Estimating annual soil carbon loss in agricultural peatland soils using a nitrogen budget approach.

Around the world, peatland degradation and soil subsidence is occurring where these soils have been converted to agriculture. Since initial drainage in the mid-1800s, continuous farming of such soils in the California Sacramento-San Joaquin Delta (the Delta) has led to subsidence of up to 8 meters in places, primarily due to soil organic matter (SOM) oxidation and physical compaction. Rice (Oryza sativa) production has been proposed as an alternative cropping system to limit SOM oxidation. Preliminary research on these soils revealed high N uptake by rice in N fertilizer omission plots, which we hypothesized was the result of SOM oxidation releasing N. Testing this hypothesis, we developed a novel N budgeting approach to assess annual soil C and N loss based on plant N uptake and fallow season N mineralization. Through field experiments examining N dynamics during growing season and winter fallow periods, a complete annual N budget was developed. Soil C loss was calculated from SOM-N mineralization using the soil C:N ratio. Surface water and crop residue were negligible in the total N uptake budget (3 - 4 % combined). Shallow groundwater contributed 24 - 33 %, likely representing subsurface SOM-N mineralization. Assuming 6 and 25 kg N ha-1 from atmospheric deposition and biological N2 fixation, respectively, our results suggest 77 - 81 % of plant N uptake (129 - 149 kg N ha-1) was supplied by SOM mineralization. Considering a range of N uptake efficiency from 50 - 70 %, estimated net C loss ranged from 1149 - 2473 kg C ha-1. These findings suggest that rice systems, as currently managed, reduce the rate of C loss from organic delta soils relative to other agricultural practices

Soil nitrogen transformations under elevated atmospheric CO2 and O3 during the soybean growing season

We investigated the influence of elevated CO2 and O3 on soil N cycling within the soybean growing season and across soil environments (i.e., rhizosphere and bulk soil) at the Soybean Free Air Concentration Enrichment (SoyFACE) experiment in Illinois, USA. Elevated O3 decreased soil mineral N likely through a reduction in plant material input and increased denitrification, which was evidenced by the greater abundance of the denitrifier gene nosZ. Elevated CO2 did not alter the parameters evaluated and both elevated CO2 and O3 showed no interactive effects on nitrifier and denitrifier abundance, nor on total and mineral N concentrations. These results indicate that elevated CO2 may have limited effects on N transformations in soybean agroecosystems. However, elevated O3 can lead to a decrease in soil N availability in both bulk and rhizosphere soils, and this likely also affects ecosystem productivity by reducing the mineralization rates of plant-derived residues

Earthworms regulate plant productivity and the efficacy of soil fertility amendments in acid soils of the Colombian Llanos

The Llanos region of Colombia represents one of the last large agricultural frontiers and is undergoing a rapid conversion from naturalized savanna to intensive agriculture with high agrochemical inputs and tillage. This massive land-use conversion has considerable impact on ecosystem services and biodiversity, particularly soil macrofauna, yet the full implications of this land-use shift for long-term agroecosystem productivity are poorly understood. To better elucidate potential land-use change impacts on agricultural production we used experimental microcosms in the greenhouse to evaluate how the common earthworm, Pontoscolex corethrurus, influences plant growth, nutrient uptake, and key soil properties relative to the application of lime and P fertilizer, both common soil fertility amendments in the region. Additionally, we aimed to explore the potential for interactions between earthworms and these amendments across distinct plant types, the grass Brachiaria decumbens and the legume Phaseolus vulgaris, which display different rooting patterns and nutrient acquisition strategies. Earthworms increased the biomass production of B. decumbens by 180% and N uptake by more than 240%, while P fertilizers and lime additions increased total biomass by less than 30% each for B. decumbens. Effects on P. vulgaris were similar, but less pronounced with earthworms increasing total biomass production by 35% and total plant N content by 70%, while neither lime nor P alone significantly influenced total biomass or N uptake. However, a significant interaction between earthworms and lime enhanced total biomass N content of P. vulgaris by more than 150% relative to microcosms without P. corethrurus, suggesting that earthworms can greatly enhance the efficacy of lime in soils. Additionally, we found that earthworms greatly improved soil aggregation, but only in the presence of plants, and that this effect was most prominent in microcosms with P. vulgaris. When testing treatment effects on soil P availability, only fertilizer P additions significantly influenced resin P, but not microbial biomass P. Our findings suggests the importance of developing management strategies that promote the activity and diversity of earthworms and other soil biota as a means to enhance crop productivity, resource use efficiency and a range of soil-based ecosystem services in the Llanos region and beyond

