Science.gov

Sample records for bacterium bacillus sp

  1. Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil.

    PubMed

    Ghosh, A; Bhardwaj, M; Satyanarayana, T; Khurana, M; Mayilraj, S; Jain, R K

    2007-02-01

    A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Growth was observed at pH 7.0-11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was with Bacillus oshimensis JCM 12663T (98.8 %). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness with the type strains of B. oshimensis (62 %), Bacillus patagoniensis (55 %), Bacillus clausii (51 %) and Bacillus gibsonii (34 %), the species with which strain MLB2T formed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species of Bacillus, for which the name Bacillus lehensis sp. nov. is proposed. The type strain is MLB2T (=MTCC 7633T=JCM 13820T). PMID:17267957

  2. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation

    PubMed Central

    Yin, Liang; Xue, Yanfen; Ma, Yanhe

    2015-01-01

    The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress. PMID:26030352

  3. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation.

    PubMed

    Yin, Liang; Xue, Yanfen; Ma, Yanhe

    2015-01-01

    The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress. PMID:26030352

  4. Bacillus shacheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    PubMed

    Lei, Zuchao; Qiu, Peng; Ye, Renyuan; Tian, Jiewei; Liu, Yang; Wang, Lei; Tang, Shu-Kun; Li, Wen-Jun; Tian, Yongqiang

    2014-01-01

    A moderately halophilic bacterium, strain HNA-14(T), was isolated from a saline-alkali soil sample collected in Shache County, Xinjiang Province. On the basis of the polyphasic taxonomic data, the isolate was considered to be a member of the genus Bacillus. The organism grew optimally at 30 °C and pH 8.0. It was moderately halophilic and its optimum growth occurred at 5-10% NaCl. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid and the predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0 and iso-C15:0 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and two unknown phospholipids. The G+C content of the genomic DNA was 48.6 mol%. Strain HNA-14(T) exhibited a low 16S rRNA gene sequence similarity of 96% with its nearest neighbors [Bacillus clausii KSM-K16 (96.5%), Bacillus xiaoxiensis DSM 21943(T)(96.2%), Bacillus clausii DSM 8716(T) (96.1%), Bacillus patagoniensis PAT05(T) (96.1%), Bacillus lehensis MLB-2(T) (96.0%), Bacillus oshimensis K11(T) (95.9%) and Bacillus hunanensis DSM 23008(T) (95.8%)] and the phenotypic characteristics indicate that strain HNA-14(T) can be distinguished from them. Therefore, a novel species of the genus Bacillus, Bacillus shacheensis sp. nov. (type strain, HNA-14(T) = KCTC 33145 = DSM 26902) is proposed. PMID:25008165

  5. Bacillus haikouensis sp. nov., a facultatively anaerobic halotolerant bacterium isolated from a paddy soil.

    PubMed

    Li, Jibing; Yang, Guiqin; Lu, Qin; Zhao, Yong; Zhou, Shungui

    2014-10-01

    A Gram-stain positive, rod-shaped, endospore-forming and facultatively anaerobic halotolerant bacterium, designated as C-89(T), was isolated from a paddy field soil in Haikou, Hainan Province, People's Republic of China. Optimal growth was observed at 37 °C and pH 7.0 in the presence of 4% NaCl (w/v). The predominant menaquinone was identified as MK-7, the major cellular fatty acids were identified as anteiso-C(15:0) and iso-C(15:0), and the major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The peptidoglycan type was determined to be based on meso-DAP. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relatives were identified as Bacillus vietnamensis JCM 11124(T) (98.8% sequence similarity), Bacillus aquimaris JCM 11545(T) (98.6%) and Bacillus marisflavi JCM 11544(T) (98.5%). The DNA G+C content of strain C-89(T) was determined to be 45.4 mol%. The DNA-DNA relatedness values of strain C-89(T) with its closest relatives were below 18%. Therefore, on the basis of phylogenetic, chemotaxonomic, and phenotypic results, strain C-89(T) can be considered to represent a novel species within the genus Bacillus, for which the name Bacillus haikouensis sp. nov., is proposed. The type strain is C-89(T) (=KCTC 33545(T) = CCTCC AB 2014076(T)). PMID:25100188

  6. Global Microarray Analysis of Carbohydrate Use in Alkaliphilic Hemicellulolytic Bacterium Bacillus sp. N16-5

    PubMed Central

    Song, Yajian; Xue, Yanfen; Ma, Yanhe

    2013-01-01

    The alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5 has a broad substrate spectrum and exhibits the capacity to utilize complex carbohydrates such as galactomannan, xylan, and pectin. In the monosaccharide mixture, sequential utilization by Bacillus sp. N16-5 was observed. Glucose appeared to be its preferential monosaccharide, followed by fructose, mannose, arabinose, xylose, and galactose. Global transcription profiles of the strain were determined separately for growth on six monosaccharides (glucose, fructose, mannose, galactose, arabinose, and xylose) and four polysaccharides (galactomannan, xylan, pectin, and sodium carboxymethylcellulose) using one-color microarrays. Numerous genes potentially related to polysaccharide degradation, sugar transport, and monosaccharide metabolism were found to respond to a specific substrate. Putative gene clusters for different carbohydrates were identified according to transcriptional patterns and genome annotation. Identification and analysis of these gene clusters contributed to pathway reconstruction for carbohydrate utilization in Bacillus sp. N16-5. Several genes encoding putative sugar transporters were highly expressed during growth on specific sugars, suggesting their functional roles. Two phosphoenolpyruvate-dependent phosphotransferase systems were identified as candidate transporters for mannose and fructose, and a major facilitator superfamily transporter was identified as a candidate transporter for arabinose and xylose. Five carbohydrate uptake transporter 1 family ATP-binding cassette transporters were predicted to participate in the uptake of hemicellulose and pectin degradation products. Collectively, microarray data improved the pathway reconstruction involved in carbohydrate utilization of Bacillus sp. N16-5 and revealed that the organism precisely regulates gene transcription in response to fluctuations in energy resources. PMID:23326578

  7. Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine.

    PubMed

    Santini, Joanne M; Streimann, Illo C A; vanden Hoven, Rachel N

    2004-11-01

    A strictly anaerobic arsenate-respiring bacterium isolated from a gold mine in Bendigo, Victoria, Australia, belonging to the genus Bacillus is described. Cells are Gram-positive, motile rods capable of respiring with arsenate and nitrate as terminal electron acceptors using a variety of substrates, including acetate as the electron donor. Reduction of arsenate to arsenite is catalysed by a membrane-bound arsenate reductase that displays activity over a broad pH range. Synthesis of the enzyme is regulated; maximal activity is obtained when the organism is grown with arsenate as the terminal electron acceptor and no activity is detectable when it is grown with nitrate. Mass of the catalytic subunit was determined to be approximately 87 kDa based on ingel activity stains. The closest phylogenetic relative, based on 16S rRNA gene sequence analysis, is Bacillus arseniciselenatis, but DNA-DNA hybridization experiments clearly show that strain JMM-4(T) represents a novel Bacillus species, for which the name Bacillus macyae sp. nov. is proposed. The type strain is JMM-4(T) (=DSM 16346(T)=JCM 12340(T)). PMID:15545465

  8. Bacillus korlensis sp. nov., a moderately halotolerant bacterium isolated from a sand soil sample in China.

    PubMed

    Zhang, Lei; Wang, Yang; Dai, Jun; Tang, Yali; Yang, Qiao; Luo, Xuesong; Fang, Chengxiang

    2009-07-01

    A Gram-positive-staining, rod-shaped, motile, spore-forming and moderately halotolerant bacterium, designated ZLC-26(T), was isolated from a sand soil sample collected from Xinjiang Province, China, and was characterized by using a polyphasic taxonomic approach. This isolate grew optimally at 30-37 degrees C and pH 7-8. It grew with 0-8% NaCl (optimum, 0-2 %). Comparative 16S rRNA gene sequence analysis showed that strain ZLC-26(T) was closely related to members of the genus Bacillus, exhibiting the highest 16S rRNA gene sequence similarities to Bacillus nealsonii DSM 15077(T) (97.1 %), B. shackletonii LMG 18435(T) (97.0 %), B. siralis 171544(T) (97.0 %), B. circulans IAM 12462(T) (96.7 %) and B. pocheonensis Gsoil 420(T) (96.7 %). Strain ZLC-26(T) contained MK-7 as the predominant menaquinone. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15 : 0), C(16 : 1)omega11c and anteiso-C(15 : 0). The DNA G+C content was 38.2 mol%. These chemotaxonomic results supported the affiliation of strain ZLC-26(T) to the genus Bacillus. However, low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain ZLC-26(T) from recognized Bacillus species. On the basis of the evidence presented, strain ZLC-26(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus korlensis sp. nov. is proposed. The type strain is ZLC-26(T) (=CCTCC AB 207172(T)=NRRL B-51302(T)). PMID:19542113

  9. A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater.

    PubMed

    Abbas, Saira; Ahmed, Iftikhar; Kudo, Takuji; Iqbal, Muhammad; Lee, Yong-Jae; Fujiwara, Toru; Ohkuma, Moriya

    2015-12-01

    The taxonomic position of a Gram-stain positive and heavy metal tolerant bacterium, designated strain NCCP-662(T), was investigated by polyphasic characterisation. Cells of strain NCCP-662(T) were observed to be rod to filamentous shaped, motile and strictly aerobic, and to grow at 10-50 °C (optimum 30-37 °C) and at pH range of 6-10 (optimum pH 7-8). The strain was found to be able to tolerate 0-12 % NaCl (w/v) and heavy metals (Cr 1200 ppm, Pb 1800 ppm and Cu 1200 ppm) in tryptic soya agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence of strain NCCP-662(T) showed that it belongs to the genus Bacillus and showed high sequence similarity (98.2 and 98.0 %, respectively) with the type strains of Bacillus niabensis 4T19(T) and Bacillus halosaccharovorans E33(T). The chemotaxonomic data showed that the major quinone is MK-7; the predominant cellular fatty acids are anteiso-C15 :0, iso-C14:0, iso-C16:0 and C16:0 and iso-C15:0; the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol along with several unidentified glycolipids, phospholipids and polar lipids. The DNA G+C content was determined to be 36.9 mol%. These data also support the affiliation of strain NCCP-662(T) with the genus Bacillus. The level of DNA-DNA relatedness between strain NCCP-662(T) and B. niabensis JCM 16399(T) was 20.5 ± 0.5 %. On the basis of physiological and biochemical characteristics, phylogenetic analyses and DNA-DNA hybridization data, strain NCCP-662(T) can be clearly differentiated from the validly named Bacillus species and thus represents a new species, for which the name Bacillus malikii sp. nov. is proposed with the type strain NCCP-662(T) (= LMG 28369(T) = DSM 29005(T) = JCM 30192(T)). PMID:26362330

  10. A Comparative biochemical study on two marine endophytes, Bacterium SRCnm and Bacillus sp. JS, Isolated from red sea algae.

    PubMed

    Ahmed, Eman Fadl; Hassan, Hossam Mokhtar; Rateb, Mostafa Ezzat; Abdel-Wahab, Noha; Sameer, Somayah; Aly Taie, Hanan Anwar; Abdel-Hameed, Mohammed Sayed; Hammouda, Ola

    2016-01-01

    Two marine endophytic bacteria were isolated from the Red Sea algae; a red alga; Acanthophora dendroides and the brown alga Sargassum sabrepandum. The isolates were identified based on their 16SrRNA sequences as Bacterium SRCnm and Bacillus sp. JS. The objective of this study was to investigate the potential anti-microbial and antioxidant activities of the extracts of the isolated bacteria grown in different nutrient conditions. Compared to amoxicillin (25μg/disk) and erythromycin (15μg/disk), the extracts of Bacterium SRCn min media II, III, IV and V were potent inhibitors of the gram-positive bacterium Sarcina maxima even at low concentrations. Also, the multidrug resistant Staphylococcus aureus(MRSA) was more sensitive to the metabolites produced in medium (II) of the same endophyte than erythromycin (15μg/disk). A moderate activity of the Bacillus sp. JS extracts of media I and II was obtained against the same pathogen. The total compounds (500ug/ml) of both isolated endophytes showed moderate antioxidant activities (48.9% and 46.1%, respectively). LC/MS analysis of the bacterial extracts was carried out to investigate the likely natural products produced. Cyclo(D-cis-Hyp-L-Leu), dihydrosphingosine and 2-Amino-1,3-hexadecanediol were identified in the fermentation medium of Bacterium SRCnm, whereas cyclo (D-Pro-L-Tyr) and cyclo (L-Leu-L-Pro) were the suggested compounds of Bacillus sp. JS. PMID:26826831

  11. Bacillus nitroreducens sp. nov., a humus-reducing bacterium isolated from a compost.

    PubMed

    Guo, Junhui; Wang, Yue Qiang; Yang, Guiqin; Chen, Yunqi; Zhou, Shungui; Zhao, Yong; Zhuang, Li

    2016-05-01

    A Gram-staining-positive, facultative anaerobic, motile and rod-shaped bacterium, designated GSS08(T), was isolated from a windrow compost pile and characterized by means of a polyphasic approach. Growth occurred with 0-4 % (w/v) NaCl (optimum 1 %), at pH 6.5-9.5 (optimum pH 7.5) and at 20-45 °C (optimum 37 °C). Anaerobic growth occurred with anthraquinone-2,6-disulphonate, fumarate and NO3 (-) as electron acceptor. The main respiratory quinone was MK-7. The predominant polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>5 %) were iso-C15:0 (43.1 %), anteiso-C15:0 (27.4 %) and iso-C16:0 (8.3 %). The DNA G + C content was 39.6 mol%. The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GSS08(T) formed a phyletic lineage with the type strain of Bacillus humi DSM 16318(T) with a high sequence similarity of 97.5 %, but it displayed low sequence similarity with other valid species in the genus Bacillus (<96.0 %). The DNA-DNA relatedness between strains GSS08(T) and B. humi DSM 16318(T) was 50.8 %. The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS08(T) represents a novel species, for which the name Bacillus nitroreducens sp. nov. is proposed. The type strain is GSS08(T) (=KCTC 33699(T) = MCCC 1K01091(T)). PMID:26832132

  12. Rapid Aggregation of Biofuel-Producing Algae by the Bacterium Bacillus sp. Strain RP1137

    PubMed Central

    Powell, Ryan J.

    2013-01-01

    Algal biofuels represent one of the most promising means of sustainably replacing liquid fuels. However, significant challenges remain before alga-based fuels become competitive with fossil fuels. One of the largest challenges is the ability to harvest the algae in an economical and low-energy manner. In this article, we describe the isolation of a bacterial strain, Bacillus sp. strain RP1137, which can rapidly aggregate several algae that are candidates for biofuel production, including a Nannochloropsis sp. This bacterium aggregates algae in a pH-dependent and reversible manner and retains its aggregation ability after paraformaldehyde fixation, opening the possibility for reuse of the cells. The optimal ratio of bacteria to algae is described, as is the robustness of aggregation at different salinities and temperatures. Aggregation is dependent on the presence of calcium or magnesium ions. The efficiency of aggregation of Nannochloropsis oceanica IMET1 is between 70 and 95% and is comparable to that obtained by other means of harvest; however, the rate of harvest is fast, with aggregates forming in 30 s. PMID:23892750

  13. Photoinhibition of Phaeocystis globosa resulting from oxidative stress induced by a marine algicidal bacterium Bacillus sp. LP-10

    PubMed Central

    Guan, Chengwei; Guo, Xiaoyun; Li, Yi; Zhang, Huajun; Lei, Xueqian; Cai, Guanjing; Guo, Jiajia; Yu, Zhiming; Zheng, Tianling

    2015-01-01

    Harmful algal blooms caused by Phaeocystis globosa have resulted in staggering losses to coastal countries because of their world-wide distribution. Bacteria have been studied for years to control the blooms of harmful alga, however, the action mechanism of them against harmful algal cells is still not well defined. Here, a previously isolated algicidal bacterium Bacillus sp. LP-10 was used to elucidate the potential mechanism involved in the dysfunction of P. globosa algal cells at physiological and molecular levels. Our results showed Bacillus sp. LP-10 induced an obvious rise of reactive oxygen species (ROS), which was supposed to be major reason for algal cell death. Meanwhile, the results revealed a significant decrease of photosynthetic physiological indexes and apparent down-regulated of photosynthesis-related genes (psbA and rbcS) and protein (PSII reaction center protein D1), after treated by Bacillus sp. LP-10 filtrates, suggesting photoinhibition occurred in the algal cells. Furthermore, our results indicated that light played important roles in the algal cell death. Our work demonstrated that the major lethal reason of P. globosa cells treated by the algicidal bacterium was the photoinhibition resulted from oxidative stress induced by Bacillus sp. LP-10. PMID:26601700

  14. Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India.

    PubMed

    Suresh, K; Prabagaran, S R; Sengupta, S; Shivaji, S

    2004-07-01

    Strain Sd/3T (=MTCC 4374T=DSM 15820T), an arsenic-resistant bacterium, was isolated from a sand sample obtained from an arsenic-contaminated aquifer in Chakdah district in West Bengal, India (23 degrees 3' N 88 degrees 35' E). The bacterium was Gram-positive, rod-shaped, non-motile, endospore-forming and yellowish-orange pigmented. It possessed all the characteristics that conform to the genus Bacillus, such as it had A4beta murein type (L-orn-D-Asp) peptidoglycan variant, MK-7 as the major menaquinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. Based on its chemotaxonomic and phylogenetic characteristics, strain Sd/3T was identified as a species of the genus Bacillus. It exhibited maximum similarity (95%) at the 16S rRNA gene level with Bacillus cohnii; however, DNA-DNA similarity with B. cohnii was 60.7%. Strain Sd/3T also exhibited a number of phenotypic differences from B. cohnii (DSM 6307T). These data suggest that Sd/3T represents a novel species of the genus Bacillus. The name Bacillus indicus sp. nov. is proposed. PMID:15280316

  15. Bacillus patagoniensis sp. nov., a novel alkalitolerant bacterium from the rhizosphere of Atriplex lampa in Patagonia, Argentina.

    PubMed

    Olivera, Nelda; Siñeriz, Faustino; Breccia, Javier D

    2005-01-01

    A Gram-positive, rod-shaped, spore-forming bacterium (PAT 05T) was isolated from the rhizosphere of the perennial shrub Atriplex lampa in north-eastern Patagonia, Argentina. Its overall biochemical and physiological characteristics indicated that this strain should be placed in the alkaliphilic Bacillus group. Strain PAT 05T grew at pH 7-10 (optimum pH 8), but not at pH 6. Its DNA G+C content was 39.7 mol%. Sequence analysis of the 16S rRNA gene of PAT 05T revealed the closest match (99.6 % similarity) with Bacillus sp. DSM 8714. The highest level of DNA-DNA relatedness (88.6 %) was also found with this strain. On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, G+C content and DNA-DNA hybridization data, strain PAT 05T is related at the species level to Bacillus sp. DSM 8714, a member of a group referred as phenon 4a by Nielsen et al. [Nielsen, P., Fritze, D. & Priest, F. G. (1995). Microbiology 141, 1745-1761], which still lacks taxonomic standing. These results support the proposal of strain PAT 05T (=DSM 16117T=ATCC BAA-965T) as the type strain of Bacillus patagoniensis sp. nov. PMID:15653916

  16. Complete genome sequence of Bacillus sp. YP1, a polyethylene-degrading bacterium from waxworm's gut.

    PubMed

    Yang, Yu; Chen, Jianwei; Wu, Wei-Min; Zhao, Jiao; Yang, Jun

    2015-04-20

    Bacillus sp. strain YP1, isolated from the gut of waxworm (the larvae of Plodia interpunctella) which ate polyethylene (PE) plastic, is capable of degrading PE and utilizing PE as sole carbon source. Here we report the complete genome sequence of strain YP1, which is relevant to polyethylene depolymerization and biodegradation. PMID:25795022

  17. Bacillus lonarensis sp. nov., an alkalitolerant bacterium isolated from a soda lake.

    PubMed

    Reddy, Sultanpuram Vishnuvardhan; Thirumala, Mothe; Farooq, Mohammed; Sasikala, Chintalapati; Ramana, Chintalapati Venkata

    2015-01-01

    A novel Gram-stain-positive, rod-shaped, motile and endospore-forming novel bacterial strain 25nlg(T) was isolated from Lonar soda lake, in India. Based on the 16S rRNA gene sequence analysis, it was identified as a member of Firmicutes, being most closely related to Bacillus patagoniensis PAT 05(T) (96.6 %) and other members in the genus Bacillus (<96.0 %). Strain 25nlg(T) was catalase and oxidase-positive. The strain grows optimally at a pH of 9.5 with 4-6 % (w/v) NaCl and temperature of 35-37 °C. The cell wall of the strain 25nlg(T) contains meso-diaminopimelic acid as the diagnostic amino acid. Polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid (PL2), an aminophospholipid (APL2) and three unknown lipids (L2-4). The predominant isoprenoid quinone was MK-7. iso-C15:0 (41.7 %) was the predominant fatty acid, and significant proportions of anteiso-C15:0 (20.8 %), C12:0 (5.5 %), anteiso-C17:0 (4.9 %), iso-C17:0 (4.5 %) were also detected in the strain 25nlg(T). The DNA G+C content of the strain 25nlg(T) was 40.5 mol%. The results of molecular, physiological and biochemical tests allowed a clear phenotypic differentiation of strain 25nlg(T) from all other members of the genus Bacillus. Strain 25nlg(T) represents a novel member of the genus Bacillus, for which the name Bacillus lonarensis sp. nov. is proposed. The type strain is 25nlg(T) (=KCTC 33413(T) = LMG 27974(T) = CGMCC = 1.12817(T)). PMID:25294189

  18. Bacillus coreaensis sp. nov.: a xylan-hydrolyzing bacterium isolated from the soil of Jeju Island, Republic of Korea.

    PubMed

    Chi, Won-Jae; Youn, Young Sang; Park, Jae-Seon; Hong, Soon-Kwang

    2015-07-01

    A xylan-degrading bacterium, designated as MS5(T) strain, was isolated from soil collected from the Jeju Island, Republic of Korea. Strain MS5(T) was Gram-stain-positive, aerobic, and motile by polar flagellum. The major fatty acids identified in this bacterium were iso-C15:0 (32.3%), C16:0 (27.3%), and anteiso-C15:0 (10.2%). A similarity search based on the 16S rRNA gene sequence revealed that the strain belongs to the class Bacilli and shared the highest similarity with the type strains Bacillus beringensis BR035(T) (98.7%) and Bacillus korlensis ZLC-26(T) (98.6%) which form a coherent cluster in a neighbor-joining phylogenetic tree. The DNA G+C content of strain MS5(T) was 43.0 mol%. The major menaquinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNADNA relatedness values between strain MS5(T) and two closely related species, B. beringensis BR035(T) and B. korlensis ZLC-26(T), were less than 70%. DNA-DNA relatedness analysis and 16S rRNA sequence similarity, as well as phenotypic and chemotaxonomic characteristics suggest that the strain MS5(T) constitutes a novel Bacillus species, for which the name Bacillus coreaensis sp. nov. is proposed. The type strain is MS5(T) (=DSM25506(T) =KCTC13895(T)). PMID:26115993

  19. Isolation and identification of chemical constituents from the bacterium Bacillus sp. and their nematicidal activities.

    PubMed

    Zeng, Liming; Jin, Hui; Lu, Dengxue; Yang, Xiaoyan; Pan, Le; Cui, Haiyan; He, Xiaofeng; Qiu, Hongdeng; Qin, Bo

    2015-10-01

    A strain SMrs28 was isolated from the rhizosphere soil of a toxic plant Stellera chamaejasme and identified as Bacillus sp. on the basis of morphological and partial 16S rRNA gene sequence analysis. The crude extract of SMrs28 fermentation broth showed strong nematocidal activities in preliminary test. To define the active nematocidal metabolites of SMrs28, a novel compound (1), 4-oxabicyclo[3.2.2]nona-1(7), 5,8-triene, along with five known compounds (2-6), were isolated from the strain by various column chromatographic techniques and characterized on the basis of spectroscopic analysis. Results of the in vitro nematicidal tests showed that the metabolites presented different levels of activity at certain exposure conditions. Compounds (1-3) displayed LC50 values of 904.12, 451.26, 232.98 µg/ml and 1594.0, 366.62, 206.38 µg/ml against Bursaphelenchus xylophilus and Ditylenchus destructor at 72 h, respectively. This is the first report of the nematicidal activity of the compounds as constituents of Bacillus sp.. Our findings help to find potential chemical structures to develop nematicides from microbial source for the management of nematode-infected plant diseases. PMID:26058971

  20. Factors affecting soluble selenium removal by a selenate-reducing bacterium Bacillus sp. SF-1.

    PubMed

    Kashiwa, M; Nishimoto, S; Takahashi, K; Ike, M; Fujita, M

    2000-01-01

    High concentrations of soluble selenium, selenate and selenite, have acute and chronic toxicity toward living things. With the aim of developing a biological process for selenium removal, the effects of a variety of parameters on the reduction of soluble selenium by a Bacillus sp. strain SF-1, which is capable of reductively transforming selenate into selenite and, subsequently, into nontoxic insoluble elemental selenium, were studied. The bacterial strain could effectively reduce 20 mM of selenate to selenite and 2 mM of selenite to elemental selenium in the presence of an appropriate carbon source and in the absence of oxygen. The reduction rate of selenate to selenite was much higher than that of selenite to elemental selenium, resulting in the transient accumulation of selenite during selenate reduction. The selenate reduction rate increased with increases in the selenate concentration up to 20 mM, while the rate of selenite reduction decreased sharply at selenite concentrations of more than 2 mM. The elemental selenium transformed from selenate via selenite was found both inside and outside the cells. Bacillus sp. SF-1 was able to utilize a variety of organic acids or sugars as a carbon source in selenate reduction. Although the copresence of sulfate did not inhibit selenate reduction, it was completely inhibited by some other oxyanions, including nitrate. A model sequencing batch system using the bacterial strain was developed and exhibited good performance in the treatment of wastewater containing high concentrations of selenate. PMID:16232792

  1. Bacillus rhizosphaerae sp. nov., an novel diazotrophic bacterium isolated from sugarcane rhizosphere soil.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Lee, Jung-Sook; Lee, Keun-Chul; Hari, Kuppusamy

    2011-10-01

    A Gram-positive, non-pigmented, rod-shaped, diazotrophic bacterial strain, designated SC-N012(T), was isolated from rhizosphere soil of sugarcane and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Bacillus. Sequence analysis of the 16S rRNA gene of SC-N012(T) revealed the closest match (98.9% pair wise similarity) with Bacillus clausii DSM 8716(T). However, DNA-DNA hybridization experiments indicated low levels of genomic relatedness (32%) with this strain. The major components of the fatty acid profile are iso-C(15:0), anteiso-C(15:0), iso-C(17:0) and anteiso-C(17:0). The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The G+C content of the genomic DNA is 43.0 mol%. The lipids present in strain SC-N012(T) are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and two unknown phospholipids. Their predominant respiratory quinone was MK-7. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing allowed strain SC-N012(T) to be described as members of novel species of the genus Bacillus, for which the name Bacillus rhizosphaerae sp. nov. is proposed. The type strain is SC-N012(T) (=DSM 21911(T) = NCCB 100267(T)). PMID:21671194

  2. Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.

    PubMed

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Xie, Changxiao; Honda, Daiske; Sun, Jianzhong; Ai, Lianzhong

    2014-05-01

    An alkaliphilic and halotolerant Gram-stain-positive bacterium, which was isolated from sediment samples from the South China Sea, was subjected to a taxonomic study. The isolate, strain L1T, grew well at a wide range of temperatures and pH values, 10.0-45.0 °C and pH 6-11, with optima at 30 °C and pH 9.0, respectively. The growth of strain L1T occurred at total salt concentrations of 0-10% (w/v) with an optimum at 2% (w/v). Phylogenetic analysis based on 16S rRNA sequence comparison indicated that the isolate represented a member of the genus Bacillus. The strains most closely related to strain L1T were Bacillus nanhaiisediminis JCM 16507T, Bacillus halodurans DSM 497T and Bacillus pseudofirmus DSM 8715T, with 16S rRNA similarities of 96.5%, 95.9% and 95.7%, respectively. DNA-DNA hybridization of strain L1T with the type strains of the most closely related species, B. nanhaiisediminis JCM 16507T, B. halodurans DSM 497T and B. pseudofirmus DSM 8715T, showed reassociation values of about 21.7%, 14.3% and 13.9%, respectively. The DNA G+C content of strain L1T was 40.76 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids of strain L1T were iso-C14 : 0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the phenotypic and phylogenetic characteristics, it is proposed that strain L1T (=JCM 18543T=DSM 26145T) should be classified as the type strain of Bacillus ligniniphilus sp. nov. PMID:24554634

  3. Bacillus oleivorans sp. nov., a diesel oil-degrading and solvent-tolerant bacterium.

    PubMed

    Azmatunnisa, M; Rahul, K; Subhash, Y; Sasikala, Ch; Ramana, Ch V

    2015-04-01

    Two Gram-stain-positive, diesel oil-degrading, solvent-tolerant, aerobic, endospore-forming, rod-shaped bacteria were isolated from a contaminated laboratory plate. Based on 16S rRNA gene sequence analysis, strains JC228(T) and JC279 were identified as belonging to the genus Bacillus within the family Bacillaceae of the phylum Firmicutes and were found to be most closely related to Bacillus carboniphilus JCM 9731(T) (98.1% 16S rRNA gene sequence similarity) and shared <96.0% 16S rRNA gene sequence similarity with other members of the genus Bacillus . The DNA-DNA hybridization value between the two strains was 88±2%. Strain JC228(T) showed 23.4±1% reassociation (based on DNA-DNA hybridization) with B. carboniphilus LMG 18001(T). The DNA G+C content of strains JC228(T) and JC279 was 39 and 38.4 mol%, respectively. Both strains were positive for catalase and oxidase activities, and negative for hydrolysis of starch and Tween 80. Strains JC228(T) and JC279 grew chemoorganoheterotrophically with optimum growth at pH 7 (range pH 7-9.5) and 35 °C (range 25-40 °C). Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid (PL2) were the major polar lipids. Major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0), iso-C(17 : 0) and C(16 : 0). Whole-cell hydrolysates contained l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. Both strains utilized diesel oil as sole carbon and energy source. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed clear differentiation of strains JC228(T) and JC279 from their closest phylogenetic neighbours. Therefore strains JC228(T) and JC279 represent a novel species of the genus Bacillus , for which the name Bacillus oleivorans sp. nov. is proposed. The type strain is JC228(T) ( = LMG 28084(T) = CCTCC AB 2013353(T)). PMID:25667390

  4. Bacillus rigiliprofundi sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust.

    PubMed

    Sylvan, Jason B; Hoffman, Colleen L; Momper, Lily M; Toner, Brandy M; Amend, Jan P; Edwards, Katrina J

    2015-06-01

    A facultatively anaerobic bacterium, designated strain 1MBB1T, was isolated from basaltic breccia collected from 341 m below the seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods, 0.5 μm wide and 1-3 μm long, that occurred singly and in chains. Strain 1MBB1T stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30 °C and pH 7.5, and could grow with up to 12 % (w/v) NaCl. The DNA G+C content was 40.5 mol%. The major cellular fatty acids were C16:1ω11c (26.5 %), anteiso-C15:0 (19.5 %), C16:0 (18.7 %) and iso-C15:0 (10.4 %), and the cell-wall diamino acid was meso-diaminopimelic acid. Endospores of strain 1MBB1T oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1T was a member of the family Bacillaceae, with Bacillus foraminis CV53T and Bacillus novalis LMG 21837T being the closest phylogenetic neighbours (96.5 and 96.2 % similarity, respectively). This is the first novel species described from deep subseafloor basaltic crust. On the basis of our polyphasic analysis, we conclude that strain 1MBB1T represents a novel species of the genus Bacillus, for which we propose the name Bacillus rigiliprofundi sp. nov. The type strain is 1MBB1T ( = NCMA B78T = LMG 28275T). PMID:25813363

  5. Bacillus daqingensis sp. nov., a halophilic, alkaliphilic bacterium isolated from saline-sodic soil in Daqing, China.

    PubMed

    Wang, Shuang; Sun, Lei; Wei, Dan; Zhou, Baoku; Zhang, Junzheng; Gu, Xuejia; Zhang, Lei; Liu, Ying; Li, Yidan; Guo, Wei; Jiang, Shuang; Pan, Yaqing; Wang, Yufeng

    2014-07-01

    An alkaliphilic, moderately halophilic, bacterium, designated strain X10-1(T), was isolated from saline-alkaline soil in Daqing, Heilongjiang Province, China. Strain X10-1(T) was determined to be a Gram-positive aerobe with rod-shaped cells. The isolate was catalase-positive, oxidase-negative, non-motile, and capable of growth at salinities of 0-16% (w/v) NaCl (optimum, 3%). The pH range for growth was 7.5-11.0 (optimum, pH 10.0). The genomic DNA G+C content was 47.7 mol%. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15:0, anteiso-C17:0, iso-C15:0, C16:0, and iso-C16:0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that X10-1(T) is a member of the genus Bacillus, being most closely related to B. saliphilus DSM15402(T) (97.8% similarity) and B. agaradhaerens DSM 8721(T) (96.2%). DNA-DNA relatedness to the type strains of these species was less than 40%. On the basis of the phylogenetic, physiological, and biochemical data, strain X10-1(T) represents a novel species of the genus Bacillus, for which the name Bacillus daqingensis sp. nov. is proposed. The type strain is X10-1(T) (=NBRC 109404(T) = CGMCC 1.12295(T)). PMID:24879344

  6. Bacillus radicibacter sp. nov., a new bacterium isolated from root nodule of Oxytropis ochrocephala Bunge.

    PubMed

    Wei, Xiu Li; Lin, Yan Bing; Xu, Lin; Han, Meng Sha; Dong, Dan Hong; Chen, Wei Min; Wang, Li; Wei, Ge Hong

    2015-10-01

    A Gram-positive, facultative anaerobic, rod-shaped, and endospore-forming strain, designated 53-2(T) was isolated from the root nodule of Oxytropis ochrocephala Bunge growing on Qilian mountain, China. The strain can grow at pH 7.0-8.0, 10-50 °C and tolerate up to 11% NaCl. Optimal growth occurred at pH 7.2 and 37 °C. The result of BLASTn search based on 16S rRNA gene sequence revealed that strain 53-2(T) , being closest related to Bacillus acidicola 105-2(T) , possessed remote similarity (less than 95.64%) to the species within genus Bacillus. The DNA G + C content was 37.8%. Chemotaxonomic data (major quinone is MK-7; major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipid, and aminoglycophospholipid; fatty acids are anteiso-C15: 0 , iso-C15:0 and anteiso-C17: 0 ) supported the affiliation of the isolate to the genus Bacillus. On the basis of physiological, phylogenetic, and biochemical properties, strain 53-2(T) represents a novel species within genus Bacillus, for which the name Bacillus radicibacter is proposed. The type strain is 53-2(T) (=DSM27302(T) =ACCC06115(T) =CCNWQLS5(T) ). PMID:26214748

  7. Bacillus subterraneus sp. nov., an iron- and manganese-reducing bacterium from a deep subsurface Australian thermal aquifer.

    PubMed

    Kanso, Sungwan; Greene, Anthony C; Patel, Bharat K C

    2002-05-01

    A facultatively anaerobic bacterium, designated strain COOI3B(T) (= ATCC BAA 136T = DSM 13966T), was isolated from the waters emitted by a bore well tapping the deep subterranean thermal waters of the Great Artesian Basin of Australia. The cells were straight to slightly curved rods (0.5-0.8 x 2-25 microm) that occurred singly and rarely in pairs or in chains. Strain COOI3B(T) was motile by peritrichous flagella. It stained gram-negative, but electron micrographs showed a gram-positive-type cell wall. Spores were never observed and cells were heat-sensitive. Yeast extract at 0.02% (w/v) was required for growth and could also be used as a sole carbon and energy source at concentrations higher than 0.1% (w/v). The strain utilized amorphous iron(III), manganese(IV), nitrate, nitrite and fumarate as electron acceptors in the presence of yeast extract, glucose, sucrose, fructose, maltose, xylose, starch, glycerol, ethanol or lactate. Electron acceptors were not obligately required and growth was better in the presence of nitrate than in its absence. Acid was not produced from growth on carbohydrates. Tryptophan deaminase, H2S, arginine dihydrolase, lysine decarboxylase, beta-galactosidase, arabinosidase, glucuronidase, glucosaminidase, nitroanilidase, xylosidase and ornithine decarboxylase were not produced. Starch and gelatin, but not casein, were hydrolysed. Aesculin and catalase, but not oxidase and urease, were produced. Strain COOI3B(T) grew optimally at temperatures between 37 and 40 degrees C (the temperature growth range was 25-45 degrees C) and at pH 7.0-9.0 (the pH growth range was 6.0 to 9.5) with 5% (w/v) NaCl (the NaCl concentration growth range was 0.9%, w/v). The DNA base composition was 43 +/- 1 mol % G+C. Phylogenetic analysis indicated that it was a member of the family Bacillaceae, Bacillus infernus and Bacillus firmus being the closest phylogenetic neighbours (having a mean similarity value of 96%); hence, strain COOI3B(T) is designated as a novel

  8. Isolation and characterization of a furfural-degrading bacterium Bacillus cereus sp. strain DS1.

    PubMed

    Zheng, Dan; Bao, Jianguo; Lu, Jueming; Gao, Chunlei

    2015-02-01

    Furfural was found to be the main organic pollutant in the wastewater coming from the Diosgenin factory. This substance is derived from acidic pentosan in Dioscorea zingiberensis and is also found in a variety of agricultural byproducts, including corncobs, oat, wheat bran, and sawdust. It is regarded as a toxicant and an inhibitor to the growth of microorganism in both sewage disposal and biological fermentation. A furfural-degrading strain (DS1) was isolated from activated sludge of wastewater treatment plant in a diosgenin factory by continuous enrichment culture. The strain was identified as Bacillus cereus based on morphological, physiological tests, as well as on 16S rDNA sequence and Biolog analyses. The capacity of this strain to grow on a mineral salt medium, utilizing furfural as the sole carbon and energy source to degrade furfural, was investigated in this study. Under the condition of pH 9.0, temperature 35 °C, with rotating speed of 150 rpm, and an inoculum of 6 %, the strain showed that the furfural degradation capacity reaches 35 % in 7 days, as measured by high-performance liquid chromatography. The addition of inorganic carbon sources could bring down the biodegradation efficiency of the furfural. The strain DS1 showed better furfural removal capacity, as compared to other inorganic carbon sources in the media. Furthermore, a furfural concentration of as high as 4,000 mg L(-1) was tolerated by the culture. The capacity to degrade furfural was demonstrated for the first time by using the genus B. cereus. This study suggests the possible application in biodegradation strategies. PMID:25274411

  9. Assessment of Bioflocculant Production by Bacillus sp. Gilbert, a Marine Bacterium Isolated from the Bottom Sediment of Algoa Bay

    PubMed Central

    Nontembiso, Piyo; Sekelwa, Cosa; Leonard, Mabinya V.; Anthony, Okoh I.

    2011-01-01

    The bioflocculant-producing potentials of a marine bacteria isolated from the bottom sediment of Algoa Bay was investigated using standard methods. The 16S rDNA sequence analysis revealed 98% similarity to that of Bacillus sp. HXG-C1 and the nucleotide sequence was deposited in GenBank as Bacillus sp. Gilbert with accession number HQ537128. Bioflocculant was optimally produced when sucrose (72% flocculating activity) and ammonium chloride (91% flocculating activity) were used as sole sources of carbon and nitrogen, respectively; an initial pH 6.2 of the production medium; and Mg2+ as cation. Chemical analysis of the purified bioflocculant revealed the compound to be a polysaccharide. PMID:21822413

  10. Antiplasmodial activity of bacilosarcin A isolated from the octocoral-associated bacterium Bacillus sp. collected in Panama

    PubMed Central

    Boya, Cristopher A.; Herrera, Liuris; Guzman, Hector M.; Gutierrez, Marcelino

    2012-01-01

    Aim: This study was designed for isolating and characterizing antiplasmodial compounds from marine octocoral-associated bacteria. Materials and Methods: The organic extract of the Bacillus sp. was subjected to purification using several chromatography techniques guided by bioassays to yield three isocoumarin derivatives (1–3). Chemical structures of the compounds were elucidated on the basis of HRMS spectra and NMR spectroscopy. The antiplasmodial activity of the isolated compounds was evaluated in vitro against the chloroquine-resistant Plasmodium falciparum strain W2. Results: Isolated compounds were identified as bacilosarcin A (1), AI77-F (2), and AI77-H (3). Bacilosarcin A (1) displayed a low micromolar activity (IC50 = 2.2 μM) against P. falciparum while compounds 2 and 3 showed no activity. Conclusions: Bacilosarcin A was found to be responsible for the antiplasmodial activity observed in the crude extract obtained from the Bacillus sp. PMID:22368402

  11. Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern.

    PubMed

    Zhou, Yan-Xia; Liu, Guo-Hong; Liu, Bo; Chen, Guan-Jun; Du, Zong-Jun

    2016-07-01

    A novel Gram-stain positive, endospore-forming bacterium, designated SA4(T), was isolated from a soil sample collected from an abandoned marine solar saltern at Wendeng, Shandong Province, PR China. Cells were observed to be rod shaped, alginase positive, catalase positive and motile. The strain was found to grow at temperatures ranging from 15 to 40 °C (optimum 35 °C), and pH 5.0-11.0 (optimum pH 8.0) with 0-7.0 % (w/v) NaCl concentration (optimum NaCl 3.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SA4(T) belongs to the genus Bacillus and exhibits 16S rRNA gene sequence similarities of 96.6, 96.5, 96.3 and 96.2 % with Bacillus horikoshii DSM 8719(T), Bacillus acidicola 105-2(T), Bacillus shackletonii LMG 18435(T) and Bacillus pocheonensis Gsoil 420(T), respectively. The menaquinone was identified as MK-7 and the major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15:0 (22.3 %), iso-C15:0 (22.6 %), iso-C16:0 (14.8 %) and iso-C14:0 (14.7 %). The DNA G+C content was determined to be 42.4 mol %. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate SA4(T) represents a novel species within the genus Bacillus, for which the name Bacillus mesophius sp. nov. is proposed. The type strain is SA4(T) (=DSM 101000(T)=CCTCC AB 2015209(T)). PMID:27084709

  12. Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil.

    PubMed

    Bao, Peng; Su, Jian-Qiang; Hu, Zheng-Yi; Häggblom, Max M; Zhu, Yong-Guan

    2014-06-15

    Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to reduce nitrate and selenite and for its resistance to arsenic under anaerobic conditions. Here we describe some key features of this organism, together with the complete genome sequence and annotation. The 3,575,797 bp long chromosome with its 3,454 protein-coding and 70 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of nitrogen, selenium and arsenic in paddy soil. PMID:25197451

  13. Genome sequence of the anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil

    PubMed Central

    Bao, Peng; Su, Jian-Qiang; Hu, Zheng-Yi; Häggblom, Max M.

    2014-01-01

    Bacillus sp. strain ZYK, a member of the phylum Firmicutes, is of interest for its ability to reduce nitrate and selenite and for its resistance to arsenic under anaerobic conditions. Here we describe some key features of this organism, together with the complete genome sequence and annotation. The 3,575,797 bp long chromosome with its 3,454 protein-coding and 70 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of nitrogen, selenium and arsenic in paddy soil. PMID:25197451

  14. Characterization of a salt-tolerant bacterium Bacillus sp. from a membrane bioreactor for saline wastewater treatment.

    PubMed

    Zhang, Xiaohui; Gao, Jie; Zhao, Fangbo; Zhao, Yuanyuan; Li, Zhanshuang

    2014-06-01

    High salt concentrations can cause plasmolysis and loss of activity of cells, but the salt-tolerant bacterium can endure the high salt concentrations in wastewater. In this research 7 salt-tolerant bacteria, which could survive in dry powder products and could degrade organic contaminants in saline wastewater, were isolated from a membrane bioreactor. The strain NY6 which showed the fastest growth rate, best property for organic matter degradation and could survive in dry powder more than 3 months was selected and characterized. It was classified as Bacillus aerius based on the analysis of the morphological and physiological properties as well as the 16S rRNA sequence and Neigh borjoining tree. The strain NY6 could survive in the salinity up to 6% and the optimal growth salinity is 2%; it belongs to a slightly halophilic bacterium. The capability of its dry powder products for COD removal was 800 mg COD/(g·day) in synthesized saline wastewater with salinity of 2%. According to salt-tolerant mechanism research, when the salinity was below 2%, the stain NY6 absorbed K(+) and Na(+) to maintain osmotic equilibrium, and when the salinity was above 2%, the NY6 kept its life by producing a large amount of spores. PMID:25079850

  15. Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils.

    PubMed

    Dou, Guiming; Liu, Hongcan; He, Wei; Ma, Yuchao

    2016-01-01

    Two alkaliphilic and halotolerant Gram-stain positive, rod-shaped and endospore-forming bacteria, designated strains 12-3(T) and 12-4, were isolated from saline and alkaline soils collected in Lindian county, Heilongjiang province, China. Both strains were observed to grow well at a wide range of temperature and pH values, 10-45 °C and pH 8-12, with optimal growth at 37 °C and pH 9.0, respectively. Growth of the two strains was found to occur at total salt concentrations of 0-12 % (w/v), with an optimum at 4 % (w/v). The G+C contents of the genomic DNA of strains 12-3(T) and 12-4 were determined to be 42.7 and 42.4 mol%, respectively, and the major cellular fatty acids were identified as anteiso-C15:0 and anteiso-C17:0. In isolate 12-3(T), meso-diaminopimelic acid was found to be the diagnostic diamino acid of the cell wall peptidoglycan; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were identified as the major cellular polar lipids; and menaquinone-7 was identified as the predominant isoprenoid quinone. Strains 12-3(T) and 12-4 share very close 16S rRNA gene sequence similarity (99.74 %) and their DNA-DNA relatedness was 95.3 ± 0.63 %, meaning that the two strains can be considered to belong to the same species. 16S rRNA gene sequence-based phylogenetic analysis revealed strains 12-3(T) and 12-4 exhibit high similarities to Bacillus pseudofirmus DSM 8715(T) (98.7 %), Bacillus marmarensis DSM 21297(T) (97.2 %) and Bacillus nanhaiisediminis CGMCC 1.10116(T) (97.1 and 97.0 %, respectively). DNA-DNA hybridization values between isolate 12-3(T) and the type strains of closely related Bacillus species were below 30 %. On the basis of the polyphasic evidence presented, strains 12-3(T) and 12-4 are considered to represent a novel species of the genus Bacillus, for which the name Bacillus lindianensis sp. nov. is proposed. The type strain is 12-3(T) (DSM 26864(T) = CGMCC 1.12717(T)). PMID:26604103

  16. Bacillus pakistanensis sp. nov., a halotolerant bacterium isolated from salt mines of the Karak Area in Pakistan.

    PubMed

    Roohi, Aneela; Ahmed, Iftikhar; Paek, Jayoung; Sin, Yeseul; Abbas, Saira; Jamil, Muhammad; Chang, Young H

    2014-06-01

    A rod shaped, non-motile, endospore forming, Gram-stain positive and moderately halotolerant strain, designated as NCCP-168(T), was isolated from salt mines sampled in the Karak district of Khyber Pakhtunkhwa Province in Pakistan. To delineate its taxonomic position, the strain was subjected to polyphasic characterization. Cells of strain NCCP-168(T) can grow at 10-40 (○)C (optimum at 30-35 (○)C), in a pH range of 5.0-9.0 (optimum at pH 8.0) and in 0-17 % (w/v) NaCl on agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NCCP-168(T) belongs to the genus Bacillus with the highest similarity to Bacillus seohaeanensis BH724(T) (97.1 %), and less than 97 % similarity with other closely related taxa (95.6 % with B. subtilis subsp. subtilis NCIB3610(T)). DNA-DNA relatedness between strain NCCP-168(T) and the type strains of closely related species was lower than 30 %. Chemotaxonomic data (major menaquinone, MK-7; cell wall peptidoglycan type, A1γ [meso-diaminopimelic acid]; major fatty acids, iso-C15:0 29.9 %, anteiso-C15:0 29.3 %, iso-C16:0 11.4 %, iso-C14:0 8.9 % and anteiso-C17:0 7.0 %; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine) support the affiliation of strain NCCP-168(T) with genus Bacillus. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain NCCP-168(T) can be distinguished from the closely related taxa and thus represents a novel species in the genus Bacillus, for which the name Bacillus pakistanensis sp. nov. is proposed, with the type strain NCCP-168(T) (= KCTC 13786(T) = DSM 24834(T) = JCM 18975(T)). PMID:24777297

  17. Bacillus herbersteinensis sp. nov.

    PubMed

    Wieser, Monika; Worliczek, Hanna; Kämpfer, Peter; Busse, Hans-Jürgen

    2005-09-01

    Two bacterial strains, designated D-1,5a(T) and D-1,5b, were isolated from a medieval wall painting in the chapel of Castle Herberstein, Styria (Austria). The Gram-positive, heterotrophic, aerobic, spore-forming rods showed nearly identical whole-cell protein patterns, identical genomic fingerprints and identical physiological profiles, demonstrating their relationship at the species level. Both strains contained meso-diaminopimelic acid in their peptidoglycan, possessed a quinone system comprising menaquinone MK-7 and had fatty acid profiles in which C(15:0) iso and C(15:0) anteiso were predominant. The 16S rRNA gene sequence of D-1,5a(T) showed the highest similarity (99.5%) to the sequence of Bacillus sp. LMG 20243, and Bacillus flexus IFO 15715(T) was the next most closely related established species (96.5%). Other type strains, such as Bacillus fastidiosus DSM 91(T), Bacillus indicus SD/3(T), Bacillus cibi JG-30(T), Bacillus megaterium IAM 13418(T), Bacillus cohnii DSM 6308(T), Bacillus bataviensis LMG 21833(T) and Bacillus soli LMG 21838(T), shared 96.0-96.1% 16S rRNA gene sequence similarity with D-1,5a(T). The combination of physiological and chemotaxonomic traits distinguishes the two strains from those species sharing the highest sequence similarities (96.0-96.5%). On the basis of these characteristics and the phylogenetic position of strain D-1,5a(T) (=DSM 16534(T)=CCM 7228(T)), this strain is assigned as the type strain of a novel species of the genus Bacillus, for which the name Bacillus herbersteinensis sp. nov. is proposed. PMID:16166719

  18. Identification and Characterization of a New Alkaline SGNH Hydrolase from a Thermophilic Bacterium Bacillus sp. K91.

    PubMed

    Yu, Tingting; Ding, Junmei; Zheng, Qingxia; Han, Nanyu; Yu, Jialin; Yang, Yunjuan; Li, Junjun; Mu, Yuelin; Wu, Qian; Huang, Zunxi

    2016-04-28

    est19 is a gene from Bacillus sp. K91 that encodes a new esterase. A comparison of the amino acid sequence showed that Est19 has typical Ser-Gly-Asn-His (SGNH) family motifs and could be grouped into the SGNH hydrolase family. The Est19 protein was functionally cloned, and expressed and purified from Escherichia coli BL21(DE3). The enzyme activity was optimal at 60°C and pH 9.0, and displayed esterase activity towards esters with short-chain acyl esters (C₂-C₆). A structural model of Est19 was constructed using phospholipase A1 from Streptomyces albidoflavus NA297 as a template. The structure showed an α/β-hydrolase fold and indicated the presence of the typical catalytic triad Ser49-Asp227-His230, which were further investigated by site-directed mutagenesis. To the best of our knowledge, Est19 is a new member of the SGNH hydrolase family identified from thermophiles, which may be applicable in the industrial production of semisynthetic β-lactam antibiotics after modification. PMID:26699742

  19. Indirect Oxidation of Co(II) in the Presence of the Marine Mn(II)-Oxidizing Bacterium Bacillus Sp. Strain SG-1

    SciTech Connect

    Murray, K.J.; Webb, S.M.; Bargar, J.R.; Tebo, B.M.; /Scripps Inst. Oceanography /SLAC, SSRL /Oregon Health Sci. U.

