Should digestion assays be used to estimate persistence of potential allergens in tests for safety of novel food proteins?

Food allergies affect an estimated 3 to 4% of adults and up to 8% of children in developed western countries. Results from in vitro simulated gastric digestion studies with purified proteins are routinely used to assess the allergenic potential of novel food proteins. The digestion of purified proteins in simulated gastric fluid typically progresses in an exponential fashion allowing persistence to be quantified using pseudo-first-order rate constants or half lives. However, the persistence of purified proteins in simulated gastric fluid is a poor predictor of the allergenic status of food proteins, potentially due to food matrix effects that can be significant in vivo. The evaluation of the persistence of novel proteins in whole, prepared food exposed to simulated gastric fluid may provide a more correlative result, but such assays should be thoroughly validated to demonstrate a predictive capacity before they are accepted to predict the allergenic potential of novel food proteins

Impact of biochar on water retention of two agricultural soils – A multi-scale analysis

The ability of soil to retain water under drought and other extreme hydrological events is critical to the sustainability of food production systems and preserving soil ecosystem services. We investigated the impact of biochar on water retention properties in California agricultural soils in a series of column, lab incubation, and field studies. Results from studies based on similar variables (soil, biochar) were used to demonstrate the impact of biochar on soil-water relations at different scales. The influences of biochar type (softwood, 600–700 °C, low surface area; walnut shell, 900 °C, high surface area), application rate (0, 0.5, 1% wt.), and particle diameter (0–0.25, 0.25–0.5, 0.5–1, 1–2 mm) were investigated. Only the higher surface area biochar increased the field capacity of a sandy soil. Neither biochar, altered the field capacity of the higher clay content soil. The walnut shell biochar with 1–2 mm particle diameter was more effective at increasing field capacity in sandy soils compare to smaller biochar size fractions. Neither biochar affected the wilting point in either soil. Neutron imaging was used to explore potential mechanisms involved in water retention by observing the spatial and temporal distribution of water in and surrounding biochar particles (~ 2 mm diameter). After wetting, water retained in the internal pores of biochar was continuously released to surrounding space (~ 2.2 mm sphere) during a 7-day air drying at room temperature, suggesting that soil water retention is improved via the biochar's intraparticle structure. In the field trial, (6 yr., corn-tomato rotation), neither walnut shell biochar amendment (10 t/ ha, equivalent to 0.5% wt. in lab scale experiments) nor agricultural management practices (organic, conventional) altered the water retention capacity of a silty clay loam soil. These data suggest that biochars with a high pore volume can temporarily increase the field capacity and plant available water in a coarse-textured soil, until biochar internal pores are filled by clay and soil organic matter. Our results suggest that biochar can have a limited impact on soil water retention when biochar pore volume is low, or soil texture is fine. High dosage (≥10 t/ha) of high pore volume biochar with bulky particle size (≥1 mm) can improve water retention of coarse-textured soil with limited capacity of water storage and may improve soil's resilience during hydrological extremes

Biodegradation of sorbed chemicals in soil.

Rates of biodegradation of sorbed chemicals are usually lower in soil than in aqueous systems, in part because sorption reduces the availability of the chemical to microorganisms. Biodegradation, sorption, and diffusion occur simultaneously and are tightly coupled. In soil, the rate of biodegradation is a function of a chemical's diffusion coefficient, sorption partition coefficient, the distance it must diffuse from the site of sorption to microbial populations that can degrade it, and its biodegradation rate constant. A model (DSB model) was developed that describes biodegradation of chemicals limited in the availability by sorption and diffusion. Different kinetics expressions describe biodegradation depending on whether the reaction is controlled by mass transfer (diffusion and sorption) or the intrinsic biodegradation rate, and whether biodegradation begins during or after the majority of sorption has occurred. We tested the hypothesis that there is a direct relationship between how strongly a chemical is sorbed and the chemical's biodegradation rate. In six soils with different organic carbon contents, there was no relationship between the extent or rate of biodegradation and the sorption partition coefficient for phenanthrene. Aging of phenanthrene residues in soil led to a substantial reduction in the rate of biodegradation compared to biodegradation rates of recently added phenanthrene. Considerable research has focused on identification and development of techniques for enhancing in situ biodegradation of sorbed chemicals. Development of such techniques, especially those involving inoculation with microbial strains, should consider physical mass transfer limitations and potential decreases in bioavailability over time

