A numerical taxonomic study of some pigmented bacteria isolated from Organic Lake,an antarctic hypersaline lake

A study was made of a group of moderately halophilic, heterotrophic, pigmented strains isolated from Organic Lake, Antarctica. These strains were Gram-negative, non-motile, had an aerobic metabolism and a mol% G+C content of their DNA in the range 35–41, indicating that they may be members of the Flavobacterium-Cytophaga group. A numerical taxonomic study involving 134 characteristics compared the antarctic strains with reference strains from Flavobacterium, Cytophaga and Flectobacillus. The antarctic strains formed two clusters that did not contain any reference strains suggesting that they may represent two new species of the genus Flavobacterium.     

纤维单胞菌属放线菌的研究进展

纤维单胞菌属(Cellulomonas)的一些菌株能够产生多种纤维素酶,在纤维素降解方面显示出明显优势。1923年Bergey等以产黄纤维单胞菌为模式菌建立了纤维单胞菌属。1991年Stackebrand和Prauser又以纤维单胞菌属为模式属建立了纤维单胞菌科(Cellulomonadaceae)。目前,纤维单胞菌属包含有从多种环境中分离培养得到的26个有效描述种。纤维单胞菌属菌株在分类学上的典型特征是:细胞壁的肽聚糖成分主要含有Orn和Glu/Asp,以MK-9(H4)为主要的甲基萘醌,主要的脂肪酸成分为anteiso-C15:0和C16:0,极性脂成分主要包括双磷脂酰甘油(DPG)和磷脂酰肌醇甘露糖甙(PIM)。基因组DNA的G+C含量为(68.5–76.0)mol%。最近,本实验室分离到2株纤维单胞菌,应用多相分类研究手段确定了他们的分类学地位。本文将结合我们的研究,对纤维单胞菌属的建立、分类学特征及其在生态和酶资源应用方面进行综述。     

Actinomycete diversity associated with foaming in activated sludge plants

Large numbers of mycolic acid-containing actinomycetes were isolated from foam and scum samples taken from three activated-sludge sewage-treatment plants using several selective isolation media. Organisms presumptively identified as gordonae formed the dominant population in all of the samples. A representative set of these strains have chemical properties consistent with their classification in the genusGordona. Forty-eight of theGordona strains were compared through 165 unit characters with the type strains of validly described species ofGordona. The resultant data were examined using the Jaccard and simple matching coefficients and clustering achieved using the unweighted pair group method with arithmetic averages algorithm. The numerical classification was only marginally affected by the statistics used or by test error, estimated as 3.92%. The isolates were assigned to five multi-membered and 28 single-membered clusters defined by the simple matching coefficient at the 89% similarity level. With few exceptions, the isolates were sharply separated from theGordona marker strains. Essentially the same classification was obtained when the test strains were examined using a Curie-point pyrolysis mass spectrometric procedure. It can be concluded that the gordonae form a heterogeneous taxonomic group, the members of which can be distinguished from representatives of validly described species ofGordona.     

Characterization of aerobic,facultative anaerobic,and anaerobic bacteria in an acidogenic phase reactor and their metabolite formation

Fifty-two aerobic and facultative anaerobic and 57 anaerobic bacterial isolates were obtained from an acidogenic phase digestion system. These isolates were characterized and the similarities between the different strains were calculated using Sokal and Michener's similarity coefficient. The aerobic and facultative anaerobic strains clustered in two major groups with the strains of the first main group being gram-negative fermentative rods, representing the generaKlebsiella, Enterobacter, Escherichia andAeromonas. Isolates of the second group were gram-positive streptococci similar toStreptococcus lactis. The strict anaerobic isolates also clustered into two main groups with strains of cluster A being identified as members of the genusFusobacterium while strains in cluster B were members of the genusBacteroides. Hypothetical mean organisms were calculated for each cluster and used in further culture studies. The major products of the continuously fed acidogenic phase reactor were ethanol and acetic, propionic, and butyric acids. In batch cultures, ethanol, acetic acid, diacetyl, and 2,3-butanediol were formed by the strains as major products both under aerobic and anaerobic conditions. The ability of the aerobic and facultative anaerobic strains to be metabolically active under anaerobic conditions indicates a prominent role in acidogenic reactors.     

