Identification of lactic acid bacteria associated with the production of plaa-som, a traditional fermented fish product of Thailand

Plaa-som is a Thai fermented fish product for which whole fish or fish fillets are fermented with either cooked rice or steamed sticky rice, salt, and garlic. A total of 762 lactic acid bacteria (LAB) were isolated during plaa-som fermentation by culture on CaCO(3)-MRS agar plates. They were screened and grouped by amplified ribosomal DNA restriction analysis (ARDRA), giving six groups that were identified by ribosomal DNA sequencing as Lactococcus garvieae, Streptococcus bovis, Weissella cibaria, Pediococcus pentosaceus, Lactobacillus plantarum, and Lactobacillus fermentum. Freshly mixed ingredients contained low populations of LAB (less than 10 CFU/g) that subsequently grew during fermentation to final populations of approximately 10(7)CFU/g. Early stages of the process were dominated by the presence of Lc. garvieae, S. bovis, and W. cibaria. At 48 h into fermentation, W. cibaria, P. pentosaceus, and Lb. plantarum were prevalent, and gave way to a dominance of Lb. plantarum that completed the fermentation. A mixture of these LAB species could be considered as species for development of a starter culture for plaa-som fermentation.

Construction and screening of marine metagenomic libraries

Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. Besides, the surfaces of marine multicellular organisms are typically covered by a consortium of epibiotic bacteria and act as barriers, where diverse interactions between microorganisms and hosts take place. Thus, microbial diversity in the water column of the oceans and the microbial consortia on marine tissues of multicellular organisms are rich sources for isolating novel bioactive compounds and genes. Here we describe the sampling, construction of large-insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomic clones.

Localization of rDNA at nucleolar structural components by immunoelectron microscopy

Fluorescence in situ hybridization (FISH) shows that DNA encoding ribosomal RNA cistron (rDNA) is localized to small speckles scattered in the nucleolus and the nucleolus-associated chromatin (NAC). This technique cannot however precisely locate rDNA in the nucleolar ultrastructural components such as the fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC). In situ hybridization at the electron microscopic level is suitable for localization of rDNA at the ultrastructural level. We have tried to determine the precise localization of rDNA in the nucleolus of a higher plant by electron microscopic (EM) in situ hybridization using biotin-labeled 18S rDNA and demonstrated that it is exclusively localized in the fibrillar centers (FCs) and the nucleolus-associated chromatin (NAC). A secondary antibody coupled to the smallest (5 nm) colloidal gold particles was used in this technique to increase the label. Another important factor to increase the label was pretreatment with proteinase. Convincing results are obtained when the samples are pretreated with 1 microg/mL proteinase K for 45 min at 37 degrees C before immunogold labeling.

Characterization of microbial communities in exhaust air treatment systems of large-scale pig housing facilities

Exhaust air treatment has gained importance as an essential factor in intensive livestock areas due to the rising emissions in the environment. Wet filter walls of multi-stage exhaust air treatment systems precipitate gaseous ammonia and dust particles from exhaust air in washing water. Microbial communities in the biomass developed in the washing water of five large-scale exhaust air treatment units of pig housing facilities, were investigated by fluorescence in situ hybridization (FISH) and 16S rDNA sequence analyses. No "standard" nitrifying bacteria were found in the washing water. Instead mainly α-Proteobacteria, aggregating β- and χ-Proteobacteria, a large number of Actinobacteria, as well as individual Planctomycetales and Crenarchaeota were detected after more than twelve months' operation. The main Proteobacteria species present were affiliated to the families Alcaligenaceae, Comamonadaceae and Xanthomonadaceae. Furthermore, we investigated the consumption of inorganic nitrogen compounds in the washing water of one exhaust air treatment unit during a fattening period with and without pH control. Maintaining the pH at 6.0 resulted in a ca. fivefold higher ammonium concentration and a ca. fourfold lower concentration of oxidized nitrogen compounds after the fattening period was finished.

[Identification of Anopheles maculipennis group species using polymerase chain reaction (PCR) in the regions of Birecik, Beyşehir and Cankiri]

Malaria is the most important vector borne disease in the world and is endemic in the southeastern Anatolia region of Turkey. Most important vector species for this disease are found within the Anopheles maculipennis group that is distributed in the Palaearctic Region. The aim of this study was to identify the species of this group distributed within the regions of Birecik, Beyşehir and Cankiri using molecular methods. The results of the molecular analysis indicated that only populations of An. sacharovi which is the main malaria vector in our country are found in Biricik. Anopheles maculipennis s.s, Anopheles melanoon and An. sacharovi were identified in the Beyşehir region and An. maculipennis s.s and An. Sacharovi, in the Cankiri region. The most abundant species in Beyşehir and Cankiri has been determined to be An. maculipennis s.s.

[Analysis of 16S rDNA sequence of Cronobacter spp]

OBJECTIVE

To analyse the sequence of 16S rDNA of twenty-nine Cronobacter spp. strains isolated from food as well as two type strains.

METHODS

Using polymerase chain reaction to obtain the sequences of 16S rDNA of all strains. The multiple cluster analysis and phylogenetic analysis of them were studied by BioNumerics software.

RESULTS

All strains, except ATCC51329 and ES 014, were clustered with the Cronobacter spp. type strain ATCC29544. The Cronobacter spp. type strain ATCC51329 and ES 014 belonged to a different branch. From the sequence analysis of 16S rDNA, all these isolates of Cronobacter spp. except ES 014 could be identified accurately by gene analysis.

CONCLUSION

All Cronobacter spp. strains isolated from food were identified on genetic level. The phylogenetic relationships among related Cronobacter spp. isolates were studied.

Nautilia nitratireducens sp. nov., a thermophilic, anaerobic, chemosynthetic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent

A thermophilic, anaerobic, chemosynthetic bacterium, designated strain MB-1(T), was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at degrees 50' N 10 degrees 17' W. The cells were Gram-negative-staining rods, approximately 1-1.5 mum long and 0.3-0.5 mum wide. Strain MB-1(T) grew at 25-65 degrees C (optimum 55 degrees C), with 10-35 g NaCl l(-1) (optimum 20 g l(-1)) and at pH 4.5-8.5 (optimum pH 7.0). Generation time under optimal conditions was 45.6 min. Growth occurred under chemolithoautotrophic conditions with H(2) as the energy source and CO(2) as the carbon source. Nitrate was used as the electron acceptor, with resulting production of ammonium. Thiosulfate, sulfur and selenate were also used as electron acceptors. No growth was observed in the presence of lactate, peptone or tryptone. Chemo-organotrophic growth occurred in the presence of acetate, formate, Casamino acids, sucrose, galactose and yeast extract under a N(2)/CO(2) gas phase. The G+C content of the genomic DNA was 36.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Nautilia profundicola AmH(T), Nautilia abyssi PH1209(T) and Nautilia lithotrophica 525(T) (95, 94 and 93 % sequence identity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Nautilia, Nautilia nitratireducens sp. nov. The type strain is MB-1(T) (=DSM 22087(T) =JCM 15746(T)).

