Characterisation of endobacterial communities in ectomycorrhizas by DNA- and RNA-based molecular methods     

Hironari Izumi  Edward R.B. Moore  Ian J. Alexander 《Soil biology & biochemistry》2007,39(4):891-899

The diversity of endobacteria associated with ectomycorrhizas of Suillus variegatus and Tomentellopsis submollis, in two Corsican pine (Pinus nigra) stands was analysed by cultivation-dependent and cultivation-independent molecular methods. Denaturing gradient gel electrophoresis (DGGE) analysis revealed the cultivable endobacterial communities associated with S. variegatus were similar within the same stand. The most abundant cultivable bacterial species belonged to the genera Pseudomonas and Burkholderia. Cultivation-independent molecular analysis indicated that the structure of the endobacterial communities in ectomycorrhizas was consistent across all samples regardless of ECM fungal species or the pine stand from which the samples were collected. However, comparison between rDNA- and rRNA-derived DGGE gels showed that metabolically active endobacterial species were not always detected in rDNA-based profiles. Clone libraries constructed from rRNA molecules indicated that Pseudomonas and Burkholderia spp. were metabolically active bacteria. As some of the most abundant cultivable bacteria, including Bacillus/Paenibacillus spp., were not detected in cultivation-independent DGGE profiles, a combination of cultivation-dependent and -independent approaches provided a more complete assessment of the diversity of endobacteria associated with ectomycorrhizas.  相似文献   

Indigenous rhizobia associated with native shrubby legumes in Taiwan     

Mei-Hua Hung  Arun A. Bhagwath  Fo-Ting Shen  Rekha P. Devasya  Chiu-Chung Young   《Pedobiologia》2005,49(6):36-584

Root-nodulating bacteria were isolated and characterized from seven native shrubby legumes growing in Taiwan. Phenotypic characteristics measured included growth rates in various media, colony morphology, and tolerances to extremes of temperature, salt and pH. The isolates were very diverse phenotypically. Among the 83 isolates that were screened, the majority were fast-growing rhizobia. Twenty eight strains tolerated high concentration of salt (4.5% NaCl) and grew well between temperatures of 37 and 45 °C. The majority of the strains also tolerated extreme pH in their medium from 3.5 to 12. All strains formed nitrogen fixing nodules, and the highest activity was detected in the legume Hedysarum crinita L. PCR restriction fragment length polymorphism (PCR-RFLP) and sequencing of the small subunit ribosomal RNAs revealed that the majority of the isolates belonged to the genera Rhizobium, Bradyrhizobium and Agrobacterium. Only a single strain represented the genus Sinorhizobium. In addition, a strain related to Burkholderia from the β-class of the Proteobacteria (CC-CC-5) was found within nodules of the legume Catenaria caudatum. The study contributes to the understanding of symbiotic nitrogen fixation in selected wild legumes that are native to Taiwan and provides insights into the distribution of nodulating and nitrogen-fixing bacteria from other distinct lineages.  相似文献   

Root-nodule bacteria from indigenous legumes in the north-west of Western Australia and their interaction with exotic legumes     

Ron J. Yates  John G. Howieson  Kemanthi G. Nandasena 《Soil biology & biochemistry》2004,36(8):1319-1329