    2009-04-29

    Cobalt(II) oxidation in aquatic environments has been shown to be linked to Mn(II) oxidation, a process primarily mediated by bacteria. This work examines the oxidation of Co(II) by the spore-forming marine Mn(II)-oxidizing bacterium Bacillus sp. strain SG-1, which enzymatically catalyzes the formation of reactive nanoparticulate Mn(IV) oxides. Preparations of these spores were incubated with radiotracers and various amounts of Co(II) and Mn(II), and the rates of Mn(II) and Co(II) oxidation were measured. Inhibition of Mn(II) oxidation by Co(II) and inhibition of Co(II) oxidation by Mn(II) were both found to be competitive. However, from both radiotracer experiments and X-ray spectroscopic measurements, no Co(II) oxidation occurred in the complete absence of Mn(II), suggesting that the Co(II) oxidation observed in these cultures is indirect and that a previous report of enzymatic Co(II) oxidation may have been due to very low levels of contaminating Mn. Our results indicate that the mechanism by which SG-1 oxidizes Co(II) is through the production of the reactive nanoparticulate Mn oxide.

  20. Isolation of a halophilic bacterium, Bacillus sp. strain NY-6 for organic contaminants removal in saline wastewater on ship

    NASA Astrophysics Data System (ADS)

    Gao, Jie; Yu, Zhenjiang; Zhang, Xiaohui; Zhao, Dan; Zhao, Fangbo

    2013-06-01

    The objective of this research was to examine if certain strains of Bacillus bacteria, could survive in dry powder products and if so, could the bacteria degrade organic contaminants in saline wastewater on a ship. As part of the study, we isolated 7 domesticated strains named NY1, NY2,..., and NY7, the strain NY6 showed to have the best performance for organic matter degradation and could survive in dry powder more than 3 months. NY6 was identified as Bacillus aerius, based on the morphological and physic-chemical properties. Its optimal growth conditions were as follows: salinity was 2%; temperature was 37°C; pH was in 6.5-7.0; best ratio of C: N: P was 100:5:1. The capability of its dry powder for Chemical Oxygen Demand (COD) removal was 800mg COD/g in synthesized marine wastewater with 2% salinity. The spores in the dry powder were 1.972×108 g -1.

  1. Bacillus oryzicola sp. nov., an Endophytic Bacterium Isolated from the Roots of Rice with Antimicrobial, Plant Growth Promoting, and Systemic Resistance Inducing Activities in Rice

    PubMed Central

    Chung, Eu Jin; Hossain, Mohammad Tofajjal; Khan, Ajmal; Kim, Kyung Hyun; Jeon, Che Ok; Chung, Young Ryun

    2015-01-01

    7007 and YC7010T represent novel species of the genus Bacillus, for which the name Bacillus oryzicola sp. nov. is proposed. The type strain is YC7010T (= KACC 18228T). Taken together, our findings suggest that novel endophytic Bacillus strains can be used for the biological control of rice diseases. PMID:26060434

  2. Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Rüger 1983 . as mMrinibacillus marinus gen nov., comb. nov.

    PubMed

    Yoon, J H; Weiss, N; Lee, K C; Lee, I S; Kang, K H; Park, Y H

    2001-11-01

    A moderately halophilic, round-endospore-forming bacterium (strain YKJ-13T) was isolated from jeotgal, a traditional Korean fermented seafood, and studied by a polyphasic taxonomic approach. This organism was related to the phylogenetic clade comprising members of Bacillus rRNA group 2 and formed a cluster with Bacillus marinus with a bootstrap fidelity value of 93.6%. The peptidoglycan type was A1alpha linked directly through L-Lys. Based on cell morphology, peptidoglycan type and phylogeny, strain YKJ-13T, together with B. marinus, is considered to be a member of Bacillus rRNA group 2. Strain YKJ-13T was also characterized by having MK-7 and MK-8 as the predominant menaquinones and iso-C15:0 as the major fatty acid. The DNA G+C content was 44 mol%. Strain YKJ-13T exhibited a 16S rDNA similarity value of 95.7% with B. marinus DSM 1297T, its closest phylogenetic relative. Levels of 16S rDNA similarity between strain YKJ-13T and other Bacillus spp. were less than 94.2%. Therefore, on the basis of the data presented, the name Jeotgalibacillus alimentarius gen. nov., sp. nov. is proposed for strain YKJ-13T (= KCCM 80002T = JCM 10872T). It is also proposed that B. marinus be reclassified in Marinibacillus gen. nov. as Marinibacillus marinus comb. nov. PMID:11760951

  3. Sporosarcina aquimarina sp. nov., a bacterium isolated from seawater in Korea, and transfer of Bacillus globisporus (Larkin and Stokes 1967), Bacillus psychrophilus (Nakamura 1984) and Bacillus pasteurii (Chester 1898) to the genus Sporosarcina as Sporosarcina globispora comb. nov., Sporosarcina psychrophila comb. nov. and Sporosarcina pasteurii comb. nov., and emended description of th.

    PubMed

    Yoon, J H; Lee, K C; Weiss, N; Kho, Y H; Kang, K H; Park, Y H

    2001-05-01

    A light-orange-coloured, facultatively anaerobic, rod-shaped bacterium (strain SW28T), which was isolated from seawater in Korea, was taxonomically studied by a polyphasic approach. This organism formed round terminal endospores in swollen sporangia. The peptidoglycan type is A4alpha, based on L-Lys-L-Ala-D-Asp. The predominant menaquinone is MK-7 and the major fatty acid is ante-C15:0. The G+C content of the DNA is 40 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain SW28T falls within the radiation of a cluster comprising the rRNA group 2 bacilli and non-Bacillus-type organisms. Strain SW28T showed the highest degree of relatedness to the type strain of Sporosarcina ureae, sharing 96.8% 16S rDNA similarity. Levels of DNA-DNA relatedness between strain SW28T and S. ureae DSM 2281T and the type strains of some Bacillus species forming a coherent phylogenetic cluster are less than 12.5%. On the basis of phenotypic and chemotaxonomic characteristics, 16S rDNA sequence analysis and DNA-DNA relatedness data, it is proposed that strain SW28T should be placed in the genus Sporosarcina as a new species, Sporosarcina aquimarina sp. nov. The type strain is SW28T (= KCCM 41039T = JCM 10887T). From the results of the taxonomic re-evaluation, it is also proposed that Bacillus globisporus, Bacillus psychrophilus and Bacillus pasteurii be transferred to the genus Sporosarcina as Sporosarcina globispora, Sporosarcina psychrophila and Sporosarcina pasteurii, respectively. PMID:11411676

  4. Gageopeptins A and B, new inhibitors of zoospore motility of the phytopathogen Phytophthora capsici from a marine-derived bacterium Bacillus sp. 109GGC020.

    PubMed

    Tareq, Fakir Shahidullah; Hasan, Choudhury M; Lee, Hyi-Seung; Lee, Yeon-Ju; Lee, Jong Seok; Surovy, Musrat Zahan; Islam, Md Tofazzal; Shin, Hee Jae

    2015-08-15

    The motility of zoospores is critical in the disease cycles of the peronosporomycetes that cause devastating diseases in plants, fishes, vertebrates, and microbes. In the course of screening for secondary metabolites regulating the motility of zoospores of Phytophthora capsici, we discovered two new inhibitors from the ethyl acetate extract of the fermentation broth of a marine-derived strain Bacillus sp. 109GGC020. The structures of these novel metabolites were elucidated as new cyclic lipopeptides and named gageopeptins A (1) and B (2) by spectroscopic analyses including high resolution MS and extensive 1D and 2D NMR. The stereoconfigurations of 1 and 2 were assigned based on the chemical derivatization studies and reviews of the literature data. Although compounds 1 and 2 impaired the motility of zoospores of P. capsici in dose- and time-dependent manners, compound 1 (IC50 = 1 μg/ml) was an approximately 400-fold stronger motility inhibitor than 2 (IC50 = 400 μg/ml). Interestingly, the zoospores halted by compound 1 were subsequently lysed at higher concentrations (IC50 = 50 μg/ml). Compounds 1 and 2 were also tested against some bacteria and fungi by broth dilution assay, and exhibited moderate antibacterial and good antifungal activities. PMID:26071635

  5. Directed Evolution and Structural Analysis of Alkaline Pectate Lyase from the Alkaliphilic Bacterium Bacillus sp. Strain N16-5 To Improve Its Thermostability for Efficient Ramie Degumming

    PubMed Central

    Zhou, Cheng; Ye, Jintong; Xue, Yanfen

    2015-01-01

    Thermostable alkaline pectate lyases have potential applications in the textile industry as an alternative to chemical-based ramie degumming processes. In particular, the alkaline pectate lyase from Bacillus sp. strain N16-5 (BspPelA) has potential for enzymatic ramie degumming because of its high specific activity under extremely alkaline conditions without the requirement for additional Ca2+. However, BspPelA displays poor thermostability and is inactive after incubation at 50°C for only 30 min. Here, directed evolution was used to improve the thermostability of BspPelA for efficient and stable degumming. After two rounds of error-prone PCR and screening of >12,000 mutants, 10 mutants with improved thermostability were obtained. Sequence analysis and site-directed mutagenesis revealed that single E124I, T178A, and S271G substitutions were responsible for improving thermostability. Structural and molecular dynamic simulation analysis indicated that the formation of a hydrophobic cluster and new H-bond networks was the key factor contributing to the improvement in thermostability with these three substitutions. The most thermostable combined mutant, EAET, exhibited a 140-fold increase in the t50 (time at which the enzyme loses 50% of its initial activity) value at 50°C, accompanied by an 84.3% decrease in activity compared with that of wild-type BspPelA, while the most advantageous combined mutant, EA, exhibited a 24-fold increase in the t50 value at 50°C, with a 23.3% increase in activity. Ramie degumming with the EA mutant was more efficient than that with wild-type BspPelA. Collectively, our results suggest that the EA mutant, exhibiting remarkable improvements in thermostability and activity, has the potential for applications in ramie degumming in the textile industry. PMID:26070675

  6. Bacillus nakamurai sp. nov., a black-pigment-producing strain.

    PubMed

    Dunlap, Christopher A; Saunders, Lauren P; Schisler, David A; Leathers, Timothy D; Naeem, Naveed; Cohan, Frederick M; Rooney, Alejandro P

    2016-08-01

    Two isolates of a Gram-stain-positive, strictly aerobic, motile, rod-shaped, endospore-forming bacterium were identified during a survey of the Bacillus diversity of the Agriculture Research Service Culture Collection. These strains were originally isolated from soil and have a phenotype of producing a dark pigment on tryptic soy agar. Phylogenetic analysis of the 16S rRNA gene indicated that these strains were related most closely to Bacillus subtilis subsp. inaquosorum (99.7 % similarity) and Bacillus axarquiensis (99.7 %). In phenotypic characterization, the novel strains were found to grow between 17 and 50 °C and can tolerate up to 9 % (w/v) NaCl. Furthermore, the strains grew in media of pH 5.5-10 (optimal growth at pH 7.0-8.0). The predominant cellular fatty acids were anteiso-C15 : 0 (34.8 %) and iso-C15 : 0 (21.9 %). The cell-wall peptidoglycan contained meso-diaminopimelic acid. A draft genome of both strains was completed. The DNA G+C content was 43.8 mol%. A phylogenomic analysis on the core genome of these two new strains and all members of the Bacillus subtilis group revealed these two strains formed a distinct monophyletic clade with the nearest neighbour Bacillus amyloliquefaciens. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations showed the two strains were conspecific (93.8 %), while values with all other species (<31.5 %) were well below the species threshold of 70 %. Based on the consensus of phylogenetic and phenotypic analyses, these strains are considered to represent a novel species within the genus Bacillus, for which the name Bacillus nakamurai sp. nov. is proposed, with type strain NRRL B-41091T (=CCUG 68786T). PMID:27150918

  7. Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft

    NASA Technical Reports Server (NTRS)

    La Duc, Myron T.; Satomi, Masataka; Venkateswaran, Kasthuri

    2004-01-01

    A round-spore-forming Bacillus species that produces an exosporium was isolated from the surface of the Mars Odyssey spacecraft. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and is a Gram-positive, aerobic, rod-shaped, endospore-forming eubacterium. Ultrathin sections of the spores showed the presence of an exosporium, spore coat, cortex and core. 16S rDNA sequence similarities between this strain, Bacillus fusiformis and Bacillus silvestris were approximately 96% and DNA-DNA reassociation values with these two bacilli were 23 and 17%, respectively. Spores of the novel species were resistant to desiccation, H2O2 and UV and gamma radiation. Of all strains tested, the spores of this strain were the most consistently resistant and survived all of the challenges posed, i.e. exposure to conditions of desiccation (100% survival), H2O2 (26% survival), UV radiation (10% survival at 660 J m(-2)) and gamma radiation (0.4% survival). The name proposed for this novel bacterium is Bacillus odysseyi sp. nov.; the type strain is 34hs-1T (=ATCC PTA-4993T=NRRL B-30641T=NBRC 100172T).

  8. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711.

    PubMed

    Shoemaker, William R; Muscarella, Mario E; Lennon, Jay T

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments. PMID:26089434

  9. Genome Sequence of the Soil Bacterium Janthinobacterium sp. KBS0711

    PubMed Central

    Shoemaker, William R.; Muscarella, Mario E.

    2015-01-01

    We present a draft genome of Janthinobacterium sp. KBS0711 that was isolated from agricultural soil. The genome provides insight into the ecological strategies of this bacterium in free-living and host-associated environments. PMID:26089434

  10. Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis.

    PubMed

    Ko, Kwan Soo; Oh, Won Sup; Lee, Mi Young; Lee, Jang Ho; Lee, Hyuck; Peck, Kyong Ran; Lee, Nam Yong; Song, Jae-Hoon

    2006-11-01

    Two Gram-positive bacilli, designated as strains SMC 4352-1T and SMC 4352-2T, were isolated sequentially from the blood of a newborn child with sepsis. They could not be identified by using conventional clinical microbiological methods. 16S rRNA gene sequencing and phylogenetic analysis revealed that both strains belonged to the genus Bacillus but clearly diverged from known Bacillus species. Strain SMC 4352-1T and strain SMC 4352-2T were found to be closely related to Bacillus firmus NCIMB 9366T (98.2% sequence similarity) and Bacillus cibi JG-30T (97.1% sequence similarity), respectively. They also displayed low DNA-DNA reassociation values (less than 40%) with respect to the most closely related Bacillus species. On the basis of their polyphasic characteristics, strain SMC 4352-1T and strain SMC 4352-2T represent two novel species of the genus Bacillus, for which the names Bacillus infantis sp. nov. (type strain SMC 4352-1T=KCCM 90025T=JCM 13438T) and Bacillus idriensis sp. nov. (type strain SMC 4352-2T=KCCM 90024T=JCM 13437T) are proposed. PMID:17082387

  11. Bacillus vini sp. nov. isolated from alcohol fermentation pit mud.

    PubMed

    Ma, Kedong; Chen, Xiaorong; Guo, Xiang; Wang, Yanwei; Wang, Huimin; Zhou, Shan; Song, Jinlong; Kong, Delong; Zhu, Jie; Dong, Weiwei; He, Mingxiong; Hu, Guoquan; Zhao, Bingqiang; Ruan, Zhiyong

    2016-08-01

    A novel aerobic, Gram-stain-positive, sporogenous, rod-shaped bacterium, designated LAM0415(T), was isolated from an alcohol fermentation pit mud sample collected from Sichuan Luzhou-flavour liquor enterprise in China. The isolate was found to be able to grow at NaCl concentrations of 0-10 % (w/v) (optimum: 1.0 %), 10-50 °C (optimum: 30-35 °C) and pH 3.0-10.0 (optimum: 7.0-8.0). Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolate belonged to the genus Bacillus and was closely related to Bacillus sporothermodurans DSM 10599(T) and Bacillus oleronius DSM 9356(T), with 98.4 and 97.2 % sequence similarity, respectively. The DNA-DNA hybridization values between strain LAM0415(T) and the two reference strains were 33.3 ± 1.2 and 42.8 ± 0.8 %, respectively. The genomic DNA G+C content was 35.2 mol% as determined by the T m method. The major fatty acids were determined to be iso-C15:0, anteiso-C15:0 and anteiso-C17:0. The predominant menaquinones were identified as MK7 and MK8. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and four unidentified glycolipids. The diagnostic amino acid of the cell wall peptidoglycan was determined to be meso-diaminopimelic acid. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0415(T) (=ACCC 06413(T) = JCM 19841(T)) represents the type strain of a novel species of the genus Bacillus, for which the name Bacillus vini sp. nov. is proposed. PMID:27055557

  12. Bacillus glycinifermentans sp. nov., isolated from fermented soybean paste.

    PubMed

    Kim, Soo-Jin; Dunlap, Christopher A; Kwon, Soon-Wo; Rooney, Alejandro P

    2015-10-01

    Two independent isolates of a Gram-stain-positive, facultatively anaerobic, motile, rod-shaped bacterium were recovered from cheonggukjang, a Korean fermented soybean paste food product. Preliminary sequencing analysis of the 16S rRNA gene indicated that these strains were related most closely to Bacillus sonorensis KCTC-13918T and Bacillus licheniformis DSM 13T. In phenotypic characterization, the novel strains were found to grow between 15 and 55 °C and to tolerate up to 8 % (w/v) NaCl. Furthermore, the strains grew in media of pH 5-10 (optimal growth at pH 7.0). The predominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0.The isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown glycolipid. Draft genomes of the two strains were determined and in silico DNA-DNA hybridizations with their nearest neighbour (B. sonorensis KCTC-13918T) revealed 29.9 % relatedness for both strains. Phylogenomic analysis of the genomes was conducted with the core genome (799 genes) of all strains in the Bacillus subtilis group and the two strains formed a distinct monophyletic cluster. In addition, the strains differed from the two most closely related species in that they did not metabolize maltose, d-galactose, d-sorbitol or d-gluconic acid. The DNA G+C content was 45.9 mol%. Based upon the consensus of phylogenetic and phenotypic analyses, these strains represent a novel species of the genus Bacillus, for which the name Bacillus glycinifermentans sp. nov. is proposed. The type strain is GO-13T ( = KACC 18425T = NRRL B-65291T). PMID:26297378

  13. Genomic, Proteomic, and Metabolite Characterization of Gemfibrozil-Degrading Organism Bacillus sp. GeD10.

    PubMed

    Kjeldal, Henrik; Zhou, Nicolette A; Wissenbach, Dirk K; von Bergen, Martin; Gough, Heidi L; Nielsen, Jeppe L

    2016-01-19

    Gemfibrozil is a widely used hypolipidemic and triglyceride lowering drug. Excess of the drug is excreted and discharged into the environment primarily via wastewater treatment plant effluents. Bacillus sp. GeD10, a gemfibrozil-degrader, was previously isolated from activated sludge. It is the first identified bacterium capable of degrading gemfibrozil. Gemfibrozil degradation by Bacillus sp. GeD10 was here studied through genome sequencing, quantitative proteomics and metabolite analysis. From the bacterial proteome of Bacillus sp. GeD10 1974 proteins were quantified, of which 284 proteins were found to be overabundant by more than 2-fold (FDR corrected p-value ≤0.032, fold change (log2) ≥ 1) in response to gemfibrozil exposure. Metabolomic analysis identified two hydroxylated intermediates as well as a glucuronidated hydroxyl-metabolite of gemfibrozil. Overall, gemfibrozil exposure in Bacillus sp. GeD10 increased the abundance of several enzymes potentially involved in gemfibrozil degradation as well as resulted in the production of several gemfibrozil metabolites. The potential catabolic pathway/modification included ring-hydroxylation preparing the substrate for subsequent ring cleavage by a meta-cleaving enzyme. The identified genes may allow for monitoring of potential gemfibrozil-degrading organisms in situ and increase the understanding of microbial processing of trace level contaminants. This study represents the first omics study on a gemfibrozil-degrading bacterium. PMID:26683816

  14. Bacillus encimensis sp. nov. isolated from marine sediment.

    PubMed

    Dastager, Syed G; Mawlankar, Rahul; Mual, Poonam; Verma, Ashish; Krishnamurthi, Srinivasan; Joseph, Neetha; Shouche, Yogesh S

    2015-05-01

    A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated SGD-V-25(T) was isolated from Veraval sediment sample, India. Strain SGD-V-25(T) was capable of growing at 25-50 °C (optimum 37 °C), pH 6-12 (optimum pH 7.0) and with 0-5% (w/v) NaCl. The taxonomic position of this strain was deduced using a polyphasic approach and the 16S rRNA gene sequence analysis showed that the isolate belongs to the phylum Firmicutes , forming the cluster with Bacillus badius MTCC 1548(T), with which it shares highest similarity of 99.1% with 13 nt differences. Other type strains of the genus Bacillus showed less than 96% similarity. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipid profile of strain SGD-V-25(T) showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phsophoglycolipid and two aminophospholipids. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 1ω11c and C16 : 0. The genomic DNA G+C content of strain SGD-V-25(T) was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA hybridization, strain SGD-V-25(T) could be clearly distinguished from closely related members of the genus Bacillus , and the name Bacillus encimensis sp. nov., is proposed to accommodate this strain. The type strain is SGD-V-25(T) ( =NCIM 5513(T) =DSM 28241(T)). PMID:25678682

  15. Bacillus gobiensis sp. nov., isolated from a soil sample.

    PubMed

    Liu, Bo; Liu, Guo-Hong; Cetin, Sengonca; Schumann, Peter; Pan, Zhi-Zhen; Chen, Qian-Qian

    2016-01-01

    A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated FJAT-4402T, was isolated from the weed rhizosphere soil of the Gobi desert in the Xinjiang Autonomous Region in the north-west of China. Isolate FJAT-4402T grew at 15-40 °C (optimum 30 °C), pH 5-10 (optimum pH 7) and in 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analyses, based on 16S rRNA gene sequences, showed that isolate FJAT-4402T was a member of the genus Bacillus and was most closely related to Bacillus licheniformis DSM 13T (96.2 %). The isolate showed 33.3 % DNA-DNA relatedness to the closest reference isolate, B. licheniformis DSM 13T. The diagnostic diamino acid of the peptidoglycan of isolate FJAT-4402T was meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (28.5 %), iso-C15 : 0 (20.1 %), anteiso-C17 : 0 (14.3 %), iso-C16 : 0 (9.6 %), C16 : 0 (8.4 %), iso-C17 : 0 (6.2 %) and iso-C14 : 0 (4.7 %) and the DNA G+C content was 42.0 mol%. The phenotypic, chemotaxonomic and genotypic properties indicated that strain FJAT-4402T represents a novel species within the genus Bacillus, for which the name Bacillus gobiensis sp. nov. is proposed. The type strain is FJAT-4402T ( = DSM 29500T = CGMCC 1.12902T). PMID:26530456

  16. Bacillus luteus sp. nov., isolated from soil.

    PubMed

    Subhash, Y; Sasikala, Ch; Ramana, Ch V

    2014-05-01

    Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5%) were anteiso-C15:0, iso-C16:0, iso-C15:0, anteiso-C17:0, iso-C14:0 and C16:0 with minor (<5 but >1%) amounts of iso-C17:0, anteiso-C17:0 B/iso-C17:0 I and C16:1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were L-alanine, D-alanine, D-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA-DNA hybridization>90%). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes. Both strains had a sequence similarity of 97.6% with Bacillus saliphilus 6AGT and <96.8% with other members of the genus Bacillus. Sequence similarity between strain JC167T and 168 was 100%. Strain JC167T showed 25.8±1% reassociation (based on DNA-DNA hybridization) with B. saliphilus DSM 15402T (=6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus, for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T (=KCTC 33100T=LMG 27257T). PMID:24478212

  17. Bacillus vanillea sp. nov., Isolated from the Cured Vanilla Bean.

    PubMed

    Chen, Yong-gan; Gu, Feng-lin; Li, Ji-hua; Xu, Fei; He, Shu-zhen; Fang, Yi-ming

    2015-02-01

    A Gram-positive bacterium, designated strain XY18(T), was isolated from a cured vanilla bean in Hainan province, China. Cells were rod-shaped, endospore producing, and peritrichous flagella. Strain XY18(T) grew at salinities of 0-8 % (w/v) NaCl (optimally 1-4 %), pH 4.0-8.0 (optimally 5.0-7.0 %) and temperature range 20-45 °C (optimally 28-35 °C). The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, and iso-C17:0. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XY18(T) was a member of the genus Bacillus, and closely related to B. amyloliquefaciens NBRC 15535(T) and B. siamensis PD-A10(T), with 99.1 and 99.2 % sequence similarity, respectively. However, the DNA-DNA hybridization value between strain XY18(T) and B. amyloliquefaciens NBRC 15535(T) was 35.7 %. The genomic DNA G+C content of strain XY18(T) was 46.4 mol%, significantly differed from B. siamensis PD-A10(T) (41.4 %), which was higher than the range of 4 % indicative of species. On the basis of polyphasic taxonomic study, including phenotypic features, chemotaxonomy, and phylogenetic analyses, strain XY18(T) represents a novel species within the genus Bacillus, for which the name Bacillus vanillea sp. nov. is proposed. The type strain is XY18(T) (=CGMCC 8629 = NCCB 100507). PMID:25292250

  18. Biodegradation of Xanthan Gum by Bacillus sp

    PubMed Central

    Cadmus, Martin C.; Jackson, Linda K.; Burton, Kermit A.; Plattner, Ronald D.; Slodki, Morey E.

    1982-01-01

    Strains tentatively identified as Bacillus sp. were isolated from sewage sludge and soil and shown to elaborate extracellular enzymes that degrade the extracellular polysaccharide (xanthan gum, polysaccharide B-1459) of Xanthomonas campestris NRRL B-1459. Enzyme production by one strain was greatly enhanced when the strain was incubated in a mixed culture. Products of degradation were identified as d-glucuronic acid, d-mannose, pyruvylated mannose, 6-O-acetyl d-mannose, and a (1→4)-linked glucan. These products correlate with the known structure of the gum. The complexity of the product mixture indicated that the xanthanase was a mixture of carbohydrases. The xanthanase complexes were similar to one another in temperature stability, pH and temperature optima, degree of substrate degradation, and enzymolysis products. Differences in pH stability, salt tolerance, recoverability, and yields of enzyme were observed. PMID:16346068

  19. Bacillus paralicheniformis sp. nov., isolated from fermented soybean paste.

    PubMed

    Dunlap, Christopher A; Kwon, Soon-Wo; Rooney, Alejandro P; Kim, Soo-Jin

    2015-10-01

    An isolate of a Gram-stain-positive, facultatively anaerobic, motile, rod-shaped, endospore-forming bacterium was recovered from soybean-based fermented paste. Phylogenetic analysis of the 16S rRNA gene indicated that the strain was most closely related to Bacillus sonorensis KCTC-13918T (99.5 % similarity) and Bacillus licheniformis DSM 13T (99.4 %). In phenotypic characterization, the novel strain was found to grow at 15–60 °C and to tolerate up to 10 % (w/v) NaCl. Furthermore, the strain grew in media with pH 6–11 (optimal growth at pH 7.0–8.0). The predominant cellular fatty acids were anteiso-C15 : 0 (37.7 %) and iso-C15 : 0 (31.5 %). The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. A draft genome sequence of the strain was completed and used for phylogenetic analysis. Phylogenomic analysis of all published genomes of species in the B. licheniformis group revealed that strains belonging to B. licheniformis clustered into two distinct groups, with group 1 consisting of B. licheniformis DSM 13T and 11 other strains and group 2 consisting of KJ-16T and four other strains. The DNA G+C content of strain KJ-16T was 45.9 % (determined from the genome sequence). Strain KJ-16T and another strain from group 2 were subsequently characterized using a polyphasic taxonomic approach and compared with strains from group 1 and another closely related species of the genus Bacillus. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Bacillus, for which the name Bacillus paralicheniformis sp. nov. is proposed, with type strain KJ-16T ( = KACC 18426T = NRRL B-65293T). PMID:26296568

  20. Draft Genome Sequencing of Bacillus sp. Strain M2-6, Isolated from the Roots of Korean Ginseng, Panax ginseng C. A. Meyer, after High-Hydrostatic-Pressure Processing

    PubMed Central

    Kim, Chong-Tai; Kim, Bong-Soo; Kim, Min-Ji; Park, Bang Heon; Kwon, Sujin; Maeng, Hack Young; Kwak, Jangyul; Chun, Jongsik; Cho, Yong-Jin; Kim, Namsoo; Kim, Chul-Jin

    2012-01-01

    A bacterium, designated M2-6, was isolated from Korean ginseng, Panax ginseng C. A. Meyer, roots after high-hydrostatic-pressure processing. On the basis of 16 rRNA gene phylogeny, the isolate was presumptively identified as a Bacillus sp. Here we report the draft genome sequence of Bacillus sp. strain M2-6 (= KACC 16563). PMID:23209247

  1. The acetylproteome of Gram-positive model bacterium Bacillus subtilis.

    PubMed

    Kim, Dooil; Yu, Byung Jo; Kim, Jung Ae; Lee, Yong-Jik; Choi, Soo-Geun; Kang, Sunghyun; Pan, Jae-Gu

    2013-05-01

    N(ε) -lysine acetylation, a reversible and highly regulated PTM, has been shown to occur in the model Gram-negative bacteria Escherichia coli and Salmonella enterica. Here, we extend this acetylproteome analysis to Bacillus subtilis, a model Gram-positive bacterium. Through anti-acetyllysine antibody-based immunoseparation of acetylpeptides followed by nano-HPLC/MS/MS analysis, we identified 332 unique lysine-acetylated sites on 185 proteins. These proteins are mainly involved in cellular housekeeping functions such as central metabolism and protein synthesis. Fifity-nine of the lysine-acetylated proteins showed homology with lysine-acetylated proteins previously identified in E. coli, suggesting that acetylated proteins are more conserved. Notably, acetylation was found at or near the active sites predicted by Prosite signature, including SdhA, RocA, Kbl, YwjH, and YfmT, indicating that lysine acetylation may affect their activities. In 2-amino-3-ketobutyrate CoA ligase Kbl, a class II aminotransferase, a lysine residue involved in pyridoxal phosphate attachment was found to be acetylated. This data set provides evidence for the generality of lysine acetylation in eubacteria and opens opportunities to explore the consequences of acetylation modification on the molecular physiology of B. subtilis. PMID:23468065

  2. Bacillus pervagus sp. nov. and Bacillus andreesenii sp. nov., isolated from a composting reactor.

    PubMed

    Kosowski, Kornelia; Schmidt, Marie; Pukall, Rüdiger; Hause, Gerd; Kämpfer, Peter; Lechner, Ute

    2014-01-01

    Two strains, 8-4-E12(T) and 8-4-E13(T), were isolated from a biowaste composting reactor. Based on 16S rRNA gene sequences, both strains belong to the genus Bacillus. Strain 8-4-E12(T) was most closely related to the type strains of Bacillus shackletonii, B. acidicola, B. sporothermodurans and B. oleronius (96.4, 96.3, 96.0 and 95.6 % 16S rRNA gene similarity, respectively), whereas strain 8-4-E13(T) was most closely related to the type strain of Bacillus humi (96.5 % sequence similarity). Strains 8-4-E12(T) and 8-4-E13(T) shared 94 % 16S rRNA gene sequence similarity. The fatty acid profile of strain 8-4-E12(T) was dominated by saturated iso- and anteiso-branched fatty acids (iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0), and also contained considerable amounts of C16 : 0. The fatty acid profile of strain 8-4-E13(T) showed a predominance of iso-C15 : 0 (65 %), with smaller amounts of other saturated branched-chain fatty acids along with an unsaturated alcohol. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids. Additionally, strain 8-4-E12(T) contained an unknown lipid and strain 8-4-E13(T) two unknown (amino-)phospholipids. The diagnostic diamino acid found in the cell-wall peptidoglycan of 8-4-E12(T) and 8-4-E13(T) was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The results of physiological and biochemical tests also allowed phenotypic differentiation of the two strains from each other and from related Bacillus species. On the basis of their phylogenetic, phenotypic and chemotaxonomic properties, strains 8-4-E12(T) and 8-4-E13(T) represent novel species of the genus Bacillus, for which the names Bacillus pervagus sp. nov. (type strain 8-4-E12(T) = DSM 23947(T) = LMG 27601(T)) and Bacillus andreesenii sp. nov. (type strain 8-4-E13(T) = DSM 23948(T) = LMG 27602(T)) are proposed. PMID:24021730

  3. Isolation and identification of antifungal peptides from Bacillus BH072, a novel bacterium isolated from honey.

    PubMed

    Zhao, Xin; Zhou, Zhi-jiang; Han, Ye; Wang, Zhan-zhong; Fan, Jie; Xiao, Hua-zhi

    2013-11-01

    A bacterial strain BH072 isolated from a honey sample showed antifungal activity against mold. Based on morphological, biochemical, physiological tests, and analysis of 16S rDNA sequence, the strain was identified to be a new subspecies of Bacillus sp. It had a broad spectrum of antifungal activity against various mold, such as Aspergillus niger, Pythium, and Botrytis cinerea. Six pairs of antifungal genes primers were designed and synthesized, and ituA, hag, tasA genes were detected by PCR analysis. The remarkable antifungal activity could be associated with the co-production of these three peptides. One of them was purified by 30-40% ammonium sulfate precipitation, Sephadex G-75 gel filtration and anion exchange chromatography on D201 resin. The purified peptide was estimated to be 35.615 kDa and identified to be flagellin by micrOTOF-Q II. By using methanol extraction, another substance was isolated from fermentation liquor, and determined to be iturin with liquid chromatography-mass spectrometry (LC-MS) method. The third possible peptide encoded by tasA was not isolated in this study. The culture liquor displayed antifungal activity in a wide pH range (5.0-9.0) and at 40-100°C. The result of the present work suggested that Bacillus BH072 might be a bio-control bacterium of research value. PMID:23545354

  4. Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a Potential Biocontrol Agent against Phytopathogens.

    PubMed

    Jeong, Haeyoung; Jo, Sung Hee; Hong, Chi Eun; Park, Jeong Mee

    2016-01-01

    ITALIC! Bacillus thuringiensisis the most widely known microbial pesticide used in agricultural applications. Herein, we report a draft genome sequence of the endophytic bacterium ITALIC! Bacillus thuringiensisstrain KB1, which exhibits antagonism against phytopathogens. PMID:27103716

  5. Genome Sequence of the Endophytic Bacterium Bacillus thuringiensis Strain KB1, a Potential Biocontrol Agent against Phytopathogens

    PubMed Central

    Jo, Sung Hee; Hong, Chi Eun

    2016-01-01

    Bacillus thuringiensis is the most widely known microbial pesticide used in agricultural applications. Herein, we report a draft genome sequence of the endophytic bacterium Bacillus thuringiensis strain KB1, which exhibits antagonism against phytopathogens. PMID:27103716

  6. Carbonate biomineralization induced by soil bacterium Bacillus megaterium

    NASA Astrophysics Data System (ADS)

    Lian, Bin; Hu, Qiaona; Chen, Jun; Ji, Junfeng; Teng, H. Henry

    2006-11-01

    Biogenic carbonates spawned from microbial activities are common occurrences in soils. Here, we investigate the carbonate biomineralization mediated by the bacterium Bacillus megaterium, a dominant strain separated from a loess profile in China. Upon completing bacterial cultivation, the ensuring products are centrifuged, and the resultant supernatant and the concentrated bacterial sludge as well as the un-separated culture are added separately into a Ca-CO 3 containing solution for crystallization experiments. Results of XRD and SEM analysis indicate that calcite is the dominant mineral phase formed when the bacteria are present. When the supernatant alone is used, however, a significant portion of vaterite is also precipitated. Experimental results further reveal that the bacteria have a strong tendency to colonize the center area of the calcite {1 0 1¯ 4} faces. Observed crystal morphology suggests that the bacterial colony may promote the growth normal to each individual {1 0 1¯ 4} face of calcite when the cell concentration is high, but may retard it or even cause dissolution of the immediate substrate surfaces when the concentration is low. SEM images taken at earlier stages of the crystallization experiments demonstrate the nucleation of calcite on the bacterial cell walls but do not show obvious morphological changes on the nanometer- to submicron-sized nuclei. δ 13C measurements unveil that the crystals grown in the presence of bacteria are further enriched in the heavy carbon isotope, implying that the bacterial metabolism may not be the carbon sources for the mineralization. Based upon these findings, we propose a mechanism for the B. megaterium mediated calcite mineralization and conclude that the whole process involves epi- and inter-cellular growth in the local microenvironments whose conditions may be controlled by cell sequestration and proton pumping during bacterial respiration.

  7. From Genome to Function: Systematic Analysis of the Soil Bacterium Bacillus Subtilis

    PubMed Central

    Crawshaw, Samuel G.; Wipat, Anil

    2001-01-01

    Bacillus subtilis is a sporulating Gram-positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. PMID:18628943

  8. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.

    PubMed Central

    Keita, Mamadou Bhoye; Diene, Seydina M.; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2013-01-01

    Strain G2T sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes. PMID:24501648

  9. Non-contiguous finished genome sequence and description of Bacillus massiliogorillae sp. nov.

    PubMed

    Keita, Mamadou Bhoye; Diene, Seydina M; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard; Bittar, Fadi

    2013-10-16

    Strain G2(T) sp. nov. is the type strain of B. massiliogorillae, a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. B. massiliogorillae is a facultative anaerobic, Gram-variable, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,431,633 bp long genome (1 chromosome but no plasmid) contains 5,179 protein-coding and 98 RNA genes, including 91 tRNA genes. PMID:24501648

  10. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern.

    PubMed

    Kumar, Rajendran Mathan; Kaur, Gurwinder; Kumar, Anand; Bala, Monu; Singh, Nitin Kumar; Kaur, Navjot; Kumar, Narender; Mayilraj, Shanmugam

    2015-10-01

    The taxonomic position of a Gram-stain positive bacterium isolated from a solar saltern sample collected from Kanyakumari, coastal region of the Bay of Bengal, India, was analysed by using a polyphasic approach. The isolated strain, designated SA2-6T, had phenotypic characteristics that matched those of the genus Bacillus. The 16S rRNA gene sequence (1493 bases) of the novel strain was compared with those of previously studied Bacillus type strains and confirmed that the strain belongs to the genus Bacillus and was moderately closely related to the type strain of Bacillus foraminis at 97.5 % 16S rRNA gene sequence similarity, followed by those of Bacillus thioparans (96.9 %), Bacillus subterraneus (96.8 %), Bacillus jeotgali (96.6 %), Bacillus selenatarsenatis (96.6 %) and Bacillus boroniphilus (96.6 %). 16S rRNA gene sequence analysis indicated that strain SA2-6T differs from all other species of the genus Bacillus by at least 2.5 %. It contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, and iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids. Major lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data from this polyphasic study, strain SA2-6T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus campisalis sp. nov. is proposed. The type strain is SA2-6T ( = MTCC 11848T = DSM 28801T). The draft genome of strain SA2-6T consisted of 5 183 363 bp with G+C content of 45.44 mol%, 5352 predicted coding sequences, 191 RNAs and 479 subsystems. PMID:26296567

  11. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome.

    PubMed

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E; Gómez-Silva, Benito; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert. PMID:26294639

  12. Five New Amicoumacins Isolated from a Marine-Derived Bacterium Bacillus subtilis

    PubMed Central

    Li, Yongxin; Xu, Ying; Liu, Lingli; Han, Zhuang; Lai, Pok Yui; Guo, Xiangrong; Zhang, Xixiang; Lin, Wenhan; Qian, Pei-Yuan

    2012-01-01

    Four novel amicoumacins, namely lipoamicoumacins A–D (1–4), and one new bacilosarcin analog (5) were isolated from culture broth of a marine-derived bacterium Bacillus subtilis, together with six known amicoumacins. Their structures were elucidated on the basis of extensive spectroscopic (2D NNR, IR, CD and MS) analysis and in comparison with data in literature. PMID:22412803

  13. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower.

    PubMed

    Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; de Souza, Rocheli; Tadra-Sfeir, Michele; Faoro, Helisson; Alvarenga, Samuel M; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi; Passaglia, Luciane M P

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake. PMID:25838494

  14. Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower

    PubMed Central

    Ambrosini, Adriana; Sant’Anna, Fernando Hayashi; de Souza, Rocheli; Tadra-Sfeir, Michele; Faoro, Helisson; Alvarenga, Samuel M.; Pedrosa, Fabio Oliveira; Souza, Emanuel Maltempi

    2015-01-01

    Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake. PMID:25838494

  15. Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1

    PubMed Central

    Hirose, Yuu; Misawa, Naomi; Hurunaka, Kohei; Kishimoto, Noriaki

    2014-01-01

    Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium, Bacillus amyloliquefaciens CMW1, which is newly isolated from a Japanese fermented soybean paste. The genome sequence will allow for a characterization of the molecular mechanism of its ionic liquid tolerance. PMID:25323721

  16. Draft Genome Sequence of a Bacillus Bacterium from the Atacama Desert Wetlands Metagenome

    PubMed Central

    Vilo, Claudia; Galetovic, Alexandra; Araya, Jorge E.; Dong, Qunfeng

    2015-01-01

    We report here the draft genome sequence of a Bacillus bacterium isolated from the microflora of Nostoc colonies grown at the Andean wetlands in northern Chile. We consider this genome sequence to be a molecular tool for exploring microbial relationships and adaptation strategies to the prevailing extreme conditions at the Atacama Desert. PMID:26294639

  17. Bacillus depressus sp. nov., isolated from soil of a sunflower field.

    PubMed

    Wei, Xuexin; Xin, Di; Xin, Yuhua; Zhang, Hao; Wang, Tianying; Zhang, Jianli

    2016-01-01

    A Gram-stain positive, rod-shaped, endospore-forming and aerobic bacterium, designated BZ1(T), was isolated from a soil sample collected from a sunflower field in Wuyuan county, Inner Mongolia, China. On the basis of 16S rRNA gene sequence analysis, the isolate was found to be a member of the genus Bacillus and the close phylogenetic relatives to be Bacillus gottheilii WCC 4585(T), Bacillus oceanisediminis H2(T), Bacillus mesonae FJAT-13985(T) and Bacillus horneckiae DSM 23495(T) with 98.3, 98.1, 98.0 and 97.6 % sequence similarity, respectively. Strain BZ1(T) was found to grow at 6-40 °C (optimum 30-33 °C), pH 6.0-9.0 (optimum pH 7.0) and 0-5.5 % (w/v) NaCl (optimum 0.5 %). The cell wall diamino acid of the peptidoglycan of strain BZ1(T) was identified as meso-diaminopimelic acid and the predominant respiratory quinone as MK-7. The major cellular fatty acids were found to be iso-C15:0, anteiso-C15:0 and iso-C14:0, and the polar lipids to consist of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The novel strain was found to have a DNA G + C content 44.5 mol%. DNA-DNA hybridization with closely related strains was low. Based on phenotypic, phylogenetic and chemotaxonomic results, it is concluded that strain BZ1(T) represents a novel species within the genus Bacillus, for which we propose the name Bacillus depressus sp. nov. The type strain is BZ1(T) (= CGMCC 1.15124(T) = KCTC 33643(T)). PMID:26452774

  18. Twenty Whole-Genome Bacillus sp. Assemblies.

    PubMed

    Daligault, H E; Davenport, K W; Minogue, T D; Bishop-Lilly, K A; Broomall, S M; Bruce, D C; Chain, P S; Coyne, S R; Frey, K G; Gibbons, H S; Jaissle, J; Koroleva, G I; Ladner, J T; Lo, C-C; Munk, C; Palacios, G F; Redden, C L; Rosenzweig, C N; Scholz, M B; Johnson, S L

    2014-01-01

    Bacilli are genetically and physiologically diverse, ranging from innocuous to highly pathogenic. Here, we present annotated genome assemblies for 20 strains belonging to Bacillus anthracis, B. atrophaeus, B. cereus, B. licheniformis, B. macerans, B. megaterium, B. mycoides, and B. subtilis. PMID:25301645

  19. Twenty Whole-Genome Bacillus sp. Assemblies

    PubMed Central

    Daligault, H. E.; Davenport, K. W.; Minogue, T. D.; Bishop-Lilly, K. A.; Broomall, S. M.; Bruce, D. C.; Chain, P. S.; Coyne, S. R.; Frey, K. G.; Gibbons, H. S.; Jaissle, J.; Koroleva, G. I.; Ladner, J. T.; Lo, C.-C.; Munk, C.; Palacios, G. F.; Redden, C. L.; Rosenzweig, C. N.; Scholz, M. B.

    2014-01-01

    Bacilli are genetically and physiologically diverse, ranging from innocuous to highly pathogenic. Here, we present annotated genome assemblies for 20 strains belonging to Bacillus anthracis, B. atrophaeus, B. cereus, B. licheniformis, B. macerans, B. megaterium, B. mycoides, and B. subtilis. PMID:25301645

  20. Bacillus taiwanensis sp. nov., isolated from a soil sample from Taiwan.

    PubMed

    Liu, Bo; Liu, Guo-Hong; Sengonca, Cetin; Schumann, Peter; Wang, Ming-Kuang; Xiao, Rong-Feng; Zheng, Xue-Fang; Chen, Zheng

    2015-07-01

    A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium (FJAT-14571(T)) was isolated from a soil sample in Taiwan. Strain FJAT-14571(T) grew at 20-40 °C (optimum 35 °C), pH 6-10 (optimum pH 8) and 0-2% (w/v) NaCl (optimum 0%). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FJAT-14571(T) was a member of the genus Bacillus and was most closely related to Bacillus oceanisediminis DSM 24771(T) (96.2%). DNA-DNA relatedness between strain FJAT-14571(T) and B. oceanisediminis DSM 24771(T) was low (32.0% ± 0.88%). The diagnostic diamino acid of the peptidoglycan of strain FJAT-14571(T) was meso-diaminopimelic acid and the predominant menaquinone was MK-7 (96.6%). The major cellular fatty acids were iso-C15 : 0 (46.4%), anteiso-C15 : 0 (7.6%), iso-C17 : 0 (8.2%) and iso-C16 : 0 (10.0 %) and the DNA G+C content was 40.8 mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that strain FJAT-14571(T) represents a novel species within the genus Bacillus, for which the name Bacillus taiwanensis sp. nov. is proposed. The type strain is FJAT-14571(T) ( = DSM 27845(T) = CGMCC1.1 2698(T)). PMID:25829330

  1. Bacillus lycopersici sp. nov., isolated from a tomato plant (Solanum lycopersicum L.).

    PubMed

    Lin, Shih-Yao; Hameed, Asif; Liu, You-Cheng; Wen, Cheng-Zhe; Lai, Wei-An; Hsu, Yi-Han; Young, Chiu-Chung

    2015-07-01

    A Gram-stain-positive, rod-shaped, endospore-forming bacterium (designated strain CC-Bw-5(T)) was isolated from chopped tomato stems. The isolate grew at 20-40 °C, pH 6.0-8.0 and tolerated 6% (w/v) NaCl. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus isabeliae (95.3%) and Bacillus oleronius (95.3%). The G+C content of the genomic DNA was 37.2 ± 3.6 mol%. Strain CC-Bw-5(T) was determined to possess C16 : 0, iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as predominant fatty acids. The polar lipid profile consisted of predominant amounts of diphosphatidylglycerol, and moderate-to-trace amounts of phosphatidylethanolamine, phosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified phosphoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid; menaquinone (MK-7) was the predominant respiratory quinone. According to distinct phylogenetic, phenotypic and chemotaxonomic features, strain CC-Bw-5(T) is proposed to represent a novel species within the genus Bacillus for which the name Bacillus lycopersici sp. nov. is proposed. The type strain is CC-Bw-5(T) ( = BCRC 80623(T) = JCM 19140(T)). PMID:25833153

  2. Bacillus mesonae sp. nov., isolated from the root of Mesona chinensis.

    PubMed

    Liu, Bo; Liu, Guo-Hong; Hu, Gui-Hing; Chen, Mei-Chun

    2014-10-01

    A Gram-stain-positive, short rod-shaped and motile, mildly halotolerant, endospore-forming bacterium, FJAT-13985(T), was isolated from the internal tissues of Mesona chinensis root. Strain FJAT-13985(T) grew at 20-45 °C (optimum 30 °C) and pH 5.7-9.0 (optimum pH 7.0) and in the presence of 0-2% (w/v) NaCl [optimum 1% (w/v)]. The strain was catalase-positive and oxidase-negative. The cell wall of strain FJAT-13985(T) contained meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7 (97.4%). The major fatty acids of the strain were anteiso-C15:0 (23.3%) and iso-C15:0 (40.8%). The DNA G+C content was 41.64 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FJAT-13985(T) is a member of the genus Bacillus and is most closely related to Bacillus drentensis DSM 15600(T) (98.4%), Bacillus vireti DSM 15602(T) (98.2%) and Bacillus novalis DSM 15603(T) (98.3%). DNA-DNA hybridization indicated that relatedness between strain FJAT-13985(T) and its closest relative, B. drentensis DSM 15600(T), was 36.63%. The phenotypic, chemotaxonomic and genotypic properties clearly indicate that strain FJAT-13985(T) represents a novel species of the genus Bacillus, for which the name Bacillus mesonae sp. nov. is proposed. The type strain is FJAT-13985(T) ( = DSM 25968(T) = CGMCC1.12238(T)). PMID:25013229

  3. Draft Genome Sequence of Bacillus murimartini LMG 21005T, an Alkalitolerant Bacterium Isolated from a Church Wall Mural in Germany

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai; Ge, Ci-bin

    2015-01-01

    Bacillus murimartini LMG 21005T is a Gram-positive, spore-forming, and alkalitolerant bacterium isolated from a church wall mural. Here, we report the 4.17-Mb genome sequence of B. murimartini LMG 21005T, which will accelerate the application of this alkalitolerant bacterium and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26494676

  4. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi.

    PubMed

    Oh, Young Joon; Lee, Hae-Won; Lim, Seul Ki; Kwon, Min-Sung; Lee, Jieun; Jang, Ja-Young; Park, Hae Woong; Nam, Young-Do; Seo, Myung-Ji; Choi, Hak-Jong

    2016-09-01

    A novel halophilic bacterium, strain K7(T), was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0-25.0% (w/v) NaCl (optimum 10-15% NaCl), pH 5.5-8.5 (optimum pH 7.0-7.5), and 15-42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7(T) and Gracilibacillus orientalis XH-63(T) (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7(T) is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7(T) (KACC 18669(T); JCM 31344(T)). PMID:27572507

  5. Draft Genome Sequence of Bacillus plakortidis P203T (DSM 19153), an Alkali- and Salt-Tolerant Marine Bacterium

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Ge, Ci-bin; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai

    2016-01-01

    Bacillus plakortidis P203T is a Gram-positive, spore-forming, and alkali- and salt-tolerant marine bacterium. Here, we report the 3.97-Mb draft genome sequence of B. plakortidis P203T, which will promote its fundamental research and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26847896

  6. Draft Genome Sequence of Bacillus pseudalcaliphilus PN-137T (DSM 8725), an Alkaliphilic Halotolerant Bacterium Isolated from Garden Soils.

    PubMed

    Wang, Jie-Ping; Liu, Bo; Liu, Guo-Hong; Xiao, Rong-Feng; Zheng, Xue-Fang; Shi, Huai; Ge, Ci-Bin

    2015-01-01

    Bacillus pseudalcaliphilus PN-137(T) (DSM 8725) is a Gram-positive, spore-forming, alkaliphilic, and halotolerant bacterium. Here, we report the 4.49-Mb genome sequence of B. pseudalcaliphilus PN-137(T), which will accelerate the application of this alkaliphile and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26272579

  7. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    PubMed Central

    Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

  8. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Xie, Gary; Dalin, Eileen; Tice, Hope; Chertkov, Olga; Land, Miriam L

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer-ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi-cellulose. This bacterium is also considered as a potential probiotic. Complete genome squence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  9. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

    SciTech Connect

    Rhee, Mun Su; Moritz, Brelan E.; Xie, Gary; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Pitluck, Sam; Land, Miriam L; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, Keelnathan T.

    2011-01-01

    Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 C and pH 5.0 and fer- ments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this spo- rogenic lactic acid bacterium to grow at 50-55 C and pH 5.0 makes this organism an attrac- tive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemi- cellulose. This bacterium is also considered as a potential probiotic. Complete genome se- quence of a representative strain, B. coagulans strain 36D1, is presented and discussed.

  10. Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1

    PubMed Central

    Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J.

    2014-01-01

    The draft genome sequence of a soil bacterium, Aquabacterium sp. strain NJ1, capable of utilizing both liquid and solid alkanes, was deciphered. This is the first report of an Aquabacterium genome sequence. PMID:25477416

  11. Kinetics of Molybdenum Reduction to Molybdenum Blue by Bacillus sp. Strain A.rzi

    PubMed Central

    Othman, A. R.; Bakar, N. A.; Halmi, M. I. E.; Johari, W. L. W.; Ahmad, S. A.; Jirangon, H.; Syed, M. A.; Shukor, M. Y.