Effects of soil management history on the rate of organic matter decomposition

In a sustainable agriculture farming systems experiment, soils managed under organic farming practices had greater microbial abundance and activity, and higher numbers of bacterial-feeding nematodes during crop growth, than those managed under conventional fanning practices. We tested rates of organic matter decomposition in the two soils and monitored the abundance and activity of soil biota during the decomposition process. Differences in soil biology between soils from organic and conventional farming systems did not persist when soils were amended with organic matter and maintained under similar conditions. Microbial communities in soil from the conventional system were sufficient and active enough to respond to organic inputs. There were minimal differences in the ability of the microbial communities of the two soils to decompose organic residues. However, when soils were removed from the field at different times, cover crop decomposition rates were more consistent in the organic soils, suggesting a greater abundance and diversity of the microbial community in those soils. Microbial activity was most suppressed when field soils were dry but responded to organic matter amendment very rapidly when favorable moisture contents were restored. The pattern of microbial activity in both organic and conventional soils following organic matter incorporation consisted of a 100 h activity phase and then a gradual decline to a relatively constant stasis phase

Compost amendment maintains soil structure and carbon storage by increasing available carbon and microbial biomass in agricultural soil – A six-year field study

Soil organic amendments in agricultural production can benefit crop production and a wide range of soil properties, including soil aggregation. Soil aggregate formation is largely driven by microbial activities, and can in-turn influence microbial communities by generating distinct microbial habitats, as well as associated impacts on water and nutrient dynamics. We investigated the long-term effects of two fertilizer management strategies (poultry manure compost vs. mineral fertilizer) and biochar amendment (0 vs. 10 t ha−1 walnut shell biochar, 900 °C pyrolysis temperature, by-product of gasification) on soil aggregation, soil organic C, and microbial community dynamics in water-stable aggregate fractions in corn-tomato rotations. Using wet-sieving, soils (0–15 cm) were divided into four size fractions: large macroaggregates (2000–8000 μm), small macroaggregates (250–2000 μm), microaggregates (53–250 μm) and silt and clay (<53 μm) for calculation of mean weight diameter in both 2014 and 2018. The total C and microbial community composition and abundance within each fraction were evaluated in 2018. Across all treatments, six years of continuous compost application maintained soil aggregate stability and C storage by increasing soil microbial biomass and associated dissolved organic C. Bacterial and fungal populations under compost treatments were significantly higher than under mineral fertilizer treatments based on 16S rRNA gene copy number and internal transcribed spacer (ITS) abundance, which likely contributed to the formation and maintenance of macroaggregates in compost treatments. Interestingly, continuous application of manure compost may increase microbial available C sources by increasing the abundance of bacteria with the potential to degrade aromatic C as predicted from 16S sequences. Soil under the mineral fertilizer treatment showed decreases in the proportion of large macroaggregates, bulk soil C, and aggregate-associated C storage compared to the compost treatment. The application of highly recalcitrant walnut shell biochar had limited long-term impacts on soil aggregation and C dynamics, likely due to its lack of microbially-available C and limited interaction with the soil environment. Our results indicate that continuous compost inputs maintained soil structure and associated physical stabilization of SOM by enlarging soil microbial available C pool, higher soil microbial biomass, and increasing aggregate formation. The soil aggregate structure, in-turn, generated diverse habitats and altered soil microbial communities. Compost inputs, in addition to or in partial replacement of mineral fertilizer inputs, can provide valuable microbial-driven ecosystem services, such as carbon storage and soil structure, while still providing fertility for crop growth

Microbial response to copper oxide nanoparticles in soils is controlled by land use rather than copper fate

Copper (Cu) products, including copper oxide nanoparticles (nCuO), are critically important agricultural fungicides and algaecides. Foliar application onto crops and subsequent aerosol drift of these Cu products, especially nCuO, on to soil may alter nutrient cycling and microbial communities in both managed and unmanaged environments. We measured the influence of land use on soil microbial biomass and respiration in response to the addition of nCuO to an alluvial soil. Different land uses included grassland, forest and both organic and conventional managed row crops. Soil samples were amended with 1000 mg Cu per kg soil as CuCl2, 16 nm CuO (16nCuO), 42 nm CuO (42nCuO), and larger than nanoparticle sized bulk CuO (bCuO). Copper availability immediately increased in all soils following Cu addition in the order of CuCl2 > 16nCuO > 42nCuO > bCuO. After 70 days Cu availability was diminished across land uses and lowest in soils treated with bCuO. Using X-ray absorption near edge structure (XANES) spectroscopy, we determined that the relatively high availability of Cu after treatment with nanoparticle sized CuO was due to the dissolution of CuO particles and subsequent adsorption by soil materials. Respiration, an indicator of microbial activity, was suppressed by Cu additions, especially CuCl2. Copper effects on soil microbial biomass were sensitive to land use. In agricultural soils, microbial biomass was unaltered by Cu form, regardless of concentration, whereas in unmanaged soils, it decreased following exposure to CuCl2 and 42nCuO. Our results suggest that land use history has little impact on Cu chemical fate in soils, but strongly modulates microbial response to Cu exposure. These results are especially important for organic agricultural systems where copper fungicides are widely used but may suppress microbial mineralization of nutrients from soil organic matter