Thermus thermophilus TMY isolated from silica scale taken from a geothermal power plant

Aims:  To identify an extreme thermophile, strain TMY, isolated from silica scale from the geothermal electric power plant and to examine microdiversity of Thermus thermophilus strains.
Materials and Results:  The isolated strain TMY was identified by morphological, biochemical and physiological tests. Phylogenetic comparison of the strain and other Thermus strains with 16S rDNA analysis, RAPD and ERIC-PCR fingerprinting were performed. Strain TMY was closely related to strain which was isolated from a hot spring in New Zealand and shown to belong to the Japanese Thermus cluster. However, there were considerable genetic differences between strain TMY and other Thermus species using DNA fingerprinting.
Conclusions:  Based on morphological, physiological and genetic properties, strain TMY could be a strain of T. thermophilus . The distinct properties of strain TMY suggest that microdiversity of T. thermophilus strains should be considered.
Significance and Impact of the Study:  The results of this study have demonstrated genetic diversity within T. thermophilus strains, which were previously masked by an almost identical 16S rDNA sequence. RAPD and ERIC-PCR could be potential methods for distinguishing between Thermus strains.     

Taxonomic composition of Lake Baikal bacterioneuston communities

The taxonomic composition of microbial communities of Lake Baikal surface microlayer was studied by pyrosequencing of the 16S rDNA amplicons. Statistically reliable differences were found between bacterioneuston of the shallow and deep-water stations. The shallow station community was characterized by higher diversity than the deep-water one. While bacterioneuston communities were shown to be less diverse than the water column communities, their diversity was comparable to that of other biofilm associations. Microbial communities of Lake Baikal surface microlayer were shown to be similar to those of the water column in the composition of predominant phyla, while differing considerably at the genus level. Bacterioneuston of Lake Baikal was comparable to microbial communities of the surface microlayer of other freshwater basins, although it was characterized by high abundance of the Alphaproteobacteria and Verrucomicrobia. High abundance of photoheterotrophs compared to the water column communities of other freshwater basins was another distinctive feature of Lake Baikal bacterioneuston. Our results showed the Lake Baikal surface microlayer to be a specific microbial community with low species diversity and relatively high abundance of photoheterotrophic microorganisms.     

Isolation and identification of new nisin-producing Lactococcus lactis subsp. lactis from milk

A method for isolating active nisin-producing strains of mesophilic lactococci was developed. Overall, 55 strains of mesophilic lactic acid bacteria were isolated from fresh cow's milk obtained from milk farms in various regions throughout Russia; of them, 36 displayed nisin-synthesizing activity. The three most active strains were studied according to morphological, cultural, physiological, and biochemical characteristics and identified as Lactococcus lactis subsp. lactis. The species attribution of the strains studied was confirmed by the similarity of the nucleotide sequences of the 16S rRNA gene. The nucleotide sequences of the 16S rRNA genes were deposited with the GenBank under accession numbers DQ255951-DQ255954. The distinctions between these strains in physiological and biochemical characteristics and the ranges of their bactericide action on the microorganisms capable of developing in agricultural materials and food products were determined. The isolated strains displayed considerably wider ranges of action, which differed from the nisin-producing strain MGU and the commercial nisin preparation (Nisaplin), used as a biological preserving agent.     

Influence of the surface microlayer on nutrients,chlorophyll and algal diversity of a small eutrophic bog pond

Nutrients, chlorophyll, phaeophytin and algal abundances were investigated in the surface microlayer and at subsurface depths in a small eutrophic bog pond. Nutrient levels were consistently higher in the microlayer while algal abundance was sometimes higher but sometimes lower in the microlayer than at near subsurface depths. Algal diversity values were strongly influenced by the depth of flagellate blooms, and in contrast to previous studies, diversity in the microlayer was higher than at near subsurface depths. These results are discussed in terms of weather parameters, affinity of algal species for the surface and differences between microlayer ecology in shallow and deep water systems.     