Terrabacter aeriphilus sp. nov., isolated from an air sample

A novel actinomycete, designated strain 5414T-18(T), was isolated from an air sample collected from the Taean region, Korea. The strain contained oxidase and grew in the presence of 7 % NaCl. A neighbour-joining tree constructed on the basis of the 16S rRNA gene sequence showed that strain 5414T-18(T) is a member of the genus Terrabacter, sharing 97.8-98.3 % 16S rRNA gene sequence similarities to type strains of species of the genus Terrabacter (98.3 % sequence similarity with Terrabacter lapilli LR-26(T)). It contained peptidoglycan containing ll-diaminopimelic acid of A3gamma type, with three glycine residues as the interpeptide bridge. Whole-cell sugars were glucose, mannose and ribose. Mycolic acids were absent. The predominant menaquinone was MK-8(H(4)). The major fatty acids (>7 % of total fatty acids) were iso-C(15 : 0), iso-C(16 : 0), C(17 : 1)omega8c and iso-C(14 : 0). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and an unidentified phosphoglycolipid. The DNA G+C content of the type strain was 73 mol%. Strain 5414T-18(T) exhibited DNA-DNA relatedness levels of 44, 43, 39, 34 and 34 % to the type strains of Terrabacter lapilli, Terrabacter aerolatus, Terrabacter terrae, Terrabacter tumescens and Terracoccus luteus, respectively. These findings suggest that strain 5414T-18(T) represents a novel species within the genus Terrabacter. The name Terrabacter aeriphilus sp. nov. is proposed for this novel species, with the type strain 5414T-18(T) (=KACC 20693(T)=DSM 18563(T)).

Staphylococcus massiliensis sp. nov., isolated from a human brain abscess

Gram-positive, catalase-positive, coagulase-negative, non-motile, non-fermentative and novobiocin-susceptible cocci were isolated from a human brain abscess sample (strain 5402776(T)). This novel strain was analysed by a polyphasic taxonomic approach. The respiratory quinones detected were MK-7 (93 %) and MK-6 (7 %) and the major fatty acids were C(15 : 0) iso (60.5 %), C(17 : 0) iso (8.96 %) C(15 : 0) anteiso (7.93 %) and C(19 : 0) iso (6.78 %). The peptidoglycan type was A3alpha l-Lys-Gly(2-3)-l-Ser-Gly. Based on cellular morphology and biochemical criteria, the new isolate was assigned to the genus Staphylococcus, although it did not correspond to any recognized species. The G+C content of the DNA was 36.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the new isolate was most closely related to Staphylococcus piscifermentans, Staphylococcus condimenti, Staphylococcus carnosus subsp. carnosus, S. carnosus subsp. utilis and Staphylococcus simulans (97.7 %, 97.6 %, 97.6 %, 97.6 % and 96.5 % sequence similarity, respectively). Comparison of tuf, hsp60, rpoB, dnaJ and sodA gene sequences was also performed. In phylogenetic analysis inferred from tuf, dnaJ and rpoB gene sequence comparisons, strain 5402776(T) clustered with Staphylococcus pettenkoferi (93.7 %, 82.5 % and 89 % sequence similarity, respectively) and on phylogenetic analysis inferred from sodA gene sequence comparisons, it clustered with Staphylococcus chromogenes (82.8 %). On the basis of phenotypic and genotypic data, this isolate represents a novel species for which the name Staphylococcus massiliensis sp. nov. is proposed (type strain 5402776(T)=CCUG 55927(T)=CSUR P23(T)).

Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata

A Gram-negative, aerobic, rod-shaped bacterium, designated strain CL-33(T), was isolated from the encrusting pore coral Montipora aequituberculata collected from seawater off the coast of southern Taiwan. 16S rRNA gene sequence analysis showed that the strain clustered closely with Endozoicomonas elysicola MKT110(T) (96.7 % similarity). The novel strain required NaCl for growth and exhibited optimal growth at 25 degrees C and in the presence of 2-3 % NaCl. Predominant cellular fatty acids were summed feature 3 (C(16 : 1)omega7c and/or C(16 : 1)omega6c; 39.6 %), summed feature 8 (C(18 : 1)omega7c and/or C(18 : 1)omega6c; 32.8 %) and C(16 : 0) (12.0 %). The DNA G+C content of strain CL-33(T) was 50.0 mol%. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of this isolate from E. elysicola. It is evident from the genotypic, phenotypic and chemotaxonomic data presented that strain CL-33(T) represents a novel species of the genus Endozoicomonas, for which the name Endozoicomonas montiporae sp. nov. is proposed. The type strain is CL-33(T) (=LMG 24815(T) =BCRC 17933(T)).

Burkholderia heleia sp. nov., a nitrogen-fixing bacterium isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps in actual acid sulfate soil areas of Vietnam

Nitrogen-fixing bacteria, strains SA41(T), SA42 and SA53, were isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps (pH 2-4) in actual acid sulfate soil areas of Vietnam. The isolates were Gram-negative, aerobic, non-spore-forming, rod-shaped bacteria, having a cell width of 0.6-0.7 microm and a length of 1.5-1.7 microm. They showed good growth between pH 3.0 and 7.0, and between 17 and 37 degrees C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone, and C(16 : 0), C(17 : 0) cyclo, C(18 : 1) omega7c and summed feature 3 (C(16 : 1) omega7c and/or iso-C(15 : 0) 2-OH) as major fatty acids. Their fatty acid profiles are similar to those reported for other Burkholderia species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Burkholderia. Although their calculated 16S rRNA gene sequence similarity values to Burkholderia silvatlantica, Burkholderia mimosarum, Burkholderia ferrariae and Burkholderia tropica were 98.5, 98.2, 98.0 and 97.0 %, respectively, the isolates formed a distinct group in phylogenetic trees, and the DNA-DNA relatedness values of strain SA41(T) to these species were 39, 41, 39 and 33 %, respectively. The results of physiological and biochemical tests, including whole-cell protein pattern analysis, allowed phenotypic differentiation of these strains from the published Burkholderia species. Therefore, strains SA41(T), SA42 and SA53 represent a novel species for which the name Burkholderia heleia sp. nov. is proposed. The type strain is SA41(T) (=NBRC 101817(T)=VTCC-D6-7(T)).

Rhodotorula arctica sp. nov., a basidiomycetous yeast from Arctic soil

Three isolates, typified by Pro94 Y29(T) (=JCM 13290(T) =CBS 9278(T) =DBVPG 7841(T)), that represent a novel species, Rhodotorula arctica sp. nov., were studied. R. arctica differed from its only close relative, Bensingtonia yamatoana, by requiring thiamine and by failing to assimilate maltose and quinate, but strain Pro94 Y29(T) could be most readily identified using the rDNA sequence of the LSU D1/D2 region, which differed from that of B. yamatoana CBS 7423(T) at four positions, and the ITS sequence, which differed at nine positions. One R. arctica isolate, Pro94 Y56 (=JCM 13292 =CBS 9280 =DBVPG Y7843), was unique in requiring either l-arginine or l-citrulline as a source of nitrogen.

