PCR-DGGE analysis reveals a distinct diversity in the bacterial population attached to the rumen epithelium

Bacteria attached to the rumen epithelium (or epimural community) are not well characterised and their role in rumen functioning is not totally understood. There is just one published report of a clone library from one cow that suggests that this epimural community differs from the bacteria associated with the rumen digestive contents. However, this time-consuming approach is not adapted for examining microbial population changes in groups of animals. In in vivo studies, when samples from several animals have to be analysed simultaneously, a simpler technique has to be used. In this study, a genetic fingerprinting technique, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), was used to characterise the structure of the bacterial population attached to the rumen epithelium. This community was compared with that present in the solid and liquid phases of rumen content under two contrasting diets. Rumen samples were obtained from four forage-fed and four high-concentrate-fed (80 : 20, wheat grain : hay) 5-month-old lambs. After slaughter, samples from five epithelial sites and the solid and liquid digesta phases were taken for DNA extraction and analysis. Bacterial communities were profiled by PCR-DGGE using bacterial-specific 16S rDNA primers. Analysis of the fingerprint revealed that the epithelial community differed from those of rumen content in both diets. As expected, the nature of the feed influenced the bacterial communities from the solid and liquid rumen phases but no diet effect was observed in the rumen epithelial profiles suggesting a strong host effect on this bacterial population. Additionally, no differences were observed among the five epithelial sampling sites taken from each animal. The profile of the bacterial population attached to the rumen epithelium presented a high inter-animal variation, whether this difference has an influence in the function of this community remains to be determined.     

麦田昆虫群落结构及多样性的季节动态

通过2年对麦田昆虫群落的系统调查,共查得昆虫11目、62科1、13种,其中植食类51种、捕食类23种、寄生类24种、腐食和食血类15种,种类数和个体数分别占群落总数的45.13,20.35,21.24,13.27%和92.89,2.19,3.63,1.35%。麦田昆虫群落可划分为4个营养层、6个功能团和19个类群,麦长管蚜Macrosiphum avenae(Fabricius)是绝对的优势种,其数量变动决定着总群落结构和多样性的季节动态。麦田昆虫群落多样性表现为前期和后期高、中期低的时间格局,类群多样性与物种多样性的变化趋势最为相似,可用类群多样性代替物种多样性进行群落分析。     

The intraruminal papillation gradient in wild ruminants of different feeding types: Implications for rumen physiology

Browsing and grazing ruminants are thought to differ in the degree their rumen contents are stratified—which may be due to different characteristics of their respective forages, to particular adaptations of the animals, or both. However, this stratification is difficult to measure in live animals. The papillation of the rumen has been suggested as an anatomical proxy for stratification—with even papillation indicating homogenous contents, and uneven papillation (with few and small dorsal and ventral papillae, and prominent papillae in the atrium ruminis) stratified contents. Using the surface enlargement factor (SEF, indicating how basal mucosa surface is increased by papillae) of over 55 ruminant species, we demonstrate that differences between the SEF_dorsal or SEF_ventral and the SEF_atrium are significantly related to the percentage of grass in the natural diet. The more a species is adapted to grass, the more distinct this difference, with extreme grazers having unpapillated dorsal and ventral mucosa. The relative SEF_dorsal as anatomical proxy for stratification, and the difference in particle and fluid retention in the rumen as physiological proxy for stratification, are highly correlated in species (n = 9) for which both kind of data are available. The results support the concept that the stratification of rumen contents varies among ruminants, with more homogenous contents in the more browsing and more stratified contents in the more grazing species. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.     

武汉地区水生蔬菜昆虫群落结构及动态分析

2008年5月至10月采用目测法与网捕法调查湖北省武汉市水生蔬菜地昆虫群落结构,共采集到11目、48科、104种,共计9169头昆虫,其中,莲缢管蚜Rhopalosiphum nymphacae(L.)、茭白长绿飞虱Prodenia litura(Fabricius)、斜纹夜蛾Saccharosyne procerus(Matsumura)、荸荠白禾螟Scirpophage praelata(Scopoli)以及菱角莹叶甲Galerucella birmanica是主要害虫,蜻蜓、瓢虫是主要天敌昆虫。通过群落结构分析表明:在不同植被类型的水生蔬菜地中,昆虫群落多样性差异较大,水芹的昆虫群落多样性最高,莲藕最低;水芹昆虫群落最稳定,荸荠次之,莲藕昆虫群落多样性前后期低,中期高,茭白前后期高,中期低。     