Numerical taxonomy of gram-negative, nonmotile, nonfermentative bacteria isolated during chilled storage of lamb carcasses.

A numerical taxonomic study using 75 characters was performed with 132 strains of gram-negative, nonmotile, nonfermentative bacteria selected on the basis of lack of motility and Gram reaction among 1,200 cultures isolated during aerobic storage of lamb carcasses. At the 80% similarity level (SSM), eight clusters were formed. Strains in clusters 1 to 6 could be identified as members of the family Moraxellaceae and, more specifically, as members of the Psychrobacter-[Moraxella] phenylpyruvica subgroup. Of these strains, clusters 1 and 2 (88 strains) were identified as [Moraxella] phenylpyruvica and cluster 3 (15 strains) was identified as Psychrobacter immobilis. Clusters 4, 5, and 6 were not identifiable with any species. Clusters 7 and 8 consisted of 14 strains considered nonmotile variants of Pseudomonas fragi. The highest separation indices corresponded to acid production from certain carbohydrates (melibiose, L-arabinose, and cellobiose). Although strains of Psychrobacter-Moraxella clusters were relatively frequently identified at the completion of slaughter, very few cultures were detected on spoiled carcasses. It appears, therefore, that this group of organisms has only low spoilage potential.     

Numerical taxonomy of gram-negative, nonmotile, nonfermentative bacteria isolated during chilled storage of lamb carcasses.

A numerical taxonomic study using 75 characters was performed with 132 strains of gram-negative, nonmotile, nonfermentative bacteria selected on the basis of lack of motility and Gram reaction among 1,200 cultures isolated during aerobic storage of lamb carcasses. At the 80% similarity level (SSM), eight clusters were formed. Strains in clusters 1 to 6 could be identified as members of the family Moraxellaceae and, more specifically, as members of the Psychrobacter-[Moraxella] phenylpyruvica subgroup. Of these strains, clusters 1 and 2 (88 strains) were identified as [Moraxella] phenylpyruvica and cluster 3 (15 strains) was identified as Psychrobacter immobilis. Clusters 4, 5, and 6 were not identifiable with any species. Clusters 7 and 8 consisted of 14 strains considered nonmotile variants of Pseudomonas fragi. The highest separation indices corresponded to acid production from certain carbohydrates (melibiose, L-arabinose, and cellobiose). Although strains of Psychrobacter-Moraxella clusters were relatively frequently identified at the completion of slaughter, very few cultures were detected on spoiled carcasses. It appears, therefore, that this group of organisms has only low spoilage potential.     

Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov.

A total of 37 actinobacteria were isolated from eighteen lichen samples collected in Thailand. Based on the 16S rRNA gene sequences, they were identified into five genera including Actinoplanes (1 strain), Actinomadura (1 strain), Pseudosporangium (1 strain), Wangella (1 strain) and Streptomyces (33 strains). Among these isolates, strain Ptm05^T, Ptm01 and Ptm12 showed low 16S rRNA gene similarity and was selected for the further taxonomic study using the polyphasic approach. These strains showed the highest 16S rRNA gene sequence similarity with Streptomyces sparsogenes ATCC 25498^T (97.44–97.72%). Strain Ptm05^T was selected for the type strain. The chemical cell composition of the strain was similar to the members of Streptomyces genus. LL-diaminopimelic acids were detected in the peptidoglycan. Menaquinones were MK-9(H₈) and MK-9(H₆). Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phospholipid, one unidentified glycolipid and one unidentified lipid were detected as the polar lipids. The predominant cellular fatty acids are anteiso-C_15:0, iso-C_15:0, iso-C_16:0, iso-C_17:0 and C_16:0. The dDNA-DNA hybridization values among strain Ptm05^T and its closely related Streptomyces type strains were 17.2–18.0%. In addition, the ANIb and ANIm between strain Ptm05^T and related Streptomyces type strains were ranged from 75.69 to 76.13% and 85.21 to 85.35%, respectively. Based on phenotypic and genomic evidence, strain Ptm05^T (=?TBRC 14546^T?=?NBRC 115203^T) represents the novel species of the genus Streptomyces for which the name Streptomyces parmotrematis sp. nov. is proposed. This study showed that the lichens are the promising source of the novel actinobacterial taxa.