    2013-01-01

    Molybdenum is very toxic to agricultural animals. Mo-reducing bacterium can be used to immobilize soluble molybdenum to insoluble forms, reducing its toxicity in the process. In this work the isolation of a novel molybdate-reducing Gram positive bacterium tentatively identified as Bacillus sp. strain A.rzi from a metal-contaminated soil is reported. The cellular reduction of molybdate to molybdenum blue occurred optimally at 4 mM phosphate, using 1% (w/v) glucose, 50 mM molybdate, between 28 and 30°C and at pH 7.3. The spectrum of the Mo-blue product showed a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of bacterial electron transport system (ETS) such as rotenone, sodium azide, antimycin A, and potassium cyanide could not inhibit the molybdenum-reducing activity. At 0.1 mM, mercury, copper, cadmium, arsenic, lead, chromium, cobalt, and zinc showed strong inhibition on molybdate reduction by crude enzyme. The best model that fitted the experimental data well was Luong followed by Haldane and Monod. The calculated value for Luong's constants pmax, Ks, Sm, and n was 5.88 μmole Mo-blue hr−1, 70.36 mM, 108.22 mM, and 0.74, respectively. The characteristics of this bacterium make it an ideal tool for bioremediation of molybdenum pollution. PMID:24369531

  12. Surfactin, Iturin, and Fengycin Biosynthesis by Endophytic Bacillus sp. from Bacopa monnieri.

    PubMed

    Jasim, B; Sreelakshmi, K S; Mathew, Jyothis; Radhakrishnan, E K

    2016-07-01

    Endophytic microorganisms which are ubiquitously present in plants may colonize intracellularly or intercellularly without causing any diseases. By living within the unique chemical environment of a host plant, they produce a vast array of compounds with a wide range of biological activities. Because of this, natural products of endophytic origin have been exploited for antimicrobial, antiviral, anticancer, and antioxidant properties. Also, they can be considered to function as an efficient microbial barrier to protect plants from various pathogens. In the present study, endophytic bacterium BmB 9 with antifungal and antibacterial activity isolated from the stem tissue of Bacopa monnieri was studied for the molecular and chemical basis of its activity. PCR-based genome mining for various biosynthetic gene clusters proved the presence of surfactin, iturin, and type I polyketide synthase (PKS) genes in the isolate. The LC-MS/MS based analysis of the extract further confirmed the production of surfactin derivatives (M + H(+)-1008.6602, 1022.6755), iturin (M + H(+)-1043.5697), and fengycin (M + H(+)-1491.8195, 1477.8055) by the selected bacterial isolate. The 16S rDNA sequence similarity based analysis identified the isolate BmB 9 as Bacillus sp. with 100 % identity to Bacillus sp. LCF1 (KP257289). PMID:27021396

  13. Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium.

    PubMed

    Rivas, Raúl; Mateos, Pedro F; Martínez-Molina, Eustoquio; Velázquez, Encarna

    2005-01-01

    During a search for xylan-degrading micro-organisms, a sporulating bacterium was recovered from xylan-containing agar plates exposed to air in a research laboratory (Salamanca University, Spain). The airborne isolate (designated strain XIL14T) was identified by 16S rRNA gene sequencing as representing a Paenibacillus species most closely related to Paenibacillus illinoisensis JCM 9907T (99.3 % sequence similarity) and Paenibacillus pabuli DSM 3036T (98 % sequence similarity). Phenotypic, chemotaxonomic and DNA-DNA hybridization data indicated that the isolate belongs to a novel species of the genus Paenibacillus. Cells of strain XIL14T were motile, sporulating, rod-shaped, Gram-positive and facultatively anaerobic. The predominant cellular fatty acids were anteiso-C(15 : 0) and C(16 : 0). The DNA G+C content of strain XIL14T was 50.5 mol%. Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. Catalase was positive and oxidase was negative. The airborne isolate produced a variety of hydrolytic enzymes, including xylanases, amylases, gelatinase and beta-galactosidase. DNA-DNA hybridization levels between strain XIL14T and P. illinoisensis DSM 11733T and P. pabuli DSM 3036T were 43.3 and 36.3 %, respectively. According to the data obtained, strain XIL14T is considered to represent a novel species for which the name Paenibacillus xylanilyticus sp. nov. is proposed (=LMG 21957T=CECT 5839T). PMID:15653909

  14. Jeongeupia chitinilytica sp. nov., a chitinolytic bacterium isolated from soil.

    PubMed

    Chen, Wen-Ming; Chang, Rey-Chang; Cheng, Chih-Yu; Shiau, Yu-Wen; Sheu, Shih-Yi

    2013-03-01

    A novel bacterium, designated strain Jchi(T), was isolated from soil in Taiwan and characterized using a polyphasic approach. Cells of strain Jchi(T) were aerobic, Gram-stain-negative, motile and rod-shaped. They contained poly-β-hydroxybutyrate granules and formed dark-yellow colonies. Growth occurred at 20-37 °C (optimum between 25 and 30 °C), at pH 6.0-8.0 (optimum between pH 7.0 and pH 8.0) and with 0-2 % NaCl (optimum between 0 and 1 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Jchi(T) belonged to the genus Jeongeupia and that its closest neighbour was Jeongeupia naejangsanensis BIO-TAS4-2(T) (98.0 % sequence similarity). The major fatty acids (>10 %) of strain Jchi(T) were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major cellular hydroxy fatty acid was C12 : 0 3-OH. The isoprenoid quinone was Q-8 and the genomic DNA G+C content was 66.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine and two unidentified phospholipids. The DNA-DNA relatedness value between strain Jchi(T) and J. naejangsanensis BIO-TAS4-2(T) was about 41.0 %. On the basis of the genotypic and phenotypic data, strain Jchi(T) represents a novel species in the genus Jeongeupia, for which the name Jeongeupia chitinilytica sp. nov. is proposed. The type strain is Jchi(T) ( = BCRC 80367(T)  = KCTC 23701(T)). PMID:22659500

  15. Novel fluorinated lipopeptides from Bacillus sp. CS93 via precursor-directed biosynthesis.

    PubMed

    O'Connor, Neil K; Hudson, Alex S; Cobb, Steven L; O'Neil, Deborah; Robertson, Jennifer; Duncan, Vanessa; Murphy, Cormac D

    2014-12-01

    While attempting to improve production of fluoro-iturin A in Bacillus sp. CS93 new mono- and di-fluorinated fengycins were detected in culture supernatants by (19)F NMR and tandem mass spectrometry, after incubation of the bacterium with 3-fluoro-L-tyrosine. The fluorinated amino acid was presumably incorporated in place of one or both of the tyrosyl residues in fengycin. Investigations to generate additional new fluorinated derivatives were undertaken using commercially available fluorinated phenylalanines and 2-fluoro- and 2,3-difluoro-tyrosine that were synthesised by Negishi cross-coupling of iodoalanine and fluorinated bromo-phenols. The anti-fungal activity of the fluorinated lipopeptides was assayed against Trichophyton rubrum and found to be similar to that of the non-fluorinated metabolites. PMID:25193167

  16. Production of L2 lipase by Bacillus sp. strain L2: nutritional and physical factors.

    PubMed

    Shariff, Fairolniza Mohd; Leow, Thean Chor; Mukred, A D; Salleh, Abu Bakar; Basri, Mahiran; Rahman, Raja Noor Zaliha Raja Abd

    2007-10-01

    A thermophilic bacterium, Bacillus sp. strain L2 was isolated from a hot spring in Perak, Malaysia. An extracellular lipase activity was detected through plate and broth assays at 70 degrees C after 28 h of incubation. The L2 lipase production was growth dependent as revealed by a number of factors affecting the secretion of extracelullar lipase. As for nutritional factors, casamino acids, trehalose, Ca(2+) and Tween 60 were found to be more effective for lipase production. The optimum physical condition for L2 lipase production was obtained at 70 degrees C after 28 h of cultivation time, at pH 7.0, 150 rpm of agitation rate and 1% of starting inoculum size. The activity staining of crude L2 lipase revealed a clearing zone at 39 kDa. PMID:17910105

  17. Biotransformation of various saccharides and production of exopolymeric substances by cloud-borne Bacillus sp. 3B6.

    PubMed

    Matulová, Mária; Husárová, Slavomíra; Capek, Peter; Sancelme, Martine; Delort, Anne-Marie

    2014-12-16

    The ability of Bacillus sp. 3B6, a bacterial strain isolated from cloudwaters, to biotransform saccharides present in the atmosphere was evaluated using in situ 1D and 2D NMR spectroscopy. Bacillus is one of the genera most frequently described in the air and in atmospheric waters. Sugars present in these environments have a biogenic origin; they include alditols, monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Bacillus sp. 3B6 was able to efficiently metabolize sugars, which could thus provide sources of energy for this bacterium and allow it to live and to be metabolically active in warm clouds. In addition, a number of these saccharides (L-arabitol, D-fructose, sucrose, D-glucose, cellotetraose, cellulose, and starch) were transformed to EPSs (exopolymeric substances). We have clearly identified the structure of two EPSs as 1,6-α-galactan and partially acetylated polyethylene glycol. 1,6-α-Galactan is a newly described polymer. The production of EPSs might protect this bacterium under hostile cloud environment conditions, including low nutrient availability, cold temperature and freeze-thaw processes, UV and radical exposure, and evaporation-condensation processes and thus desiccation and osmolarity changes. EPSs could also have a potential role in atmospheric processes because they can be considered as secondary organic aerosols and efficient cloud condensation nuclei. PMID:25390890

  18. Bacillus sp. BS061 Suppresses Powdery Mildew and Gray Mold

    PubMed Central

    Kim, Young-Sook; Song, Ja-Gyeong; Lee, In-Kyoung; Yeo, Woon-Hyung

    2013-01-01

    The use of a microorganism, or its secretions, to prevent plant disease offers an attractive alternative or supplement to synthetic fungicides for the management of plant disease without the negative effects of chemical control mechanisms. During a screening for microorganisms with the potential to be used as microbial fungicides, Bacillus sp. BS061 was isolated from a plant leaf. The strain BS061 potently inhibited the mycelial growth of Botrytis cinerea, and significantly reduced disease incidence of powdery mildew in cucumber and strawberry. We also found that the culture filtrate of BS061 inhibited the mycelial growth of various plant pathogens. PMID:23874134

  19. Structure of the detoxification catalyst mercuric ion reductase from Bacillus sp. strain RC607

    NASA Astrophysics Data System (ADS)

    Schiering, N.; Kabsch, W.; Moore, M. J.; Distefano, M. D.; Walsh, C. T.; Pai, E. F.

    1991-07-01

    SEVERAL hundred million tons of toxic mercurials are dispersed in the biosphere1. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase2 and mercuric ion reductase (MerA) 3-5. The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases6, catalyses the reaction NADPH + Hg(II) --> NADP+ + H+Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase7,8 serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure9 and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), pI258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved10,11. All MerAs have a C-terminal extension about 15 residues long but have very varied N termini. Although the enzyme from Streptomyces lividans has no addition, from Pseudomonas aeruginosa Tn5Ol and Bacillus sp. strain RC607 it has one and two copies respectively of a domain of 80-85 residues, highly homologous to MerP, the periplasmic component of proteins encoded by the mer operon11. These domains can be proteolytically cleaved off without changing the catalytic efficiency3. We report here the crystal structure of MerA from the Gram-positive bacterium Bacillus sp. strain RC607. Analysis of its complexes with nicotinamide dinucleotide substrates and the inhibitor Cd(II) reveals how limited structural changes enable an enzyme to accept as substrate what used to be a dangerous inhibitor. Knowledge of the mode of mercury ligation is a prerequisite for understanding this unique detoxification mechanism.

  20. Geobacillus zalihae sp. nov., a thermophilic lipolytic bacterium isolated from palm oil mill effluent in Malaysia

    PubMed Central

    Rahman, Raja Noor Zaliha Raja Abd; Leow, Thean Chor; Salleh, Abu Bakar; Basri, Mahiran

    2007-01-01

    Background Thermophilic Bacillus strains of phylogenetic Bacillus rRNA group 5 were described as a new genus Geobacillus. Their geographical distribution included oilfields, hay compost, hydrothermal vent or soils. The members from the genus Geobacillus have a growth temperatures ranging from 35 to 78°C and contained iso-branched saturated fatty acids (iso-15:0, iso-16:0 and iso-17:0) as the major fatty acids. The members of Geobacillus have similarity in their 16S rRNA gene sequences (96.5–99.2%). Thermophiles harboring intrinsically stable enzymes are suitable for industrial applications. The quest for intrinsically thermostable lipases from thermophiles is a prominent task due to the laborious processes via genetic modification. Results Twenty-nine putative lipase producers were screened and isolated from palm oil mill effluent in Malaysia. Of these, isolate T1T was chosen for further study as relatively higher lipase activity was detected quantitatively. The crude T1 lipase showed high optimum temperature of 70°C and was also stable up to 60°C without significant loss of crude enzyme activity. Strain T1T was a Gram-positive, rod-shaped, endospore forming bacterium. On the basic of 16S rDNA analysis, strain T1T was shown to belong to the Bacillus rRNA group 5 related to Geobacillus thermoleovorans (DSM 5366T) and Geobacillus kaustophilus (DSM 7263T). Chemotaxonomic data of cellular fatty acids supported the affiliation of strain T1T to the genus Geobacillus. The results of physiological and biochemical tests, DNA/DNA hybridization, RiboPrint analysis, the length of lipase gene and protein pattern allowed genotypic and phenotypic differentiation of strain T1T from its validly published closest phylogenetic neighbors. Strain T1T therefore represents a novel species, for which the name Geobacillus zalihae sp. nov. is proposed, with the type strain T1T (=DSM 18318T; NBRC 101842T). Conclusion Strain T1T was able to secrete extracellular thermostable lipase into

  1. Bacillus invictae sp. nov., isolated from a health product.

    PubMed

    Branquinho, Raquel; Sousa, Clara; Osório, Hugo; Meirinhos-Soares, Luís; Lopes, João; Carriço, João A; Busse, Hans-Jürgen; Abdulmawjood, Amir; Klein, Günter; Kämpfer, Peter; Pintado, Manuela E; Peixe, Luísa V

    2014-11-01

    A Gram-positive, rod-shaped, endospore-forming Bacillus isolate, Bi.(FFUP1) (T), recovered in Portugal from a health product was subjected to a polyphasic study and compared with the type strains of Bacillus pumilus, Bacillus safensis, Bacillus altitudinis and Bacillus xiamenensis, the phenotypically and genotypically most closely related species. Acid production from cellobiose, D-glucose and D-mannose and absence of acid production from D-arabinose, erythritol, inositol, maltose, mannitol, raffinose, rhamnose, sorbitol, starch and L-tryptophan discriminated this new isolate from the type strains of the most closely related species. Additionally, a significant different protein and carbohydrate signature was evidenced by spectroscopic techniques, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Fourier transform IR spectroscopy with attenuated total reflectance. Using a chemometric approach, the score plot generated by principal component analysis clearly delineated the isolate as a separate cluster. The quinone system for strain Bi.(FFUP1) (T) comprised predominantly menaquinone MK-7 and major polar lipids were diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. Strain Bi.(FFUP1) (T) showed ≥ 99% 16S rRNA gene sequence similarity to B. safensis FO-036b(T), B. pumilus (7061(T) and SAFR-032), B. altitudinis 41KF2b(T) and B. xiamenensis HYC-10(T). Differences in strain Bi.FFUP1 (T) gyrB and rpoB sequences in comparison with the most closely related species and DNA-DNA hybridization experiments with Bi.FFUP1 (T) and B. pumilus ATCC 7061(T), B. safensis FO-036b(T), B. altitudinis 41KF2b(T) and B. xiamenensis HYC-10(T) gave relatedness values of 39.6% (reciprocal 38.0%), 49.9% (reciprocal 42.9%), 61.9% (reciprocal 52.2%) and 61.7% (reciprocal 49.2%), respectively, supported the delineation of strain Bi.(FFUP1) (T) as a representative of a novel species of the genus Bacillus, for which the name Bacillus

  2. A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1.

    PubMed

    Noor, Yusuf Muhammad; Samsulrizal, Nurul Hidayah; Jema'on, Noor Azah; Low, Kheng Oon; Ramli, Aizi Nor Mazila; Alias, Noor Izawati; Damis, Siti Intan Rosdianah; Fuzi, Siti Fatimah Zaharah Mohd; Isa, Mohd Noor Mat; Murad, Abdul Munir Abdul; Raih, Mohd Firdaus Mohd; Bakar, Farah Diba Abu; Najimudin, Nazalan; Mahadi, Nor Muhammad; Illias, Rosli Md

    2014-07-25

    Bacillus lehensis G1 is a Gram-positive, moderately alkalitolerant bacterium isolated from soil samples. B. lehensis produces cyclodextrin glucanotransferase (CGTase), an enzyme that has enabled the extensive use of cyclodextrin in foodstuffs, chemicals, and pharmaceuticals. The genome sequence of B. lehensis G1 consists of a single circular 3.99 Mb chromosome containing 4017 protein-coding sequences (CDSs), of which 2818 (70.15%) have assigned biological roles, 936 (23.30%) have conserved domains with unknown functions, and 263 (6.55%) have no match with any protein database. Bacillus clausii KSM-K16 was established as the closest relative to B. lehensis G1 based on gene content similarity and 16S rRNA phylogenetic analysis. A total of 2820 proteins from B. lehensis G1 were found to have orthologues in B. clausii, including sodium-proton antiporters, transport proteins, and proteins involved in ATP synthesis. A comparative analysis of these proteins and those in B. clausii and other alkaliphilic Bacillus species was carried out to investigate their contributions towards the alkalitolerance of the microorganism. The similarities and differences in alkalitolerance-related genes among alkalitolerant/alkaliphilic Bacillus species highlight the complex mechanism of pH homeostasis. The B. lehensis G1 genome was also mined for proteins and enzymes with potential viability for industrial and commercial purposes. PMID:24811681

  3. Lead biotransformation potential of allochthonous Bacillus sp. SKK11 with sesame oil cake in mine soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was aimed at assessing the potential of allochthonous Bacillus sp. SKK11 and sesame oil cake extract for transformation of Pb in mine soil. The bacteria were isolated from a brackish environment and identified as Bacillus sp. based on partial 16S rDNA sequences. The isolate SKK11 exhibite...

  4. Draft Genome Sequence of Bacillus sp. GZT, a 2,4,6-Tribromophenol-Degrading Strain Isolated from the River Sludge of an Electronic Waste-Dismantling Region.

    PubMed

    Liang, Zhishu; Li, Guiying; An, Taicheng; Das, Ranjit

    2016-01-01

    Here, we report the draft genome sequence of Bacillus sp. strain GZT, a 2,4,6-tribromophenol (TBP)-degrading bacterium previously isolated from an electronic waste-dismantling region. The draft genome sequence is 5.18 Mb and has a G+C content of 35.1%. This is the first genome report of a brominated flame retardant-degrading strain. PMID:27257197

  5. Draft Genome Sequence of Bacillus sp. GZT, a 2,4,6-Tribromophenol-Degrading Strain Isolated from the River Sludge of an Electronic Waste-Dismantling Region

    PubMed Central

    Liang, Zhishu; Li, Guiying; Das, Ranjit

    2016-01-01

    Here, we report the draft genome sequence of Bacillus sp. strain GZT, a 2,4,6-tribromophenol (TBP)-degrading bacterium previously isolated from an electronic waste-dismantling region. The draft genome sequence is 5.18 Mb and has a G+C content of 35.1%. This is the first genome report of a brominated flame retardant-degrading strain. PMID:27257197

  6. Complete genome of Martelella sp. AD-3, a moderately halophilic polycyclic aromatic hydrocarbons-degrading bacterium.

    PubMed

    Cui, Changzheng; Li, Zhijie; Qian, Jiangchao; Shi, Jie; Huang, Ling; Tang, Hongzhi; Chen, Xin; Lin, Kuangfei; Xu, Ping; Liu, Yongdi

    2016-05-10

    Martelella sp. strain AD-3, a moderate halophilic bacterium, was isolated from a petroleum-contaminated soil with high salinity in China. Here, we report the complete genome of strain AD-3, which contains one circular chromosome and two circular plasmids. An array of genes related to metabolism of polycyclic aromatic hydrocarbons and halophilic mechanism in this bacterium was identified by the whole genome analysis. PMID:26988395

  7. Antitumor activity of bacterial exopolysaccharides from the endophyte Bacillus amyloliquefaciens sp. isolated from Ophiopogon japonicus

    PubMed Central

    CHEN, YI-TAO; YUAN, QIANG; SHAN, LE-TIAN; LIN, MEI-AI; CHENG, DONG-QING; LI, CHANG-YU

    2013-01-01

    The endophytic bacterium, MD-b1, was isolated from the medicinal plant Ophiopogon japonicas and identified as the Bacillus amyloliquefaciens sp. with 99% similarity based on the partial sequence analysis of 16S rDNA. Exopolysaccharides were extracted from the endophyte for the evaluation of its antitumor activity against gastric carcinoma cell lines (MC-4 and SGC-7901). 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays and microscopy were performed to estimate the cell viability and morphological changes of the MC-4 and SGC-7901 cells following treatment with the exopolysaccharides at 14, 22 and 30 μg/μl. The results revealed that the exopolysaccharides displayed concentration-dependent inhibitory effects against the MC-4 and SGC-7901 cells, with an IC50 of 19.7 and 26.8 μg/μl, respectively. The exopolysaccharides also induced morphological abnormalities in the cells. These effects indicated the the exopolysaccharides had an antitumoral mechanism of action associated with the mitochondrial dysfunction of the treated cells. This is the first study to investigate the endophytic microorganism isolated from O. japonicas and also the first discovery of such antitumoral exopolysaccharides derived from the genus Bacillus. This provides a promising and reproducible natural product source with high therapeutic value for anticancer treatment, thereby facilitating the development of new anticancer agents. PMID:23833642

  8. Genome Sequence of Bacillus butanolivorans K9T (DSM 18926), an n-Butanol-Consuming Bacterium Isolated from Soil

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Chen, De-ju; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai; Ge, Ci-bin

    2015-01-01

    Bacillus butanolivorans K9T (DSM 18926) is a Gram-positive, spore-forming, strictly aerobic, and n-butanol-consuming bacterium. Here, we report the 5.68-Mb genome sequence of B. butanolivorans K9T, which is the first genomic information of this species that will provide useful information for the genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26494675

  9. Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

    PubMed Central

    Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric; Thijs, Sofie; Balseiro-Romero, Maria; Monterroso, Carmela; Kidd, Petra Suzan; Rineau, Francois; Weyens, Nele; Sillen, Wouter

    2016-01-01

    We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:27340073

  10. Draft Genome Sequence of Bacillus licheniformis Strain GB2, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium.

    PubMed

    Gkorezis, Panagiotis; Van Hamme, Jonathan; Bottos, Eric; Thijs, Sofie; Balseiro-Romero, Maria; Monterroso, Carmela; Kidd, Petra Suzan; Rineau, Francois; Weyens, Nele; Sillen, Wouter; Vangronsveld, Jaco

    2016-01-01

    We report the 4.39 Mb draft genome of Bacillus licheniformis GB2, a hydrocarbonoclastic Gram-positive bacterium of the family Bacillaceae, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain GB2 is an effective plant-growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:27340073

  11. Biogenesis of antibacterial silver nanoparticles using the endophytic bacterium Bacillus cereus isolated from Garcinia xanthochymus

    PubMed Central

    Sunkar, Swetha; Nachiyar, C Valli

    2012-01-01

    Objective To synthesize the ecofriendly nanoparticles, which is viewed as an alternative to the chemical method which initiated the use of microbes like bacteria and fungi in their synthesis. Methods The current study uses the endophytic bacterium Bacillus cereus isolated from the Garcinia xanthochymus to synthesize the silver nanoparticles (AgNPs). The AgNPs were synthesized by reduction of silver nitrate solution by the endophytic bacterium after incubation for 3-5 d at room temperature. The synthesis was initially observed by colour change from pale white to brown which was confirmed by UV-Vis spectroscopy. The AgNPs were further characterized using FTIR, SEM-EDX and TEM analyses. Results The synthesized nanoparticles were found to be spherical with the size in the range of 20-40 nm which showed a slight aggregation. The energy-dispersive spectra of the nanoparticle dispersion confirmed the presence of elemental silver. The AgNPs were found to have antibacterial activity against a few pathogenic bacteria like Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi and Klebsiella pneumoniae. Conclusions The endophytic bacteria identified as Bacillus cereus was able to synthesize silver nanoparticles with potential antibacterial activity. PMID:23593575

  12. Bacillus plakortidis sp. nov. and Bacillus murimartini sp. nov., novel alkalitolerant members of rRNA group 6.

    PubMed

    Borchert, Martin S; Nielsen, Preben; Graeber, Ingeborg; Kaesler, Ines; Szewzyk, Ulrich; Pape, Thomas; Antranikian, Garabed; Schäfer, Thomas

    2007-12-01

    The Gram-positive, alkali- and salt-tolerant marine bacterium strain P203(T) is described together with its closest phylogenetic neighbour, terrestrial isolate LMG 21005(T). Strain P203(T) was isolated from material from the sponge Plakortis simplex that was obtained from the Sula-Ridge, Norwegian Sea. Strain LMG 21005(T) was an undescribed strain that was isolated from a church wall mural in Germany. Strains P203(T) and LMG 21005(T) were identified as novel alkalitolerant members of the Bacillus rRNA group 6 with a 16S rRNA gene sequence similarity of 99.5 %. The closest described neighbour, Bacillus gibsonii DSM 8722(T), showed 99.0 % gene sequence similarity with P203(T) and 98.8 % similarity with strain LMG 21005(T). Despite the high 16S rRNA gene sequence similarity, DNA-DNA cross-hybridization revealed only 25.8-34.1 % similarity amongst the three strains. The DNA G+C contents were 41.1 mol% for strain P203(T) and 39.6 mol% for strain LMG 21005(T). Both strains grew well between pH 7 and pH 11. Strain P203(T) showed growth at moderate temperatures (from 4 to 30 degrees C) and in the presence of up to 12 % (w/v) NaCl at pH 9.7, whereas strain LMG 21005(T) was not salt tolerant (up to 4 % NaCl) and no growth was observed at 4 degrees C. The major fatty acids of strains P203(T), LMG 21005(T) and the type strain of B. gibsonii were the saturated terminally methyl-branched compounds iso-C(15 : 0) (19.8, 15.6 and 28.0 %, respectively) and anteiso-C(15 : 0) (57.1, 48.6 and 45.2 %, respectively). Physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains P203(T) and LMG 21005(T) from the six related Bacillus species with validly published names and supported the proposal of two novel species, Bacillus plakortidis [type strain P203(T) (=DSM 19153(T)=NCIMB 14288(T))] and Bacillus murimartini [type strain LMG 21005(T) (=NCIMB 14102(T))]. PMID:18048744

  13. Degradation of polyester polyurethane by a newly isolated soil bacterium, Bacillus subtilis strain MZA-75.

    PubMed

    Shah, Ziaullah; Krumholz, Lee; Aktas, Deniz Fulya; Hasan, Fariha; Khattak, Mutiullah; Shah, Aamer Ali

    2013-11-01

    A polyurethane (PU) degrading bacterial strain MZA-75 was isolated from soil through enrichment technique. The bacterium was identified through 16S rRNA gene sequencing, the phylogenetic analysis indicated the strain MZA-75 belonged to genus Bacillus having maximum similarity with Bacillus subtilis strain JBE0016. The degradation of PU films by strain MZA-75 in mineral salt medium (MSM) was analyzed by scanning electron microscopy (SEM), fourier transform infra-red spectroscopy (FT-IR) and gel permeation chromatography (GPC). SEM revealed the appearance of widespread cracks on the surface. FTIR spectrum showed decrease in ester functional group. Increase in polydispersity index was observed in GPC, which indicates chain scission as a result of microbial treatment. CO2 evolution and cell growth increased when PU was used as carbon source in MSM in Sturm test. Increase in both cell associated and extracellular esterases was observed in the presence of PU indicated by p-Nitrophenyl acetate (pNPA) hydrolysis assay. Analysis of cell free supernatant by gas chromatography-mass spectrometry (GC-MS) revealed that 1,4-butanediol and adipic acid monomers were produced. Bacillus subtilis strain MZA-75 can degrade the soft segment of polyester polyurethane, unfortunately no information about the fate of hard segment could be obtained. Growth of strain MZA-75 in the presence of these metabolites indicated mineralization of ester hydrolysis products into CO2 and H2O. PMID:23536219

  14. Decolourization of 4-Chloro-2-Nitrophenol by a Soil Bacterium, Bacillus subtilis RKJ 700

    PubMed Central

    Arora, Pankaj Kumar

    2012-01-01

    A 4-Chloro-2-nitrophenol (4C2NP) decolourizing strain RKJ 700 was isolated from soil collected from a pesticide contaminated site of India and identified as Bacillus subtilis on the basis of the 16S rRNA gene sequence analysis. Bacillus subtilis RKJ 700 decolourized 4C2NP up to concentration of 1.5 mM in the presence of additional carbon source. The degradation pathway of 4C2NP was studied and 4-chloro-2-aminophenol, 4-chloro-2-acetaminophenol and 5-chloro-2-methylbenzoxazole (5C2MBZ) were identified as metabolites by high performance liquid chromatography and gas chromatography-mass spectrometry. Resting cell studies showed that Bacillus subtilis RKJ 700 depleted 4C2NP completely with stoichiometric formation of 5C2MBZ. This is the first report of (i) the degradation of 4C2NP at high concentration (1.5 mM) and, (ii) the formation of 5C2MBZ by a soil bacterium. PMID:23251673

  15. Direct transesterification of Oedogonium sp. oil be using immobilized isolated novel Bacillus sp. lipase.

    PubMed

    Sivaramakrishnan, Ramachandran; Muthukumar, Karuppan

    2014-01-01

    This work emphasizes the potential of the isolated Bacillus sp. lipase for the production of fatty acid methyl ester by the direct transesterification of Oedogonium sp. of macroalgae. Dimethyl carbonate was used as the extraction solvent and also as the reactant. The effect of solvent/algae ratio, water addition, catalyst, temperature, stirring and time on the direct transesterification was studied. The highest fatty acid methyl ester yield obtained under optimum conditions (5 g Oedogonium sp. powder, 7.5 ml of solvent (dimethyl carbonate)/g of algae, 8% catalyst (%wt/wt of oil), distilled water 1% (wt/wt of algae), 36 h, 55°C and 180 rpm) was 82%. Final product was subjected to thermogravimetric analysis and (1)H NMR analysis. The results showed that the isolated enzyme has good potential in catalyzing the direct transesterification of algae, and the dimethyl carbonate did not affect the activity of the isolated lipase. PMID:23890544

  16. Draft Genome Sequence of Bacillus humi LMG 22167T (DSM 16318), an Endospore-Forming Bacterium Isolated from Soil

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Pan, Zhizhen; Xiao, Rong-feng; Chen, Meichun; Chen, De-ju

    2016-01-01

    Bacillus humi LMG 22167T is a Gram-positive, aerobic, and spore-forming bacterium Here, we report the 4.80-Mb draft genome sequence of B. humi LMG 22167T, which is the first genome sequence of this species and will promote its fundamental research. PMID:26847898

  17. Draft Genome Sequence of Bacillus farraginis R-6540T (DSM 16013), a Spore-Forming Bacterium Isolated at Dairy Farms

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Ge, Ci-bin; Xiao, Rong-feng; Zheng, Xue-fang; Shi, Huai

    2016-01-01

    Bacillus farraginis R-6540T is a Gram-positive, aerobic, and spore-forming bacterium with very high intrinsic heat resistance. Here, we report the 5.32-Mb draft genome sequence of B. farraginis R-6540T, which is the first genome sequence of this species and will promote its fundamental research. PMID:27313303

  18. Complete genome sequence of the bioleaching bacterium Leptospirillum sp. group II strain CF-1.

    PubMed

    Ferrer, Alonso; Bunk, Boyke; Spröer, Cathrin; Biedendieck, Rebekka; Valdés, Natalia; Jahn, Martina; Jahn, Dieter; Orellana, Omar; Levicán, Gloria

    2016-03-20

    We describe the complete genome sequence of Leptospirillum sp. group II strain CF-1, an acidophilic bioleaching bacterium isolated from an acid mine drainage (AMD). This work provides data to gain insights about adaptive response of Leptospirillum spp. to the extreme conditions of bioleaching environments. PMID:26853478

  19. Draft Genome Sequence of Pontibacter sp. nov. BAB1700, a Halotolerant, Industrially Important Bacterium

    PubMed Central

    Joshi, M. N.; Sharma, A. C.; Pandya, R. V.; Patel, R. P.; Saiyed, Z. M.; Saxena, A. K.

    2012-01-01

    Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

  20. Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008

    PubMed Central

    Joshi, M. N.; Pandit, A. S.; Sharma, A.; Pandya, R. V.; Saxena, A. K.

    2013-01-01

    The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

  1. Draft genome sequence of Pontibacter sp. nov. BAB1700, a halotolerant, industrially important bacterium.

    PubMed

    Joshi, M N; Sharma, A C; Pandya, R V; Patel, R P; Saiyed, Z M; Saxena, A K; Bagatharia, S B

    2012-11-01

    Pontibacter sp. nov. BAB1700 is a halotolerant, Gram-negative, rod-shaped, pink-pigmented, menaquinone-7-producing bacterium isolated from sediments of a drilling well. The draft genome sequence of the strain, consisting of one chromosome of 4.5 Mb, revealed vital gene clusters involved in vitamin biosynthesis and resistance against various metals and antibiotics. PMID:23105068

  2. Draft Genome Sequence of the Halophilic Bacterium Halobacillus sp. Strain BAB-2008.

    PubMed

    Joshi, M N; Pandit, A S; Sharma, A; Pandya, R V; Saxena, A K; Bagatharia, S B

    2013-01-01

    The Halobacillus sp. strain BAB-2008 is a moderately halophilic, rod-shaped, Gram-positive, orange-pigmented, carotenoid-producing bacterium isolated from saline soil near Zazam-Solar Park Road, Gujarat, India. Here we present the 3.7-Mb genome sequence to provide insights into its functional genomics and potential applications for carotenoid and enzyme production. PMID:23469348

  3. Complete Genome Sequence of a γ-Hexachlorocyclohexane-Degrading Bacterium, Sphingobium sp. Strain MI1205

    PubMed Central

    Tabata, Michiro; Ohhata, Satoshi; Nikawadori, Yuki; Sato, Takuya; Kishida, Kouhei; Ohtsubo, Yoshiyuki; Tsuda, Masataka

    2016-01-01

    Here, we report the complete genome sequence of a γ-hexachlorocyclohexane (γ-HCH)-degrading bacterium, Sphingobium sp. strain MI1205. The genome of MI1205 consists of two chromosomes and four plasmids with sizes of 33 to 292 kb. All the lin genes for γ-HCH metabolism are dispersed on the four plasmids. PMID:27056230

  4. Complete Genome Sequence of Sphingomonas sp. Strain NIC1, an Efficient Nicotine-Degrading Bacterium

    PubMed Central

    Zhu, Xiongyu; Wang, Weiwei; Xu, Ping

    2016-01-01

    Sphingomonas sp. strain NIC1, an efficient nicotine-degrading bacterium, was isolated from tobacco leaves. Here, we present the complete genome sequence of strain NIC1, which contains one circular chromosome and two circular plasmids. The genomic information will provide insights into its molecular mechanism for nicotine degradation. PMID:27417841

  5. Draft Genome Sequence of a Benzo[a]pyrene-Degrading Bacterium, Olleya sp. Strain ITB9

    PubMed Central

    Okai, Masahiko; Watanabe, Akihiro; Ishida, Masami

    2015-01-01

    Olleya sp. ITB9 is a benzo[a]pyrene-degrading bacterium, isolated from surface water near a waste treatment plant at Tokyo Bay, Japan. Here, we present the draft genome sequence of this strain, which consists of 58 contigs corresponding to 3.4 Mb and a G+C content of 31.2%. PMID:26564047

  6. Uncoupling effect of fatty acids in halo- and alkalotolerant bacterium Bacillus pseudofirmus FTU.

    PubMed

    Popova, I V; Bodrova, M E; Mokhova, E N; Muntyan, M S

    2004-10-01

    Natural uncouplers of oxidative phosphorylation, long-chain non-esterified fatty acids, cause uncoupling in the alkalo- and halotolerant bacterium Bacillus pseudofirmus FTU. The uncoupling effect in the bacterial cells was manifested as decrease of membrane potential and increase of respiratory activity. The membrane potential decrease was detected only in bacterial cells exhausted by their endogenous substrates. In proteoliposomes containing reconstituted bacterial cytochrome c oxidase, fatty acids caused a "mild" uncoupling effect by reducing membrane potential only at low rate of membrane potential generation. "Free respiration" induced by the "mild" uncouplers, the fatty acids, can be considered as possible mechanism responsible for adaptation of the bacteria to a constantly changed environment. PMID:15527418

  7. Beneficial soil bacterium Bacillus subtilis (GB03) augments salt tolerance of white clover

    PubMed Central

    Han, Qing-Qing; Lü, Xin-Pei; Bai, Jiang-Ping; Qiao, Yan; Paré, Paul W.; Wang, Suo-Min; Zhang, Jin-Lin; Wu, Yong-Na; Pang, Xiao-Pan; Xu, Wen-Bo; Wang, Zhi-Liang

    2014-01-01

    Soil salinity is an increasingly serious problem worldwide that reduces agricultural output potential. Selected beneficial soil bacteria can promote plant growth and augment tolerance to biotic and abiotic stresses. Bacillus subtilis strain GB03 has been shown to confer growth promotion and abiotic stress tolerance in the model plant Arabidopsis thaliana. Here we examined the effect of this beneficial soil bacterium on salt tolerance in the legume forage crop, white clover. Plants of white clover (Trifolium repens L. cultivar Huia) were grown from seeds with or without soil inoculation of the beneficial soil bacterium Bacillus subtilis GB03 supplemented with 0, 50, 100, or 150 mM NaCl water into soil. Growth parameters, chlorophyll content, malondialdehyde (MDA) content and osmotic potential were monitored during the growth cycle. Endogenous Na+ and K+ contents were determined at the time of harvest. White clover plants grown in GB03-inoculated soil were significantly larger than non-inoculated controls with respect to shoot height, root length, plant biomass, leaf area and chlorophyll content; leaf MDA content under saline condition and leaf osmotic potential under severe salinity condition (150 mM NaCl) were significantly decreased. Furthermore, GB03 significantly decreased shoot and root Na+ accumulation and thereby improved K+/Na+ ratio when GB03-inoculated plants were grown under elevated salt conditions. The results indicate that soil inoculation with GB03 promotes white clover growth under both non-saline and saline conditions by directly or indirectly regulating plant chlorophyll content, leaf osmotic potential, cell membrane integrity and ion accumulation. PMID:25339966

  8. Complete Genome Sequence of Antarctic Bacterium Psychrobacter sp. Strain G

    PubMed Central

    Che, Shuai; Song, Lai; Song, Weizhi; Yang, Meng

    2013-01-01

    Here, we report the complete genome sequence of Psychrobacter sp. strain G, isolated from King George Island, Antarctica, which can produce lipolytic enzymes at low temperatures. The genomics information of this strain will facilitate the study of the physiology, cold adaptation properties, and evolution of this genus. PMID:24051316

  9. Isolation, Identification and Characteristics of an Endophytic Quinclorac Degrading Bacterium Bacillus megaterium Q3

    PubMed Central

    Wang, Yunsheng; Zeng, Aiping; Zhou, Xiaomao; Luo, Feng; Bai, Lianyang

    2014-01-01

    In this study, we isolated an endophytic quinclorac-degrading bacterium strain Q3 from the root of tobacco grown in quinclorac contaminated soil. Based on morphological characteristics, Biolog identification, and 16S rDNA sequence analysis, we identified strain Q3 as Bacillus megaterium. We investigated the effects of temperature, pH, inoculation size, and initial quinclorac concentration on growth and degrading efficiency of Q3. Under the optimal degrading condition, Q3 could degrade 93% of quinclorac from the initial concentration of 20 mg/L in seven days. We analyzed the degradation products of quinclorac using liquid chromatography–tandem mass spectrometry (LC-MS/MS). The major degradation products by Q3 were different from those of previously identified quinclorac degrading strains, which suggests that Q3 may employ new pathways for quinclorac degradation. Our indoor pot experiments demonstrated that Q3 can effectively alleviate the quinclorac phytotoxicity in tobacco. As the first endophytic microbial that is capable of degrading quinclorac, Q3 can be a good bioremediation bacterium for quinclorac phytotoxicity. PMID:25244184

  10. Genome sequence of Bacillus sp. CHD6a, isolated from the shallow-sea hydrothermal vent.

    PubMed

    Lin, Wenxin; Chen, Hong; Chen, Qi; Liu, Yanting; Jiao, Nianzhi; Zheng, Qiang

    2016-02-01

    Bacillus sp. CHD6a, which can produce oval endosperms, isolated from the shallow-sea hydrothermal vent systems off northeast Taiwan's coast. Here, we report the draft genome sequence of Bacillus sp. CHD6a. It comprises ~3.97Mb in 55 contigs with the G+C content of 39.9%, and a total of 3740 protein-coding genes were obtained. PMID:26508672

  11. Gene identification and molecular characterization of solvent stable protease from a moderately haloalkaliphilic bacterium, Geomicrobium sp. EMB2.

    PubMed

    Karan, Ram; Singh, Raj Kumar Mohan; Kapoor, Sanjay; Khare, S K

    2011-02-01

    Cloning and characterization of the gene encoding a solvent-tolerant protease from the haloalkaliphilic bacterium Geomicrobium sp. EMB2 are described. Primers designed based on the N-terminal amino acid sequence of the purified EMB2 protease helped in the amplification of a 1,505-bp open reading frame that had a coding potential of a 42.7-kDa polypeptide. The deduced EMB2 protein contained a 35.4-kDa mature protein of 311 residues, with a high proportion of acidic amino acid residues. Phylogenetic analysis placed the EMB2 gene close to a known serine protease from Bacillus clausii KSM-K16. Primary sequence analysis indicated a hydrophobic inclination of the protein; and the 3D structure modeling elucidated a relatively higher percentage of small (glycine, alanine, and valine) and borderline (serine and threonine) hydrophobic residues on its surface. The structure analysis also highlighted enrichment of acidic residues at the cost of basic residues. The study indicated that solvent and salt stabilities in Geomicrobium sp. protease may be accorded to different structural features; that is, the presence of a number of small hydrophobic amino acid residues on the surface and a higher content of acidic amino acid residues, respectively. PMID:21364294

  12. Further studies on a human intestinal bacterium Ruminococcus sp. END-1 for transformation of plant lignans to mammalian lignans.

    PubMed

    Jin, Jong-Sik; Hattori, Masao

    2009-08-26

    A human intestinal bacterium Ruminococcus (R.) sp. END-1 capable of oxidizing (-)-enterodiol to (-)-enterolactone, enantioselectively, was further investigated from the perspective of transformation of plant lignans to mammalian lignans; A cell-free extract of the bacterium transformed (-)-enterodiol to (-)-enterolactone through an intermediate, enterolactol. The bacterium showed not only oxidation but also demethylation and deglucosylation activities for plant lignans. Arctiin and secoisolariciresinol diglucoside were converted to (-)-dihydroxyenterolactone and (+)-dihydroxyenterodiol, respectively. Moreover, by coincubation with Eggerthella sp. SDG-2, the bacterium transformed arctiin and secoisolariciresinol diglucoside to (-)-enterolactone and (+)-enterodiol, respectively. PMID:19630415

  13. A halotolerant thermostable lipase from the marine bacterium Oceanobacillus sp. PUMB02 with an ability to disrupt bacterial biofilms.

    PubMed

    Seghal Kiran, George; Nishanth Lipton, Anuj; Kennedy, Jonathan; Dobson, Alan D W; Selvin, Joseph

    2014-01-01

    A halotolerant thermostable lipase was purified and characterized from the marine bacterium Oceanobacillus sp. PUMB02. This lipase displayed a high degree of stability over a wide range of conditions including pH, salinity, and temperature. It was optimally active at 30 °C and pH 8.0 respectively and was stable at higher temperatures (50-70 °C) and alkaline pH. The molecular mass of the lipase was approximately 31 kDa based on SDS-PAGE and MALDI-ToF fingerprint analysis. Conditions for enhanced production of lipase by Oceanobacillus sp. PUMB02 were attained in response surface method-guided optimization with factors such as olive oil, sucrose, potassium chromate, and NaCl being evaluated, resulting in levels of 58.84 U/ml being achieved. The biofilm disruption potential of the PUMB02 lipase was evaluated and compared with a marine sponge metagenome derived halotolerant lipase Lpc53E1. Good biofilm disruption activity was observed with both lipases against potential food pathogens such as Bacillus cereus MTCC1272, Listeria sp. MTCC1143, Serratia sp. MTCC4822, Escherichia coli MTCC443, Pseudomonas fluorescens MTCC1748, and Vibrio parahemolyticus MTCC459. Phase contrast microscopy, scanning electron microscopy, and confocal laser scanning microscopy showed very effective disruption of pathogenic biofilms. This study reveals that marine derived hydrolytic enzymes such as lipases may have potential utility in inhibiting biofilm formation in a food processing environment and is the first report of the potential application of lipases from the genus Oceanobacillus in biofilm disruption strategies. PMID:25482232

  14. A halotolerant thermostable lipase from the marine bacterium Oceanobacillus sp. PUMB02 with an ability to disrupt bacterial biofilms

    PubMed Central

    Seghal Kiran, George; Nishanth Lipton, Anuj; Kennedy, Jonathan; Dobson, Alan DW; Selvin, Joseph

    2014-01-01

    A halotolerant thermostable lipase was purified and characterized from the marine bacterium Oceanobacillus sp. PUMB02. This lipase displayed a high degree of stability over a wide range of conditions including pH, salinity, and temperature. It was optimally active at 30 °C and pH 8.0 respectively and was stable at higher temperatures (50–70 °C) and alkaline pH. The molecular mass of the lipase was approximately 31 kDa based on SDS-PAGE and MALDI-ToF fingerprint analysis. Conditions for enhanced production of lipase by Oceanobacillus sp. PUMB02 were attained in response surface method-guided optimization with factors such as olive oil, sucrose, potassium chromate, and NaCl being evaluated, resulting in levels of 58.84 U/ml being achieved. The biofilm disruption potential of the PUMB02 lipase was evaluated and compared with a marine sponge metagenome derived halotolerant lipase Lpc53E1. Good biofilm disruption activity was observed with both lipases against potential food pathogens such as Bacillus cereus MTCC1272, Listeria sp. MTCC1143, Serratia sp. MTCC4822, Escherichia coli MTCC443, Pseudomonas fluorescens MTCC1748, and Vibrio parahemolyticus MTCC459. Phase contrast microscopy, scanning electron microscopy, and confocal laser scanning microscopy showed very effective disruption of pathogenic biofilms. This study reveals that marine derived hydrolytic enzymes such as lipases may have potential utility in inhibiting biofilm formation in a food processing environment and is the first report of the potential application of lipases from the genus Oceanobacillus in biofilm disruption strategies. PMID:25482232

  15. Properties of an amylase from thermophilic Bacillus SP

    PubMed Central

    de Carvalho, Raquel Vieira; Côrrea, Thamy Lívia Ribeiro; da Silva, Júlia Caroline Matos; de Oliveira Mansur, Luciana Ribeiro Coutinho; Martins, Meire Lelis Leal

    2008-01-01

    α-Amylase production by thermophilic Bacillus sp strain SMIA-2 cultivated in liquid cultures containing soluble starch as a carbon source and supplemented with 0.05% whey protein and 0.2% peptone reached a maximum activity at 32 h, with levels of 37 U/mL. Studies on the amylase characterization revealed that the optimum temperature of this enzyme was 90°C. The enzyme was stable for 1 h at temperatures ranging from 40-50°C while at 90°C, 66% of its maximum activity was lost. However, in the presence of 5 mM CaCl2, the enzyme was stable at 90°C for 30 min and retained about 58% residual activity after 1 h. The optimum pH of the enzyme was found to be 8.5. After incubation of enzyme for 2 h at pH 9.5 and 11.0 was observed a decrease of about 6.3% and 16.5% of its original activity. At pH 6.0 the enzyme lost about 36% of its original activity. The enzyme was strongly inhibited by Co2+, Cu2+ and Ba2+, but less affected by Mg2+, Na+ and K+. In the presence of 2.0 M NaCl, 63% of amylase activity was retained after 2 h incubation at 45°C. The amylase exhibited more than 70% activity when incubated for 1 h at 50°C with sodium dodecyl sulphate. However, very little residual activity was obtained with sodium hypochlorite and with hydrogen peroxide the enzyme was completely inhibited. The compatibility of Bacillus sp SMIA-2 amylase with certain commercial detergents was shown to be good as the enzyme retained 86%, 85% and 75% of its activity after 20 min incubation at 50°C in the presence of the detergent brands Omo®, Campeiro® and Tide®, respectively. PMID:24031188

  16. Geobacillus sp., a thermophilic soil bacterium producing volatile antibiotics.

    PubMed

    Ren, Yuhao; Strobel, Gary; Sears, Joe; Park, Melina

    2010-07-01

    Geobacillus, a bacterial genus, is represented by over 25 species of Gram-positive isolates from various man-made and natural thermophilic areas around the world. An isolate of this genus (M-7) has been acquired from a thermal area near Yellowstone National Park, MT and partially characterized. The cells of this organism are globose (ca. 0.5 mu diameter), and they are covered in a matrix capsule which gives rise to elongate multicelled bacilliform structures (ranging from 3 to 12 mum) as seen by light and atomic force microscopy, respectively. The organism produces unique petal-shaped colonies (undulating margins) on nutrient agar, and it has an optimum pH of 7.0 and an optimum temperature range of 55-65 degrees C. The partial 16S rRNA sequence of this organism has 97% similarity with Geobacillus stearothermophilus, one of its closest relatives genetically. However, uniquely among all members of this genus, Geobacillus sp. (M-7) produces volatile organic substances (VOCs) that possess potent antibiotic activities. Some of the more notable components of the VOCs are benzaldehyde, acetic acid, butanal, 3-methyl-butanoic acid, 2-methyl-butanoic acid, propanoic acid, 2-methyl-, and benzeneacetaldehyde. An exposure of test organisms such as Aspergillus fumigatus, Botrytis cinerea, Verticillium dahliae, and Geotrichum candidum produced total inhibition of growth on a 48-h exposure to Geobacillus sp.(M-7) cells (ca.10(7)) and killing at a 72-h exposure at higher bacterial cell concentrations. A synthetic mixture of those available volatile compounds, at the ratios occurring in Geobacillus sp. (M-7), mimicked the bioactivity of this organism. PMID:20091406

  17. Yersinia ruckeri sp. nov., the redmouth (RM) bacterium

    USGS Publications Warehouse

    Ewing, W.H.; Ross, A.J.; Brenner, Don J.; Fanning, G. R.

    1978-01-01

    Cultures of the redmouth (RM) bacterium, one of the etiological agents of redmouth disease in rainbow trout (Salmo gairdneri) and certain other fishes, were characterized by means of their biochemical reactions, by deoxyribonucleic acid (DNA) hybridization, and by determination of guanine-plus-cytosine (G+C) ratios in DNA. The DNA relatedness studies confirmed the fact that the RM bacteria are members of the family Enterobacteriaceae and that they comprise a single species that is not closely related to any other species of Enterobacteriaceae. They are about 30% related to species of both Serratia and Yersinia. A comparison of the biochemical reactions of RM bacteria and serratiae indicated that there are many differences between these organisms and that biochemically the RM bacteria are most closely related to yersiniae. The G+C ratios of RM bacteria were approximated to be between 47.5 and 48.5% These values are similar to those of yersiniae but markedly different from those of serratiae. On the basis of their biochemical reactions and their G+C ratios, the RM bacteria are considered to be a new species of Yersinia, for which the name Yersinia ruckeri is proposed. Strain 2396-61 (= ATCC 29473) is designated the type strain of the species.

  18. Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium.