豚草发生地土壤昆虫群落结构及动态

采用分层取样法、大类群分类法和数理统计方法,研究了普通豚草Ambrosia artemisiifolia和三裂叶豚草A．trifida发生地土壤昆虫的群落结构及动态。共采集土壤昆虫46个科（成虫与幼虫分开单列）,隶属于12个目,其中弹尾目个体数占绝对优势（占土壤昆虫总个体数的80.879%）,其次是膜翅目（8.765%）、鞘翅目幼虫（3.951%）和双翅目虫（3.093%）,其余合计占3.312%。在46个科中,优势类群有3科：棘跳虫科（Onychiuridae）（占土壤昆虫总个体数的32.756%）、鳞跳虫科（Tomoceridae）（18.869%）和节跳虫科（Isotomidae）（18.178%）。土壤昆虫个体数和类群数,随着豚草生长季的推进而增加,8月达到最高值。豚草降低了土壤昆虫的个体数量和群落多样性,根据逐月方差分析和多重比较,8月和9月对照样地土壤昆虫个体数量和多样性指数均显著高于豚草样地。豚草表现出对某些土壤昆虫类群的驱避作用,步甲科（Carabidae）成虫、拟花萤科（Dasytidae）幼虫、叶蝉科（Jassidae）、阎甲科（Histeridae）和管蓟马科（Phloeothripidae）在豚草整个生长季从未在豚草样地中出现。豚草对于土壤昆虫的抑制作用在豚草纯群落和植物生长旺季更为明显。土壤昆虫的垂直分布具有明显的表聚性。     

Molecular diversity analysis of rumen methanogenic Archaea from goat in eastern China by DGGE methods using different primer pairs

Aims:  To screen a pair of primers suitable for denaturing gradient gel electrophoretic (DGGE) analysis of ruminal methanogenic Archaea and to detect the archaeal communities in the rumen of goat.
Methods and Results:  Nine primer pairs for 16S rDNA of methanogenic Archaea , including six for directed polymerase chain reaction (PCR) and three for nested PCR were first evaluated by PCR amplification of the total DNA from rumen fluids and bacteria. The DGGE analysis of rumen fluids was then conducted with three primer sets (344fGC/915r, 1106fGC/1378r and 519f/915rGC) of the nine pairs tested. Good separation and quality of patterns were obtained in DGGE analysis with primer pairs 1106fGC/1378r and 519f/915rGC. A total of 40 DNA fragments were excised from the DGGE gels and their sequences were determined. All fragments belonged to methanogenic Archaea while primer pair 519f/915rGC had better amplification ranges than the other two primer pairs.
Conclusions:  The procedure of DGGE analysis with primer pair 519f/915rGC was more suitable for investigating methanogenic archaeal community in the rumen. The dominant methanogenic Archaea in the rumen of goat was Methanobrevibacter sp. and an unidentified methanogenic Archaea .
Significance and Impact of the Study:  One pair of primers suitable for DGGE analysis of ruminal methanogenic Archaea was obtained and the molecular diversity of ruminal methanogenic Archaea in goat was investigated by PCR-DGGE.     

不同烟草品种烟田捕食性节肢动物群落的结构和动态研究

应用群落结构特性参数和主分量分析对Nc89、Nc82和K326烟田中捕食性节肢动物群落的结构和动态进行了研究.结果表明,蜘蛛和捕食性昆虫构成烟田主要捕食性节肢动物群落,其相对丰盛度分别为83.25%～86.87%和13.13%～16.38%.烟田捕食性节肢动物群落主要类群平均密度(头/8株)品种间差异显著,K326显著高于Nc82,Nc82显著高于Nc89.皿蛛和瓢虫的个体数量在烟田捕食性节肢动物群落中起主导作用.Nc89和Nc82烟田捕食性节肢动物群落的丰富度(S)差异显著,其它群落结构特性指数三品种烟田之间无显著差异.群落丰富度(S)和优势集中性(C)的时序动态三品种烟田呈低高低趋势,多样性(H')和均匀度(E)的时序动态三品种烟田呈高低高趋势.     