Brucella inopinata sp. nov., isolated from a breast implant infection

A Gram-negative, non-motile, non-spore-forming coccoid bacterium (strain BO1(T)) was isolated recently from a breast implant infection of a 71-year-old female patient with clinical signs of brucellosis. Affiliation of strain BO1(T) to the genus Brucella was confirmed by means of polyamine pattern, polar lipid profile, fatty acid profile, quinone system, DNA-DNA hybridization studies and by insertion sequence 711 (IS711)-specific PCR. Strain BO1(T) harboured four to five copies of the Brucella-specific insertion element IS 711, displaying a unique banding pattern, and exhibited a unique 16S rRNA gene sequence and also grouped separately in multilocus sequence typing analysis. Strain BO1(T) reacted with Brucella M-monospecific antiserum. Incomplete lysis was detected with bacteriophages Tb (Tbilisi), F1 and F25. Biochemical profiling revealed a high degree of enzymic activity and metabolic capabilities. In multilocus VNTR (variable-number tandem-repeat) analysis, strain BO1(T) showed a very distinctive profile and clustered with the other 'exotic' Brucella strains, including strains isolated from marine mammals, and Brucella microti, Brucella suis biovar 5 and Brucella neotomae. Comparative omp2a and omp2b gene sequence analysis revealed the most divergent omp2 sequences identified to date for a Brucella strain. The recA gene sequence of strain BO1(T) differed in seven nucleotides from the Brucella recA consensus sequence. Using the Brucella species-specific multiplex PCR assay, strain BO1(T) displayed a unique banding pattern not observed in other Brucella species. From the phenotypic and molecular analysis it became evident that strain BO1( T) was clearly different from all other Brucella species, and therefore represents a novel species within the genus Brucella. Because of its unexpected isolation, the name Brucella inopinata with the type strain BO1(T) (=BCCN 09-01(T)=CPAM 6436(T)) is proposed.

Enrichment of bacteria possessing catechol dioxygenase genes in the rhizosphere of Spirodela polyrrhiza: a mechanism of accelerated biodegradation of phenol

The bacterial community structure in bulk water and in rhizosphere fractions of giant duckweed, Spirodela polyrrhiza, was quantitatively and qualitatively investigated by PCR-based methods using 6 environmental water samples to elucidate the mechanisms underlying selective accumulation of aromatic compound-degrading bacteria in the rhizosphere of S. polyrrhiza. S. polyrrhiza selectively accumulated a diverse range of aromatic compound-degrading bacteria in its rhizosphere, regardless of the origin of water samples, despite no exposure to phenol. The relative abundances of the catechol 1,2-dioxygenase (C12O) gene (C12O DNA) and catechol 2,3-dioxygenase (C23O) gene (C23O DNA) were calculated as the ratios of the copy numbers of these genes to the copy number of 16S rDNA and are referred to as the rhizosphere effect (RE) value. The RE values for C12O DNA and C23O DNA were 1.0 x 10(1)-9.3 x 10(3) and 1.7 x 10(2)-1.5 x 10(4) times as high, respectively, in rhizosphere fractions as in bulk water fractions, and these higher values were associated with a notably higher sequence diversity of C12O DNA and C23O DNA. The RE values during phenol degradation were 3.6 x 10(0)-4.3 x 10(2) and 2.2 x 10(0)-1.7 x 10(2), respectively, indicating the ability of S. polyrrhiza to selectively accumulate aromatic compound-degrading bacteria in its rhizosphere during phenol degradation. The bacterial communities in the rhizosphere fractions differed from those in the bulk water fractions, and those in the bulk water fractions were notably affected by the rhizosphere bacterial communities. S. polyrrhiza released more than 100 types of phenolic compound into its rhizosphere as root exudates at the considerably high specific release rate of 1520mg TOC and 214mg phenolic compounds/d/g root (wet weight). This ability of S. polyrrhiza might result in the selective recruitment and accumulation of a diverse range of bacteria harboring genes encoding C12O and C23O, and the subsequent accelerated degradation of phenol in the rhizosphere.

Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent

A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T)).

Gordonibacter pamelaeae gen. nov., sp. nov., a new member of the Coriobacteriaceae isolated from a patient with Crohn's disease, and reclassification of Eggerthella hongkongensis Lau et al. 2006 as Paraeggerthella hongkongensis gen. nov., comb. nov

A strictly anaerobic, Gram-positive, short-rod/coccobacillus-shaped bacterial strain, designated 7-10-1-b(T), was isolated from the colon of a patient suffering from acute Crohn's disease. The isolate formed small, pale-white, semi-translucent colonies on solid cultivation media. The strain was catalase-positive and metabolized only a small number of carbon sources. Whole-cell fatty acids consisted predominantly of saturated fatty acids (89 %), of which 15 : 0 anteiso was the major component. The polar lipids phosphatidylglycerol and diphosphatidylglycerol as well as four glycolipids were identified. 16S rRNA gene sequence analysis revealed that the isolate represents a distinct lineage within the family Coriobacteriaceae and has 94.6 % identity to the type strain of [Eggerthella] hongkongensis, the phylogenetically closest bacterial species. On the basis of the analyses performed, the new genus and species Gordonibacter pamelaeae gen. nov., sp. nov. is described, with strain 7-10-1-b(T) (=DSM 19378(T) =CCUG 55131(T)) as the type and only strain of Gordonibacter pamelaeae. Also, based on the chemotaxonomic data obtained for all type strains of the neighbouring genus Eggerthella, we propose that Eggerthella hongkongensis Lau et al. 2006 be transferred to a new genus as Paraeggerthella hongkongensis gen. nov., comb. nov.; the type strain of Paraeggerthella hongkongensis is HKU10(T) (=DSM 16106(T) =CCUG 49250(T)).

Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis

During a search for exo-enzyme-producing bacteria in the gut of an insect, Diestrammena apicalis, a novel bacterium capable of degrading pectin was isolated. The isolate, designated strain RCB-08(T), comprised Gram-positive, endospore-forming, motile rods capable of growth at 15-30 degrees C and pH 6.0-8.7. The DNA G+C content of the isolate was 51.5 mol% and the predominant cellular fatty acid was anteiso-C(15 : 0) (74.1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RCB-08(T) was affiliated with a cluster within the Paenibacillaceae, and was related most closely to Paenibacillus chondroitinus NBRC 15376(T), with a sequence similarity of 96.7 %. The DNA-DNA relatedness value for strain RCB-08(T) with P. chondroitinus NBRC 15376(T) was 15.0 %. Strain RCB-08(T) hydrolysed pectin, but not cellulose, casein, starch or xylan. Strain RCB-08(T) could be clearly distinguished from other Paenibacillus species on the basis of characteristics observed using a polyphasic approach. Therefore strain RCB-08(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus pectinilyticus sp. nov. is proposed. The type strain is RCB-08(T) (=KCTC 13222(T)=CECT 7358(T)).

Roseovarius pacificus sp. nov., isolated from deep-sea sediment

An aerobic, Gram-negative, ovoid to rod-shaped bacterial isolate, strain 81-2(T), was isolated from deep-sea sediment of the Western Pacific Ocean. Strain 81-2(T) was motile, formed faint pink colonies, and was catalase-positive, weakly positive for oxidase and required NaCl for growth. It did not synthesize bacteriochlorophyll a and its DNA G+C content was 62.3 mol%. The 16S rRNA gene sequence of strain 81-2(T) indicated that it was a member of the Roseobacter clade of the class Alphaproteobacteria, with moderate bootstrap support for inclusion in the genus Roseovarius. Its closest phylogenetic neighbour was the type strain of Roseovarius nubinhibens, which shared 95.8 % 16S rRNA gene sequence similarity; strain 81-2(T) was <95.0 % similar to strains of other related species and genera. Phenotypic, chemotaxonomic and phylogenetic data support assignment of this strain to the genus Roseovarius as a representative of a novel species. The name Roseovarius pacificus sp. nov. is proposed, with strain 81-2(T) (=MCCC 1A00293(T)=CGMCC 1.7083(T)=LMG 24575(T)) as the type strain.

