Recharacterization of Pseudomonas fulva Iizuka and Komagata 1963, and proposals of Pseudomonas parafulva sp. nov. and Pseudomonas cremoricolorata sp. nov

Seven Pseudomonas fulva strains obtained from culture collections were taxonomically studied. The seven strains were separated into three clusters (Clusters I to III) on the basis of 16S rRNA gene sequences, and located phylogenetically in the genus Pseudomonas sensu stricto. Further, the strains were classified into 4 groups (Groups I to IV) on the basis of DNA-DNA similarity. As a result, Cluster I was split into Groups I and II. Group I included the type strain of P. fulva and two strains, and levels of DNA-DNA similarity ranged from 88 to 100% among the strains. Group II contained two strains, and the level between the two strains ranged from 91 to 100%. Group III consisted of one strain. Group IV included one strain, and this strain showed a high level of DNA-DNA similarity with the type strain of Pseudomonas straminea NRIC 0164(T). Clusters II and III corresponded to Groups III and IV, respectively. The four groups were separated from one another and from related Pseudomonas species at the level from 3 to 45% of DNA-DNA similarity. The strains of Groups I, II, and III had ubiquinone 9 as the major quinone. According to numerical analysis by the use of 133 phenotypic characteristics, the seven P. fulva strains were split into four phenons (Phenons I to IV). The groups by DNA-DNA similarity corresponded well with the phenons produced by numerical taxonomy, and differential characteristics were recognized. Consequently, Group I was regarded as P. fulva because the type strain (NRIC 0180(T)) of this species was included in this group. Strains in Group II were identified as a new species, Pseudomonas parafulva sp. nov., and the type strain is AJ 2129 (=IFO 16636=JCM 11244=NRIC 0501). NRIC 0181 in Group III was identified as a new species, Pseudomonas cremoricolorata sp. nov., and the type strain is NRIC 0181 (=IFO 16634=JCM 11246). NRIC 0182 in Group IV was identified as P. straminea on the basis of the high level of DNA-DNA similarity with the type strain of this species.     

Lactic acid bacteria isolated from soy sauce mash in Thailand

Fourteen sphere-shaped and 30 rod-shaped lactic acid bacteria were isolated from soy sauce mash of two factories in Thailand. These strains were separated into two groups, Group A and Group B, by cell shape and DNA-DNA similarity. Group A contained 14 tetrad-forming strains, and these strains were identified as Tetragenococcus halophilus by DNA similarity. Group B contained 30 rod-shaped bacteria, and they were further divided into four Subgroups, B1, B2, B3, and B4, and three ungrouped strains by phenotypic characteristics and DNA similarity. Subgroup B1 contained 16 strains, and these strains were identified as Lactobacillus acidipiscis by DNA similarity. Subgroup B2 included two strains, and the strains were identified as Lactobacillus farciminis by DNA similarity. Subgroup B3 contained five strains. The strains had meso-diaminopimelic acid in the cell wall, and were identified as Lactobacillus pentosus by DNA similarity. The strains tested produced DL-lactic acid from D-glucose. Subgroup B4 contained four strains. The strains had meso-diaminopimelic acid in the cell wall, and they were identified as Lactobacillus plantarum by DNA similarity. Two ungrouped strains were homofermentative, and one was heterofermentative. They showed a low degree of DNA similarity with the type strains tested, and were left unnamed. The distribution of lactic acid bacteria in soy sauce mash in Thailand is discussed.     

中国香菇自然种质遗传多样性的RAPD分析*

用RAPD技术分析了收集自中国14个省份、分属于8个不同植物区系的53个野生香菇菌株的DNA多态性。用10个随机引物共扩增出147条DNA带,其中94%具有多态性。供试菌株在RAPD带型及DNA相似性上的差异表明,中国香菇自然群体具有丰富的遗传多样性。其中,横断山脉、云南高原、台湾及华南地区菌株的多样性尤为丰富。用平均连锁聚类法构建了样本的遗传相关聚类图。大多数来自同一区域或相邻区域的菌株优先聚成小类,表明菌株的分组与其地理来源明显相关。以0.66的相似性为切割点,53个菌株可分成4大类群。类群Ⅰ和类群Ⅱ主要由横断山脉、云南高原和华中地区菌株组成,类群Ⅲ包含其他地区的菌株。类群Ⅳ则是由来自华北和四川省的共5个菌株组成的一个小的分支。     

rep-PCR fingerptinting as a tool for the analysis of genomic diversity in Escherichia coli strains isolated from an aqueous/freshwater environment