    PubMed

    Lee, Myungjin; Kim, Myung Kyum; Vancanneyt, Marc; Swings, Jean; Kim, Seong-Hye; Kang, Myung Suk; Lee, Sung-Taik

    2005-07-01

    A Gram-positive, non-motile, non-spore-forming coccus (strain JS(T)) was isolated from kimchi (a traditional Korean food) and investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between strain JS(T) and its closest relative, Tetragenococcus halophilus IAM 1676(T), was 98.1%. The level of DNA-DNA relatedness between the two strains was 9.7%. Strain JS(T) had a DNA G+C content of 38.3% and a cellular fatty acid profile containing 16:0, 18:1 and cyclo fatty acids. Phylogenetic data and genomic and phenotypic features demonstrated that strain JS(T) represents a novel species, for which the name Tetragenococcus koreensis sp. nov. is proposed. The type strain is JS(T) (=KCTC 3924(T)=DSM 16501(T)=LMG 22864(T)). PMID:16014460

  19. Mechanism of algal aggregation by Bacillus sp. strain RP1137.

    PubMed

    Powell, Ryan J; Hill, Russell T

    2014-07-01

    Alga-derived biofuels are one of the best alternatives for economically replacing liquid fossil fuels with a fungible renewable energy source. Production of fuel from algae is technically feasible but not yet economically viable. Harvest of dilute algal biomass from the surrounding water remains one of the largest barriers to economic production of algal biofuel. We identified Bacillus sp. strain RP1137 in a previous study and showed that this strain can rapidly aggregate several biofuel-producing algae in a pH- and divalent-cation-dependent manner. In this study, we further characterized the mechanism of algal aggregation by RP1137. We show that aggregation of both algae and bacteria is optimal in the exponential phase of growth and that the density of ionizable residues on the RP1137 cell surface changes with growth stage. Aggregation likely occurs via charge neutralization with calcium ions at the cell surface of both algae and bacteria. We show that charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. The addition of calcium also renders both algae and bacteria more able to bind to hydrophobic beads, suggesting that aggregation may occur through hydrophobic interactions. Knowledge of the aggregation mechanism may enable engineering of RP1137 to obtain more efficient algal harvesting. PMID:24771029

  20. Mechanism of Algal Aggregation by Bacillus sp. Strain RP1137

    PubMed Central

    Powell, Ryan J.

    2014-01-01

    Alga-derived biofuels are one of the best alternatives for economically replacing liquid fossil fuels with a fungible renewable energy source. Production of fuel from algae is technically feasible but not yet economically viable. Harvest of dilute algal biomass from the surrounding water remains one of the largest barriers to economic production of algal biofuel. We identified Bacillus sp. strain RP1137 in a previous study and showed that this strain can rapidly aggregate several biofuel-producing algae in a pH- and divalent-cation-dependent manner. In this study, we further characterized the mechanism of algal aggregation by RP1137. We show that aggregation of both algae and bacteria is optimal in the exponential phase of growth and that the density of ionizable residues on the RP1137 cell surface changes with growth stage. Aggregation likely occurs via charge neutralization with calcium ions at the cell surface of both algae and bacteria. We show that charge neutralization occurs at least in part through binding of calcium to negatively charged teichoic acid residues. The addition of calcium also renders both algae and bacteria more able to bind to hydrophobic beads, suggesting that aggregation may occur through hydrophobic interactions. Knowledge of the aggregation mechanism may enable engineering of RP1137 to obtain more efficient algal harvesting. PMID:24771029

  1. Anaerobic utilization of phosphite and hypophosphite by Bacillus sp.

    PubMed Central

    Foster, T L; Winans, L; Helms, S J

    1978-01-01

    A Bacillus sp. capable of utilizing phosphite and hypophosphite under anaerobic conditions was isolated from Cape Canerval soil samples. The organism was isolated on a glucose-mineral salts medium with phosphate deleted. Anaerobic cultivation of this isolate resulted in decreases in the hypophosphite or phosphite concentration, increases in turbidity, cell count, and dry-cell weight, and decreases in pH and glucose concentration. The optimum hypophosphite concentration for this isolate was 60 microgram/ml, whereas the optimum phosphate concentration was greater than 1,000 microgram/ml, suggesting that higher concentrations of hypophosphite may be toxic to this isolate. Hypophosphite or phosphite utilization was accompanied by little or no detectable accumulation of phosphate in the medium, and 32P-labeled hypophosphite was incorporated into the cell as organic phosphate. When phosphate was present in the medium, the isolate failed to metabolize phosphite. In the presence of phosphite and hypophosphite, the isolate first utilized phosphite and then hypophosphite. PMID:26310

  2. Bacillus cihuensis sp. nov., isolated from rhizosphere soil of a plant in the Cihu area of Taiwan.

    PubMed

    Liu, Bo; Liu, Guo-Hong; Sengonca, Cetin; Schumann, Peter; Wang, Ming-Kuang; Tang, Jian-Yang; Chen, Mei-Chun

    2014-12-01

    A Gram-positive, moderately halotolerant, rod-shaped, spore forming bacterium, designated strain FJAT-14515(T) was isolated from a soil sample in Cihu area, Taoyuan County, Taiwan. The strain grew at 10-35 °C (optimum at 30 °C), pH 5.7-9.0 (optimum at pH 7.0) and at salinities of 0-5 % (w/v) NaCl (optimum at 1 % w/v). The diagnostic diamino acid of the peptidoglycan of the isolated strain was meso-diaminopimelic acid and major respiratory isoprenoid quinone was MK-7. Major cellular fatty acids were anteiso-C15:0 (40.6 %), iso-C15:0 (20.7 %) and the DNA G+C content of strain FJAT-14515(T) was 37.1 mol %. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FJAT-14515(T) belongs to the genus Bacillus, and was most closely related to the reference strains of Bacillus muralis DSM 16288(T) (97.6 %) and Bacillus simplex DSM 1321(T) (97.5 %). Levels of DNA-DNA relatedness between strain FJAT-14515(T) and the reference strains of B. muralis DSM 16288(T) and B. simplex DSM 1321(T) were 27.9 % ± 3.32 and 44.1 % ± 0.57, respectively. Therefore, on the basis of phenotypic, chemotaxonomic and genotypic properties, strain FJAT-14515(T) represents a novel species of the genus Bacillus, for which the name Bacillus cihuensis sp. nov. is proposed. The type strain is FJAT-14515(T) (=DSM 25969(T) = CGMCC 1.12697(T)). PMID:25256951

  3. Coarse grained simulation reveals antifreeze properties of hyperactive antifreeze protein from Antarctic bacterium Colwellia sp.

    NASA Astrophysics Data System (ADS)

    Nguyen, Hung; Van, Thanh Dac; Le, Ly

    2015-10-01

    The novel hyperactive antifreeze protein (AFP) of Antarctic sea ice bacterium Colwellia sp. provides a target for studying the protection of psychrophilic microgoranisms against freezing environment. Interestingly, the Colwellia sp. hyperactive antifreeze protein (ColAFP) was crystallized without the structural dynamic characteristics. Here, the result indicated, through coarse grained simulation of ColAFP under various subfreezing temperature, that ColAFP remains active at temperature of equal and greater than 275 K (∼2 °C). Extensive simulation analyses also revealed the adaptive mechanism of ColAFP in subfreezing environment. Our result provides a structural dynamic understanding of the ColAFP.

  4. Massilia sp. BS-1, a novel violacein-producing bacterium isolated from soil.

    PubMed

    Agematu, Hitosi; Suzuki, Kazuya; Tsuya, Hiroaki

    2011-01-01

    A novel bacterium, Massilia sp. BS-1, producing violacein and deoxyviolacein was isolated from a soil sample collected from Akita Prefecture, Japan. The 16S ribosomal DNA of strain BS-1 displayed 93% homology with its nearest violacein-producing neighbor, Janthinobacterium lividum. Strain BS-1 grew well in a synthetic medium, but required both L-tryptophan and a small amount of L-histidine to produce violacein. PMID:21979084

  5. Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, Bacillus sp. isolated from salt flat sediments of Soap Lake.

    PubMed

    Pollock, Jarrod; Weber, Karrie A; Lack, Joe; Achenbach, Laurie A; Mormile, Melanie R; Coates, John D

    2007-12-01

    A halotolerant, alkaliphilic dissimilatory Fe(III)-reducing bacterium, strain SFB, was isolated from salt flat sediments collected from Soap Lake, WA. 16S ribosomal ribonucleic acid gene sequence analysis identified strain SFB as a novel Bacillus sp. most similar to Bacillus agaradhaerens (96.7% similarity). Strain SFB, a fermentative, facultative anaerobe, fermented various hexoses including glucose and fructose. The fructose fermentation products were lactate, acetate, and formate. Under fructose-fermenting conditions in a medium amended with Fe(III), Fe(II) accumulated concomitant with a stoichiometric decrease in lactate and an increase in acetate and CO(2). Strain SFB was also capable of respiratory Fe(III) reduction with some unidentified component(s) of Luria broth as an electron donor. In addition to Fe(III), strain SFB could also utilize nitrate, fumarate, or O(2) as alternative electron acceptors. Optimum growth was observed at 30 degrees C and pH 9. Although the optimal salinity for growth was 0%, strain SFB could grow in a medium with up to 15% NaCl by mass. These studies describe a novel alkaliphilic, halotolerant organism capable of dissimilatory Fe(III) reduction under extreme conditions and demonstrate that Bacillus species can contribute to the microbial reduction of Fe(III) in environments at elevated pH and salinity, such as soda lakes. PMID:17943280

  6. Sporosarcina saromensis sp. nov., an aerobic endospore-forming bacterium.

    PubMed

    An, Sun-Young; Haga, Tomomi; Kasai, Hiroaki; Goto, Keiichi; Yokota, Akira

    2007-08-01

    Two Gram-positive, endospore-forming, rod-shaped bacterial strains, HG645(T) and HG711, were respectively isolated from surface water of a brackish lake and sediment of a fishery harbour in Japan and were subsequently characterized taxonomically using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains HG645(T) and HG711 are affiliated phylogenetically to the genus Sporosarcina, and they exhibit sequence similarities of 95.7-97.3 % to the type strains of Sporosarcina species. DNA-DNA relatedness between strain HG645(T) and the type strain of the phylogenetically related species Sporosarcina aquimarina was less than 10 %. The DNA G+C content of strains HG645(T) and HG711 were respectively 46.0 and 45.2 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell-wall peptidoglycan type (Lys-Glu), major cellular fatty acids (iso-C(15 : 0) and anteiso-C(15 : 0)) and quinone type (MK-7) of the isolates support their affiliation to the genus Sporosarcina. On the basis of phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent a novel species of the genus Sporosarcina, for which the name Sporosarcina saromensis sp. nov. is proposed. The type strain is strain HG645(T) (=MBIC08270(T)=IAM 15429(T) =KCTC 13119(T)). PMID:17684272

  7. Immobilization of Bacillus sp. in mesoporous activated carbon for degradation of sulphonated phenolic compound in wastewater.

    PubMed

    Sekaran, G; Karthikeyan, S; Gupta, V K; Boopathy, R; Maharaja, P

    2013-03-01

    Xenobiotic compounds are used in considerable quantities in leather industries besides natural organic and inorganic compounds. These compounds resist biological degradation and thus they remain in the treated wastewater in the unaltered molecular configurations. Immobilization of organisms in carrier matrices protects them from shock load application and from the toxicity of chemicals in bulk liquid phase. Mesoporous activated carbon (MAC) has been considered in the present study as the carrier matrix for the immobilization of Bacillus sp. isolated from Effluent Treatment Plant (ETP) employed for the treatment of wastewater containing sulphonated phenolic (SP) compounds. Temperature, pH, concentration, particle size and mass of MAC were observed to influence the immobilization behavior of Bacillus sp. The percentage immobilization of Bacillus sp. was the maximum at pH 7.0, temperature 20 °C and at particle size 300 μm. Enthalpy, free energy and entropy of immobilization were -46.9 kJ mol(-1), -1.19 kJ mol(-1) and -161.36 JK(-1)mol(-1) respectively at pH 7.0, temperature 20 °C and particle size 300 μm. Higher values of ΔH(0) indicate the firm bonding of the Bacillus sp. in MAC. Degradation of aqueous sulphonated phenolic compound by Bacillus sp. immobilized in MAC followed pseudo first order rate kinetics with rate constant 1.12 × 10(-2) min(-1). PMID:25427481

  8. Draft Genome Sequence of Arthrobacter sp. Strain SPG23, a Hydrocarbon-Degrading and Plant Growth-Promoting Soil Bacterium

    PubMed Central

    Gkorezis, Panagiotis; Bottos, Eric M.; Van Hamme, Jonathan D.; Thijs, Sofie; Rineau, Francois; Balseiro-Romero, Maria; Weyens, Nele

    2015-01-01

    We report here the 4.7-Mb draft genome of Arthrobacter sp. SPG23, a hydrocarbonoclastic Gram-positive bacterium belonging to the Actinobacteria, isolated from diesel-contaminated soil at the Ford Motor Company site in Genk, Belgium. Strain SPG23 is a potent plant growth promoter useful for diesel fuel remediation applications based on plant-bacterium associations. PMID:26701084

  9. Terribacillus aidingensis sp. nov., a moderately halophilic bacterium.

    PubMed

    Liu, Wenyan; Jiang, Linlin; Guo, Chunjing; Yang, Su Sheng

    2010-12-01

    Three Gram-positive, moderately halophilic bacteria, designated YI7-61(T), IA7 and DB2, were isolated from sediments of Aiding salt lake in the Xinjiang region of China. Cells of the strains were rod-shaped, motile by means of peritrichous flagella and produced ellipsoidal spores. Colonies were pale yellow in colour. The strains grew optimally at 30-37 °C, pH 6-7 and 3-7 % (w/v) NaCl. The diamino acid in the murein was meso-diaminopimelic acid and the major quinone system was MK-7. The major cellular fatty acids were anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 44.6-45.0 mol%. 16S rRNA gene sequence analysis revealed that strains YI7-61(T), IA7 and DB2 were closely related to members of the genus Terribacillus and showed 96.8-97.6, 96.4-97.2 and 95.4-95.5 % 16S rRNA gene sequence similarity with Terribacillus halophilus 002-051(T), Terribacillus saccharophilus RB589 and Terribacillus goriensis CL-GR16(T), respectively. DNA-DNA relatedness among the isolates was 88-92 % and strain YI7-61(T) shared 24, 18 and 18 % DNA-DNA relatedness with T. halophilus JCM 21760(T), T. saccharophilus JCM 21759(T) and T. goriensis DSM 18252(T), respectively. On the basis of phenotypic and phylogenetic distinctiveness, the three isolates should be placed in the genus Terribacillus as representatives of a novel species, for which the name Terribacillus aidingensis sp. nov. is proposed. The type strain is YI7-61(T) (=CGMCC 1.8913(T) =NBRC 105790(T)). PMID:20118295

  10. Flavobacterium tistrianum sp. nov., a gliding bacterium isolated from soil.

    PubMed

    Suwannachart, Chatrudee; Rueangyotchanthana, Kanjana; Srichuay, Suksan; Pheng, Sophea; Fungsin, Bundit; Phoonsiri, Chantara; Kim, Song-Gun

    2016-06-01

    A novel gliding bacterial strain, GB 56.1T, was obtained from soil at the Sakaerat Biosphere Reserve, in Nakhon Ratchasima province, Thailand; the strain was characterized using a polyphasic approach. Cells were Gram-stain-negative, yellow, rod shaped and devoid of flagella, but showed gliding motility. Phylogenetic analysis based on 16S rRNA gene sequences found that GB 56.1T was a member of the genus Flavobacterium and that the strain shared the highest sequence similarities with Flavobacterium nitrogenifigens (98.4 %), Flavobacterium anhuiense(98.3 %) and Flavobacterium ginsenosidimutans (97.9 %). The similarities of the sequences of all other species of the genus Flavobacterium were below 97.4 %. The major respiratory quinone of strain GB 56.1T was MK-6; fatty acids were iso-C15:0, C16:1ω6c/C16:1ω7c, C16:0 and C16:0 3-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylserine, an unidentified amino lipid and four polar lipids. The DNA G+C content of this strain was 34.2 mol%. The DNA-DNA relatedness of GB 56.1T was highest against F.anhuiense, with a value of 37.6 %. On the basis of morphological, physiological and chemotaxonomic characteristics, DNA-DNA hybridization relatedness and 16S rRNA gene sequence analysis, we conclude that strain GB 56.1T represents a novel species, for which the name Flavobacterium tistrianum sp. nov. is proposed. The type strain is GB 56.1T (=TISTR 1612T =KCTC 42679T). PMID:26970735

  11. Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge.

    PubMed

    Deng, Shi-Kai; Ye, Xiao-Mei; Chu, Cui-Wei; Jiang, Jin; He, Jian; Zhang, Jun; Li, Shun-Peng

    2014-08-01

    A Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, aerobic bacterial strain, designated BUT-2(T), was isolated from activated sludge of one herbicide-manufacturing wastewater-treatment facility in Kunshan, Jiangsu province, China, and subjected to polyphasic taxonomic studies. Analysis of the 16S rRNA gene sequence indicated that strain BUT-2(T) shared the highest similarity with Chryseomicrobium amylolyticum (98.98%), followed by Chryseomicrobium imtechense (98.88%), with less than 96% similarlity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain BUT-2(T) clustered with C. amylolyticum JC16(T) and C. imtechense MW10(T), occupying a distinct phylogenetic position. The major fatty acid (>10% of total fatty acids) type of strain BUT-2(T) was iso-C(15 : 0). The quinone system comprised menaquinone MK-7 (77.8%), MK-6 (11.9%) and MK-8 (10.3%). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and some unidentified phospholipids. The cell-wall peptidoglycan type of strain BUT-2(T) was L-Orn-D-Glu. The genomic DNA G+C content of strain BUT-2(T) was 48.5 mol%. Furthermore, the DNA-DNA relatedness in hybridization experiments against the reference strain was lower than 70%, confirming that strain BUT-2(T) did not belong to previously described species of the genus Chryseomicrobium. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strain BUT-2(T) is considered to represent a novel species of the genus Chryseomicrobium, for which the name Chryseomicrobium aureum sp. nov. is proposed. The type strain is BUT-2(T) ( = CCTCC AB2013082(T) = KACC 17219(T)). PMID:24827708

  12. Chitinophaga jiangningensis sp. nov., a mineral-weathering bacterium.

    PubMed

    Wang, Qi; Cheng, Cheng; He, Lin-Yan; Huang, Zhi; Sheng, Xia-Fang

    2014-01-01

    A Gram-stain-negative, rod-shaped bacterial strain, JN53(T), was isolated from the surfaces of weathered rock (potassic trachyte) from Nanjing, Jiangsu Province, PR China. Strain JN53(T) grew optimally at 30 °C, pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JN53(T) belonged to the genus Chitinophaga in the family Chitinophagaceae. It was most closely related to Chitinophaga terrae KP01(T) (97.3 % 16S rRNA gene sequence similarity), Chitinophaga eiseniae YC6729(T) (96.3 %). Strain JN53(T) contained MK-7 as the major menaquinone and homospermidine as the major polyamine. The main fatty acids of strain JN53(T) were iso-C15 : 0, C16 : 1ω5c, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 0 3-OH and C16 : 0 3-OH. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids and unknown lipids. The total DNA G+C content of strain JN53(T) was 49.7 mol%. The low level of DNA-DNA relatedness to other species of the genus Chitinophaga and the many phenotypic properties that distinguished strain JN53(T) from recognized species of this genus demonstrated that isolate JN53(T) should be classified as representing a novel species of the genus Chitinophaga, for which the name Chitinophaga jiangningensis sp. nov. is proposed. The type strain is JN53(T) ( = CCTCC AB 2013166(T) = JCM 19354(T)). PMID:24052630

  13. Bacillus coahuilensis sp. nov., a moderately halophilic species from a desiccation lagoon in the Cuatro Ciénegas Valley in Coahuila, Mexico.

    PubMed

    Cerritos, René; Vinuesa, Pablo; Eguiarte, Luis E; Herrera-Estrella, Luis; Alcaraz-Peraza, Luis D; Arvizu-Gómez, Jackeline L; Olmedo, Gabriela; Ramirez, Enrique; Siefert, Janet L; Souza, Valeria

    2008-04-01

    A moderately halophilic, Gram-positive and rod-shaped bacterium, strain m4-4T, was isolated from a Chihuahuan desert lagoon in Cuatro Ciénegas, Coahuila, Mexico. Strain m4-4T was found to grow optimally at 30-37 degrees C, pH 7.0-8.0 and 5 % NaCl and to tolerate from 0.5 % to 10 % NaCl. It was shown to be aerobic. The genomic DNA G+C content was about 37 mol%. Strain m4-4T exhibited minimal or no growth on most sugars tested. Its major cellular fatty acids were C14 : 0, C16 : 0 and C18 : 1. Based on phylogenetic analysis of 16S rRNA and recA gene sequences, we observed that the closest relatives of the isolate are moderately halophilic Bacillus species, with 16S rRNA gene sequence similarity ranging from 96.6 to 97.4 % (Bacillus marisflavi, Bacillus aquimaris and Bacillus vietnamensis). Additionally, using genomic data it was determined that the type strain contains a total of nine rRNA operons with three slightly different sequences. On the basis of phenotypic and molecular properties, strain m4-4T represents a novel species within the genus Bacillus, for which the name Bacillus coahuilensis sp. nov. is proposed, with the type strain m4-4T (=NRRL B-41737T =CECT 7197T). PMID:18398195

  14. Isolation and characterization of Leu[7]-Surfactin from the endophytic bacterium Bacillus mojavensis RRC 101, a biocontrol agent for Fusarium verticillioides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacillus mojavensis is an endophytic bacterium patented for control of fungal diseases in maize and other plants. Culture extracts and filtrates from this bacterium were antagonistic to the pathogenic and mycotoxic fungus Fusarium verticillioides. However, the identity of the inhibitory substance ...

  15. A Pathway Closely Related to the d-Tagatose Pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis

    PubMed Central

    Van der Heiden, Edwige; Lebrun, Sarah; Freichels, Régine; Brans, Alain; Vastenavond, Christian M.; Galleni, Moreno; Joris, Bernard

    2013-01-01

    We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. PMID:23524682

  16. Rhodococcus biphenylivorans sp. nov., a polychlorinated biphenyl-degrading bacterium.

    PubMed

    Su, Xiaomei; Liu, Yindong; Hashmi, Muhammad Zaffar; Hu, Jinxing; Ding, Linxian; Wu, Min; Shen, Chaofeng

    2015-01-01

    A Gram-positive, aerobic, non-motile and rod-coccus shaped novel actinobacterial strain, designated as TG9(T), was isolated from a polychlorinated biphenyl (PCB)-contaminated sediment in Taizhou city, Zhejiang province, eastern China. The isolate was observed to grow at 10-45 °C (optimum 28-32 °C), pH 5.0-11.0 (optimum pH 7.0-8.0) and with 0-9.0 % (w/v) NaCl (optimum 0-3.0 %). Comparison of the 16S rRNA gene sequences of strain TG9(T) and other members of the genus Rhodococcus showed that strain TG9(T) shared highest similarities with Rhodococcus pyridinivorans DSM 44555(T) (99.4 %), R. rhodochrous DSM 43241(T) (99.2 %), R. gordoniae DSM 44689(T) (99.2 %) and R. artemisiae DSM 45380(T) (98.2 %). However, low levels of DNA-DNA relatedness (15-48 %), which are below the 70 % limit for prokaryotic species identification, were obtained by DNA-DNA hybridization. Strain TG9(T) was found to contain meso-diaminopimelic acid as the diagnostic diamino acid and arabinose and galactose in the whole-cell hydrolysate. Mycolic acids were found to be present. The major fatty acids were identified as C16:0, C16:1 ω7c and/or iso-C15:0 2-OH, 10-methyl C18:0 and C18:1 ω9c. The only menaquinone detected was MK-8 (H2). The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycolipid and traces of some unknown lipids. The genomic DNA G+C content of strain TG9(T) was determined to be 62.8 %. The combined phenotypic and genotypic data show that the strain represents a novel species of the genus Rhodococcus for which the name Rhodococcus biphenylivorans sp. nov. is proposed, with the type strain TG9(T) (=CGMCC 1.12975(T) = KCTC 29673(T) = MCCC 1K00286(T)). PMID:25315102

  17. Biodegradation of exploded cotton stalk by Bacillus sp.

    PubMed

    Zheng, Lianshuang; Han, Xiaofang; Du, Yumin

    2003-10-01

    The exploded bast, branch and stem of cotton stalk were degraded by alkalophilic Bacillus NT-19, with weight losses of 24%, 20% and 14%, respectively, after 14 d. Compared with a white-rot fungus (Phanerochaete chrysosporium), Bacillus NT- 19 preferentially degraded the non-cellulose components of cotton stem. The relative degree of crystallinity of bast fibers decreased by 8% and the middle lamella was partially removed from the fiber bundle by the Bacillus. PMID:14626420

  18. Augmenting iron accumulation in cassava by the beneficial soil bacterium Bacillus subtilis (GBO3).

    PubMed

    Freitas, Mônica A; Medeiros, Flavio H V; Carvalho, Samuel P; Guilherme, Luiz R G; Teixeira, William D; Zhang, Huiming; Paré, Paul W

    2015-01-01

    Cassava (Manihot esculenta), a major staple food in the developing world, provides a basic carbohydrate diet for over half a billion people living in the tropics. Despite the iron abundance in most soils, cassava provides insufficient iron for humans as the edible roots contain 3-12 times less iron than other traditional food crops such as wheat, maize, and rice. With the recent identification that the beneficial soil bacterium Bacillus subtilis (strain GB03) activates iron acquisition machinery to increase metal ion assimilation in Arabidopsis, the question arises as to whether this plant-growth promoting rhizobacterium also augments iron assimilation to increase endogenous iron levels in cassava. Biochemical analyses reveal that shoot-propagated cassava with GB03-inoculation exhibit elevated iron accumulation after 140 days of plant growth as determined by X-ray microanalysis and total foliar iron analysis. Growth promotion and increased photosynthetic efficiency were also observed for greenhouse-grown plants with GB03-exposure. These results demonstrate the potential of microbes to increase iron accumulation in an important agricultural crop and is consistent with idea that microbial signaling can regulate plant photosynthesis. PMID:26300897

  19. Augmenting iron accumulation in cassava by the beneficial soil bacterium Bacillus subtilis (GBO3)

    PubMed Central

    Freitas, Mônica A.; Medeiros, Flavio H. V.; Carvalho, Samuel P.; Guilherme, Luiz R. G.; Teixeira, William D.; Zhang, Huiming; Paré, Paul W.

    2015-01-01

    Cassava (Manihot esculenta), a major staple food in the developing world, provides a basic carbohydrate diet for over half a billion people living in the tropics. Despite the iron abundance in most soils, cassava provides insufficient iron for humans as the edible roots contain 3–12 times less iron than other traditional food crops such as wheat, maize, and rice. With the recent identification that the beneficial soil bacterium Bacillus subtilis (strain GB03) activates iron acquisition machinery to increase metal ion assimilation in Arabidopsis, the question arises as to whether this plant-growth promoting rhizobacterium also augments iron assimilation to increase endogenous iron levels in cassava. Biochemical analyses reveal that shoot-propagated cassava with GB03-inoculation exhibit elevated iron accumulation after 140 days of plant growth as determined by X-ray microanalysis and total foliar iron analysis. Growth promotion and increased photosynthetic efficiency were also observed for greenhouse-grown plants with GB03-exposure. These results demonstrate the potential of microbes to increase iron accumulation in an important agricultural crop and is consistent with idea that microbial signaling can regulate plant photosynthesis. PMID:26300897

  20. Development of a gene cloning system for the hydrogen-producing marine photosynthetic bacterium Rhodopseudomonas sp.

    PubMed Central

    Matsunaga, T; Matsunaga, N; Tsubaki, K; Tanaka, T

    1986-01-01

    Seventy-six strains of marine photosynthetic bacteria were analyzed by agarose gel electrophoresis for plasmid DNA content. Among these strains, 12 carried two to four different plasmids with sizes ranging from 3.1 to 11.0 megadaltons. The marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 had two plasmids, pRD06S and pRD06L. The smaller plasmid, pRD06S, had a molecular weight of 3.8 megadaltons and was cut at a single site by restriction endonucleases SalI, SmaI, PstI, XhoI, and BglII. Moreover, the marine photosynthetic bacterium Rhodopseudomonas sp. NKPB002106 containing plasmid pRD06 had a satisfactory growth rate (doubling time, 7.5 h), a hydrogen-producing rate of 0.96 mumol/mg (dry weight) of cells per h, and nitrogen fixation capability. Plasmid pRD06S, however, had neither drug resistance nor heavy-metal resistance, and its copy number was less than 10. Therefore, a recombinant plasmid consisting of pRD06S and Escherichia coli cloning vector pUC13 was constructed and cloned in E. coli. The recombinant plasmid was transformed into Rhodopseudomonas sp. NKPB002106. As a result, Rhodopseudomonas sp. NKPB002106 developed ampicillin resistance. Thus, a shuttle vector for gene transfer was constructed for marine photosynthetic bacteria. PMID:3020006

  1. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring.

    PubMed

    Slobodkin, A; Reysenbach, A L; Strutz, N; Dreier, M; Wiegel, J

    1997-04-01

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7T; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 microns, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74 degrees C with an optimum at 65 degrees C. The pH range for growth at 65 degrees C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO2, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H2 was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO2, nitrate, sulfate, sulfite, or elemental sulfur. The G + C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type-positive Bacillus-Clostridium subphylum. PMID:9103646

  2. Thermoterrabacterium ferrireducens gen. nov., sp. nov., a thermophilic anaerobic dissimilatory Fe(III)-reducing bacterium from a continental hot spring

    SciTech Connect

    Slobodkin, A.; Wiegel, J.; Reysenbach, A.L.

    1997-04-01

    A strain of a thermophilic, anaerobic, dissimilatory, Fe(III)-reducing bacterium, Thermoterrabacterium ferrireducens gen. nov., sp. nov. (type strain JW/AS-Y7{sup T}; DSM 11255), was isolated from hot springs in Yellowstone National Park and New Zealand. The gram-positive-staining cells occurred singly or in pairs as straight to slightly curved rods, 0.3 to 0.4 by 1.6 to 2.7 {mu}m, with rounded ends and exhibited a tumbling motility. Spores were not observed. The temperature range for growth was 50 to 74{degrees}C with an optimum at 65{degrees}C. The pH range for growth at 65{degrees}C was from 5.5 to 7.6, with an optimum at 6.0 to 6.2. The organism coupled the oxidation of glycerol to reduction of amorphous Fe(III) oxide or Fe(III) citrate as an electron acceptor. In the presence as well as in the absence of Fe(III) and in the presence of CO{sub 2}, glycerol was metabolized by incomplete oxidation to acetate as the only organic metabolic product; no H{sub 2} was produced during growth. The organism utilized glycerol, lactate, 1,2-propanediol, glycerate, pyruvate, glucose, fructose, mannose, and yeast extract as substrates. In the presence of Fe(III) the bacterium utilized molecular hydrogen. The organism reduced 9,10-anthraquinone-2,6-disulfonic acid, fumarate (to succinate), and thiosulfate (to elemental sulfur) but did not reduce MnO{sub 2}, nitrate, sulfate, sulfite, or elemental sulfur. The G+C content of the DNA was 41 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolated strain as a member of a new genus within the gram-type positive Bacillus-Clostridium subphylum.

  3. Draft Genome Sequence of Limnobacter sp. Strain CACIAM 66H1, a Heterotrophic Bacterium Associated with Cyanobacteria.

    PubMed

    da Silva, Fábio Daniel Florêncio; Lima, Alex Ranieri Jerônimo; Moraes, Pablo Henrique Gonçalves; Siqueira, Andrei Santos; Dall'Agnol, Leonardo Teixeira; Baraúna, Anna Rafaella Ferreira; Martins, Luisa Carício; Oliveira, Karol Guimarães; de Lima, Clayton Pereira Silva; Nunes, Márcio Roberto Teixeira; Vianez-Júnior, João Lídio Silva Gonçalves; Gonçalves, Evonnildo Costa

    2016-01-01

    Ecological interactions between cyanobacteria and heterotrophic prokaryotes are poorly known. To improve the genomic studies of heterotrophic bacterium-cyanobacterium associations, the draft genome sequence (3.2 Mbp) of Limnobacter sp. strain CACIAM 66H1, found in a nonaxenic culture of Synechococcus sp. (cyanobacteria), is presented here. PMID:27198027

  4. N-Acyl Dehydrotyrosines, Tyrosinase Inhibitors from the Marine Bacterium Thalassotalea sp. PP2-459.

    PubMed

    Deering, Robert W; Chen, Jianwei; Sun, Jiadong; Ma, Hang; Dubert, Javier; Barja, Juan L; Seeram, Navindra P; Wang, Hong; Rowley, David C

    2016-02-26

    Thalassotalic acids A-C and thalassotalamides A and B are new N-acyl dehydrotyrosine derivatives produced by Thalassotalea sp. PP2-459, a Gram-negative bacterium isolated from a marine bivalve aquaculture facility. The structures were elucidated via a combination of spectroscopic analyses emphasizing two-dimensional NMR and high-resolution mass spectrometric data. Thalassotalic acid A (1) displays in vitro inhibition of the enzyme tyrosinase with an IC50 value (130 μM) that compares favorably to the commercially used control compounds kojic acid (46 μM) and arbutin (100 μM). These are the first natural products reported from a bacterium belonging to the genus Thalassotalea. PMID:26824128

  5. Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.

    PubMed

    Bendjama, Esma; Loucif, Lotfi; Diene, Seydina M; Michelle, Caroline; Gacemi-Kirane, Djamila; Rolain, Jean-Marc

    2014-06-15

    Strain EB01(T) sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes. PMID:25197482

  6. Non-contiguous finished genome sequence and description of Bacillus massilioalgeriensis sp. nov.

    PubMed Central

    Bendjama, Esma; Loucif, Lotfi; Diene, Seydina M.; Michelle, Caroline; Gacemi-Kirane, Djamila; Rolain, Jean-Marc

    2014-01-01

    Strain EB01T sp. nov. is the type strain of Bacillus massilioalgeriensis, a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from sediment sample of the hypersaline lake Ezzemoul sabkha in northeastern Algeria. B. massilioalgeriensis is a facultative anaerobic Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,269,577 bp long genome contains 5,098 protein-coding and 95 RNA genes, including 12 rRNA genes. PMID:25197482

  7. Tetrodotoxin-producing Bacillus sp. from the ribbon worm (Nemertea) Cephalothrix simula (Iwata, 1952).

    PubMed

    Magarlamov, Timur Yu; Beleneva, Irina A; Chernyshev, Alexey V; Kuhlevsky, Andrey D

    2014-07-01

    Specimens of the toxic ribbon worm Cephalothrix simula from the Sea of Japan were screened for tetrodotoxin-producing bacteria. A single TTX-producing bacterial strain (No 1839) was isolated from tissues of C. simula and studied by immunohistochemical methods (including immunoelectron and immunofluorescent microscopies) with anti-TTX antibodies. Sequencing of 16S rRNA gene of the strain 1839 showed that it is most likely Bacillus sp. CU040510-015 and Bacillus asahii. Based on its morphological and biochemical properties, however we suppose that the isolated Bacillus sp. 1839 should be classified as representing a new species. Microdistribution of TTX in bacterial cell was investigated under electron microscope by immunoenzymatic methods. TTX was concentrated in the forespore and free spores, but it was not detected in the vegetative cells of Bacillus sp. 1839. We suggest that release of free mature spores from sporangium of Bacillus sp. 1839 leads to appearance of toxin in tissues of C. simula. Confocal laser-scanning microscopy (CLSM) method with anti-TTX antibodies can be recommended for preliminary detection of apparent TTX accumulation. PMID:24813332

  8. Antibiofilm Activity of the Marine Bacterium Pseudoalteromonas sp. Strain 3J6▿

    PubMed Central

    Dheilly, Alexandra; Soum-Soutéra, Emmanuelle; Klein, Géraldine L.; Bazire, Alexis; Compère, Chantal; Haras, Dominique; Dufour, Alain

    2010-01-01

    Biofilm formation results in medical threats or economic losses and is therefore a major concern in a variety of domains. In two-species biofilms of marine bacteria grown under dynamic conditions, Pseudoalteromonas sp. strain 3J6 formed mixed biofilms with Bacillus sp. strain 4J6 but was largely predominant over Paracoccus sp. strain 4M6 and Vibrio sp. strain D01. The supernatant of Pseudoalteromonas sp. 3J6 liquid culture (SN3J6) was devoid of antibacterial activity against free-living Paracoccus sp. 4M6 and Vibrio sp. D01 cells, but it impaired their ability to grow as single-species biofilms and led to higher percentages of nonviable cells in 48-h biofilms. Antibiofilm molecules of SN3J6 were able to coat the glass surfaces used to grow biofilms and reduced bacterial attachment about 2-fold, which might partly explain the biofilm formation defect but not the loss of cell viability. SN3J6 had a wide spectrum of activity since it affected all Gram-negative marine strains tested except other Pseudoalteromonas strains. Biofilm biovolumes of the sensitive strains were reduced 3- to 530-fold, and the percentages of nonviable cells were increased 3- to 225-fold. Interestingly, SN3J6 also impaired biofilm formation by three strains belonging to the human-pathogenic species Pseudomonas aeruginosa, Salmonella enterica, and Escherichia coli. Such an antibiofilm activity is original and opens up a variety of applications for Pseudoalteromonas sp. 3J6 and/or its active exoproducts in biofilm prevention strategies. PMID:20363799

  9. Antioxidative and radioprotective activities of semiquinone glucoside derivative (SQGD) isolated from Bacillus sp. INM-1.

    PubMed

    Kumar, Raj; Bansal, Deen Dayal; Patel, Dev Dutt; Mishra, Saurabh; Karamalakova, Yana; Zheleva, A; Gadjeva, Vessilina; Sharma, Rakesh Kumar

    2011-03-01

    A semiquinone glucoside derivative (SQGD) was isolated from a radioresistant bacterium Bacillus sp. INM-1 and its antioxidant and radioprotective activities were evaluated using in vitro assays. Natural stable free radical properties of SQGD in solid as well as in solution form were estimated using Electron Paramagnetic Resonance (EPR) spectrometry. Results of the study were demonstrated high reducing power (1.267 ± 0.03356 U(abs)) and nitric oxide radicals scavenging activity (34.684 ± 2.132%) of SQGD. Maximum lipid peroxidation inhibitory activity of SQGD was found to be 74.09 ± 0.08% at 500 μg/ml concentration. Similarly, significant (39.54%; P < 0.05) protection to the liposomal artificial membrane against gamma radiation was observed by SQGD in terms of neutralization of gamma radiation-induced TBARS radicals in vitro. OH(-) radicals scavenging efficacy of SQGD was estimated in terms of % inhibition in deoxy D: -ribose degradation by non-site-specific and site-specific assay. The maximum (54.01 ± 1.01%) inhibition of deoxy D: -ribose degradation was observed in non-site-specific manner, whereas, site-specific inhibition was observed to be 46.36 ± 0.5% at the same concentration (250 μg/ml) of SQGD. EPR spectroscopic analysis of the SQGD indicated ~80% reduction of DPPH radicals at 6.4% concentration. EPR spectral analysis of SQGD was revealed an appearance of very strong EPR signal of 2.00485 (crystalline form) and 2.00520 (solution form) g(y) tensor value, which were an established characteristic of o-semiquinone radicals. Therefore, it can be concluded that SQGD is a natural stable o-semiquinone-type radical, possessing strong antioxidant activities and can effectively neutralize radiation induced free radicals in biological system. PMID:21116688

  10. Bioethanol production from mannitol by a newly isolated bacterium, Enterobacter sp. JMP3.

    PubMed

    Wang, Jing; Kim, Young Mi; Rhee, Hong Soon; Lee, Min Woo; Park, Jong Moon

    2013-05-01

    In this study a new bacterium capable of growing on brown seaweed Laminaria japonica, Enterobacter sp. JMP3 was isolated from the gut of turban shell, Batillus cornutus. In anaerobic condition, it produced high yields of ethanol (1.15 mol-EtOH mol-mannitol(-1)) as well as organic acids from mannitol, the major carbohydrate component of L. japonica. Based on carbon distribution and metabolic flux analysis, it was revealed that mannitol was more favorable than glucose for ethanol production due to their different redox states. This indicates that L. japonica is one of the promising feedstock for bioethanol production. Additionally, the mannitol dehydrogenation pathway in Enterobacter sp. JMP3 was examined and verified. Finally, an attempt was made to explore the possibility of controlling ethanol production by altering the redox potential via addition of external NADH in mannitol fermentation. PMID:23186687

  11. Metabolism of Kaempferia parviflora polymethoxyflavones by human intestinal bacterium Bautia sp. MRG-PMF1.

    PubMed

    Kim, Mihyang; Kim, Nayoung; Han, Jaehong

    2014-12-24

    Poylmethoxyflavones (PMFs) are major bioactive flavonoids, which exhibit various biological activities, such as anticancer effects. The biotransformation of PMFs and characterization of a PMF-metabolizing human intestinal bacterium were studied herein for the first time. Hydrolysis of aryl methyl ether functional groups by human fecal samples was observed from the bioconversion of various PMFs. Activity-guided screening for PMF-metabolizing intestinal bacteria under anaerobic conditions resulted in the isolation of a strict anaerobic bacterium, which was identified as Blautia sp. MRG-PMF1. The isolated MRG-PMF1 was able to metabolize various PMFs to the corresponding demethylated flavones. The microbial conversion of bioactive 5,7-dimethoxyflavone (5,7-DMF) and 5,7,4'-trimethoxyflavone (5,7,4'-TMF) was studied in detail. 5,7-DMF and 5,7,4'-TMF were completely metabolized to 5,7-dihydroxyflavone (chrysin) and 5,7,4'-trihydroxyflavone (apigenin), respectively. From a kinetics study, the methoxy group on the flavone C-7 position was found to be preferentially hydrolyzed. 5-Methoxychrysin, the intermediate of 5,7-DMF metabolism by Blautia sp. MRG-PMF1, was isolated and characterized by nuclear magnetic resonance spectroscopy. Apigenin was produced from the sequential demethylation of 5,7,4'-TMF, via 5,4'-dimethoxy-7-hydroxyflavone and 7,4'-dihydroxy-5-methoxyflavone (thevetiaflavone). Not only demethylation activity but also deglycosylation activity was exhibited by Blautia sp. MRG-PMF1, and various flavonoids, including isoflavones, flavones, and flavanones, were found to be metabolized to the corresponding aglycones. The unprecedented PMF demethylation activity of Blautia sp. MRG-PMF1 will expand our understanding of flavonoid metabolism in the human intestine and lead to novel bioactive compounds. PMID:25437273

  12. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    PubMed Central

    Taghavi, Safiyh; van der Lelie, Daniel; Hoffman, Adam; Zhang, Yian-Biao; Walla, Michael D.; Vangronsveld, Jaco; Newman, Lee; Monchy, Sébastien

    2010-01-01

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa×deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT–PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  13. Draft genome sequence of Bacillus okhensis Kh10-101T, a halo-alkali tolerant bacterium from Indian saltpan.

    PubMed

    Krishna, Pilla Sankara; Sreenivas, Ara; Singh, Deepak Kumar; Shivaji, Sisinthy; Prakash, Jogadhenu S S

    2015-12-01

    We report the 4.86-Mb draft genome sequence of Bacillus okhensis strain Kh10-101T, a halo-alkali tolerant rod shaped bacterium isolated from a salt pan near port of Okha, India. This bacterium is a potential model to study the molecular response of bacteria to salt as well as alkaline stress, as it thrives under both high salt and high pH conditions. The draft genome consist of 4,865,284 bp with 38.2% G + C, 4952 predicted CDS, 157 tRNAs and 8 rRNAs. Sequence was deposited at DDBJ/EMBL/GenBank under the project accession JRJU00000000. PMID:26697400

  14. Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India.

    PubMed

    Shashidhar, Ravindranath; Bandekar, Jayant R

    2006-01-01

    A radiation-resistant, Gram-negative and pleomorphic bacterium (CON-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. It was red pigmented, nonmotile, nonsporulating, and aerobic, and contained MK-8 as respiratory quinone. The cell wall of this bacterium contained ornithine. The major fatty acids were C16:0, C16:1, C17:0, C18:1 and iso C18:0. The DNA of CON-1 had a G+C content of 70 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that CON-1 exhibited a maximum similarity (94.72%) with Deinococcus grandis. Based on the genotypic, phenotypic and chemotaxonomic characteristics, the bacterium CON-1 was identified as a new species of the genus Deinococcus, for which the name Deinococcus mumbaiensis sp. nov. is proposed. The type strain of D. mumbaiensis is CON-1 (MTCC 7297(T)=DSM 17424(T)). PMID:16445756

  15. Pseudomonas sp. strain 273, and aerobic {alpha},{omega}-dichloroalkane-degrading bacterium

    SciTech Connect

    Wischnak, C.; Mueller, R.; Loeffler, F.E. |; Li, J.; Urbance, J.W.

    1998-09-01

    A gram-negative, aerobic bacterium was isolated from soil; this bacterium grew in 50% (vol/vol) suspensions of 1,10-dichlorodecane (1,10-DCD) as the sole source of carbon and energy. Phenotypic and small-subunit ribosomal RNA characterizations identified the organism, designated strain 273, as a member of the genus Pseudomonas. After induction with 1,10-DCD, Pseudomonas sp. strain 273 released stoichiometric amounts of chloride from C{sub 5} to C{sub 12} {alpha},{omega}-dichloroalkanes in the presence of oxygen. No dehalogenation occurred under anaerobic conditions. The best substrates for dehalogenation and growth were C{sub 9} to C{sub 12} chloroalkanes. The isolate also grew with nonhalogenated aliphatic compounds, and decane-grown cells dechlorinated 1,10-DCD without a lag phase. In addition, cells grown on decane dechlorinated 1,10-DCD in the presence of chloramphenicol, indicating that the 1,10-DCD-dechlorinating enzyme system was also induced by decane. Other known alkane-degrading Pseudomonas species did not grow with 1,10-DCD as a carbon source. Dechlorination of 1,10-DCD was demonstrated in cell extracts of Pseudomonas sp. strain 273. Cell-free activity was strictly oxygen dependent, and NADH stimulated dechlorination, whereas EDTA had an inhibitory effect.

  16. Characterization of acetonitrile-tolerant marine bacterium Exiguobacterium sp. SBH81 and its tolerance mechanism.

    PubMed

    Kongpol, Ajiraporn; Kato, Junichi; Tajima, Takahisa; Vangnai, Alisa S

    2012-01-01

    A Gram-positive marine bacterium, Exiguobacterium sp. SBH81, was isolated as a hydrophilic organic-solvent tolerant bacterium, and exhibited high tolerance to various types of toxic hydrophilic organic solvents, including acetonitrile, at relatively high concentrations (up to 6% [v/v]) under the growing conditions. Investigation of its tolerance mechanisms illustrated that it does not rely on solvent inactivation processes or modification of cell surface characteristics, but rather, increase of the cell size lowers solvent partitioning into cells and the extrusion of solvents through the efflux system. A test using efflux pump inhibitors suggested that secondary transporters, i.e. resistance nodulation cell division (RND) and the multidrug and toxic compound extrusion (MATE) family, are involved in acetonitrile tolerance in this strain. In addition, its acetonitrile tolerance ability could be stably and significantly enhanced by repetitive growth in the presence of toxic acetonitrile. The marked acetonitrile tolerance of Exiguobacterium sp. SBH81 indicates its potential use as a host for biotechnological fermentation processes as well as bioremediation. PMID:21971080

  17. Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site.

    PubMed

    Sharma, Ashwani; Thakur, Indu Shekhar; Dureja, Prem

    2009-09-01

    Three pentachlorophenol (PCP) degrading bacterial strains were isolated from sediment core of pulp and paper mill effluent discharge site. The strains were continuously enriched in mineral salts medium supplemented with PCP as sole source of carbon and energy. One of the acclimated strains with relatively high PCP degradation capability was selected and characterized in this study. Based on morphology, biochemical tests, 16S rDNA sequence analysis and phylogenetic characteristics, the strains showed greatest similarity with Acinetobacter spp. The strain was identified as Acinetobacter sp. ISTPCP-3. The physiological characteristics and optimum growth conditions of the bacterial strain were investigated. The results of optimum growth temperature revealed that it was a mesophile. The optimum growth temperature for the strain was 30 degrees C. The preferential initial pH for the strain was ranging at 6.5-7.5, the optimum pH was 7. The bacterium was able to tolerate and degrade PCP up to a concentration of 200 mg/l. Increase in PCP concentration had a negative effect on biodegradation rate and PCP concentration above 250 mg/l was inhibitory to its growth. Acinetobacter sp. ISTPCP-3 was able to utilize PCP through an oxidative route with ortho ring-cleavage with the formation of 2,3,5,6-tetrachlorohydroquinone and 2-chloro-1,4-benzenediol, identified using gas chromatograph-mass spectrometric (GC-MS) analysis. The degradation pathway followed by isolated bacterium is different from previously characterized pathway. PMID:19214760

  18. The phototrophic bacterium Rhodopseudomonas capsulata sp108 encodes an indigenous class A beta-lactamase.

    PubMed Central

    Campbell, J I; Scahill, S; Gibson, T; Ambler, R P

    1989-01-01

    The nucleotide sequence of a 2.37 kb DNA fragment derived from cloning a total DNA digest of Rhodopseudomonas capsulata sp108 was determined. The DNA codes for a beta-lactamase, a protein showing sequence similarity to the ampR protein of Enterobacter cloacae and an unidentified open reading frame. Hybridization experiments with a probe carrying DNA from within the beta-lactamase gene suggests a chromosomal location for the coding sequences in strain sp108 and in sp109, a penicillin-sensitive revertant of sp108 in which the enzyme is not inducible. A protein-sequence comparison of the deduced amino acid sequence of the Rps. capsulata beta-lactamase indicates that it is a Class A enzyme and that its sequence can be aligned with those of the characterized beta-lactamases from Staphylococcus aureus, Bacillus licheniformis and the Escherichia coli plasmid (R-TEM enzyme), with only a few insertions or deletions. The corresponding DNA sequence is, however, characteristically rhodopseudomonad, suggesting that it is not a recently transposed gene. Images Fig. 4. PMID:2788410

  19. Whole-Genome Sequence of Bacillus sp. SDLI1, Isolated from the Social Bee Scaptotrigona depilis

    PubMed Central

    Paludo, Camila R.; Silva-Junior, Eduardo A.; Pishchany, Gleb; Currie, Cameron R.; Nascimento, Fábio S.; Kolter, Roberto G.

    2016-01-01

    We announce the complete genome sequence of Bacillus sp. strain SDLI1, isolated from larval gut of the stingless bee Scaptotrigona depilis. The 4.13-Mb circular chromosome harbors biosynthetic gene clusters for the production of antimicrobial compounds. PMID:27013050

  20. Functional genomic approaches for understanding the mode of action of Bacillus sp biocontrol strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequencing of several Bacillus sp. strains has shed new light on the mode of action of these antagonists of plant pathogens. The use of genomic data mining tools provided the ability to quickly determine the potential of these strains to produce bioactive secondary metabolites. Our B...

  1. Draft Genome Sequence of the Nitrate- and Phosphate-Accumulating Bacillus sp. Strain MCC0008

    PubMed Central

    DebRoy, Shreya; Bhattacharjee, Amrita; Thakur, Ashoke Ranjan

    2013-01-01

    Here, we report the draft genome sequence of the nitrate- and phosphate-accumulating Bacillus sp. strain MCC0008, isolated from a consortium enriched from municipal sewage in nitrate broth (HiMedia M439). The total size of the genome is 5,609,456 bp, with a G+C content of 35.1%. PMID:23409265

  2. Bacillus glycinifermentans sp. nov., isolated from fermented soybean paste

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two independent isolates of a Gram-positive, aerobic, motile rod-shaped bacterium were recovered from soybean-based fermented foodstuffs. Two were isolated from cheonggukjang, a Korean fermented soybean food product. Multilocus sequencing analysis of the 16S rRNA gene and 5 protein coding genes indi...

  3. Bacillus paralicheniformis sp. nov., isolated from fermented soybean paste

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An isolate of a Gram-positive, facultatively anaerobic, motile, rod-shaped, endospore forming bacterium was recovered from soybean-based fermented paste. It was isolated from cheonggukjang, a Korean fermented soybean food product. Phylogenetic analysis of the 16S rRNA gene indicated that the strain ...

  4. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638

    SciTech Connect

    Taghavi, S.; van der Lelie, D.; Hoffman, A.; Zhang, Y.-B.; Walla, M. D.; Vangronsveld, J.; Newman, L.; Monchy, S.

    2010-05-13

    Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpa x deltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to

  5. Optimization of Chromium Removal by the Indigenous Bacterium Bacillus spp. REP02 Using the Response Surface Methodology

    PubMed Central

    Venil, C. K.; Mohan, V.; Lakshmanaperumalsamy, P.; Yerima, M. B.

