Streptomyces daliensis sp. nov. from soil

A novel actinomycete strain YIM 31724^T was isolated from a soil sample collected from Dali, Yunnan Province, People’s Republic of China. The strain is characterized by white to yellow white aerial mycelia, spiral spore chains and smooth spore surface. The cell wall of strain YIM 31724^T contained LL-diaminopimelic acid (A₂pm) and traces of meso-A₂pm. Whole-cell hydrolysates contained mainly glucose and small amounts of galactose and xylose. The menaquinones were MK-9(H₆) (31%) and MK-9(H₈) (69%). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 31724^T was 67.2 mol%. Phylogenetic analysis indicated that the strain belongs to the genus Streptomyces, with highest similarity to Streptomyces rimosus subsp. rimosus JCM 4667^T (rRNA gene sequence similarity value of 98.9%) and Streptomyces erumpens DSM 40941^T (rRNA gene sequence similarity value of 98.7%). Based on its phenotypic and genotypic characteristics, including low DNA–DNA hybridization results, strain is proposed as the type strain of a novel species, Streptomyces daliensis sp. nov.     

Chromium accumulation by two Streptomyces spp. isolated from riverine sediments

Strains designated R22 and R25, isolated from Salí River sediments, Argentina, were highly resistant to chromium. These strains were shown by 16S rRNA sequencing studies to be Streptomyces spp.; this affiliation was consistent with morphological and chemical characteristics. Growth of strains R22 and R25 in medium containing 100 mg l⁻¹ chromate was reduced by only 23% and 34%, respectively, compared with growth in medium without added chromium. Streptomyces sp. strains R22 and R25 both accumulated chromium with yields of 10.0 and 5.6 mg Cr g⁻¹ of dry weight, respectively, and a chromate concentration of 50 mg ml⁻¹. Cell fractionation studies with strain R22 showed that the great majority of the chromium were associated with the cell wall fraction. Streptomyces strains R22 and R25 may have applications in bioremediation of chromium contamination. Journal of Industrial Microbiology & Biotechnology (2001) 26, 210–215. Received 23 June 2000/ Accepted in revised form 24 January 2000     

Chemical profiling of Streptomyces sp. Al-Dhabi-2 recovered from an extreme environment in Saudi Arabia as a novel drug source for medical and industrial applications

Filamentous bacterial belonged to Streptomyces species were novel drug source for medical and industrial applications. However, the detailed identification of Streptomyces species from Saudi Arabian extreme environment for the identification novel drug source for medical and industrial applications were rarely studied. The Streptomyces strain Al-Dhabi-2 obtained from the thermophilic region kingdom of Saudi Arabia, exhibited antimicrobial potentials against the pathogenic microorganism were characterized. Biochemical and phylogenetic analysis confirmed that the strain was closely associated to the Streptomyces species. The chromatogram of GC-MS analysis of this ethyl acetate extract (EA) had diverse of chemical compounds namely benzene acetic acid (7.81%), acetic acid, methoxy-, 2-phenylethyl ester (6.01%) were the major compounds. EA of Al-Dhabi-2 showed inhibition zone ranged from 14 to 25 mm at 5 mg/well concentration against the tested microbial pathogens. Results revealed that the significant MIC values were observed against B. cereus, and E. faecalis by (less than 39 μg/ml) and against S. agalactiae with (78 μg/ml). Minimum inhibitory concentrations (MIC) for fungi: were also reported against Cryptococcus neoformans and Trichophyton mentagrophytes by (156 μg/ml), whilst Candida albicans and Aspergillus niger by (312 μg/ml). Results of this study showed that thermophilic actinobacteria could be promise source in the context of searching for unique antimicrobial agents with novel properties.     