     

Multi-gene analysis reveals previously unrecognized phylogenetic diversity in Aliivibrio

The “Vibrio fischeri species group” recently was reclassified as a new genus, Aliivibrio, comprising four species, Aliivibrio fischeri, Aliivibrio logei, Aliivibrio salmonicida, and Aliivibrio wodanis. Only limited phylogenetic analysis of strains within Aliivibrio has been carried out, however, and taxonomic ambiguity is evident within this group, especially for phenotypically unusual strains and certain strains isolated from bioluminescent symbioses. Therefore, to examine in depth the evolutionary relationships within Aliivibrio and redefine the host affiliations of symbiotic species, we examined several previously identified and newly isolated strains using phylogenetic analysis based on multiple independent loci, gapA, gyrB, pyrH, recA, rpoA, the luxABE region, and the 16S rRNA gene. The analysis resolved Aliivibrio as distinct from Vibrio, Photobacterium, and other genera of Vibrionaceae, and resolved A. fischeri, A. salmonicida, A. logei, and A. wodanis as distinct, well-supported clades. However, it also revealed that several previously reported strains are incorrectly identified and that substantial unrecognized diversity exists in this genus. Specifically, strain ATCC 33715 (Y-1) and several other strains having a yellow-shifted luminescence were not members of A. fischeri. Furthermore, no strain previously identified as A. logei grouped with the type strain (ATCC 29985^T), and no bona-fide strain of A. logei was identified as a bioluminescent symbiont. Several additional strains identified previously as A. logei group instead with the type strain of A. wodanis (ATCC BAA-104^T), or are members of a new clade. Two strongly supported clades were evident within A. fischeri, a phylogenetic structure that might reflect differences in the host species or differences in the ecological incidence of strains. The results of this study highlight the importance of basing taxonomic conclusions on examination of type strains.     

Geobacillus galactosidasius sp. nov., a new thermophilic galactosidase-producing bacterium isolated from compost

Two thermophilic spore-forming strains, with optimum growth temperature at 70 °C, were isolated from compost of the “Experimental System of Composting” (Teora, Avellino, Italy). A phylogenetic analysis based on 16S rRNA gene sequences showed that these organisms represented a new species of the genus Geobacillus. Based on polyphasic taxonomic data the strains represented a novel species for which the name Geobacillus galactosidasius sp. nov. is proposed. The type strain is CF1B^T (= ATCC BAA-1450^T = DSM 18751^T).     

Karyotaxonomic study of some species ofPeucedanum (Umbelliferae)

A study of morphometric karyotype characters was carried out in 14 species ofPeucedanum s. lat. (Umbelliferae — Apioideae) and in one species of the related genusLomatium. The differences of the species in their karyotype characters are correlated only to a limited degree with their similarities of dissimilarities in morphological (i. a. carpological) characters, and thus with their taxonomic position. The evolution of these two sets of characters seems to have proceeded not synchronously or even in different directions in the group of platycarpousUmbelliferae united in the genusPeucedanum. Therefore, it is unlikely that morphometric chromosome characters revealed by monochrome staining can be used appropriately in the taxonomic revision of the polymorphous genusPeucedanum.     