The rep-PCR fingerprinting method, with the support of ERIC and REP primers, was used to analyse the genomic diversity of 93 E. coli strains isolated from lake water samples drawn at two different depths. The applied UPGMA for DNA analysis did not reveale any genomic similarities between the 48 E. coli strains derived from the subsurface-zone water and the 43 of the bottom-zone water. The considerable genomic diversity of the E. coli of the surface zone was expressed as a dendrogram in the form of 8 similarity groups comprising strains isolated from samples drawn over one month. The bottom-zone strains, which display a lesser degree of genomic diversity (5 similarity groups), showed distinct common features in their DNA fingerprints. In the similarity dendrogram for the bottom-zone, strains derived in different months of sampling were segregated into the same similarity groups. Applying REP primers in rep-PCR generates more complex fingerprints increasing the discriminatory power of the analysis, whereas the ERIC primer generates less complex fingerprint patterns, and is thus clearer to interpret.     

Investigation of persistent colonization by Pseudomonas aeruginosa-like strains in a spring water bottling plant.

Ninety-seven strains, producing a fluorescent pigment under UV light and/or a green diffusive pigment on cetrimide-naladixic acid agar, were isolated from a spring water bottling plant. These strains were presumptively identified as Pseudomonas aeruginosa, but they could not be confirmed as strains of this species nor identified by the API 20NE identification system. The isolates and reference strains were clustered by computer-assisted whole-cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The numerical analysis of the protein electrophoregrams resulted in the formation of four clusters at a similarity level of 80% and two unclustered type strains. One cluster included strains isolated during a 4-month period and reference strains of several biotypes of P. fluorescens. The remaining isolates formed another cluster with a very high similarity of level, which included two groups of strains based on biochemical characterization by the API 20NE Test System. Strains were typed by random amplified polymorphic DNA (RAPD)-PCR and two different RAPD patterns were obtained, corresponding to each biochemical profile. This persistent colonization seems to be caused by a single species present in the bottling system, with two clonal origins, not related to P. aeruginosa or to any of the other type strains tested. Partial 16S rDNA sequence of a representative strain of one cluster of isolates had a level of similarity of 99.3% with P. alcaligenes. This study shows that characteristics similar to P. aeruginosa on cetrimide-naladixic acid agar can be exhibited by several groups of fluorescent pseudomonads that do not belong to this species, clearly showing that confirmation tests must be performed before a decision regarding the water quality is made.     

Characterization of new mouse V kappa groups

A lambda gt10 BXSB spleen cDNA library was screened with a DNA probe for the C kappa region. Forty individual C kappa+ phages were tested for hybridization with DNA probes representing 11 V kappa region groups. Of the phage inserts large enough to contain V kappa region sequences, 3 were negative for hybridization with all 11 V kappa region probes. The inserts from those three were subcloned, sequenced, and compared with V kappa region sequences in the gene bank. One was identical to 87.92.6 for the region sequenced (a member of V kappa RF). The second showed 93.8% sequence similarity with AN04 and called V kappa 32. The third called V kappa 33 showed 76% sequence similarity with the human sequence V52 and 73.2% sequence similarity with the mouse sequence L6. An insert from V kappa 32 containing the 5' untranslated regions through the codon for Cys 88 of the V kappa region was used as a probe in Southern blot analysis of genomic DNA from inbred and congenic strains of mice. V kappa 32 is a four to eight member group and some of the members are retained in the B6.PL-Ly2a congenic and missing from the B6.PL (85NS) congenic consistent with a map location near V kappa 28. The same filters were hybridized with the insert from V kappa 33 containing 5' untranslated region through the codon for Ser 93 of the V kappa region. V kappa 33 is a one to three member group and using the B6.PL congenics maps with the polymorphic fragments of V kappa 32 and V kappa 28.     

Use of tRNA consensus primers to indicate subgroups of Pseudomonas solanacearum by polymerase chain reaction amplification.

Polymerase chain reaction amplification of DNA from 112 Pseudomonas solanacearum strains with the tRNA consensus primers T3A and T5A divided the species into three fingerprint groups. These groups correspond well with previous divisions made by restriction fragment length polymorphism analysis. This polymerase chain reaction test is a facile method for rapidly classifying P. solanacearum strains.     