    2011-01-01

    An indigenous bacterium, Bacillus REP02, was isolated from locally sourced chromium electroplating industrial effluents. Response surface methodology was employed to optimize the five critical medium parameters responsible for higher % Cr2+ removal by the bacterium Bacillus REP02. A three-level Box-Behnken factorial design was used to optimize K2HPO4, yeast extract, MgSO4, NH4NO3, and dextrose for Cr2+ removal. A coefficient of determination (R2) value (0.93), model F-value (3.92) and its low P-value (F < 0.0008) along with lower value of coefficient of variation (5.39) indicated the fitness of response surface quadratic model during the present study. At optimum parameters of K2HPO4 (0.6 g L−1), yeast extract (5.5 g L−1), MgSO4 (0.04 g L−1), NH4NO3 (0.20 g L−1), and dextrose (12.50 g L−1), the model predicted 98.86% Cr2+ removal, and experimentally, 99.08% Cr2+ removal was found. PMID:23724315

  6. Pyruvatibacter mobilis gen. nov., sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122.

    PubMed

    Wang, Guanghua; Tang, Mingxing; Wu, Hualian; Dai, Shikun; Li, Tao; Chen, Chenghao; He, Hui; Fan, Jiewei; Xiang, Wenzhou; Li, Xiang

    2016-01-01

    A Gram-stain-negative, aerobic bacterium, designated strain GYP-11T, was isolated from the culture broth of a marine microalga, Picochloruma sp. 122. Cells were dimorphic rods; free living cells were motile by means of a single polar flagellum, and star-shaped-aggregate-forming cells were attached with stalks and non-motile. Sodium pyruvate or Tween 20 was required for growth on marine agar 2216.16S rRNA gene sequence analysis revealed that this isolate shared 94.07 % similarity with its closest type strain, Parvibaculum hydrocarboniclasticum EPR92T. Phylogenetic analyses indicated that strain GYP-11T represents a distinct lineage in a robust clade consisting of strain GYP-11T, alphaproteobacterium GMD21A06 and Candidatus Phaeomarinobacter ectocarpi Ec32. This clade was close to the genera Parvibaculum and Tepidicaulis in the order Rhizobiales. Chemotaxonomic and physiological characteristics, including cellular fatty acids and carbon source profiles, also readily distinguished strain GYP-11T from all established genera and species. Thus, it is concluded that strain GYP-11T represents a novel species of a new genus in the order Rhizobiales, for which the name Pyruvatibacter mobilis gen. nov., sp. nov. is proposed. The type strain of Pyruvatibacter mobilis is GYP-11T ( = CGMCC 1.15125T = KCTC 42509T). PMID:26476620

  7. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions

    PubMed Central

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Hosseini Salekdeh, Ghasem; Karimi, Keikhosro

    2016-01-01

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated. PMID:26725518

  8. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions.

    PubMed

    Amiri, Hamid; Azarbaijani, Reza; Parsa Yeganeh, Laleh; Shahzadeh Fazeli, Abolhassan; Tabatabaei, Meisam; Salekdeh, Ghasem Hosseini; Karimi, Keikhosro

    2016-01-01

    The moderately halophilic bacterium Nesterenkonia sp. strain F, which was isolated from Aran-Bidgol Lake (Iran), has the ability to produce acetone, butanol, and ethanol (ABE) as well as acetic and butyric acids under aerobic and anaerobic conditions. This result is the first report of ABE production with a wild microorganism from a family other than Clostridia and also the first halophilic species shown to produce butanol under aerobic cultivation. The cultivation of Nesterenkonia sp. strain F under anaerobic conditions with 50 g/l of glucose for 72 h resulted in the production of 105 mg/l of butanol, 122 mg/l of acetone, 0.2 g/l of acetic acid, and 2.5 g/l of butyric acid. Furthermore, the strain was cultivated on media with different glucose concentrations (20, 50, and 80 g/l) under aerobic and anaerobic conditions. Through fermentation with a 50 g/l initial glucose concentration under aerobic conditions, 66 mg/l of butanol, 125 mg/l of acetone, 291 mg/l of ethanol, 5.9 g/l of acetic acid, and 1.2 g/l of butyric acid were produced. The enzymes pertaining to the fermentation pathway in the strain were compared with the enzymes of Clostridium spp., and the metabolic pathway of fermentation used by Nesterenkonia sp. strain F was investigated. PMID:26725518

  9. Ieodoglucomide C and Ieodoglycolipid, New Glycolipids from a Marine-Derived Bacterium Bacillus licheniformis 09IDYM23.

    PubMed

    Tareq, Fakir Shahidullah; Lee, Hyi-Seung; Lee, Yeon-Ju; Lee, Jong Seok; Shin, Hee Jae

    2015-05-01

    Chemical examination of the ethyl acetate extract from the fermentation broth of the marine-derived bacterium Bacillus licheniformis resulted in the isolation of two new glycolipids, ieodoglucomide C (1) and ieodoglycolipid (2). The structural characterization of 1 and 2 was achieved by extensive spectroscopic evidence, including 2D NMR experiments. A combination of chemical derivatization techniques followed by NMR studies, LC-MS data analysis and a literature review was deployed for the establishment of the stereo-configurations of 1 and 2. Compounds 1 and 2 exhibited good antibiotic properties against Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, Salmonella typhi, Escherichia coli and Pseudomonas aeruginosa with MICs ranging from 0.01 to 0.05 μM. Furthermore, the antifungal activity of 1 and 2 was evaluated against plant pathogenic fungi Aspergillus niger, Rhizoctonia solani, Botrytis cinerea and Colletotrichum acutatum as well as the human pathogen Candida albicans. Compounds 1 and 2 inhibited the mycelial growth of these pathogens with MIC values of 0.03-0.05 μM, revealing that these compounds are good candidates for the development of new fungicides. PMID:25893812

  10. Selective inhibition of toxic cyanobacteria by β-carboline-containing bacterium Bacillus flexus isolated from Saudi freshwaters

    PubMed Central

    Alamri, Saad A.; Mohamed, Zakaria A.

    2013-01-01

    A bacterial strain SSZ01 isolated from a eutrophic lake in Saudi Arabia dominated by cyanobacterial blooms, showed an antialgal activity against cyanobacteria species. Based on the analysis of the 16S rDNA gene sequence, the isolated strain (SSZ01) most likely belonged to the genus Bacillus with a 99% similarity to Bacillus flexus strain EMGA5. The thin layer chromatography (TLC) analysis of the ethyl acetate extract of this bacterium revealed that this strain can produce harmine and norharmane compared to different β-carboline analog standards. Harmine and norharmane were also detected in considerable amounts in bacterial growth medium, indicating a potential excretion of these compounds into the aquatic environment. The crude extract of Bacillus flexus as well as pure materials of harmine and norharmane inhibited the growth of tested species of cyanobacteria. However, the bacterial crude extract has a higher toxicity against tested species of cyanobacteria than harmine and norharmane. In addition, harmine was more toxic to cyanobacteria than norharmane. On the other hand, neither pure compounds of harmine and norharmane nor crude bacterial extract showed any antialgal activity against tested species of green algae. The results of the present study suggest that B. flexus SSZ01 or its crude extract containing harmine and norharmane could be a candidate for the selective control of cyanobacterial blooms without affecting other algal species. PMID:24235872

  11. Cloning and expression in Escherichia coli of chromosomal mercury resistance genes from a Bacillus sp

    SciTech Connect

    Wang, Y.; Mahler, I.; Levinson, H.S.; Halvorson, H.O.

    1987-10-01

    A 7.9-kilobase (kb) chromosomal fragment was cloned from a mercury-resistant Bacillus sp. In Escherichia coli, in the presence of a second plasmid carrying functional transport genes, resistance to HgCl/sub 2/ and to phenylmercury acetate (PMA) was expressed. Shortening the cloned fragment to 3.8 kb abolished resistance to PMA but not to HgCl/sub 2/. In Bacillus subtilis, the 3.8-kb fragment produced mercuric reductase constitutively but did not produce resistance to HgCl/sub 2/ or to PMA.

  12. Continuous Cultivation for Apparent Optimization of Defined Media for Cellulomonas sp. and Bacillus cereus

    PubMed Central

    Summers, R. J.; Boudreaux, D. P.; Srinivasan, V. R.

    1979-01-01

    Steady-state continuous culture was used to optimize lean chemically defined media for a Cellulomonas sp. and Bacillus cereus strain T. Both organisms were extremely sensitive to variations in trace-metal concentrations. However, medium optimization by this technique proved rapid, and multifactor screening was easily conducted by using a minimum of instrumentation. The optimized media supported critical dilution rates of 0.571 and 0.467 h−1 for Cellulomonas and Bacillus, respectively. These values approximated maximum growth rate values observed in batch culture. PMID:16345417

  13. NH4+ transport system of a psychrophilic marine bacterium, Vibrio sp. strain ABE-1.

    PubMed

    Chou, M; Matsunaga, T; Takada, Y; Fukunaga, N

    1999-05-01

    NH4(+) transport system of a psychrophilic marine bacterium Vibrio sp. strain ABE-1 (Vibrio ABE-1) was examined by measuring the uptake of [14C]methylammonium ion (14CH3NH3+) into the intact cells. 14CH3NH3+ uptake was detected in cells grown in medium containing glutamate as the sole nitrogen source, but not in those grown in medium containing NH4Cl instead of glutamate. Vibrio ABE-1 did not utilize CH3NH3+ as a carbon or nitrogen source. NH4Cl and nonradiolabeled CH3NH3+ completely inhibited 14CH3NH3+ uptake. These results indicate that 14CH3NH3+ uptake in this bacterium is mediated via an NH4+ transport system and not by a specific carrier for CH3NH3+. The respiratory substrate succinate was required to drive 14CH3NH3+ uptake and the uptake was completely inhibited by KCN, indicating that the uptake was energy dependent. The electrochemical potentials of H+ and/or Na+ across membranes were suggested to be the driving forces for the transport system because the ionophores carbonylcyanide m-chlorophenylhydrazone and monensin strongly inhibited uptake activities at pH 6.5 and 8.5, respectively. Furthermore, KCl activated 14CH3NH3+ uptake. The 14CH3NH3+ uptake activity of Vibrio ABE-1 was markedly high at temperatures between 0 degrees and 15 degrees C, and the apparent Km value for CH3NH3+ of the uptake did not change significantly over the temperature range from 0 degrees to 25 degrees C. Thus, the NH4+ transport system of this bacterium was highly active at low temperatures. PMID:10356994

  14. Pontibacter diazotrophicus sp. nov., a Novel Nitrogen-Fixing Bacterium of the Family Cytophagaceae

    PubMed Central

    Xu, Linghua; Zeng, Xian-Chun; Nie, Yao; Luo, Xuesong; Zhou, Enmin; Zhou, Lingli; Pan, Yunfan; Li, Wenjun

    2014-01-01

    Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod-shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15∶0, C16∶1ω5c, summed feature 3 (containing C16∶1ω6c and/or C16∶1ω7c) and summed feature 4 (comprising anteiso-C17∶1B and/or iso-C17∶1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium. PCR amplification suggested that the bacterium possesses at least one type of nitrogenase gene. Acetylene reduction assay showed that H4XT actually possesses nitrogen-fixing activity. Therefore, it can be concluded that H4XT is a new diazotroph. We thus referred it to as Pontibacter diazotrophicus sp. nov. The type strain is H4XT ( = CCTCC AB 2013049T = NRRL B-59974T). PMID:24647674

  15. Roseovarius aquimarinus sp. nov., a slightly halophilic bacterium isolated from seawater.

    PubMed

    Kang, Hyeonji; Kim, Jong-Hwa; Jeon, Che Ok; Yoon, Jung-Hoon; Kim, Wonyong

    2015-12-01

    A Gram-stain-negative, non-spore-forming, rod-shaped, motile, facultatively anaerobic bacterium, designated CAU 1059T, was isolated from a seawater sample from Jeju Island, Republic of Korea. The bacterium grew optimally at 37 °C, at pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1059T belonged to the genus Roseovarius. It exhibited only 91.5-96.9 % sequence similarity to the type strains of recognized Roseovarius species. Similar to other species of the genus Roseovarius, strain CAU 1059T had ubiquinone-10 (Q-10) as the predominant ubiquinone and C16 : 0 and summed feature 8 (C18 : 1ω7c/ω6c) as the major fatty acids. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine; three unidentified phospholipids, two aminolipids, an aminophospholipid and nine other lipids were also found. The G+C content of the genomic DNA was 61.9 mol%. On the basis of the data provided, strain CAU 1059T should be classified as representing a novel species of the genus Roseovarius, for which the name Roseovarius aquimarinus sp. nov. is proposed. The type strain is CAU 1059T ( = KCTC 32014T = CCUG 64792T). PMID:26374629

  16. Alicyclobacillus vulcanalis sp. nov., a thermophilic, acidophilic bacterium isolated from Coso Hot Springs, California, USA.

    PubMed

    Simbahan, Jessica; Drijber, Rhae; Blum, Paul

    2004-09-01

    A thermo-acidophilic Gram-positive bacterium, strain CsHg2T, which grows aerobically at 35-65 degrees C (optimum 55 degrees C) and at pH 2.0-6.0 (optimum 4.0), was isolated from a geothermal pool located in Coso Hot Springs in the Mojave Desert, California, USA. Phylogenetic analysis of 16S rRNA gene sequences showed that this bacterium was most closely related to the type strains of Alicyclobacillus acidocaldarius (97.8 % identity) and Alicyclobacillus sendaiensis (96.9 %), three Japanese strains denoted as UZ-1, KHA-31 and MIH 332 (96.1-96.5 %) and Alicyclobacillus genomic species FR-6 (96.3 %). Phenotypic characteristics including temperature and pH optima, G+C composition, acid production from a variety of carbon sources and sensitivity to different metal salts distinguished CsHg2T from A. acidocaldarius, A. sendaiensis and FR-6. The cell lipid membrane was composed mainly of omega-cyclohexyl fatty acid, consistent with membranes from other Alicyclobacillus species. Very low DNA-DNA hybridization values between CsHg2T and the type strains of Alicyclobacillus indicate that CsHg2T represents a distinct species. On the basis of these results, the name Alicyclobacillus vulcanalis sp. nov. is proposed for this organism. The type strain is CsHg2T (ATCC BAA-915T = DSM 16176T). PMID:15388732

  17. Co-metabolism of DDT by the newly isolated bacterium, Pseudoxanthomonas sp. wax

    PubMed Central

    Wang, Guangli; Zhang, Ji; Wang, Li; Liang, Bin; Chen, Kai; Li, Shunpeng; Jiang, Jiandong

    2010-01-01

    Microbial degradation of 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) is the most promising way to clean up DDT residues found in the environment. In this paper, a bacterium designated as wax, which was capable of co-metabolizing DDT with other carbon sources, was isolated from a long-term DDT-contaminated soil sample by an enrichment culture technique. The new isolate was identified as a member of the Pseudoxanthomonas sp., based on its morphological, physiological and biochemical properties, as well as by 16S rRNA gene analysis. In the presence of 100 mg l-1 glucose, the wax strain could degrade over 95% of the total DDT, at a concentration of 20 mg l-1, in 72 hours, and could degrade over 60% of the total DDT, at a concentration of 100 mg l-1, in 144 hours. The wax strain had the highest degradation efficiency among all of the documented DDT-degrading bacteria. The wax strain could efficiently degrade DDT at temperatures ranging from 20 to 37°C, and with initial pH values ranging from 7 to 9. The bacterium could also simultaneously co-metabolize 1,1-dichloro-2,2-bis(p-chlorophenyl)ethane (DDD), 2,2-bis(p-chlorophenyl)-1,1-dichlorethylene (DDE), and other organochlorine compounds. The wax strain could also completely remove 20 mg kg-1 of DDT from both sterile and non-sterile soils in 20 days. This study demonstrates the significant potential use of Pseudoxanthomonas sp. wax for the bioremediation of DDT in the environment. PMID:24031514

  18. Rhizobium sp. strain BN4 (a selenium oxyanion-reducing bacterium) 16S rRNA gene complete sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study used 1482 base pair 16S rRNA gene sequence methods in conjunction with other biochemical and morphological studies to confirm the identification of a bacterium (refer to as the BN4 strain) as a Rhizobium sp. The 16S rRNA gene sequence places it with the Rhizobium clade that includes R. d...

  19. Draft Genome Sequence of Chryseobacterium sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste.

    PubMed

    Park, Gun-Seok; Hong, Sung-Jun; Lee, Chang-Hyun; Khan, Abdur Rahim; Ullah, Ihsan; Jung, Byung Kwon; Choi, JungBae; Kwak, Yunyoung; Back, Chang-Gi; Jung, Hee-Young; Shin, Jae-Ho

    2014-01-01

    Chryseobacterium sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes. PMID:25428979

  20. Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium.

    PubMed

    Smith, Heidi; Akiyama, Tatsuya; Foreman, Christine; Franklin, Michael; Woyke, Tanja; Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Goodwin, Lynne; Gu, Wei; Xu, Yan; Chain, Patrick

    2013-01-01

    Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight as to the mechanisms necessary for bacteria to survive in UV-stressed icy environments. PMID:24265494

  1. Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil.

    PubMed

    Tonomura, Mimori; Ehara, Ayaka; Suzuki, Haruo; Amachi, Seigo

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified. PMID:25977440

  2. Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil

    PubMed Central

    Tonomura, Mimori; Ehara, Ayaka; Suzuki, Haruo

    2015-01-01

    Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified. PMID:25977440

  3. Draft Genome Sequence of Vibrio sp. Strain Evh12, a Bacterium Retrieved from the Gorgonian Coral Eunicella verrucosa

    PubMed Central

    Franco, Telma; Califano, Gianmaria; Gonçalves, Ana C. S.; Cúcio, Catarina

    2016-01-01

    To shed light on the associations established between Vibrio species and soft corals in coastal ecosystems, we report here the draft genome sequence of Vibrio sp. strain Evh12, a bacterium that has been isolated from the gorgonian coral Eunicella verrucosa and that shows antagonistic activity against Escherichia coli. PMID:26868405

  4. Draft Genome Sequence and Description of Janthinobacterium sp. Strain CG3, a Psychrotolerant Antarctic Supraglacial Stream Bacterium

    PubMed Central

    Smith, Heidi; Akiyama, Tatsuya; Franklin, Michael; Woyke, Tanja; Teshima, Hazuki; Davenport, Karen; Daligault, Hajnalka; Erkkila, Tracy; Goodwin, Lynne; Gu, Wei; Xu, Yan; Chain, Patrick

    2013-01-01

    Here we present the draft genome sequence of Janthinobacterium sp. strain CG3, a psychrotolerant non-violacein-producing bacterium that was isolated from the Cotton Glacier supraglacial stream. The genome sequence of this organism will provide insight as to the mechanisms necessary for bacteria to survive in UV-stressed icy environments. PMID:24265494

  5. Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus).

    PubMed

    Jeong, Jin-Ju; Park, Byeong Hyeok; Park, Hongjae; Choi, In-Geol; Kim, Ki Deok

    2016-01-01

    Chryseobacterium sp. strain GSE06 is a biocontrol endophytic bacterium against the destructive soilborne oomycete Phytophthora capsici, which causes Phytophthora blight of pepper. Here, we present its draft genome sequence, which contains genes related to biocontrol traits, such as colonization, antimicrobial activity, plant growth promotion, and abiotic or biotic stress adaptation. PMID:27313310

  6. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment.

    PubMed

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant'Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano; Passaglia, Luciane M P

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. PMID:25838495

  7. Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment

    PubMed Central

    Pereira, Jamile Queiroz; Ambrosini, Adriana; Sant’Anna, Fernando Hayashi; Tadra-Sfeir, Michele; Faoro, Helisson; Pedrosa, Fábio Oliveira; Souza, Emanuel Maltempi; Brandelli, Adriano

    2015-01-01

    Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments. PMID:25838495

  8. Draft Genome Sequence of Chryseobacterium sp. Strain GSE06, a Biocontrol Endophytic Bacterium Isolated from Cucumber (Cucumis sativus)

    PubMed Central

    Jeong, Jin-Ju; Park, Byeong Hyeok; Park, Hongjae

    2016-01-01

    Chryseobacterium sp. strain GSE06 is a biocontrol endophytic bacterium against the destructive soilborne oomycete Phytophthora capsici, which causes Phytophthora blight of pepper. Here, we present its draft genome sequence, which contains genes related to biocontrol traits, such as colonization, antimicrobial activity, plant growth promotion, and abiotic or biotic stress adaptation. PMID:27313310

  9. Anaerobic utilization of phosphite and hypophosphite by Bacillus sp.

    NASA Technical Reports Server (NTRS)

    Foster, T. L.; Winans, L., Jr.; Helms, S. J. S.

    1978-01-01

    A Bacillus species capable of using phosphite and hypophosphite under anaerobic conditions was isolated from Cape Canaveral soil samples and grown on a glucose-mineral salts medium with phosphate omitted. The optimum hypophosphite concentration was 60 microg/ml, while the optimum phosphite concentration was greater than 1000 microg/ml. P-32-labeled hypophosphite was incorporated into the cell as organic phosphate, and little or no phosphate appeared in the medium when either hypophosphite or phosphite was the phosphorus source. When phosphate was present in the medium, phosphite was not metabolized. When both phosphite and hypophosphite were present, phosphite was used first and then hypophosphite.

  10. Isolation of proline-based cyclic dipeptides from Bacillus sp. N strain associated with rhabditid [corrected] entomopathogenic nematode and its antimicrobial properties.

    PubMed

    Kumar, Nishanth; Mohandas, C; Nambisan, Bala; Kumar, D R Soban; Lankalapalli, Ravi S

    2013-02-01

    Entomopathogenic nematodes (EPN) are well-known as biological control agents and are found to have associated bacteria which can produce a wide range of bioactive secondary metabolites. We report herewith isolation of six proline containing cyclic dipeptides cyclo(D-Pro-L-Leu), cyclo(L-Pro-L-Met), cyclo(D-Pro-L-Phe), cyclo(L-Pro-L-Phe), cyclo(L-Pro-L-Tyr) and cyclo(L-Pro-D-Tyr) from ethyl acetate extract of the Luria Broth (LB) cell free culture filtrate of Bacillus sp. strain N associated with a new EPN Rhabditis sp. from sweet potato weevil grubs collected from Central Tuber Crops Research Institute farm. Antimicrobial studies of these 2,5-diketopiperazines (DKPs) against both medicinally and agriculturally important bacterium and fungi showed potent inhibitory values in the range of μg/mL. Cyclic dipeptides showed significantly higher activity than the commercial fungicide bavistin against agriculturally important fungi, viz., Fusarium oxysporum, Rhizoctonia solani, and Pencillium expansum. The highest activity of 2 μg/mL by cyclo(L-Pro-L-Phe) was recorded against P. expansum, a plant pathogen responsible for causing post harvest decay of stored apples and oranges. To our knowledge, this is the first report on the isolation of these DKPs from Rhabditis EPN bacterial strain Bacillus sp. PMID:23065379

  11. [Probiotic features of carotene producing strains Bacillus sp. 1.1 and B. amyloliquefaciens UCM B-5113].

    PubMed

    Avdeeva, L V; Nechypurenko, O O; Kharhota, M A

    2015-01-01

    Researched probiotic properties of carotinproducing strains Bacillus sp. 1.1 and B. amyloliquefaciens UCM B-5113. It was established that Bacillus sp. 1.1 characterized by high and middle antagonistic activity against museums and actual test cultures and B. amyloliquefaciens UCM B-5113 shown middle and low activity. They grew up and formed a pigment at pH 6.0 in the presence of 0.4% bile. Bacillus sp. 1.1 and B. amyloliquefaciens UCM B-5113 were avirulent, had low antagonistic activity and characterized by susceptibility to antimicrobial agents, excluding colistin. The results suggested the possibility to create based on Bacillus sp. 1.1 and B. amyloliquefaciens UCM B-5113 probiotic preparation. PMID:26036029

  12. Efficient Degradation of Feather by Keratinase Producing Bacillus sp.

    PubMed Central

    Jeevana Lakshmi, P.; Kumari Chitturi, Ch. M.; Lakshmi, V. V.

    2013-01-01

    Keratinase producing microorganisms are being increasingly utilized for degradation and recycling of poultry feather waste. Two native strains BF11 (Bacillus subtilis) and BF21 (Bacillus cereus) degrading keratin completely were characterized. The native strains produced more than 10 KU/mL of enzyme. Strain improvement resulted in isolation of MBF11 and MBF21 from BF11 and BF21 isolates, respectively. Optimization of nutritional and physical parameters of these MBF isolates at laboratory scale increased the overall keratinase activity by 50-fold resulting in a yield of 518–520 KU/mL. Fermentation media designed with starch as carbon source and soya bean meal as nitrogen source supported high levels of enzyme production. The optimum conditions for enzyme production were determined to be pH 8.5 and temperatures of 45–55°C for MBF11 and 37°C for MBF21, respectively. Culture filtrate showed a significant increase in the amounts of cysteine, cystine, methionine, and total free amino acids during the fermentation period. The ratio of organic sulphur concentration was also considerably higher than that of the inorganic sulphate in the culture filtrate suggesting the hydrolysis of disulphide by the isolates. PMID:24298284

  13. Draft Genome Sequence of Bacillus cecembensis PN5T (DSM 21993), a Psychrotolerant Bacterium Isolated from Soil Samples near the Pindari Glacier

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Ge, Ci-bin; Chen, Qian-qian; Che, Jian-mei; Chen, De-ju

    2016-01-01

    Bacillus cecembensis PN5T is a Gram-positive, aerobic, and spore-forming bacterium with very high intrinsic heat resistance. Here, we report the 4.72-Mb draft genome sequence of B. cecembensis PN5T, the first genome sequence of this species, which will promote its fundamental research. PMID:26847893

  14. Draft Genome Sequence of Bacillus muralis LMG 20238T (DSM 16288), a Spore-Forming Bacterium Isolated from Deteriorated Mural Paintings

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Chen, Qianqian; Pan, Zhizhen; Zheng, Xue-fang; Chen, Meichun

    2016-01-01

    Bacillus muralis LMG 20238T is a Gram-positive, aerobic, and spore-forming bacterium. Here, we report the 5.18-Mb draft genome sequence of B. muralis LMG 20238T, which is the first genome sequence of this species and will promote its fundamental research. PMID:26847897

  15. Complete Genome Sequence of Bacillus velezensis CBMB205, a Phosphate-Solubilizing Bacterium Isolated from the Rhizoplane of Rice in the Republic of Korea

    PubMed Central

    Hwangbo, Kyeong; Um, Yurry; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min

    2016-01-01

    Bacillus velezensis CBMB205 (= KACC 13105T = NCCB 100236T) was isolated from the rhizoplane of rice (Oryza sativa L. cv. O-dae). According to previous studies, this bacterium has several genes that can promote plant growth, such as the phosphorus-solubilizing protein-coding gene. Here, we present the first complete genome of B. velezensis CBMB205. PMID:27417835

  16. Formulations of the endophytic bacterium Bacillus subtilis Tu-100 suppress Sclerotinia sclerotiorum on oilseed rape and improve plant vigor in field trials conducted at separate locations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sclerotinia sclerotiorum causes serious yield losses in crops in The People’s Republic of China. Two formulations of oilseed rape seed containing the endophytic bacterium Bacillus subtilis Tu-100 were evaluated for suppression of this pathogen in field trials conducted at two independent locations....

  17. Biosynthesis of silver nanoparticles by a Bacillus sp. of marine origin

    NASA Astrophysics Data System (ADS)

    Janardhanan, A.; Roshmi, T.; Varghese, Rintu T.; Soniya, E. V.; Mathew, Jyothis; Radhakrishnan, E. K.

    2013-04-01

    This study was aimed to explore the nanoparticle synthesizing properties of a silver resistant Bacillus sp. isolated from a marine water sample. The 16SrDNA sequence analysis of the isolate proved it as a Bacillus strain. Very interestingly, the isolate was found to have the ability to form intracellular silver nanoparticles at room temperature within 24 hours. This was confirmed by the UV-Vis absorption analysis which showed a peak at 430 nm corresponding to the plasmon absorbance of silver nanoparticles. Further characterization of the nanoparticles was carried out by transmission electron microscopy (TEM) and scanning electron microscopy (SEM) analysis. The presence of silver nanoparticles with the size less than 100 nm was confirmed. These particles were found to be extremely stable as confirmed by the TEM analysis after three months of purification. So, the current study is the demonstration of an efficient synthesis of stable silver nanoparticles by a marine Bacillus strain.

  18. Development of a genetic system for the deep-sea psychrophilic bacterium Pseudoalteromonas sp. SM9913

    PubMed Central

    2014-01-01

    Background Pseudoalteromonas species are a group of marine gammaproteobacteria frequently found in deep-sea sediments, which may play important roles in deep-sea sediment ecosystem. Although genome sequence analysis of Pseudoalteromonas has revealed some specific features associated with adaptation to the extreme deep-sea environment, it is still difficult to study how Pseudoalteromonas adapt to the deep-sea environment due to the lack of a genetic manipulation system. The aim of this study is to develop a genetic system in the deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913, making it possible to perform gene mutation by homologous recombination. Results The sensitivity of Pseudoalteromonas sp. SM9913 to antibiotic was investigated and the erythromycin resistance gene was chosen as the selective marker. A shuttle vector pOriT-4Em was constructed and transferred into Pseudoalteromonas sp. SM9913 through intergeneric conjugation with an efficiency of 1.8 × 10-3, which is high enough to perform the gene knockout assay. A suicide vector pMT was constructed using pOriT-4Em as the bone vector and sacB gene as the counterselective marker. The epsT gene encoding the UDP-glucose lipid carrier transferase was selected as the target gene for inactivation by in-frame deletion. The epsT was in-frame deleted using a two-step integration–segregation strategy after transferring the suicide vector pMT into Pseudoalteromonas sp. SM9913. The ΔepsT mutant showed approximately 73% decrease in the yield of exopolysaccharides, indicating that epsT is an important gene involved in the EPS production of SM9913. Conclusions A conjugal transfer system was constructed in Pseudoalteromonas sp. SM9913 with a wide temperature range for selection and a high transfer efficiency, which will lay the foundation of genetic manipulation in this strain. The epsT gene of SM9913 was successfully deleted with no selective marker left in the chromosome of the host, which thus make it

  19. Filobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts.

    PubMed

    Ike, Fumio; Sakamoto, Mitsuo; Ohkuma, Moriya; Kajita, Ayako; Matsushita, Satoru; Kokubo, Toshiaki

    2016-01-01

    Strain SMR-CT, which was originally isolated from rats as the SMR strain, had been named 'cilia-associated respiratory bacillus' ('CAR bacillus'). 'CAR bacillus' was a Gram-stain-negative, filamentous argentophilic bacterium without flagella. SMR-CT grew at 37 °C under microaerobic conditions, showed gliding activity, hydrolysed urea and induced chronic respiratory diseases in rodents. The dominant cellular fatty acids detected were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 47.7 mol%. 16S rRNA gene sequence analysis revealed SMR-CT and other strains of 'CAR bacillus' isolated from rodents all belonged to the phylum Bacteroidetes. The nearest known type strain, with 86 % 16S rRNA gene sequence similarity, was Chitinophaga pinensis DSM 2588T in the family Chitinophagaceae. Strain SMR-CT and closely related strains of 'CAR bacillus' rodent-isolates formed a novel family-level clade in the phylum Bacteroidetes with high bootstrap support (98-100 %). Based on these results, we propose a novel family, Filobacteriaceae fam. nov., in the order Sphingobacteriales as well as a novel genus and species, Filobacterium rodentium gen. nov., sp. nov., for strain SMR-CT. The type strain is SMR-CT ( = JCM 19453T = DSM 100392T). PMID:26476525

  20. Noncontiguous finished genome sequence and description of Bacillus testis strain SIT10 sp. nov.

    PubMed

    Cimmino, T; Traore, S I; Valentini, C; le Page, S; Sokhna, C; Diallo, A; Raoult, D; Rolain, J M

    2016-07-01

    Bacillus testis strain SIT10 (= CSUR P1492 = DSMZ 101190) is the new type strain collected from stool from a 2-year-old boy from Senegal during a culturomics study. This Gram-positive bacterium is a facultative anaerobic rod and a member of the Bacillaceae family. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 3 987 349 bp long genome (one chromosome but no plasmid) with 42.8% GC content contains 4005 protein-coding and 171 sRNA genes, including 19 5S rRNA gene, 15 16S rRNA genes and ten 23S rRNA genes. PMID:27222713

  1. Identification of strains Bacillus aerophilus MTCC 7304T as Bacillus altitudinis and Bacillus stratosphericus MTCC 7305T as a Proteus sp. and the status of the species Bacillus aeriusShivaji et al. 2006. Request for an Opinion.

    PubMed

    Liu, Yang; Ramesh Kumar, N; Lai, Qiliang; Du, Juan; Dobritsa, Anatoly P; Samadpour, Mansour; Shao, Zongze

    2015-09-01

    On the basis of 16S rRNA, rpoB, gyrB and pycA gene sequence analyses, characterization of biochemical features and other phenotypic traits and pulsed-field gel electrophoresis (PFGE) fingerprinting, it was ascertained that strains Bacillus aerius MTCC 7303T, Bacillus aerophilus MTCC 7304(T) and Bacillus stratosphericus MTCC 7305(T) do not conform to the descriptions of the type strains of the respective species. Strains MTCC 7303(T) and MTCC 7304(T) were indistinguishable from Bacillus altitudinis DSM 21631(T), while strain MTCC 7305(T) should be classified as a representative of a Proteus sp. Our attempts to find other deposits of the type strains of these species were unsuccessful. Therefore, the results support the Request for an Opinion on the status of the species Bacillus aerophilus and Bacillus stratosphericus by Branquinho et al. [Branquinho, R., Klein, G., Kämpfer, P. & Peixe, L. V. (2015). Int J Syst Evol Microbiol 65, 1101]. It is also proposed that the Judicial Commission should place the name Bacillus aerius on the list of rejected names if a suitable replacement type strain cannot be found or a neotype is not proposed within two years following the publication of this Request (Rule 18c). PMID:26297145

  2. The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4.

    PubMed

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J; Glick, Bernard R

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated "housekeeping" genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

  3. The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

    PubMed Central

    Duan, Jin; Jiang, Wei; Cheng, Zhenyu; Heikkila, John J.; Glick, Bernard R.

    2013-01-01

    The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup. PMID:23516524

  4. Bacillus rubiinfantis sp. nov. strain mt2T, a new bacterial species isolated from human gut

    PubMed Central

    Tidjiani Alou, M.; Rathored, J.; Khelaifia, S.; Michelle, C.; Brah, S.; Diallo, B.A.; Raoult, D.; Lagier, J.-C.

    2015-01-01

    Bacillus rubiinfantis sp. nov. strain mt2T is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid) contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes. PMID:27076912

  5. Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut

    PubMed Central

    Tidjani Alou, M.; Rathored, J.; Traore, S.I.; Khelaifia, S.; Michelle, C.; Brah, S.; Diallo, B.A.; Raoult, D.; Lagier, J.-C.

    2015-01-01

    Bacillus niameyensis sp. nov. strain SIT3T (= CSUR P1266 = DSM 29725) is the type strain of B. niameyensis sp. nov. This Gram-positive strain was isolated from the digestive flora of a child with kwashiorkor and is a facultative anaerobic rod and a member of the Bacillaceae family. This organism is hereby described alongside its complete genome sequence and annotation. The 4  286  116 bp long genome (one chromosome but no plasmid) contains 4130 protein-coding and 66 RNA genes including five rRNA genes. PMID:27076913

  6. Ferrovibrio xuzhouensis sp. nov., a cyhalothrin-degrading bacterium isolated from cyhalothrin contaminated wastewater.

    PubMed

    Song, Man; Zhang, Long; Sun, Bin; Zhang, Hao; Ding, Hui; Li, Qiang; Guo, Suhui; Huang, Xing

    2015-08-01

    A novel cyhalothrin-degrading strain, designated as LM-6(T), was isolated from a cyhalothrin contaminated wastewater sample. The bacterium was found to be Gram stain-negative, non-spore-forming, vibrio-shaped, and motile with a single polar flagellum. Strain LM-6(T) was observed to grow optimally at 28-30 °C, pH 6.0 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain LM-6(T) is a member of the genus Ferrovibrio, and showed the highest sequence similarity with Ferrovibrio denitrificans Sp-1(T) (97.7 %), followed by Taonella mepensis H1(T) (93.3 %). The major fatty acids of strain LM-6(T) (>5 %) were determined to be C18:1 ω7c and/or C18:1 ω6c, C16:0, C18:1 2-OH and C17:1 iso I and/or anteiso B. The major polar lipids were identified to be phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmethylethanolamine. The major respiratory quinone was determined to be ubiquinone-10. The genomic DNA G+C content of strain LM-6(T) is 66.5 mol %. Strain LM-6(T) showed low DNA-DNA relatedness with F. denitrificans Sp-1(T) (53.1 ± 0.5 %). On the basis of phylogenetic, genomic, phenotypic and chemotaxonomic data, strain LM-6(T) is considered to represent a novel species of the genus Ferrovibrio, for which the name Ferrovibrio xuzhouensis sp. nov. is proposed. The type strain is Ferrovibrio xuzhouensis LM-6(T) (=KCTC 42182(T) = ACCC 19710(T)). PMID:26002076

  7. Efficient industrial dye decolorization by Bacillus sp. VUS with its enzyme system.

    PubMed

    Dawkar, Vishal V; Jadhav, Umesh U; Tamboli, Dhawal P; Govindwar, Sanjay P

    2010-10-01

    This work presents role of different enzymes in decolorization of industrial dye Orange T4LL by Bacillus sp. VUS. Bacillus sp. strain VUS decolorized dye Orange T4LL, under static anoxic condition in 24 h. During decolorization of Orange T4LL a significant induction in the activities of lignin peroxidase, tyrosinase, and reductases (NADH-DCIP, azo, and riboflavin) was observed. The biodegradation was monitored by Ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy, and high performance liquid chromatography. The final products 4-methyl-2-o-tolylazo-benzene-1,3-diamine and [3-(phenyl-hydrazono)-cyclohexa-1,4-dienyl]-methanol were characterized by gas chromatography-mass spectroscopy. Phytotoxicity, COD, and BOD revealed non-toxicity of degraded products. Phytotoxicity study demonstrated non-toxicity of the biodegraded products for crop plants with respect to Triticum aestivum and Sorghum bicolor. Bacillus sp. VUS with its enzyme system could be a useful tool for textile effluent treatment. PMID:20655588

  8. Evaluation of Bacillus sp. MZS10 for decolorizing Azure B dye and its decolorization mechanism.

    PubMed

    Li, Huixing; Zhang, Ruijing; Tang, Lei; Zhang, Jianhua; Mao, Zhonggui

    2014-05-01

    To evaluate decolorization and detoxification of Azure B dye by a newly isolated Bacillus sp. MZS10 strain, the cultivation medium and decolorization mechanism of the isolate were investigated. The decolorization was discovered to be dependent on cell density of the isolate and reached 93.55% (0.04 g/L) after 14 hr of cultivation in a 5 L stirred-tank fermenter at 2.0 g/L yeast extract and 6.0 g/L soluble starch and a small amount of mineral salts. The decolorization metabolites were identified with ultra performance liquid chromatography-tandem mass spectroscopy (UPLC-MS). A mechanism for decolorization of Azure B was proposed as follows: the C=N in Azure B was initially reduced to -NH by nicotinamide adenine dinucleotide phosphate (NADPH)-dependent quinone dehydrogenase, and then the -NH further combined with -OH derived from glucose to form a stable and colorless compound through a dehydration reaction. The phytotoxicity was evaluated for both Azure B and its related derivatives produced by Bacillus sp. MZS10 decolorization, indicating that the decolorization metabolites were less toxic than original dye. The decolorization efficiency and mechanism shown by Bacillus sp. MZS10 provided insight on its potential application for the bioremediation of the dye Azure B. PMID:25079643

  9. A New Alkali-Thermostable Azoreductase from Bacillus sp. Strain SF

    PubMed Central

    Maier, Jürgen; Kandelbauer, Andreas; Erlacher, Angelika; Cavaco-Paulo, Artur; Gübitz, Georg M.

    2004-01-01

    A screening for dye-decolorizing alkali-thermophilic microorganisms resulted in a Bacillus sp. strain isolated out of the wastewater drain of a textile finishing company. An NADH-dependent azoreductase of this strain, Bacillus sp. strain SF, was found to be responsible for the decolorization of azo dyes. This enzyme was purified by a combination of ammonium sulfate precipitation and anion-exchange and affinity chromatography and had a molecular mass of 61.6 kDa and an isoelectric point at pH 5.3. The pH optimum of the azoreductase depended on the substrate and was within the range of pHs 8 to 9, while the temperature maximum was reached at 80°C. Decolorization only took place in the absence of oxygen and was enhanced by FAD, which was not consumed during the reaction. A 26% similarity of this azoreductase to chaperonin Cpn60 from a Bacillus sp. was found by peptide mass mapping experiments. Substrate specificities of the azoreductase were studied by using synthesized model substrates based on di-sodium-(R)-benzyl-azo-2,7-dihydroxy-3,6-disulfonyl-naphthaline. Those dyes with NO2 substituents, especially in the ortho position, were degraded fastest, while analogues with a methyl substitution showed the lowest degradation rates. PMID:14766562

  10. Biosorption of uranium on Bacillus sp. dwc-2: preliminary investigation on mechanism.

    PubMed

    Li, Xiaolong; Ding, Congcong; Liao, Jiali; Lan, Tu; Li, Feize; Zhang, Dong; Yang, Jijun; Yang, Yuanyou; Luo, Shunzhong; Tang, Jun; Liu, Ning

    2014-09-01

    In this paper, the biosorption mechanisms of uranium on an aerobic Bacillus sp. dwc-2, isolated from a potential disposal site for (ultra-) low uraniferous radioactive waste in Southwest China, was explored by transmission electron microscopy (TEM), energy dispersive X-ray (EDX) analysis, FT-IR spectroscopy, proton induced X-ray emission (PIXE) and enhanced proton backscattering spectrometry (EPBS). The biosorption experiments for uranium were carried out at a low pH (pH 3.0), where the uranium solution speciation is dominated by highly mobile uranyl ions. The bioaccumulation was found to be the potential mechanism involved in uranium biosorption by Bacillus sp. dwc-2, and the bioaccumulated uranium was deposited in the cell interior as needle shaped particles at pH 3.0, as revealed by TEM analysis as well as EDX spectra. FTIR analysis further suggested that the absorbed uranium was bound to amino, phosphate and carboxyl groups of bacterial cells. Additionally, PIXE and EPBS results confirmed that ion-exchange also contributed to the adsorption process of uranium. All the results implied that the biosorption mechanism of uranium on Bacillus sp. is complicated and at least involves bioaccumulation, ion exchange and complexation process. PMID:24727549

  11. Bacillus cibi sp. nov., isolated from jeotgal, a traditional Korean fermented seafood.

    PubMed

    Yoon, Jung-Hoon; Lee, Choong-Hwan; Oh, Tae-Kwang

    2005-03-01

    A Gram-variable, motile, endospore-forming, halotolerant bacillus, strain JG-30(T), was isolated from the traditional Korean fermented seafood jeotgal, and was subjected to a polyphasic taxonomic study. This organism grew optimally at 37 degrees C and in the presence of 0-1 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain JG-30(T) forms a distinct phylogenetic lineage within the evolutionary radiation encompassed by the genus Bacillus. Strain JG-30(T) was characterized chemotaxonomically as having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C(15 : 0) and iso-C(14 : 0) as the major fatty acids. The DNA G+C content was 45 mol%. Strain JG-30(T) exhibited levels of 16S rRNA gene sequence similarity of less than 95.7 % to Bacillus species with validly published names. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JG-30(T) (=KCTC 3880(T)=DSM 16189(T)) was classified within the genus Bacillus as a novel species, for which the name Bacillus cibi sp. nov. is proposed. PMID:15774653

  12. Growth of hydroxyapatite on the cellular membrane of the bacterium Bacillus thuringiensis for the preparation of hybrid biomaterials.

    PubMed

    Cervantes, Eric Reyes; Torres, Maykel González; Muñoz, Susana Vargas; Rosas, Efraín Rubio; Vázquez, Candelario; Talavera, Rogelio Rodríguez

    2016-01-01

    This study aimed to grow hydroxyapatite (HAp) crystals on the cellular wall of the Gram-positive bacterium Bacillus thuringiensis using a bio-mimetic method. Several strains were phenotypically and genotypically characterized using multilocus sequence typing (MLST) gene markers to differentiate the strains and confirm the identity of the isolated species to guarantee that the selected species was not harmful to human health or the environment. Three of the analyzed strains were selected because they exhibited the best nucleation and growth of HAp on the bacterial surface. This innovative method to grow HAp crystals on a cellular membrane helps to elucidate the mechanisms by which osseous tissue is formed in nature. The optimum concentration for the simulated physiological fluid (SPF) was 1.5×. The hybrid materials were characterized by optical microscopy, atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray powder diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). PMID:26478352

  13. Complete genome sequence of Bacillus amyloliquefaciens L-S60, a plant growth-promoting and antifungal bacterium.

    PubMed

    Qin, Yuxuan; Han, Yuzhu; Yu, Yaqiong; Shang, Qingmao; Zhang, Bao; Li, Pinglan

    2015-10-20

    Bacillus amyloliquefaciens L-S60, a gram-positive plant-associated bacterium, which could stimulate plant growth and shows strong antifungal function, was isolated from the turfy soil in Beijing, China. The genome of B. amyloliquefaciens L-S60 comprises a 3903,017bp long circular chromosome that consists of 3909 protein-coding genes and 117 RNA genes. Based on genomic analysis, we identified gene clusters responsible for the biosynthesis of numerous bioactive metabolites with well-established in-vitro activity such as surfactin, iturin and fengycins. Additionally, we also found functionally related genes in the genome of L-S60, which play key roles in the process of plant growth promotion hormone secretion, biofilm formation and volatile compounds production. PMID:26297906

  14. Enzymatic Properties of an Alkaline and Chelator Resistant alpha-amylase from the Alkaliphilic Bacillus sp. Isolate L1711

    NASA Technical Reports Server (NTRS)

    Bernhardsdotter, Eva C. M. J.; Pusey, Marc L.; Ng, Joseph D.; Garriott, Owen K.

    2004-01-01

    An alkaliphilic amylase producing bacterium, Bacillus sp. strain L 711, was selected among 13 soda lakes isolates. When grown at pH 10.5 and 37 C, strain L711 produced multiple forms of amylases in the culture broth. One of these, BAA, was purified from the culture supernatant by QAE column chromatography and preparative native gel electrophoresis. The molecular weight of BAA was determined to be 51 kDa by denaturing gel electrophoresis. The pH optima for activity below and above 40 C were 9.5 - 10.0 and 7.0 - 7.5 respectively. BAA was stable in the pH range 6-11 and was completely inactivated at 55 C. The thermostability was not increased in the presence of Ca(2+). The enzyme was strongly inhibited by Ca(2+), Zn(2+), Mg(2+), Mn(2+), Ba(2+) and Cu(2+), whereas the presence of Na(+), Co(2+) and EDTA (10 mM) enhanced enzymatic activity. The K(sub m), and specific activity of BAA on soluble starch were 1.9 mg/ml and 18.5 U/mg respectively. The main end products of hydrolysis were maltotetraose, maltose and glucose.

  15. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress

    PubMed Central

    Chen, Yanmei; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong

    2016-01-01

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd2+ MIC, >250 mg liter−1) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. PMID:26729719

  16. Survival Strategies of the Plant-Associated Bacterium Enterobacter sp. Strain EG16 under Cadmium Stress.

    PubMed

    Chen, Yanmei; Chao, Yuanqing; Li, Yaying; Lin, Qingqi; Bai, Jun; Tang, Lu; Wang, Shizhong; Ying, Rongrong; Qiu, Rongliang

    2016-01-01

    Plant-associated bacteria are of great interest because of their potential use in phytoremediation. However, their ability to survive and promote plant growth in metal-polluted soils remains unclear. In this study, a soilborne Cd-resistant bacterium was isolated and identified as Enterobacter sp. strain EG16. It tolerates high external Cd concentrations (Cd(2+) MIC, >250 mg liter(-1)) and is able to produce siderophores and the plant hormone indole-3-acetic acid (IAA), both of which contribute to plant growth promotion. Surface biosorption in this strain accounted for 31% of the total Cd accumulated. The potential presence of cadmium sulfide, shown by energy-dispersive X-ray (EDX) analysis, suggested intracellular Cd binding as a Cd response mechanism of the isolate. Cd exposure resulted in global regulation at the transcriptomic level, with the bacterium switching to an energy-conserving mode by inhibiting energy-consuming processes while increasing the production of stress-related proteins. The stress response system included increased import of sulfur and iron, which become deficient under Cd stress, and the redirection of sulfur metabolism to the maintenance of intracellular glutathione levels in response to Cd toxicity. Increased production of siderophores, responding to Cd-induced Fe deficiency, not only is involved in the Cd stress response systems of EG16 but may also play an important role in promoting plant growth as well as alleviating the Cd-induced inhibition of IAA production. The newly isolated strain EG16 may be a suitable candidate for microbially assisted phytoremediation due to its high resistance to Cd and its Cd-induced siderophore production, which is likely to contribute to plant growth promotion. PMID:26729719

  17. Integrated Bacillus sp. immobilized cell reactor and Synechocystis sp. algal reactor for the treatment of tannery wastewater.

    PubMed

    Sekaran, G; Karthikeyan, S; Nagalakshmi, C; Mandal, A B

    2013-01-01

    The wastewater discharged from leather industries lack biodegradability due to the presence of xenobiotic compounds. The primary clarification and aerobic treatment in Bacillus sp. immobilized Chemo Autotrophic Activated Carbon Oxidation (CAACO) reactor removed considerable amount of pollution parameters. The residual untreated organics in the wastewater was further treated in algal batch reactor inoculated with Synechocystis sp. Sodium nitrate, K(2)HPO(4), MgSO(4).7H(2)O, NH(4)Cl, CaCl(2)·2H(2)O, FeCl(3) (anhydrous), and thiamine hydrochloride, rice husk based activated carbon (RHAC), immobilization of Bacillus sp. in mesoporous activated carbon, sand filter of dimensions diameter, 6 cm and height, 30 cm; and the CAACO reactor of dimensions diameter, 5.5 cm and height, 30 cm with total volume 720 ml, and working volume of 356 ml. In the present investigation, the CAACO treated tannery wastewater was applied to Synechocystis sp. inoculated algal batch reactor of hydraulic residence time 24 h. The BOD(5), COD, and TOC of treated wastewater from algal batch reactor were 20 ± 7, 167 ± 29, and 78 ± 16 mg/l respectively. The integrated CAACO system and Algal batch reactor was operated for 30 days and they accomplished a cumulative removal of BOD(5),COD, TOC, VFA and sulphide as 98 %, 95 %, 93 %, 86 %, and 100 %, respectively. The biokinetic constants for the growth of algae in the batch reactor were specific growth rate, 0.095(day(-1)) and yield coefficient, 3.15 mg of algal biomass/mg of COD destructed. The degradation of xenobiotic compounds in the algal batch reactor was confirmed through HPLC and FT-IR techniques. The integrated CAACO-Algal reactor system established a credible reduction in pollution parameters in the tannery wastewater. The removal mechanism is mainly due to co-metabolism between algae and bacterial species and the organics were completely metabolized rather than by adsorption. PMID:22528997

  18. Isolation and characterization of the homoacetogenic thermophilic bacterium Moorella glycerini sp. nov.

    SciTech Connect

    Slobodkin, A.; Wiegel, J.; Reysenbach, A.L.

    1997-10-01

    A thermophilic, anaerobic, spore-forming bacterium (strain JW/AS-Y6) was isolated from a mixed sediment-water sample from a hot spring (Calcite Spring area) at Yellowstone National Park. The vegetative cells of this organism were straight rods, 0.5 to 0.6 by 3.0 to 6.5 {mu}m. Cells occurred singly and exhibited a slight tumbling motility. They formed round refractile endospores in terminal swollen sporangia. Cells stained gram positive. The temperature range for growth at pH 6.8 was 43 to 65{degrees}C, with optimum growth at 58{degrees}C. The range for growth at 60{degrees}C (pH{sup 60C}; with the pH meter calibrated at 60{degrees}C) was 5.9 to 7.8, with an optimum pH{sub 60C} of 6.3 to 6.5. The substrates utilized included glycerol, glucose, fructose, mannose, galactose, xylose, lactate, glycerate, pyruvate, and yeast extract. In the presence of CO{sub 2}, acetate was the only organic product from glyerol and carbohydrate fermentation. No H{sub 2} was produced during growth. The strain was not able to grow chemolithotrophically at the expense of H{sub 2}-CO{sub 2}; however, suspensions of cells in the exponential growth phase consumed H{sub 2}. The bacterium reduced fumarate to succinate and thiosulfate to elemental sulfur. Growth was exhibited by ampicillin, chloramphenicol, erythromycin, rifampin, and tetracycline, but not by streptomycin. The G+C content of the DNA was 54.5 mol% (as determined by high-performance liquid chromatography). The 16S ribosomal DNA sequence analysis placed the isolate in the Gram type-positive Bacillus-Clostridium subphylum. On the basis of physiological properties and phylogenetic analysis we propose that the isolated strain constitutes a new species, Moorella glycerini; the type strain is JW/AS-Y6 (= DSM 11254 = ATCC 700316).