Unravelling the immune signature of Plasmodium falciparum transmission-reducing immunity

Infection with Plasmodium can elicit antibodies that inhibit parasite survival in the mosquito, when they are ingested in an infectious blood meal. Here, we determine the transmission-reducing activity (TRA) of naturally acquired antibodies from 648 malaria-exposed individuals using lab-based mosquito-feeding assays. Transmission inhibition is significantly associated with antibody responses to Pfs48/45, Pfs230, and to 43 novel gametocyte proteins assessed by protein microarray. In field-based mosquito-feeding assays the likelihood and rate of mosquito infection are significantly lower for individuals reactive to Pfs48/45, Pfs230 or to combinations of the novel TRA-associated proteins. We also show that naturally acquired purified antibodies against key transmission-blocking epitopes of Pfs48/45 and Pfs230 are mechanistically involved in TRA, whereas sera depleted of these antibodies retain high-level, complement-independent TRA. Our analysis demonstrates that host antibody responses to gametocyte proteins are associated with reduced malaria transmission efficiency from humans to mosquitoes

Science in the Supply Chain: Collaboration Opportunities for Advancing Sustainable Agriculture in the United States

Consumers and corporations are increasingly interested in understanding the sustainability of agricultural supply chains and reducing the environmental impacts of food, fiber, feed, and fuel production. This emerging need to quantify environmental impacts from agricultural production creates an opportunity for collaboration with the scientific community. Without such collaboration, sustainability efforts risk failure by adopting unrealistic goals or misguided approaches. This commentary explores the role of science in Field to Market, a nonprofit organization developing a sustainability program for US commodity crops, and highlights opportunities to address emerging science challenges. We evaluate changes over the past 35 years in key environmental impacts of crop production used to inform land managers as well as companies that are committed to improvements. Achieving improvements will only be possible if three key gaps are addressed regarding available simulation models and data, scale of implementation and uncertainty, and effectiveness of conservation practices. Filling these gaps presents an opportunity for dialogue between scientists, farmers, and private-sector stakeholders to advance scientific knowledge and promote the common objective of sustainable agriculture

Switchgrass is a promising, high-yielding crop for California biofuel

Ethanol use in California is expected to rise to 1.62 billion gallons per year in 2012, more than 90% of which will be trucked or shipped into the state. Switchgrass, a nonnative grass common in other states, has been identified as a possible high-yielding biomass crop for the production of cellulosic ethanol. The productivity of the two main ecotypes of switchgrass, lowland and upland, was evaluated under irrigated conditions across four diverse California ecozones - from Tulelake in the cool north to warm Imperial Valley in the south. In the first full year of production, the lowland varieties yielded up to 17 tons per acre of biomass, roughly double the biomass yields of California rice or maize. The yield response to nitrogen fertilization was statistically insignificant in the first year of production, except for in the Central Valley plots that were harvested twice a year. The biomass yields in our study indicate that switchgrass is a promising biofuel crop for California

Improved mycobacterial protein production using a Mycobacterium smegmatis groEL1ΔC expression strain

<p>Abstract</p> <p>Background</p> <p>The non-pathogenic bacterium <it>Mycobacterium smegmatis </it>is widely used as a near-native expression host for the purification of <it>Mycobacterium tuberculosis </it>proteins. Unfortunately, the Hsp60 chaperone GroEL1, which is relatively highly expressed, is often co-purified with polyhistidine-tagged recombinant proteins as a major contaminant when using this expression system. This is likely due to a histidine-rich C-terminus in GroEL1.</p> <p>Results</p> <p>In order to improve purification efficiency and yield of polyhistidine-tagged mycobacterial target proteins, we created a mutant version of GroEL1 by removing the coding sequence for the histidine-rich C-terminus, termed GroEL1ΔC. GroEL1ΔC, which is a functional protein, is no longer able to bind nickel affinity beads. Using a selection of challenging test proteins, we show that GroEL1ΔC is no longer present in protein samples purified from the <it>groEL1ΔC </it>expression strain and demonstrate the feasibility and advantages of purifying and characterising proteins produced using this strain.</p> <p>Conclusions</p> <p>This novel <it>Mycobacterium smegmatis </it>expression strain allows efficient expression and purification of mycobacterial proteins while concomitantly removing the troublesome contaminant GroEL1 and consequently increasing the speed and efficiency of protein purification.</p

Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites.

Plasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available 'omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated "gold standards" of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P. falciparum genes. To illustrate the utility of the gametocyte score, we explored newly predicted gametocyte-specific genes as potential biomarkers of gametocyte carriage and exposure. We analyzed the humoral immune response in field samples against 30 novel gametocyte-specific antigens and found five antigens to be differentially recognized by gametocyte carriers as compared to malaria-infected individuals without detectable gametocytes. We also validated the gametocyte-specificity of 15 identified gametocyte transcripts on culture material and samples from naturally infected individuals, resulting in eight transcripts that were >1000-fold higher expressed in gametocytes compared to asexual parasites and whose transcript abundance allowed gametocyte detection in naturally infected individuals. Our integrated genome-wide gametocyte-specificity scores provide a comprehensive resource to identify targets and monitor P. falciparum gametocytemia

A multiplex assay for the sensitive detection and quantification of male and female Plasmodium falciparum gametocytes.

BACKGROUND: The transmission of malaria to mosquitoes depends on the presence of gametocytes that circulate in the peripheral blood of infected human hosts. Sensitive estimates of the densities of female gametocytes (FG) and male gametocytes (MG) may allow the prediction of infectivity to mosquitoes and thus a molecular estimate of the human infectious reservoir for transmission. METHODS: A novel multiplex qRT-PCR assay with intron-spanning primers was developed for the parallel quantification of FG and MG. CCp4 (PF3D7_0903800) transcripts specific for FG and PfMGET (PF3D7_1469900) transcripts specific for MG were quantified in total nucleic acids. The assay was validated on sex-sorted gametocytes from culture material and on samples from clinical trials with gametocytocidal drugs. Synthetic RNA standards were generated for the two targets genes and calibrated against known gametocyte quantities. RESULTS: The limit of detection was determined at 0.1 male and 0.1 female gametocyte/µL, which was equal to the limit of quantification (LOQ) for MG, while the LOQ for FG was 1 FG/µL. Results from previously reported clinical trials that used separate gametocyte qRT-PCR assays for FG (targeting Pfs25) and MG (targeting PfMGET) were reproduced with the multiplex assay. High levels of agreement between separate assays and the multiplex approach were observed (R2 = 0.9473, 95% CI 0.9314-0.9632, for FG measured by transcript levels of Pfs25 in qRT-PCR or CCp4 in multiplex; R2 = 0.8869, 95% CI 0.8541-0.9197, for MG measured by PfMGET in either single or multiplex qRT-PCR). FG and MG transcripts were detected in pure ring stage parasites at 10,000- and 100,000-fold reduced frequency for CCp4 and PfMGET, respectively. The CCp4 and PfMGET transcripts were equally stable under suboptimal storage conditions. CONCLUSIONS: Gametocyte densities and their sex ratios can be determined in the presented one-step multiplex assay with higher throughput than single assays. The interpretation of low gametocyte densities at asexual parasite densities above 1000 parasites/µL requires caution to avoid false positive gametocyte signals from spurious transcript levels in ring stage parasites

Multiseason recoveries of organic and inorganic nitrogen-15 in tropical cropping systems

In tropical agroecosystems, limited N availability remains a major impediment to increasing yield. A 15N-recovery experiment was conducted in 13 diverse tropical agroecosystems. The objectives were to determine the total recovery of one single 15N application of inorganic or organic N during three to six growing seasons and to establish whether the losses of N are governed by universal principles. Between 7 and 58% (average of 21%) of crop N uptake duringthe first growing season was derived from fertilizer. On average, 79% of crop N was derived from the soil. When 15N-labeled residues were applied, in the first growing season 4% of crop N was derived from the residues. Average recoveries of 15N- labeled fertilizer and residue in crops after the first growing season were 33 and 7%, respectively. Corresponding recoveries in the soil were 38 and 71 %. An additional 6% of the fertilizer and 9.1 % of the residue was recovered by crops during subsequent growing seasons. There were no significant differences in total 15N recovery (average 54%) between N from fertilizer and N from residue. After five growing seasons, more residue N (40%) than fertilizer N (18%) was recovered in the soil, better sustaining the soil organic matter N content. Long-term total recoveries of 15N-labeled fertilizer or residue in the crop and soil were similar. Soil N remained the primary source of N for crops. As higher rainfall and temperature tend to cause higher N losses, management practices to improve N use efficiency and reduce losses in wet tropical regions will remain a challenge