Assays for mitotic chromosome condensation in live yeast and mammalian cells

The dynamic reorganization of chromatin into rigid and compact mitotic chromosomes is of fundamental importance for faithful chromosome segregation. Owing to the difficulty of investigating this process under physiological conditions, the exact morphological transitions and the molecular machinery driving chromosome condensation remain poorly defined. Here, we review how imaging-based methods can be used to quantitate chromosome condensation in vivo, focusing on yeast and animal tissue culture cells as widely used model systems. We discuss approaches how to address structural dynamics of condensing chromosomes and chromosome segments, as well as to probe for mechanical properties of mitotic chromosomes. Application of such methods to systematic perturbation studies will provide a means to reveal the molecular networks underlying the regulation of mitotic chromosome condensation.

Phylogenetic analysis of the sequences of rDNA internal transcribed spacer (ITS) of Phytophthora sojae

The internal transcribed spacer (ITS) region (ITS1, ITS2 and 5.8S rDNA) of the nuclear ribosomal DNA (nrDNA) was amplified via the PCR method in seventeen different isolates of Phytophthora sojae using the common primers of the ITS of fungi. Around 800 bp-1,000 bp fragments were obtained based on the DL2000 marker and the sequences of the PCR products were tested. Taking isolate USA as outgroup, the phylogenetic tree was constructed by means of maximum parsimony analysis, and the genetic evolution among isolates was analyzed. The results showed that there is a great difference between the base constitution of ITS1 and ITS2 among various isolates. The seventeen isolates are classified into three groups, and the isolates from the same region belong to the same group, which shows the variation in geography.

Study on sequences of ribosomal DNA internal transcribed spacers of clams belonging to the Veneridae family (Mollusca: Bivalvia)

The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA from four species, Meretrix meretrix L., Cyclina sinensis G., Mercenaria mercenaria L., and Protothaca jedoensis L., belonging to the family Veneridae were amplified by PCR and sequenced. The size of the ITS1 PCR amplification product ranged from 663 bp to 978 bp, with GC contents ranging from 60.78% to 64.97%. The size of the ITS1 sequence ranged from 585 bp to 900 bp, which is the largest range reported thus far in bivalve species, with GC contents ranging from 61.03% to 65.62%. The size of the ITS2 PCR amplification product ranged from 513 bp to 644 bp, with GC contents ranging from 61.29% to 62.73%. The size of the ITS2 sequence ranged from 281 bp to 412 bp, with GC contents ranging from 65.21% to 67.87%. Extensive sequence variation and obvious length polymorphisms were noted for both regions in these species, and sequence similarity of ITS2 was higher than that of ITS1 across species. The complete sequences of 5.8S ribosomal RNA gene were obtained by assembling ITS1 and ITS2 sequences, and the sequence length in all species was 157 bp. The phylogenetic tree of Veneridae clams was reconstructed using ITS2-containing partial sequences of both 5.8S and 28S ribosomal DNA as markers and the corresponding sequence information in Arctica islandica as the outgroup. Tree topologies indicated that P. jedoensis shared a close relationship with M. mercenaria and C. sinensis, a distant relationship with other species.

The identity of Anisakis type II larvae with Anisakis physeteris confirmed by restriction fragment length polymorphism analysis of genomic DNA

The identity of Anisakis type II larvae with adult A. physeteris was confirmed by comparison of restriction fragment length polymorphisms (RFLPs) of 25S ribosomal DNA (rDNA). Patterns of RFLPs in larvae were almost identical with those in adult worms. Directly labelled 25S rDNA might serve as an appropriate probe with highly specific activity for examining RFLPs of larvae and adult worms.

[Isolation and characterisation of Spiroplasma sp. from Phytomia zonata (Diptera: Syrphidae)]

OBJECTIVE

To obtain the spiroplasma resources and characterize the spiroplasmas from insects in China, as well as study the taxonomy of spiroplasma based on biological characteristics.

METHODS

We determined morphology by using dark field and transmission electron microscopy. The biological characteristics of the spiroplasmas were studied by using conventional culture-dependent method and phylogenetic analysis based on 16S rDNA.

RESULTS

Based on morphological characteristics, biological characteristics and phylogenetic evidences, we studied the taxonomy of the strain YY0801 isolated from Phytomia zonata (Diptera: Syrphidae). The isolate grew well in R2 liquid medium and could pass through 0.22 microm and 0.45 microm filtrate membranes. The colony was grain-like in solid medium. Through electron microscopy, the isolate YY0801 exhibited helicity during their exponential growth phase. The isolate YY0801 was able to ferment glucose and D-fructose and to catabolize arginine, but did not to hydrolyse urea. The isolate was resistant to ampicillin (2000 U/mL). The phylogenetic relationships based on 16S rDNA supported YY0801 grouped with the serogroup I and was close to S. melliferum.

CONCLUSION

The result indicated that the spiroplasma isolate YY0801 was close to S. melliferum, but further designation need support of serological analyses.

[Endophytic bacterial diversity in Glycyrrhiza inflata Bat. from Xinjiang by culture-independent method]

OBJECTIVE

We investigated endophytic bacterial diversity in Glycyrrhiza inflata Bat. from Xinjiang.

METHODS

We investigated endophytic bacterial diversity in root of Glycyrrhiza inflata Bat. from Xingjian by culture-independent method. Total DNA genome of Glycyrrhiza sample was extracted using CTAB (Hexadecyl trimethyl ammonium Bromide) procedure with some modifications. A pair of bacterial PCR primers were used for endophytic bacterial 16S rDNA gene amplification and a clone library was constructed for the Glycyrrhiza DNA samples. Clones screened from clone library on the basis of Hae III digestion patterns were sequenced and compared, flowed by constructing Neighbor-Joining tree.

RESULTS

In total 150 clones were grouped to 32 operational taxonomic units, most of the clones showed high similarity to the known cultured bacteria. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, gamma subclasses of the Proteobacteria, Bacteroides, Firmicutes, Actinobacteria, and Uncultured bacteria; 74% of the clones were highly related to the known bacteria in the genus Sphingobium, Phyllobacterium, Hyphomonas, Agrobacterium etc (> 96% sequence similarity); whereas 26% of the clones showed lower affiliation with known genus (< 96% sequence similarity) and may represent novel taxa.

CONCLUSION

There was abundant endophytic bacterial diversity in Glycyrrhiza inflata Bat. from Xinjiang as well as many unknown organisms.

Identification of airborne bacterial and fungal species in the clinical microbiology laboratory of a university teaching hospital employing ribosomal DNA (rDNA) PCR and gene sequencing techniques

Universal or "broad-range" PCR-based ribosomal DNA (rDNA) was performed on a collection of 58 isolates (n = 30 bacteria + 28 fungi), originating from environmental air from several locations within a busy clinical microbiology laboratory, supporting a university teaching hospital. A total of 10 bacterial genera were identified including both Gram-positive and Gram-negative genera. Gram-positive organisms accounted for 27/30 (90%) of total bacterial species, consisting of seven genera and included (in descending order of frequency) Staphylococcus, Micrococcus, Corynebacterium, Paenibacillus, Arthrobacter, Janibacter and Rothia. Gram-negative organisms were less frequently isolated 3/30 (10%) and comprised three genera, including Moraxella, Psychrobacter and Haloanella. Eight fungal genera were identified among the 28 fungal organisms isolated, including (in descending order of frequency) Cladosporium, Penicillium, Aspergillus, Thanatephorus, Absidia, Eurotium, Paraphaeosphaeria and Tritirachium, with Cladosporium accounting for 10/28 (35.7%) of the total fungal isolates. In conclusion, this study identified the presence of 10 bacterial and eight fungal genera in the air within the laboratory sampled. Although this reflected diversity of the microorganisms present, none of these organisms have been described previously as having an inhalational route of laboratory-acquired infection. Therefore, we believe that the species of organisms identified and the concentration levels of these airborne contaminants determined, do not pose a significant health and safety threat for immunocompotent laboratory personnel and visitors.