  19. Synergistic Effect of Simple Sugars and Carboxymethyl Cellulose on the Production of a Cellulolytic Cocktail from Bacillus sp. AR03 and Enzyme Activity Characterization.

    PubMed

    Manfredi, Adriana P; Pisa, José H; Valdeón, Daniel H; Perotti, Nora I; Martínez, María A

    2016-04-01

    A cellulase-producing bacterium isolated from pulp and paper feedstock, Bacillus sp. AR03, was evaluated by means of a factorial design showing that peptone and carbohydrates were the main variables affecting enzyme production. Simple sugars, individually and combined with carboxymethyl cellulose (CMC), were further examined for their influence on cellulase production by strain AR03. Most of the mono and disaccharides assayed presented a synergistic effect with CMC. As a result, a peptone-based broth supplemented with 10 g/L sucrose and 10 g/L CMC maximized enzyme production after 96 h of cultivation. This medium was used to produce endoglucanases in a 1-L stirred tank reactor in batch mode at 30 °C, which reduced the fermentation period to 48 h and reaching 3.12 ± 0.02 IU/mL of enzyme activity. Bacillus sp. AR03 endoglucanases showed an optimum temperature of 60 °C and a pH of 6.0 with a wide range of pH stability. Furthermore, presence of 10 mM Mn(2+) and 5 mM Co(2+) produced an increase of enzyme activity (246.7 and 183.7 %, respectively), and remarkable tolerance to NaCl, Tween 80, and EDTA was also observed. According to our results, the properties of the cellulolytic cocktail from Bacillus sp. AR03 offer promising features in view of potential biorefinery applications. PMID:26797928

  20. Crystal structure of stable protein CutA1 from psychrotrophic bacterium Shewanella sp. SIB1

    PubMed Central

    Sato, Aya; Yokotani, Sonoko; Tadokoro, Takashi; Tanaka, Shun-ichi; Angkawidjaja, Clement; Koga, Yuichi; Takano, Kazufumi; Kanaya, Shigenori

    2011-01-01

    CutA1 is widely found in bacteria, plants and animals, including humans. The functions of CutA1, however, have not been well clarified. It is known that CutA1s from Pyrococcus horikoshii, Thermus thermophilus and Oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. In this work the crystal structure of CutA1 from the psychrotrophic bacterium Shewanella sp. SIB1 (SIB1–CutA1) in a trimeric form was determined at 2.7 Å resolution. This is the first crystal structure of a psychrotrophic CutA1. The overall structure of SIB1–CutA1 is similar to those of CutA1 from Homo sapiens, Escherichia coli, Pyrococcus horikoshii, Thermus thermophilus, Termotoga maritima, Oryza sativa and Rattus norvergicus. A peculiarity is observed in the β2 strand. The β2 strand is divided into two short β strands, β2a and β2b, in SIB1–CutA1. A thermal denaturation experiment revealed that SIB1–CutA1 does not unfold completely at 363 K at pH 7.0, although Shewanella sp. SIB1 cannot grow at temperatures exceeding 303 K. These results indicate that the trimeric structural motif of CutA1 is the critical factor in its unusually high stability and suggest that CutA1 needs to maintain its high stability in order to function, even in psychrotrophs. PMID:21169681

  1. The Extracytoplasmic Function Sigma Factor SigY Is Important for Efficient Maintenance of the Spβ Prophage That Encodes Sublancin in Bacillus subtilis

    PubMed Central

    Mendez, Rebecca; Gutierrez, Alba; Reyes, Jasmin

    2012-01-01

    Many strains of the soil bacterium Bacillus subtilis are capable of producing and being resistant to the antibiotic sublancin because they harbor the Spβ prophage. This 135 kb viral genome is integrated into the circular DNA chromosome of B. subtilis, and contains genes for the production of and resistance to sublancin. We investigated the role of SigY in sublancin production and resistance, finding that it is important for efficient maintenance of the Spβ prophage. We were unable to detect the prophage in mutants lacking SigY. Additionally, these mutants were no longer able to produce sublancin, were sensitive to killing by this factor, and displayed a delay in sporulation. Wild-type cells with normal SigY activity were found to partially lose the Spβ prophage during growth and early sporulation, suggesting a mechanism for the bistable outcome of sibling cells capable of killing and of being killed. The appropriate regulation of SigY appears to be essential for growth as evidenced by the inability to disrupt the gene for its putative antisigma. Our results confirm a role for SigY in antibiotic production and resistance, as has been found for other members of the extracytoplasmic function sigma factor family in B. subtilis, and shows that this role is achieved by affecting maintenance of the Spβ prophage. PMID:22400495

  2. Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.

    PubMed

    Behrendt, Undine; Kämpfer, Peter; Glaeser, Stefanie P; Augustin, Jürgen; Ulrich, Andreas

    2016-06-01

    In the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium. The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola. The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA-DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788T) is proposed. PMID:27030972

  3. Exopolysaccharides Play a Role in the Swarming of the Benthic Bacterium Pseudoalteromonas sp. SM9913

    PubMed Central

    Liu, Ang; Mi, Zi-Hao; Zheng, Xiao-Yu; Yu, Yang; Su, Hai-Nan; Chen, Xiu-Lan; Xie, Bin-Bin; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Qin, Qi-Long

    2016-01-01

    Most marine bacteria secrete exopolysaccharide (EPS), which is important for bacterial survival in the marine environment. However, it is still unclear whether the self-secreted EPS is involved in marine bacterial motility. Here we studied the role of EPS in the lateral flagella-driven swarming motility of benthic bacterium Pseudoalteromonas sp. SM9913 (SM9913) by a comparison of wild SM9913 and ΔepsT, an EPS synthesis defective mutant. Reduction of EPS production in ΔepsT did not affect the growth rate or the swimming motility, but significantly decreased the swarming motility on a swarming plate, suggesting that the EPS may play a role in SM9913 swarming. However, the expression and assembly of lateral flagella in ΔepsT were not affected. Instead, ΔepsT had a different swarming behavior from wild SM9913. The swarming of ΔepsT did not have an obvious rapid swarming period, and its rate became much lower than that of wild SM9913 after 35 h incubation. An addition of surfactin or SM9913 EPS on the surface of the swarming plate could rescue the swarming level. These results indicate that the self-secreted EPS is required for the swarming of SM9913. This study widens our understanding of the function of the EPS of benthic bacteria. PMID:27092127

  4. Genome sequence of Enterobacter sp. ST3, a quorum sensing bacterium associated with marine dinoflagellate

    PubMed Central

    Zhou, Jin; Lao, Yong-Min; Ma, Zhi-Ping; Cai, Zhong-Hua

    2016-01-01

    Phycosphere environment is a typical marine niche, harbor diverse populations of microorganisms, which are thought to play a critical role in algae host and influence mutualistic and competitive interactions. Understanding quorum sensing-based acyl-homoserine lactone (AHL) language may shed light on the interaction between algal-associated microbial communities in the native environment. In this work, we isolated an epidermal bacterium (was tentatively named Enterobacter sp. ST3, and deposited in SOA China, the number is MCCC1K02277-ST3) from the marine dinoflagellate Scrippsiella trochoidea, and found it has the ability to produce short-chain AHL signal. In order to better understand its communication information at molecular level, the genomic map was investigated. The genome size was determined to be 4.81 Mb with a G + C content of 55.59%, comprising 6 scaffolds of 75 contigs containing 4647 protein-coding genes. The functional proteins were predicted, and 3534 proteins were assigned to COG functional categories. An AHL-relating gene, LuxR, was found in upstream position at contig 1. This genome data may provide clues to increase understanding of the chemical characterization and ecological behavior of strain ST3 in the phycosphere microenvironment. PMID:26981407

  5. Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater.

    PubMed

    Zhang, Wen-wu; Fang, Ming-xu; Tan, Hai-qin; Zhang, Xin-qi; Wu, Min; Zhu, Xu-fen

    2012-09-01

    A novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TY(T), was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l(-1). Strain TY(T) produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C(14 : 0) DMA (18.7 %), C(15 : 0) (15.4 %), anteiso-C(18 : 1) (15.2 %), C(11 : 0) (13.3 %) and summed feature 5 (C(17 : 1)ω7c and/or C(17 : 2)) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TY(T) represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TY(T) is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TY(T) = JCM 17499(T) = DSM 24661(T)). PMID:22058316

  6. Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces.

    PubMed

    Velázquez, Encarna; de Miguel, Trinidad; Poza, Margarita; Rivas, Raúl; Rosselló-Mora, Ramón; Villa, Tomás G

    2004-01-01

    During a search for xylan-degrading micro-organisms, a sporulated bacterium was recovered from recent and old cow dung and rectal samples. The isolates were identified as members of a novel species of the genus Paenibacillus, based on 16S rRNA gene sequences. According to the results of phylogenetic analysis, the most closely related species was Paenibacillus azoreducens. Phenotypic and chemotaxonomic analyses and DNA-DNA hybridization experiments also showed that the isolates belonged to a novel species of the genus Paenibacillus. The novel species is a facultatively anaerobic, motile, Gram-variable, sporulated rod. The spores of this rod-shaped micro-organism occur in slightly swollen sporangia and are honeycomb-shaped. The main fatty acid is anteiso-branched C(15:0). Growth was observed with many carbohydrates, including xylan, as the only carbon source and gas production was not observed from glucose. The novel species produces a wide variety of hydrolytic enzymes, such as xylanases, cellulases, amylases, gelatinase, urease and beta-galactosidase. On the contrary, it does not produce caseinase, phenylalanine deaminase or lysine decarboxylase. According to the data obtained in this work, the strains belong to a novel species, for which the name Paenibacillus favisporus sp. nov. is proposed (type strain, GMP01T=LMG 20987T=CECT 5760T). PMID:14742459

  7. Colwellia asteriadis sp. nov., a marine bacterium isolated from the starfish Asterias amurensis.

    PubMed

    Choi, Eun Ju; Kwon, Hak Cheol; Koh, Hye Yeon; Kim, Young Sug; Yang, Hyun Ok

    2010-08-01

    A marine bacterial strain, KMD 002T, was isolated from an Amur starfish, Asterias amurensis, collected in the East Sea of Korea. Strain KMD 002T was a Gram-negative, beige-pigmented, rod-shaped bacterium. The strain was capable of growth at relatively low temperatures (4-25 degrees C) and over a broad pH range (pH 4.0-10.0). The major fatty acids were C16:1omega7c and/or iso-C15:0 2-OH and C16:0 and the predominant isoprenoid quinone was Q-8. The DNA G+C content of strain KMD 002T was 40.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain KMD 002T belonged to the genus Colwellia. However, various phenotypic properties as well as low 16S rRNA gene sequence similarities to members of the genus Colwellia (94.1-96.7%) suggested that strain KMD 002T is a representative of a novel species, for which the name Colwellia asteriadis sp. nov. is proposed. The type strain is KMD 002T (=KCCM 90077T =JCM 15608T). PMID:19801395

  8. Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium

    SciTech Connect

    Wada, M.; Fukunaga, N.; Sasaki, S. )

    1989-08-01

    Biosynthesis of palmitic, palmitoleic, and cis-vaccenic acids in Pseudomonas sp. strain E-3 was investigated with in vitro and in vivo systems. (1-{sup 14}C)palmitic acid was aerobically converted to palmitoleate and cis-vaccenate, and the radioactivities on their carboxyl carbons were 100 and 43%, respectively, of the total radioactivity in the fatty acids. Palmitoyl coenzyme A desaturase activity was found in the membrane fraction. (1-{sup 14}C)stearic acid was converted to octadecenoate and C16 fatty acids. The octadecenoate contained oleate and cis-vaccenate, but only oleate was produced in the presence of cerulenin. (1-{sup 14}C)lauric acid was aerobically converted to palmitate, palmitoleate, and cis-vaccenate. Under anaerobic conditions, palmitate (62%), palmitoleate (4%), and cis-vaccenate (34%) were produced from (1-{sup 14}C)acetic acid, while they amounted to 48, 39, and 14%, respectively, under aerobic conditions. In these incorporation experiments, 3 to 19% of the added radioactivity was detected in released {sup 14}CO{sub 2}, indicating that part of the added fatty acids were oxidatively decomposed. Partially purified fatty acid synthetase produced saturated and unsaturated fatty acids with chain lengths of C10 to C18. These results indicated that both aerobic and anaerobic mechanisms for the synthesis of unsaturated fatty acid are operating in this bacterium.

  9. Paenibacillus pini sp. nov., a cellulolytic bacterium isolated from the rhizosphere of pine tree.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Min, Sung Ran; Kim, Hyun Soon; Shin, Kee-Sun

    2009-12-01

    Strain S22(T), a novel cellulolytic bacterium was isolated from the rhizosphere of pine trees. This isolate was Gram-reaction positive, motile and rods, and formed terminal or subterminal ellipsoidal spores. S22(T) represented positive activity for catalase, oxidase, esterase (C4), esterase lipase (C8), beta-galactosidase, leucine arylamidase, and hydrolysis of esculin. It contained meso-diaminopimelic acid as the diagnostic dia-mino acid in the cell-wall. The predominant isoprenoid quinone was menaquinone 7 (MK-7), and the major cellular fatty acids were anteiso-C(15:0) (52.9%), iso-Ci(16:0) (11.3%), and iso-C(15:0) (10.0%). The DNA G+C content was 43.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that this isolate belonged to the family Paenibacillaceae. S22(T) exhibited less than 97.0% 16S rRNA gene similarity with all relative type strains in the genus Paenibacillus, and the most closely related strains were Paenibacillus anaericanus MH21(T) and Paenibacillus ginsengisoli Gsoil 1638(T), with equal similarities of 95.8%. This polyphasic evidence suggested that strain S22(T) should be considered a novel species in the genus Paenibacillus, for which the name, Paenibacillus pini sp. nov., is proposed. The type strain is S22(T) (=KCTC 13694(T) =KACC 14198(T) =JCM 16418(T)). PMID:20127462

  10. Aurantiacicella marina gen. nov., sp. nov., a myxol-producing bacterium from surface seawater.

    PubMed

    Teramoto, Maki; Onodera, Ken-Ichi; Moriyama, Hironori; Komatsu, Ayumi; Akakabe, Mai; Nishijima, Miyuki

    2016-01-01

    A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped bacterium, strain 2A-8T, was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced myxol as a major carotenoid. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and was related most closely to the genus Aquimarina (91.0-94.4 % 16S rRNA gene sequence similarity to the type strains of species of this genus). The DNA G+C content was 35 mol%. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and five unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-8T represents a novel genus and species, for which the name Aurantiacicella marina gen. nov., sp. nov. is proposed. The type strain of Aurantiacicella marina is 2A-8T ( = NBRC 111187T = KCTC 42676T). PMID:26493321

  11. Mageeibacillus indolicus gen. nov., sp. nov.: a novel bacterium isolated from the female genital tract.

    PubMed

    Austin, Michele N; Rabe, Lorna K; Srinivasan, Sujatha; Fredricks, David N; Wiesenfeld, Harold C; Hillier, Sharon L

    2015-04-01

    Three isolates of a bacterium recovered from human endometrium using conventional culture methods were characterized biochemically and subjected to 16S rRNA gene sequencing and phylogenetic analysis. Isolates were non-motile, obligately anaerobic, non-spore forming, asaccharolytic, non-cellulolytic, indole positive, Gram positive rods. Cell wall fatty acid profiling revealed C14:0, C16:0, C18:2 ω6, 9c, C18:1 ω9c and C18:0 to be the major fatty acid composition. The DNA mol % G+C was determined to be 44.2%. 16S rRNA gene sequence analysis revealed only 91% sequence similarity with the closest cultivated bacterial isolate, Saccharofermentans acetigenes. Based on genotypic and phenotypic data, all three isolates are considered to be members of the same species and data suggest it represents a novel genus and species in the order Clostridiales with an association with Clostridium rRNA cluster III within the family Ruminococcaceae. We propose the name, Mageeibacillus indolicus gen. nov., sp. nov. The type strain is BAA-2120(T) and CCUG 59143(T). PMID:25482717

  12. Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid.

    PubMed

    Oelschlägel, Michel; Rückert, Christian; Kalinowski, Jörn; Schmidt, Gert; Schlömann, Michael; Tischler, Dirk

    2015-09-01

    Strain Kp5.2(T) is an aerobic, Gram-negative soil bacterium that was isolated in Freiberg, Saxony, Germany. The cells were motile and rod-shaped. Optimal growth was observed at 20-30 °C. The fatty acids of strain Kp5.2(T) comprised mainly C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The major respiratory quinone was Q-10. The major polar lipids of strain Kp5.2(T) were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.7%. Sequencing of the 16S rRNA gene of strain Kp5.2(T) allowed its classification into the family Sphingomonadaceae, and the sequence showed the highest similarity to those of members of the genus Sphingopyxis, with Sphingopyxis italica SC13E-S71(T) (99.15% similarity), Sphingopyxis panaciterrae Gsoil 124(T) (98.96%), Sphingopyxis chilensis S37(T) (98.90%) and Sphingopyxis bauzanensis BZ30(T) (98.51%) as the nearest neighbours. DNA-DNA hybridization and further characterization revealed that strain Kp5.2(T) can be considered to represent a novel species of the genus Sphingopyxis. Hence, the name Sphingopyxis fribergensis sp. nov. is proposed, with the type strain Kp5.2(T) ( = DSM 28731(T) = LMG 28478(T)). PMID:26040579

  13. Sphingomonas psychrolutea sp. nov., a psychrotolerant bacterium isolated from glacier ice.

    PubMed

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2015-09-01

    A Gram-stain-negative, rod-shaped, orange bacterium (strain MDB1-A(T)) was isolated from ice samples collected from Midui glacier in Tibet, south-west China. Cells were aerobic and psychrotolerant (growth occurred at 0-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that it was a member of the genus Sphingomonas, with its closest relative being Sphingomonas glacialis C16y(T) (98.9% similarity). Q-10 was the predominant ubiquinone. C17 : 1ω6c and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) were the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The polyamines detected were sym-homospermidine, spermidine and spermine. The G+C content of the genomic DNA was 63.6%. Based on data from this polyphasic analysis, strain MDB1-A(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas psychrolutea sp. nov. is proposed. The type strain is MDB1-A(T) ( = CGMCC 1.10106(T) = NBRC 109639(T)). PMID:26025946

  14. Deinococcus puniceus sp. nov., a bacterium isolated from soil-irradiated gamma radiation.

    PubMed

    Lee, Jae-Jin; Srinivasan, Sathiyaraj; Lim, Sangyong; Joe, Minho; Im, Seonghun; Kim, Myung Kyum

    2015-04-01

    A Gram-positive, coccus-shaped, crimson-color-pigmented bacterium was isolated from soil irradiated with 5 kGy gamma radiation and was designated strain DY1(T). Cells showed growth at 10-30 °C and pH 7-11 and were oxidase-negative and catalase-positive. Phylogenetic analyses of the 16S rRNA gene showed that the strain DY1(T) belonged to the genus Deinococcus with sequence similarities to Deinococcus aquatilis CCUG 53370(T) (96.2 %) and Deinococcus navajonensis KR-114(T) (94.1 %). Strain DY1(T) showed low level of DNA relatedness with D. aquatilis CCUG 53370(T) (41.3 ± 3.9 %). The DNA G + C content of DY1(T) was 58.7 mol%. Predominant fatty acids were summed feature 3 (C16:1 ω7c/ω6c), C16:0, and C17:0. The major amino acids were D-alanine, L-glutamic acid, glycine, and L-ornithine in the peptidoglycan. The major polar lipids were unknown phosphoglycolipids (PGL). Strain DY1(T) has resistance to gamma radiation and was found to be a novel species. Therefore, the strain was designated as DY1(T) (=KCTC 33027(T) = JCM 18576(T)), and the name Deinococcus puniceus sp. nov. is herein proposed. PMID:25477066

  15. Luteimonas arsenica sp. nov., an arsenic-tolerant bacterium isolated from arsenic-contaminated soil.

    PubMed

    Mu, Yao; Pan, Yunfan; Shi, Wanxia; Liu, Lan; Jiang, Zhao; Luo, Xuesong; Zeng, Xian-Chun; Li, Wen-Jun

    2016-06-01

    A Gram-stain-negative, rod-shaped bacterium that formed yellow and viscous colonies was isolated from arsenic-contaminated soil of the Jianghan plain, Hubei Province, China, and it was designated 26-35T. This strain was capable of resisting arsenate and arsenite with MICs of 40 and 20 mM, respectively. The 16S rRNA gene of the novel isolate displayed 96.7-94.2 % sequence similarities to those of other known species of the genus Luteimonas. The respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content was 71.4 mol%. The predominant cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, iso-C11 : 0, iso-C11 : 0 3-OH and iso-C17 : 1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic and physiological analysis indicated that the isolate represents a novel species of the genus Luteimonas, for which the name Luteimonas arsenica sp. nov. is proposed. The type strain is 26-35T (=KCTC 42824T=CCTCC AB 2014326T). PMID:26978245

  16. Purification and characterization of catalase from marine bacterium Acinetobacter sp. YS0810.

    PubMed

    Fu, Xinhua; Wang, Wei; Hao, Jianhua; Zhu, Xianglin; Sun, Mi

    2014-01-01

    The catalase from marine bacterium Acinetobacter sp. YS0810 (YS0810CAT) was purified and characterized. Consecutive steps were used to achieve the purified enzyme as follows: ethanol precipitation, DEAE Sepharose ion exchange, Superdex 200 gel filtration, and Resource Q ion exchange. The active enzyme consisted of four identical subunits of 57.256 kDa. It showed a Soret peak at 405 nm, indicating the presence of iron protoporphyrin IX. The catalase was not apparently reduced by sodium dithionite but was inhibited by 3-amino-1,2,4-triazole, hydroxylamine hydrochloride, and sodium azide. Peroxidase-like activity was not found with the substrate o-phenylenediamine. So the catalase was determined to be a monofunctional catalase. N-terminal amino acid of the catalase analysis gave the sequence SQDPKKCPVTHLTTE, which showed high degree of homology with those of known catalases from bacteria. The analysis of amino acid sequence of the purified catalase by matrix-assisted laser desorption ionization time-of-flight mass spectrometry showed that it was a new catalase, in spite of its high homology with those of known catalases from other bacteria. The catalase showed high alkali stability and thermostability. PMID:25045672

  17. Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost.

    PubMed

    Kang, Myung-Suk; Im, Wan-Taek; Jung, Hae-Min; Kim, Myung Kyum; Goodfellow, Michael; Kim, Kwang Kyu; Yang, Hee-Chan; An, Dong-Shan; Lee, Sung-Taik

    2007-06-01

    A bacterial strain, TR7-06(T), which has cellulase and beta-glucosidase activities, was isolated from compost at a cattle farm near Daejeon, Republic of Korea. It was a Gram-positive, aerobic or facultatively anaerobic, non-motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belongs to the genus Cellulomonas, with highest sequence similarity to Cellulomonas uda DSM 20107(T) (98.5 %). Cell wall analysis revealed the presence of type A4beta, L-orn-D-Glu peptidoglycan. The cell-wall sugars detected were mannose and glucose. The predominant menaquinone was MK-9(H(4)); MK-8(H(4)) was detected in smaller quantities. The major fatty acids were anteiso-C(15 : 0), C(16 : 0), C(14 : 0) and C(18 : 0). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that TR7-06(T) represents a novel species. The combined genotypic and phenotypic data show that strain TR7-06(T) (=KCTC 19030(T)=NBRC 100758(T)) merits description as the type strain of a novel Cellulomonas species, Cellulomonas composti sp. nov. PMID:17551039

  18. Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium.

    PubMed

    van Gelder, Antonie H; Sousa, Diana Z; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Stams, Alfons J M; Sánchez-Andrea, Irene

    2014-07-01

    A novel anaerobic succinate-producing bacterium, strain ZWB(T), was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4-0.5 µm in diameter and 2-3 µm in length), and stained Gram-negative. The temperature range for growth was 25-40 °C, with an optimum at 37 °C. The pH range for growth was 7.0-9.0, with an optimum at pH 7.5. Strain ZWB(T) was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWB(T). The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14 : 0 and iso-C16 : 0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWB(T) belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006(T) (92.1%). Based on the physiological features and phylogenetic analysis, strain ZWB(T) represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWB(T) ( = DSM 27333(T) = JCM 19283(T)). PMID:24776531

  19. Biodegradation of the neonicotinoid insecticide Acetamiprid by bacterium Pigmentiphaga sp. strain AAP-1 isolated from soil.

    PubMed

    Wang, Guangli; Yue, Wenlong; Liu, Yuan; Li, Feng; Xiong, Minhua; Zhang, Hui

    2013-06-01

    The Acetamiprid-degrading bacterium AAP-1 was isolated from contaminated soil, and identified as Pigmentiphaga sp. combined traditionary categorization method with modern molecule method. The strain could utilize Acetamiprid as the sole carbon, nitrogen and energy source for growth and metabolized 100 mgL(-1) Acetamiprid within 2.5h. During the degradation of Acetamiprid, one N-deacetylation metabolite, was characterized by FT-IR, GC-MS and NMR analysis. A novel microbial biodegradation pathway for Acetamiprid was proposed on the basis of the metabolite. Compared with uninoculated soils, the addition of the AAP-1 strain into soils treated with Acetamiprid gained a higher degradation rate, and the bacteria community analysis by T-RFLP in contaminated soil recovered after inoculation of the AAP-1 strain. On the basis of these results, strain AAP-1 has the potential to be used in the bioremediation of Acetamiprid-contaminated environments. This is the first report of Acetamiprid-degrading isolate from the genus of Pigmentiphaga. PMID:23624055

  20. Dysgonomonas alginatilytica sp. nov., an alginate-degrading bacterium isolated from a microbial consortium.

    PubMed

    Kita, Akihisa; Miura, Toyokazu; Okamura, Yoshiko; Aki, Tsunehiro; Matsumura, Yukihiko; Tajima, Takahisa; Kato, Junichi; Nakashimada, Yutaka

    2015-10-01

    Gram-stain-negative, facultatively anaerobic, non-motile, non-spore-forming, rod-shaped bacterium, designated strain HUA-2T, was isolated from an alginate-degrading microbial consortium. Strain HUA-2T was related to Dysgonomonas capnocytophagoides JCM 16697T, Dysgonomonas macrotermitis JCM 19375T and Dysgonomonas mossii CCUG 43457T with 95.1 %, 94.1 % and 92.1 % 16S rRNA gene sequence similarity, respectively. The optimal growth temperature and pH for strain HUA-2T were 35 °C and pH 8.0, respectively. Enzyme production, major fermentation products from glucose, and the major cellular fatty acids were different from those of D. capnocytophagoides CCUG 17966T or other members of the genus Dysgonomonas. Therefore, strain HUA-2T is proposed to represent a novel species of the genus Dysgonomonas, for which we propose the name Dysgonomonas alginatilytica sp. nov. The type strain is HUA-2T ( = DSM 100214T = HUT 8134T). PMID:26297040

  1. A new κ-carrageenase CgkS from marine bacterium Shewanella sp. Kz7

    NASA Astrophysics Data System (ADS)

    Wang, Linna; Li, Shangyong; Zhang, Shilong; Li, Jiejing; Yu, Wengong; Gong, Qianhong

    2015-08-01

    A new κ-carrageenase gene cgkS was cloned from marine bacterium Shewanella sp. Kz7 by using degenerate and site-finding PCR. The gene was comprised of an open reading frame of 1224 bp, encoding 407 amino acid residues, with a signal peptide of 24 residues. Based on the deduced amino acid sequence, the κ-carrageenase CgkS was classified into the Glycoside Hydrolase family 16. The cgkS gene was expressed in Escherichia coli, and the recombinant enzyme was purified to homogeneity with a specific activity of 716.8 U mg-1 and a yield of 69%. Recombinant CgkS was most active at 45°C and pH 8.0. It was stable at pH 6.0-9.0 and below 30°C. The enzyme did not require NaCl for activity, although its activity was enhanced by NaCl. CgkS degraded κ-carrageenan in an endo-fashion releasing tetrasaccharides and disaccharides as main hydrolysis products.

  2. Pseudomonas glareae sp. nov., a marine sediment-derived bacterium with antagonistic activity.

    PubMed

    Romanenko, Lyudmila A; Tanaka, Naoto; Svetashev, Vassilii I; Mikhailov, Valery V

    2015-06-01

    An aerobic, Gram-negative, motile, rod-shaped bacterium designated KMM 9500(T) was isolated from a sediment sample collected from the Sea of Japan seashore. Comparative 16S rRNA gene sequence analysis affiliated strain KMM 9500(T) to the genus Pseudomonas as a distinct subline clustered with Pseudomonas marincola KMM 3042(T) and Pseudomonas segetis KCTC 12331(T) sharing the highest similarities of 98 and 97.9 %, respectively. Strain KMM 9500(T) was characterized by mainly possessing ubiquinone Q-9, and by the predominance of C18:1 ω7c, C16:1 ω7c, and C16:0 followed by C12:0 in its fatty acid profile. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminophospholipid, and unknown phospholipids. Strain KMM 9500(T) was found to inhibit growth of Gram-negative and Gram-positive indicatory microorganisms. Based on the phylogenetic analysis and distinctive phenotypic characteristics, strain 9500(T) is concluded to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas glareae sp. nov. is proposed. The type strain of the species is strain KMM 9500(T) (=NRIC 0939(T)). PMID:25787010

  3. Marinobacter piscensis sp. nov., a moderately halophilic bacterium isolated from salty food in Tunisia.

    PubMed

    Hedi, Abdeljabbar; Cayol, Jean Luc; Sadfi, Najla; Fardeau, Marie-Laure

    2015-04-01

    An aerobic, Gram-negative, moderately halophilic bacterium, oxidase, and catalase positive-designated Abdou3(T), was isolated from salted traditional foods (Anchovies) in Tunisia. Cells were rod-shaped, non-spore-forming and motile. Growth occurred at 15-45 °C (optimum, 37 °C), pH 5.5-8.75 (optimum, 7.3), and in the presence of 1-15 % NaCl (optimum, 10 %). Strain Abdou3(T) used glucose, D-arabinose, and sucrose. Strain Abdou3(T) had Q9 as the major respiratory quinone and C18:1 ω9c and C16:0 as predominant fatty acids. The DNA G+C content was 55.2 mol%. Phylogenetic analysis of the small-subunit ribosomal RNA (rRNA) gene sequence indicated that strain Abdou3(T) had as its closest relative Marinobacter maritimus (identity of 96 %). Based on phenotypic, phylogenetic, and taxonomic characteristics, strain Abdou3(T) is proposed as a novel species of the genus Marinobacter within the order Alteromonadales, for which the name M. piscensis sp. nov. is proposed. The type strain is Abdou3(T) (=DSM 26804(T)). PMID:25510172

  4. Melghiribacillus thermohalophilus gen. nov., sp. nov., a novel filamentous, endospore-forming, thermophilic and halophilic bacterium.

    PubMed

    Addou, Nariman Ammara; Schumann, Peter; Spröer, Cathrin; Ben Hania, Wajdi; Hacene, Hocine; Fauque, Guy; Cayol, Jean-Luc; Fardeau, Marie-Laure

    2015-04-01

    A novel filamentous, endospore-forming, thermophilic and moderately halophilic bacterium designated strain Nari2A(T) was isolated from soil collected from an Algerian salt lake, Chott Melghir. The novel isolate was Gram-staining-positive, aerobic, catalase-negative and oxidase-positive. Optimum growth occurred at 50-55 °C, 7-10% (w/v) NaCl and pH 7-8. The strain exhibited 95.4, 95.4 and 95.2% 16S rRNA gene sequence similarity to Thalassobacillus devorans G19.1(T), Sediminibacillus halophilus EN8d(T) and Virgibacillus kekensis YIM-kkny16(T), respectively. The major menaquinone was MK-7. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, three unknown phosphoglycolipids and two unknown phospholipids. The predominant cellular fatty acids were iso-C(15 : 0) and iso-C(17 : 0). The DNA G+C content was 41.9 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain Nari2A(T) is considered to represent a novel species of a new genus in the family Bacillaceae , order Bacillales , for which the name Melghiribacillus thermohalophilus gen. nov., sp. nov. is proposed. The type strain of Melghiribacillus thermohalophilus is Nari2A(T) ( = DSM 25894(T) = CCUG 62543(T)). PMID:25604343

  5. Roseimarinus sediminis gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from coastal sediment.

    PubMed

    Wu, Wen-Jie; Liu, Qian-Qian; Chen, Guan-Jun; Du, Zong-Jun

    2015-07-01

    A Gram-stain-negative, facultatively anaerobic, non-motile and pink-pigmented bacterium, designated strain HF08(T), was isolated from marine sediment of the coast of Weihai, China. Cells were rod-shaped, and oxidase- and catalase-positive. The isolate grew optimally at 33 °C, at pH 7.5-8.0 and with 2-3% (w/v) NaCl. The dominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C14 : 0. Menaquinone 7 (MK-7) was the major respiratory quinone and the DNA G+C content was 44.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the class Bacteroidia, and shared 88-90% sequence similarity with the closest genera Sunxiuqinia, Prolixibacter, Draconibacterium, Mariniphaga and Meniscus. Based on the phylogenetic and phenotypic evidence presented, a novel species in a new genus of the family Prolixibacteraceae is proposed, with the name Roseimarinus sediminis gen. nov., sp. nov. The type strain of Roseimarinus sediminis is HF08(T) ( = KCTC 42261(T) = CICC 10901(T)). PMID:25866024

  6. Flavobacterium arsenatis sp. nov., a novel arsenic-resistant bacterium from high-arsenic sediment.

    PubMed

    Ao, Lian; Zeng, Xian-Chun; Nie, Yao; Mu, Yao; Zhou, Lingli; Luo, Xuesong

    2014-10-01

    A novel bacterial strain Z(T) was isolated from the high-arsenic sediment in Jianghan Plain, China. The strain was Gram-staining-negative, rod-shaped and formed yellow colonies. This bacterium is capable of tolerating arsenate and arsenite, with MICs of 40 mM and 20 mM, respectively. The strain also possesses catalase and does not produce oxidase. The nucleotide sequence of the 16S rRNA gene of the isolate showed the highest similarity (96.9%) to that of the type strain of Flavobacterium soli. On the basis of the 16S rRNA gene sequence analysis and the phenotypic properties of strain Z(T), it was assigned to the genus Flavobacterium. The major respiratory menaquinone was MK-6 and the predominant fatty acids were iso-C15:0, summed feature 3 (containing C16:1ω6c and/or C16:1ω7c) and iso-C15:1G. The major polar lipids were phosphatidylethanolamine, three uncharacterized aminophospholipids and four unidentified phospholipids. The DNA G+C content was 32.1 mol%. Based on the phenotypic and genotypic data presented in this article, it can be concluded that this isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenatis sp. nov. is proposed. The type strain is Z(T) ( = CCTCC AB 2013048(T) = KCTC 32397(T)). PMID:25013224

  7. Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen.

    PubMed

    Oh, Tae-Jin; Han, So-Ra; Ahn, Do-Hwan; Park, Hyun; Kim, Augustine Yonghwi

    2016-06-10

    A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment. PMID:27063139

  8. Bacillus jeotgali sp. nov., isolated from jeotgal, Korean traditional fermented seafood.

    PubMed

    Yoon, J H; Kang, S S; Lee, K C; Kho, Y H; Choi, S H; Kang, K H; Park, Y H

    2001-05-01

    Two Gram-variable, rod-shaped, endospore-forming bacterial strains, which are motile with peritrichous flagella, were isolated from a Korean traditional fermented seafood, jeotgal. The two isolates (strains YKJ-1OT and YKJ-11) were proven to be members of the same species on the basis of the results of phenotypic and phylogenetic analyses and DNA relatedness. Strains YKJ-10T and YKJ-11 were characterized by having cell wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone, and iso-C15:0 as the major fatty acid. The G+C content of the DNA was 41 mol%. Strains YKJ-10T and YKJ-11 showed only a 1 bp sequence difference in the 16S rDNA sequences. The two strains formed distinct phylogenetic lineages within the radiation of the cluster comprising Bacillus species. Levels of 16S rDNA similarity between strains YKJ-10T and YKJ-11 and Bacillus species were less than 96.6%. Levels of DNA-DNA relatedness were found to be low enough to distinguish strains YKJ-10T and YKJ-11 from some phylogenetically related Bacillus species. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strains YKJ-10T and YKJ-11 represent a new species of the genus Bacillus, for which a new name, Bacillusjeotgali sp. nov., is proposed. The type strain of the new species is strain YKJ-10T (= KCCM 41040T = JCM 10885T). PMID:11411677

  9. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis

    NASA Astrophysics Data System (ADS)

    Li, Yongxin; Li, Zhongrui; Yamanaka, Kazuya; Xu, Ying; Zhang, Weipeng; Vlamakis, Hera; Kolter, Roberto; Moore, Bradley S.; Qian, Pei-Yuan

    2015-03-01

    Bacilli are ubiquitous low G+C environmental Gram-positive bacteria that produce a wide assortment of specialized small molecules. Although their natural product biosynthetic potential is high, robust molecular tools to support the heterologous expression of large biosynthetic gene clusters in Bacillus hosts are rare. Herein we adapt transformation-associated recombination (TAR) in yeast to design a single genomic capture and expression vector for antibiotic production in Bacillus subtilis. After validating this direct cloning ``plug-and-play'' approach with surfactin, we genetically interrogated amicoumacin biosynthetic gene cluster from the marine isolate Bacillus subtilis 1779. Its heterologous expression allowed us to explore an unusual maturation process involving the N-acyl-asparagine pro-drug intermediates preamicoumacins, which are hydrolyzed by the asparagine-specific peptidase into the active component amicoumacin A. This work represents the first direct cloning based heterologous expression of natural products in the model organism B. subtilis and paves the way to the development of future genome mining efforts in this genus.

  10. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis

    PubMed Central

    Li, Yongxin; Li, Zhongrui; Yamanaka, Kazuya; Xu, Ying; Zhang, Weipeng; Vlamakis, Hera; Kolter, Roberto; Moore, Bradley S.; Qian, Pei-Yuan

    2015-01-01

    Bacilli are ubiquitous low G+C environmental Gram-positive bacteria that produce a wide assortment of specialized small molecules. Although their natural product biosynthetic potential is high, robust molecular tools to support the heterologous expression of large biosynthetic gene clusters in Bacillus hosts are rare. Herein we adapt transformation-associated recombination (TAR) in yeast to design a single genomic capture and expression vector for antibiotic production in Bacillus subtilis. After validating this direct cloning “plug-and-play” approach with surfactin, we genetically interrogated amicoumacin biosynthetic gene cluster from the marine isolate Bacillus subtilis 1779. Its heterologous expression allowed us to explore an unusual maturation process involving the N-acyl-asparagine pro-drug intermediates preamicoumacins, which are hydrolyzed by the asparagine-specific peptidase into the active component amicoumacin A. This work represents the first direct cloning based heterologous expression of natural products in the model organism B. subtilis and paves the way to the development of future genome mining efforts in this genus. PMID:25807046

  11. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis.

    PubMed

    Li, Yongxin; Li, Zhongrui; Yamanaka, Kazuya; Xu, Ying; Zhang, Weipeng; Vlamakis, Hera; Kolter, Roberto; Moore, Bradley S; Qian, Pei-Yuan

    2015-01-01

    Bacilli are ubiquitous low G+C environmental Gram-positive bacteria that produce a wide assortment of specialized small molecules. Although their natural product biosynthetic potential is high, robust molecular tools to support the heterologous expression of large biosynthetic gene clusters in Bacillus hosts are rare. Herein we adapt transformation-associated recombination (TAR) in yeast to design a single genomic capture and expression vector for antibiotic production in Bacillus subtilis. After validating this direct cloning "plug-and-play" approach with surfactin, we genetically interrogated amicoumacin biosynthetic gene cluster from the marine isolate Bacillus subtilis 1779. Its heterologous expression allowed us to explore an unusual maturation process involving the N-acyl-asparagine pro-drug intermediates preamicoumacins, which are hydrolyzed by the asparagine-specific peptidase into the active component amicoumacin A. This work represents the first direct cloning based heterologous expression of natural products in the model organism B. subtilis and paves the way to the development of future genome mining efforts in this genus. PMID:25807046

  12. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    SciTech Connect

    Bollmann, Annette; Sedlacek, Christopher J; Laanbroek, Hendrikus J; Suwa, Yuichi; Stein, Lisa Y; Klotz, Martin G; Arp, D J; Sayavedra-Soto, LA; Lu, Megan; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos C; Mavromatis, K; Markowitz, Victor; Szeto, Ernest; Ivanova, N; Mikhailova, Natalia; Pagani, Ioanna; Pati, Amrita; Peters, Lin; Ovchinnikova, Galina; Goodwin, Lynne A.

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

  13. Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil

    PubMed Central

    Ehara, Ayaka; Suzuki, Haruo

    2015-01-01

    Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance. PMID:25635012

  14. Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.

    PubMed

    Ehara, Ayaka; Suzuki, Haruo; Amachi, Seigo

    2015-01-01

    Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance. PMID:25635012

  15. Isolation and identification of berberine and berberrubine metabolites by berberine-utilizing bacterium Rhodococcus sp. strain BD7100.

    PubMed

    Ishikawa, Kazuki; Takeda, Hisashi; Wakana, Daigo; Sato, Fumihiko; Hosoe, Tomoo

    2016-05-01

    Based on the finding of a novel berberine (BBR)-utilizing bacterium, Rhodococcus sp. strain BD7100, we investigated the degradation of BBR and its analog berberrubine (BRU). Resting cells of BD7100 demethylenated BBR and BRU, yielding benzeneacetic acid analogs. Isolation of benzeneacetic acid analogs suggested that BD7100 degraded the isoquinoline ring of the protoberberine skeleton. This work represents the first report of cleavage of protoberberine skeleton by a microorganism. PMID:26882131

  16. Tenacibactins A-D, hydroxamate siderophores from a marine-derived bacterium, Tenacibaculum sp. A4K-17.

    PubMed

    Jang, Jae-Hyuk; Kanoh, Kaneo; Adachi, Kyoko; Matsuda, Satoru; Shizuri, Yoshikazu

    2007-04-01

    Four new hydroxamate siderophores, tenacibactins A-D (1-4), were isolated from a culture broth of the marine-derived bacterium Tenacibaculum sp. A4K-17. The structures of these tenacibactins were determined by NMR analyses and ESIMS/MS experiments. The iron-binding (chelating) activity of 1-4 was evaluated by the chrome azurol sulfonate (CAS) assay. PMID:17319723

  17. Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi).

    PubMed

    Thiel, Vera; Hamilton, Trinity L; Tomsho, Lynn P; Burhans, Richard; Gay, Scott E; Schuster, Stephan C; Ward, David M; Bryant, Donald A

    2014-01-01

    The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons. PMID:25189583

  18. Draft Genome Sequence of a Sulfide-Oxidizing, Autotrophic Filamentous Anoxygenic Phototrophic Bacterium, Chloroflexus sp. Strain MS-G (Chloroflexi)

    PubMed Central

    Thiel, Vera; Hamilton, Trinity L.; Tomsho, Lynn P.; Burhans, Richard; Gay, Scott E.; Schuster, Stephan C.; Ward, David M.

    2014-01-01

    The draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain MS-G (Chloroflexi), isolated from Mushroom Spring (Yellowstone National Park, WY, USA) was sequenced and comprises 4,784,183 bp in 251 contigs. The draft genome is predicted to encode 4,059 protein coding genes, 49 tRNA encoding genes, and 3 rRNA operons. PMID:25189583

  19. Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

    SciTech Connect

    Arai, Shigeki; Yonezawa, Yasushi; Ishibashi, Matsujiro; Matsumoto, Fumiko; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko; Blaber, Michael; Tokunaga, Masao; Kuroki, Ryota

    2014-03-01

    In order to clarify the structural basis of the halophilic characteristics of an alkaline phosphatase derived from the moderate halophile Halomonas sp. 593 (HaAP), the tertiary structure of HaAP was determined to 2.1 Å resolution by X-ray crystallography. The structural properties of surface negative charge and core hydrophobicity were shown to be intermediate between those characteristic of halophiles and non-halophiles, and may explain the unique functional adaptation to a wide range of salt concentrations. Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1–4 M NaCl). In order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique ‘crown’ domain containing an extended ‘arm’ structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (C{sup α} r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior

  20. Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability.

    PubMed

    Uroz, Stéphane; Oger, Phil

    2015-01-01

    We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France). PMID:26205858

  1. Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability

    PubMed Central

    Oger, Phil

    2015-01-01

    We report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France). PMID:26205858

  2. Activation of Pathogenesis-related Genes by the Rhizobacterium, Bacillus sp. JS, Which Induces Systemic Resistance in Tobacco Plants.

    PubMed

    Kim, Ji-Seong; Lee, Jeongeun; Lee, Chan-Hui; Woo, Su Young; Kang, Hoduck; Seo, Sang-Gyu; Kim, Sun-Hyung

    2015-06-01

    Plant growth promoting rhizobacteria (PGPR) are known to confer disease resistance to plants. Bacillus sp. JS demonstrated antifungal activities against five fungal pathogens in in vitro assays. To verify whether the volatiles of Bacillus sp. JS confer disease resistance, tobacco leaves pre-treated with the volatiles were damaged by the fungal pathogen, Rhizoctonia solani and oomycete Phytophthora nicotianae. Pre-treated tobacco leaves had smaller lesion than the control plant leaves. In pathogenesis-related (PR) gene expression analysis, volatiles of Bacillus sp. JS caused the up-regulation of PR-2 encoding β-1,3-glucanase and acidic PR-3 encoding chitinase. Expression of acidic PR-4 encoding chitinase and acidic PR-9 encoding peroxidase increased gradually after exposure of the volatiles to Bacillus sp. JS. Basic PR-14 encoding lipid transfer protein was also increased. However, PR-1 genes, as markers of salicylic acid (SA) induced resistance, were not expressed. These results suggested that the volatiles of Bacillus sp. JS confer disease resistance against fungal and oomycete pathogens through PR genes expression. PMID:26060440

  3. Molecular characterization of alkaline protease of Bacillus amyloliquefaciens SP1 involved in biocontrol of Fusarium oxysporum.

    PubMed

    Guleria, Shiwani; Walia, Abhishek; Chauhan, Anjali; Shirkot, C K

    2016-09-01

    An alkaline protease gene was amplified from genomic DNA of Bacillus amyloliquefaciens SP1 which was involved in effective biocontrol of Fusarium oxysporum. We investigated the antagonistic capacity of protease of B. amyloliquifaciens SP1, under in vitro conditions. The 5.62 fold purified enzyme with specific activity of 607.69U/mg reported 24.14% growth inhibition of F. oxysporum. However, no antagonistic activity was found after addition of protease inhibitor i.e. PMSF (15mM) to purified enzyme. An 1149bp nucleotide sequence of protease gene encoded 382 amino acids of 43kDa and calculated isoelectric point of 9.29. Analysis of deduced amino acid sequence revealed high homology (86%) with subtilisin E of Bacillus subtilis. The B. amyloliquefaciens SP1 protease gene was expressed in Escherichiax coli BL21. The expressed protease was secreted into culture medium by E. coli and exhibited optimum activity at pH8.0 and 60°C. The most reliable three dimensional structure of alkaline protease was determined using Phyre 2 server which was validated on the basis of Ramachandran plot and ERRAT value. The expression and structure prediction of the enzyme offers potential value for commercial application in agriculture and industry. PMID:27294522

  4. Isolation and characterization of mesotrione-degrading Bacillus sp. from soil.

    PubMed

    Batisson, Isabelle; Crouzet, Olivier; Besse-Hoggan, Pascale; Sancelme, Martine; Mangot, Jean-François; Mallet, Clarisse; Bohatier, Jacques

    2009-04-01

    Dissipation kinetics of mesotrione, a new triketone herbicide, sprayed on soil from Limagne (Puy-de-Dôme, France) showed that the soil microflora were able to biotransform it. Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods. Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it. PMID:19121884

  5. Halomonas urumqiensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake.

    PubMed

    Zhang, Shanshan; Pan, Jiao; Lu, Weidong; Yan, Yanchun; Wang, Haisheng; Wiegel, Jurgen; Zhao, Baisuo

    2016-05-01

    A moderately halophilic, aerobic bacterium, strain BZ-SZ-XJ27T, belonging to the genus Halomonas, was isolated from a saline-alkaline lake in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences and a multilocus sequence analysis using the 16S rRNA, gyrB and rpoD genes demonstrated that strain BZ-SZ-XJ27T represents a member of the genus Halomonas. On the basis of 16S rRNA gene sequence similarity, the closest relatives were Halomonas campaniensis 5AGT, H. fontilapidosi 5CRT, H. korlensis XK1T and H. sinaiensis ALO SharmT, with similarities of 96.2-97.2 %. DNA-DNA hybridization with H. korlensis CGMCC 1.6981T (the nearest phylogenetic neighbour) and H. campaniensis DSM 15293T (the highest 16S rRNA gene sequence similarity) showed relatedness values of 53 and 38 %, respectively, demonstrating the separateness of the three taxa. The bacterium stained Gram-negative and the cells were motile and rod-shaped. The strain formed creamy-white colonies and grew under optimal conditions of 1.42 M Na+ (range 0.22-4.32 M Na+), pH 8.0-8.5 (range pH 6.0-10.0) and 39 °C (range 4-43 °C). The dominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 36.6 %), C16 : 0 (25.9 %) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.2 %). The dominant polar lipids were two unknown phospholipids, phosphatidylethanolamine and phosphatidylglycerol, and the main respiratory quinones were ubiquinone 9 (Q-9; 89 %) and ubiquinone 8 (Q-8; 10 %). The genomic DNA G+C content was 61.7 ± 0.8 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ27T is proposed to represent a novel species, Halomonas urumqiensis sp. nov., within the genus Halomonas of the family Halomonadaceae. The type strain is BZ-SZ-XJ27T ( = JCM 30202T = CGMCC 1.12917T). PMID:26873696

  6. Cloning and nucleotide sequence of the gene coding for citrate synthase from a thermotolerant Bacillus sp

    SciTech Connect

    Schendel, F.J.; August, P.R.; Anderson, C.R.; Flickinger, M.C. ); Hanson, R.S. )

    1992-01-01

    Acetate salts are emerging as potentially attractive bulk chemicals for a variety of environmental applications, for example, as catalysts to facilitate combustion of high-sulfur coal by electrical utilities and as the biodegradable noncorrosive highway deicing salt calcium magnesium acetate. The structural gene coding for citrate synthase from the gram-positive soil isolate Bacillus sp. strain C4 (ATCC 55182) capable of secreting acetic acid at pH 5.0 to 7.0 in the presence of dolime has been cloned from a genomic library by complementation of an Escherichia coli auxotrophic mutant lacking citrate synthase. The nucleotide sequence of the entire 3.1-kb HindIII fragment has been determined, and one major open reading frame was found coding for citrate synthase (ctsA). Citrate synthase from Bacillus sp. strain C4 was found to be a dimer (M{sub r}, 84,500) with a sub unit with an M{sub r} of 42,000. The N-terminal sequence was found to be identical with that predicted from the gene sequence. The kinetics were best fit to a bisubstrate enzyme with an ordered mechanism. Bacillus sp. strain C4 citrate synthase was not activated by potassium chloride and was not inhibited by NADH, ATP, ADP, or AMP at levels up to 1 mM. The predicted amino acid sequence was compared with that of the E. coli, Acinetobacter anitratum, Pseudomonas aeruginosa, Rickettsia prowazekii, porcine heart, and Saccharomyces cerevisiae cytoplasmic and mitochondrial enzymes.