Streptomyces sp. strain isolated from river water has high bisphenol A degradability

AIMS: We report the identification of the bisphenol A (BPA) biodegradability in Streptomyces sp. strain isolated from river water. METHODS AND RESULTS: The water samples spiked with BPA (1 mg l(-1)) and the culture solution of Streptomyces sp. strain were placed at 30 degrees C for 10 days and were analysed by high-performance liquid chromatography. A half-life for BPA degradation was between 3 and 4 days. The removal rate of BPA was >90% for 10 days. CONCLUSIONS: These results show that the Streptomyces sp. strain isolated from river water has high BPA degradability. SIGNIFICANCE AND IMPACT OF THE STUDY: To our knowledge, this is the first report of BPA degradation by Streptomyces sp. strain.     

Alkalibacillus halophilus sp. nov., a new halophilic species isolated from hypersaline soil in Xin-Jiang province, China

A halophilic, Gram-positive, spore-forming motile Bacillus-like strain YIM 012(T), was isolated from one of the hypersaline soil samples collected in Xin-jiang province, China. Its optimum growth occurred at 10-20% of NaCl concentration (w/v), pH 7.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 012(T) is a member of the genus of Alkalibacillus, which is well supported by its chemotaxonomic and molecular characteristics. Based on its phenotypic evidence and genotypic data, Alkalibacillus halophilus sp. nov. was proposed and strain YIM 012(T) (=DSM 17369(T)=KCTC 3990(T)) was assigned as the type strain of the novel species.     

<Emphasis Type="Italic">Streptomyces gulbargensis</Emphasis> sp. nov., isolated from soil in Karnataka,India

During the course of screening for industrially important microorganisms, an alkali-tolerant and thermotolerant actinomycete, strain DAS 131T, was isolated from a soil sample collected from the Gulbarga region, Karnataka province, India. The strain was characterized by a polyphasic approach that showed that it belonged to the genus Streptomyces. Growth was observed over a wide pH range (pH 6-12) and at 45 degrees C. The 16S rRNA gene sequence of strain DAS 131T was deposited in the GenBank database under the accession number DQ317411. 16S rRNA gene sequence analysis revealed that strain DAS 131T was most closely related to Streptomyces venezuelae ISP 5230T (AY999739) with a sequence similarity of 99.5% (8 nucleotide differences out of 1,477). Despite this very high sequence similarity, strain DAS 131T was phenetically distinct from S. venezuelae. The DNA relatedness between these strains was 54%, indicating that strain DAS 131T is a distinct genomic species. On the basis of phenetic and genetic analyses, strain DAS 131T is classified as a new species in the genus Streptomyces, for which we propose the name Streptomyces gulbargensis sp. nov.     

A new isolate of Nosema sp. (Microsporidia, Nosematidae) from Phyllobrotica armata Baly (Coleoptera, Chrysomelidae) from China

We studied the spore morphology and molecular systematics of a novel microsporidian isolate from Phyllobrotica armata Baly collected in China. The spores were long-oval and measured 4.7 × 2.6 μm on fresh smears. Ultrastructure of the spores was characteristic for the genus Nosema: 13-14 polar filament coils, posterior vacuole, and a diplokaryon. The complete rRNA gene sequence of the isolate was 4308 bp long. The organization of the rRNA gene was 5′-LSU rRNA-ITS-SSU rRNA-IGS-5S-3′, which corresponds to that of the Nosema species. Phylogenetic analysis based on the rRNA gene sequence indicated that this isolate, designated as Nosema sp. PA, is closely related to Nosemabombycis and is correctly assigned to the “true” Nosema group.     

Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.     

Cellulase from Bacillus licheniformis and Brucella sp. isolated from mangrove soils of Mahanadi river delta,Odisha, India