[Selective isolation and diversity of acidophilic filamentous actinomycetes from acidic soils]

OBJECTIVE

To establish effective methods for selective isolation of acidophilic filamentous actinomycetes from acidic soils, and to investigate their genus and species diversity.

METHODS

Four pretreatments and 5 media supplemented with different inhibitors were used for isolation. The best combination of methods was determined according to the number and ratio of actinomycete colonies on plates, and was applied to isolate actinomycetes from 17 acidic soil samples collected in Jiangxi Province. The isolates were grouped based on cultural characteristics. The micromorphology and pH growth range of each group were studied to choose the representative isolates, which were subsequently subjected to 16S rRNA gene analysis to investigate their diversity.

RESULTS

We found the best isolation approach involved Dispersion and Differential Centrifugation (DDC) pretreatment and GTV medium supplemented with cycloheximide, nalidixic acid nystatin (each at 50 mg/L). 369 isolates were obtained, and were assigned to 10 color groups. 6.6% of the isolates were strictly acidophilic actinomycetes, 72.4% were neutrotolerant acidophilic actinomycetes, and 21.0% were acidotolerant ones. The 52 representative isolates belong to 12 recognized genera: 30 of them fall within the genus Streptomyces, 6 belong to Micromonospora, 3 belong to Nocardia, 3 belong to Nonomuraea, 2 belong to Kribbella, 2 belong to Microbispora, and the other 6 strains belong to Actinomadura, Amycolatopsis, Dactylosporangium, Lentzea, Planotetraspora and Streptacidiphilus, respectivley. The Streptomyces isolates formed 12 evolutionary groups in the Streptomyces 16S rRNA gene tree.

CONCLUSION

The selective isolation approach established here is robust for isolating various acidophilic filamentous actinomycetes from soil. Acidic soils in Jiangxi Province harbor abundant and diverse acidophilic actinomycetes.

Monophyly of the family Desmoscolecidae (Nematoda, Demoscolecida) and its phylogenetic position inferred from 18S rDNA sequences

To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia longicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct sub-groups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].

Utility of 16S ribosomal DNA sequencing in the diagnosis of Staphylococcus lugdunensis native valve infective endocarditis: case report and literature review

We report a case of possible infective endocarditis without fever presenting with an acutely ischemic limb with prior antimicrobial therapy preventing identification by culture of a microorganism. 16S ribosomal DNA sequencing led to the identification of Staphylococcus lugdunensis from an embolus removed at surgery and subsequent successful antibiotic treatment. We review the utility of 16S ribosomal DNA sequencing in diagnosing infective endocarditis and other infectious conditions.

Pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in Flanders

Bacterial midrib rot of greenhouse-grown butterhead lettuce (Lactuca sativa L. var. capitata) is an emerging disease in Flanders (Belgium) and fluorescent pseudomonads are suspected to play an important role in the disease. Isolations from infected lettuces, collected from 14 commercial greenhouses in Flanders, yielded 149 isolates that were characterized polyphasically, which included morphological characteristics, pigmentation, pathogenicity tests by both injection and spraying of lettuce, LOPAT characteristics, FAME analysis, BOX-PCR fingerprinting, 16S rRNA and rpoB gene sequencing, as well as DNA-DNA hybridization. Ninety-eight isolates (66%) exhibited a fluorescent pigmentation and were associated with the genus Pseudomonas. Fifty-five of them induced an HR+ (hypersensitive reaction in tobacco leaves) response. The other 43 fluorescent isolates were most probably saprophytic bacteria and about half of them were able to cause rot on potato tuber slices. BOX-PCR genomic fingerprinting was used to assess the genetic diversity of the Pseudomonas midrib rot isolates. The delineated BOX-PCR patterns matched quite well with Pseudomonas morphotypes defined on the basis of colony appearance and variation in fluorescent pigmentation. 16S rRNA and rpoB gene sequence analyses allowed most of the fluorescent isolates to be allocated to Pseudomonas, and they belonged to either the Pseudomonas fluorescens group, Pseudomonas putida group, or the Pseudomonas cichorii/syringae group. In particular, the isolates allocated to this latter group constituted the vast majority of HR+ isolates and were identified as P. cichorii by DNA-DNA hybridization. They were demonstrated by spray-inoculation tests on greenhouse-grown lettuce to induce the midrib rot disease and could be re-isolated from lesions of inoculated plants. Four HR+ non-fluorescent isolates associated with one sample that showed an atypical midrib rot were identified as Dickeya sp.

[Etiology of off-plate syndrome in cultured larval Apostichopus japonicus at attachment stage and analysis of reservoir of pathogens]

OBJECTIVE

To clarify pathogens and sources of the off-plate syndrome at the attachment stage in the larval culture of Apostichopus japonicus, and further to find out effective medicines for this disease.

METHODS

Etiological analysis was performed on larvae with typical off-plate syndrome from three larvae culture factories. Suspicious pathogens were used for artificial infection test, and were identified through morphological, physiological and biochemical tests, and 16S rDNA sequence analysis. Quantitative bacterial analysis was done on the culture systems of the three factories, including water sources, rearing water, ordure (in the pond floor), attachments and feeds. Finally, drug-sensitive tests were done against the pathogens.

RESULTS

A common dominant bacterium strain was isolated from all ill larvae included in the study. Artificial infection test showed it was the causative pathogen associated with the disease, and the artificially infected sea cucumbers had same syndromes to the naturally ill ones. The bacterium was identified as Vibrio sp. Bacterial quantity of water sources was in the qualified range (<50 cfu/mL), while out of the standard range in others (> 1 x 10(5) cfu/mL). The sources of the pathogen were complicated, since pathogens were discovered in the water sources, rearing water, ordure, attachments and feeds. However, the density of causative bacteria was the highest in the feeds, middle in the attachments, and lowest in the water sources. Twelve antibiotics could inhibit growth of the pathogens.

CONCLUSION

The possible pathogen for off-plate syndrome was Vibrio sp. Feeds may be the main source of the pathogen. Twelve antibiotics besides nalidixic acid could be applied for disease prevention and treatment of Apostichopus japonicus.

[Taxonomic position of bifidobacteria and modern methods for their identification]

Literature data, concerning current state of taxonomy of microorganisms of genus Bifidobacterium are presented in the review. The question of creation of necessary conditions for accurate identification of these bacteria has been revealed, as well as the basic principles of novel molecular-genetic approaches for microorganisms' typing (as they are used for the detection and identification of bifidobacteria) have been described. Main information sources in systematics, classification and nomenclature have been listed. The paper is presented in Ukrainian.

Modern subsurface bacteria in pristine 2.7 Ga-old fossil stromatolite drillcore samples from the Fortescue Group, Western Australia

Background

Several abiotic processes leading to the formation of life-like signatures or later contamination with actual biogenic traces can blur the interpretation of the earliest fossil record. In recent years, a large body of evidence showing the occurrence of diverse and active microbial communities in the terrestrial subsurface has accumulated. Considering the time elapsed since Archaean sedimentation, the contribution of subsurface microbial communities postdating the rock formation to the fossil biomarker pool and other biogenic remains in Archaean rocks may be far from negligible.