Isolation and identification of new nisin-producing Lactococcus lactis subsp. lactis from milk

A method for isolating active nisin-producing strains of mesophilic lactococci was developed. Overall, 55 strains of mesophilic lactic acid bacteria were isolated from fresh cow’s milk obtained from milk farms in various regions throughout Russia; of them, 36 displayed nisin-synthesizing activity. The three most active strains were studied according to morphological, cultural, physiological, and biochemical characteristics and identified as Lactococcus lactis subsp. lactis. The species attribution of the strains studied was confirmed by the similarity of the nucleotide sequences of the 16S rRNA gene. The nucleotide sequences of the 16S rRNA genes were deposited with the GenBank under accession numbers DQ255951–DQ255954. The distinctions between these strains in physiological and biochemical characteristics and the ranges of their bactericide action on the microorganisms capable of developing in agricultural materials and food products were determined. The isolated strains displayed considerably wider ranges of action, which differed from the nisin-producing strain MGU and the commercial nisin preparation (Nisaplin), used as a biological preserving agent.     

广东中山地区气单胞菌环境株的分离、鉴定及系统发生关系

从广东省中山市的池塘水样、底泥、健康鱼、肠道及稻田土样中用Aeromonas的选择培养基分离到10株气单胞菌。通过生理生化测试、16S rDNA序列测定、与气单胞菌典型菌株的16S rDNA序列进行比对和聚类分析,对它们进行了鉴定,并研究了它们之间的系统发生关系。结果显示该地区环境中气单胞菌的优势种除A.hydrophila(HG1组)外,还有A.caviae(HG4组)、A.jandaei(HG9组)和A.veronii(HG10组),其中后两种是国内新记录。这是国内首次对环境中气单胞菌多样性进行研究。     

净化养殖水体紫色非硫光合细菌的筛选与鉴定

本研究从杭州养鱼塘水样及底泥样品中富集分离得到三株紫色非硫光合细菌,分别命名为HZ-3,HZ-4,HZ-5。 通过比较这三株菌对鱼、虾养殖水体的净化效果,筛选出菌株HZ-5 净化能力较强 ,经过5天的处理,该菌株使养鱼塘水样的COD 降低24.87%;使养虾池塘水样的COD 降低 36.99%;使养鱼塘水样的亚硝态氮的降解率达到97.79%。对菌株HZ-5进行了形态学观察、生理生化鉴定、活细胞吸收光谱以及16S rDNA序列分析。16S rDNA序列分析结果表明该菌株与沼泽红假单胞菌的16S rDNA序列有高达99％的同源性,结合形态特征和生理生化特性以及活细胞吸收光谱特征等,将其鉴定为沼泽红假单胞菌（Rhodopseudomonas palustris）。     

新疆罗布泊周边地区极端环境嗜盐菌的研究

为了研究分析新疆罗布泊周边地区pH值5-6的盐湖嗜盐古菌资源。从湖中分离筛选出一批嗜盐古菌,对其进行了生理生化特性研究,发现其中6株菌的生理特性和产酶特性比较特殊,并采用PCR方法扩增出其16SrRNA基因（16S rDNA）,并测定了基因的核苷酸序列。基于16S rDNA序列的同源性比较以及16S rDNA序列的系统发育学研究表明,菌株B20-RDX是盐盒菌属Haloarchaeon属中新种成员,GenBank登录号为FJ561285,该菌株为革兰氏阴性菌,最适盐浓度25%,最适pH 8.0,能产过氧化氢酶、淀粉酶,对四环素有抗性,能利用精氨酸和丁二酸盐。迄今为止,国内极少有关罗布泊周边地区极端环境微生物研究的报道,该研究可为今后研究同类极端环境中新的物种资源开发应用以及微生物多样性研究提供素材和参考。     

