Detection of Phytophthora nicotianae in Soil with Real-time Quantitative PCR

Phytophthora nicotianae is one of the most important soil-borne plant pathogens. A rapid, specific and sensitive real-time polymerase chain reaction (PCR) detection method for P. nicotianae was established, which used primers targeting the internal transcribed spacer (ITS) regions of rDNA genes of Phytophthora spp. Based on the nucleotide sequences of ITS2 of 15 different species of Phytophthora , the primers and probe were designed specifically to amplify DNA from P. nicotianae. With a series of 10-fold DNA dilutions extracted from P. nicotianae pure cultures, the detection limit was 10 pg/μl in conventional PCR, whereas in SYBR Green I PCR the detection limit was 0.12 fg/μl and in TaqMan PCR 1.2 fg/μl, and real-time PCR was 10⁴–10⁵ times more sensitive than conventional PCR. The simple and rapid procedures maximized the yield and quality of recovered DNA from soil and allowed the processing of many samples in a short time. The direct DNA extractions from soil were utilized to yield DNA suitable for PCR. By combining this protocol with the real-time PCR procedure it has been possible to specifically detect P. nicotianae in soil, and the degree of sensitivity was 1.0 pg/μl. The system was applied to survey soil samples from tobacco field sites in China for the presence of P. nicotianae and the analyses of naturally infested soil showed the reliability of the real-time PCR method.     

Patterns of introduction and adaptation during the invasion of Aegilops triuncialis (Poaceae) into Californian serpentine soils

Multiple introductions can play a prominent role in explaining the success of biological invasions. One often cited mechanism is that multiple introductions of invasive species prevent genetic bottlenecks by parallel introductions of several distinct genotypes that, in turn, provide heritable variation necessary for local adaptation. Here, we show that the invasion of Aegilops triuncialis into California, USA, involved multiple introductions that may have facilitated invasion into serpentine habitats. Using microsatellite markers, we compared the polymorphism and genetic structure of populations of Ae. triuncialis invading serpentine soils in California to that of accessions from its native range. In a glasshouse study, we also compared phenotypic variation in phenological and fitness traits between invasive and native populations grown on loam soil and under serpentine edaphic conditions. Molecular analysis of invasive populations revealed that Californian populations cluster into three independent introductions (i.e. invasive lineages). Our glasshouse common garden experiment found that all Californian populations exhibited higher fitness under serpentine conditions. However, the three invasive lineages appear to represent independent pathways of adaptation to serpentine soil. Our results suggest that the rapid invasion of serpentine habitats in California may have been facilitated by the existence of colonizing Eurasian genotypes pre‐adapted to serpentine soils.     

贵州省土壤中的暗色丝孢菌Ⅰ(英文)

采用土壤平板法和稀释平板法,从采自贵州省的20份土壤样品中分离得到14个暗色丝孢菌分离物,隶属于11属12种。其中,浅色腐殖霉Humicola pallescens为一新种,绿色暗梗单孢霉厚垣变种Chloridium virescens var.chlamy dosporum和印度粘束霉Graphiumindicum为中国新记录。对新种及中国新记录作了较详细的描述并绘图。其余9个国内已报道种亦作了生境和分布地点的引证。所有研究菌株的干制培养物标本与活菌种均存放在山东农业大学植物病理学标本室(HSAUP)。     

The distribution and abundance of wheat roots in a dense,structured subsoil – implications for water uptake

We analysed the abundance, spatial distribution and soil contact of wheat roots in dense, structured subsoil to determine whether incomplete extraction of subsoil water was due to root system limitations. Intact soil cores were collected to 1.6 m below wheat crops at maturity on a red Kandosol in southern Australia. Wheat roots, remnant roots, soil pores and root–soil contact were quantified at fresh breaks in the soil cores. In surface soil layers (<0.6 m) 30–40% of roots were clumped within pores and cracks in the soil, increasing to 85–100% in the subsoil (>0.6 m), where 44% of roots were in pores with at least three other roots. Most pores contained no roots, with occupancy declining from 20% in surface layers to 5% in subsoil. Wheat roots clumped into pores contacted the surrounding soil via numerous root hairs, whereas roots in cracks were appressed to the soil surface and had very few root hairs. Calculations assuming good root–soil contact indicated that root density was sufficient to extract available subsoil water, suggesting that uptake is constrained at the root–soil interface. To increase extraction of subsoil water, genetic targets could include increasing root–soil contact with denser root hairs, and increasing root proliferation to utilize existing soil pores.     