Actinoplanes capillaceus sp. nov., a new species of the genus Actinoplanes

Two motile actinomycete strains, K95–5561^T and K95–5562, were isolated from a soil sample collected at Sayama City, Saitama Prefecture, Japan. They produced bell shaped spore vesicles (sporangia) with hairy surfaces on substrate hyphae. When released into water, the sporangiospores became motile by a tuft of polar flagella. The chemotaxonomic and morphological characteristics together with 16S rRNA gene sequence data indicated that the two isolates belonged to the genus Actinoplanes. The two strains were assigned to a single species on the basis of phenotypic, notably cultural, morphological and physiological characteristics, and DNA-DNA pairing data. The two strains were distinguished from representatives of all validly described species of Actinoplanes using a combination of genotypic and phenotypic properties. It is, therefore, proposed that strains K95–5561 and K95–5562 be recognized as a new species of the genus Actinoplanes with the name Actinoplanes capillaceus sp. nov. The type strain of the species is strain K95–5561^T (=JCM 10268^T =IFO 16408^T). The invalidly proposed species `Ampullariella cylindrica', `Ampullariella pekinensis' and `Ampullariella pilifera' were assigned to Actinoplanes capillaceus on the basis of genotypic and phenotypic data.     

The classification of luminescent bacteria

Summary The luminescent bacteria are logically placed in two genera. The common coccoid and frequently non-motile species placed byBeije-rinck first in his genusPhotobacterium, 1889 under the namePhotobacterium phosphorescens syn.Bacterium phosphorescens Fischer, should be recognized as the type species ofPhotobacterium. Other characters indicate that this genus should be placed in the FamilyPseudomonadaceae Winslowet al.. and should include other straight, rod-shaped, luminescent, polar flagellate bacteria that ferment glucose without, however, necessarily producing gas (H₂ and CO₂) as does the type species. The species that have the form of vibrios should be accepted as members of the genusVibrio as suggested by several previous investigators. They have characters much like those ofVibrio comma, the type species of the genusVibrio.     

Molecular phylogenetic study of the basidiomycetous anamorphic yeast genusTrichosporon and related taxa based on small subunit ribosomal DNA sequences

Small subunit ribosomal DNA sequences of all species of the basidiomycetous anamorphic yeast genusTrichosporon were determined, and phylogenetic trees were constructed by the neighbor-joining and maximum likelihood methods. The sequence data showed that, with the exception ofT. pullulans, the genus is monophyletic, although its members have two different major ubiquinones, Q9 and Q10. The genus can be divided phylogenetically into three major clusters. Species with Q10 as the major ubiquinone constitute a single cluster, while those with Q9 form two clusters.Trichosporon pullulans was phylogenetically distinct from other taxa of the genus. It is located in a cluster containingCystofilobasidium capitatum, Mrakía frigida, Xanthophyllomyces dendrorhous and three species ofUdeniomyces. This result sugests thatT. pullulans does not belong to the genusTrichosporon.     

Srinivasan’s coagulation test in taxonomically classified streptomycetes

Srinivasan’s coagulation test was performed in 18 strains of the genusStreptomyces and one strain of the genusActinoplanes. The highest coagulation activity was detected in strains systematically classified in a series of streptomycetes with pink or red aerial mycelium:S. erythreus, Streptomyces sp. AJ/22,S. roseo-luteus andS. griseofuscus. With the exception ofS. griseofuscus these three cultures also exhibited the highest inhibitory activity againstB. subtilis. When using hemoglobin as substrate it was possible to detect acid, neutral and alkaline proteinases with the highest proteolytic activity at pH 3.0 to 4.0 in the most active strain ofS. erythreus.     

<Emphasis Type="Italic">Halobacillus locisalis</Emphasis> sp. nov., a halophilic bacterium isolated from a marine solar saltern of the Yellow Sea in Korea