津巴布韦烟叶中淀粉酶和蛋白酶产生菌的分离及鉴定

目的:从津巴布韦烟叶中分离产蛋白酶菌和产淀粉酶能力最高的菌株,并对其进行鉴定。方法:采用淀粉富集培养基和酪蛋白富集培养基分别分离津巴布韦烟叶中的产淀粉酶和产蛋白酶菌株,通过生理生化实验和16SrRNA序列分析鉴定分离的菌株。结果:产蛋白酶菌株菌体不透明、表面有褶皱,蛋白酶酶活为52.10±0.13 U/mL;产淀粉酶菌株菌体表面呈黏状,淀粉酶酶活为3.69±0.07 U/mL;产蛋白酶与产淀粉酶的2株菌均与枯草芽孢杆菌的16S rRNA序列有100%的相似性,结合生理生化指标初步鉴定为枯草芽孢杆菌。结论:获得的2株菌在降解烟叶的蛋白质和淀粉过程中可能起重要作用。     

Genetic Diversity of Escherichia coli Isolated from Urban Rivers and Beach Water

Repetitive element anchored PCR was used to evaluate the genetic profiles of Escherichia coli isolated from surface water contaminated with urban stormwater, sanitary sewage, and gull feces to determine if strains found in environmental samples reflect the strain composition of E. coli obtained from host sources. Overall, there was less diversity in isolates collected from river and beach sites than with isolates obtained from human and nonhuman sources. Unique strain types comprised 28.8, 29.2, and 15.0% of the isolate data sets recovered from stormwater, river water, and beach water, respectively. In contrast, 50.4% of gull isolates and 41.2% of sewage isolates were unique strain types. River water, which is expected to contain E. coli strains from many diffuse sources of nonpoint source pollution, contained strains most closely associated with other river water isolates that were collected at different sites or on different days. However, river sites impacted by sewage discharge had approximately 20% more strains similar to sewage isolates than did sites impacted by stormwater alone. Beach sites with known gull fecal contamination contained E. coli most similar to other beach isolates rather than gull isolates collected at these same sites, indicating underrepresentation of possible gull strains. These results suggest large numbers of strains are needed to represent contributing host sources within a geographical location. Additionally, environmental survival may influence the composition of strains that can be recovered from contaminated waters. Understanding the ecology of indicator bacteria is important when interpreting fecal pollution assessments and developing source detection methodology.     

Differentiation of Staphylococcus aureus from freshly slaughtered poultry and strains 'endemic'to processing plants by biochemical and physiological tests

A comparison was made of 27 'endemic' strains of Staphylococcus aureus and 35 strains from freshly slaughtered birds, isolated at five commercial slaughterhouses processing chickens or turkeys. Of 112 biochemical and physiological tests used, 74 gave results which differed among the strains. Cluster analysis revealed several distinct groupings which were influenced by strain type, processing plant and bird origin; these included a single group at the 72% level of similarity containing most of the 'endemic' strains. In comparison with strains from freshly slaughtered birds, a higher proportion of 'endemic' strains produced fibrinolysin, aP-glucosidase and urease and were β-haemolytic on sheep-blood agar. The 'endemic' type also showed a greater tendency to coagulate human but not bovine plasma, and to produce mucoid growth and clumping. The last two properties, relevant to colonization of processing equipment, were less evident in heart infusion broth than in richer media or process water collected during defeathering of the birds.     

Characteristics and utilities of luminescent bacteria from the Black sea

Luminescent bacteria, isolated from summer specimens of water of the Black sea, have been identified as strains of Photobacterium phosphoreum and Vibrio fischeri (two of each). Morphological, physiological, and biochemical properties of the four strains have been characterized, and the kinetic behavior of luciferases isolated therefrom has been studied. The sensitivity of the luminescence of the strains to certain toxic agents has been compared to that of the test strain Ph. phosphoreum (Cohn) Ford. The results obtained indicate that the new strains show promise as bioindicators.     