小溪自然保护区非盐环境土壤中嗜盐和耐盐菌多样性

【目的】研究湖南小溪国家级自然保护区普通非盐环境(ordinary non-saline environment)土壤样品中可培养嗜盐及耐盐细菌(含放线菌)多样性。【方法】采用纯培养法和基于16S rRNA基因序列的系统发育分析对样品中嗜盐及耐盐细菌多样性进行研究。【结果】用补充5%-20%(w/v)NaCl的MA、ISP2、ISP5、NA和HAA培养基从土壤样品中分离到114株细菌,其中8株为中度嗜盐菌,19株为轻度嗜盐菌,87株为耐盐菌。根据形态观察和部分生理生化实验结果去冗余,选取61个代表性菌株进行基于16S rRNA基因序列的系统发育多样性分析。结果表明,这些菌株属于细菌域(Bacteria)的3个大的系统发育类群(门;phylum)(Actinobacteria,Firmicutes,Proteobacteria)的16个科、18个属,代表了41个物种。多数菌株属于Firmicutes门(38株,62.3%)和Actinobacteria门(18株,29.5%)。大多数菌株与其系统发育关系最密切的已知物种的典型菌株之间存在一定的遗传差异(16S rRNA基因序列相似性为96.9%-99.8%),其中有7个菌株(JSM070026,JSM081004,JSM081006,JSM081008,JSM083058,JSM083085,JSM084035)代表7个潜在新种(potential novel species)。【结论】研究结果表明,湖南小溪国家级自然保护区普通非盐环境土壤中存在较为丰富的可培养嗜盐及耐盐细菌多样性,并且潜藏着较多新的微生物类群(物种)。     

红海榄根际土壤来源的泡盛曲霉（Aspergillus awamori）F12及其代谢产物的抗菌活性分析

摘要：【目的】鉴定一株来自于红海榄根际土壤并具有分泌抑菌活性代谢产物的真菌菌株F12,并从其发酵液乙酸乙酯浸膏中分离抑菌活性成分。【方法】通过形态学观察以及ITS序列分析方法对菌株F12进行鉴定;利用色谱技术分离发酵液乙酸乙酯浸膏中的次生代谢产物,根据化合物的质谱、氢谱、碳谱以及理化性质确定其结构,并检测它们对细菌生长的抑制作用。【结果】菌株F12被鉴定为Aspergillus awamori strain F12;从其发酵液乙酸乙酯浸膏中分离到3种化合物：1,4-二甲氧基苯（1）、大黄素（2）和3,6-二苯甲基哌嗪-2,5-二酮（3）,其中化合物1属于在本属真菌中首次报道。化合物2对金黄色葡萄球菌和枯草芽孢杆菌的生长具有明显的抑制作用,最低抑菌浓度（MIC）分别为16ng/L和32ng/L,化合物1和3对上述菌株的生长无明显的抑制活性。【结论】首次发现从红海榄根际土壤中分离到的泡盛曲霉（Aspergillus awamori）菌株F12具有合成1,4-二甲氧基苯和大黄素的能力,其中后者对微生物的生长具有明显的抑制作用。     

Quantification of soil organic carbon sequestration potential in cropland: A model approach

Agroecosystems have a critical role in the terrestrial carbon cycling process. Soil organic carbon (SOC) in cropland is of great importance for mitigating atmospheric carbon dioxide increases and for global food security. With an understanding of soil carbon saturation, we analyzed the datasets from 95 global long-term agricultural experiments distributed across a vast area spanning wide ranges of temperate, subtropical and tropical climates. We then developed a statistical model for estimating SOC sequestration potential in cropland. The model is driven by air temperature, precipitation, soil clay content and pH, and explains 58% of the variation in the observed soil carbon saturation (n=76). Model validation using independent data observed in China yielded a correlation coefficient R ² of 0.74 (n=19, P<0.001). Model sensitivity analysis suggested that soils with high clay content and low pH in the cold, humid regions possess a larger carbon sequestration potential than other soils. As a case study, we estimated the SOC sequestration potential by applying the model in Henan Province. Model estimations suggested that carbon (C) density at the saturation state would reach an average of 32 t C ha⁻¹ in the top 0–20 cm soil depth. Using SOC density in the 1990s as a reference, cropland soils in Henan Province are expected to sequester an additional 100 Tg C in the future.     

Mitigating the greenhouse gas balance of ruminant production systems through carbon sequestration in grasslands