A Gram-positive, motile, endospore-forming and rod-shaped halophilic bacterial strain MSS-155 (KCTC 3788 and KCCM 41687) was isolated from a marine solar saltern of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic study. This organism grew at temperature of 10.0–42.0°C with an optimum of 35°C. Strain MSS-155 grew optimally in the presence of 10% NaCl and did not grow in the absence of NaCl. The cell wall peptidoglycan type of strain MSS-155 was A4 based on l-Orn-d-Asp. Strain MSS-155 was also characterized chemotaxonomically by having menaquinone-7 (MK-7) as the predominant isoprenoid quinone and anteiso-C_15:0 as the major fatty acid. The DNA G+C content was 44.0 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain MSS-155 falls within the radiation of the cluster comprising Halobacillus species. Levels of 16S rDNA sequence similarity between strain MSS-155 and the type strains of four Halobacillus species were in the range 97.6–98.8%. Strain MSS-155 exhibited levels of DNA-DNA relatedness of 6.2–11.2% to the type strains of Halobacillus species described previously. On the basis of phenotypic properties, phylogeny, and genomic data, strain MSS-155 should be placed in the genus Halobacillus as a member of a novel species, for which we propose the name Halobacillus locisalis sp. nov.Communicated by W.D. Grant     

Struvite precipitation by soil and fresh water bacteria

Struvite precipitation by 161 bacterial strains isolated from soil and fresh water was analyzed. The results showed that the ability to form struvite is not widespread among these bacteria. Struvite precipitation was influenced by environmental factors and could be enhanced by changing the experimental conditions. There was no clear relationship between the taxonomic status of a given strain and its ability to precipitate struvite. However, bacteria of the genusPseudomonas showed a greater tendency to precipitate struvite than organisms of the remaining genera studied, and five new genera were identified as struvite producers.     

Isoprenoid quinones and fatty acids ofZoogloea

NineZoogloea strains including the type strain ofZ. ramigera (IAM 12136=ATCC 19544=N.C. Dondero 106) and newly isolated strains were investigated for isoprenoid quinone composition and whole-cell fatty acid profiles. Seven of the tested strains, having phenotypic properties typical ofZoogloea, were characterized by their production of both ubiquinone-8 and rhodoquinone-8 as major quinones, whereas the remaining two strains,Z. ramigera IAM 12669 (=K. Crabtree I-16-M) and IAM 12670 (=P.R. Dugan 115), formed ubiquinone-10 and ubiquinone-8, respectively, as the sole quinone. All rhodoquinone-producing strains contained palmitoleic acid and 3-hydroxy-decanoic acid as the major components of nonpolar and hydroxylated fatty acids, respectively. Marked differences were noted in the fatty acid composition between the strains with and without rhodoquinones. The chemotaxonomic data suggested that the rhodoquinonelacking strains should be excluded from the genusZoogloea. Since there have been no reliable taxonomic tools forZoogloea, rhodoquinone analysis may provide a new criterion of great promise for identifyingZoogloea strains.     

Thermus 2S from Thai hot springs: isolation and immobilization

Three strains of thermophilic bacteria producing extracellular protease have been isolated from hot springs in Chiang Mai, Thailand. The bacterium producing the highest amount of protease has been selected and identified as belonging to the genusThermus, and is tentatively calledThermus 2S. The isolate is a Gram-negative, rod shaped bacterium. It exhibited maximum growth around 60°C at pH 7. Entrapment of the microbial cells in calcium alginate maintained the cell viability. Protease production from immobilized cells using 2 g wet cells per 10 ml 3% (w/v) sodium alginate was higher than that from a free-cell system using 2% inoculum.     

Identification and Discrimination of Oral Asaccharolytic Eubacterium spp. by Pyrolysis Mass Spectrometry and Artificial Neural Networks

Curie-point pyrolysis mass spectra were obtained from 29 oral asaccharolytic Eubacterium strains and 6 abscess isolates previously identified as Peptostreptococcus heliotrinreducens. Pyrolysis mass spectrometry (PyMS) with cluster analysis was able to clarify the taxonomic position of this group of organisms. Artificial neural networks (ANNs) were then trained by supervised learning (with the back-propagation algorithm) to recognize the strains from their pyrolysis mass spectra; all Eubacterium strains were correctly identified, and the abscess isolates were identified as un-named Eubacterium taxon C₂ and were distinct from the type strain of P. heliotrinreducens. These results demonstrate that the combination of PyMS and ANNs provides a rapid and accurate identification technique.