一株来自蚯蚓的产纤溶酶蜡状芽孢杆菌Bacillus cereus的筛选及鉴定

对来自4个不同省份的5条蚯蚓的肠道及体表细菌进行分离,共获得122株细菌。通过脱脂奶粉平板法初筛,纤维蛋白平板法复筛,以透明圈为筛选标记,共筛选出产纤溶酶菌株12株,其中菌株SC-3-W-3的纤溶酶活力较高,达到了538.64 U/mL(相当于尿激酶的活力单位)。通过对其形态、培养、生理生化特征进行研究,发现其与蜡状芽孢杆菌Bacillus cereus Frankland的特征很相符。进一步对SC-3-W-3的16S rDNA序列及系统发育分析表明,该菌株与蜡状芽孢杆菌的同源性高达100%。综合生理生化及16S rDNA序列比对结果,将SC-3-W-3菌株鉴定为蜡状芽孢杆菌。     

一株耐盐葡萄球菌的分离鉴定及其特性分析

本文旨在分离筛选出在高盐环境中具有潜在应用可能性的菌株。在筛选耐盐酵母的过程中分离出一株耐盐菌株,采用形态特征观察、生理生化实验和16S rDNA基因测序进行菌株鉴定,鉴定结果显示该菌为沃氏葡萄球菌(Staphylooccus warneri),命名为SW-1。进一步对其药敏特性、耐盐性和表面疏水性进行检测,结果表明,该菌株对大部分抗生素极敏感,在含20%(质量分数)NaCl的LB培养基中仍能良好生长,对氯仿、乙酸乙酯和正丁醇的疏水率依次为43%、34%和39%。沃氏葡萄球菌SW-1在高盐条件下能快速适应环境积累生物量,具有优良的生物学特性,为开发和利用耐盐菌株提供参考。     

Differentiation of Staphylococcus aureus from freshly slaughtered poultry and strains 'endemic' to processing plants by biochemical and physiological tests

A comparison was made of 27 'endemic' strains of Staphylococcus aureus and 35 strains from freshly slaughtered birds, isolated at five commercial slaughterhouses processing chickens or turkeys. Of 112 biochemical and physiological tests used, 74 gave results which differed among the strains. Cluster analysis revealed several distinct groupings which were influenced by strain type, processing plant and bird origin; these included a single group at the 72% level of similarity containing most of the 'endemic' strains. In comparison with strains from freshly slaughtered birds, a higher proportion of 'endemic' strains produced fibrinolysin, alpha-glucosidase and urease and were beta-haemolytic on sheep-blood agar. The 'endemic' type also showed a greater tendency to coagulate human but not bovine plasma, and to produce mucoid growth and clumping. The last two properties, relevant to colonization of processing equipment, were less evident in heart infusion broth than in richer media or process water collected during defeathering of the birds.     

斑点叉尾鮰一株致病菌的分离鉴定及系统发育分析

从发生急性流行性传染病的斑点叉尾肝、肾分离到一高致病性的菌株(CCF00024),经人工感染实验证实其为该病的病原菌。对该菌的形态、生理生化及16S rDNA序列分析结果表明,其为非发酵型,严格需氧,革兰氏阴性杆菌,极生多鞭毛,对除麦芽糖和甘露糖以外的多种糖类不能利用产酸,氧化酶阴性,DNA酶、蛋白酶、脲酶、赖氨酸脱羧酶阳性,MR阴性。在以该菌16S rDNA序列(GenBank登录号AY970826)和GenBank及RDP数据库内同源性较高的细菌16S rDNA序列构建的系统发育树中,分离菌CCF00024与嗜麦芽寡养单胞菌(Stenotrophomonasmaltophilia)聚在一簇,特别是与S.maltophiliaM5-1的同源性最高,其序列相似性达99.6%,结合形态和生理生化特点将其鉴定为嗜麦芽寡养单胞菌(Stenotrophomonas maltophilia)。     

Taxonomy of obligately homofermentative and facultatively heterofermentative lactobacilli in pig faeces

AIMS: Identification and characterization of obligately homofermentative and facultatively heterofermentative strains of Lactobacillus spp. isolated from the faeces of pigs that had been raised under different conditions. METHODS AND RESULTS: The phenotypic relatedness of the isolated strains and reference strains were determined by numerical analysis of total soluble cell protein patterns and simple physiological and biochemical tests. Of the 23 strains isolated from faeces, nine were obligately homofermentative and 14 facultatively heterofermentative. The strains clustered at r > or = 0.61 with Lactobacillus amylovorus (seven strains), Lactobacillus crispatus (one strain), Lactobacillus plantarum (14 strains) and Lactobacillus intestinalis (one strain). CONCLUSIONS: Results obtained from the physiological and biochemical tests confirmed the identity of the isolates as determined by numerical analysis of total soluble cell protein profiles. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report on the association of Lact. crispatus and Lact. intestinalis with the gastro-intestinal tract of pigs.     

