Fingerprinting of Cyanobacteria Based on PCR with Primers Derived from Short and Long Tandemly Repeated Repetitive Sequences

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.     

PCR fingerprinting for epidemiological studies of Staphylococcus aureus

Staphylococcus aureus isolates (n = 126), collected during two different periods from patients hospitalised in pediatric wards, were analysed using polymerase chain reaction (PCR) mediated genotyping. These isolates were compared with 29 isolates from individuals attending the out-patient clinic of the same hospital and 13 isolates from pediatric hospital personnel. Within a group of 99 isolates gathered from 48 individuals during surveillance period I, 22 distinct genotypes were identified by application of two PCR assays. Among the 58 isolates collected in surveillance period II from pediatric and out-clinic patients, 25 genotypes were detected by a single PCR assay only. Based on these results it was demonstrated that patients can be colonised with multiple strains that may persist in a certain anatomical location for prolonged periods of time. It is shown that persistence of a S. aureus strain in a pediatric ward can be deduced from the PCR genotyping studies. As such PCR can be used for longitudinal monitoring of bacterial infections in hospital departments, analysis of patient-to-patient and personnel-to-patient transmission and for detection of genetic variation in general in S. aureus. Also, isolate-specific DNA probes can be generated for S. aureus by PCR genotyping. The probes can be used for the recognition of re-emerging S. aureus epidemics.     

用传统分离培养法和高通量测序技术分析印度块菌子囊果内细菌的群落结构

块菌是重要的经济真菌, 在其生长发育过程中, 细菌扮演了重要角色。本文利用传统分离培养方法和高通量测序技术分析了印度块菌(Tuber indicum)子囊果内细菌的群落结构。共分离得到细菌532株, 根据物种累积曲线, 选取其中的112株细菌进行了16S rRNA基因序列分析, 共鉴定出4属40种, 其中假单胞菌属(Pseudomonas)菌株占所测菌株数的80%, 不动杆菌属(Acinetobacter)占12.5%, 链霉菌属(Streptomyces)占5%, 贪噬菌属(Variovorax)占2.5%。通过对印度块菌子囊果16S rRNA基因的V1-V3区高通量测序分析, 共获得细菌序列9,862条, 分属于7门43属220种, 其中变形菌门、拟杆菌门和放线菌门的物种占总物种数的99.7%, 是印度块菌子囊果内的优势细菌。黄杆菌属(Flavobacterium)、壤霉菌属(Agromyces)、微杆菌属(Microbacterium)、剑菌属(Ensifer)和寡养食单胞菌属(Stenotrophomonas)的物种数占总物种的86.3%, 是印度块菌子囊果内细菌的优势属。研究结果表明, 采用胰蛋白大豆培养基仅分离得到印度块菌子囊果内少数细菌物种, 而采用高通量测序技术分析发现, 印度块菌子囊果内细菌物种种类丰富, 群落结构复杂。     

Genetic Relatedness among Environmental, Clinical, and Diseased-Eel Vibrio vulnificus Isolates from Different Geographic Regions by Ribotyping and Randomly Amplified Polymorphic DNA PCR

Genetic relationships among 132 strains of Vibrio vulnificus (clinical, environmental, and diseased-eel isolates from different geographic origins, as well as seawater and shellfish isolates from the western Mediterranean coast, including reference strains) were analyzed by random amplified polymorphic DNA (RAPD) PCR. Results were validated by ribotyping. For ribotyping, DNAs were digested with KpnI and hybridized with an oligonucleotide probe complementary to a highly conserved sequence in the 23S rRNA gene. Random amplification of DNA was performed with M13 and T3 universal primers. The comparison between ribotyping and RAPD PCR revealed an overall agreement regarding the high level of homogeneity of diseased-eel isolates in contrast to the genetic heterogeneity of Mediterranean isolates. The latter suggests the existence of autochthonous clones present in Mediterranean coastal waters. Both techniques have revealed a genetic proximity among Spanish fish farm isolates and a close relationship between four Spanish eel farm isolates and some Mediterranean isolates. Whereas the differentiation within diseased-eel isolates was only possible by ribotyping, RAPD PCR was able to differentiate phenotypically atypical isolates of V. vulnificus. On the basis of our results, RAPD PCR is proposed as a better technique than ribotyping for rapid typing in the routine analysis of new V. vulnificus isolates.     

