Investigating the Relationship Between Climate and Valley Fever (Coccidioidomycosis)

Valley fever (coccidioidomycosis) is a disease caused by inhalation of spores from the soil-dwelling Coccidioides fungal species. The disease is endemic to semiarid areas in the western USA and parts of Central and South America. The region of interest for this study, Kern County, California, accounts for approximately 14% of the reported valley fever cases in the USA each year. It is hypothesized that the weather conditions that foster the growth and dispersal of the fungus influence the number of cases in the endemic area. This study uses regression-based analysis to model and assess the seasonal relationships between valley fever incidence and climatic variables including concurrent and lagged precipitation, temperature, Palmer Drought Severity Index, wind speed, and PM₁₀ using data from 2000 to 2015. We find statistically significant links between disease incidence and climate conditions in Kern County, California. The best performing seasonal model explains up to 76% of the variability in fall valley fever incidence based on concurrent and antecedent climate conditions. Findings are consistent with previous studies, suggesting that antecedent precipitation is an important predictor of disease. The significant relationships found support the “grow and blow” hypothesis for climate-related coccidioidomycosis incidence risk that was originally developed for Arizona.     

Statistical modeling of valley fever data in Kern County,California

Coccidioidomycosis (valley fever) is a fungal infection found in the southwestern US, northern Mexico, and some places in Central and South America. The fungus that causes it (Coccidioides immitis) is normally soil-dwelling but, if disturbed, becomes air-borne and infects the host when its spores are inhaled. It is thus natural to surmise that weather conditions that foster the growth and dispersal of the fungus must have an effect on the number of cases in the endemic areas. We present here an attempt at the modeling of valley fever incidence in Kern County, California, by the implementation of a generalized auto regressive moving average (GARMA) model. We show that the number of valley fever cases can be predicted mainly by considering only the previous history of incidence rates in the county. The inclusion of weather-related time sequences improves the model only to a relatively minor extent. This suggests that fluctuations of incidence rates (about a seasonally varying background value) are related to biological and/or anthropogenic reasons, and not so much to weather anomalies.     

Environmental vVariability and coccidioidomycosis (valley fever)

Coccidioidomycosis (valley fever) is a disease endemic to arid regions in the western hemisphere, and is caused by the soil-dwellingfungus Coccidioides immitis (C. immitis). In this paper, we provide an overview of the current state of knowledge regarding valley fever and C. immitis as related to climatic conditions and habitat requirements. Previous research shows there is a relationship between temperature and precipitation, and outbreaks of coccidioidomycosis. Incidence of the disease varies seasonally as well as annually due to changing climatic conditions. However, the specific environmental conditions that may produce an outbreak of coccidioidomycosis are not well understood in space and time. Previous studies have attempted characterize C. immitis' habitat. Temperature, moisture, salinity, and pH of the soil have all been considered separately in the geographic distribution of the fungus. Medical and proactive intervention are served best, however, by an integrative strategy that folds climate and surface variables into spatially-explicit models. We conclude with recommendations for future research directions.     

Combining Forces - The Use of Landsat TM Satellite Imagery,Soil Parameter Information,and Multiplex PCR to Detect Coccidioides immitis Growth Sites in Kern County,California

Coccidioidomycosis is a fungal disease acquired through the inhalation of spores of Coccidioides spp., which afflicts primarily humans and other mammals. It is endemic to areas in the southwestern United States, including the San Joaquin Valley portion of Kern County, California, our region of interest (ROI). Recently, incidence of coccidioidomycosis, also known as valley fever, has increased significantly, and several factors including climate change have been suggested as possible drivers for this observation. Up to date details about the ecological niche of C. immitis have escaped full characterization. In our project, we chose a three-step approach to investigate this niche: 1) We examined Landsat-5-Thematic-Mapper multispectral images of our ROI by using training pixels at a 750 m×750 m section of Sharktooth Hill, a site confirmed to be a C. immitis growth site, to implement a Maximum Likelihood Classification scheme to map out the locations that could be suitable to support the growth of the pathogen; 2) We used the websoilsurvey database of the US Department of Agriculture to obtain soil parameter data; and 3) We investigated soil samples from 23 sites around Bakersfield, California using a multiplex Polymerase Chain Reaction (PCR) based method to detect the pathogen. Our results indicated that a combination of satellite imagery, soil type information, and multiplex PCR are powerful tools to predict and identify growth sites of C. immitis. This approach can be used as a basis for systematic sampling and investigation of soils to detect Coccidioides spp.     

