454焦磷酸测序技术对不同猪种肠道菌群差异的分析（英文）

454焦磷酸测序用于分析比较巴马香猪(BAMA)、黑香猪(BLACK)与外三元猪(CROSS)的肠道菌群差异。结果表明:三个猪种的肠道细菌多样性与丰度各有不同,差异较大。威克氏菌属、丛毛单胞菌属与光岗菌属等病原菌在BAMA肠道内检测到,而在BLACK与CROSS肠道内未检测到。BAMA肠道中丝状杆菌属与瘤胃球菌属等纤维素分解菌的多样性与丰度远大于在BLACK与CROSS肠道中的分布量。BAMA肠道内高含量的潜在病原菌与纤维分解菌表明BAMA对恶劣环境的适应性与抗病力较强,以及耐粗饲性强,容易饲养管理。     

Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw

Addition of organic matter such as livestock manures and plant residues is a feasible practice to mitigate soil degradation caused by long-term application of chemical fertilizers, and the mitigation is largely mediated though activities of the soil-dwelling microorganisms. However, the roles of different kinds of organic matter in maintaining bacterial community structure have not been assessed in a comparative manner. In this study, 454 pyrosequencing of 16S rRNA gene was employed to compare the bacterial community structure among soils that had been subjected to 30 years of NPK fertilization under six treatment regimes: non-fertilization control, fertilization only, and fertilization combined with the use of pig manure, cow manure or low- and high-level of wheat straws. Consistent with expectation, long-term application of NPK chemical fertilizers caused a significant decrease of bacterial diversity in terms of species richness (i.e. number of unique operational taxonomic units (OTU)), Faith's index of phylogenetic diversity and Chao 1 index. Incorporation of wheat straw into soil produced little effects on bacterial community, whereas addition of either pig manure or cow manure restored bacterial diversity to levels that are comparable to that of the non-fertilization control. Moreover, bacterial abundance determined by quantitative PCR was positively correlated with the nutritional status of the soil (e.g., nitrate, total nitrogen, total carbon, available phosphorus); however, bacterial diversity was predominantly determined by soil pH. Together, our data implicate the role of livestock manures in preventing the loss of bacterial diversity during long-term chemical fertilization, and highlight pH as the major deterministic factor for soil bacterial community structure.     

基于Special-Base模型检测转基因作物nos/plamid构建特异性

以转基因作物中常见的nos/plamid构建特异性序列为研究对象,通过同源性比较和焦磷酸测序dispensation order设计,建立Special-Base焦磷酸测序检测模型;利用转基因大豆Roundup Ready Soybean和转基因玉米Bt11、GA21、NK603等4种转基因作物为试验材料,针对nos/plamid构建特异性序列设计引物,经复合PCR扩增及焦磷酸测序,验证Special-Base焦磷酸测序检测模型有效性。结果表明:本研究建立的Special-Base焦磷酸测序模型能检测出样品中单一或多种转基因作物成分,提高了转基因作物检测的精确性、检测通量和自动化程度。     

长期围封对不同放牧强度下草地植物和AM真菌群落恢复的影响

为探明人为干扰对草地生态系统生态恢复的影响,以不同放牧强度试验草地为研究对象,调查了围封14a后草地植物群落的多样性,并应用第二代高通量测序技术454测序法分析了植物根际土壤中AM真菌的群落结构。研究结果显示,14a围封保育使得不同放牧强度小区与长期封育小区植被盖度及植物多样性指数基本恢复至同一水平。土壤速效磷含量在重度放牧小区最低(1.00 mg/kg),轻度放牧区最高(2.25 mg/kg),其它土壤理化性质指标在不同小区之间没有显著差异。通过分子鉴定发现所有土壤样品中AM真菌共有87个分类单元(VT),隶属于Diversispora、Otospora、Scutellospora、Glomeraceae Glomus、Rhizophagus、Paraglomus和Archaeospora 等7个属。对不同放牧强度小区AM真菌进行多样性分析,结果表明长期封育小区AM真菌Shannon多样性指数和Pielou均匀度指数最低,且显著低于中度放牧区,而AM真菌多样性在各放牧小区之间差异不显著。本研究表明长期围封可以有效促进退化草地植物群落的恢复,而AM真菌表现出与植物群落恢复的不同步性。对于草地生态系统退化及恢复过程中植物和土壤功能微生物类群的协同关系还需要进一步系统深入的研究。     