Macrophyte disturbance alters aquatic surface microlayer structure,metabolism, and fate

Macrophytes drive the functioning of many salt marsh ecosystem components. We questioned how temporary clearing of the macrophyte community, during restoration, would impact processes at the scale of the aquatic surface microlayer. Development, deposition, and breakup of the tidal creek surface microlayer were followed over tidal cycles seasonally in a cleared “former” Phragmites marsh and an adjacent restored Spartina marsh. Metabolic and physical processes of the mobile surface microlayers and underlying water were compared, along with distribution of organic and inorganic components onto simulated plant stems. In July and October, chlorophyll-a quantities were less on simulated stems in the cleared site than in the restored site. The aquatic microlayer in the cleared site creek exhibited lower photosynthesis and respiration rates, fewer diatoms and green algae, and less chlorophyll-a. There was a lower concentration (250 times) and reduced diversity of fatty acids in the surface microlayer of the cleared site, reflecting a smaller and less diverse microbial community and reduced food resources. Fiddler crab activity was an order of magnitude higher where macrophytes had been cleared. Their consumption of edaphic algae on the mud surface may account for the reduced algae and other organics in the creek surface microlayer, thus representing a redirection of this food resource from creek consumers. Overall, there were less total particulates in the creek surface microlayer at the cleared site, and they dropped out of the surface microlayer sooner in the tidal cycle, resulting in a lower sediment load available for deposit onto marsh surfaces.     

Microbial communities in the saturated groundwater environment I: Methods of isolation and characterization of heterotrophic bacteria

In this paper we present a method of isolation and morphological and physiological characterization of groundwater bacteria based on numerical taxonomy and cluster analysis, and using a miniaturized test system (microtiter plates). Bacteria were isolated randomly on P-agar, and each strain was characterized in regard to 155 features. The media for biochemical differentiation are listed as well as methods of morphological discrimination. 246 strains of heterotrophic and oligotrophic bacteria, isolated from five water samples from different depths of the saturated groundwater area, were used for optimizing media and test reactions.     

Habitat Segregation and Biochemical Activities of Marine Members of the Family Vibrionaceae

A comparative study of marine members of the family Vibrionaceae with the technique of numerical taxonomy revealed habitat segregation as well as a cosmopolitan nature of species distribution among the vibrios in different marine environments. The bacterial strains analyzed were isolated from seawater, sediments, phyto- and zooplankton, and fish in the Indian Ocean, the South and East China Sea, and West Pacific Ocean, and coastal areas of Japan. A total of 155 morphological, physiological, and biochemical tests were carried out for each of 405 strains examined. The results showed that most of the large taxonomical clusters which emerged from the computation corresponded to ecological groups which have particular niches. For instance, each group of seawater vibrios inhabited a particular water layer of limited depth range, in spite of the fact that strains of the group were isolated from sampling locations spread over a wide area from the Indian Ocean to Japanese coast. Various vibrio groups showed remarkable differences in their physiological and biochemical activities, and the activities of each group seemed to correspond with its ecological niche. The strains which inhabited surface-water layers grew fast and actively utilized many high-molecular-weight organic compounds and carbohydrates that are derived from fresh, easily degradable organic matter present in the surface waters, whereas the middle- and deep-water vibrios did not decompose most of the high-molecular-weight organic compounds except chitin but, rather, utilized some carbohydrates and organic acids which seemed to be derived from refractory particulate organic matter present in the deeper waters.