Methodology/Principal Findings

In order to evaluate the degree of potential contamination of Archean rocks by modern microorganisms, we looked for the presence of living indigenous bacteria in fresh diamond drillcores through 2,724 Myr-old stromatolites (Tumbiana Formation, Fortescue Group, Western Australia) using molecular methods based on the amplification of small subunit ribosomal RNA genes (SSU rDNAs). We analyzed drillcore samples from 4.3 m and 66.2 m depth, showing signs of meteoritic alteration, and also from deeper “fresh” samples showing no apparent evidence for late stage alteration (68 m, 78.8 m, and 99.3 m). We also analyzed control samples from drilling and sawing fluids and a series of laboratory controls to establish a list of potential contaminants introduced during sample manipulation and PCR experiments. We identified in this way the presence of indigenous bacteria belonging to Firmicutes, Actinobacteria, and Alpha-, Beta-, and Gammaproteobacteria in aseptically-sawed inner parts of drillcores down to at least 78.8 m depth.

Conclusions/Significance

The presence of modern bacterial communities in subsurface fossil stromatolite layers opens the possibility that a continuous microbial colonization had existed in the past and contributed to the accumulation of biogenic traces over geological timescales. This finding casts shadow on bulk analyses of early life remains and makes claims for morphological, chemical, isotopic, and biomarker traces syngenetic with the rock unreliable in the absence of detailed contextual analyses at microscale.

Ginsenoside Rb1 in asymmetric somatic hybrid calli of Daucus carota with Panax quinquefolius

American ginseng (Panax quinquefolius L.) is one of the most valuable herbs in the world. Its major active components are ginsenosides. In order to produce ginsenoside heterogeneously, somatic hybridization, a novel approach for genetic introgression, was employed in this study. Protoplasts derived from respective calli of carrot (Daucus carota var. sativus Hoffm.) and American ginseng (P. quinquefolius L.) were used as the fusion partners. Hybrid calli derived from single cell lines containing chromatin of American ginseng were confirmed by the analyses of isozyme, Random amplified polymorphic DNA (RAPD) and genomic in situ hybridization (GISH). High performance liquid chromatography (HPLC) results showed that the ginseng monomer Rb(1) was synthesized in seven of the hybrid calli identified as well as in the parent American ginseng calli but not in the parent carrot calli. Results indicated that hybrid introgression lines could produce ginsenoside Rb(1) and the ginsenoside Rb(1) biosynthesis pathway has been introgressed into carrot cells via somatic hybridization. From the point of biosafety view concerning the consumer acceptance, the potential predominance to produce ginsenosides with somatic hybridization other than with genetic transformation is discussed.

[Effects of enrofloxacin on DNA sequence diversity of soil cultural bacterial community]

In order to understand the effects of remained enrofloxacin (ENR) in environment on the diversity of soil microbial communities, amplified ribosomal DNA restriction analysis (ARDRA) approach and genomic fingerprinting technique enterobacterial repetitive intergenic consensus sequence-polymerase chain reaction (ERIC-PCR) were used to analyze the molecular diversity of 16S rDNA from soil bacteria after ENR addition. The results showed that after the ENR addition for 35 days, the total count of soil bacteria was less than that of CK, and decreased with increasing ENR concentration. The ARDRA divided the separated soil bacteria into different operational taxonomic units (OTU) groups, and the count of group I to group VI was 15, 13, 10, 8, 6, and 6, respectively. Genomic fingerprinting analysis indicated that the Shannon-Wiener index of group I to group VI was 2.78, 2.14, 1.78, 1.11, 0.69 and 0.31, respectively, and the Margalef index, Simpson index, and Pielou index of soil microbial community in CK were higher than that in the soils in which ENR was added.

Significant performance variation among PCR systems in diagnosing congenital toxoplasmosis in São Paulo, Brazil: analysis of 467 amniotic fluid samples

INTRODUCTION

Performance variation among PCR systems in detecting Toxoplasma gondii has been extensively reported and associated with target genes, primer composition, amplification parameters, treatment during pregnancy, host genetic susceptibility and genotypes of different parasites according to geographical characteristics.

PATIENTS

A total of 467 amniotic fluid samples from T. gondii IgM- and IgG-positive Brazilian pregnant women being treated for 1 to 6 weeks at the time of amniocentesis (gestational ages of 14 to 25 weeks).

METHODS

One nested-B1-PCR and three one-round amplification systems targeted to rDNA, AF146527 and the B1 gene were employed.

RESULTS

Of the 467 samples, 189 (40.47%) were positive for one-round amplifications: 120 (63.49%) for the B1 gene, 24 (12.69%) for AF146527, 45 (23.80%) for both AF146527 and the B1 gene, and none for rDNA. Fifty previously negative one-round PCR samples were chosen by computer-assisted randomization analysis and re-tested (nested-B1-PCR), during which nine additional cases were detected (9/50 or 18%).

DISCUSSION

The B1 gene PCR was far more sensitive than the AF146527 PCR, and the rDNA PCR was the least effective even though the rDNA had the most repetitive sequence. Considering that the four amplification systems were equally affected by treatment, that the amplification conditions were optimized for the target genes and that most of the primers have already been reported, it is plausible that the striking differences found among PCR performances could be associated with genetic diversity in patients and/or with different Toxoplasma gondii genotypes occurring in Brazil.

CONCLUSION

The use of PCR for the diagnosis of fetal Toxoplasma infections in Brazil should be targeted to the B1 gene when only one gene can be amplified, preferably by nested amplification with primers B22/B23.

Rhizobial resource associated with epidemic legumes in Tibet

A total of 128 bacterial test strains originated from Astragalus, Caragana, Gueldenstaedtia, Medicago, Melilotus, Oxytropis, Trifolium, and Vicia grown in Tibet were characterized phenotypically and genomically. Based upon the consensus of grouping results, they were identified as 16 putative species. Twenty-five test strains belonging to seven putative species of Agrobacterium, Bradyrhizobium, and Rhizobium might be nonsymbiotic bacteria and the remaining 103 test strains were symbiotic bacteria belonging to Mesorhizobium, Rhizobium, and Sinorhizobium meliloti. Although no novel taxon was detected in the symbiotic bacteria, several characters including the alkaliphilic psychrotolerance revealed that the Tibetan rhizobia could be ecotypes adapted to the local conditions. The results also demonstrated that frequent lateral transfer of symbiotic genes might have happened in the Tibetan rhizobia since nodC genes similar to that of S. meliloti were found in several Rhizobium test strains and all the Mesorhizobium species had very similar nodC genes despite their genomic background. All of these findings demonstrated that the Tibetan rhizobia were an important resource for further studies on rhizobial ecology and application.

Erwinia amylovora: modern methods for detection and differentiation

Erwinia amylovora is the causative agent of fire blight, a very destructive disease of numerous members of the rosaceae. The primary route of infection for host species, including commercially grown apple and pear, is the newly opened blossom. Susceptibility of flowers to infection for only a few days creates narrow window for infection. Not surprisingly, the risk of disease is related to E. amylovora population size. As a result, methods that supply quick, accurate and sensitive quantification of the pathogen population are important tools for determining the need for and the efficacy of disease control intervention. Plating samples and assessing colony-forming units constitutes an accurate and sensitive but slow method. Endpoint PCR is quick and sensitive but is not particularly amenable to quantification. We describe a real-time PCR procedure that provides all requirements. This method is based on chromosomal genes rather than on the pEa29 plasmid and so can be used to measure isolates that have been cured of the plasmid. The method has been used very successfully in directly quantify whole E. amylovora cells, in a variety of tissues from the orchard environment.