稻作条件下不同施肥模式对盐碱化土壤细菌和古菌群落结构的影响

为探讨稻作条件下不同施肥模式对盐碱化土壤细菌和古菌群落结构的影响,实验选取脱硫废弃物(T1)、脱硫废弃物和有机肥混合不同梯度(T2、T3和T4)4个施肥处理盐碱土壤,不施肥土壤(CK)作为对照,利用Illumina Hiseq高通量测序技术解析不同处理土壤特性和细菌、古菌群落结构关系的特征,并对细菌和古菌群落结构与环境因子进行相关性分析。试验结果表明:与CK相比,4种处理均降低了古菌多样性,T2、T3和T4处理增加了细菌的多样性;变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)是所有土样中的优势菌群,占细菌总量的25.7%~31.2%和22.9%~28.1%。施用脱硫废弃物和有机肥料的处理Proteobacteria相对丰度提高了14.0%~36.4%,T1处理降低了9.2%。T1、T2和T3处理的Euryarchaeota相对丰度提高了41.6%~115.2%。不同施肥处理土壤细菌和古菌群落结构存在显著差异。施用脱硫废弃物和有机肥改变了土壤化学性质,其中T4提高了有机碳(6.74%)、碱解氮(37.20%)、速效磷(47.83%)和铵态氮(96.26%)。RDA分析结果显示,硝态氮对土壤细菌和古菌群落结构的影响最大,其次分别是全磷、pH、速效钾、电导率。研究解析了稻作条件下不同施肥模式对盐碱化土壤细菌和古菌群落结构的特征,确定了影响土壤细菌和古菌区系的主效环境因子,脱硫废弃物与有机肥最佳配比模式为T4处理组,该处理不仅提高了土壤养分含量,同时也增加了土壤细菌的多样性,有利于维持良好的土壤生态环境。     

Bacterial diversity in the sediment of Crescent Moon Spring,Kumtag Desert,Northwest China

Desert lake, a unique oasis in desert ecosystems, harbours different bacterial communities. Thus, it is considered as a hub of bacterial diversity. In this study, bacterial diversity in the sediment of Crescent Moon Spring, Kumtag Desert, Northwest China was analyzed using high-throughput amplicon pyrosequencing analysis. The sequences of the most abundant OUTs(Operational Taxonomic Units) in the sediment of Crescent Moon Spring were compared with the sequences of those most abundant OUTs of various origins from NCBI Gen Bank database to detect the origins of bacteria in the sediment of Crescent Moon Spring. Also, bacterial compositions between sediment of Crescent Moon Spring and other desert and lake ecosystems(including desert lakes) worldwide were compared using cluster analysis to determine the possible factors affecting bacterial compositions. In total, 11,855 sequences were obtained and 30 phyla were identified. At the phylum level, the dominant phylum was Proteobacteria with α-Proteobacteria being the first dominant class and the second dominant phylum was Planctomycetes. Our finding that α-Proteobacteria being the first dominant class of Proteobacteria and Planctomycetes being the second dominant phyla are somewhat contradictory with reports from other desert lake sediments. This difference could be resulted from water hydration and conductivity, as well as oligotrophic conditions of Crescent Moon Spring. At the genus level, Rhodobacter, Caldilinea, Planctomyces, and Porphyrobacter were the dominant genera in the sediment of Crescent Moon Spring. Comparisons on sequences of the most abundant OUTs(including OTU3615, OTU6535, and OTU6646) between sediment of Crescent Moon Spring and various origins from NCBI Gen Bank database indicate that the origins of bacteria in the sediment of Crescent Moon Spring are likely from the underground water. Furthermore, cluster analysis on comparisons of bacteria compositions between sediment of Crescent Moon Spring and other desert and lake ecosystems(including desert lakes) worldwide shows that at regional scales, bacterial compositions may be mainly affected by geographical patterns, precipitation amounts, and p H values. Collectively, our results provide new knowledge on the bacterial diversity in desert lake ecosystems.     