Modeling valley fever (coccidioidomycosis) incidence on the basis of climate conditions

Valley fever (coccidioidomycosis) is a disease endemic to arid regions within the Western Hemisphere, and is caused by a soil-dwelling fungus, Coccidioides immitis. Incidence data for Pima County, reported to the Arizona Department of Health Services as new cases of valley fever, were used to conduct exploratory analyses and develop monthly multivariate models of relationships between valley fever incidence and climate conditions and variability in Pima County, Arizona, USA. Bivariate and compositing analyses conducted during the exploratory portion of the study revealed that antecedent temperature and precipitation in different seasons are important predictors of incidence. These results were used in the selection of candidate variables for multivariate predictive modeling, which was designed to predict deviation from mean incidence on the basis of past, current, and forecast climate conditions. The models were specified using a backward stepwise procedure, and were most sensitive to key predictor variables in the winter season and variables that were time-lagged 1 year or more prior to the month being predicted. Model accuracy was generally moderate ( r(2) values for the monthly models, tested on independent data, ranged from 0.15 to 0.50), and months with high incidence can be predicted more accurately than months with low incidence.     

气候变化背景下入侵植物曼陀罗在西藏的潜在风险区预测

生物安全与外来物种入侵是国门生物安全的重大生态学问题,生物入侵造成了巨大的经济损失与生物多样性快速丧失,还影响着人类的身体健康。西藏是我国重要的生态安全屏障,生态类型复杂且丰富多样,明确西藏区域尺度上外来入侵植物的潜在分布格局及其对气候变化的响应对入侵植物的预防和控制具有重要意义。为了探究入侵植物曼陀罗(Datura stramonium L.)对西藏生态安全的影响风险,基于野外实地调查数据,采用最大熵(Maxent) 模型,应用R语言和SPSS软件对模型参数和数据进行优化筛选,探讨影响其地理分布的主要环境因子,并模拟预测了当代及2种气候变化情景(RCP 45、RCP 85)下2050年和2070年, 其在西藏的潜在入侵风险区分布情况。结果表明:下层土壤酸碱度、年平均气温、最暖月最高温度与土壤有效含水量是影响曼陀罗分布的主导环境因子,海拔和人类活动影响强度也有重要作用;朗县、加查县、乃东区、城关区、八宿县、贡嘎县、巴宜区、波密县、察隅县、芒康县等地为入侵高风险地区;两种气候背景下曼陀罗的各级风险区面积和总风险区面积均呈持续增加的变化趋势,且在最高碳排放情景(RCP 85情景)下响应更为敏感;主要沿着低海拔河谷区域东南向西北方向入侵扩散的趋势,分布中心由当前的墨脱县域向工布江达县域转移。综合来说,曼陀罗在西藏分布受土壤环境、温度和降水影响较大,气候变化和人类活动影响强度将使其向西藏西部、北部扩散。研究结果可为西藏地区综合防控曼陀罗的入侵危害与动态监测提供生态学基础理论依据。     

增加降水对干旱河谷区云南松人工林土壤呼吸的影响

2013年5月至2014年6月,对干旱河谷区云南松(Pinus yunnanensis)人工林进行增加降水试验,试验设置对照(CK,0 mm m~(-2)a~(-1))、增水10%(A1,80 mm m~(-2)a~(-1))、增水20%(A2,160 mm m~(-2)a~(-1))和增水30%(A3,240 mm m~(-2)a~(-1))4个处理水平。采用LI-8100开路式土壤碳通量测量系统测定每月土壤呼吸速率。结果表明,4个处理云南松人工林土壤呼吸速率均呈明显的季节变化,7月最高,2月最低。与CK相比,A1年均土壤呼吸速率无显著性差异(P0.05),A2显著增加了12.88%(P0.05),而A3明显减少了17.71%(P0.05)。3个增水处理均提高了土壤呼吸的温度敏感性,减弱了土壤呼吸与土壤湿度的关系。与土壤温度相比,土壤湿度对土壤呼吸的影响相对较小。增水增加了湿季土壤微生物碳、氮含量,干季对微生物碳含量无影响,但明显降低了微生物氮含量。这说明,降水增加对干旱河谷区云南松人工林土壤呼吸的影响是不尽相同的,适当的增水会促进土壤呼吸,而过量的增水会抑制土壤呼吸。     

Gene exchange between two divergent species of the fungal human pathogen,Coccidioides