Phylogenetic analysis of bacterial communities associated with larvae of the Atlantic halibut propose succession from a uniform normal flora

Halibut, the largest of all flatfishes is a valuable species with a great potential for aquaculture. Bacteria play an important role in regulating the health of the early life stages. The present article is the first broad-range molecular analysis of bacterial communities in larvae of the Atlantic halibut (Hippoglossus hippoglossus). DNA was extracted from larvae, water and silo biofilm from hatcheries in Norway, Scotland, Iceland and Canada. Eubacterial 16S rRNA gene fragments were amplified by polymerase chain reaction (PCR) with broad-range primers. Sequences spanning the hyper variable V3 region representing individual bacterial species were separated into community profiles by denaturing gradient gel electrophoresis (DGGE). The profiles revealed simple communities after hatching and bacterial succession following growth. Sequencing and phylogenetic analysis of excised DGGE bands suggested aerobic heterotrophs related to groups of Pseudomonas, Janthinobacterium and possibly Marinomonas to be the primary colonisers of the larvae. After onset of feeding, fermentative species (Vibrio) were detected as well. Comparative analysis of bacterial communities from different geographical regions indicated that larvae of the Atlantic halibut possess a distinct and specific normal flora.     

基于SSR标记的琅琊山球孢白僵菌寄主专化性

球孢白僵菌Beauveria bassiana是一类常见的昆虫病原真菌,其自然侵染的寄主昆虫众多,达15目149科750种。为了解球孢白僵菌自然种群的遗传多样性,探讨种群异质性和寄主来源之间的关系,分析其寄主专化性的强弱,本研究利用SSR分子标记技术,比较了安徽琅琊山国家森林公园的85株球孢白僵菌（寄主种类涉及7目24种）群体遗传多样性差异,通过构建聚类树分析菌株基因型和寄主关联性。结果表明琅琊山球孢白僵菌群体Nei’s基因多样性指数h=0.2906,Shannon信息指数I_s=0.4510,多态位点百分率P为100%。不同寄主目球孢白僵菌遗传多样性水平由高至低为鞘翅目>膜翅目>同翅目>双翅目>鳞翅目>直翅目>半翅目,其中菌株数量较多的鞘翅目、膜翅目和同翅目3个亚种群的遗传多样性较高且水平接近。聚类分析发现8对SSR引物将85株球孢白僵菌分成29个基因型,并在遗传相似系数0.70处分别聚为3个分支。分析寄主类型发现相同基因型的株系可侵染不同目的寄主,而同一类型寄主也可被不同基因型的菌株侵染。球孢白僵菌种群的总体遗传多样性较高,遗传谱系与寄主来源无明显相关性,菌株的寄主专化性弱。     

Adaptive coloration, behavior and predation vulnerability in three juvenile north Pacific flatfishes

Adaptive color change in flatfish has long been of interest to scientists, yet rarely studied from an ecological perspective. Because color change can take a day or so in some species, movement between sediments with differing color or texture may render fish more conspicuous to predators. We conducted laboratory experiments to test the following hypotheses related to adaptive color change in flatfish: 1) fish which do not cryptically match sediment will be more vulnerable to predation, 2) fish will reduce activity and bury to minimize conspicuousness when on a sediment they mismatch, and 3) fish will choose a sediment they match when given a choice. Experiments were conducted using three co-occurring north Pacific juvenile flatfishes: English sole Parophrys vetulus, northern rock sole Lepidopsetta polyxystra and Pacific halibut Hippoglossus stenolepis. As per expectations, juvenile flatfish were more vulnerable to visual predators when they mismatched sediment. Mismatched fish tended to behave differently than fish which matched the sediment. Rather than burying and becoming inactive, they became more active and less likely to bury, perhaps contributing to their predation vulnerability. This increased activity may have represented search for better matching sediment, a stress response, or conspicuousness-related density dependent behavior. Fish which had acclimated to light colored sediment preferred light over dark sediment in choice trials. In contrast, fish acclimated to dark sediment demonstrated no preference. These experiments demonstrate that adaptive coloration is an integral part of the flatfish detection minimization strategy and that movement between habitats can increase risk of predation.     

