Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal Lake in the Indian trans-Himalayas

The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852^T and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852^T and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596^T (97.8% and 97.7%) and less than 95.9% similarity to other species of the genus Paenibacillus. DNA-DNA relatedness among strains IHBB 9852^T and IHBB 9951 was 90.2%, and with P. lactis DSM 15596^T, was 52.7% and 52.4%, respectively. The novel strains contain anteiso-C_15:0, iso-C_15:0, C_16:0 and iso-C_16:0 as major fatty acids, and phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol were predominant polar lipids. The DNA G+C content for IHBB 9852T and IHBB 9951 was 52.1 and 52.2 mol%. Based on the results of phenotypic and genomic characterisations, we concluded that strains IHBB 9852^T and IHBB 9951 belong to a novel Paenibacillus species, for which the name Paenibacillus ihbetae sp. nov. is proposed. The type strain is IHBB 9852^T (=MTCC 12459^T = MCC 2795^T = JCM 31131^T = KACC 19072^T; DPD TaxonNumber TA00046) and IHBB 9951 (=MTCC 12458 = MCC 2794 = JCM 31132 = KACC 19073) is a reference strain.     

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.     

宁夏枸杞内生细菌的多样性及其抑菌活性研究

【目的】对宁夏枸杞各药用部位内生细菌的分布特征、遗传多样性和抑菌活性进行分析。【方法】采用菌落计数和16S rRNA基因序列分析法研究枸杞内生细菌的分布特征、遗传多样性,采用琼脂扩散法测定其抑菌活性。【结果】从各药用组织器官中分离出内生细菌34株,隶属于7科11属,内生细菌的数量和群落组成存在明显的组织特异性,其数量表现为根皮>叶>花>果实,而多样性则表现为花>根皮>叶>果实。芽孢杆菌属为枸杞优势内生菌群,分布于所有组织中;抑菌实验结果表明有76.5%的内生菌对一种或多种病原菌的生长有抑制作用,芽孢杆菌属菌株R2、R7、L3和短波单胞菌属的R3拮抗番茄炭疽杆菌和玉米大斑病菌的能力较强,而多数菌株对大肠杆菌和金黄色葡萄球菌的抑制能力较弱。【结论】枸杞可培养内生细菌遗传多样性丰富,对植物病原菌有较强的抑制活性。     

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.     

Antimicrobial potential of phylogenetically unique actinomycete,Streptomyces sp. JRG-04 from marine origin

Due to the emergence of severe infectious diseases and thriving antibiotic resistance, there is a need to explore microbial-derived bioactive secondary metabolites from unexplored regions. Present study deals with a mangrove estuary derived strain of Streptomyces sp. with potent antimicrobial activity against various pathogens, including methicillin resistant Staphylococcus aureus. Bioactive compound was effective even at low MIC level, damages the membrane of methicillin resistant S. aureus and causes cell death, however it has no cytotoxic effect on H9C2 cells. 16S rRNA shared 99.5% sequence similarity to Streptomyces longispororuber. Optimum biomass and antimicrobial compound production were observed in production medium supplemented with 1.0% maltose and 0.5% yeast extract. The active compound purified from the chloroform extract of the cell-free supernatant was studied by FT-IR, 1H NMR, 13C NMR and LC ESI-MS and identified as aromatic polyketide. β-ketosynthase (KS) domain of the Streptomyces strain revealed 93.2% sequence similarity to the benzoisochromanequinone, an actinorhodin biosynthetic gene cluster of Streptomyces coelicolor A3(2). However, the region synthesizing the secondary metabolite produced by the S. longispororuber was not related to the KS domain of the strain, due to the phenomenon of horizontal gene transfer over the period of evolutionary process, thus generating metabolic compound diversity.     

Bacillus onubensis sp. nov., isolated from the air of two Andalusian caves

Two Gram-positive, catalase-positive, oxidase-negative, motile, endospore-forming, rod-shaped bacteria, designated as 0911MAR22V3T and 0911TES10J4, were isolated from air samples collected in two show caves, located in Andalusia, Southern Spain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains were indistinguishable and they were most closely related to Bacillus humi DSM 16318T (98%). DNA–DNA hybridization values of the strain 0911MAR22V3T with respect to strain 0911TES10J4 and B. humi DSM 16318T were 76.8% (73.9%, reciprocal) and 56.9% (63.3%, reciprocal analysis), respectively. Whole genome average nucleotide identity (ANI) values of both strains were in the threshold value for species delineation and less than 85% with B. humi. Strains 0911MAR22V3T and 0911TES10J4 grew at 10–47 °C (optimum 37 °C), at pH 6–9.5 and with 0–8% (w/v) NaCl (optimum 1%). In both strains the dominant isoprenoid quinone was MK-7, the major cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and two more phospholipids, the predominant fatty acids were iso-C15:0 and anteiso-C15:0 and the DNA G + C content was 38 mol%. On the basis of their phylogenetic relatedness and their phenotypic and genotypic features, the strains 0911MAR22V3T and 0911TES10J4 should be attributed to a novel species within the genus Bacillus, for which the name Bacillus onubensis sp. nov. is proposed. The type strain is 0911MAR22V3T (=LMG 27963T = CECT 8479T); and strain 0911TES10J4 (CECT 8478) is a reference strain.     

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.     