In the present study, two cellulose-degrading bacteria (CDB-5 and CDB-12) were isolated from mangrove soils of Mahanadi river delta, based on halo zone formation in Congo red agar medium and evaluation for cellulase production in CMC broth medium. Based on morphological, biochemical and 16S rRNA gene sequencing, the two strains, CDB-5 and CDB-12, were identified as Brucella sp. and Bacillus licheniformis, respectively. The gene bank accession number of the strains CDB-5 and CDB-12 are KR632646 and KR632645, respectively. The strain Brucella sp. and B. licheniformis showed an enzyme activity of 96.37?U/ml and 98.25?U/ml, respectively, after 72?h of incubation period. Enzyme production was optimized under different growth conditions such as pH, temperature, agitation rate, carbon source, sodium chloride (NaCl), and nitrogen sources. Maximum cellulase production by both the strains was obtained in the same parameter condition such as pH (7.0), rpm (150), and NaCl (2%, w/v) which varies for other parameters. The strain, CDB-5, produced maximum cellulase at 35?°C temperature, maltose as a carbon source, and yeast extract as a nitrogen source where as the strain CDB-12 produces maximum cellulase at 45?°C temperature, carboxyl methyl cellulose (CMC) as carbon source and trypton as a nitrogen source. The bacterial crude enzyme was purified by ammonium sulfate precipitation followed by overnight dialysis. SDS-PAGE analysis of the partially purified cellulase enzyme exhibited band sizes of approximately 55 and 72?kDa.     

Ruminococcus luti sp. nov., isolated from a human faecal sample

A strain of an unidentified strictly anoxic, gram-postive, non-motile Ruminococcus-like bacterium was isolated from a human faecal sample. The organism used carbohydrates as fermentable substrates, produced acetate, succinate, and hydrogen as the major products of glucose metabolism, and possessed a G + C content of 43.3 mol%. The morphological and biochemical characteristics of the organism were consistent with its assignment to the genus Ruminococcus but it did not correspond to any recognized species of this genus. Comparative 16S rRNA gene sequencing showed the unidentified bacterium represents a previously unrecognised sub-line within the Clostridium coccoides rRNA group of organisms. The nearest relative of the unknown bacterium corresponded to Ruminococcus obeum but a 16S rRNA sequence divergence value of >3% demonstrated it represents a different species. Based on the presented findings a new species, Ruminococcus luti, is described. The type strain of Ruminococcus luti is BInIX(T) (DSM 14534T, CCUG 45635T).     

<Emphasis Type="Italic">Streptomyces serianimatus</Emphasis> sp. nov., isolated from a rhizophere soil

A novel actinomycete strain, designated YIM 45720^T, was isolated from a Cephalotaxus fortunei rhizophere soil sample collected from Yunnan Province, southwest China. The strain formed well-differentiated aerial and substrate mycelia. Chemotaxonomically, it contained LL-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose, mannose, and galactose with traces of glucose and xylose. Phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol. MK-9 (H₈) was the predominant menaquinone. The major fatty acids (>10%) were iso-C_16:0, iso-C_15:1 and anteiso-C_15:0. The G + C content of the DNA was 70 mol%. Phylogenetic analysis data based on 16S rRNA gene sequence showed that strain YIM 45720^T formed a distinct branch with the type strain of Streptomyces scabrisporus JCM 11712^T within the genus Streptomyces. On the basis of the phenotypic and genotypic characteristics, strain YIM 45720^T (=DSM 41883^T = CCTCC AA 206006^T) is proposed as the type strain of a novel species, Streptomyces serianimatus sp. nov.     

Sphingobacterium canadense sp. nov., an isolate from corn roots

A free-living Gram-negative bacterial strain CR11(T) was isolated from corn roots. Polyphasic taxonomy was performed, including API20 NE and API50 CH bacterial identification kits, Biolog analysis, lipids and fatty acid analysis, DNA-DNA hybridization, 16S rRNA and cpn60 gene sequence analyses. 16S rRNA gene sequence analysis indicated that strain CR11(T) belonged to the genus Sphingobacterium and was closely related to Sphingobacterium multivorum IFO 14947(T) (98% similarity) and Sphingobacterium. thalpophilum ATCC 43320(T) (97% similarity). DNA-DNA hybridization showed 11% and 13% DNA re-association with S. multivorum LMG 8342(T) and S. thalpophilum LMG 11520(T), respectively. Major fatty acids (16:0, 15:0 iso and 17:0 iso 3-OH) and the G+C content of the DNA (40.5 mol%), were also similar to those of the genus Sphingobacterium. The predominant respiratory quinone was MK-7. In all analyses, including phenotypic characterization, this isolate was found to be different from the closely related species, S. multivorum and S. thalpophilum. On the basis of these results, this strain represents a new species within the genus Sphingobacterium. The name Sphingobacterium canadense sp. nov. is suggested and the type strain is CR11(T) (=NCCB 100125(T)=LMG 23727(T)).     