Characterization of 1,3-regiospecific lipases from new Pseudomonas and Bacillus isolates

Lipase producing ability of 120 bacterial isolates was examined qualitatively, resulting in 32 lipase producers, which were further screened for 1,3-regiospecificity. Three Bacillus (GK-8, GK-31 and GK-42) and one Pseudomonas (GK-80) were found to produce 1,3-regiospecific lipases. These lipases were alkaline in nature as they showed pH optima of 9.0 and high stability in the alkaline pH range of 8.0–11.0. The lipases from three Bacillus isolates, viz. GK-8, GK-31 and GK-42 showed temperature optima of 37 °C, whereas the Pseudomonas (GK-80) lipase showed optimum activity at 50 °C. The lipase of GK-8 was highly stable and showed enhanced activity in different organic solvents like petroleum ether (172%), diethyl ether (143%) and acetone (135%).     

北部湾雷州近海春、夏季鱼类群落结构初探

根据2005年4月、7月和8月在北部湾雷州近海进行的渔业资源刺网和底拖网调查,对该海域春、夏季鱼类群落结构进行了初步研究.结果表明,银鲳(Stromateoides argenteus)是当地绝对的优势种,其它鱼类优势种随区域和季节有着较大的差异.分别计算了北部湾雷州近海春、夏季鱼类生物多样性指数的种类丰度指数(R)、多样性指数(H')、均匀度指数(J').聚类分析表明该水域鱼类群落结构存在一定程度的时空异质性,但空间异质性不如时间异质性明显.此外,不同群落中的鱼类呈现出不同的生态型特征.同时部分结果表明,在不同网具的调查下,有的结果会出现较大变化.     

Variations in chromosome size and organization in Candida albicans and Candida stellatoidea

Candida albicans and the closely related species Candida stellatoidea are medically important diploid asexual yeasts. Clinical isolates frequently show variant electrophoretic karyotypes, apparently due largely to chromosomal translocations. These translocations seem to occur at hot spots characterized by the repeated DNA sequence RSP1. A programmed karyotypic rearrangement occurs in C. stellatoidea. Karyotypic rearrangement may serve as a source of genetic variation in these asexual yeasts.     

Reduction of hyperhydricity in tissue cultures of oregano (Origanum vulgare) by extracellular polysaccharide isolated from Pseudomonas spp

Hyperhydricity or vitrification is a physiological malformation affecting tissue culture-based propagation of several plant species. A Pseudomonas spp-mediated approach was recently developed to control hyperhydricity in oregano. This bacterium-induced prevention of hyperhydricity helped the establishment of clonal plants in the greenhouse without extensive acclimatization. The prevention of hyperhydricity was specifically linked to mucoid Pseudomonas spp and was characterized by high chlorophyll and reduced water content in oregano shoots. The focus of research reported in this paper was to purify the extracellular mucoid component from Pseudomonas spp and evaluate the effect on hyperhydricity in oregano tissue culture. The extracellular mucoid component was purified by ethanol precipitation. This extracellular mucoid component was confirmed to be a polysaccharide using gas chromatography-mass spectrometry. The effect of purified polysaccharide to prevent or reduce hyperhydricity was tested in oregano clone 0–1. The polysaccharide prevented hyperhydricity in oregano with reduced efficiency compared to bacterial inoculation. This was characterized by higher chlorophyll and reduced water content when compared to uninoculated/untreated oregano shoots. This confirms that the Pseudomonas spp-mediated hyperhydricity reduction in oregano is partially due to its extracellular polysaccharide. This provides a novel approach to develop a media formulation to control hyperhydricity in wide number of plant species where tissue culture is used for clonal propagation.     

Is Aeromonas hydrophila the dominant motile Aeromonas species that causes disease outbreaks in aquaculture production in the Zhejiang Province of China?

