Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Here, we examine soil-borne microbial biogeography as a function of the features that define an American Viticultural Area (AVA), a geographically delimited American wine grape-growing region, defined for its distinguishing features of climate, geology, soils, physical features (topography and water), and elevation. In doing so, we lay a foundation upon which to link the terroir of wine back to the soil-borne microbial communities. The objective of this study is to elucidate the hierarchy of drivers of soil bacterial community structure in wine grape vineyards in Napa Valley, California. We measured differences in the soil bacterial and archaeal community composition and diversity by sequencing the fourth variable region of the small subunit ribosomal RNA gene (16S V4 rDNA). Soil bacterial communities were structured with respect to soil properties and AVA, demonstrating the complexity of soil microbial biogeography at the landscape scale and within the single land-use type. Location and edaphic variables that distinguish AVAs were the strongest explanatory factors for soil microbial community structure. Notably, the relationship with TC and TN of the <53 μm and 53–250 μm soil fractions offers support for the role of bacterial community structure rather than individual taxa on fine soil organic matter content. We reason that AVA, climate, and topography each affect soil microbial communities through their suite of impacts on soil properties. The identification of distinctive soil microbial communities associated with a given AVA lends support to the idea that soil microbial communities form a key in linking wine terroir back to the biotic components of the soil environment, suggesting that the relationship between soil microbial communities and wine terroir should be examined further.     

S‐locus diversity and cross‐compatibility of wild Prunus avium for timber breeding

Prunus avium is primarily cultivated for its fruit, sweet cherries. However, it is also used to produce high‐quality timber. In a P. avium seed orchard, gametophytic self‐incompatibility is a restriction for free pollen flow and should be considered when establishing basic forest materials. In this study, S‐locus diversity and cross‐incompatibility of wild cherry individuals in clonal banks established for breeding for timber production were investigated. Wild cherry trees (140) with outstanding forest growth habit, collected in northern Spain, grafted and planted in two clonal banks, were genotyped at the S‐locus. The self‐incompatibility S‐locus genes, S‐RNase and SFB, were analysed by PCR. Twenty‐two S‐haplotypes, resulting in 72 different S‐genotypes, were identified. The genotypes were grouped into 33 incompatibility groups and 39 unique genotypes. This initial S‐locus analysis revealed large genetic diversity of wild cherry trees from the Spanish northern deciduous forest, and provides useful information for seed orchard design. Wild P. avium displays significantly more genetic diversity than what is detected in local cultivars, revealing a narrowing of genetic diversity during local domestication.     

细菌鞭毛蛋白作为佐剂的研究进展

细菌鞭毛蛋白作为Toll样受体5(TLR5)或NOD样受体C4(NLRC4)的配体,其结构决定了其既有抗原性又具有佐剂效应。将细菌鞭毛蛋白与外源抗原混合或融合表达,已获得多种有效的候选疫苗。细菌鞭毛蛋白佐剂效应主要是通过TLR5和NLRC4信号途径协同实现的。TLR5位于细胞表面,可触发炎性因子、趋化因子和Ⅰ型干扰素的分泌,启动天然免疫应答。NLRC4是细胞质中的模式识别受体,可识别细胞质中的多种配体并诱导相应免疫应答。另外,细菌鞭毛蛋白能募集T淋巴细胞和B淋巴细胞至次级淋巴器官,促进DCs和T淋巴细胞的活化。细菌鞭毛蛋白的可塑性将会使得以细菌鞭毛蛋白为基础的疫苗成为当前和未来研究的热点。     

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO₂ respiration were determined. The second manure input resulted in higher CO₂ respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.     

普通荞麦染色体的原位PCR技术研究

[目的]探索一种适合荞麦的简单易行的染色体原位PCR技术。[方法]采用16S套式引物、4．5S套式引物与psbA引物，以栽培甜荞为材料，进行染色体原位PCR、原位套式PCR与多次原位PCR试验。[结果]高温干燥可以起到与包埋类似的作用；染色体的原位套式PCR效果比原位PCR明显，多次原位PCR次数为5-6效果较佳。16S引物和4．5S引物均显示了4对信号，但位置不同；而psbA引物是单拷贝的，仅显示出1对信号。根据这些信号的位置差异可以区分普通荞麦的5对染色体。[结论]所使用的荞麦染色体原位PCR技术简单易行。     

