Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri-udic ferrosols with pH (H(2)O) ranging from 3.7 to 6.0, was sampled in summer and winter from long-term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia-oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira-like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long-term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of both AOB and AOA in the cycling of nitrogen and other nutrients in terrestrial ecosystems.     

引入显式水分子对接提高蛋白质配体复合物结构的预测精度

在蛋白质复合物界面一般都会存在着一定量的水分子,这些水分子通过空间占据和氢键方式影响蛋白质与配体的位置关系。应用现有的计算机方法研究蛋白质-配体对接时,一般不会显式地考虑水分子的作用。本文显式地将水分子引入蛋白质-配体对接过程,考虑水分子空间占据和氢键能量对复合物对接结构的影响,提出了一种包含水分子的蛋白质-配体对接算法。实验结果表明引入水分子使蛋白质-配体对接质量有明显提高。     

Factors influencing soil enzyme activity in China’s forest ecosystems

Enzyme activity (EA) mediates soil organic matter (SOM) degradation, transformation, and mineralization, thereby maintaining the biogeochemical cycles and energy flow of ecosystems. To determine the main factors explaining EA variations in China’s forest ecosystems, we created a database of soil EAs and relevant variables using data from the literature and analysed relationships between EAs and both climatic and edaphic variables. Catalase, phenol oxidase, acid (alkaline) phosphatase, and protease activities differed significantly among different types of forests. Catalase and urease activities were generally higher in primosols, cambisols, and argosols than in ferrosols. EA largely decreased with soil depth and increased with SOM. Phenol oxidase and urease activities were negatively correlated with mean annual temperature (MAT); in contrast, catalase, invertase, and protease activities first decreased (< 2.5 °C), increased (2.5–17.5 °C), and then decreased (> 17.5 °C) with increasing MAT. Although protease activity was slightly positively correlated with mean annual precipitation (MAP), catalase, phenol oxidase, and urease activities were all negatively related to MAP. Catalase, invertase, acid (alkaline) phosphatase, urease, and protease activities first increased (< 2000 m.a.s.l.) and then decreased (2000–4100 m.a.s.l.) with increasing elevation. Principal component analysis revealed most EAs to be correlated with climate conditions and soil pH. These findings suggest that climatic and edaphic variables directly and indirectly correlate with forest type and greatly impact soil EA.     

<Emphasis Type="Italic">Pm61</Emphasis>: a recessive gene for resistance to powdery mildew in wheat landrace Xuxusanyuehuang identified by comparative genomics analysis

Key message

A single recessive powdery mildew resistance gene Pm61 from wheat landrace Xuxusanyuehuang was mapped within a 0.46-cM genetic interval spanning a 1.3-Mb interval of the genomic region of chromosome arm 4AL.

Abstract

Epidemics of powdery mildew incited by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt) have caused significant yield reductions in many wheat (Triticum aestivum)-producing regions. Identification of powdery mildew resistance genes is required for sustainable improvement of wheat for disease resistance. Chinese wheat landrace Xuxusanyuehuang was resistant to several Bgt isolates at the seedling stage. Genetic analysis based on the inoculation of Bgt isolate E09 on the F₁, F₂, and F_2:3 populations produced by crossing Xuxusanyuehuang to susceptible cultivar Mingxian 169 revealed that the resistance of Xuxusanyuehuang was controlled by a single recessive gene. Bulked segregant analysis and simple sequence repeat (SSR) mapping placed the gene on chromosome bin 4AL-4-0.80-1.00. Comparative genomics analysis was performed to detect the collinear genomic regions of Brachypodium distachyon, rice, sorghum, Aegilops tauschii, T. urartu, and T. turgidum ssp. dicoccoides. Based on the use of 454 contig sequences and the International Wheat Genome Sequence Consortium survey sequence of Chinese Spring wheat, four EST-SSR and seven SSR markers were linked to the gene. An F₅ recombinant inbred line population derived from Xuxusanyuehuang?×?Mingxian 169 cross was used to develop the genetic linkage map. The gene was localized in a 0.46-cM genetic interval between Xgwm160 and Xicsx79 corresponding to 1.3-Mb interval of the genomic region in wheat genome. This is a new locus for powdery mildew resistance on chromosome arm 4AL and is designated Pm61.

