Fire Effects on Soil Properties: Amending Post-Fire Soils with Native Microbial Communities and Biochar to Improve Sagebrush Performance

Within the sagebrush steppe, fire has been shown to affect biogeochemical properties and the microbial community composition in soils. However, there is uncertainty about the magnitude and direction of these effects, since they vary by sites that differ in abiotic and biotic conditions. Moreover, differences in post-fire management strategies are likely to mediate the effect of fire on soil properties, thus further compounding this uncertainty. Any changes in soil biogeochemical properties following fire can prevent successful restoration of Artemisia tridentata sp. wyomingensis (sagebrush), leading to variable outcomes of restoration success in the sagebrush steppe. Previous research has shown that addition of native soil microbes and biochar can improve ecosystem restoration efforts, but the effects of these soil amendments on post-fire soil properties and sagebrush performance across sites are uncertain. With this study, I investigated how fire impacts soil properties (i.e., soil organic matter (SOM), soil structure, carbon (C) and nitrogen (N) concentrations, soil pH, net mineral N, microbial richness and composition) at a variety of sites that differ in time since exposure to fire, post-fire plant communities, and post-fire site management. I then implemented a greenhouse study to evaluate how amending soils with native microbial community inocula and biochar impact soil properties of the post-burn sites and sagebrush germination and growth. Taken together, these findings capture the influences of multiple fires and separate management strategies on soil properties, and how certain soil amendments may redirect soil recovery to aid in sagebrush restoration. In my first chapter, I asked two questions: (1) how does fire affect soil biochemical properties across sites that differ in fire history, post-fire plant communities, and post-fire site management, and (2) how does fire affect soil microbial richness and community composition across sites that differ in post-fire plant communities, and post-fire site management. To assess these questions, soils were collected from three south of Boise, Idaho within the Orchard Combat Training Center (OCTC) that contrasted in fire history, plant community, and post-fire management. The northern part of the Union Fire (180 acres; hereafter: UFN2011) burned in 2011, and was treated with a mix of imazapic and glyphosate during the spring of 2019, after which sagebrush was handplanted 8 months later that yea. The southern part of the Union Fire (160 acres; hereafter: UFS2011) burned in 2011 and seeded with native grass species and planted with sagebrush. The Christmas Fire (hereafter: CF2018) burned in 2018, and was subjected to the same seeding and handplanting treatments as UFS2011. At each site, I selected five locations within the perimeter of the burn, and five locations outside the burn, representing the unburned control plots. In these unburned control plots, the five locations were stratified by sagebrush canopy and interspace microsites separately. At each one of the five locations, I collected four soil cores (10cm depth, 2.5cm diameter). I evaluated differences in soil pH, soil organic matter (SOM), soil carbon (C) and nitrogen (N) contents, soil structure, N cycling, and soil microbial communities between burned and unburned sites. Fire reduced SOM and soil C contents, and these losses were greater in burned areas that received an herbicide treatment. This suggests that suppression of plant growth using herbicides may limit the recovery of soil properties that are foundational to sagebrush steppe ecosystem functioning. Furthermore, I found a loss of arbuscular mycorrhizal fungi (AMF) richness with fire and significant changes in soil microbial community structure when herbicide had been used. Finally, increased soil mineral N concentrations across all burned sites indicate that fire may significantly reduce ecosystem stability and increase the risk of invasion. These changes in soil properties are likely to lead to a persistent ecosystem state-changes in the sagebrush steppe, and future studies should evaluate which management approaches could be used to restore both soils and plant communities. In my second chapter, I investigated two management approaches that may be used to restore the soils and plant communities impacted by fire. I asked (1) How does a live native soil microbial inoculum impact sagebrush performance and soil properties, (2) how do biochar additions impact sagebrush performance and soil properties, and (3) how does prior management (e.g., herbicide) mediate the impact of soil microbial inoculation and biochar amendment on sagebrush performance? A full factorial greenhouse experiment was conducted for three months with soils collected from the three post-burn sites described in Chapter 1. In the greenhouse experiment I incorporated the following treatments: (1) sterile native inoculum [-Inoculum] and no biochar [-Biochar], (2) live native inoculum [+Inoculum] and no biochar [-Biochar], (3) sterile native inoculum [-Inoculum] and biochar [+Biochar], and (4) live native inoculum [+Inoculum] and biochar [+Biochar]. Inocula was derived from sagebrush canopies at unburned sites and either added as live native inocula or autoclaved to sterilize the microbial community. Biochar was crushed into planted, watered daily until cotyledons showed, and continually monitored throughout the growing period. Germination, soil moisture content and pH, above- and below-ground measurements, total mineral N, fungal root colonization proportional abundances, and microbial richness and composition were assessed. I found that inoculations did not significantly benefit sagebrush performance, most likely due to the ratio of inocula administered. In contrast, biochar consistently enhanced soil moisture, pH, sagebrush germination and other performance variables while its effects on total mineral N and fungal root colonization varied by site location. Lastly, presence of herbicide in post-burn soils significantly altered soil bacterial and fungal community composition, and its effects persisted enough to inhibit sagebrush performance. Together, my data show that addition of biochar has a greater positive impact on sagebrush germination and performance than addition of soil microbial inocula, and that herbicide addition has persistent negative impacts on sagebrush performance. My study captured the varying levels at which fire impacts ecosystem structure and function, and how different soil amendments affected sagebrush performance at these post-fire soils. My findings support the notion that soil properties will remain degraded without appropriate management strategies supporting restoration, and herbicide may actually suppress successful restoration, residing longer in the soil than previously documented. When growing sagebrush in post-burn soils within the greenhouse, biochar enabled soil recovery, and this benefited sagebrush performance. However, herbicide impacts persisted and decreased sagebrush biomass even when soil amendments were incorporated. Fire can have profound, yet vastly different, influences on soil properties, and soil amendments may be able to augment soil recovery. Future studies should investigate various soil amendments and their impacts on sagebrush performance in the midst of changing fire regimes, post-fire vegetation shifts, and current post-fire management