Inhella inkyongensis gen. nov., sp. nov., a new freshwater bacterium in the order Burkholderiales

A freshwater bacterium, designated IMCC1713(T), was isolated from a highly eutrophic artificial pond. Cells of the strain were Gram-negative, chemoheterotrophic, polybeat and obligately aerobic short rods that were motile with a single polar flagellum. The 16S rRNA gene sequence similarity analysis showed that the novel strain was most closely related to the species Roseateles depolymerans (96.3%), Mitsuaria chitosanitabida (96.2%), Ideonella dechloratans (96.2%), and Pelomonas saccharophila (96.1%) in the Sphaerotilus-Leptothrix group within the order Burkholderiales. Phylogenetic trees based on 16S rRNA gene sequences indicated that the isolate formed an independent monophyletic clade within the order Burkholderiales. The relatively low DNA G+C content (57.4 mol%), together with several phenotypic characteristics, differentiated the novel strain from other members of the Sphaerotilus-Leptothrix group. From the taxonomic data, therefore, the strain should be classified as a novel genus and species, for which the name Inhella inkyongensis gen. nov., sp. nov. is proposed. The type strain of the proposed species is strain IMCC1713(T) (=KCTC 12791(T)=NBRC 103252(T)=CCUG 54308(T)).

[Diversity and bioactivity analysis of actinomycetes isolated from grand Shangri-La soil]

OBJECTIVE

To obtain new pharmaceuticals and enzymes with high activity,we studied the composition as well as antimicrobial and enzyme activities of actinomycetes in Grand Shangri-La.

METHODS

Using 4 media,we isolated mesophilic and psychrophilic actinomycetes from 220 soil samples collected from areas with different altitudes in Grand Shangri-La. Twenty-five representative isolates were phylogenetically analyzed based on their 16S rRNA gene sequences. Antimicrobial activities against four bacteria and seven fungi were tested using agar well diffusion method. Genes encoding type I and II polyketide synthases (PKS I, PKS II), nonribosomal peptide synthase (NRPS) and polyene cytochrome P450 hydroxylase (CYP) were screened by PCR. Furthermore,several enzyme activities of psychrophilic actinomycetes were examined.

RESULTS

The 25 representative strains belonged to 6 suborders, 12 families and 15 genera of the order Actinomycetals. For NRPS and CYP genes screening, positive strains were 14 and 11, respectively. Among the 111 actinomycetes isolated under low-temperature conditions, 88% were psychrotroph strains, 12% were psychrophilic actinomycetes, and most of them utilized gelatin, cellulose and chitin.

CONCLUSION

Actinomycetes diversity is rich in Grand Shangri-la, and has the potential for conservation and utilization of actinomycetes resources.

Diversity of aerobic methanotrophic bacteria in a permafrost active layer soil of the Lena Delta, Siberia

With this study, we present first data on the diversity of aerobic methanotrophic bacteria (MOB) in an Arctic permafrost active layer soil of the Lena Delta, Siberia. Applying denaturing gradient gel electrophoresis and cloning of 16S ribosomal ribonucleic acid (rRNA) and pmoA gene fragments of active layer samples, we found a general restriction of the methanotrophic diversity to sequences closely related to the genera Methylobacter and Methylosarcina, both type I MOB. In contrast, we revealed a distinct species-level diversity. Based on phylogenetic analysis of the 16S rRNA gene, two new clusters of MOB specific for the permafrost active layer soil of this study were found. In total, 8 out of 13 operational taxonomic units detected belong to these clusters. Members of these clusters were closely related to Methylobacter psychrophilus and Methylobacter tundripaludum, both isolated from Arctic environments. A dominance of MOB closely related to M. psychrophilus and M. tundripaludum was confirmed by an additional pmoA gene analysis. We used diversity indices such as the Shannon diversity index or the Chao1 richness estimator in order to compare the MOB community near the surface and near the permafrost table. We determined a similar diversity of the MOB community in both depths and suggest that it is not influenced by the extreme physical and geochemical gradients in the active layer.

[Diversity of bacteria isolated from the South China Sea sediments]

OBJECTIVE

To isolate bacteria from Nansha area of South China sea,

METHODS

Sediment samples of 22 sites were used. Bacterial isolation was conducted on plates of marine medium, followed by 16S rRNA identification and phylogenetic analysis.

RESULTS

In total 349 bacteria were obtained, belonging to 87 species. Analyses of 16S rRNA sequence showed that Bacillus and other spore-forming bacteria occupied the majority of isolates in 10 sites. Bacillus was the most abundant bacterium and of high diversity; with 34 species and 8 possible novel species. Halobacillus also occurred frequently while other spore-forming bacteria including Brevibacillus, Paenibacillus, Pontibacillus and Thalassobacillus were also found, but less occurred in this area. In addition to these low-G+C-content bacteria, gamma-Proteobacteria were the second subgroup of high occurrence, among which Pseudomonas, Marinobacter and Alcanivorax were relatively abundant. Generally, isolates of 750-2000 m deep mainly consist of low-G+C-content bacteria, while mainly composed of gamma-Proteobacteria when the depth is over 2000 m.

CONCLUSION

Marine sediments of South China Sea are rich in spore-forming bacteria, which deserve further study and exploitation.

[Isolation and characterization of Bdellovibrio strains from the ocean]

OBJECTIVE

To isolate and identify the new Bdellovibrio strains from the sea mud of Shenzhen bay and to preliminarily study their biological characteristics.

METHODS

We isolated Bdellovibrio strains by DNB(dilute nutrient broth) double-layer plate method. Their 16S rDNAs were sequenced and their morphologies were examined under electron microscope. We identified these strains according to the ninth edition of Bergey's manual of determinative bacteriology. We also studied their biological characteristics through physiological tests.

RESULTS

We isolated 2 strains of Bdellovibrio sp. (5#-12 and 5#-sh06) from sea mud of Shenzhen bay. Both strains grew between 209C and 35 degrees C, with 259C and 309C as optimal temperature for 5#-12 and 5#-sh06, respectively. They grew between pH 6.1 and 8.6, and the opticCmal pH for both was 7.2. Lysis experiments on 58 strains of pathogens were conducted and the results showed that 5#-12 and 5#-sh06 lysed 46 and 48 strains, corresponding to 79.3% and 82.8% of lysis abilities. Taken both two Bdellovibrio strains together, they lysed 96.6% (56 strains) of tested pathogens and 100% of tested vibrios (39 strains).

CONCLUSION

The results demonstrated that Bdellovibrio have potential and significant application prospect for elimination of pathogens.

[Identification of the Burkholderia cepacia complex genomovars and their virulence in an alfalfa infection model]

OBJECTIVE

To confirm Burkholderia cepacia complex (Bcc) genomovars from agricultural niches and clinical samples, and to evaluate their possible virulence to human body on alfalfa infection model in China.

METHODS

A total of 57 Bcc strains were isolated and collected from the rhizosphere, soil and clinical samples in China. The genomovars composition of the Bcc strains was analyzed by species-specific PCR tests, and the virulence of the Bce strains was tested on alfalfa seedlings.