     

Overexpression of a Common Wheat Gene <Emphasis Type="Italic">GALACTINOL SYNTHASE3</Emphasis> Enhances Tolerance to Zinc in <Emphasis Type="Italic">Arabidopsis</Emphasis> and Rice Through the Modulation of Reactive Oxygen Species Production

Galactinol synthase (GolS, EC 2.4.1.123), a key enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs), plays roles in plant growth and developmental processes. The in vitro roles of GolS in plant responses against heavy metal stress are not well clarified. In the present study, a suppression-subtractive hybridization (SSH) cDNA library has been constructed using RNA extracted from wheat cultivar Jinan 18 treated with ZnCl₂ as the tester and RNA from untreated seedlings as the driver. Sixteen expressed sequence tags (ESTs) highly homologous with known proteins associated with stress tolerance have been obtained. Among these, a 1000-bp cDNA sequence encoding GolS protein has been isolated and designated as TaGolS3. Real-time quantitative PCR (qPCR) analysis revealed that TaGolS3 was mainly expressed in young roots and upregulated by exogenous ABA treatment and several abiotic stresses, such as ZnCl₂, CuCl₂, low temperature, and NaCl. Subcellular localization analysis showed that TaGolS3 protein is a nuclear-localized protein. A detailed analysis of Arabidopsis and rice transgenic plants overexpressing TaGolS3 gene displayed that transgenic plants exhibited increased lateral root number, primary root length, plant survival rate, and plant height. Moreover, in comparison with the wild-type (WT) plants, the TaGolS3-overexpressing lines showed a higher expression of ROS-scavenging genes, activities of antioxidative enzymes, proline contents, and a lower level of malondialdehyde (MDA) contents and electrolyte leakage under zinc stress. These results confirmed the positive roles of TaGolS3 in improving plant tolerance to heavy metal stress, indicating a potential resource in the transgenic breeding to enhance heavy metal stress tolerance in crop plants.     

The Functional and Regulatory Mechanisms of the Thellungiella salsuginea Ascorbate Peroxidase 6 (TsAPX6) in Response to Salinity and Water Deficit Stresses

Soil salinization is a resource and ecological problem in the world. Thellungiella salsuginea is becoming a new model plant because it resembles its relative species, Arabidopsis thaliana, in small genome and short life cycle. It is highly tolerant to salinity and drought stresses. Ascorbate peroxidase (APX) is an enzyme that clears H₂O₂ in plants. The function and molecular and regulation mechanisms of APX in T. salsuginea have rarely been reported. In this study, an APX gene, TsApx6, was cloned from T. salsuginea and its responses to abiotic stresses in transgenic Arabidopsis were studied. Under high salinity treatment, the expression of TsApx6 was significantly induced. Under drought treatment, overexpression of TsApx6 increased the survival rate and reduced leaf water loss rate in Arabidopsis. Compared to the wild type plants, high salinity treatment reduced the concentrations of MDA, H₂O₂ and proline but elevated the activities of APX, GPX, CAT and SOD in the TsApx6-overexpressing plants. Meanwhile, germination rate, cotyledon greening, and root length were improved in the transgenic plants compared to the wild type plants under salt and water deficit conditions. Based on these findings, TsApx6 has an important function in the resistance of plants to certain abiotic stresses. The TsApx6 promoter sequence was obtained using Genome Walking technology. Bioinformatics analysis indicated that it contains some cis-acting elements related to stress response. The treatments of salt, dehydration, and ABA induced the expression of Gus gene under the regulation of the TsApx6 promoter. Mutation analysis showed that the MBS motif present in the TsApx6 promoter might be a key negative regulatory element which has an important effect on the growth and developmental process of plants.     

Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study

Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality worldwide in children aged <5 years and older adults with acute lower respiratory infections (ALRIs). However, few studies regarding the epidemiology of hospitalizations for RSV infection have been performed previously in China. Here, we aimed to describe the clinical and epidemiologic characteristics of hospitalized patients with laboratory-confirmed RSV infection in eastern China. Active surveillance for hospitalized ALRI patients using a broad case definition based on symptoms was performed from 2009–2013 in 12 sentinel hospitals in eastern China. Clinical and epidemiologic data pertaining to hospitalized patients of all ages with laboratory-confirmed RSV infection by PCR assay were collected and analyzed in this study. From 2009 to 2013, 1046 hospitalized patients with laboratory-confirmed RSV infection were enrolled in this study, and 14.7% of patients had subtype A, 24.2% of patients had subtype B, 23.8% of patients with subtype not performed, and 37.3% of patients had RSV coinfections with other viruses. RSV and influenza coinfections (33.3%) were the most common coinfections noted in this study. Moreover, young children aged <5 years (89.1%, 932/1046), particularly young infants aged <1 year (43.3%, 453/1046), represented the highest proportion of patients with RSV infections. In contrast, older adults aged ≥60 years (1.1%, 12/1046) represented the lowest proportion of patients with RSV infections among enrolled patients. The peak RSV infection period occurred mainly during autumn and winter, and 57% and 66% of patients exhibited symptoms such as fever (body temperature ≥38°C) and cough separately. Additionally, only a small number of patients were treated with broad-spectrum antiviral drugs, and most of patients were treated with antimicrobial drugs that were not appropriate for RSV infection. RSV is a leading viral pathogen and a common cause of viral infection in young children aged <5 years with ALRIs in eastern China. Effective vaccines and antiviral agents targeting RSV are needed to mitigate its large public health impact.     

The COVID-19 outbreak in Sichuan,China: Epidemiology and impact of interventions

In January 2020, a COVID-19 outbreak was detected in Sichuan Province of China. Six weeks later, the outbreak was successfully contained. The aim of this work is to characterize the epidemiology of the Sichuan outbreak and estimate the impact of interventions in limiting SARS-CoV-2 transmission. We analyzed patient records for all laboratory-confirmed cases reported in the province for the period of January 21 to March 16, 2020. To estimate the basic and daily reproduction numbers, we used a Bayesian framework. In addition, we estimated the number of cases averted by the implemented control strategies. The outbreak resulted in 539 confirmed cases, lasted less than two months, and no further local transmission was detected after February 27. The median age of local cases was 8 years older than that of imported cases. We estimated R₀ at 2.4 (95% CI: 1.6–3.7). The epidemic was self-sustained for about 3 weeks before going below the epidemic threshold 3 days after the declaration of a public health emergency by Sichuan authorities. Our findings indicate that, were the control measures be adopted four weeks later, the epidemic could have lasted 49 days longer (95% CI: 31–68 days), causing 9,216 more cases (95% CI: 1,317–25,545).     

五大连池火山色木槭叶功能性状特征

植物功能性状反映了植物对生长环境的响应和适应, 是连接植物与环境的桥梁, 研究植物功能性状特征及其随坡向的变化规律, 对认识不同微地形生境下植物群落空间格局形成及适应机制具有重要意义。本文以五大连池不同历史年代的8座火山共有树种色木槭(Acer mono)为研究对象, 测定了9类叶功能性状, 研究了植物叶功能性状在火山间及火山坡向间(阴坡-阳坡)的变化规律, 以期揭示生境对火山植物主要叶功能性状的影响, 以及阴阳坡植物生存策略的变化, 初步探讨了植物对环境的适应机制。结果表明: (1)坡向的变化是造成色木槭叶功能性状差异的重要原因; (2)火山间叶功能性状的差异反映了它们具有不同的资源环境, 色木槭生长主要受氮元素的限制; (3)南北坡向及火山间叶片厚度与叶面积均呈极显著的正相关关系, 叶片厚度与比叶面积在不同火山间均呈显著的正相关关系, 这与色木槭在火山土壤条件下的自我保护密切相关, 色木槭通过这些指标间的功能调节来适应环境的变化, 并形成最佳功能组合。五大连池不同历史年代火山的色木槭采用增加植物叶片叶干物质浓度、叶面积、叶片厚度、叶氮和叶磷浓度提高固碳能力, 通过降低比叶面积和氮磷比来适应干旱、土壤养分贫瘠的环境。