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Biochar Effects on Mycorrhizal Fungi in Sagebrush Roots

Non-native annual grasses such as cheatgrass (Bromus tectorum) are fueling more extensive and frequent fires in sagebrush-steppe ecosystems. These disturbances have changed soil biological properties inhibiting native sagebrush (Artemisia tridentata) reestablishment. Sagebrush depends on symbiotic soil fungi (AMF) to enhance nutrient uptake. Biochar, a plant-based charcoal used as an ameliorant for soil health, can positively impact AMF colonization in some plants. We hypothesized that adding soil from an intact sagebrush stand, which harbors AMF, in combination with biochar would increase root colonization by AMF in sagebrush seedlings grown in post-fire soil. We grew sagebrush seedlings in post-fire soil in the greenhouse for three months. We added an inoculum of sagebrush soil that had not burned, and half of the pots received a biochar treatment (dose). Upon harvest, we measured the percent of fungal colonization in roots via the line intercept method. Our preliminary findings show no significant increase in root colonization by AMF with biochar added to post-fire field soil. Similar studies conducted in other fires showed contradictory results, suggesting an interaction between biochar and soil microbial communities that vary among ecosystems. Further research into soil amendments and their influence on AMF could greatly benefit post-fire sagebrush restoration efforts

Soil Recovery After Fire and Invasion: Implications for Sagebrush Reestablishment