The fungal genus Coccidioides is composed of two species, Coccidioides immitis and Coccidioides posadasii. These two species are the causal agents of coccidioidomycosis, a pulmonary disease also known as valley fever. The two species are thought to have shared genetic material due to gene exchange in spite of their long divergence. To quantify the magnitude of shared ancestry between them, we analyzed the genomes of a population sample from each species. Next, we inferred what is the expected size of shared haplotypes that might be inherited from the last common ancestor of the two species and find a cutoff to find what haplotypes have conclusively been exchanged between species. Finally, we precisely identified the breakpoints of the haplotypes that have crossed the species boundary and measure the allele frequency of each introgression in this sample. We find that introgressions are not uniformly distributed across the genome. Most, but not all, of the introgressions segregate at low frequency. Our results show that divergent species can share alleles, that species boundaries can be porous, and highlight the need for a systematic exploration of gene exchange in fungal species.     

中国四齿芥属一新记录种——帕米尔四齿芥

报道了十字花科(Brassicaceae)四齿芥属(Tetracme Bunge)一中国新记录种——帕米尔四齿芥(Tetracme pamirica Vassilcz.)。标本采自西藏自治区札达县底雅乡,生于干燥的河谷坡地。该种与相近种四齿芥的区别是,角果长10~13 mm,种子长1~2 mm。凭证标本保存在内蒙古大学植物标本馆(HIMC)。     

Radial growth responses to drought of Pinus sylvestris and Quercus pubescens in an inner‐Alpine dry valley

Question: Lower montane treeline ecotones such as the inner Alpine dry valleys are regarded as sensitive to climate change. In the dry Valais valley (Switzerland) the composition of the widespread, low altitude Pinus forests is shifting towards a mixed deciduous state. The sub‐boreal P. sylvestris shows high mortality rates, whereas the deciduous sub‐mediterranean Quercus pubescens is spreading. These species may act as early indicators of climate change. We evaluate this hypothesis by focusing on their differences in drought tolerance, which are hardly known, but are likely to be crucial in the current forest shift and also for future forest development. Methods: We used dendroecological methods to detect species‐specific patterns in the growth response to drought. The relationship between radial growth of 401 trees from 15 mixed stands and drought was analysed by calculating response functions using yearly tree‐ring indices and monthly drought indices. PCA was applied to the response ratios to discover spatial patterns of drought response. Results: A species‐specific response to moisture as well as a sub‐regional differentiation of the response patterns were found. While Quercus showed a response mainly to the conditions of the previous autumn and those of current spring, Pinus did not start responding before May, but showed responses throughout the whole summer. Quercus may restrict physiological activity to moist periods; growth of Pinus was much more dependent on prior growth. Conclusions: Given that the climate is changing towards (1) longer summer drought periods, (2) higher mean temperatures and (3) shifted seasonally of moisture availability, Quercus may benefit from adapting better to drier conditions. Pinus may increasingly face problems related to drought stress as it depends on summer moisture and has a smaller adaptive capacity due to its long‐lived photosynthetic tissue.     

Edaphic limitations to growth and photosynthesis in Sierran and Great Basin vegetation

Summary Soils derived from hydrothermally altered andesite support unique communities of Sierran conifers (Pinus ponderosa Laws. and P. jeffreyi Grev. and Balf.) amongst sagebrush (Artemisia tridentata Nutt.) vegetation in the western Great Basin. Plants grown in soil derived from hydrothermally altered bedrock had lower growth rates, total biomass, and net photosynthetic rates than plants grown in soil derived from unaltered andesite of the same formation. Total dry mass was 10 to 28% lower for conifers grown in altered soil whereas dry mass of Artemisia tridentata and Bromus tectorum L. was reduced by over 90%. Results from a nutrient amendment experiment indicated that low phosphorus was the dominant limitation in altered soil, and phosphorus-deficiency affected growth primarily by limiting leaf area development rather than direct inhibition of photosynthesis. The proportionately greater reduction of biomass for Artemisia and Bromus grown in altered soil supports our hypothesis that Great Basin vegetation is excluded from altered soil by intolerance to nutrient deficiency. The Sierran conifers growing on this rock type are therefore free of competition for water with Great Basin vegetation and are able to persist in an exceptionally dry climate.     