Microbial degradation in the rumen of wheat straw and anhydrous ammonia treated wheat straw observed by electron microscopy

With the exception of the phloem and the crown of the parenchyma, which borders the medullary lacuna, the walls of the tissues of both treated and untreated straw were lignified. The walls of the treated straw were not fluorescent in the ultraviolet probably because the treatment had modified the phenolic acids. They also had a stronger reaction to Schiff reagent particularly in the sclerenchyma indicating that their polysaccharides were more accessible. The tissues of the treated straw degraded faster in the rumen. The walls of the sclerenchyma of the treated straw were attacked by micro-organisms. Both treated and normal straw were abundantly colonized by rumen fungi, especially in the sclerenchyma. The increase in the digestibility of the treated straw was due to the greater access the micro-organisms had to the polysaccharides of the lignified walls.     

不同碳源诱导下牦牛瘤胃厌氧真菌Orpinomyces sp. YF3的产酶机制

为探究体外发酵牦牛瘤胃源厌氧真菌Orpinomyces sp. YF3在不同碳源诱导下的产酶机制,本研究利用厌氧培养管在10 mL基础培养基中分别添加不同碳源复杂度的葡萄糖(glucose, Glu)、滤纸(filter paper, Flp)、微晶纤维素(avicel, Avi)各8 g/L作为唯一碳源进行体外发酵,检测发酵液中的纤维降解酶活性和挥发性脂肪酸,并利用转录组学探究Orpinomyces sp. YF3的产酶机制。结果表明葡萄糖诱导下的发酵液中羧甲基纤维素酶、微晶纤维素酶、滤纸酶和木聚糖酶的活性,及乙酸的比例显著升高(P＜0.05),丙酸、丁酸、异丁酸的比例显著降低(P＜0.05)。进一步分析发现与纤维降解酶相关的差异表达基因(differentially expressed genes, DEGs)在Glu组中显著上调。基因本体论(gene ontology, GO)功能富集显示DEGs主要集中在木聚糖酶、纤维素酶、葡萄糖和碳水化合物等的分解代谢过程及相关酶活性,京都基因和基因组百科全书(Kyoto Encyclopedia of Genes and Genomes, KEGG)通路分析富集到的纤维降解酶相关的差异通路主要是淀粉和蔗糖代谢途径、其他聚糖降解途径。以上结果表明,以葡萄糖为碳源底物的Orpinomyces sp. YF3可增加纤维素降解酶活性,提高乙酸比例,通过调控纤维降解酶基因的表达及相关代谢通路来提高对底物的降解能力,提高能量利用效率。这为Orpinomyces sp. YF3在实际生产中的应用提供了理论基础。     

新疆阜康绿洲不同生境土壤动物群落多样性及其季节动态

为了查明阜康绿洲不同生境土壤动物群落多样性特征及其变化动态,2010年4、7、9及11月中旬分别以该绿洲的用材林、防护林、苗圃、耕地、盐碱地、灌木林及荒草地生境为研究对象,采用手捡法、改良干漏斗法和湿漏斗法分离0～20 cm土层中的土壤动物,并分析了不同生境土壤动物的群落结构、分布特征及季节动态.共获得土壤动物1 1098只,共35类,其中线虫类、轮虫类和弹尾类为优势类群.在7种不同生境土壤动物类群、个体数和多样性以及不同季节之间均存在显著差异(P＜0.05),其中Shannon多样性指数依次为用材林＞防护林＞灌木林＞耕地＞盐碱地＞苗圃＞荒草地;时空分布调查发现,不同生境土壤动物群落分布具有明显的表聚性特征,并在不同土层及季节间均有显著性差异(P＜0.05),季节动态变化依次为秋季最多、其次春季和冬季,夏季最少;不同生境土壤动物群落间的Jaccard相似性指数属于中等不相似(处于0.25～0.50).不同生境组间聚类和排序结果表明,将7种不同生境分为人工林生境型、人为干扰生境型、灌木生境型及荒漠生境型4大类型.结果表明,阜康绿洲不同生境土壤动物群落组成和多样性具有明显的生境和季节差异特征.     