  7. Influence of plaque-forming bacterium, Rhodobacteraceae sp. on the growth of Chlorella vulgaris.

    PubMed

    Chen, Zhangran; Zhang, Jingyan; Lei, Xueqian; Zhang, Bangzhou; Cai, Guanjing; Zhang, Huajun; Li, Yi; Zheng, Wei; Tian, Yun; Xu, Hong; Zheng, Tianling

    2014-10-01

    Experiments were conducted to find out the molecular features, infection process of a special alga plaque-forming microorganism and its potential influence on the biomass of Chlorella vulgaris during the infection process. Direct contact between the algal cell and the bacterium may be the primary steps needed for the bacterium to lyse the alga. Addition of C. vulgaris cells into f/2 medium allowed us obtain the object bacterium. The 16S rRNA gene sequence comparisons results showed that the plaque-forming bacterium kept the closest relationship with Labrenzia aggregata IAM 12614(T) at 98.90%. The existence of the bacterium could influence both the dry weight and lipid content of C. vulgaris. This study demonstrated that direct cell wall disruption of C. vulgaris by the bacterium would be a potentially effective method to utilize the biomass of microalgae. PMID:25086475

  8. Influence of culture conditions on thermostable lipase production by a thermophilic alkalitolerant strain of Bacillus sp.

    PubMed

    Kambourova, M; Emanuilova, E; Dimitrov, P

    1996-01-01

    The effect of different culture conditions on thermostable lipase production by Bacillus sp. was studied in shake flasks. A maximum enzyme activity of 67-75 nkat/mL was observed in a medium consisting of 0.5% soybean flour and 0.1% stearyl glycerol esters or natural fats. A lipase activity of about 117 nkat/mL was established when the cultivation was carried out in a laboratory fermentor at 20% minimal dissolved oxygen level, the enzyme production being increased 1.5 fold compared to that in a flask culture. PMID:9138309

  9. Draft Genome Sequence of Bacillus marisflavi TF-11T (JCM 11544), a Carotenoid-Producing Bacterium Isolated from Seawater from a Tidal Flat in the Yellow Sea

    PubMed Central

    Wang, Jie-ping; Liu, Guo-hong; Chen, De-ju; Chen, Qian-qian; Zhu, Yu-jing; Chen, Zheng; Che, Jian-mei

    2015-01-01

    Bacillus marisflavi TF-11T (JCM 11544) is a Gram-positive, spore-forming, and carotenoid-producing bacterium isolated from seawater from a tidal flat in the Yellow Sea. Here, we report the first draft genome sequence of B. marisflavi TF-11T, which comprises 4.31 Mb in 11 scaffolds with a G+C content of 48.57%. PMID:26659687

  10. Antioxidant Properties of Fish Protein Hydrolysates Prepared from Cod Protein Hydrolysate by Bacillus sp.

    PubMed

    Godinho, I; Pires, C; Pedro, S; Teixeira, B; Mendes, R; Nunes, M L; Batista, I

    2016-03-01

    Fermentative protein hydrolysates (FPH) were prepared with a proteolytic bacterium, Bacillus strain exhibiting high proteolytic activity. Three FPH with 1, 2, and 4 % of cod protein hydrolysate (CPH) and 0.5 % of yeast extract in the culture were prepared. The yields achieved varied between 30 and 58 % based on protein content. A general decrease of leucine, isoleucine, valine, alanine, arginine, threonine, proline, and glutamic acid was observed. All FPHs showed higher reducing power and DPPH radical scavenging activity than CPH, but similar ABTS radical scavenging activity. However, FPHs exhibited lower Cu(+2)-chelating activity than CPH. The ACE inhibitory activity of FPHs was not improved relatively to that recorded in CPH. The fermentative process seems to have potential to obtaining hydrolysates with improved biological activities or even to produce protein hydrolysates from native fish proteins. PMID:26590847

  11. Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

    PubMed Central

    Arai, Shigeki; Yonezawa, Yasushi; Ishibashi, Matsujiro; Matsumoto, Fumiko; Adachi, Motoyasu; Tamada, Taro; Tokunaga, Hiroko; Blaber, Michael; Tokunaga, Masao; Kuroki, Ryota

    2014-01-01

    Alkaline phosphatase (AP) from the moderate halophilic bacterium Halomonas sp. 593 (HaAP) catalyzes the hydrolysis of phosphomonoesters over a wide salt-concentration range (1–4 M NaCl). In order to clarify the structural basis of its halophilic characteristics and its wide-range adaptation to salt concentration, the tertiary structure of HaAP was determined by X-ray crystallography to 2.1 Å resolution. The unit cell of HaAP contained one dimer unit corresponding to the biological unit. The monomer structure of HaAP contains a domain comprised of an 11-stranded β-sheet core with 19 surrounding α-helices similar to those of APs from other species, and a unique ‘crown’ domain containing an extended ‘arm’ structure that participates in formation of a hydrophobic cluster at the entrance to the substrate-binding site. The HaAP structure also displays a unique distribution of negatively charged residues and hydrophobic residues in comparison to other known AP structures. AP from Vibrio sp. G15-21 (VAP; a slight halophile) has the highest similarity in sequence (70.0% identity) and structure (Cα r.m.s.d. of 0.82 Å for the monomer) to HaAP. The surface of the HaAP dimer is substantially more acidic than that of the VAP dimer (144 exposed Asp/Glu residues versus 114, respectively), and thus may enable the solubility of HaAP under high-salt conditions. Conversely, the monomer unit of HaAP formed a substantially larger hydrophobic interior comprising 329 C atoms from completely buried residues, whereas that of VAP comprised 264 C atoms, which may maintain the stability of HaAP under low-salt conditions. These characteristics of HaAP may be responsible for its unique functional adaptation permitting activity over a wide range of salt concentrations. PMID:24598750

  12. Gordonibacter urolithinfaciens sp. nov., a urolithin-producing bacterium isolated from the human gut.

    PubMed

    Selma, María V; Tomás-Barberán, Francisco A; Beltrán, David; García-Villalba, Rocio; Espín, Juan C

    2014-07-01

    Urolithins are dibenzopyranone metabolites that exert anti-inflammatory activity in vivo and are produced by the gut microbiota from the dietary polyphenols ellagic acid (EA) and ellagitannins. However, the bacteria involved in this process remain unknown. We report here a novel bacterium, strain CEBAS 1/15P(T), capable of metabolizing EA to urolithins, that was isolated from healthy human faeces and characterized by determining phenotypic, biochemical and molecular methods. The strain was related to Gordonibacter pamelaeae 7-10-1-b(T), the type and only reported strain of the only species of the genus Gordonibacter, with about 97% 16S rRNA gene sequence similarity; they were both obligately anaerobic, non-spore-forming, Gram-stain-positive, short-rods/coccobacilli and metabolized only small numbers of carbon sources. L-Fucose, D-fructose, turanose, D-galacturonic acid and α-ketobutyric acid were metabolized by strain CEBAS 1/15P(T), while G. pamelaeae was negative for metabolism of these compounds. The whole-cell fatty acids consisted predominantly of saturated fatty acids (70%); strain CEBAS 1/15P(T) differed significantly from G. pamelaeae in the major fatty acid, which was C18 : 1ω9c, while anteiso-C15 : 0 was the major component for G. pamelaeae. The presence of a number of different fatty acid peaks, especially C19 : 0 cyclo and C18 : 1ω6c, was also indicative of distinct species. Six glycolipids (GL1-6) were recognized, while, in G. pamelaeae, only four glycolipids were described. On the basis of these data, the novel species Gordonibacter urolithinfaciens sp. nov. is described, with strain CEBAS 1/15P(T) ( = DSM 27213(T) = CCUG 64261(T)) as the type strain. PMID:24744017

  13. Arenimonas taoyuanensis sp. nov., a novel bacterium isolated from rice-field soil in China.

    PubMed

    Zhang, Shi-Ying; Xiao, Wei; Xia, Yun-Sheng; Wang, Yong-Xia; Cui, Xiao-Long; Zhang, Nai-Ming

    2015-05-01

    A Gram-stain negative, aerobic, rod-shaped bacterial strain, YN2-31A(T), was isolated from rice-field soil, Taoyuan Village, Yunnan province of China. The bacterium was observed to grow at 20-45 °C (optimum 28 °C), at pH 5.0-10.0 (optimum 7.0), and in the presence of 0-2% (w/v) NaCl (optimum 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2-31A(T) is most closely related to Arenimonas daejeonensis DSM 18060(T) (96.1%), Arenimonas malthae DSM 21305(T) (95.9%), Arenimonas donghaensis DSM 18148(T) (95.1%), Arenimonas composti DSM 18010(T) (94.8%) and Arenimonas maotaiensis JCM 19710(T) (94.8%). The major cellular fatty acids (>10%) were found to be iso-C(18:1) ω9c, iso-C(15:0), Sum In Feature 3 (C(16:1) ω7c/C(16:1) ω6c), and C(16:0). The major ubiquinone was identified as Q-8 and the major cellular polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The genomic DNA G+C content was determined to be 72.3 mol%. The results of the phylogenetic, genetic, phenotypic and chemotaxonomic analyses suggest that strain YN2-31A(T) represents a novel species of the genus Arenimonas, for which the name Arenimonas taoyuanensis sp. nov. is proposed. The type strain is YN2-31A(T) (=DSM 26777(T) = CCTCC AB2012964(T)). PMID:25731739

  14. Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba.

    PubMed

    Han, Tong-Yan; Tong, Xiao-Mei; Wang, Yan-Wei; Wang, Hui-Min; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; Ruan, Zhi-Yong

    2015-09-01

    A novel aerobic bacterium, designated strain LAM0705(T), was isolated from the rhizosphere of Populus alba in the Peking University Third Hospital. Cells of strain LAM0705(T) were observed to be Gram-stain positive, motile, spore-forming and rod-shaped. The optimal temperature and pH for growth were found to be 30 °C and pH 7.5, respectively. Strain LAM0705(T) was found to be able to grow in the presence 0-5 % NaCl (w/v) (optimum 1.0 %). The major fatty acids of strain LAM0705(T) were identified as anteiso-C15:0, C16:0 and iso-C16:0. The dominant polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The cell wall peptidoglycan of strain LAM0705(T) was found to contain meso-diaminopimelic acid. The predominant menaquinone was identified as MK-7. The G+C content of genomic DNA was found to be 48 mol% when determined by the T m method. The 16S rRNA gene sequence similarity analysis indicated that strain LAM0705(T) is closely related to Paenibacillus agaridevorans DSM 1355(T) and Paenibacillus thailandensis KCTC 13043(T) with 97.8 and 96.1 % sequence similarity, respectively. The DNA-DNA hybridization value between strain LAM0705(T) and P. agaridevorans DSM 1355(T) was 47 ± 0.8 %. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0705(T) is concluded to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus populi sp. nov. is proposed. The type strain is LAM0705(T) (=ACCC 06427(T) = JCM 19843(T)). PMID:26133115

  15. Thermosipho activus sp. nov., a thermophilic, anaerobic, hydrolytic bacterium isolated from a deep-sea sample.

    PubMed

    Podosokorskaya, Olga A; Bonch-Osmolovskaya, Elizaveta A; Godfroy, Anne; Gavrilov, Sergey N; Beskorovaynaya, Daria A; Sokolova, Tatyana G; Kolganova, Tatyana V; Toshchakov, Stepan V; Kublanov, Ilya V

    2014-09-01

    A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3(T), was isolated from a deep-sea sample containing Riftia pachyptila sheath from Guaymas Basin, Gulf of California. Cells of the novel isolate were rods, 0.3-0.8 µm in width and 1.5-10 µm in length, surrounded by a sheath-like structure (toga). Strain Rift-s3(T) grew at temperatures ranging from 44 to 75 °C, at pH 5.5 to 8.0, and with NaCl concentrations of 3 to 60 g l(-1). Under optimum conditions (65 °C, pH 6.0, NaCl 25 g l(-1)), the doubling time was 30 min. The isolate was able to ferment mono-, oligo- and polysaccharides including cellulose, chitin, xylan and pectin, and proteins including β-keratins, casein and gelatin. Acetate, hydrogen and carbon dioxide were the main products of glucose fermentation. The G+C content of the DNA was 30 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed the affiliation of strain Rift-s3(T) with the genus Thermosipho, with Thermosipho atlanticus Ob7(T) as the closest relative (96.5 % 16S rRNA gene sequence similarity). Based on the phylogenetic analysis and physiological properties of the novel isolate we propose a novel species of the genus Thermosipho, Thermosipho activus sp. nov., with Rift-s3(T) ( = DSM 26467(T) = VKM B-2803(T)) as the type strain. PMID:24994778

  16. Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal.

    PubMed

    Chang, Chi-huan; Chen, Yi-sheng; Lee, Tzu-tai; Chang, Yu-chung; Yu, Bi

    2015-01-01

    A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215(T), was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215(T) had 98.74-99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus (Lactobacillus farciminis BCRC 14043(T), Lactobacillus futsaii BCRC 80278(T) and Lactobacillus crustorum JCM 15951(T)). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215(T) was well separated from the reference strains of species of the genus Lactobacillus. DNA-DNA hybridization results indicated that strain S215(T) had DNA related to the three type strains of species of the genus Lactobacillus (33-66 % relatedness). The DNA G+C content of strain S215(T) was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus, for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215(T) ( = NBRC 109509(T) = BCRC 80582(T)). PMID:25281727

  17. Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample.

    PubMed

    Chen, Wei; Zhao, Ying-Liang; Cheng, Juan; Zhou, Xing-Kui; Salam, Nimaichand; Fang, Bao-Zhu; Li, Qing-Qing; Hozzein, Wael N; Li, Wen-Jun

    2016-07-01

    A Gram-staining negative, aerobic, rod-shaped bacterium, designated YIM C01544(T), was isolated from a soil sample collected from Sigangli Cave, Yunnan province, South-West China. The strain was able to grow over a range of temperatures (4-30 °C), pH (6.0-10.0) and NaCl concentration (0-2 %, w/v). Comparative 16S rRNA gene sequence analysis revealed that strain YIM C01544(T) should be a member of the genus Lysobacter. The strain is closely related to Lysobacter niastensis GH41-7(T) (97.6 %), Lysobacter soli DCY21(T) (97.5 %), Lysobacter enzymogenes DSM 2043(T) (97.3 %), Lysobacter antibioticus DSM 2044(T) (97.1 %) and Lysobacter panacisoli CJ29(T) (97.1 %). The genomic DNA relatedness values (<47 %) as indicated by DNA-DNA hybridization studies were below the threshold limit for characterization of new bacterial species. The chemotaxonomic features of the new isolate include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and two unidentified polar lipids as its characteristic polar lipids and Q-8 as the only quinone. The major fatty acids detected were iso-C15:0 and iso-C17:1 ω9c. The DNA G + C content of the strain was determined to be 64.9 mol %. Based on the data from phenotypic, chemotaxonomic and molecular studies, strain YIM C01544(T) merits recognition as novel species in the genus Lysobacter for which the name Lysobacter cavernae sp. nov. is proposed. The type strain of Lysobacter cavernae is YIM C01544(T) (= KCTC 42875(T) = DSM 101561(T) = CPCC 100816(T)). PMID:27180096

  18. Metabolism of 2-Methylpropene (Isobutylene) by the Aerobic Bacterium Mycobacterium sp. Strain ELW1

    PubMed Central

    Kottegoda, Samanthi; Waligora, Elizabeth

    2015-01-01

    An aerobic bacterium (Mycobacterium sp. strain ELW1) that utilizes 2-methylpropene (isobutylene) as a sole source of carbon and energy was isolated and characterized. Strain ELW1 grew on 2-methylpropene (growth rate = 0.05 h−1) with a yield of 0.38 mg (dry weight) mg 2-methylpropene−1. Strain ELW1 also grew more slowly on both cis- and trans-2-butene but did not grow on any other C2 to C5 straight-chain, branched, or chlorinated alkenes tested. Resting 2-methylpropene-grown cells consumed ethene, propene, and 1-butene without a lag phase. Epoxyethane accumulated as the only detected product of ethene oxidation. Both alkene consumption and epoxyethane production were fully inhibited in cells exposed to 1-octyne, suggesting that alkene oxidation is initiated by an alkyne-sensitive, epoxide-generating monooxygenase. Kinetic analyses indicated that 1,2-epoxy-2-methylpropane is rapidly consumed during 2-methylpropene degradation, while 2-methyl-2-propen-1-ol is not a significant metabolite of 2-methylpropene catabolism. Degradation of 1,2-epoxy-2-methylpropane by 2-methylpropene-grown cells led to the accumulation and further degradation of 2-methyl-1,2-propanediol and 2-hydroxyisobutyrate, two sequential metabolites previously identified in the aerobic microbial metabolism of methyl tert-butyl ether (MTBE) and tert-butyl alcohol (TBA). Growth of strain ELW1 on 2-methylpropene, 1,2-epoxy-2-methylpropane, 2-methyl-1,2-propanediol, and 2-hydroxyisobutyrate was fully inhibited when cobalt ions were omitted from the growth medium, while growth on 3-hydroxybutyrate and other substrates was unaffected by the absence of added cobalt ions. Our results suggest that, like aerobic MTBE- and TBA-metabolizing bacteria, strain ELW1 utilizes a cobalt/cobalamin-dependent mutase to transform 2-hydroxyisobutyrate. Our results have been interpreted in terms of their impact on our understanding of the microbial metabolism of alkenes and ether oxygenates. PMID:25576605

  19. Thermus anatoliensis sp. nov., a thermophilic bacterium from geothermal waters of Buharkent, Turkey.

    PubMed

    Kacagan, Murat; Inan, Kadriye; Canakci, Sabriye; Guler, Halil Ibrahim; Belduz, Ali Osman

    2015-12-01

    A Gram-stain-negative, lack of motility, catalase- and oxidase- positive bacterium (strain MT1(T)) was isolated from Buharkent hot spring in Aydin, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain was able to grow at 45-80 °C, pH 5.5-10.5 and with a NaCI tolerance up to 2.0% (w/v). Strain MT1(T) was able to utilize d-mannitol and l-arabinose, not able to utilize d-cellobiose as sole carbon source. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Thermus; strain MT1(T) detected low-level similarities of 16S rRNA gene sequences (below 97%) compared with all other species in this genus. The predominant fatty acids of strain MT1(T) were iso-C(15:0) (43.0%) and iso-C(17:0) (27.4%). Polar lipid analysis revealed a major phospholipid, one major glycolipid, one major aminophospholipid, two minor aminolipids, one minor phospholipid, and several minor glycolipids. The major isoprenoid quinone was MK-8. The DNA G+C content of MT1(T) was 69.6 mol%. On the basis of a taxonomic study using a polyphasic approach, strain MT1(T) is considered to represent a novel species of the genus Thermus, for which the name Thermus anatoliensis sp. nov. is proposed. The type strain is MT1(T) (=NCCB 100425(T) =LMG 26880(T)). PMID:26272788

  20. Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae.

    PubMed

    Zhang, Gaiyun; Yang, Yanliu; Wang, Shuang; Sun, Zhilei; Jiao, Kailin

    2015-08-01

    A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4-50 °C, pH 6-11 and 0-10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4%), followed by Ponticoccus litoralis CL-GR66T (96.4%), Antarctobacter heliothermus EL-219T (96.3%) and Thalassococcus lentus YCS-24T (96.0%). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2%), anteiso-C15 : 0 (30.4%) and anteiso-C17 : 0 (9.7%). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T). PMID:25908713

  1. Chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.

    PubMed

    Akter, Shahina; NGO, Hien T T; Du, Juan; Won, KyungHwa; Singh, Hina; Yin, Chang Shik; Kook, MooChang; Yi, Tae-Hoo

    2015-10-01

    A Gram-reaction-negative, non-motile and rod-shaped bacterium, designated as THG-DN3.6(T), was isolated from an ancient tree trunk from Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain THG-DN3.6(T) was shown to belong to the genus Chryseobacterium and the highest similarity to Chryseobacterium indoltheticum LMG 4025(T) (97.2%) and the closest phylogenetic relatives were Chryseobacterium scophthalmum (96.8%), Chryseobacterium piscium (96.7%) and Chryseobacterium balustinum KCTC 2903(T) (96.3%). The DNA G + C content of the isolate was 33.2 mol%. The predominant isoprenoid quinone was menaquinone-6. The major fatty acids were iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω7t and/or iso-C15:0 2-OH), iso-C17:1 ω9c and iso-C17:0 3-OH. The major polar lipids of strain THG-DN3.6(T) were phosphatidylethanolamine. The mean DNA-DNA relatedness of strain THG-DN3.6(T) to C. indoltheticum LMG 4025(T) was 52 ± 0.5%. Based on the results of polyphasic characterization, strain THG-DN3.6(T) represented a novel species within the genus Chryseobacterium, for which the name Chryseobacterium formosus sp. nov. is proposed. The type strain is THG-DN3.6(T) (=KCTC 42606 = CCTCC AB 2015118). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain THG-DN3.6(T) is KM035938. PMID:26210236

  2. Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae.

    PubMed

    Menes, Rodolfo Javier; Viera, Claudia Elizabeth; Farías, María Eugenia; Seufferheld, Manfredo J

    2016-01-01

    A Gram-negative, halophilic, heterotrophic, rod-shaped, non-spore-forming bacterium (SV525T) was isolated from the sediment of a hypersaline lake located at 4600 m above sea level (Laguna Vilama, Argentina). Strain SV525T was strictly aerobic and formed pink-to-magenta colonies. Growth occurred at 10–35 °C (optimum 25–30 °C), at pH levels 6.0–8.5 (optimum 7.0) and at NaCl concentrations of 7.5–25 % (w/v) with an optimum at 10–15 % (w/v). The strain required sodium and magnesium but not potassium ions for growth. Grows with tryptone, or Bacto Peptone as sole carbon and energy source and requires yeast extract for growth. It produced catalase and oxidase. The predominant ubiquinone was Q-8 and the major fatty acids comprised C18:1 ω7c, C16:0 and C18:0. The DNA G+C content was 60.4 mol% and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene indicated that strain SV525T belongs to the family Ectothiorhodospiraceae within the class Gammaproteobacteria. On the basis of phylogenetic and phenotypic data, SV525T represents a novel genus and species, for which the name Halopeptonella vilamensis gen. nov., sp. nov. is proposed. The type strain is SV525T (=DSM 21056T =JCM 16388T =NCIMB 14596T). PMID:26475627

  3. Paenibacillus lemnae sp. nov., an endophytic bacterium of duckweed (Lemna aequinoctialis).

    PubMed

    Kittiwongwattana, Chokchai; Thawai, Chitti

    2015-01-01

    A Gram-stain-variable, rod-shaped and endospore-forming bacterium, designated strain L7-75, was isolated from duckweed (Lemna aequinoctialis). Cells were motile with a monopolar flagellum. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain L7-75(T) belonged to the genus Paenibacillus, and the closest phylogenetically related species were Paenibacillus uliginis N3/975(T) (98.5% 16S rRNA gene sequence similarity), Paenibacillus purispatii ES_M17(T) (98.5%), Paenibacillus lactis MB 1871(T) (98.2%), Paenibacillus campinasensis 324(T) (97.7%), Paenibacillus glucanolyticus S93(T) (97.7%) and Paenibacillus lautus ATCC 43898(T) (97.4%). Growth of strain L7-75(T) was observed at pH 7-10 and at 20-40 °C, and NaCl concentrations up to 5% (w/v) were tolerated. Major cellular fatty acids included anteiso-C15 : 0, C16 : 0 and anteiso-C17:0 that were present at 36.0%, 14.2 % and 10.0% of the total cellular fatty acid profile, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. MK-7 was the predominant menaquinone. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA G+C content was 49.1 mol% (Tm). DNA-DNA relatedness values between strain L7-75(T) and its closest relatives ranged from 4.4 to 47.8%. These results indicate that strain L7-75(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lemnae sp. nov. is proposed. The type strain is L7-75(T) ( = BCC 67838(T) = NBRC 109972(T)). PMID:25288280

  4. Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil.

    PubMed

    Li, Qin-Fen; Sun, Li-Na; Kwon, Soon-Wo; Chen, Qing; He, Jian; Li, Shun-Peng; Zhang, Jun

    2014-06-01

    A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8(T), was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97% sequence similarity to strains of the environmental species Xenophilus azovorans, Xenophilus aerolatus, Simplicispira metamorpha, Variovorax soli, and Xylophilus ampelinus. However, the phylogenetic tree indicated that strain YW8(T) formed a separate clade from Xenophilus azovorans. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain YW8(T) and its closest phylogenetic neighbours were below 24.2-35.5%, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8(T) were C(16 : 0), C(17 : 0) cyclo, C(18 : 1)ω7c, and summed feature 3(C(16 : 1)ω6c and/or C(16 : 1)ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA-DNA hybridization and chemotaxonomic data, strain YW8(T) is considered to represent a novel species of the genus Xenophilus, for which the name Xenophilus arseniciresistens sp. nov. is proposed; the type strain is YW8(T) ( = CCTCC AB2012103(T) = KACC 16853(T)). PMID:24585373

  5. Desulfonatronum Thiodismutans sp. nov., a Novel Alkaliphilic, Sulfate-reducing Bacterium Capable of Lithoautotrophic Growth

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.; Bej, Asim K.; Marsic, Damien; Whitman, William B.; Cleland, David; Krader, Paul

    2003-01-01

    A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(sup T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7 x 1.2-2.7 microns in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 C (optimum, 37 C), > 1-7 % NaCI, w/v (optimum, 3%) and pH 8.0-10.0 (optimum, 9.5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1(sup T) uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1(sup T) is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63.0 mol% (HPLC). DNA-DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951(sup T), exhibited 51 % homology. Also, the genome size (1.6 x 10(exp 9) Da) and T(sub m) value of the genomic DNA (71 +/- 2 C) for strain MLF1(sup T) were significantly different from the genome size (2.1 x 10(exp 9) Da) and T(sub m) value (63 +/- 2 C) for Desulfonatronum lacustre Z-7951(sup T). On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1(sup T) = ATCC BAA-395(sup T) = DSM 14708(sup T)).

  6. Celeribacter naphthalenivorans sp. nov., a naphthalene-degrading bacterium from tidal flat sediment.

    PubMed

    Taek Oh, Young; Avedoza, Catherine; Lee, Sang-Suk; Jeong, Sang Eun; Jia, Baolei; Jeon, Che Ok

    2015-09-01

    A Gram-stain-negative, aerobic and moderately halophilic bacterium, designated strain EMB201(T), was isolated from tidal flat sediment of the South Sea in Korea. Cells were motile rods with a single polar flagellum and had catalase- and oxidase-positive activities. Growth of strain EMB201(T) was observed at 15-37 °C (optimum, 30 °C), at pH 5.0-9.5 (optimum, pH 7.0-7.5) and in the presence of 1-7% (w/v) NaCl (optimum, 2-3%). Strain EMB201(T) contained ubiquinone-10 as the sole isoprenoid quinone and summed feature 8 (comprising C18 : 1ω7c/ω6c), C18 : 0ω7c 11-methyl and C10 : 0 3-OH as the major fatty acids. Phosphatidylglycerol and an unidentified amino lipid were identified as the major polar lipids and an unidentified phospholipid and three unidentified lipids were detected as minor components. The G+C content of the genomic DNA was approximately 58.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB201(T) formed a phylogenetic lineage with members of the genus Celeribacter. Strain EMB201(T) was related most closely to Celeribacter halophilus ZXM137(T) with a 16S rRNA gene sequence similarity of 98.3%, and the level of DNA-DNA relatedness between the two strains was 17.0 ± 2.0%. The combined chemotaxonomic and molecular properties suggest that strain EMB201(T) represents a novel species of the genus Celeribacter, for which the name Celeribacter naphthalenivorans sp. nov. is proposed. The type strain is EMB201(T) ( = KACC 18393(T) = JCM 30679(T)). PMID:26297231

  7. Marinobacter nitratireducens sp. nov., a halophilic and lipolytic bacterium isolated from coastal surface sea water.

    PubMed

    Vaidya, Bhumika; Kumar, Ravinder; Korpole, Suresh; Tanuku, Naga Radha Srinivas; Pinnaka, Anil Kumar

    2015-07-01

    A novel Gram-stain-negative, rod-shaped, motile bacterium, designated strain AK21(T), was isolated from coastal surface sea water at Visakhapatnam, India. The strain was positive for oxidase, catalase, lipase, L-proline arylamidase and tyrosine arylamidase activities. The predominant fatty acids were C12:0, C12:0 3-OH, C16:0, C16:1ω9c, C18:1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, two unidentified phospholipids and one unidentified lipid. Q-10 was the predominant respiratory quinone. The DNA G+C content of the strain was 54.6 mol%. 16S rRNA gene sequence analysis indicated that strain AK21(T) was a member of the genus Marinobacter and was closely related to Marinobacter xestospongiae, with pairwise sequence similarity of 97.2% to the type strain, with similarity to other members of the genus of 94.0-96.8%. The mean DNA-DNA relatedness of strain AK21(T) with M. xestospongiae JCM 17469(T) was 34.5%, and relatedness with Marinobacter mobilis JCM 15154(T) was 40.5%. Phylogenetic analysis showed that strain AK21(T) clustered with the type strains of M. xestospongiae and M. mobilis at distances of 2.9 and 2.8% (97.1 and 97.2% similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, it appears that strain AK21(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter nitratireducens sp. nov. is proposed. The type strain of Marinobacter nitratireducens is AK21(T) ( = MTCC 11704(T ) = JCM 18428(T)). PMID:25835026

  8. Thermoanaerobacter siderophilus sp. nov., a novel dissimilatory Fe(III)-reducing, anaerobic, thermophilic bacterium.

    PubMed

    Slobodkin, A I; Tourova, T P; Kuznetsov, B B; Kostrikina, N A; Chernyh, N A; Bonch-Osmolovskaya, E A

    1999-10-01

    A thermophilic, anaerobic, spore-forming, dissimilatory Fe(III)-reducing bacterium, designated strain SR4T, was isolated from sediment of newly formed hydrothermal vents in the area of the eruption of Karymsky volcano on the Kamchatka peninsula. Cells of strain SR4T were straight-to-curved, peritrichous rods, 0.4-0.6 micron in diameter and 3.5-9.0 microns in length, and exhibited a slight tumbling motility. Strain SR4T formed round, refractile, heat-resistant endospores in terminally swollen sporangia. The temperature range for growth was 39-78 degrees C, with an optimum at 69-71 degrees C. The pH range for growth was 4.8-8.2, with an optimum at 6.3-6.5. Strain SR4T grew anaerobically with peptone as carbon source. Amorphous iron(III) oxide present in the medium stimulated the growth of strain SR4T; cell numbers increased with the concomitant accumulation of Fe(II). In the presence of Fe(III), strain SR4T grew on H2/CO2 and utilized molecular hydrogen. Strain SR4T reduced 9,10-anthraquinone-2,6-disulfonic acid, sulfite, thiosulfate, elemental sulfur and MnO2. Strain SR4T did not reduce nitrate or sulfate and was not capable of growth with O2. The fermentation products from glucose were ethanol, lactate, H2 and CO2. The G + C content of DNA was 32 mol%. 16S rDNA sequence analysis placed the organism in the genus Thermoanaerobacter. On the basis of physiological properties and phylogenetic analysis, it is proposed that strain SR4T (= DSM 12299T) should be assigned to a new species, Thermoanaerobacter siderophilus sp. nov. PMID:10555328

  9. Shewanella algicola sp. nov., a marine bacterium isolated from brown algae.

    PubMed

    Kim, Ji-Young; Yoo, Han-Su; Lee, Dong-Heon; Park, So-Hyun; Kim, Young-Ju; Oh, Duck-Chul

    2016-06-01

    A Gram-stain-negative, aerobic, rod-shaped bacterium motile by means of a single polar flagella, strain ST-6T, was isolated from a brown alga (Sargassum thunbergii) collected in Jeju, Republic of Korea. Strain ST-6T was psychrotolerant, growing at 4-30 °C (optimum 20 °C). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences revealed that strain ST-6T belonged to a distinct lineage in the genus Shewanella. Strain ST-6T was related most closely to Shewanella basaltis J83T, S. gaetbuli TF-27T, S. arctica IT12T, S. vesiculosa M7T and S. aestuarii SC18T, showing 96-97 % and 85-70 % 16S rRNA and gyrB gene sequences similarities, respectively. DNA-DNA relatedness values between strain ST-6T and the type strains of two species of the genus Shewanella were <22.6 %. The major cellular fatty acids (>5 %) were summed feature 3 (comprising C16:1ω7c and/ or iso-C15:0 2-OH), C16:0, iso-C13:0 and C17:1ω8c. The DNA G+C content of strain ST-6Twas 42.4 mol%, and the predominant isoprenoid quinones were menaquinone MK-7 and ubiquinones Q-7 and Q-8. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain ST-6T is considered to represent a novel species of the genus Shewanella, for which the name Shewanella algicola sp. nov. is proposed. The type strain is ST-6T (= KCTC 23253T = JCM 31091T). PMID:26962005

  10. Sphingobium phenoxybenzoativorans sp. nov., a 2-phenoxybenzoic-acid-degrading bacterium.

    PubMed

    Cai, Shu; Shi, Chao; Zhao, Jia-Dong; Cao, Qin; He, Jian; Chen, Li-Wei

    2015-06-01

    A Gram-stain-negative, aerobic, yellow-pigmented, rod-shaped bacterium, designated strain SC_3T, was isolated from pesticide-contaminated soil sediment. The strain was able to mineralize 2-phenoxybenzoic acid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SC_3T formed a monophyletic lineage in the genus Sphingobium, and showed highest similarity to the type strains of Sphingobium abikonense (97.0 %), followed by Sphingobium lactosutens (96.8 %) and Sphingobium cloacae (96.7 %). The DNA-DNA relatedness between strain SC_3T and its closest phylogenetic neighbours was lower than 70 %. The major fatty acids (>5 % of the total) were summed feature 8 (comprising C18:1ω7c/C18:1ω6c), summed feature 3 (comprising C16:1ω7c/C16:1ω6c), C14:0 2-OH, C16:0 and C17:1ω6c. The predominant quinone was ubiquinone Q-10, and the major polyamine was spermidine. The polar lipid profile contained diphosphatidylglycerol (DPG), sphingoglycolipid (SGL), phosphatidylethanolamine (PDME), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), an unknown aminolipid (AL), two unknown lipids (L1, L2) and several unknown phospholipids (PL1-6). The genomic DNA G+C content of strain SC_3T was 62.9 mol%. On the basis of phenotypic, chemotaxonomic, phylogenetic and genotypic data, strain SC_3T represents a novel species of the genus Sphingobium, for which the name Sphingobium phenoxybenzoativorans sp. nov. is proposed. The type strain is SC_3T ( = CCTCC AB 2014349T = KACC 42448T). PMID:25807977

  11. Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba.

    PubMed

    Ahn, Young-Beom; Kerkhof, Lee J; Häggblom, Max M

    2009-09-01

    A reductively dehalogenating, strictly anaerobic, sulfate-reducing bacterium, designated strain AA1T, was isolated from the marine sponge Aplysina aerophoba collected in the Mediterranean Sea and was characterized phenotypically and phylogenetically. Cells of strain AA1T were Gram-negative, short, curved rods. Growth of strain AA1T was observed between 20 and 37 degrees C (optimally at 28 degrees C) at pH 7-8. NaCl was required for growth; optimum growth occurred in the presence of 25 g NaCl l(-1). Growth occurred with lactate, propionate, pyruvate, succinate, benzoate, glucose and sodium citrate as electron donors and carbon sources and either sulfate or 2-bromophenol as electron acceptors, but not with acetate or butyrate. Strain AA1T was able to dehalogenate several different bromophenols, and 2- and 3-iodophenol, but not monochlorinated or fluorinated phenols. Lactate, pyruvate, fumarate and malate were not utilized without an electron acceptor. The G+C content of the genomic DNA was 58.5 mol%. The predominant cellular fatty acids were C14:0, iso-C14:0, C14:0 3-OH, anteiso-C15:0, C16:0, C16:1omega7c and C18:1omega7c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons placed the novel strain within the class Deltaproteobacteria. Strain AA1T was related most closely to the type strains of Desulfoluna butyratoxydans (96% 16S rRNA gene sequence similarity), Desulfofrigus oceanense (95%) and Desulfofrigus fragile (95%). Based on its phenotypic, physiological and phylogenetic characteristics, strain AA1T is considered to represent a novel species of the genus Desulfoluna, for which the name Desulfoluna spongiiphila sp. nov. is proposed. The type strain is AA1T (=DSM 17682T=ATCC BAA-1256T). PMID:19605712

  12. Marinococcus tarijensis sp. nov., a moderately halophilic bacterium isolated from a salt mine.

    PubMed

    Balderrama-Subieta, Andrea; Guzmán, Daniel; Minegishi, Hiroaki; Echigo, Akinobu; Shimane, Yasuhiro; Hatada, Yuji; Quillaguamán, Jorge

    2013-09-01

    A Gram-stain-positive, coccoid-shaped, halophilic bacterium, strain SR-1(T), was isolated from a salt crystal obtained from a mine located in Tarija, Bolivia. The strain was investigated using a polyphasic approach. The optimum conditions for growth of strain SR-1(T) were reached at 5% (w/v) NaCl, pH 7.6 and 37-40 °C. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The isoprenoid quinone was MK-7. The major cellular fatty acids of strain SR-1(T) were anteiso-C(15:0), anteiso-C(17:0) and iso-C(16:0). The DNA G+C content of strain SR-1(T) was 48.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed a close relationship between strain SR-1(T) and Marinococcus halophilus JCM 2479(T) (99.7% 16S rRNA gene sequence similarity), Marinococcus halotolerans KCTC 19045(T) (99.4%) and Marinococcus luteus KCTC 13214(T) (99.8%). However, strain SR-1(T) also showed low levels of DNA-DNA relatedness with these reference strains (47, 61 and 58%, respectively). On the basis of phenotypic differences and DNA-DNA hybridization results, strain SR-1(T) is considered to represent a novel species of the genus Marinococcus, for which the name Marinococcus tarijensis sp. nov. is proposed. The type strain is SR-1(T) ( =LMG 26930(T) =CECT 8130(T)). PMID:23504966

  13. Thermoactinomyces khenchelensis sp. nov., a filamentous bacterium isolated from soil sediment of a terrestrial hot spring.

    PubMed

    Mokrane, Salim; Bouras, Noureddine; Meklat, Atika; Lahoum, Abdelhadi; Zitouni, Abdelghani; Verheecke, Carol; Mathieu, Florence; Schumann, Peter; Spröer, Cathrin; Sabaou, Nasserdine; Klenk, Hans-Peter

    2016-02-01

    A novel thermophilic filamentous bacterium, designated strain T36(T), was isolated from soil sediment sample from a hot spring source collected in Khenchela province, Algeria. Strain T36(T) was identified as a member of the genus Thermoactinomyces by a polyphasic approach. Strain T36(T) was observed to form white aerial mycelium and non-coloured to pale yellow substrate mycelium, both producing endospores, sessile or borne by short sporophores. The optimum growth temperature and pH were found to be 37-55 °C and 7.0-9.0, respectively and the optimum NaCl concentration for growth was found to be 0-7 % (w/v). The diagnostic diamino acid in the cell wall peptidoglycan was identified as meso-diaminopimelic acid. The predominant menaquinone of strain T36(T) was identified as MK-7 (H0). The major fatty acids were found to be iso-C15:0 and iso-C17:0. The phospholipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphoglycolipid. The chemotaxonomic properties of strain T36(T) are consistent with those shared by members of the genus Thermoactinomyces. 16S rRNA gene sequence analysis indicated that the sequence similarities between strain T36(T) and Thermoactinomyces species with validly published names were less than 98 %. Based on the combined genotypic and phenotypic evidence, it is proposed that strain T36(T) should be classified as representative of a novel species, for which the name Thermoactinomyces khenchelensis sp. nov. is proposed. The type strain is T36(T) (=DSM 45951(T) = CECT 8579(T)). PMID:26678783

  14. Mobilitalea sibirica gen. nov., sp. nov., a halotolerant polysaccharide-degrading bacterium.

    PubMed

    Podosokorskaya, O A; Bonch-Osmolovskaya, E A; Beskorovaynyy, A V; Toshchakov, S V; Kolganova, T V; Kublanov, I V

    2014-08-01

    A novel strictly anaerobic, halotolerant, organotrophic bacterium, strain P3M-3(T), was isolated from a microbial mat formed under the flow of hot water emerging from a 2775 m-deep well in Tomsk region (western Siberia, Russia). Cells of strain P3M-3(T) were straight and curved rods, 0.2-0.4 µm in width and 1.5-20 µm in length. Strain P3M-3(T) grew optimally at 37 °C, pH 7.0-7.5 and in a NaCl concentration of 15 g l(-1). Under optimum growth conditions, the doubling time was 1 h. The isolate was able to ferment a variety of mono-, di- and polysaccharides, including microcrystalline cellulose. Acetate, ethanol, H2 and CO2 were the main products of glucose fermentation. The DNA G+C content was 33.4 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain P3M-3(T) was a member of family Lachnospiraceae, whose representatives are also found in Clostridium cluster XIVa. 16S rRNA gene sequence similarity with Clostridium jejuense HY-35-12(T), the closest relative, was 93.9%. A novel genus and species, Mobilitalea sibirica gen. nov., sp. nov., are proposed based on phylogenetic analysis and physiological properties of the novel isolate. The type strain of the type species is P3M-3(T) ( = DSM 26468(T) = VKM B-2804(T)). PMID:24827706

  15. Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India.

    PubMed

    Saha, P; Mondal, A K; Mayilraj, S; Krishnamurthi, S; Bhattacharya, A; Chakrabarti, T

    2005-11-01

    A polyphasic approach was used to characterize a bacterium, GPTSA 11(T), isolated from a warm spring located in a reserve forest in Assam, India. The cells are Gram-variable, strictly aerobic, sporulating motile rods. The major fatty acids of the strain are C(15 : 0) anteiso (48.42 %), C(16 : 0) iso (11.59 %), C(16 : 1)omega11c (6.16 %), C(15 : 0) iso (6.03 %), C(17 : 0) anteiso (5.68 %) and C(16 : 1)omega7c alcohol (5.01 %). The presence of the fatty acid C(16 : 1)omega7c alcohol distinguishes this strain from other closely related species of the genus Paenibacillus. The strain contains MK-7 as the diagnostic menaquinone. The G+C content of the genomic DNA is 41.2 mol%. Analysis of the 16S rRNA gene sequence (1466 nt) revealed the presence of signature sequences PAEN 515F (5'-GAGTAACTGCTCTCGGAATGACGGTACTTGAGAAGAAAGCCCC-3') and PAEN 862F (5'-TCGATACCCTTGGTGCCGAAGT-3'), which were found in the species of the genus Paenibacillus surveyed by Shida et al. [Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997). Int J Syst Bacteriol 47, 289-298]. The sequence shows closest similarity (95.85 %) to that of Paenibacillus apiarius, followed by Paenibacillus alvei (94.34 %), Paenibacillus cineris (93.87 %), Paenibacillus favisporus (93.80 %), Paenibacillus chibensis (93.47 %) and Paenibacillus azoreducens (93.40 %). Biochemical, physiological, chemotaxonomic and phylogenetic analyses justify placement of the strain in the genus Paenibacillus but not within any existing species. It should, therefore, be considered as representing a novel species, for which the name Paenibacillus assamensis sp. nov. is proposed. The type strain is GPTSA 11T (=MTCC 6934T=JCM 13186T). PMID:16280530

  16. Methylobacterium pseudosasae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the bamboo phyllosphere.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj

    2014-02-01

    A pink-pigmented, Gram negative, aerobic, facultatively methylotrophic bacterium, strain BL44(T), was isolated from bamboo leaves and identified as a member of the genus Methylobacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed similarity values of 98.7-97.0 % with closely related type strains and showed highest similarity to Methylobacterium zatmanii DSM 5688(T) (98.7 %) and Methylobacterium thiocyanatum DSM 11490(T) (98.7 %). Methylotrophic metabolism in this strain was confirmed by PCR amplification and sequencing of the mxaF gene coding for the α-subunit of methanol dehydrogenase. Strain BL44(T) produced three known quorum sensing signal molecules with similar retention time to C8, C10 and C12-HSLs when characterized by GC-MS. The fatty acid profiles contained major amounts of C18:1 ω7c, iso-3OH C17:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), which supported the grouping of the isolate in the genus Methylobacterium. The DNA G+C content was 66.9 mol%. DNA relatedness of the strain BL44(T) to its most closely related strains ranged from 12-43.3 %. On the basis of the phenotypic, phylogenetic and DNA-DNA hybridization data, strain BL44(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium pseudosasae sp. nov. is proposed (type strain BL44(T) = NBRC 105205(T) = ICMP 17622(T)). PMID:24297603

  17. Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake.

    PubMed

    Dimitriu, Pedro A; Shukla, Sanjay K; Conradt, Jennifer; Márquez, M Carmen; Ventosa, Antonio; Maglia, Anne; Peyton, Brent M; Pinkart, Holly C; Mormile, Melanie R

    2005-11-01

    A novel alkaliphilic bacterium, strain 4CAT, was isolated from decomposing wood taken from the shore of Soap Lake, a saline, alkaline lake in Grant County, WA, USA. Cells of the isolate were Gram-negative, asporogenous, short, motile rods that utilized only a limited range of organic acids as sole carbon and energy sources. In addition to oxygen, the strain possessed the ability to reduce in the presence of acetate. Strain 4CAT was oxidase- and catalase-positive; it degraded Tween 60, but not DNA, urea, gelatin or starch. It grew at pH values from 7.5 to 11.0, with optimum growth occurring at pH 9.0, and growth was observed in NaCl concentrations of 0.2-1.3 M, with optimum growth at 0.8 M NaCl. The optimum temperature for growth was 37 degrees C. Strain 4CAT was resistant to erythromycin, bacitracin, novobiocin, polymyxin B, neomycin, gentamicin, streptomycin, carbenicillin, rifampicin and tetracycline, and was susceptible to nalidixic acid, chloramphenicol, ampicillin and penicillin. The isolate's 16S rRNA gene sequence indicated that it belonged to the gamma-Proteobacteria, showing 90-94 % similarity to its closest relatives. Maximum-likelihood phylogenetic inferences placed strain 4CAT within a novel lineage related to the marine bacterial genera Neptunomonas and Marinobacterium. The DNA G+C content of the isolate was 47.4 mol%. On the basis of genotypic and phenotypic characterization, it was concluded that strain 4CAT should be placed in a separate taxon as a novel genus and species, with the proposed name Nitrincola lacisaponensis gen. nov., sp. nov. The type strain is 4CAT (=ATCC BAA-920T=DSM 16316T). PMID:16280482

  18. Lentibacillus amyloliquefaciens sp. nov., a halophilic bacterium isolated from saline sediment sample.

    PubMed

    Wang, Jing-Li; Ma, Ke-Dong; Wang, Yan-Wei; Wang, Hui-Min; Li, Yan-Bin; Zhou, Shan; Chen, Xiao-Rong; Kong, De-Long; Guo, Xiang; He, Ming-Xiong; Ruan, Zhi-Yong

    2016-02-01

    A Gram-stain positive, non-motile, non-sporogenous, aerobic, rod-shaped and halophilic bacterium, designated LAM0015(T), was isolated from a saline sediment sample collected from Yantai City in China. The isolate was found to be able to grow at NaCl concentrations of 5-25 % (w/v) (optimum: 7-12 %), 15-45 °C (optimum: 35 °C) and pH 5.0-9.0 (optimum: 7.0). The major fatty acids were determined to be anteiso-C15:0 and anteiso-C17:0. The predominant respiratory quinone was identified as MK-7. The cell wall peptidoglycan was determined to contain meso-diaminopimelic acid. The polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, five phospholipids and one glycolipid. The DNA G+C content was 43.1 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate belongs within the genus Lentibacillus and is closely related to Lentibacillus persicus DSM 22530(T), Lentibacillus salicampi JCM 11462(T) and Lentibacillus jeotgali JCM 15795(T) with 97.3, 96.7 and 96.4 % sequence similarity, respectively. The DNA-DNA hybridization value between LAM0015(T) and L. persicus DSM 22530(T) was 51.2 ± 1.4 %. Based on its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0015(T) is concluded to represent a novel species of the genus Lentibacillus, for which the name Lentibacillus amyloliquefaciens sp. nov. is proposed. The type strain is LAM0015(T) (=ACCC 06401(T) = JCM 19838(T)). PMID:26545789

  19. Halomonas xinjiangensis sp. nov., a halotolerant bacterium isolated from a salt lake.

    PubMed

    Guan, Tong-Wei; Xiao, Jing; Zhao, Ke; Luo, Xiao-Xia; Zhang, Xiao-Ping; Zhang, Li-Li

    2010-02-01

    A novel bacterium, TRM 0175(T), belonging to the genus Halomonas, was isolated from a soil sample taken from a salt lake in Xinjiang Province, north-west China. The isolate was Gram-negative, aerobic, rod-shaped and motile by means of peritrichous flagella. It was catalase-positive and oxidase-negative. Growth occurred at NaCl concentrations of 0-20 % (optimum at 10-13 %), at 15-50 degrees C (optimum at 37 degrees C) and at pH 6.0-9.0 (optimum at pH 7.0). Metabolism was respiratory with oxygen as terminal electron acceptor. Acid was produced from D-ribose, D- and L-arabinose, D-xylose, D-galactose, D-mannose, L-rhamnose, cellobiose, maltose, trehalose and D- and L-fucose and was produced weakly from aesculin. The predominant ubiquinone was Q-9. The major fatty acids were C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The G+C content of the genomic DNA was 60.0 mol%. The affiliation of strain TRM 0175(T) with the genus Halomonas was confirmed by 16S rRNA gene sequence comparisons. The most closely related species was Halomonas anticariensis; 16S rRNA gene sequence similarity between H. anticariensis FP35(T) and strain TRM 0175(T) was 95.3 %. Phenotypically, some characteristics of TRM 0175(T) differed from those of H. anticariensis. On the basis of data from this polyphasic study, strain TRM 0175(T) represents a novel species of the genus Halomonas, for which the name Halomonas xinjiangensis sp. nov. is proposed; the type strain is TRM 0175(T) (=CCTCC AB 208329(T) =KCTC 22608(T)). PMID:19651733

  20. Dethiosulfovibrio salsuginis sp. nov., an anaerobic, slightly halophilic bacterium isolated from a saline spring.

    PubMed

    Díaz-Cárdenas, C; López, G; Patel, B K C; Baena, S

    2010-04-01

    A mesophilic, strictly anaerobic, slightly halophilic bacterium, designated strain USBA 82(T), was isolated from a terrestrial saline spring in the Colombian Andes. The non-spore-forming curved rods (5-7 x 1.3 microm) with pointed or rounded ends, stained Gram-negative and were motile by means of laterally inserted flagella. The strain grew optimally at 30 degrees C (growth range 20-40 degrees C), pH 7.3 (growth range pH 5.5-8.5) and 2 % (w/v) NaCl (growth range 0.1-7 % NaCl). The strain fermented peptides, amino acids and a few organic acids, but growth was not observed on carbohydrates, alcohols or fatty acids. The strain reduced thiosulfate and sulfur to sulfide. Sulfate, sulfite, nitrate and nitrite were not used as electron acceptors. On peptone alone, acetate, succinate, propionate and traces of ethanol were formed, but in the presence of thiosulfate, acetate and succinate were formed. The G+C content of the chromosomal DNA was 52 mol% (T(m)). 16S rRNA gene sequence analysis indicated that strain USBA 82(T) was affiliated to Dethiosulfovibrio peptidovorans within the phylum Synergistetes with a similarity value of approximately 93 %. Based on the differences between the new strain and the type species of the genus Dethiosulfovibrio, we suggest that strain USBA 82(T) represents a novel species of the genus for which the name Dethiosulfovibrio salsuginis sp. nov. is proposed. The type strain is USBA 82(T) (=DSM 21565(T)=KCTC 5659(T)). PMID:19661517

  1. Rufibacter glacialis sp. nov., a psychrotolerant bacterium isolated from glacier soil.

    PubMed

    Liu, Qing; Liu, Hong-Can; Zhang, Jian-Li; Zhou, Yu-Guang; Xin, Yu-Hua

    2016-01-01

    A Gram-stain-negative, rod-shaped, red-pigmented bacterium (MDT1-10-3T) was isolated from Midui glacier in Tibet, China. Cells were aerobic and psychrotolerant (growth occurred at 4-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that it was a member of the genus Rufibacter, with Rufibacter immobilis MCC P1T (96.7 % similarity) as its closest phylogenetic relative. MK-7 was the predominant respiratory menaquinone. The major cellular fatty acids were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C17 : 1ω6c, iso-C16 : 0, iso-C15 : 0 and C16 : 1ω5c. The predominant polar lipids were phosphatidylethanolamine, two unidentified aminophospholipids, one glycolipid and four unidentified lipids. The G+C content of the genomic DNA was 49 mol%. On the basis of the phenotypic characteristics and phylogenetic analysis, strain MDT1-10-3T represents a novel species of the genus Rufibacter, for which the name Rufibacter glacialis sp. nov. is proposed. The type strain is MDT1-10-3T ( = CGMCC 1.9789T = NBRC 109705T). PMID:26510965

  2. Ectothiorhodospira variabilis sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes.

    PubMed

    Gorlenko, Vladimir M; Bryantseva, Irina A; Rabold, Sandra; Tourova, Tatjana P; Rubtsova, Dariya; Smirnova, Ekaterina; Thiel, Vera; Imhoff, Johannes F

    2009-04-01

    During studies of moderately halophilic strains of Ectothiorhodospira from steppe soda lakes, we found a novel group of bacteria related to Ectothiorhodospira haloalkaliphila with salt optima at 50-80 g NaCl l(-1). Phylogenetic analysis using 16S rRNA gene sequences of strains from soda lakes in Mongolia, Egypt and Siberia revealed separation of the group of new isolates from other Ectothiorhodospira species, including the closely related Ect. haloalkaliphila. DNA-DNA hybridization studies demonstrated that the new isolates form a homogeneous group at the species level, but at the same time are distinct from related species such as Ect. haloalkaliphila, Ect. vacuolata, Ect. shaposhnikovii and Ect. marina. The new isolates are considered to be strains of a novel species, for which the name Ectothiorhodospira variabilis sp. nov. is proposed, with the type strain WN22(T) (=VKM B-2479(T) =DSM 21381(T)). Photosynthetic pigments of the novel species are bacteriochlorophyll a and carotenoids of the spirilloxanthin series with spirilloxanthin and derivatives thereof, together with small amounts of lycopene and rhodopin. Gas vesicles are formed by most of the strains, particularly in media containing yeast extract (0.5 g l(-1)) and acetate (0.5-2.0 g l(-1)). Sequence analysis of nifH (nitrogenase) and cbbL (RuBisCO) confirmed the assignment of the strains to the genus Ectothiorhodospira and in particular the close relationship to Ect. haloalkaliphila. The novel species Ect. variabilis is found in soda lakes separated by great geographical distances and is an alkaliphilic and halophilic bacterium that tolerates salt concentrations up to 150-200 g NaCl l(-1). PMID:19329583

  3. Fusibacter fontis sp. nov., a sulfur-reducing, anaerobic bacterium isolated from a mesothermic Tunisian spring.

    PubMed

    Fadhlaoui, Khaled; Ben Hania, Wajdi; Postec, Anne; Fauque, Guy; Hamdi, Moktar; Ollivier, Bernard; Fardeau, Marie-Laure

    2015-10-01

    Strain KhalAKB1T, a mesophilic, anaerobic, rod-shaped bacterium, was isolated from water collected from a mesothermic Tunisian spring. Cells were Gram-staining-positive rods, occurring singly or in pairs and motile by one lateral flagellum. Strain KhalAKB1T grew at 15-45 °C (optimum 30 °C), at pH 5.5-8.5 (optimum pH 7.0) and in the presence of 0-35 g NaCl l- 1 (optimum 1 g NaCl l- 1). It fermented yeast extract and a wide range of carbohydrates including cellobiose, d-glucose, d-ribose, sucrose, d-xylose, maltose, d-galactose and starch as electron donors. Acetate, ethanol, CO2 and H2 were end products of glucose metabolism. It reduced elemental sulfur, but not sulfate, thiosulfate or sulfite, into sulfide. The DNA G+C content was 37.6 mol%. The predominant cellular fatty acids were C14 : 0 and C16 : 0. Phylogenetic analysis of the 16S rRNA gene sequence suggested Fusibacter bizertensis as the closest relative of this isolate (identity of 97.2 % to the type strain). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain KhalAKB1T is proposed to be assigned to a novel species within the genus Fusibacter, order Clostridiales, Fusibacter fontis sp. nov. The type strain is KhalAKB1T ( = DSM 28450T = JCM 19912T). PMID:26296995

  4. Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots.