The significance of Aeromonas hydrophila in association with disease outbreaks in aquaculture production in the Zhejiang province of China was investigated. Bacteriological examination of moribund fish and crabs resulted in 95 bacterial isolates: 88 bacterial isolates from fish and 7 isolates from crabs. PCR and traditional biochemical methods were used for identification of A. hydrophila. Out of 69 motile aeromonads, 35 isolates were identified as A. hydrophila by biochemical tests. However, 6 of those were not identified as A. hydrophila by a species specific PCR method. Serotyping revealed 2 dominant serotypes (O9 and O97) among A. hydrophila isolates. The data presented show that approximately 42% of the motile aeromonads isolated from disease outbreaks among various fish species were A. hydrophila. It is noteworthy that A. hydrophila accounted for more than 50% of the isolated aeromonands isolated from crucian carp Carassius carassius and Wuchang bream Megalobrama amblycephala with haemorrhagic septicaemia. Although this species was the most frequently isolated organism from internal organs of diseased fish and crabs in the present study, other motile Aeromonas spp. were also found. The PCR assay was useful in preventing misidentification of A. hydrophila, which may occur when only phenotypic tests are employed.     

乳杆菌对致病假单胞菌的抑制作用研究进展*

假单胞菌污染事件在临床就医和日常饮食中频发,屡次产生致病、致死等恶劣后果,有效抑制致病假单胞菌并降低其耐药性作为解决该问题的关键手段,是目前的研究重点。相关研究表明益生菌等天然活性成分对假单胞菌产生多方面影响,以应用范围最广的益生菌——乳杆菌为例,综合国内外最新研究进展,论述了乳杆菌对假单胞菌的生物膜结构、生长活性、生物毒性、黏附细胞表面能力及被假单胞菌感染后的小鼠等产生的影响。深入挖掘乳杆菌等益生菌及其代谢产物成分的作用机制,是防治假单胞菌等微生物污染和感染的关键。     

Genetic differentiation of populations of the copepod sea louse Lepeophtheirus salmonis (Krøyer) ectoparasitic on wild and farmed salmonids around the coasts of Scotland: Evidence from RAPD markers

Sea trout are the sea-going migratory form of the freshwater brown trout (Salmo trutta L.) and since 1989 there have been marked declines in their stocks on the west coasts both of Scotland and Ireland. Various factors have been attributed as possible causal agents in these stock declines, including fresh water acidification, overfishing, climatic fluctuations, habitat degradation and sea lice parasitic burdens. The putative impact of infestations of sea trout by the ectoparasitic copepod sea louse, Lepeophtheirus salmonis (Krøyer), has featured prominently in the controversy, especially with regard to the role of inshore commercial salmon farms as a possible source of infestation of wild salmonids by sea lice. This study focused on the population genetics of L. salmonis around the coasts of Scotland: We sampled fish from wild and cultured stocks and included salmon (Salmo salar L.), rainbow trout (Oncorhynchus mykiss Walbaum) and sea trout as host species. Analyses of allozyme variation of sea lice were confined to data for two polymorphic loci (Fum, Got-2) and conformed to our initial expectation — that the inclusion of a planktonic larval phase in the life cycle of the copepod, in addition to the high mobility of the host fish, would enhance gene flow and preclude genetic differentiation of L. salmonis populations as a result of random drift alone. DNA polymorphism was quantified by means of PCR and RAPD analysis. Six primers were screened for 16 samples (from wild and farmed salmon, wild sea trout and farmed rainbow trout) — including the east, north and west coasts of Scotland — and the data analyzed by AMOVA (Analysis of Molecular Variance). In contrast to the allozyme results, the RAPD analysis showed striking patterns of genetic differentiation around the coasts of Scotland. The overall pattern was one of genetic homogeneity of L. salmonis populations sampled from wild salmon and sea trout. All of the L. salmonis samples taken from farmed salmon and rainbow trout did, however, show highly significant levels of genetic differentiation, both between wild and farmed salmonids and among the various farms themselves. Evidence of high levels of small-scale spatial or temporal heterogeneity of RAPD marker band frequencies was shown for the one farm from which repeat samples (July and November, 1995) were analysed. Samples of sea lice taken from west coast wild sea trout subjected to RAPD analysis also revealed the occurrence of putative “farm markers” in some individual parasites, indicating that they had possibly originated from salmon farms.     