Nocardia rhamnosiphila sp. nov., isolated from soil

In this study two actinomycete strains were isolated in Cape Town (South Africa), one from a compost heap (strain 202GMO^T) and the other from within the fynbos-rich area surrounded by the horseracing track at Kenilworth Racecourse (strain C2). Based on 16S rRNA gene sequence BLAST analysis, the strains were identified as members of the genus Nocardia. Phylogenetic analysis showed that the strains clustered together and are most closely related to Nocardia flavorosea NRRL B-16176^T, Nocardia testacea JCM 12235^T, Nocardia sienata IFM 10088^T and Nocardia carnea DSM 43397^T. This association was also supported by gyrB based phylogenetic analysis. The results of DNA–DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of both strains 202GMO^T and C2 from related species. However, their high DNA relatedness showed that they belong to the same species. Strain 202GMO^T was selected as the type strain to represent this novel species, for which the name Nocardia rhamnosiphila is proposed (=DSM 45147^T = NRRL B-24637^T).     

Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant

A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03(T), was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and beta-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005(T) (95.9% sequence similarity), Comamonas nitrativorans DSM 13191(T) (95.7%), and Comamonas odontotermitis LMG 23579(T) (95.7%). Strain Ko03(T) had a genomic DNA G+C content of 68.4 mol% and the predominant respiratory quinone was Q-8. The major fatty acids were C(16:1) omega7c (44.7%), C(16:0) (28.1%), C(18:1) (16.1%), and C(10:0) 3-OH (3.5%). These chemo-taxonomic results supported the affiliation of strain Ko03(T) to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03(T) from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03(T) represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03(T) (= KCTC 12199(T) = NBRC 101663(T)).     

Seminibacterium arietis gen. nov., sp. nov., isolated from the semen of rams

Two gram-negative, catalase- and oxidase-positive, bacillus-shaped bacterial strains were isolated from the semen of two rams. 16S rRNA gene sequencing demonstrated that both isolates represented a distinct subline within the family Pasteurellaceae with <95% sequence similarity to any recognized member of this family. Sequencing of rpoB and infB genes confirmed this finding with the semen isolates representing a new sub-line within the family Pasteurellaceae. The main cell fatty acids of strain DICM-00342^T were C_14:0, C_16:0, C_18:1ω7c and summed feature 3 (C_16:1ω7c/iso-C_15:0 2OH). Ubiquinone Q-8 was the major quinone and 1,3-diaminopropane was the predominat polyamine. Major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The new genus can be phenotypically distinguished from currently described genera of this family based on physiological traits and a combination of signature amino acids in the RpoB protein sequence. On the basis of these results we describe a new genus and species for which we propose the name of Seminibacterium arietis gen. nov., sp. nov. (DICM11-00342^T = CCUG 61707^T = CECT 8033^T).     

Isolation and characterization of Bacillus sp. strain BC01 from soil displaying potent antagonistic activity against plant and fish pathogenic fungi and bacteria