Effect of dietary supplementation of probiotic on performance and intestinal microflora of Chinese soft‐shelled turtle (Trionyx sinensis)

This experiment was conducted to study the effect of dietary supplementation of probiotic on performance and intestinal microflora of Chinese soft‐shelled turtle. Healthy Chinese soft‐shelled turtles (6000 pieces with average weight of 5 g) were selected and randomly divided into two groups: control and treatment with three replicates each. The control was fed on normal basal diet, whereas treatment was fed on basal diet supplemented with 1 × 10⁸ cfu.g^?1 Bacillus subtilis preparation. The results showed that the final mean weight of treatment (265.84 ± 3.48 g) was significantly higher (P < 0.05) than that of control (240.45 ± 4.32 g). There was significant difference (P < 0.05) in FCR, and DGs were obtained in probiotics fed group as compared to control. The level of sucrase, maltase, amylase, lipase and ATPase of treatment was significantly higher (P < 0.05) than that of control. Pyrosequencing showed that the dietary supplementation of probiotic Bacillus strain decreased microbial diversity. Phylum Firmicutes was dominant in both groups. Compared with the control, Firmicutes was increased, while others were decreased in treatment group. The results indicated that dietary supplementation of probiotic can improve growth performance, digestibility and intestinal microflora in Chinese soft‐shelled turtle.     

用焦磷酸测序技术研究猪KIT基因的基因型

为了探讨猪KIT基因等位基因的识别及KIT基因和毛色的关系,为实现猪毛色的定向分子育种奠定基础。以皮特兰、棕色杜洛克、白色杜洛克、长白猪、大白猪、B系猪、荣昌猪、盆周山地猪共8个品种(系)98头猪为试验材料,利用焦磷酸测序技术检测了猪KIT基因第17内含子区第一核苷酸处G→A突变的比例,推测了猪在KIT基因座位上的基因型或基因型组合。结果表明,A/A+G呈现明显的品种特征:棕色杜洛克、盆周山地猪、荣昌猪、皮特兰猪KIT基因A/A+G均在20%以下,推测棕色杜洛克和盆周山地猪在KIT基因座位上的基因型为ii,荣昌猪、皮特兰在KIT基因座位上的基因型为ii、IPi和IPIP;白色杜洛克、大白猪、长白猪、B系猪KIT基因A/A+G呈现散在分布,依据理论基因型下A/A+G将其聚类。通过探讨KIT基因和毛色的关系,证实荣昌猪的全白毛色并非受传统的显性白等位基因控制。     

Pineapple–banana rotation reduced the amount of Fusarium oxysporum more than maize–banana rotation mainly through modulating fungal communities

Continuous cropping with banana results in an enrichment of Fusarium oxysporum f. sp. cubense race 4 (FOC) in soil, causing the soil-borne disease Fusarium wilt. Crop rotation has been an effective method of controlling various soil-borne diseases. However, no information is currently available concerning variations in soil microbial community structure in banana crop rotations. Thus, the influence of two-year crop rotation systems of pineapple–banana and maize–banana on the population density of FOC and soil microbial community structure was investigated to identify which rotation system is more effective in FOC suppression and differences in microbial community composition among different rotations. Bacterial and fungal communities were interrogated by pyrosequencing of the 16 S RNA gene and the internal transcribed spacer (ITS) region. The pineapple–banana rotation was more effective than maize–banana in reducing FOC abundances and suppressing Fusarium wilt disease incidence. Allelopathic effects of pineapple root exudates on FOC were not observed. Greater fungal community variations than bacterial were identified between the two rotation systems, suggesting that fungal communities may play a more important role in regulating FOC abundances. Furthermore, in the pineapple–banana rotation, Acidobacteria, Planctomycetes, Chloroflexi phyla, Gp1, Gp2 and Burkholderia bacterial genera increased while the fungal phyla Basidiomycota, (esp. Gymnopilus) increased and Sordariomycetes decreased. Such changes may be important microbial factors in the decrease in FOC.