Effect of yak rumen content treatments on seed germination of 11 alpine meadow species on the Qinghai-Tibetan Plateau

The Qinghai-Tibetan Plateau is located in the ‘Third Pole’ of the world, characterized by a harsh environment. Despite this, the alpine meadow ecosystem have developed over a wide area but serious grassland degradation is threatening the ecological environment on the Plateau. Recruitment of new plants to the population, via germination and establishment, is vital to plant community survival. Previous work on the seeds in this area has mainly focused on community-wide germination strategies, seed germination characteristics and their correlations with seed size and seed mass. However, there have been no studies on the effects of soaking in rumen contents on the plant seed germination characteristics of alpine meadow species. The present study had two main objectives: (i) to determine the effect of fresh rumen content from yaks on seed germination characteristics and seedling growth of species common to the eastern Tibetan Plateau alpine meadow, and (ii) to develop an effective method to enhance seed germination. Seeds of 11 common species were collected together with fresh rumen content from three yaks that grazed there. Seed germination tests were conducted after they had been soaked in rumen content for one of six soaking periods (12, 24, 36, 48, 60 or 72 h). The seeds were incubated under natural light conditions of 8 h light at 25 °C and 16 h darkness at 15 °C, for the germination period of 34 days. The results showed that seed germination and seedling growth were affected by soaking time, seed coat completeness and seed type. After soaking in rumen content, the germination percentages of scarified (peeled or with the seed coat cut through) seeds of some species (true seeds Oxytropis ochrocephala and Medicago ruthenia var inschanica, nutlet Carex enervis, achenes Anemone rivularis and Polygonum sibiricum) and complete seeds of C. enervis, and A. rivularis were improved but the duration of soaking was also important. Seed germination of caryopsis Achnatherum inebrians (a toxic grass) was significantly inhibited by any exposure to rumen fluids. Scarified seeds generally had higher germination percentages than complete ones after treatment, but with the increase in soaking time, germination percentages declined and scarified seeds were more sensitive to the treatment than the complete seeds. After soaking in yak rumen content, the germination indices of scarified M. ruthenia at 12 h treatment, O. ochrocephala and achene Rumex acetosa at 12–24 h treatment, nutlet Kobresia humilis at 24 h treatment, P. sibiricum at 24–48 h treatment, C. enervis at 12–48 h treatment and A. rivularis at 12–60 h treatment were significantly higher than the control (P < 0.05), while the germination indices of complete C. enervis seeds at 12 h and 36 h treatment, and A. rivularis at 12–60 h treatment were significantly higher compared with the control. The germination indices of other species gradually decreased with the increase in soaking time. We concluded that yak rumen digestion could enhance, inhibit or not affect seed germination and seedling growth of the alpine meadow species, which might influence seedling recruitment, interspecific competition, and the plant community structure of the eastern Tibetan Plateau alpine meadow. Overall, yak digestion has a positive effect on alpine meadow seed germination and seed dispersal.     

Diversity and dynamics of microbial communities in brown planthopper at different developmental stages revealed by high‐throughput amplicon sequencing

The microbiome associated with brown planthopper (BPH) plays an important role in mediating host health and fitness. Characterization of the microbial community and its structure is prerequisite for understanding the intricate symbiotic relationships between microbes and host insect. Here, we investigated the bacterial and fungal communities of BPH at different developmental stages using high‐throughput amplicon sequencing. Our results revealed that both the bacterial and fungal communities were diverse and dynamic during BPH development. The bacterial communities were generally richer than fungi in each developmental stage. At 97% similarly, 19 phyla and 278 genera of bacteria were annotated, while five fungal phyla comprising 80 genera were assigned. The highest species richness for the bacterial communities was detected in the nymphal stage. The taxonomic diversity of the fungal communities in female adults was generally at a relatively higher level when compared to other developmental stages. The most dominant phylum of bacteria and fungi at each developmental stage all belonged to Proteobacteria and Ascomycota, respectively. A significantly lower abundance of bacterial genus Acinetobacter was recorded in the egg stage when compared to other developmental stages, while the dominant fungal genus Wallemia was more abundant in the nymph and adult stages than in the egg stage. Additionally, the microbial composition differed between male and female adults, suggesting that the microbial communities in BPH were gender‐dependent. Overall, our study enriches our knowledge on the microbial communities associated with BPH and will provide clues to develop potential biocontrol techniques against this rice pest.     