干热河谷车桑子光合生理特性对氮磷添加的响应

氮磷养分是限制干热河谷植物生长的重要元素,不同土壤上植物受到的养分限制类型不同。光合作用作为植物生长发育的基础,不同土壤上氮磷养分添加对干热河谷植物光合生理特征的影响还没有报道。因此,以干热河谷优势植物——车桑子为研究对象,在元谋县不同海拔处采集土壤,设置加氮（+N）、加磷（+P）、氮磷同时添加（+NP）和不添加（CK）四个处理,研究车桑子光合响应曲线、叶绿素含量和叶绿素荧光特性对氮、磷添加的响应规律,并探讨光合响应特征与车桑子生长的关系：研究结果显示：1）不同海拔土壤上,车桑子光合生理特性对氮磷添加具有不同的响应。在低海拔燥红土上,氮添加处理（+N和+NP）提高了车桑子净光合速率、叶绿素含量和PSII活性;中海拔紫色土上,+NP促进了车桑子光合速率和叶绿素含量的提高;高海拔黄棕壤上,+N处理降低了车桑子净光合速率和PSII活性,而磷添加处理（+P和+NP）提高了车桑子净光合速率。2）车桑子光合特性对养分添加的响应取决于土壤的养分限制类型,限制性养分添加可以提高车桑子的净光合速率。3）燥红土上+P以及黄棕壤上+N对PSⅡ最大光化学效率（Fv/Fm）的降低更大程度上归于可变荧光Fv的减少而不是最小荧光F₀的增加,可减少养分限制对光系统II造成的伤害。4）三种土壤类型上车桑子的叶绿素含量和组成差异极显著,相比于燥红土和紫色土,黄棕壤上车桑子的叶绿素含量显著更高,而叶绿素a/b显著更低。综上,本研究结果表明,车桑子光合能力受到氮和磷的共同调节,不同土壤上光合生理特性的响应可增强植物对限制性养分的适应性,影响植物生长发育。     

基于可培养方法分析云南腾冲小空山火山谷芽胞杆菌分布特征

【目的】为了解云南腾冲小空山火山谷土壤中可培养芽胞杆菌种类分布特征。【方法】采用可培养手段对小空山火山谷阳坡、谷底和阴坡土壤中的芽胞杆菌进行分离培养,根据16S rRNA基因序列同源性对分离菌株进行鉴定,并分析系统发育地位。利用Canoco5软件分析采样点芽胞杆菌种类分布特征与土壤样品理化性质的相关性。【结果】从火山谷土壤样品中共分离获得180株芽胞杆菌,16S rRNA基因测序鉴定结果表明分离菌株隶属于芽胞杆菌纲2个科(芽胞杆菌科和类芽胞杆菌科)、6个属、34个种,其中芽胞杆菌属(Bacillus) 11个种,类芽胞杆菌属(Paenibacillus) 14个种,短芽胞杆菌属(Brevibacillus)3个种,赖氨酸芽胞杆菌属(Lysinibacillus)4个种,嗜冷芽胞杆菌属(Psychrobacillus)1个种和绿芽胞杆菌属(Viridibacillus)2个种,其中7个菌株与其最近模式菌株16SrRNA相似性低于种的界定阈值(98.65%),为芽胞杆菌潜在新物种。优势属为芽胞杆菌属和类芽胞杆菌属,优势种为蕈状芽胞杆菌(Bacillusmycoides),图瓦永芽胞杆菌(Bacillustoyonensis),蜡状芽胞杆菌(Bacilluscereus),解木糖赖氨酸芽胞杆菌(Lysinibacillusxylanilyticus),蜂房类芽胞杆菌(Paenibacillusalvei)和沙地绿芽胞杆菌(Viridibacillus arenosi)。其中16个种分离自阳坡,29个种分离自阴坡,9个种分离自谷底,三者共同种类为6种。阳坡、谷底和阴坡的芽胞杆菌种群分布Bray-Curtis相似性为62.4%,多样性分析结果表明,Shannon指数(H′)大小次序为阴坡阳坡谷底。环境因子分析发现,芽胞杆菌种群分布多样性特征与其土壤的海拔高度、碳氮比和硫含量呈负相关,而和碳源和氮源含量呈正相关。【结论】从以上结果得出,云南腾冲火山谷有着较为丰富的芽胞杆菌资源,且还存在可分离培养的芽胞杆菌的潜在新物种,为利用火山微生物资源提供了保障。     

Development of Pusa 5SD for seed dressing and Pusa Biopellet 10G for soil application formulations of Trichoderma harzianum and their evaluation for integrated management of dry root rot of mungbean (Vigna radiata)