Genetic diversity of Vibrio cholerae in Chesapeake Bay determined by amplified fragment length polymorphism fingerprinting

Vibrio cholerae is indigenous to the aquatic environment, and serotype non-O1 strains are readily isolated from coastal waters. However, in comparison with intensive studies of the O1 group, relatively little effort has been made to analyze the population structure and molecular evolution of non-O1 V. cholerae. In this study, high-resolution genomic DNA fingerprinting, amplified fragment length polymorphism (AFLP), was used to characterize the temporal and spatial genetic diversity of 67 V. cholerae strains isolated from Chesapeake Bay during April through July 1998, at four different sampling sites. Isolation of V. cholerae during the winter months (January through March) was unsuccessful, as observed in earlier studies (J. H. L. Kaper, R. R. Colwell, and S. W. Joseph, Appl. Environ. Microbiol. 37:91-103, 1979). AFLP fingerprints subjected to similarity analysis yielded a grouping of isolates into three large clusters, reflecting time of the year when the strains were isolated. April and May isolates were closely related, while July isolates were genetically diverse and did not cluster with the isolates obtained earlier in the year. The results suggest that the population structure of V. cholerae undergoes a shift in genotype that is linked to changes in environmental conditions. From January to July, the water temperature increased from 3 degrees C to 27.5 degrees C, bacterial direct counts increased nearly an order of magnitude, and the chlorophyll a concentration tripled (or even quadrupled at some sites). No correlation was observed between genetic similarity among isolates and geographical source of isolation, since isolates found at a single sampling site were genetically diverse and genetically identical isolates were found at several of the sampling sites. Thus, V. cholerae populations may be transported by surface currents throughout the entire Bay, or, more likely, similar environmental conditions may be selected for a specific genotype. The dynamic nature of the population structure of this bacterial species in Chesapeake Bay provides new insight into the ecology and molecular evolution of V. cholerae in the natural environment.     

Genetic variability among Alexandrium tamarense and Alexandrium minutum strains studied by RAPD banding pattern analysis

We performed random amplification of polymorphic DNA (RAPD) analysis on five strains of Alexandrium tamarense and nine strains of Alexandrium minutum. Arbitrary 10-mer oligonucleotides were used as primers for the PCR. Electrophoresis on denaturing acrylamide gels improved RAPD reproducibility and increased the band number. Eight of the 20 primers assayed gave reproducible results and the band profiles generated by them were used for constructing a similarity matrix. Analyses were performed independently for the strains of each species and jointly for all the strains of both species. Results for A. tamarense showed the highest similarity for two distinct clones isolated from the same water sample in the Baltic Sea during a bloom (KAC01 and KAC02). The highest similarity among A. minutum clones was found for three strains (AL1V, AL2V and AL3V) isolated in the Ria de Vigo in NW Spain. The results show a high genetic diversity within a single species. We have shown the potential of the RAPD technique to discriminate between two conspecific strains, as well as for establishing similarities that are related to the biogeographic origin of the strains.     

Alterations in the major heterotrophic bacterial populations isolated from a still bottled mineral water

M orais , P.V. & D a C osta , M.S. 1990. Alterations in the major heterotrophic bacterial populations isolated from a. still bottled mineral water. Journal of Applied Bacteriology 69 , 750–757.
The heterotrophic bacterial population of a bottled mineral water stored in returnable glass bottles and in polyvinyl chloride (PVC) bottles at room temperature was studied over 9–12 months. The plate counts in R₂A medium incubated at 22 and 37C were low initially, increasing to 10⁴-10⁵ cfu/ml within a few days of bottling. The number of bacteria recovered at 22C from PVC bottles was fairly constant during the storage period, but the population isolated at 37C decreased markedly after storage for 1 year. The major components of the population were Pseudomonas strains, one of which was identified as Pseudomonas vesicularis . Major changes took place during storage; two groups of bacteria (B and C) were dominant initially, but during the latter period of storage other groups (F, G and H) increased in number.     

Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker

Genetic diversity and relationship of Lycoris species were investigated using SCoT marker analysis. Of 57 SCoT primers screened, 23 SCoT primers were identified to be high polymorphism. A total of 154 DNA bands with size varied from 0.2 kb to 2.5 kb were amplified, and 131 (82.5%) of them were polymorphic. The average number of polymorphic DNA band per primer was 5.7. Based on Nei's similarity coefficients and genetic distances, total of 43 accessions from 14 species of the genus Lycoris tested were clustered into four groups. Group I consisting of 17 accessions was further divided into two subgroup (Ia and Ib). Subgroup Ia included four species with red flower and 22 (2n) chromosomes. Subgroup Ib contained Lycoris haywardii and Lycoris albiflora which were natural hybrids with oyster white flower. Group II consisted of three species with yellow flower and 16 (2n) chromosomes. Group III was composed of Lycoris Squamigera, Lycoris incarnata and all of hybrids whose flower color was variegated. Group IV only has one species (Lycoris sprengeri) whose petal was a mixture of pink and blue. Notably, the polymorphism generated by SCoT was associated with flower color and chromosome number in this genus plants. The present data provide high-valued information for the management of germplasm, genetic improvement, and conservation of the genetic resources of Lycoris species, important horticulture and medical plants.     