Utilization of drought-tolerant bacterial strains isolated from harsh soils as a plant growth-promoting rhizobacteria (PGPR)

Drought stress adversely affects plant health and productivity. Recently, drought-resistant bacterial isolates are used to combat drought resistance in crops. In this in vitro study, 20 bacterial isolates were isolated from harsh soil; their drought tolerance was evaluated using four concentrations of polyethylene glycol (PEG) 6000. The two most efficient isolates (DS4 and DS9) were selected and identified using 16S rRNA genetic sequencing. They were registered in the NCBI database and deposited under accession numbers MW916285 and MW916307 for Bacillus cereus (DS4) and Bacillus albus (DS9), respectively. These isolates were screened for plant growth-promoting properties compared to non-stressed conditions. Biochemical parameters; Proline, salicylic acid, gibberellic acid (GA), indole acetic acid (IAA), antioxidant activity, and antioxidant enzymes were measured under the same conditions, and in vitro seed germination was tested under stress conditions and inoculation with selected isolates. The results showed that under the harsh conditions of PEG6000, DS4 produced the highest amount of IAA of 1.61 µg/ml, followed by DS9 with 0.9 µg/ml. The highest amount of GA (49.95 µg/ml) was produced by DS9. On the other hand, the highest amount of siderophore was produced from DS4 isolate followed by DS9. Additionally, DS4 isolate recorded the highest exopolysaccharide (EPS) content of 3.4 mg/ml under PEG (-1.2 MPa) followed by DS9. The antioxidant activity increased in PEG concentrations depending manner, and the activity of the antioxidant enzymes increased, as catalase (CAT) recorded the highest activity in DS4 with an amount of 1.095 mg/ml. additionally, an increase in biofilm formation was observed under drought conditions. The isolated mixture protected the plant from the harmful effects of drought and showed an increase in the measured variables. Under unstressed conditions, the highest rates of emulsification index (EI 24%) were obtained for DS4 and DS9, at 14.92 and 11.54, respectively, and decreased under stress. The highest values of germination, total seedling length, and vigor index were obtained upon inoculation with the combination of two strains, and were 100%, 4.10 cm, and 410, respectively. Therefore, two strains combination is an effective vaccine capable of developing and improving drought tolerance in dryland plants.     

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.     

Anoxybacillus amylolyticus sp. nov., a thermophilic amylase producing bacterium isolated from Mount Rittmann (Antarctica)

A new thermophilic spore-forming strain MR3CT was isolated from geothermal soil located on Mount Rittmann in Antarctica. Strain MR3CT was Gram-positive, rod-shaped, occurring in pairs or filamentous. Growth was observed between 45 and 65 degrees C (optimum 61 degrees C) and at pH 5.0-6.5 (optimum pH 5.6). It was capable of utilizing galactose, trehalose, maltose and sucrose. The microorganism produced an exopolysaccharide and synthesized an extracellular constitutive amylolytic activity. The G + C content of DNA was 43.5 mol%. On the basis of 16S rRNA gene sequence similarity, strain MR3CT was shown to be related most closely to Anoxybacillus species. Chemotaxonomic data (major isoprenoid quinone-menaquinone-7; major fatty acid-iso-C15:0 and iso-C17:0) supported the affiliation of strain MR3C1T to the genus Anoxybacillus. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MR3CT from the validly published Anoxybacillus species. MR3CT therefore represents a new species, for which the name Anoxybacillus amylolyticus sp. nov., is proposed, with the type strain MR3CT (= ATCC BAA-872T = DSM 15939T = CIP 108338T).     

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.     

Drouetiella epilithica sp. nov. and Drouetiella lurida (Oculatellaceae,Synechococcales) isolated in the Republic of Korea based on the polyphasic approach

Five strains of Drouetiella (ACKU666, 667, 668, 669 and 670) were isolated from gravels in water, stone monument and coastal mudflat in Korea, and were studied using morphological and molecular traits. All five strains had thin and simple trichomes and exhibited false branching. From these strains, four strains (ACKU666, 667, 668 and 669) exhibited similar cell lengths with reddish–brown colored cells such as Drouetiella lurida. The 16S rRNA gene phylogeny showed the four strains formed a clade with Drouetiella lurida, and their DNA similarity was calculated to be 99.1–100%. The color of strain ACKU670 appeared to be in bright blue–green color like Drouetiella fasciculata, and their thylakoids showed a parietal arrangement, which is a characteristic feature of the family Oculatellaceae. Strain ACKU670 turned out to be a sister clade to the D. lurida according to the phylogenetic analysis of the 16S rRNA gene. The 16–23S rRNA internal transcribed spacer secondary folding structure (D1–D1′, Box-B and V3 helices) confirmed the uniqueness of strain ACKU670, therefore indicating differences from the related species. Considering all the results, we described our strain ACKU670 as Drouetiella epilithica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.     

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).     

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.     

<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.     

Description and phylogeny of Namalycastis jaya sp. n. (Polychaeta,Nereididae, Namanereidinae) from the southwest coast of India

Namalycastis jaya sp. n. (Polychaeta: Nereididae: Namanereidinae)is described from the southern coast of Kerala in southwest India. One important characteristic feature of the species is the lack of notochaetae in all parapodia, a characteristic that it shares with at least two other species, Namalycastis elobeyensis Glasby, 1999and Namalycastis hawaiiensis Johnson, 1903. It differs from Namalycastis elobeyensis by virtue of its smaller antennae, unequal eye size, bilobed acicular neuropodial ligule and multi-incised pygidium rim. Moreover, it differs from Namalycastis hawaiiensis by having fewer teeth on the serrated blades of the sub-neuroacicular falciger in chaetiger 10, and by possessing finely serrated falcigers in posterior segments. Beyond morphological analyses, molecular phylogenetics was used for the first time for Namalycastis to support population monophyly and recognition of the new species.The analysis, using both mitochondrial and nuclear data, corroborated the morphological analysis in suggesting that our specimens represent an as yet undescribed species, Namalycastis jaya sp. n., which forms a monophyletic group among the sampled nereidid taxa. Finally, a taxonomic key for Namalycastis species recorded from the Indian region is provided.