Fungal and bacterial pathogens infect a diverse range of hosts including various plant and animal species. Fungal and bacterial diseases, especially of plants and aquatic animals, such as fish, lead to significant damage to crops and aquaculture, respectively, worldwide. The present study was conducted to isolate and characterize potent Bacillus strains with significant antagonistic activity against the major plant and fish pathogenic fungi and bacteria. We randomly collected 22 isolates of Bacillus from the soil, rhizosphere, and sediment from different parts of Bangladesh. Initial characterization, based on in vitro antagonistic activity on the culture plate, resulted in the selection of four gram-positive Bacillus sp. isolates. Among these, the isolate BC01, obtained from soil demonstrated the highest broad-spectrum anti-bacterial and anti-fungal activities. We confirmed the genus of BC01 to be Bacillus by morphological and biochemical tests as well as using molecular data analysis tools, including the study of 16s rDNA, phylogenetic relationship, and evolutionary divergence scores. The isolate significantly inhibited the mycelial growth of the plant pathogen, Penicillium digitatum and fish pathogen, Aphanomyces invadans in vitro. The anti-bacterial effect of the isolate was also evaluated against Pseudomonas spp. and Xanthomonas spp., the two deadliest plant pathogens, and Aeromonas veronii, Pseudomonas fluorescens, and Streptococcus iniae, three major fish pathogens that are primarily responsible for global aquaculture loss. The results of the present study could pave the way for developing potent drugs to combat microbial infection of plants and fish.     

Genetic variability of plant-associated proteobacteria isolated from Slovak (Central European) territory

Genetic variability of 17 wild strains of γ-proteobacteria isolated from different host plants, locations and seasons, identified via routine diagnostics as Erwinia amylovora, was analysed. The ERIC-PCR confirmed the genetic homogeneity among 15 virulent strains while 2 avirulent strains were genetically distinct. These two avirulent strains differed in their antibiotic susceptibility from all virulent strains. The only avirulent Ra1051/98 strain showed significant ampicillin resistance. All 15 virulent strains were confirmed via the ERIC-PCR and MALDI-TOF MS, as closely related to the reference strain NCPPB 683 of E. amylovora. Avirulent strains were identified as Rahnella aquatilis and L. quercina subsp. britannica (formerly Brenneria quercina), by MALDI-TOF MS and the identification was confirmed by 16S rRNA gene sequence analysis. For the first time, L. quercina subsp britannica was identified in the fire blight-symptomatic samples in Central Europe, and for the first time this bacterium was isolated from the host different than oak.     

Antimicrobial and antiviral activities of an actinomycete (Streptomyces sp.) isolated from a Brazilian tropical forest soil

A promising producer of bioactive compounds isolated from a Brazilian tropical soil was tested for its range of antimicrobial activities. Strain 606, classified as Streptomyces sp., could not be identified up to species level, suggesting a possible new taxon. The supernatant and 10 extracts and fractions, obtained by extraction and chromatographic techniques, presented antimicrobial activity using antibiograms. The methanolic fraction was highly active against pathogenic bacteria, phytopathogenic fungi and the human pathogenic yeast Candida albicans. It also possessed high antiviral activity inhibiting the propagation of an acyclovir-resistant herpes simplex virus type 1 strain on HEp-2 cells at non-cytotoxic concentration. The strong cytotoxic effect suggests an antitumour action. This revised version was published online in August 2006 with corrections to the Cover Date.     

Rhodococcus cercidiphylli sp. nov., a new endophytic actinobacterium isolated from a Cercidiphyllum japonicum leaf

An endophytic actinobacterium, designated YIM 65003(T), was isolated from a surface sterilized leaf sample of Cercidiphyllum japonicum collected from Yunnan province, south-west China. The morphological and chemotaxonomic properties of the isolate were typical of members of the genus Rhodococcus. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Rhodococcus fascians DSM 20669(T) (99.6%) and Rhodococcus yunnanensis YIM 70056(T) (99.0%). DNA-DNA hybridization with the above microorganisms (46.3% and 48.8%, respectively), in combination with differences in the biochemical and physiological properties, suggested that strain YIM 65003(T) should be classified within a novel species of the genus Rhodococcus, for which the name Rhodococcus cercidiphylli sp. nov. is proposed, with YIM 65003(T) (=CCTCC AB 207160(T)=DSM 45141(T)) as the type strain. The 16S rRNA gene sequence of strain YIM 65003(T) has been deposited in GenBank under the accession number EU325542.