Identification of Acetobacter strains isolated from Indonesian sources,and proposals of Acetobacter syzygii sp. nov., Acetobacter cibinongensis sp. nov., and Acetobacter orientalis sp. nov

Forty-six strains of acetic acid bacteria newly isolated from flowers, fruits, and fermented foods collected in Indonesia were taxonomically studied. They were Gram-negative rods, produced acetic acid from ethanol, oxidized acetate and lactate to CO(2) and H(2)O, and had Q-9 as the major ubiquinone system. On the basis of DNA-DNA similarity, all strains studied, including type strains and reference strains of the genus Acetobacter, were separated into eleven groups (Groups I to XI). Of the 46 isolates, two isolates were included in Group II and identified as Acetobacter pasteurianus, five in Group IV as A. orleanensis, 16 in Group V as A. lovaniensis, five in Group VII as A. indonesiensis, and three in Group VIII as A. tropicalis. The remaining 15 isolates constituted three new groups based on DNA-DNA similarity; four isolates were included in Group IX, two in Group X, and nine in Group XI. No isolates were identified as A. aceti (Group I), A. peroxydans (Group III), and A. estunensis (Group VI). Phylogenetic analysis based on 16S rDNA sequences of representative strains of the Groups indicated belonging to the strains of the genus Acetobacter. On the basis of DNA base composition, DNA-DNA similarity, and 16S rDNA sequences, three new species of the genus Acetobacter are proposed: Acetobacter syzygii sp. nov. for Group IX, Acetobacter cibinongensis sp. nov. for Group X, and Acetobacter orientalis sp. nov. for Group XI. The distribution of Acetobacter strains in Indonesia is discussed in light of isolation sources.     

Three new species of the genus Peptostreptococcus isolated from humans: Peptostreptococcus vaginalis sp. nov., Peptostreptococcus lacrimalis sp. nov., and Peptostreptococcus lactolyticus sp. nov.

We describe three new species of the genus Peptostreptococcus which were isolated from human specimens and were tentatively identified as Peptostreptococcus prevotii. These three organisms were not homologous with previously described type strains of the genus Peptostreptococcus. A total of 12 strains that were identified biochemically as P. prevotii were divided into five independent DNA similarity groups; 10 of these strains were divided into three similarity groups which exhibited significant phenotypic differences from previously described species. Therefore, we propose the following new species: Peptostreptococcus vaginalis for group 1 strains, Peptostreptococcus lacrimalis for group 2 strains, and Peptostreptococcus lactolyticus for group 3 strains. The type strain of P. vaginalis is strain GIFU 12669 (= JCM 8138), the type strain of P. lacrimalis is strain GIFU 7667 (= JCM 8139), and the type strain of P. lactolyticus is strain GIFU 8586 (= JCM 8140).     

Genetic characterization of morphologically variant strains of Paracoccidioides brasiliensis

Molecular characterization of Paracoccidioides brasiliensis variant strains that had been preserved under mineral oil for decades was carried out by random amplified polymorphic DNA analysis (RAPD). On P. brasiliensis variants in the transitional phase and strains with typical morphology, RAPD produced reproducible polymorphic amplification products that differentiated them. A dendrogram based on the generated RAPD patterns placed the 14 P. brasiliensis strains into five groups with similarity coefficients of 72%. A high correlation between the genotypic and phenotypic characteristics of the strains was observed. A 750 bp-RAPD fragment found only in the wild-type phenotype strains was cloned and sequenced. Genetic similarity analysis using BLASTx suggested that this RAPD marker represents a putative domain of a hypothetical flavin-binding monooxygenase (FMO)-like protein of Neurospora crassa.     

