传染性造血器官坏死病毒焦磷酸测序检测技术的建立

根据传染性造血器官坏死病毒(IHNV)基因序列,设计了IHNV最为保守的指纹序列,以及测序引物,建立了IHNV焦磷酸测序检测方法。对所构建的IHNV焦磷酸检测方法进行特异性试验和灵敏度检测。结果表明,所建立的方法特异性好,在8种鱼类病毒中能够特异性检测出目的病毒,检测方法灵敏度高,最低检出核酸量为10pg/μL。对建立的焦磷酸测序检测方法进行了实际应用研究,选取国内采集与进口的鱼类样本共计80批次进行IHNV检测。结果显示,焦磷酸测序检测方法可以有效的检出常规RTPCR不能检出的假阴性样本和弱阳性样本,该方法的灵敏度和特异性可以满足水生动物疫病检测的需要。     

Effects of different dietary copper sources on the growth and intestinal microbial communities of Pacific white shrimp (Litopenaeus vannamei)

An 8‐week feeding trial was conducted to evaluate the effects of dietary copper sources on growth performance and intestinal microbial communities of juvenile Pacific white shrimp (Litopenaeus vannamei). Four isonitrogenous (420 g/kg crude protein) and isolipidic (70 g/kg crude lipid) experimental diets were formulated to contain different copper sources, Diet NSC (no‐supplemented copper), Diet CS (copper sulphate), Diet Availa (copper amino acid complex from Availa^®Cu100) and Diet M (1:1, copper sulphate + copper amino acid complex). A total of 360 Pacific white shrimp juveniles (initial weight: 1.86 ± 0.03 g) were randomly allocated into four groups, with three replicates per group and 30 shrimps each replicate. An Illumina‐based sequencing method was used to analyse the intestinal bacterial composition of shrimp juveniles. The results revealed that shrimps fed Diet M had significantly higher percent weight gain (PWG) than that fed Diet NSC and Diet CS, while there were no significant differences between Diet M and Diet Availa. Survival was not affected by the dietary copper sources. Proteobacteria and Bacteroidetes were dominant in the intestines of Pacific white shrimp. Shrimps fed Diet M and Diet Availa had higher bacterial richness and diversity than those fed Diet NSC and Diet CS with no significant differences among all treatments. Furthermore, Diet M and Diet Availa which contained copper amino acid complex reduced the relative abundance of Vibrionaceae in shrimp intestinal tract. This study indicated that dietary copper sources could affect the intestinal microbial communities and diets supplemented with Availa^®Cu100 could have a positive impact on the growth performance and decrease the potential risk of disease in Pacific white shrimp.     

不同季节土庄绣线菊根围丛枝菌根真菌群落差异性研究

土庄绣线菊(Spiraea pubescens)是内蒙古大青山干旱生态系统重要的护土灌木,研究季节变化对土庄绣线菊根围丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)群落的影响,有助于进一步探讨AMF在土庄绣线菊生长发育过程中发挥的作用。采用传统染色检测与Illumina Mi Seq测序相结合的方法,研究季节变化对内蒙古大青山土庄绣线菊AMF侵染率、孢子密度、丰富度、多样性和群落组成的影响。结果显示:在春季、夏季和秋季,AMF侵染率和丛枝丰度不存在显著差异,而孢子密度却存在显著差异。AMF丰富度和多样性在夏季显著低于春季和秋季,但在春季和秋季间差异并不显著;主成分分析(principal coordinate analysis,PCo A)和PERMANOVA分析表明,春季和秋季AMF群落组成与夏季存在显著差异,而在春季和秋季间差异并不显著。     

Intestinal Microbiota in Large Yellow Croaker,Larimichthys crocea,at Different Ages

The polymerase chain reaction–denaturing gradient gel electrophoresis (PCR‐DGGE) of 16S ribosomal RNA gene was used to investigate bacterial communities in the intestines of large yellow croaker at six different ages (12 d, 18 d, 26 d, 40 d, 3 mo, and 1 yr old) as well as within the corresponding feed and culture water. In addition, Illumina Miseq sequencing was utilized to compare intestinal microbiota between 12‐d‐old and 1‐yr‐old individuals. PCR‐DGGE results revealed that the culture water had the highest bacterial diversity, followed by the feed, while the intestines had the lowest diversity. The intestinal microbiota at six ages changed severely; however, the change did not follow any trend. The large yellow croaker intestines harbored specific bacterial communities that differed from those in both feed and water. Illumina Miseq sequencing results revealed that the diversity of intestinal bacteria in 12‐d‐old fish was higher than that in 1‐yr‐old fish, and the bacterial composition differed significantly between them. γ‐Proteobacteria and Pseudoalteromonas supplied the most abundant phylum and genus in the 12‐d‐old fish intestine. However, in the 1‐yr‐old fish intestine, Firmicutes and Clostridium were the most dominant, respectively. The study may contribute to a better understanding of gut microbiota and dynamics of the large yellow croaker and the relationship with their surrounding environment.     