RESULTS

Four genomovars of the ten genomovars were detected among the Bcc strains, including B. cepacia (genomovar I), B. cenocepacia (genomovar III), B. vietnamiensis (genomovarV) and B. pyrrocinia (genomovar IX). Bcc genomovars I and III A from clinic, and genomovar III B from rhizosphere were the most virulent in the alfalfa infection model, and caused symptoms in 69%, 68% and 55% of seedlings, respectively. There were significant variances in the mean percentage of seedlings with symptoms for genomovars I , III A and III B compared to those for genomovar V and IX.

CONCLUSION

There was difference in the ability to cause disease in alfalfa for different genomovar strains from agricultural inches. The strains of Bcc genomovar III B from rhizosphere were more virulent similar to those of Bcc genomovar III A from clinic.

Description of Croceitalea gen. nov. in the family Flavobacteriaceae with two species, Croceitalea eckloniae sp. nov. and Croceitalea dokdonensis sp. nov., isolated from the rhizosphere of the marine alga Ecklonia kurome

Two novel bacterial strains, designated DOKDO 025(T) and DOKDO 023(T), were isolated on Dokdo Island, Korea, from the rhizosphere of the brown alga Ecklonia kurome. The strains were subjected to a polyphasic taxonomy study and were found to be Gram-negative, aerobic, rod-shaped, non-motile and orange-coloured. The isolates shared 96.3 % 16S rRNA gene sequence similarity. They showed 93.8-95.6 % 16S rRNA gene sequence similarity with respect to members of the genus Muricauda in the family Flavobacteriaceae, but formed a distinct phyletic line. Moreover, the cellular appendages reported for all Muricauda species were absent from strains DOKDO 025(T) and DOKDO 023(T). The predominant cellular fatty acids of strain DOKDO 025(T) were iso-C(15 : 0), iso-C(15 : 1) and one with an equivalent chain-length of 13.565 and those of strain DOKDO 023(T) were iso-C(15 : 0), iso-C(15 : 1) and iso-C(17 : 0) 3-OH. The DNA G+C content of strains DOKDO 025(T) and DOKDO 023(T) were 59.5 and 66.5 mol%, respectively, higher than any values found in recognized members of the family Flavobacteriaceae. The major respiratory quinone was MK-6. On the basis of evidence from the polyphasic study, strains DOKDO 025(T) and DOKDO 023(T) represent two novel species in a new genus, Croceitalea gen. nov., for which the names Croceitalea eckloniae sp. nov. (the type species) and Croceitalea dokdonensis sp. nov. are proposed. The type strain of Croceitalea eckloniae sp. nov. is DOKDO 025(T) (=KCCM 42309(T) =JCM 13827(T)) and that of Croceitalea dokdonensis sp. nov. is DOKDO 023(T) (=KCCM 42308(T) =JCM 13826(T)).

[Cloning and phylogenetic analysis of small subunit ribosomal RNA core sequence of Vairimorpha ceraces (Microspora: Burenellidae) from the insect of Lepidoptera, Cerace Stipatana (Walker)]

OBJECTIVE

Vairimorpha ceraces is a new microsporidium that isolated from the insect of Lepidoptera, Cerace Stipatana (Walker). We used 16S rDNA sequence to explore genetic status of Vairimorpha ceraces.

METHODS

SSU rDNA (small subunit ribosomal RNA) of Vairimorpha ceraces was cloned and sequenced for constructing phylogenetic tree through Neighbor-joining.

RESULTS

The core sequence of SSU rRNA of Vairimorpha ceraces with a length of 1228 nucleotides (GenBank EU267796) was successfully cloned and sequenced. Phylogenetic analysis showed that Vairimorpha ceraces was closer to the species of Vairimorpha sp. Germany (GenBank AF124331) and Vairimorpha imperfecta (GenBank AJ131645), both isolated from Plutella xylostella. The three species of genera Vairimorpha included Vairimorpha ceraces formed a clade with the Nosema spp. which from Lepidoptera host in phylogenetic tree. Conversely, other three Vairimorpha spp. from Lepidoptera (Vairimorpha necatrix, Vairimorpha sp. NISM12 and Vairimorpha lymantriae) were mixed with Nosema spp. from non-lepidopteran host in the other clade.

CONCLUSION

Combined with the biological characters, Vairimorpha ceraces was a member of genera Vairimorpha, Family Nosematidae.

Colwellia polaris sp. nov., a psychrotolerant bacterium isolated from Arctic sea ice

A novel psychrotolerant, Gram-negative, aerobic bacterium, designated strain 537T, was isolated from sea-ice samples from the Arctic. Strain 537T was able to grow at 4-26 degrees C, with optimum growth occurring at 20-21 degrees C. Strain 537T had Q-8 as the major respiratory quinone and contained iso-C15:0 2-OH and/or C16:1 omega7c (22.95 %), C15:1 (17.64 %) and C17:1 omega8c (13.74 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 38.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 537T formed a coherent cluster within the genus Colwellia. The highest level of 16S rRNA gene sequence similarity (97.5 %) exhibited by strain 537T was obtained with respect to the type strain of Colwellia aestuarii. On the basis of phenotypic, chemotaxonomic and phylogenetic properties and DNA-DNA relatedness data, strain 537T represents a novel species of the genus Colwellia, for which the name Colwellia polaris sp. nov. is proposed. The type strain is 537T (=CGMCC 1.6132T =JCM 13952T).

Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella

A bacterial strain designated GSPC1 T was isolated from root nodules of Phaseolus coccineus in Segovia (Spain). The 16S rRNA gene sequence of this strain showed 95.9 and 94.7 % sequence similarity, respectively, with those of the type strains of Cohnella hongkongensis and Cohnella thermotolerans. Strain GSPC1 T presented phenotypic, chemotaxonomic and molecular differences with respect to Cohnella species which indicated that it belonged to a different species. The isolate was a Gram-positive, aerobic, sporulated rod, motile by means of peritrichous flagella. The strain was catalase-positive and showed weak oxidase activity. It grew in the presence of 2 % NaCl. MK-7 was the predominant menaquinone. anteiso-C15:0, iso-C15:0, iso-C16: 0 and C16:0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content was 60.3 mol%. The results of this study suggest that isolate GSPC1 T should be classified within a novel Cohnella species, for which the name Cohnella phaseoli sp. nov. is proposed, with strain GSPC1T (=LMG 24086T =DSM 19269T) as the type strain.

Study of a Bordetella hinzii isolate from a laboratory mouse

Bordetella hinzii isolated from the trachea and lungs of a laboratory mouse with a respiratory infection was identified based on its phenotypic and genetic traits. The mouse showed sneezing with a chattering sound but without nasal discharge, and histopathologic examination revealed rhinitis, tracheitis, and bronchopneumonia. The isolate was a gram-negative, oxidase- and catalase-positive, short rod-shaped organism that produced alkali from malonate. The results of biochemical identification, an alkali production test from malonate, and partial sequence analysis of the 16S rRNA gene (1523 bp) were consistent with those reported previously for B. hinzii. The isolate induced sneezing in ICR mice and sneezing and slight to severe dyspnea in NOD-SCID mice after experimental infection. Histopathologic examination revealed catarrhal rhinitis and bronchopneumonia in both strains of mice and interstitial pneumonia in NOD-SCID mice. In light of these findings, B. hinzii was deemed to be a novel causative agent of respiratory disease in mice. This report describes the first isolation of B. hinzii from a mouse and confirms the organism's pathogenicity in mice.