大连市两种来源的副溶血性弧菌分子分型

目的 分析食品来源、患者来源及2种来源的副溶血性弧菌之间的PFGE图谱的关系,从分子流行病学角度探讨2种来源的副溶血性弧菌的关联。 方法 收集患者和食品2种来源的副溶血性弧菌178株,经限制性内切酶SfiI酶切,用脉冲场凝胶电泳方法进行电泳,凝胶成像仪获得电泳图谱,利用BioNumerics软件对图谱进行聚类分析。 结果 食品来源的96株菌,有13株降解,83株菌被限制性内切酶SfiI酶切出83个PFGE types(PT),聚类分析发现各菌株间相似系数为55.6%～97.4%,按带型相似系数为85%标准划分为1~67共67个克隆群。患者来源的82株菌,有5株降解,77株菌被限制性内切酶SfiI酶切出46个PFGE types(PT),聚类分析发现各菌株间相似系数为64.1%～100.0%,按带型相似系数为85.0%标准划分为A～O群共15个克隆群。将2种来源的共160株副溶血性弧菌的PFGE图谱进行聚类分析,各菌株间相似系数为41.7%～100.0%,按带型相似系数为85.0%标准划分为79个克隆群。 结论 多数食品来源菌株间相似系数较低,患者来源菌株间相似系数高,而食品和患者来源菌株间相似系数较低,只有少数食品来源与患者来源菌株相似系数较高。     

Using SSR markers to evaluate the genetic diversity of Lentinula edodes’ natural germplasm in China

In this study, microsatellite markers were utilized to reveal the genetic diversity of 56 strains of Lentinula edodes grown in China. A total of 224 DNA bands were detected through 25 primer pairs, of which, 223 bands (99.6%) were polymorphic between two or more strains. The variation in SSR (Simple Sequence Repeat) DNA band patterns and average genetic similarity among the wild strains of L. edodes obtained from the same region uncovered a vast genetic diversity in the natural germplasm found in China. Compared with L. edodes strains from other areas, the genetic diversity of those from the Yunnan Plateau, Hengduanshan mountains, Taiwan, and south China was significantly greater. Based on cluster analysis and principal coordinate analysis, the results indicated that all L. edodes strains could be divided into three major groups. These results effectively displayed the differences between the strains from North and South China, and those from the same or adjoining regions could cluster preferentially into small groups in most cases, suggesting the positive correlation between the cluster results and the geographical origin for the natural germplasm of Chinese L. edodes. To our knowledge, this is a pioneering report on the utilization of the SSR marker technique in analyzing L. edodes’ genetic diversity.     

Identification of Trichoderma strains from building materials by ITS1 ribotyping, UP-PCR fingerprinting and UP-PCR cross hybridization

To study the role of Trichoderma in sick building syndrome, it is essential to be able to accurately identify species. Forty-four strains of Trichoderma spp. isolated from Danish buildings damaged by water leaks were identified using ITS1 ribotyping and universally primed PCR, UP-PCR. Ribotyping allowed the assignment of the strains into three distinct groups. High similarity of UP-PCR banding profiles of the strains allowed species designation for almost all strains (43 out of 44) when compared with the UP-PCR banding profiles obtained from reference strains of T. atroviride, T. citrinoviride, T. harzianum, T. longibrachiatum and T. viride. However, cross hybridization of UP-PCR products showed that the latter strain had high DNA homology to the ex-type strain of T. hamatum. The combined approach is a convenient way for reliable identification of Trichoderma strains.     

Genetic exchange in soil between introduced chlorobenzoate degraders and indigenous biphenyl degraders.

Pseudomonas aeruginosa JB2, a chlorobenzoate degrader, was inoculated into soil having indigenous biphenyl degraders but no identifiable 2-chlorobenzoate (2CBa) or 2,5-dichlorobenzoate (2,5DCBa) degraders. The absence of any indigenous chlorobenzoate degraders was noted by the failure to obtain enrichment cultures with the addition of 2CBa, 3CBa, or 2,5DCBa and by the failure of soil DNA to hybridize to the tfdC gene, which encodes ortho fission of chlorocatechols. In contrast, DNA extracted from inoculated soils hybridized to this probe. Bacteria able to utilize both biphenyl and 2CBa as growth substrates were absent in uninoculated soil, but their presence increased with time in the inoculated soils. This increase was related kinetically to the growth of biphenyl degraders. Pseudomonas sp. strain AW, a dominant biphenyl degrader, was selected as a possible parental strain. Eight of nine recombinant strains, chosen at random, had high phenotypic similarity (90% or more) to the inoculant; the other, strain JB2-M, had 78% similarity. Two hybrid strains, P. aeruginosa JB2-3 and Pseudomonas sp. JB2-M, were the most effective of all strains, including strain AW, in metabolizing polychlorinated biphenyls (Aroclor 1242). Repetitive extragenic palindromic-PCR analysis of putative parental strains JB2 and AW and the two recombinant strains JB2-3 and JB2-M showed similar fragments among the recombinants and JB2 but not AW. These results indicate that the bph genes were transferred to the chlorobenzoate-degrading inoculant from indigenous biphenyl degraders.