Long and Short-Term Effects of Fire on Soil Charcoal of a Conifer Forest in Southwest Oregon

In 2002, the Biscuit Wildfire burned a portion of the previously established, replicated conifer unthinned and thinned experimental units of the Siskiyou Long-Term Ecosystem Productivity (LTEP) experiment, southwest Oregon. Charcoal C in pre and post-fire O horizon and mineral soil was quantified by physical separation and a peroxide-acid digestion method. The abrupt, short-term fire event caused O horizon charcoal C to increase by a factor of ten to >200 kg C ha⁻¹. The thinned wildfire treatment produced less charcoal C than unthinned wildfire and thinned prescribed fire treatments. The charcoal formation rate was 1 to 8% of woody fuels consumed, and this percentage was negatively related to woody fuels consumed, resulting in less charcoal formation with greater fire severity. Charcoal C averaged 2000 kg ha⁻¹ in 0–3 cm mineral soil and may have decreased as a result of fire, coincident with convective or erosive loss of mineral soil. Charcoal C in 3–15 cm mineral soil was stable at 5500 kg C ha⁻¹. Long-term soil C sequestration in the Siskiyou LTEP soils is greatly influenced by the contribution of charcoal C, which makes up 20% of mineral soil organic C. This research reiterates the importance of fire to soil C in a southwestern Oregon coniferous forest ecosystem.Keywords: Soil carbon, Soil change, Wildfire, Pre- and post-fire measurement, Black carbon, Biscuit Wildfire, Charcoal, Peroxide-acid digestio

Forest Structure Affects Soil Mercury Losses in the Presence and Absence of Wildfire

Soil is an important, dynamic component of regional and global mercury (Hg) cycles. This study evaluated how changes in forest soil Hg masses caused by atmospheric deposition and wildfire are affected by forest structure. Pre and postfire soil Hg measurements were made over two decades on replicate experimental units of three prefire forest structures (mature unthinned, mature thinned, clear-cut) in Douglas-fir dominated forest of southwestern Oregon. In the absence of wildfire, O-horizon Hg decreased by 60% during the 14 years after clearcutting, possibly the result of decreased atmospheric deposition due to the smaller-stature vegetative canopy; in contrast, no change was observed in mature unthinned and thinned forest. Wildfire decreased O-horizon Hg by >88% across all forest structures and decreased mineral-soil (0 to 66 mm depth) Hg by 50% in thinned forest and clear-cut. The wildfire-associated soil Hg loss was positively related to the amount of surface fine wood that burned during the fire, the proportion of area that burned at >700 °C, fire severity as indicated by tree mortality, and soil C loss. Loss of soil Hg due to the 200 000 ha wildfire was more than four times the annual atmospheric Hg emissions from human activities in Oregon

Postwildfire Soil Trajectory Linked to Prefire Ecosystem Structure in Douglas-Fir Forest

Changes in soil C and N pools following wildfire are quite varied, but there is little understanding of the causes of the variation. We examined how the legacies of prefire ecosystem structure may explain the variation in soil trajectories during the first decade following wildfire. Five years prior to wildfire in a southwestern Oregon forest dominated by mature Douglas-fir [Pseudotsuga menziesii var. menziesii (Mirb.) Franco], ecosystem structure was experimentally manipulated by thinning or clearcutting for comparison with unthinned forest. Repeated measurements of replicated experimental units were made before wildfire and during the first decade following wildfire. In the unthinned forest, the O-horizon soil C and N pools were decreased to 24–39% of prefire levels by wildfire, then increased to 53–70% during the first year postwildfire by deposition of fire-killed needles from overstory trees. The mineral soil (0–6 cm depth) C pool was decreased by wildfire, then increased in the following decade, while no change in the N pool was detected. In contrast, in the clearcut treatment, the O-horizon soil C and N pools were nearly totally consumed during the wildfire, lacked fire-killed overstory as a source of needle and fine and coarse wood inputs, but regained 20% of prefire masses in the following decade via foliar and root inputs from regenerated shrubs and herbaceous vegetation. Surface mineral soil C and N pools were decreased 35–50% by wildfire and showed no sign of recovery during the following decade. In contrast to wildfire, unburned ecosystem structures showed no changes in O horizon and increased mineral-soil N pool in the clearcut. We propose a conceptual model of soil C and N response following wildfire that includes legacy influences resulting from prefire ecosystem structures: residual live trees that generate continual litterfall and root turnover; fire-killed trees that produce needle-fall, dead roots, and fine- and coarse-wood detritus; and surviving roots and burls that contribute to postwildfire shrub regeneration. Consideration of prefire ecosystem structure and legacies in quantitative models may improve forecasts of postwildfire C budgets at stand to regional scales.Keywords: legacy, soil nitrogen, fine woody debris, soil carbon, postwildfire change, forest management, wildfir

Managing early succession for biodiversity and long-term productivity of conifer forests in southwestern Oregon