Soil carbon sequestration (enhanced sinks) is the mechanism responsible for most of the greenhouse gas (GHG) mitigation potential in the agriculture sector. Carbon sequestration in grasslands can be determined directly by measuring changes in soil organic carbon (SOC) stocks and indirectly by measuring the net balance of C fluxes. A literature search shows that grassland C sequestration reaches on average 5 ± 30 g C/m2 per year according to inventories of SOC stocks and -231 and 77 g C/m2 per year for drained organic and mineral soils, respectively, according to C flux balance. Off-site C sequestration occurs whenever more manure C is produced by than returned to a grassland plot. The sum of on- and off-site C sequestration reaches 129, 98 and 71 g C/m2 per year for grazed, cut and mixed European grasslands on mineral soils, respectively, however with high uncertainty. A range of management practices reduce C losses and increase C sequestration: (i) avoiding soil tillage and the conversion of grasslands to arable use, (ii) moderately intensifying nutrient-poor permanent grasslands, (iii) using light grazing instead of heavy grazing, (iv) increasing the duration of grass leys; (v) converting grass leys to grass-legume mixtures or to permanent grasslands. With nine European sites, direct emissions of N2O from soil and of CH4 from enteric fermentation at grazing, expressed in CO2 equivalents, compensated 10% and 34% of the on-site grassland C sequestration, respectively. Digestion inside the barn of the harvested herbage leads to further emissions of CH4 and N2O by the production systems, which were estimated at 130 g CO2 equivalents/m2 per year. The net balance of on- and off-site C sequestration, CH4 and N2O emissions reached 38 g CO2 equivalents/m2 per year, indicating a non-significant net sink activity. This net balance was, however, negative for intensively managed cut sites indicating a source to the atmosphere. In conclusion, this review confirms that grassland C sequestration has a strong potential to partly mitigate the GHG balance of ruminant production systems. However, as soil C sequestration is both reversible and vulnerable to disturbance, biodiversity loss and climate change, CH4 and N2O emissions from the livestock sector need to be reduced and current SOC stocks preserved.     

Net greenhouse gas fluxes in Brazilian ethanol production systems

Biofuels are both a promising solution to global warming mitigation and a potential contributor to the problem. Several life cycle assessments of bioethanol have been conducted to address these questions. We performed a synthesis of the available data on Brazilian ethanol production focusing on greenhouse gas (GHG) emissions and carbon (C) sinks in the agricultural and industrial phases. Emissions of carbon dioxide (CO₂) from fossil fuels, methane (CH₄) and nitrous oxide (N₂O) from sources commonly included in C footprints, such as fossil fuel usage, biomass burning, nitrogen fertilizer application, liming and litter decomposition were accounted for. In addition, black carbon (BC) emissions from burning biomass and soil C sequestration were included in the balance. Most of the annual emissions per hectare are in the agricultural phase, both in the burned system (2209 out of a total of 2398 kg C_eq), and in the unburned system (559 out of 748 kg C_eq). Although nitrogen fertilizer emissions are large, 111 kg C_eq ha^?1 yr^?1, the largest single source of emissions is biomass burning in the manual harvest system, with a large amount of both GHG (196 kg C_eq ha^?1 yr^?1). and BC (1536 kg C_eq ha^?1 yr^?1). Besides avoiding emissions from biomass burning, harvesting sugarcane mechanically without burning tends to increase soil C stocks, providing a C sink of 1500 kg C ha^?1 yr^?1 in the 30 cm layer. The data show a C output: input ratio of 1.4 for ethanol produced under the conventionally burned and manual harvest compared with 6.5 for the mechanized harvest without burning, signifying the importance of conservation agricultural systems in bioethanol feedstock production.     

Paleoenvironmental conditions preceding the Messinian Salinity Crisis in the Central Mediterranean: Integrated data from the Upper Miocene Trave section (Italy)

Integrated data of calcareous plankton and benthic foraminifers from the pre-evaporitic interval of Trave section (Central Italy) allowed the reconstruction of surface and bottom-water conditions in the Central Mediterranean during the interval from 7.61 to 6.33 Ma, preceding the Messinian Salinity Crisis.Our data point out a three-step paleoenvironmental evolution. During the first stage (7.61-7.02 Ma) benthic foraminiferal assemblages depict stable, well-oxygenated and ventilated bottom-water conditions, while the surface water records variable temperature and high nutrient conditions, probably associated with strong seasonality. The second stage (7.02-6.70 Ma) points to unfavourable bottom-water condition, triggered by deep-sea stagnation. This is witnessed by a significant decrease in oxygen concentration and biotic diversity, and by the presence of stress-tolerant taxa. A general warming of the surface water and a strongly stratified water column, characterized by an expanded mixed layer, are also recorded.From 6.70 Ma onwards (third stage), a prominent change to more restricted, low-oxygenated, hypersaline conditions at the sea floor is testified by the total disappearance of deep-dwelling planktonic foraminifers and the increasing abundance of stress-tolerant species. Calcareous plankton reflects high instability of the surface water in terms of nutrients, temperature and salinity. During this stage the environmental deterioration reaches intermediate depths in the water column.The initial change toward a step-wise isolation of the Central Mediterranean bottom-waters is probably related to a general warming, responsible for a first slowing-down of the vertical circulation, favouring stratification of surface and intermediate waters and stagnation of bottom-waters. This warming is related to the restricted connection between the Mediterranean Sea and the Atlantic Ocean, which occurred since 7.146 Ma.In the Trave section, the isolation of bottom-waters most likely occurred at the same time as in other Mediterranean sections. However, due to the presence of a hiatus it cannot be excluded that it occurred with a delay of ~ 100 kyr, probably related to the shallower paleodepth of the basin.