The sagebrush steppe ecosystem has been heavily impacted by disturbance, including fires and the invasion of cheatgrass (Bromus tectorum). Both fire and changes in the plant community can impact soil properties that reduce sagebrush (Artemisia tridentate) reestablishment success, but in the long-term, these soil properties may recover thus allowing for sagebrush re-establishment. With this study we ask: how do soil properties change in a recovering sagebrush ecosystem? To quantify soil properties and changes therein as succession progresses, I will investigate a 1983 fire on the Orchard Combat Training Center that is experiencing re-establishment of sagebrush. Soil samples have been collected from three areas: (1) areas of no sagebrush regrowth, (2) areas with sagebrush regrowth, and (3) unburned areas adjacent to the fire. I will measure physical, chemical, and biological soil properties that are critical to sagebrush re-establishment. These include soil structure, organic matter content, pH, nitrogen and carbon content, and microbial and arbuscular mycorrhizal fungi (AMF) communities. These results will allow us to evaluate the process of succession following fire and invasion, and the importance of recovery of soil properties in enabling this process

Swiss Evaluation Registry for Pediatric Infective Endocarditis (SERPIE) - Risk factors for complications in children and adolescents with infective endocarditis.

BACKGROUND Infective endocarditis (IE) in pediatric patients is a severe cardiac disease and its actual epidemiology and clinical outcome in Switzerland is scarcely studied. METHODS Retrospective nationwide multicenter data analysis of pediatric IE in children (<18 years) between 2011 and 2020. RESULTS 69 patients were treated for definite (40/69;58%) or possible IE (29/69;42%). 61% (42/69) were male. Diagnosis was made at median 6.4 years (IQR 0.8-12.6) of age with 19 patients (28%) during the first year of life. 84% (58/69) had congenital heart defects. IE was located on pulmonary (25/69;35%), mitral (10/69;14%), tricuspid (8/69;12%) and aortic valve (6/69;9%), and rarely on ventricular septal defect (VSD;4/69;6%) and atrial septal defect (ASD;1/69;1%). In 22% (16/69) localization was unknown. 70% (48/69) had postoperative IE, with prosthetic material involved in 60% (29/48; right ventricular to pulmonary artery conduit (24), VSD (4), ASD (1)). Causative organisms were mostly Staphylococci spp. (25;36%) including Staphylococcus aureus (19;28%), and Streptococci spp. (13;19%). 51% (35/69) suffered from severe complications including congestive heart failure (16;23%), sepsis (17;25%) and embolism (19;28%). Staphylococcus aureus was found as a predictor of severe complications in univariate and multivariate analysis (p = 0.02 and p = 0.033). In 46% (32/69) cardiac surgery was performed. 7% (5/69) died. CONCLUSIONS IE in childhood remains a severe cardiac disease with relevant mortality. The high morbidity and high rate of complications is associated with Staphylococcus aureus infections. Congenital heart defects act as a risk factor for IE, in particular the high number of cases associated with prosthetic pulmonary valve needs further evaluation and therapeutic alternatives

The CD4(+) T-cell response of melanoma patients to a MAGE-A3 peptide vaccine involves potential regulatory T cells.

Melanoma patients were injected with various vaccines containing a MAGE-A3 peptide presented by HLA-DP4. Anti-MAGE-A3.DP4 T cells were not detectable in the blood before vaccination, but their frequencies after vaccination ranged from 2 x 10(-6) to 2 x 10(-3) among the CD4(+) blood T lymphocytes of the patients. The CD4(+) blood T lymphocytes that stained ex vivo with HLA-DP4 tetramers folded with the MAGE-A3 peptide were selected by flow cytometry and amplified under clonal conditions. About 5% of the CD4(+) T-cell clones that recognized the MAGE-A3.DP4 antigen had a CD25(+) phenotype in the resting state. These CD25(+) clones had a high capacity to suppress the proliferation of another T-cell clone after peptide stimulation in vitro. Most of them had high FOXP3 expression in the resting state and an unmethylated FOXP3 intron 1. They produced active transforming growth factor-beta but none of cytokines IFN-gamma, interleukin-2 (IL-2), IL-4, IL-5, and IL-10. About 20% of CD25(-) clones had a significant but lower suppressive activity. Most of the CD25(-) clonal populations contained cells that expressed FOXP3 in the resting state, but FOXP3 demethylation was not observed. We conclude that MAGE-A3.DP4 vaccination can produce CD4(+) T cells that may exert regulatory T-cell function in vivo.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe