario planning workshops to engage stakeholders in participatory design and consensus-based decision-making driven by geospatial science.     

Improved speciation of dissolved organic nitrogen in natural waters: amide hydrolysis with fluorescence derivatization

The objective of this study was to improve primary-amine nitrogen (1°-N) quantification in dissolved organic matter (DOM) originating from natural waters where inorganic forms of N, which may cause analytical interference, are commonly encountered. Efforts were targeted at elucidating organic-N structural criteria influencing the response of organic amines to known colorimetric and fluorescent reagents and exploring the use of divalent metal-assisted amide hydrolysis in combination with fluorescence analyse...     

Cobalt and secondary poisoning in the terrestrial food chain: data review and research gaps to support risk assessment

Cobalt is a naturally occurring element found in rocks, soil, water, plants, and animals and has diverse industrial importance. It is cycled in surface environments through many natural processes (e.g. volcanic eruptions, weathering) and can be introduced through numerous anthropogenic activities (e.g. burning of coal or oil, or the production of cobalt alloys). The environmental behaviour of cobalt in terrestrial environment is relatively poorly studied and in particular where Co is used in industrial processes, the baseline information to support wider and long-term environmental impacts is widely dispersed. To support the adoption of new EU regulations on the risk assessment of chemicals, we review here the various aspects of the environmental chemistry, fate and transport of Co across environmental interfaces and discuss the toxicology and potential for bio magnification and food chain accumulation. The soil-to-plant transfer of Co appears to be viable route to expose lower trophic levels to biologically significant concentrations and Co is potentially accumulated in biomass and top soil. Evidence for further accumulation through soil-invertebrate transfer and to higher trophic levels is suggested by some studies but this is obscured by the relatively high variability of published transfer data. This variation is not due to one particular aspect of the transfer of Co in terrestrial environments. Influences are from the variability of geological sources within soil systems; the sensitivity of Co mobility to environmental factors (e.g. pH) and the variety of life strategies for metal elimination/use within biological species. Toxic effects of Co have been suggested for some soil-plant animal studies however, uncertainty in the extrapolation from laboratory to field is a major limitation.     

Radiation-induced adaptive response in fish cell lines

There is considerable interest at present in low-dose radiation effects in non-human species. In this study gamma radiation-induced adaptive response, a low-dose radiation effect, was examined in three fish cell lines, (CHSE-214 (Chinook salmon), RTG-2 (rainbow trout) and ZEB-2J (zebrafish)). Cell survival after exposure to direct radiation with or without a 0.1 Gy priming dose, was determined using the colony forming assay for each cell line. Additionally, the occurrence of a bystander effect was examined by measuring the effect of irradiated cell culture medium from the fish cell lines on unexposed reporter cells. A non-linear dose response was observed for all cell lines. ZEB-2J cells were very sensitive to low doses and a hyper-radiosensitive (HRS) response was observed for doses <0.5 Gy. A typical protective adaptive response was not detected in any of the three fish cell lines tested. Rather, it was found that pre-exposure of these cells to 0.1 Gy radiation sensitized the cells to subsequent high doses. In CHSE-214 cells, increased sensitivity to subsequent high doses of radiation was observed when the priming and challenge doses were separated by 4 h; however, this sensitizing effect was no longer present when the interval between doses was greater than 8 h. Additionally, a "protective" bystander response was observed in these cell lines; exposure to irradiated medium from fish cells caused increased cloning efficiency in unirradiated reporter cells. The data confirm previous conclusions for mammalian cells that the adaptive response and bystander effect are inversely correlated and contrary to expectations probably have different underlying mechanisms.     

An integrated approach to the toxicity assessment of Irish marine sediments: validation of established marine bioassays for the monitoring of Irish marine sediments

This paper describes the ecotoxicological evaluation of marine sediments from three sites around Ireland representative of a range of contaminant burdens. A comprehensive assessment of potential sediment toxicity requires the consideration of multiple exposure phases. In addition to the evaluation of multi-exposure phases the use of a battery of multi-trophic test species has been advocated by a number of researchers as testing of single or few organisms may not detect toxicants with a specific mode of action. The Microtox(R) solid phase test (SPT) and the 10-d acute amphipod test with Corophium volutator were used to assess whole sediment toxicity. Porewater and elutriates were assessed with the Microtox(R) acute test, the marine prasinophyte Tetraselmis suecica, and the marine copepod Tisbe battagliai. Solvent extracts were assayed with the Microtox(R) and T. battagliai acute tests. Alexandra Basin was identified as the most toxic site according to all tests, except the Microtox(R) SPT which identified the Dunmore East site as being more toxic. However, it was not possible to correlate the observed ecotoxicological effects with a specific and/or class of contaminants based on sediment chemistry alone. Therefore porewaters found to elicit significant toxicity (Dunmore East and Alexandra Basin) with the test battery were selected for further TIE assessment with T. battalgiai and the Microtox(R) system. The results of this study have important implications for risk assessment in estuarine and coastal waters in Ireland, where, at present the monitoring of sediment and water quality is predominantly reliant on chemical analysis alone.     

Real-time quantification of mcrA, pmoA for methanogen, methanotroph estimations during composting

Composting is the controlled biological decomposition of organic matter by microorganisms during predominantly aerobic conditions. It is being increasingly adopted due to its benefits in nutrient recycling, soil reclamation, and urban land use. However, it poses an environmental concern related to its contribution to greenhouse gas production. During composting, activities of methanogenic and methanotrophic communities influence the net methane (CH4) release into the atmosphere. Using quantitative polymerase chain reaction (qPCR), this study was aimed at assessing the changes in the methyl-coenzyme M reductase (mcrA) and particulate methane monooxygenase (pmoA) copy numbers for estimation of methanogenic and methanotrophic communities, respectively. Open-windrow composting of beef cattle (Bos Taurus L.) manure with temperatures reaching > 55 degrees C was effective indegrading commensal Escherichia coli within the first week. Quantification of community DNA revealed significant differences in mcrA and pmoA copy numbers between top and middle sections. Consistent mcrA copy numbers (7.07 to 8.69 log copy number g(-1)) were detected throughout the 15-wk composting period. However, pmoA copy number varied significantly over time, with higher values during Week 0 and 1 (6.31 and 5.41 log copy number g(-1), respectively) and the lowest at Week 11 (1.6 log copy number g(-1)). Net surface CH4 emissions over the 15-wk period were correlated with higher mcrA copy number. Higher net ratio of mrA: pmoA copy numbers was observed when surface CH4 flux was high. Our results indicate that mcrA and pmoA copy numbers vary during composting and that methanogen and methanotroph populations need to be examined in conjunction with net CH4 emissions from open-windrow composting of cattle feedlot manure.     

A landscape-scale framework to identify refugia from multiple stressors

From a conservation perspective, quantifying potential refugial capacity has been predominantly focused on climate refugia, which is critical for maintaining the persistence of species and ecosystems. However, protection from other stressors, such as human-induced changes in fire and hydrology, that cause habitat loss, degradation, and fragmentation is also necessary to ensure that conservation efforts focused on climate are not undermined by other threats. Thus, conceptual and methodological advances for quantifying potential refugia from multiple anthropogenic stressors are important to support conservation efforts. We devised a new conceptual approach, the domains of refugia, for assessing refugial capacity that identifies areas where exposure to multiple stressors is low. In our framework, patterns of environmental variability (e.g., increased frequency of warm summers), thresholds of resilience, and extent and intensity of stressors are used to identify areas of potential refugia from a suite of ongoing anthropogenic stressors (e.g., changes in fire regime). To demonstrate its utility, we applied the framework to a Southern California landscape. Sites with high refugial capacity (super-refugia sites) had on average 30% fewer extremely warm summers, 20% fewer fire events, 10% less exposure to altered river channels and riparian areas, and 50% fewer recreational trails than the surrounding landscape. Our results suggest that super-refugia sites (∼8200 km²) for some natural communities are underrepresented in the existing protected area network, a finding that can inform efforts to expand protected areas. Our case study highlights how considering exposure to multiple stressors can inform planning and practice to conserve biodiversity in a changing world.