Early-successional stages have been truncated and altered in many western U.S. forest landscapes by planting conifers, controlling competing vegetation, suppressing fire, and focusing on maintaining late-seral species and undisturbed riparian zones. Declining area of early-successional stages may be reducing resilience and sustainability on landscapes that experience elevated disturbance related to future climate changes. In this study, two post-harvest early-successional treatments were compared to each other and to two mature-forest treatments using 20 years of evidence from replicated 7-ha experimental units in a southwestern Oregon forest dominated by Douglas-fir (Pseudotsuga menziesii Mirb. Franco). One early-successional treatment (Douglas-fir plantation) planted Douglas-fir and was followed by a brushing to reduce hardwood competition to move quickly to the conifer stem-exclusion stage; the other (Early-seral plantation) favored natural sprouting and regeneration of hardwood shrubs and trees and planted scattered knobcone pines (Pinus attenuata Lemmon) and Douglas-fir. Plant diversity in the Early-seral plantation was 56% (year 2) and 26% (year 6) higher than in the Douglas-fir plantation. Both early-successional treatments far exceeded plant diversity in Unaltered and Thinned mature stands. Fifteen years of growth of shrubs and hardwood trees in the Early-seral plantation was remarkable, resulting in total aboveground biomass increment (18 Mg ha⁻¹ yr⁻¹) double that of the Douglas-fir plantations. Important process effects related to primary productivity were noted: losses of soil organic matter from the B horizon in young Douglas-fir, and, after wildfire, increases in N₂-fixing plant cover in Early-seral plantation. The burl-sprouting and deep rooting of many hardwoods also created opportunities for nutrient retention and release from primary minerals as well as deep-profile water supply. Recognizing the importance of intentionally managing for shrubs and hardwood trees is particularly relevant at this site, because stand reconstruction and historical records indicate these species, along with knobcone pine, dominated the site for 40 years before the current mature Douglas-fir forest started gaining dominance. In contrast, the prolific natural regeneration of Douglas-fir after recent harvest and wildfire suggests that what comes back ‘‘naturally’’ in modern times will not allow this history to be repeated.Keywords: N₂ fixation, Early-seral, Long-term productivity, Biodiversity, Early successionKeywords: N₂ fixation, Early-seral, Long-term productivity, Biodiversity, Early successio

Induction of Protective CD4+ T Cell-Mediated Immunity by a Leishmania Peptide Delivered in Recombinant Influenza Viruses

The available evidence suggests that protective immunity to Leishmania is achieved by priming the CD4+ Th1 response. Therefore, we utilised a reverse genetics strategy to generate influenza A viruses to deliver an immunogenic Leishmania peptide. The single, immunodominant Leishmania-specific LACK158–173 CD4+ peptide was engineered into the neuraminidase stalk of H1N1 and H3N2 influenza A viruses. These recombinant viruses were used to vaccinate susceptible BALB/c mice to determine whether the resultant LACK158–173-specific CD4+ T cell responses protected against live L. major infection. We show that vaccination with influenza-LACK158–173 triggers LACK158–173-specific Th1-biased CD4+ T cell responses within an appropriate cytokine milieu (IFN-γ, IL-12), essential for the magnitude and quality of the Th1 response. A single intraperitoneal exposure (non-replicative route of immunisation) to recombinant influenza delivers immunogenic peptides, leading to a marked reduction (2–4 log) in parasite burden, albeit without reduction in lesion size. This correlated with increased numbers of IFN-γ-producing CD4+ T cells in vaccinated mice compared to controls. Importantly, the subsequent prime-boost approach with a serologically distinct strain of influenza (H1N1->H3N2) expressing LACK158–173 led to a marked reduction in both lesion size and parasite burdens in vaccination trials. This protection correlated with high levels of IFN-γ producing cells in the spleen, which were maintained for 6 weeks post-challenge indicating the longevity of this protective effector response. Thus, these experiments show that Leishmania-derived peptides delivered in the context of recombinant influenza viruses are immunogenic in vivo, and warrant investigation of similar vaccine strategies to generate parasite-specific immunity

The Functions of Mediator in Candida albicans Support a Role in Shaping Species-Specific Gene Expression

The Mediator complex is an essential co-regulator of RNA polymerase II that is conserved throughout eukaryotes. Here we present the first study of Mediator in the pathogenic fungus Candida albicans. We focused on the Middle domain subunit Med31, the Head domain subunit Med20, and Srb9/Med13 from the Kinase domain. The C. albicans Mediator shares some roles with model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, such as functions in the response to certain stresses and the role of Med31 in the expression of genes regulated by the activator Ace2. The C. albicans Mediator also has additional roles in the transcription of genes associated with virulence, for example genes related to morphogenesis and gene families enriched in pathogens, such as the ALS adhesins. Consistently, Med31, Med20, and Srb9/Med13 contribute to key virulence attributes of C. albicans, filamentation, and biofilm formation; and ALS1 is a biologically relevant target of Med31 for development of biofilms. Furthermore, Med31 affects virulence of C. albicans in the worm infection model. We present evidence that the roles of Med31 and Srb9/Med13 in the expression of the genes encoding cell wall adhesins are different between S. cerevisiae and C. albicans: they are repressors of the FLO genes in S. cerevisiae and are activators of the ALS genes in C. albicans. This suggests that Mediator subunits regulate adhesion in a distinct manner between these two distantly related fungal species

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves.The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats.We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data

Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season

The dry season is a major challenge for Plasmodium falciparum parasites in many malaria endemic regions, where water availability limits mosquito vectors to only part of the year. How P. falciparum bridges two transmission seasons months apart, without being cleared by the human host or compromising host survival, is poorly understood. Here we show that low levels of P. falciparum parasites persist in the blood of asymptomatic Malian individuals during the 5- to 6-month dry season, rarely causing symptoms and minimally affecting the host immune response. Parasites isolated during the dry season are transcriptionally distinct from those of individuals with febrile malaria in the transmission season, coinciding with longer circulation within each replicative cycle of parasitized erythrocytes without adhering to the vascular endothelium. Low parasite levels during the dry season are not due to impaired replication but rather to increased splenic clearance of longer-circulating infected erythrocytes, which likely maintain parasitemias below clinical and immunological radar. We propose that P. falciparum virulence in areas of seasonal malaria transmission is regulated so that the parasite decreases its endothelial binding capacity, allowing increased splenic clearance and enabling several months of subclinical parasite persistence