Various seed dressing and soil application formulations were developed from Trichoderma viride, T. virens and T. harzianum to increase the shelf life of bio-formulations used to manage dry root rot (Rhizoctonia bataticola) of mungbean (Vigna radiata), a major yield limiting factor in mungbean production. The shelf life of the formulations developed in the present study was monitored by counting colony forming units (cfu) up to 25 months of storage at room temperature (26 ± 8 °C). A newly developed seed dressing formulation, Pusa 5SD based on peat powder (47.5%), Sabudana powder (Manihot esculenta) (47.5%) and carboxymethyl cellulose (5%) and a newly developed soil application formulation, Pusa Biopellet (PBP) based on sodium alginate, aluminium silicate, Sabudana powder and tap water (1:5:5:100 w/w/w/v) exhibited longer shelf life. Another formulation Pusa Biogranule (PBG) based on wheat and pulse brans varied in cfu counts during different periods of storage. Pusa 5SD could be used up to 25 months of storage while PBP 10G and PBG 5 could be used up to 15 months of storage (>10⁵ cfu). The efficacy of the formulations was evaluated in pot experiments against the disease. In these experiments, T. harzianum based PBP 10G and PBG 5 for soil application, and Pusa 5SD for seed treatment were found to be superior to others in reducing the dry root rot incidence, and increasing the seed germination and shoot and root lengths. However, a combination of soil application of PBP 10G (T. harzianum) and seed treatment with T. harzianum based Pusa 5SD + carboxin was found superior to the use of any of these formulations alone in reducing the dry root rot incidence (87.2%) and increasing the seed germination (43.0%), shoot length (40.3%), root length (37.0%) and grain yield (54.6%) of mungbean crop over those of untreated control under sick field conditions.     

Survival ofXanthomonas campestris pv.vesictoria in pepper seeds and roots in symptomless and dry leaves in non-host plants and in the soil

Summary A population ofXanthomonas campestris pv.vesicatoria developed as endophytes in the leaves and rhizosphere of apparently symptomless plants grown under mist but not under dry conditions. The pathogen survired for long periods on, and could be isolated from, the surface of infested dried seeds, inoculated sandy loam soil, dried leaves, and the rhizosphere of pepper and of other non-host plants. In addition, small numbers of the pathogen survived for 18 months in a field previously cropped with pepper diseased with bacterial scab. Healthy nursery or mature plants developed symptoms while growing in soil containing infested leaves, either buried or placed on the soil surface.     

Ecophysiological observations on Drosophyllum lusitanicum

The carnivorous plant Drosophyllum lusitanicum inhabits heathland and ruderal sites in Portugal, Spain and Morocco. In the literature, various theories have been discussed concerning the ability of Drosophyllum to survive the annual dry period in summer. In August 2004, we examined: (1) the microclimate, (2) soil parameters and (3) the physiological conditions of the plants on two sites in Portugal and Spain. First, during the day, plants are exposed to very high air and soil temperatures and very low air humidity. The climatic extremes are not significantly softened by the population, only the wind speed is drastically decreased. During the night, on the other hand, very high air humidity and dew formation could be observed. The harsh climate is accompanied by stressful soil conditions. Second, the soil is completely dry, poor in fine earth, calcium and nutrients and more or less acid. Third, in spite of these climatic and edaphic extremes, all plants were green, produced trapping mucilage and caught numerous animals. Far from being affected by these conditions, Drosophyllum showed even better growth and reproduction on more extreme sites. We analysed the root system and found living fine roots missing. The osmotic value of the plants is rather low and water storage organs are absent. Therefore we conclude that in summer Drosophyllum is nourished by the dew at night.     

Ubiquinone system,GC contents and cellular fatty acid composition of species of the form-genusMalbranchea andCoccidioides immitis for chemotaxonomic study

Ubiquinone system, GC contents and cellular fatty acid (CFA) composition were analyzed as criteria for chemotaxonomy ofMalbranchea species andCoccidioides immitis, which are suggested to be phylogenetically related. Based on the major ubiquinone,Malbranchea spp. were divided into two groups, of which one group possessed the same major ubiquinone asC. immitis. Similar GC contents and CFA profiles were obtained for the species ofMalbranchea andC. immitis. On the basis of these criteria the relationships between the fungi are discussed.     

Elastase activity of fungi with anamorphs similar to Coccidioides immitis

The elastin digestion assay was examined to determine if it would facilitate the identification of Coccidioides immitis when non-pathogenic fungi resembling C. immitis are encountered. Fungal isolants tested have anamorphs that closely resemble the macroscopic or microscopic morphology of C. immitis. Elastin hydrolysis was measured by elastin-agar plate assays. Approximately 80% of the isolants hydrolyzed elastin; thus, the elastin digestion assay as a differential test appears to have little value.