鲍曼不动杆菌雏鸡分离株CCGGD201101的分离、鉴定及致病性研究简

试验旨在鉴定吉林省某雏鸡孵育基地病死雏鸡组织中分离出的1株致病性菌CCGGD201101株并测定其致病性。对疑似致病菌进行生理生化试验、16S rDNA测序鉴定，并人工接种昆明鼠，测定其半数致死量，验证细菌毒力。经鉴定该菌为鲍曼不动杆菌（Acinetobacter baumannii）。以鲍曼不动杆菌CCGGD201101分离株为研究对象，并以鲍曼不动杆菌标准株（ATCC 19606）为对照，测得半数致死量，进一步证明鲍曼不动杆菌病死鸡分离株CCGGD201101具有较强致病性。     

基于RFID技术的电动车充电系统

本文设计了基于RFID技术的一种刷卡式的充电服务终端硬件装置,实现刷卡自动计费。本程序以AT89S52单片机为主控制器,用MFRC500射频识别芯片进行识别,并与射频卡进行通信。     

秸秆纤维素分解细菌的筛选与鉴定

利用纤维素琼脂选择培养基和刚果红染色方法,从不同来源的土样中分离出2个菌株,测定了其纤维素酶活性、小麦秸秆降解能力,并对纤维素降解能力强的两个菌株进行了分子鉴定。结果表明,两株高效纤维素分解菌在纤维素刚果红培养基上均能形成透明水解圈,利用16S r RNA序列测序并分析Genbank中的同源性,结合形态和理化性质确定为Bacillus thuringiensis和Bacillus anthracis。在37℃,p H为7的条件下测定了纤维素酶活力,SC1-3和XR2-5-4分别为1.41和1.59。这两株37℃下经15 d后小麦秸秆失重率达19.92%和22.83%。     

Mapping soil salinity and pH across an estuarine and alluvial plain using electromagnetic and digital elevation model data

Increasing pressures from agriculture and urbanization have resulted in drainage of many floodplains along the eastern Australian coastline, which are underlain by sulphidic sediments, to lower water tables and reduce soil salinity. This leads to oxidation of the sediments with a rapid decline in pH and an increase in salinity. Accurately mapping soil salinity and pH in coastal acid sulphate soil (CASS) landscapes is therefore important. One required map is the extent of highly acidic (i.e. pH < 4.5) areas, so that the application of alkaline amendments (e.g. lime) to neutralize the acid produced can be specifically targeted to the variation in pH. One approach is to use digital soil mapping (DSM) using ancillary information, such as an EM38, digital elevation models (DEM – elevation) and trend surface parameters (east and north). We used an EM38 in the horizontal (EM38h) and vertical (EM38v) modes together with elevation data to develop multiple linear regressions (MLR) for predicting EC_1:5 and pH. For pH, best results were achieved when the EM38 EC_a data were log‐transformed. By comparing MLR models using REML analysis, we found that using all ancillary data was optimal for mapping EC_1:5, whereas the best predictors for pH were north, log‐EM38v and elevation. Using residual maximum likelihood (REML), the final EC_1:5 and pH maps produced were consistent with previously defined soil landscape units, particularly CASS. The DSM approach used is amenable for mapping saline soils and identifying areas requiring the application of lime to manage acidic soil conditions in CASS landscape.     

Devastation of sesame (Sesamum indicum L.) crops in different agroclimatic zones of India by genetically diverse subgroups of phytoplasma

The sesame crop is highly susceptible to infection by phytoplasmas, a class of cell wall-less plant pathogenic bacteria (Mollicutes), which is responsible for widespread loss of sesame crops in both North and South India in recent years. Therefore, characterizing the pathogen population is required before the control measures can be devised and implemented. With molecular tools based on nested polymerase chain reaction (PCR) assays, sequencing, restriction profiling, and phylogenetic analysis, phyllody-affected sesame plants collected from nine different states of India were found to be infected by phytoplasmas belonging to two 16Sr groups, namely 16SrI and II. Two subgroups of phytoplasma −16SrI-B and 16SrII-D— were prevalent in symptomatic sesame samples collected from North India, whereas phytoplasma of only the 16SrII group was found in South India. However, the latter samples were diverse, belonging to three different subgroups (16SrII-A, II-C, and II-D). In addition, yearly phyllody-affected sesame samples from Delhi for 4 consecutive years (2007–2010) showed variation in the infecting phytoplasma: the subgroup 16SrII-D was detected in samples collected in 2007, and 16SrI-B was predominantly found in the samples collected in the subsequent years. The study also provides molecular evidence for the association between 16SrI-B phytoplasma and different symptoms in sesame crops such as fasciation, little leaf, and stunting. This is the first study to report the association of the phytoplasma subgroups 16SrII-A and II-D with sesame crops in India. This study provides a baseline for designing specific detection and molecular analysis strategies for quarantine purposes. It also highlights the need for examining the dynamics of seasonal or location-specific variation in vector populations to determine the pattern of infection outbreaks.