麦田昆虫群落的结构与时序动态

采用目测法和网捕法 ,通过对小麦整个生长季节内昆虫群落的系统调查 ,共查得昆虫11目 2 3科 36种 ,其中捕食性昆虫有 4目 5科 12种、寄生性昆虫有 2目 3科 4种、植食性昆虫有 5目 12科 15种、粪食性等其他类昆虫有 1目 3科 5种。在捕食性天敌昆虫中 ,瓢虫的种类和数量最多 ,其次为草蛉和食蚜蝇 ;在寄生性天敌昆虫中 ,蚜茧蜂为优势种 ,其次为寄蝇 ;在植食性昆虫中 ,麦长管蚜为绝对的优势种 ,其次为赤须盲蝽、灰飞虱和麦蓟马。天敌昆虫对害虫具有明显的跟随现象 ,不能有效地控制麦长管蚜的发生与危害。依据昆虫群落的组成与结构 ,结合小麦生育期 ,采用最优分割法将麦田昆虫群落动态划分为 5个阶段 ,并指出不同阶段昆虫群落特点及相应的害虫防治策略。     

Local deformations revealed by dynamics simulations of DNA polymerase Beta with DNA mismatches at the primer terminus

Nanosecond dynamics simulations for DNA polymerase beta (pol beta)/DNA complexes with three mismatched base-pairs, namely GG, CA, or CC (primer/template) at the DNA polymerase active site, are performed to investigate the mechanism of polymerase opening and how the mispairs may affect the DNA extension step; these trajectories are compared to the behavior of a pol beta/DNA complex with the correct GC base-pair, and assessed with the aid of targeted molecular dynamics (TMD) simulations of all systems from the closed to the open enzyme state. DNA polymerase conformational changes (subdomain closing and opening) have been suggested to play a critical role in DNA synthesis fidelity, since these changes are associated with the formation of the substrate-binding pocket for the nascent base-pair. Here we observe different large C-terminal subdomain (thumb) opening motions in the simulations of pol beta with GC versus GG base-pairs. Whereas the conformation of pol beta in the former approaches the observed open state in the crystal structures, the enzyme in the latter does not. Analyses of the motions of active-site protein/DNA residues help explain these differences. Interestingly, rotation of Arg258 toward Asp192, which coordinates both active-site metal ions in the closed "active" complex, occurs rapidly in the GG simulation. We have previously suggested that this rotation is a key slow step in the closed to open transition. TMD simulations also point to a unique pathway for Arg258 rotation in the GG mispair complex. Simulations of the mismatched systems also reveal distorted geometries in the active site of all the mispair complexes examined. The hierarchy of the distortions (GG>CC>CA) parallels the experimentally deduced inability of pol beta to extend these mispairs. Such local distortions would be expected to cause inefficient DNA extension and polymerase dissociation and thereby might lead to proofreading by an extrinsic exonuclease. Thus, our studies on the dynamics of pol beta opening in mismatch systems provide structural and dynamic insights to explain experimental results regarding inefficient DNA extension following misincorporation; these details shed light on how proofreading may be invoked by the abnormal active-site geometry.     

田间不同防治方法对麦蚜种群动态的影响

【目的】从保护生态环境兼顾防治害虫的角度出发,研究不同防治方法对麦蚜种群动态的影响,为麦蚜的田间防治提供理论依据。【方法】本试验分别设置不同的麦蚜防治田(空白对照田、黄板田、糖醋液田、诱芯田、诱虫灯田、综合防治田),在小麦生长期观察不同的防治田内麦蚜的种群动态的变化。【结果】诱虫灯对有翅蚜的防治效果要好于黄板和糖醋液,但对禾谷缢管蚜Rhopalosiphum padi(Linnaeus)有翅蚜的诱捕效果不明显,黄板和糖醋液对有翅蚜和无翅蚜均有防治效果,多种防治方法共同利用对麦蚜种群数量有一定的防治效果。【结论】多种防治方法共同使用的防治效果优于单一防治方法,诱虫灯、糖醋液、黄板、诱芯对不同种类麦蚜的防治效果不同。在田间使用时应注意不同时期采用不同的防治方法。     

Genetic diversity and population structure of Buddleja crispa Bentham in the Himalaya-Hengduan Mountains region revealed by AFLP

Buddleja crispa Benth. is one of the most morphologically variable species in genus Buddleja, and it is widely distributed in the Himalaya-Hengduan Mountains (HHM) region. This study used AFLPs as a tool to examine the genetic variation among and within 25 populations of B. crispa. Analysis of population genetics of the species aimed to clarify morphological variation, current distribution patterns, strong adaptability to habitats, and the effects of geological factors in the HHM region. The genetic structure results, based on PCoA and NJ cluster analyses, revealed that the populations of B. crispa were divided into two genetic groups. Furthermore, the peripheral populations had lower genetic diversity than the populations in the center of the distribution areas (Three Parallel Rivers). We conclude that the gene flow (predominantly seed and pollen flow) and the population differentiation of B. crispa might be more affected by the barriers formed by rivers and mountains than by geographic distance.