Phenotypic characterization of raw milk-associated psychrotrophic bacteria

Among the 68 isolates, selected from 13 raw-milk samples in Finland (that originate from farm, truck or silo tanks), 60 (88%) were psychrotrophs. All the isolates were characterized by the determination of their spoilage and phenotypic features: proteolytic and lipolytic activities, the production of lecithinases and hemolytic factors were considered. Phenotypic characterization of the isolates was mainly performed with API 20NE and BIOLOG GN2 identification systems; the results were system-dependent, although the presence of representatives of the Pseudomonas genus (for the majority of the isolates) was suggested by both systems. The results of the numerical profile analyses by API 20NE proposed that some strains might be members of Stenotrophomonas, Burkholderia and Acinetobacter genera; however, the identity of many isolates remained doubtful or controversial.     

Characterization of Methyl tert-Butyl Ether-Degrading Bacteria from a Gasoline-Contaminated Aquifer

Molecular microbial community analysis was combined with traditional cultivation strategies to investigate the presence of methyl tert-butyl ether (MTBE)-degrading bacteria in a gasoline-contaminated aquifer (Ronan, MT). A bacterial consortium, RS24, which is capable of complete mineralization of MTBE as a sole carbon and energy source was enriched from soil and aquifer materials taken from the contaminated site. The consortium was capable of degrading MTBE at rates up to 0.66 mg d^-1, with corresponding gross biomass yields of 0.25±0.02 mg dry biomass (mg MTBE)^-1. Two MTBE-degrading isolates identified as Pseudomonas Ant9 and Rhodococcus koreensis were obtained from the consortium. However, both isolates required the presence of 2-propanol as a cosubstrate for MTBE degradation. Denaturing gradient gel electrophoresis (DGGE) of Poly-merase Chain Reaction (PCR)-amplified 16S rDNA confirmed the presence of both isolates in the initial consortium and indicated their disappearance with transfer and subculturing. MTBE degradation and cell growth by the consortium was stimulated by the presence of spent culture medium, suggesting the production of a growth factor during MTBE degradation. These results indicate the presence of naturally occurring MTBE-degrading bacteria in a contaminated aquifer and suggest the potential for natural attenuation or enhanced aerobic oxidation.     

Rapid and reliable identification of Staphylococcus equorum by a species-specific PCR assay targeting the sodA gene

Rapid and reliable identification of Staphylococcus (S.) equorum was achieved by species-specific PCR assays. A set of primers targeting the manganese-dependent superoxide dismutase (sodA) gene of S.equorum was designed. Species-specificity of the primer set was evaluated by using a total of 112 strains (including 27 reference strains of the DSM collection), representing 26 different species of the genus Staphylococcus, 3 species of the genus Kocuria, and different strains of Macrococcus caseolyticus. By using primers SdAEqF and SdAEqR the expected PCR fragment was obtained only when DNA from S. equorum strains was used as template. The rapidity (about 4 h from DNA isolation to results) and reliability of the PCR procedures established suggests that the method may be profitably applied for specific detection and identification of S. equorum strains.     

Limited Roles for Salicylate and Phthalate in Bacterial PAH Bioremediation

We have isolated and identified 12 previously unreported strains of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria. Three of these isolates belong to the genus Burkholderia, with the remainder comprised of two Pseudomonas species, and seven strains from the genus Sphingomonas. These isolates were examined for their ability to utilize a variety of three- to five-ring PAHs as sole sources of carbon and energy. All were also checked for the ability to grow on salicylic acid and phthalic acid, two compounds that are key intermediates in almost all published PAH degradative pathways. Only 3 of the 12 strains were able to grow on both of these monoaromatic acids, while three others (all Sphingomonas) could not grow on either. The implications of these findings on the universal applicability of known PAH catabolic pathways, and on possible induction of PAH degradation by pathway intermediates, are discussed.     

野生鸡油菌子实体可培养微生物多样性及其功能分析

采用多种培养基对采自贵州省贵阳市3个样地的鸡油菌Cantharellus cibarius子实体内细菌和真菌进行分离、培养、鉴定和多样性分析.利用FAPROTAX和FUNGuild数据库分别对其功能类群进行注释,从而探究微生物群对鸡油菌生长发育的影响.结果 表明,鸡油菌子实体内共分离获得细菌49株,分属于2门、4纲、6...