Bacteria were isolated from root-nodules collected from indigenous legumes at 38 separate locations in the Gascoyne and Pilbara regions of Western Australia. Authentication of cultures resulted in 31 being ascribed status as root-nodule bacteria based upon their nodulation of at least one of eight indigenous legume species. The authenticated isolates originated from eight legume genera from 19 sites. Isolates were characterised on the basis of their growth and physiology; 20 isolates were fast-growing and 11 were slow-growing (visible growth within 3 and 7 d, respectively). Fast-growers were isolated from Acacia, Isotropis, Lotus and Swainsona, whilst slow-growers were from Muelleranthus, Rhynchosia and Tephrosia. Indigofera produced one fast-growing isolate and seven slow-growing isolates. Three indigenous legumes (Swainsona formosa, Swainsona maccullochiana and Swainsona pterostylis) nodulated with fast-growing isolates and four species (Acacia saligna, Indigofera brevidens, Kennedia coccinea and Kennedia prorepens) nodulated with both fast- and slow-growing isolates. Swainsona kingii did not form nodules with any isolates. Fast-growing isolates were predominantly acid-sensitive, alkaline- and salt-tolerant. All slow-growing isolates grew well at pH 9.0 whilst more than half grew at pH 5.0, but all were salt-sensitive. All isolates were able to grow at 37 °C. The fast-growing isolates utilised disaccharides, whereas the slow-growing isolates did not. Symbiotic interactions of the isolates were assessed on three annual, one biennial and nine perennial exotic legume species that have agricultural use, or potential use, in southern Australia. Argyrolobium uniflorum, Chamaecytisus proliferus, Macroptilium atropurpureum, Ononis natrix, Phaseolus vulgaris and Sutherlandia microphylla nodulated with one or more of the authenticated isolates. Hedysarum coronarium, Medicago sativa, Ornithopus sativus, Ornithopus compressus, Trifolium burchellianum, Trifolium polymorphum and Trifolium uniflorum did not form nodules. Investigation of the 31 authenticated isolates by polymerase chain reaction with three primers resulted in the RPO1 primer distinguishing 20 separate banding patterns, while ERIC and PucFor primers distinguished 26 separate banding patterns. Sequencing the 16S rRNA gene for four fast- and two slow-growing isolates produced the following phylogenetic associations; WSM1701 and WSM1715 (isolated from Lotus cruentus and S. pterostylis, respectively) displayed 99% homology with Sinorhizobium meliloti, WSM1707 and WSM1721 (isolated from Sinorhizobium leeana and Indigofera sp., respectively) displayed 99% homology with Sinorhizobium terangae, WSM1704 (isolated from Tephrosia gardneri) shared 99% sequence homology with Bradyrhizobium elkanii, and WSM1743 (isolated from Indigofera sp.) displayed 99% homology with Bradyrhizobium japonicum.  相似文献   

苎麻木质纤维高效降解菌的分离与鉴定     

王超群  陈洪高  张运鹏 《湖北农业科学》2015,54(3):565-568

利用羧甲基纤维素钠培养基,从腐烂苎麻秆堆中分离到1株高效纤维降解细菌,形态学观察结合16S r RNA基因分子鉴定。结果表明,该菌属于蜡样芽孢杆菌(Bacillus cereus),发酵进行产酶的最适温度和p H分别为42℃和7.0,在该条件下,于100 m L发酵体系中发酵降解苎麻纤维,发酵96 h后纤维素酶活力达到最高值24.3 U/m L,发酵8 d后其纤维降解率为45.1%。  相似文献   

固氮、解磷复合菌剂对小麦根际土壤细菌群落的影响     

贺国强  陈三凤 《中国农业大学学报》2015,20(5):81-88

为研究固氮芽孢杆菌、固氮巨大芽孢杆菌、解磷假单胞菌、巴西固氮螺菌组成的复合菌剂对小麦根际土壤细菌群落多样性的影响,通过构建16SrRNA克隆文库及采用核糖体DNA扩增片段酶切分析(ARDRA)的方法,以文库库容值(C)、Rarefaction曲线(R)对克隆文库进行评价。系统发育分析表明,对照及菌剂处理样品均检测到酸杆菌门、变形菌门、浮霉菌门、厚壁菌门、拟杆菌门、疣微菌门、放线菌门和芽单胞菌门8个细菌类群,并且优势菌群均为变形菌门和酸杆菌门。接种菌剂后小麦根际土壤检出了绿弯菌门、蓝藻门、产水菌门和硝化螺旋菌门,而梭杆菌门未被检出。假单胞菌属由1.59%增加至21.28%。芽孢杆菌属由未检出增至3.05%。两样品中均未检出固氮螺菌属。多样性分析表明,接种菌剂后,小麦根际土壤细菌多样性指数和丰富度指数均提高。因此,接种菌剂对小麦根际土壤细菌类群的组成及所占比例有较大影响。  相似文献   

驯鹿18S rRNA基因的克隆测序   总被引：1，自引：1，他引：0  

张敏  白秀娟 《经济动物学报》2003,7(1):15-17

对驯鹿 (Rangifertarandus)的 1 8SrRNA基因片段进行了克隆测序 ,序列长度为 1 1 47bp ,并且已被发送到Genebank上 ,其登录号是AY1 45 5 2 7。  相似文献   

The Application of Microbiome Culturomics in Veterinary Medicine     

PENG Na  PENG Xianqi  YUE Min 《畜牧兽医学报》1956,51(12):2942-2953

Under laboratory conditions, the number of cultured microorganisms accounts for about 1% of the total number of microorganisms in nature, which limits people's understanding and utilization of 99% of the unknown microorganisms. However, relevant researches show that those "uncultured microorganisms" can be developed and utilized, and the uncultured microorganisms are the main body of the unknown microorganisms. The microbial culturomics explored the application of multiple culture conditions and long-term culture, it was combined with Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) and 16S ribosomal RNA (rRNA) sequencing to identify all kinds of microorganisms on a large scale. At the same time, whole-genome sequencing (WGS) and Metagenomics sequencing technology were used to analyze unknown microorganisms in depth. In this paper, the latest progress of culturomics in the ruminant gastrointestinal tract, poultry cecum, and livestock nasal microflora in recent years was reviewed, and the feasibility of applying the method of microflora culturomics in animal disease prevention and control was discussed. As a new research idea, culturomics has some immature aspects, but its development prospect is very broad. The complementary of microflora culturomics and other research methods have gradually become a breakthrough in the development of veterinary microbiology.  相似文献   