Within‐ and across‐breed imputation of high‐density genotypes in dairy and beef cattle from medium‐ and low‐density genotypes

The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower‐ to higher‐density genotypes in dairy and beef cattle. High‐density genotypes consisting of 777 962 single‐nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein‐Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower‐ to higher‐density genotype platforms was undertaken within and across breeds exploiting population‐wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD.     

白菜型油菜和菜薹的InDel 标记开发及其RILs群体遗传连锁图谱的构建

 通过白菜型油菜‘R-O-18’和菜薹‘L58’的基因组重测序数据与白菜基因组的参考序列（‘Chiifu-401-42’的基因组序列）的比对,在全基因组范围内检测到了18 479 个短插入缺失变异位点（≤5 bp）。从中挑选了500 个插入/缺失片段为4 ~ 5 bp 的InDel 变异位点,将其设计成InDel 分子标记并进行试验验证,结果有452 个标记通过PCR 扩增出单一条带,但仅有106 个在‘R-O-18’和‘L58’间表现出多态性,346 个没有多态性,48 个在PCR 中没有扩增。亲本间具有多态性的106 个InDel 标记可用来检测以‘R-O-18’和‘L58’为亲本构建的RILs 基因型,并构建了一张包含99 个标记的遗传连锁图谱。     

饲粮中性洗涤纤维/淀粉比值对荷斯坦公牛瘤胃古菌和甲烷排放量的影响

本试验旨在通过Illumina HiSeq测序技术和实时定量PCR研究饲粮中性洗涤纤维(NDF)/淀粉比值对荷斯坦公牛瘤胃古菌和甲烷排放量的影响.选取36头体重[(282±37)kg]相近、健康的荷斯坦奶公牛,随机分为3组,每组12头.各组分别饲喂NDF/淀粉比值为1.13(Ⅰ组)、1.38(Ⅱ组)、1.63(Ⅲ组)的...     

The microbial diversity and structure in peatland forest in Indonesia

The microbial community structure and function under forest in tropical peatlands are poorly understood. In this study, we investigated the microbial community structure and diversity in natural peat swamp forest soil, disturbed peat soil and mineral soil in Central Kalimantan, Indonesia, using 454 pyrosequencing. The results showed that the natural peat soil had the greatest fungal species richness (Chao1), which was significantly (p < .05) larger than that in the other two soils. Community structure of both fungi and bacteria in natural peat soil differed significantly from that in the disturbed peat soil (p = .039 and p = .045, respectively). Ascomycota (40.5%) was the most abundant phylum across the three soils followed by Basidiomycota (18.8%), Zygomycota (<0.1%) and Glomeromycota (<0.1%). The linear discriminant analysis with effect size (LEfSe) showed that Ascomycota (p < .05) and genus Gliocephalotrichum (p < .05) dominated in natural peat soil. Functionally, pathotrophs were more abundant in disturbed peat soil (p < .05). Proteobacteria (43.8%) were the most abundant phylum followed by Acidobacteria (32.6%), Actinobacteria (9.8%), Planctomycetes (1.7%). Methylocystis, Telmatospirillum, Syntrophobacter, Sorangium and Opitutus were the more abundant genera in disturbed peat soil, whereas Nevskia and Schlesneria were more abundant in mineral soil and natural peat soil, respectively. The natural peat forest soil supported a more diverse microbiology; however, the land use of such a soil can change its microbial community structure. The results provide evidence that the disturbance of tropical peat land could lead to the introduction and spread of a large number of fungal diseases     

Fine root decomposition,nutrient mobilization and fungal communities in a pine forest ecosystem

Despite its importance to energy flow and nutrient cycling the process of fine root decomposition has received comparatively little detailed research. Disruption of the fine root-soil interface during preparation of root litterbags for decomposition studies could affect decay rates and nutrient mobilization in part by altering the community of decay organisms. We compared rates of decomposition and nutrient release from fine roots of pine between litterbags and intact cores and characterized the fungal community in the decomposing roots. Fine root decomposition was about twice as fast overall for intact cores than litterbags, and rapid mobilization of N and P was observed for roots in cores whereas nutrients were immobilized in litterbags. Fungal communities characterized using 454 pyrosequencing were considerably different between decaying roots in intact cores and litterbags. Most interesting, taxa from ectomycorrhizal fungal orders such as Boletales, Thelephorales and Cantharellales appeared to be more common in decaying roots from cores than litterbags. Moreover, the rate of N and P mobilization from decaying fine roots was highly correlated with taxa from two orders of ectomycorrhizal fungi (Thelephorales, Cantharellales). Although we caution that DNA identified from the decaying roots cannot be conclusively ascribed to active fungi, the results provide tentative support for a significant role of ectomycorrhizal fungi in decomposition and nutrient mobilization from fine roots of pine.