Ribotyping of Indian Isolates of <Emphasis Type="Italic">Pasteurella multocida</Emphasis> Based on 16S and 23S rRNA Genes     

Saxena MK  Kumar AA  Chaudhari P  Shivachandra SB  Singh VP  Sharma B 《Veterinary research communications》2005,29(6):527-535

The applicability of ribotyping based on 16S and 23S rRNA was evaluated for molecular epidemiological studies. Forty-eight isolates of Pasteurella multocida isolated from different hosts and geographical locations and one reference isolate were ribotyped. Only four ribotypes were found. All the isolates including reference isolate from wild carnivores had the same ribotype, though they had different serotypes. The isolate from a tiger had one band in addition to the bands present in the major ribotype. The isolates from lions represented two ribotypes; of these ribotypes, one (r2) had an additional band of 3.6 kbp, which was absent in all other ribotypes. The second ribotype (r4) from a lion had one band missing (6 kbp) that was present in the other ribotypes. These isolates were further typed using ERIC-PCR and REP-PCR. With ERIC-PCR and REP-PCR, higher D values of 0.83 and 0.89 were obtained. The current study revealed that ribotyping is not a very efficient typing tool for use in molecular epidemiology for differentiation of isolates.  相似文献   

Study on some molecular characterization of Babesia orientalis     

Liu Q  Zhao JL  Zhou YQ  Liu EY  Yao BA  Fu Y 《Veterinary parasitology》2005,130(3-4):191-198

The study on buffalo babesiosis indicated that its pathogen was different from other Babesia on many aspects such as morphology, transmission and pathogenicity. Therefore, it was named as a new species—Babesia orientalis. In order to prove the validity of this taxon, molecular taxonomic study on the pathogen was done in this experiment. The complete 18S rRNA gene sequence of B. orientalis was determined by PCR. It was sequenced and blasted. The results indicated that the classification of the parasite belonged to the genus Babesia. The 1700 bp complete sequence was compared with 15 other Babesia sp. available in GenBank. The data were analyzed and a phylogenetic tree was established. The results indicated that the hereditary distance of the parasite was close to that of Babesia sp. from South Africa and Babesia ovis, and the hereditary distance was far from Babesia bigemina and B. bovis.  相似文献   

Detection of bacterial DNA in synovial fluid from horses with infectious synovitis     

Pille F  Martens A  Schouls LM  Peelman L  Gasthuys F  Schot CS  De Baere C  Desmet P  Vandenberghe F 《Research in veterinary science》2004,77(3):189-195

Standard culturing techniques are often unrewarding in confirming diagnosis of synovial infection in the equine patient. Several human studies report the use of sensitive polymerase chain reaction (PCR) techniques for the detection of bacterial involvement in acute synovitis. However, successful extraction of bacterial DNA directly from clinical samples from horses without prior culture has not been reported yet. The goal of this study was to develop a sensitive and reliable method for molecular detection and identification of bacterial species in synovial fluid from horses with infectious synovitis. Synovial fluid samples from 6 horses with culture confirmed synovial infection were used for broad range 16S rRNA gene PCR. Synovial aspirates of 2 healthy horses were used as negative controls. Following extraction and purification of synovial fluid DNA, all samples were processed by touchdown PCR. Amplicons were detected by reverse line blot hybridisation and visualised with chemiluminescence. Pathogen-specific detection of 16S rRNA gene sequences was successful in all 6 synovial fluid samples. No bacterial DNA was detected in the aspirates from the negative control horses using touchdown PCR followed by 25 additional cycles of amplification. The identity of the pathogens was confirmed by DNA sequencing of the amplicons. It can be concluded that broad range 16S rRNA gene PCR followed by reverse line blot hybridisation is a promising technique for detection of bacterial DNA in synovial fluid samples. Further research should aim at the detection of bacterial DNA in synovial fluid samples suspected of infection but having negative culture results. When the 16S PCR proves to be reliable and more sensitive than standard culturing techniques, it may become a powerful tool in the diagnosis of synovial infection.  相似文献