    PubMed

    Zhang, Lei; Gao, Ju-Sheng; Kim, Song-Gun; Zhang, Cai-Wen; Jiang, Ju-Quan; Ma, Xiao-Tong; Zhang, Jun; Zhang, Xiao-Xia

    2016-01-01

    A novel endophytic bacterium, strain ZYY112T, isolated from rice roots, was characterized by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, ZYY112T showed highest sequence similarity to Novosphingobium sediminicola HU1-AH51T (97.2 %) and less than 97 % similarity with respect to other Novosphingobium species with validly published names. The DNA G+C content of strain ZYY112T was 60.8 mol%. The level of DNA-DNA relatedness between strain ZYY112T and N. sediminicola DSM 27057T was 33.7 % (reciprocal 5.2 %), which supported the suggestion that ZYY112T represented a novel species of the genus Novosphingobium. Ubiquinone Q-10 was the unique respiratory quinone (100 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, an unknown aminolipid and an unknown phospholipid. The major fatty acids of strain ZYY112T were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c), C14 : 0 2-OH and C16 : 0. The major polyamine of ZYY112T was spermidine, which is a characteristic trait of the genus Novosphingobium. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain ZYY112T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium oryzae sp. nov. is proposed. The type strain is ZYY112T ( = ACCC 06131T = JCM 30537T). PMID:26514117

  5. A novel perchlorate- and nitrate-reducing bacterium, Azospira sp. PMJ.

    PubMed

    Nam, Ji-Hyun; Ventura, Jey-R S; Yeom, Ick Tae; Lee, Yongwoo; Jahng, Deokjin

    2016-07-01

    A novel perchlorate-reducing bacterium (PCRB), PMJ, was isolated from the mixed liquor suspended solids in the aerobic tank of a wastewater treatment plant. The 16S ribosomal RNA (rRNA), perchlorate reductase, and chlorite dismutase gene sequences revealed that PMJ belonged to the genus Azospira. PMJ was removed high-strength (700 mg/L) perchlorate and also removed low-strength (≤50 mg/L) perchlorate below the detection limit (2 μg/L) when acetate was used as a sole and carbon source. The maximum specific perchlorate utilization rate, q max, was 0.96 mg ClO4 (-)/mg dry cell weight day, and the half-saturation constant, K S , was lower than 0.002 mg ClO4 (-)/L. PMJ also utilized inorganic electron donors [(H2, S(0), and Fe(II)] with perchlorate as an electron acceptor. Perchlorate reduction by PMJ was completely inhibited by oxygen and chlorate but was not inhibited by nitrate. In the presence of similar concentrations (100∼140 mg/L) of nitrate and perchlorate, PMJ simultaneously removed both electron acceptors. Therefore, it was concluded that the strains PMJ might possess separate pathways for perchlorate and nitrate reduction. These results indicated that Azospira sp. PMJ could be efficiently used for treating perchlorate-contaminated groundwater and wastewater because many of these water bodies are known to contain both perchlorate and nitrate. In addition, low K S value and autotrophic perchlorate reduction of PMJ might be useful to design the biological treatment systems. PMID:26971497

  6. Antibiofilm Activity of an Exopolysaccharide from Marine Bacterium Vibrio sp. QY101

    PubMed Central

    Han, Feng; Duan, Gaofei; Lu, Xinzhi; Gu, Yuchao; Yu, Wengong

    2011-01-01

    Bacterial exopolysaccharides have always been suggested to play crucial roles in the bacterial initial adhesion and the development of complex architecture in the later stages of bacterial biofilm formation. However, Escherichia coli group II capsular polysaccharide was characterized to exert broad-spectrum biofilm inhibition activity. In this study, we firstly reported that a bacterial exopolysaccharide (A101) not only inhibits biofilm formation of many bacteria but also disrupts established biofilm of some strains. A101 with an average molecular weight of up to 546 KDa, was isolated and purified from the culture supernatant of the marine bacterium Vibrio sp. QY101 by ethanol precipitation, iron-exchange chromatography and gel filtration chromatography. High performance liquid chromatography traces of the hydrolyzed polysaccharides showed that A101 is primarily consisted of galacturonic acid, glucuronic acid, rhamnose and glucosamine. A101 was demonstrated to inhibit biofilm formation by a wide range of Gram-negative and Gram-positive bacteria without antibacterial activity. Furthermore, A101 displayed a significant disruption on the established biofilm produced by Pseudomonas aeruginosa, but not by Staphylococcus aureus. Importantly, A101 increased the aminoglycosides antibiotics' capability of killing P. aeruginosa biofilm. Cell primary attachment to surfaces and intercellular aggregates assays suggested that A101 inhibited cell aggregates of both P. aeruginosa and S. aureus, while the cell-surface interactions inhibition only occurred in S. aureus, and the pre-formed cell aggregates dispersion induced by A101 only occurred in P. aeruginosa. Taken together, these data identify the antibiofilm activity of A101, which may make it potential in the design of new therapeutic strategies for bacterial biofilm-associated infections and limiting biofilm formation on medical indwelling devices. The found of A101 antibiofilm activity may also promote a new recognition

  7. Geobacter soli sp. nov., a dissimilatory Fe(III)-reducing bacterium isolated from forest soil.

    PubMed

    Zhou, Shungui; Yang, Guiqin; Lu, Qin; Wu, Min

    2014-11-01

    A novel Fe(III)-reducing bacterium, designated GSS01(T), was isolated from a forest soil sample using a liquid medium containing acetate and ferrihydrite as electron donor and electron acceptor, respectively. Cells of strain GSS01(T) were strictly anaerobic, Gram-stain-negative, motile, non-spore-forming and slightly curved rod-shaped. Growth occurred at 16-40 °C and optimally at 30 °C. The DNA G+C content was 60.9 mol%. The major respiratory quinone was MK-8. The major fatty acids were C(16:0), C(18:0) and C(16:1)ω7c/C(16:1)ω6c. Strain GSS01(T) was able to grow with ferrihydrite, Fe(III) citrate, Mn(IV), sulfur, nitrate or anthraquinone-2,6-disulfonate, but not with fumarate, as sole electron acceptor when acetate was the sole electron donor. The isolate was able to utilize acetate, ethanol, glucose, lactate, butyrate, pyruvate, benzoate, benzaldehyde, m-cresol and phenol but not toluene, p-cresol, propionate, malate or succinate as sole electron donor when ferrihydrite was the sole electron acceptor. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSS01(T) was most closely related to Geobacter sulfurreducens PCA(T) (98.3% sequence similarity) and exhibited low similarities (94.9-91.8%) to the type strains of other species of the genus Geobacter. The DNA-DNA relatedness between strain GSS01(T) and G. sulfurreducens PCA(T) was 41.4 ± 1.1%. On the basis of phylogenetic analysis, phenotypic characterization and physiological tests, strain GSS01(T) is believed to represent a novel species of the genus Geobacter, and the name Geobacter soli sp. nov. is proposed. The type strain is GSS01(T) ( =KCTC 4545(T) =MCCC 1K00269(T)). PMID:25139417

  8. Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water.

    PubMed

    Albert, Richard A; Waas, Nancy E; Pavlons, Shawn C; Pearson, Jamie L; Ketelboeter, Laura; Rosselló-Móra, Ramon; Busse, Hans-Jürgen

    2013-03-01

    A psychrophilic, Gram-negative bacterium, designated MOL-1(T), was isolated from water of Lake Michigan. 16S rRNA gene sequence analysis revealed that the sequence of strain MOL-1(T) has sequence similarity of 95.6, 94.8, 94.3, 94.3, 94.2 and 93.9 %, respectively, to the 16S rRNA gene sequences of Sphingobacterium shayense HS39(T), S. lactis WCC 4512(T), S. composti T5-12(T), S. daejeonense TR6-04(T), S. bambusae IBFC2009(T) and S. alimentarium WCC 4521(T). The major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone MK-7 is the predominant respiratory quinone, while sym-homospermidine is the predominant polyamine. The polar lipid profile is composed of the predominant lipids phosphatidylethanolamine and unidentified polar lipid L2, with moderate amounts of unidentified polar lipids L1, L5 and L6 and unidentified aminophospholipids APL1 and APL2 and minor to trace amounts of unidentified polar lipids L3, L4, L7, L8, L9 and L10, unidentified phospholipid PL4 and unidentified aminophospholipid APL3. After molecular and phenotypic studies, including chemotaxonomic analyses, it was concluded that strain MOL-1(T) represents a novel Sphingobacterium species, for which the name Sphingobacterium psychroaquaticum sp. nov. is proposed. The type strain is MOL-1(T) ( = NRRL B-59232(T)  = DSM 22418(T)). PMID:22659507

  9. Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge.

    PubMed

    Sun, Le-Ni; Wang, Dao-Sheng; Yang, En-Dong; Fang, Lian-Cheng; Chen, Yi-Fei; Tang, Xin-Yun; Hua, Ri-Mao

    2016-06-01

    A Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus, and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2-98.2 % with other species of the genus Cupriavidus. The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA-DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and 'Cupriavidus yeoncheonense' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA-DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus, for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T). PMID:27001671

  10. Caldicoprobacter guelmensis sp. nov., a thermophilic, anaerobic, xylanolytic bacterium isolated from a hot spring.

    PubMed

    Bouanane-Darenfed, Amel; Ben Hania, Wajdi; Hacene, Hocine; Cayol, Jean-Luc; Ollivier, Bernard; Fardeau, Marie-Laure

    2013-06-01

    A hyperthermophilic anaerobic bacterium, designated D2C22(T), was isolated from the hydrothermal hot spring of Guelma in north-east Algeria. The isolate was a Gram-stain-positive, non-sporulating, non-motile rod, appearing singly or in pairs (0.3-0.4 × 8.0-9.0 µm). Strain D2C22(T) grew anaerobically at 45-85 °C (optimum 65 °C), at pH 5-9 (optimum pH 6.8) and with 0-20 g NaCl l(-1). Strain D2C22(T) used glucose, galactose, lactose, fructose, ribose, xylose, arabinose, maltose, cellobiose, mannose, melibiose, sucrose, xylan and pyruvate (only in the presence of yeast extract or biotrypticase) as electron donors. The end products from glucose fermentation were acetate, lactate, CO2 and H2. Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate and sulfite were not used as electron acceptors. The predominant cellular fatty acids were iso-C15:0 and iso-C17:0. The DNA G+C content was 41.6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain D2C22(T) was most closely related to Caldicoprobacter oshimai JW/HY-331(T), Caldicoprobacter algeriensis TH7C1(T) and Acetomicrobium faecale DSM 20678(T) (95.5, 95.5 and 95.3% 16S rRNA gene sequence similarity, respectively). Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain D2C22(T) is proposed to be a representative of a novel species of the genus Caldicoprobacter within the order Clostridiales, for which the name Caldicoprobacter guelmensis sp. nov. is proposed. The type strain is D2C22(T) (=DSM 24605(T)=JCM 17646(T)). PMID:23041645

  11. Asticcacaulis endophyticus sp. nov., a prosthecate bacterium isolated from the root of Geum aleppicum.

    PubMed

    Zhu, Lingfang; Long, Mingxiu; Si, Meiru; Wei, Linfang; Li, Changfu; Zhao, Liang; Shen, Xihui; Wang, Yao; Zhang, Lei

    2014-12-01

    A strictly aerobic, light-yellow-coloured, stalked bacterium, designated strain ZFGT-14(T), was isolated from the root of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi province, north-west China, and was subjected to a taxonomic study using a polyphasic approach. This novel isolate grew at 7-33 °C (optimum 25-28 °C) and pH 6.0-10.0 (optimum pH 7.0-8.0). Flexirubin-type pigments were not produced. Cells were Gram-stain-negative, rod-shaped and motile with a single polar flagellum. The predominant respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C19 : 0 cyclo ω8c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and the major polar lipids were phosphatidylglycerol and glycolipids. The DNA G+C content was 57.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFGT-14(T) was most closely related to the genus Asticcacaulis and had low sequence similarity (95.0-95.9 %) with all species with validly published names within the genus Asticcacaulis. Based on the phenotypic, phylogenetic and genotypic data, strain ZFGT-14(T) is considered to represent a novel species of the genus Asticcacaulis, for which the name Asticcacaulis endophyticus sp. nov. is proposed. The type strain is ZFGT-14(T) ( = CCTCC AB 2013012(T) = KCTC 32296(T) = LMG 27605(T)). PMID:25205798

  12. Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand.

    PubMed

    Ramaprasad, E V V; Bharti, Dave; Sasikala, Ch; Ramana, Ch V

    2015-12-01

    A red-pigmented bacterium producing a metallic green sheen, designated strain JC333T, was isolated from a sand sample collected from Shivrajpur-Kachigad beach, Gujarat, India. Phylogenetic analyses based on the 16S rRNA gene sequence of strain JC333T showed highest sequence similarity to Zooshikella ganghwensis JC2044T (99.24 %) and less than 91.94 % similarity with other members of the class Gammaproteobacteria. DNA-DNA hybridizations between JC333T and Z. ganghwensis JC2044T showed low relatedness values of 19 ± 1.3 % (reciprocal 21 ± 2.2 %). The major respiratory quinone was ubiquinone-9 (Q9) and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The presence of C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C18 : 1ω7c and C12 : 0 as major fatty acids supported the affiliation of strain JC333T to the genus Zooshikella. Prodigiosin, cycloprodigiosin and eight other prodigiosin analogues were the pigments of JC333T. Characterization based on 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, ubiquinone, and polar lipid and fatty acid compositions revealed that JC333T represents a novel species of the genus Zooshikella, for which the name Zooshikella marina sp. nov. is proposed. The type strain is JC333T ( = KCTC 42659T = LMG 28823T). PMID:26409875

  13. Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring.

    PubMed

    Kämpfer, P; Arun, A B; Rekha, P D; Busse, H-J; Young, C-C; Glaeser, S P

    2013-07-01

    A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2(T), was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus Ruegeria with 97.4 % similarity to Ruegeria lacuscaerulensis ITI-1157(T), and a lower sequence similarity to all other species of the genus Ruegeria. Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2(T) clustered within the genus Ruegeria. Robust tree topology for the genus Ruegeria including the new strain was only obtained by including all Rhodobacteraceae type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2(T) represents a novel species of the genus Ruegeria, for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2(T) ( = CCUG 59209(T) = LMG 25539(T) = CCM 7758(T)). PMID:23243093

  14. Plant-Microbe Communication Enhances Auxin Biosynthesis by a Root-Associated Bacterium, Bacillus amyloliquefaciens SQR9.

    PubMed

    Liu, Yunpeng; Chen, Lin; Zhang, Nan; Li, Zunfeng; Zhang, Guishan; Xu, Yu; Shen, Qirong; Zhang, Ruifu

    2016-04-01

    Mechanisms by which beneficial rhizobacteria promote plant growth include tryptophan-dependent indole-3-acetic acid (IAA) synthesis. The abundance of tryptophan in the rhizosphere, however, may influence the level of benefit provided by IAA-producing rhizobacteria. This study examined the cucumber-Bacillus amyloliquefaciens SQR9 system and found that SQR9, a bacterium previously shown to enhance the growth of cucumber, increased root secretion of tryptophan by three- to fourfold. Using a split-root system, SQR9 colonization of roots in one chamber not only increased tryptophan secretion from the noninoculated roots but also increased the expression of the cucumber tryptophan transport gene but not the anthranilate synthesis gene in those roots. The increased tryptophan in isolated rhizosphere exudates was sufficient to support increased IAA production by SQR9. Moreover, SQR9 colonization of roots in one chamber in the split-root system resulted in sufficient tryptophan production by the other roots to upregulate SQR9 IAA biosynthesis genes, including a 27-fold increase in the indole-3-acetonitrilase gene yhcX during subsequent colonization of those roots. Deletion of yhcX eliminated SQR9-mediated increases in root surface area, likely by reducing IAA-stimulated lateral root growth. This study demonstrates a chemical dialogue between B. amyloliquefaciens and cucumber in which this communication contributes to bacteria-mediated plant-growth enhancement. PMID:26808445

  15. Microbial metabolism of polycyclic aromatic hydrocarbons: Isolation and characterization of a pyrene-degrading bacterium. [Mycobacterium sp

    SciTech Connect

    Heitkamp, M.A.; Franklin, W.; Cerniglia, C.E. )

    1988-10-01

    Microbiological analyses of sediments located near a point source for petrogenic chemicals resulted in the isolation of a pyrene-mineralizing bacterium. This isolate was identified as a Mycobacterium sp. on the basis of its cellular and colony morphology, gram-positive and strong acid-fast reactions, diagnostic biochemical tests, 66.6% G+C content of the DNA, and high-molecular-weight mycolic acids (C{sub 58} to C{sub 64}). The mycobacterium mineralized pyrene when grown in a mineral salts medium supplemented with nutrients but was unable to utilize pyrene as a sole source of carbon and energy. The mycobacterium grew well at 24 and 30{degree}C and minimally at 35{degree}C. No growth was observed at 5 or 42{degree}C. The mycobacterium grew well at salt concentrations up to 4%. Pyrene-induced Mycobacterium cultures mineralized 5% of the pyrene after 6 h and reached a maximum of 48% mineralization within 72 h. Treatment of induced and noninduced cultures with chloramphenicol showed that pyrene-degrading enzymes were inducible in this Mycobacterium sp. This bacterium could also mineralize other polycyclic aromatic hydrocarbons and alkyl- and nitro-substituted polycyclic aromatic hydrocarbons including naphthalene, phenanthrene, fluoranthene, 3-methylcholanthrene, 1-nitropyrene, and 6-nitrochrysene. This is the first report of a bacterium able to extensively mineralize pyrene and other polycyclic aromatic hydrocarbons containing four aromatic rings.

  16. Biosorption of metal ions from aqueous solution and tannery effluent by Bacillus sp. FM1.

    PubMed

    Masood, Farhana; Malik, Abdul

    2011-01-01

    The metal binding capacity of Bacillus sp. FM1 isolated from soil irrigated with tannery effluent was assessed using synthetic metal solutions and tannery wastewater. Biosorption of Cr(VI) and Cu(II) ions from aqueous solutions using Bacillus was investigated as a function of pH, initial metal ion concentration and contact time. The optimum adsorption pH value observed for Cr(VI) and Cu(II) ions was 2 and 5, respectively. Metal ion uptake increased with increasing initial metal concentration but no significant difference was observed by increasing the time after 60 min. Maximum uptake capacity of chromium was estimated as 64.102 mg g(-1), and of copper to 78.125 mg g(-1). Equilibrium data were well described by the Langmuir and Freundlich adsorption relations. The presence of functional groups on the cell wall surface of the biomass that may interact with the metal ion was confirmed by Fourier Transform Infrared (FTIR) spectroscopy. The application of Bacillus to remove Cr(VI) and Cu(II) in tannery effluent revealed that the biomass was capable of removing both the metal ions. However, the biosorption performance was slightly lower compared to that of synthetic metal solutions. Several factors may be responsible for this difference. However, the most important factor appears to be the presence of other contaminants such as anions, organics, and other trace metals in the effluent. PMID:22126236

  17. Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile.

    PubMed

    Yumoto, Isao; Hirota, Kikue; Goto, Toshitaka; Nodasaka, Yoshinobu; Nakajima, Kenji

    2005-03-01

    A halophilic and halotolerant, facultatively alkaliphilic strain, K11(T), was isolated from soil obtained from Oshyamanbe, Oshima, Hokkaido, Japan. The isolate grew at pH 7-10. It was non-motile, Gram-positive and aerobic. Cells comprised straight rods and produced ellipsoidal spores. The isolate grew in 0-20 % NaCl, with optimum growth at 7 % NaCl, and hydrolysed casein, gelatin, starch, DNA and Tweens 20, 40, 60 and 80. The major isoprenoid quinone was menaquinone-7, and the cellular fatty acid profile consisted of significant amounts of C(15) branched-chain acids, iso C(15 : 0) and anteiso C(15 : 0). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain K11(T) was a member of group 6 [Nielsen et al., FEMS Microbiol Lett 117 (1994), 61-66] (alkaliphiles) of the genus Bacillus. DNA-DNA hybridization revealed a low relatedness (14 %) of the isolate to its closest phylogenetic neighbour, Bacillus clausii. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA-DNA relatedness data, it was concluded that K11(T) (=JCM 12663(T)=NCIMB 14023(T)) merits classification as the type strain of a novel species, for which the name Bacillus oshimensis sp. nov. is proposed. PMID:15774684

  18. Isolation and characterization of a novel poly(vinyl alcohol)-degrading bacterium, Sphingopyxis sp. PVA3.

    PubMed

    Yamatsu, Atsushi; Matsumi, Rie; Atomi, Haruyuki; Imanaka, Tadayuki

    2006-10-01

    We have isolated a poly(vinyl alcohol) (PVA)-degrading bacterium from an activated sludge sample obtained from the drainage of a dyeing factory. Enrichment cultures were performed in media containing PVA as the sole or major carbon source. After several rounds of cultivation on liquid and solid media, we were able to isolate a single colony with PVA-degrading ability (strain PVA3). The bacterium could degrade PVA in the absence of symbionts or cofactors such as pyrroloquinoline quinone (PQQ). Over 90% of PVA, at an initial concentration of 0.1%, was degraded within a 6-day cultivation. Degradation was confirmed by both iodometric methods and gel permeation chromatography. Examination of the PVA attached to the cells revealed a large increase in carbonyl groups, suggesting the oxidation of hydroxyl groups of the polymer on the surfaces of cells. Addition of PQQ to the culture medium did not enhance the growth and the PVA-degrading rates of strain PVA3. Furthermore, we found that cells grown on PVA generated hydrogen peroxide upon the addition of PVA. The results strongly suggest that the initial oxidation of PVA is mediated via a PVA oxidase, and not a PQQ-dependent dehydrogenase. A biochemical and phylogenetic characterization of the bacterium was performed. The sequence of the 16S ribosomal RNA gene of the bacterium indicated a phylogenetic position of the strain within the genus Sphingopyxis, and the strain was therefore designated Sphingopyxis sp. PVA3. PMID:16583228

  19. Protease with collagenolytic activity produced by Bacillus sp. DPUA 1728 from Amazonian soil

    PubMed Central

    Lima, Lorena A.; Cruz, Raimundo F.; dos Santos, Januário G.; Silva, Wilson C.

    2015-01-01

    Qualitative analyses were carried out on solid medium with insoluble collagen 0.25% (w/v) to detect proteases with collagenolytic activity produced by Bacillus sp. In cultures incubated for 24 h, a 23 full factorial design with four repetitions at the center point was developed to analyze the effects and interactions between initial pH, temperature and the concentration of gelatin. Based on the results of the first 23 full factorial design, a successive 23 full factorial design was performed. The most favorable production conditions were found to be 1.5% (w/v) gelatin, pH 9.0 and 37 °C with enzymatic activity of 86.27 U/mL. The enzyme showed optimal activity at 50 °C and pH 9.0, and it was stable over wide pH (7.2-10.0) and temperature (45 °C-60 °C) ranges. These results indicate that Bacillus sp DPUA 1728 is a potential source for producing collagenolytic protease with possible biotechnological applications, such as in the food, cosmetics and leather industries. PMID:26691484

  20. Transcriptional and posttranscriptional regulation of Bacillus sp. CDB3 arsenic-resistance operon ars1

    PubMed Central

    Yu, Xuefei; Zheng, Wei; Bhat, Somanath; Aquilina, J. Andrew

    2015-01-01

    Bacillus sp. CDB3 possesses a novel eight-gene ars cluster (ars1, arsRYCDATorf7orf8) with some unusual features in regard to expression regulation. This study demonstrated that the cluster is a single operon but can also produce a short three-gene arsRYC transcript. A hairpin structure formed by internal inverted repeats between arsC and arsD was shown to diminish the expression of the full operon, thereby probably acting as a transcription attenuator. A degradation product of the arsRYC transcript was also identified. Electrophoretic mobility shift analysis demonstrated that ArsR interacts with the ars1 promoter forming a protein-DNA complex that could be impaired by arsenite. However, no interaction was detected between ArsD and the ars1 promoter, suggesting that the CDB3 ArsD protein may not play a regulatory role. Compared to other ars gene clusters, regulation of the Bacillus sp. CDB3 ars1 operon is more complex. It represents another example of specific mRNA degradation in the transporter gene region and possibly the first case of attenuator-mediated regulation of ars operons. PMID:26355338

  1. An effective method for the detoxification of cyanide-rich wastewater by Bacillus sp. CN-22.

    PubMed

    Wu, Chou-Fei; Xu, Xiao-Ming; Zhu, Qing; Deng, Mao-Cheng; Feng, Lei; Peng, Juan; Yuan, Jian-Ping; Wang, Jiang-Hai

    2014-04-01

    The biodetoxification of cyanide-rich wastewater has become increasingly popular because of its cost-effectiveness and environmental friendliness. Therefore, we have developed an effective method, optimised by response surface methodology, for detoxifying cyanide-rich wastewater using Bacillus sp. CN-22, which was newly isolated from a cyanide-contaminated electroplating sludge and could tolerate a CN⁻ concentration of 700 mg L⁻¹. The concentration of CN⁻ in the treated wastewater decreased from 200 to 6.62 mg L⁻¹ after cultivation with 2.38 % inocula for 72 h on the medium, consisting of 0.05 % KH₂PO₄, 0.15 % K₂HPO₄, 1.0 mM MgCl₂, 1.0 mM FeCl₃, 0.1 % NH₄Cl, and 0.1 % glycerol. The CN⁻ degradability of 96.69 % is similar to the predicted value of 96.82 %. The optimal cultivation conditions were controlled as follows: initial pH, 10.3; temperature, 31 °C; and rotary speed, 193 rpm. The maintenance of higher pH in the overall treatment procedures may avoid the production of volatile HCN and the risk associated with cyanide detoxification. Additionally, the bacterial strain Bacillus sp. CN-22, with its potent cyanide-degrading activity at the initial CN⁻ concentration of 200 mg L⁻¹, may be employed to effectively treat cyanide-rich wastewater, especially electroplating effluent. PMID:24337345

  2. Transcriptional and posttranscriptional regulation of Bacillus sp. CDB3 arsenic-resistance operon ars1.

    PubMed

    Yu, Xuefei; Zheng, Wei; Bhat, Somanath; Aquilina, J Andrew; Zhang, Ren

    2015-01-01

    Bacillus sp. CDB3 possesses a novel eight-gene ars cluster (ars1, arsRYCDATorf7orf8) with some unusual features in regard to expression regulation. This study demonstrated that the cluster is a single operon but can also produce a short three-gene arsRYC transcript. A hairpin structure formed by internal inverted repeats between arsC and arsD was shown to diminish the expression of the full operon, thereby probably acting as a transcription attenuator. A degradation product of the arsRYC transcript was also identified. Electrophoretic mobility shift analysis demonstrated that ArsR interacts with the ars1 promoter forming a protein-DNA complex that could be impaired by arsenite. However, no interaction was detected between ArsD and the ars1 promoter, suggesting that the CDB3 ArsD protein may not play a regulatory role. Compared to other ars gene clusters, regulation of the Bacillus sp. CDB3 ars1 operon is more complex. It represents another example of specific mRNA degradation in the transporter gene region and possibly the first case of attenuator-mediated regulation of ars operons. PMID:26355338

  3. Metal ion activated lipase from halotolerant Bacillus sp. VITL8 displays broader operational range.

    PubMed

    Balaji, Lavanya; Jayaraman, Gurunathan

    2014-06-01

    Lipase producing halo tolerant Bacillus sp. VITL8 was isolated from oil contaminated areas of Vellore. The identity of the organism was established by 16S rDNA sequence, in addition to the morphological and biochemical characterization. The purified enzyme (22kDa, 8680U/mg) exhibited optimal activity at pH 7.0 and 40°C and retained more than 50% of its activity in the NaCl concentration range of 0-3.0M, pH 6.0-10.0 and 10-60°C. Secondary structure analysis, using circular dichroism, revealed that the enzyme is composed of 38% α-helix and 29% β-turns. The lipase activity significantly increased in the presence of (1mM) Mn(2+) (139%), Ca(2+) (134%) and Mg(2+) (130%). Organic solvents such as butanol and acetonitrile (25%, v/v) enhanced the activity whereas DMSO (25% v/v) retained the activity. The Km of enzyme-p-Nitrophenyl palmitate complex was determined to be 191μM with a Vmax of 68μM/mg/min. Though halotolerant Bacillus sp. has been explored for hydrocarbon degradation, to our knowledge this is the first report on the lipase activity of the isolate. The characteristics of the enzyme presented in this report, imply broader operational range of the enzyme and therefore could be suitable for many of the industrial chemical processes. PMID:24704541

  4. Nitrogen removal capability through simultaneous heterotrophic nitrification and aerobic denitrification by Bacillus sp. LY.

    PubMed

    Zhao, Bin; He, Yi Liang; Zhang, Xiao Fan

    2010-04-01

    The heterotrophic nitrification and aerobic denitrification capabilities of Bacillus sp. LY were investigated under the aerobic condition. The results indicate that Bacillus sp. LY is not only a heterotrophic nitrifier, but also an aerobic denitrifier. Experiments were carried out in an attempt to determine and quantify the contribution of heterotrophic nitrification and aerobic denitrification to total N removal. By taking the nitrogen balance under the culture condition of 41.1 mg/L of initial NH(4+)-N at a C/N ratio of 15 in 96 h, 8.0% of the initial NH(4)+-N still remained in the medium in the forms of hydroxylamine, nitrite, nitrate and organic N; 40.5% of NH(4+)-N was converted to biomass and 45.9% of NH(4+)-N was estimated to be finally removed in the formation of N2. This conversion of ammonium to N2 with the intermediate formation of N2O under the aerobic condition was confirmed by gas chromatography. Single step nitrogen removal by simultaneous heterotrophic nitrification and aerobic denitrification has great potential in wastewater treatment. PMID:20450115

  5. Purification and Partial characterization of manganese peroxidase from Bacillus pumilus AND Paenibacillus sp.

    PubMed Central

    de Oliveira, Patrícia Lopes; Duarte, Marta Cristina Teixeira; Ponezi, Alexandre Nunes; Durrant, Lúcia Regina

    2009-01-01

    The production of manganese peroxidase (MnP) from Bacillus pumilus and Paenibacillus sp. was studied under absence and presence of the inducers indulin AT, guayacol, veratryl alcohol, lignosulfonic acid and lignosulfonic acid desulfonated. Indulin AT increased the activity of B. pumilus MnP up to 31.66 U/L after 8 h, but no improve was observed for Paenibacillus sp., which reached maximum activity (12.22 U/L) after 20 h. Both MnPs produced by these microorganisms were purified in phenyl sepharose resin and the proteins from crude extracts were eluted in two fractions. However, only the first fraction of each extract exhibited MnP activities. Tests in different pH and temperature values, from pH 5.0 to pH 10.0 and 30 °C to 60 °C, respectively, were carried out with the purified MnP. The maximum activity reached for B. pumilus and Paenibacillus sp. MnPs were 4.3 U/L at pH 8.0 and 25 °C and 11.74 U/L at pH 9.0 and 35 °C, respectively. The molar masses determined by SDS-PAGE gel eletrophoresis were 25 kDa and 40 kDa, respectively, for the purified enzyme from B. pumilus and Paenibacillus sp. PMID:24031429

  6. Genome Sequence of Desulfovibrio sp. A2, a Highly Copper Resistant, Sulfate-Reducing Bacterium Isolated from Effluents of a Zinc Smelter at the Urals

    PubMed Central

    Mancini, Stefano; Abicht, Helge K.; Karnachuk, Olga V.; Solioz, Marc

    2011-01-01

    Desulfovibrio sp. A2 is an anaerobic Gram-negative sulfate-reducing bacterium with remarkable tolerance to copper. It was isolated from wastewater effluents of a zinc smelter at the Urals. Here, we report the 4.2-Mb draft genome sequence of Desulfovibrio sp. A2 and identify potential copper resistance mechanisms. PMID:22072648

  7. Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix

    PubMed Central

    Alzbutas, Gediminas; Kaniusaite, Milda; Lagunavicius, Arunas

    2016-01-01

    In our previous work we showed that DNaseI-like protein from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix retained its activity at salt concentrations as high as 4 M NaCl and the key factor allowing this was the C-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix) motifs. The further investigations revealed that this domain originated from proteins related to bacterial competence ComEA/ComE proteins. It is likely that in the course of evolution the DNA-binding domain from these proteins was fused to a metallo-β-lactamase superfamily domain. Very likely such domain organization having proteins subsequently “donated” the DNA-binding domain to bacterial DNases. In this study we have mimicked this evolutionary step by fusing bovine DNaseI and DNA-binding domains. We have created two fusions: one harboring the DNA-binding domain of DNaseI-like protein from Thioalkalivibrio sp. K90mix and the second one harboring the DNA-binding domain of bacterial competence protein ComEA from Bacillus subtilis. Both domains enhanced salt tolerance of DNaseI, albeit to different extent. Molecular modeling revealed the essential differences between their interaction with DNA shedding some light on the differences in salt tolerance. In this study we have enhanced salt tolerance of bovine DNaseI; thus, we successfully mimicked the Nature’s evolutionary engineering that created the extremely halotolerant bacterial DNase. We have demonstrated that the newly engineered DNaseI variants can be successfully used in applications where activity of the wild type bovine DNaseI is impeded by buffers used. PMID:26939122

  8. Enhancement of DNaseI Salt Tolerance by Mimicking the Domain Structure of DNase from an Extremely Halotolerant Bacterium Thioalkalivibrio sp. K90mix.

    PubMed

    Alzbutas, Gediminas; Kaniusaite, Milda; Lagunavicius, Arunas

    2016-01-01

    In our previous work we showed that DNaseI-like protein from an extremely halotolerant bacterium Thioalkalivibrio sp. K90mix retained its activity at salt concentrations as high as 4 M NaCl and the key factor allowing this was the C-terminal DNA-binding domain, which comprised two HhH (helix-hairpin-helix) motifs. The further investigations revealed that this domain originated from proteins related to bacterial competence ComEA/ComE proteins. It is likely that in the course of evolution the DNA-binding domain from these proteins was fused to a metallo-β-lactamase superfamily domain. Very likely such domain organization having proteins subsequently "donated" the DNA-binding domain to bacterial DNases. In this study we have mimicked this evolutionary step by fusing bovine DNaseI and DNA-binding domains. We have created two fusions: one harboring the DNA-binding domain of DNaseI-like protein from Thioalkalivibrio sp. K90mix and the second one harboring the DNA-binding domain of bacterial competence protein ComEA from Bacillus subtilis. Both domains enhanced salt tolerance of DNaseI, albeit to different extent. Molecular modeling revealed the essential differences between their interaction with DNA shedding some light on the differences in salt tolerance. In this study we have enhanced salt tolerance of bovine DNaseI; thus, we successfully mimicked the Nature's evolutionary engineering that created the extremely halotolerant bacterial DNase. We have demonstrated that the newly engineered DNaseI variants can be successfully used in applications where activity of the wild type bovine DNaseI is impeded by buffers used. PMID:26939122

  9. Biomass Yield Efficiency of the Marine Anammox Bacterium, “Candidatus Scalindua sp.,” is Affected by Salinity

    PubMed Central

    Awata, Takanori; Kindaichi, Tomonori; Ozaki, Noriatsu; Ohashi, Akiyoshi

    2015-01-01

    The growth rate and biomass yield efficiency of anaerobic ammonium oxidation (anammox) bacteria are markedly lower than those of most other autotrophic bacteria. Among the anammox bacterial genera, the growth rate and biomass yield of the marine anammox bacterium “Candidatus Scalindua sp.” is still lower than those of other anammox bacteria enriched from freshwater environments. The activity and growth of marine anammox bacteria are generally considered to be affected by the presence of salinity and organic compounds. Therefore, in the present study, the effects of salinity and volatile fatty acids (VFAs) on the anammox activity, inorganic carbon uptake, and biomass yield efficiency of “Ca. Scalindua sp.” enriched from the marine sediments of Hiroshima Bay, Japan, were investigated in batch experiments. Differences in VFA concentrations (0–10 mM) were observed under varying salinities (0.5%–4%). Anammox activity was high at 0.5%–3.5% salinity, but was 30% lower at 4% salinity. In addition, carbon uptake was higher at 1.5%–3.5% salinity. The results of the present study clearly demonstrated that the biomass yield efficiency of the marine anammox bacterium “Ca. Scalindua sp.” was significantly affected by salinity. On the other hand, the presence of VFAs up to 10 mM did not affect anammox activity, carbon uptake, or biomass yield efficiency. PMID:25740428

  10. Respiratory chain of the alkalophilic bacterium Bacillus firmus RAB and its non-alkalophilic mutant derivative.

    PubMed Central

    Kitada, M; Lewis, R J; Krulwich, T A

    1983-01-01

    The membrane-bound respiratory chain components of alkalophilic Bacillus firmus RAB were studied by difference spectroscopy and oxidation-reduction potentiometric titrations. Cytochromes with the following midpoint potentials were identified at pH 9.0: a-type cytochromes, +110 and +210 mV; b-type cytochromes, +20, -120, -280, and -400 mV; and cytochrome c, +60 mV. Only the higher-potential cytochrome a showed an upward shift in midpoint potential when titrated at pH 7.0. Parallel studies of a non-alkalophilic mutant derivative of B. firmus RAB, strain RABN, revealed the presence of only one species each of a-, b-, and c-type cytochromes which exhibited midpoint potentials of +110, -150, and +160 mV, respectively, at pH 7.0. Membranes of both strains were found to contain menaquinone. At pH 9.0, NADH caused the reduction of essentially all of the cytochromes that were seen in fully reduced preparations of wild-type B. firmus RAB membranes. By contrast, at pH 7.0, NADH failed to appreciably reduce the b-type cytochromes. These findings may relate to our recent proposal that an inadequacy in energy transduction (production of a proton motive force) by the alkalophilic respiratory chain at pH 7.0 is what precludes the growth of B. firmus RAB at a neutral pH. PMID:6833181

  11. Biophysical characterization of a recombinant aminopeptidase II from the thermophilic bacterium Bacillus stearothermophilus.

    PubMed

    Wang, Tzu-Fan; Lin, Min-Guan; Lo, Huei-Fen; Chi, Meng-Chun; Lin, Long-Liu

    2014-01-01

    In the present study, the biophysical properties of His6-tagged Bacillus stearothermophilus aminopeptidase II (His6-tagged BsAmpII) are characterized in detail by gel-filtration, analytical ultracentrifugation, and various spectroscopic techniques. Using size-exclusion chromatography and analytical ultracentrifugation, we demonstrate that His6-tagged BsAmpII exists predominantly as a dimer in solution. The enzyme is active and stable at pHs ranging from 6.5 to 8.5. Far-UV circular dichroism analysis reveals that the secondary structures of His6-tagged BsAmpII are significantly altered in the presence of SDS, whereas the presence of 5-10% acetone and ethanol was harmless to the folding of the enzyme. Thermal unfolding of His6-tagged BsAmpII was found to be irreversible and led to the formation of aggregates. The native enzyme started to unfold beyond 0.6 M guanidine hydrochloride and had a midpoint of denaturation at 1.34 M. This protein remained active at concentrations of urea below 2.7 M but experienced an irreversible unfolding by >5 M denaturant. Taken together, this work lays a foundation for potential biotechnological applications of His6-tagged BsAmpII. PMID:24165863

  12. Characteristics of recombinant α-carbonic anhydrase of polyextremophilic bacterium Bacillus halodurans TSLV1.

    PubMed

    Faridi, Shazia; Satyanarayana, T

    2016-08-01

    Carbonic anhydrase (CA) is a biocatalyst that catalyzes the hydration of CO2 to bicarbonate and protons, thus useful in mitigating green house effect by sequestering CO2 from various point sources. An alkalistable and moderately thermostable α- carbonic anhydrase encoding gene (BhCA) from Bacillus halodurans TSLV1 has been cloned and expressed in Escherichia coli. A 31.4-fold enhancement in CA production was achieved due to cloning and expression in E. coli. About 50% of the CA produced was secreted when recombinant E. coli with BhCA-pET22b was cultivated in a medium with EDTA and lysozyme because of the efficient pelB leader sequence. rBhCA is a ∼75kDa homodimeric protein with a Tm of 72°C and T1/2 values of 66 and 24min at 50 and 60°C, respectively. SDM analysis revealed that H137, H139, H156 and H110 present in the active site play an important role in catalysis. Mineralization of CO2 using rBhCA led to the accelerated precipitation of CaCO3 in calcite form. rBhCA also functions as an efficient virtual peroxidase when Zn(2+) is substituted with Mn(2+). PMID:27174908

  13. Streptomyces olivicoloratus sp. nov., an antibiotic-producing bacterium isolated from soil.

    PubMed

    Nguyen, Tuan Manh; Kim, Jaisoo

    2015-10-01

    Strain T13T, isolated from forest soil in Jeollabuk-do, South Korea, exhibited antibiotic production on yeast extract-malt extract-glucose (YMG) medium containing magnesium chloride as a trace mineral, and inhibited the growth of Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, Staphylococcus epidermidis, Paenibacillus larvae, Escherichia coli, Candida albicans and Aspergillus niger. Growth occurred at 15-45 °C, pH 4-11 and in the presence of up to 2 % (w/v) NaCl. Biochemical analyses indicated that the predominant menaquinones produced by this strain were MK-9(H6) and MK-9(H8); small amounts of MK-10(H2) and MK-10(H4) were also detected. The polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine, and the cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates contained glucose, galactose, ribose and rhamnose. The fatty-acid profile of strain T13T was made up predominantly of iso- and anteiso-branched fatty acids. Genetic analyses demonstrated that strain T13T is closely related to Streptomyces gramineus JR-43T (98.29 % 16S rRNA gene sequence similarity), S. graminisoli JR-19T (97.99 %), S. rhizophilus JR-41T (97.86 %), S. longwoodensis LMG 20096T (97.84 %), S. graminifolii JL-22T (97.79 %) and S. yaanensis Z4T (97.56 %), and DNA-DNA hybridization yielded relatedness values of 35.27-43.42 % when T13T was compared to related strains. The results of morphological, chemotaxonomic, phylogenetic and phenotypic analyses confirm that this strain represents a novel species of the genus Streptomyces, for which the name Streptomyces olivicoloratus sp. nov. is proposed. The type strain is T13T ( = KEMB 9005-210T = KACC 18227T = NBRC 110901T). PMID:26296874

  14. Halobacillus salicampi sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.

    PubMed

    Kim, Su-Jin; Lee, Jae-Chan; Han, Song-Ih; Whang, Kyung-Sook

    2016-05-01

    A Gram-positive, moderately halophilic bacterium, designated strain TGS-15(T), was isolated from the sediment of a solar saltern pond located in Shinan, Korea. Strain TGS-15(T) was found to be a strictly aerobic, non-motile rod which can grow at pH 6.0-10.0 (optimum, pH 9.0), at 20-35 °C (optimum, 28 °C) and at salinities of 1-20 % (w/v) NaCl (optimum, 9 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain TGS-15(T) belongs to the genus Halobacillus, with sequence similarity of 98.5-96.0 % to known type strains, showing high sequence similarity to Halobacillus locisalis MSS-155(T) (98.5 %), Halobacillus faecis IGA7-4(T) (98.2 %) and Halobacillus alkaliphilus FP5(T) (98.0 %), and less than 98.0 % sequence similarity to other currently recognised type strains of the genus. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and an unidentified lipid. The cell wall peptidoglycan was found to be based on L-Orn-D-Asp, the predominant isoprenoid quinone was identified as menaquinone-7 (MK-7) and the major fatty acids were identified as anteiso-C15:0, iso-C15:0, anteiso-C17:0 and C16:1 ω7c alcohol. The DNA G+C content of this novel isolate was determined to be 45.3 mol %. Levels of DNA:DNA relatedness between strain TGS-15(T) and the type strains of 13 other species of the genus ranged from 52 to 9 %. On the basis of the polyphasic analysis conducted in this study, strain TGS-15(T) is concluded to represent a novel species of the genus Halobacillus, for which the name Halobacillus salicampi sp. nov. is proposed. The type strain is TGS-15(T) (=KACC 18264(T) = NBRC 110640(T)). PMID:26942918

  15. Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil.

    PubMed

    Pham, Van Hong Thi; Jeong, Seung-Woo; Kim, Jaisoo

    2015-10-01

    Strain NHI-1T is a Gram-negative, motile, non-spore-forming bacterium isolated from oil-contaminated soil in South Korea. The strain was able to grow by using gasoline, diesel and kerosene as energy and carbon sources. After incubation for 14 days, cells (1 g l- 1) degraded approximately 58 % of oil present at concentration of 1500 p.p.m. at pH 8 and 28 °C. Strain NHI-1T grew well under aerobic conditions, with optimal growth at pH 7-9 and 28 °C-37 °C but grew poorly in the presence of ≥ 0.5 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest relatives of strain NHI-1T were Aquabacterium fontiphilum CS-6T (97.96 % sequence similarity), Aquabacterium parvum B6T (96.39 %), Aquabacterium commune B8T (95.76 %), Aquabacterium limnoticum ABP-4T (95.72 %) and Aquabacterium citratiphilum B4T (95.25 %). DNA-DNA relatedness was 41-53 % between strain NHI-1T and its closest type strains. The major fatty acids present in strain NHI-1T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 44.5 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c, 21.5 %) and C16 : 0 (16.2 %), and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol and uncharacterized aminophospholipids. Strain NHI-1T was distinguishable from other members of genus Aquabacterium based on phenotypic, chemotaxonomic and genotypic characteristics. Therefore, strain NHI-1T represents a novel species of the genus Aquabacterium for which the name Aquabacterium olei sp. nov. is proposed. The type strain is NHI-1T ( = KEMB 9005-082T =  KACC 18244T = NBRC 110486T). PMID:26297008

  16. Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.

    PubMed

    Chen, Qing; Zhang, Jun; Wang, Cheng-Hong; Jiang, Jin; Kwon, Soon-Wo; Sun, Li-Na; Shen, Wen-Biao; He, Jian

    2014-08-01

    Strain BUT-14(T), a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90% of butachlor, acetochlor and alachlor (100 mg l(-1)) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14(T) was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821(T) (97.9%), N. naphthalenivorans KACC 15258(T) (97.4%), N. pentaromativorans JCM 12182(T) (97.4%) and N. barchaimii DSM 25411(T) (97.1%) and lower (<97%) sequence similarities to all other species of the genus Novosphingobium. Chemotaxonomic analysis revealed that strain BUT-14(T) possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C(18 : 1)ω7c (46.9%), C(17 : 1)ω6c (17.9%), summed feature 3, C(14 : 0) 2-OH (4.4%), C(15 : 0) 2-OH (3.1%) and C(16 : 0) (5.51%) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14(T) showed low DNA-DNA relatedness with N. soli DSM 22821(T) (41.5±2.9%), N. naphthalenivorans JCM 12182(T) (49.2±4.2%), N. pentaromativorans KACC 12295(T) (53.2±1.9%) and N. barchaimii DSM 25411 (51.2±4.5%). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA-DNA hybridization supports the suggestion that strain BUT-14(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14(T) ( = CCTCC AB 2013086(T) = KACC 17147(T) = JCM 19923(T)). PMID

  17. Salipiger nanhaiensis sp. nov., a bacterium isolated from deep sea water.

    PubMed

    Dai, Xiaofeng; Shi, Xiaochong; Gao, Xin; Liang, Jing; Zhang, Xiao-Hua

    2015-04-01

    A Gram-stain-negative, facultatively anaerobic, chemoheterotrophic, moderately halophilic, exopolysaccharide (EPS)-producing, cream, non-motile and rod-shaped bacterium, designated strain ZH114(T), was isolated from deep water of the South China Sea, and was subjected to a polyphasic taxonomic study. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that this strain belongs to the genus Salipiger with the highest sequence similarity to Salipiger mucescens LMG 22090(T) (96.83%), followed by Pseudodonghicola xiamenensis LMG 24574(T) (96.12%). Growth occurred at 4-37 °C (optimum 32 °C), pH 6.0-10.0 (optimum pH 9.0-10.0) and in the presence of 0-19% NaCl (w/v) (optimum 6%, w/v). It did not produce poly-β-hydroxyalkanoate granules or bacteriochlorophyll a. Acid was produced from glycerol, erythrose, ribose, D-xylose, galactose, glucose, fructose, mannitol, cellobiose, maltose, lactose, melibiose, turanose, D-lyxose, D-tagatose, D-fucose, D-arabitol and L-arabitol after inoculating for 24 h and weakly positive results were also detected after 48 h in API 50CH strips with D-arabinose, L-arabinose, L-xylose, adonitol, mannose, aesculin, salicin, sucrose, mycose and L-fucose. The predominant fatty acids were C(18 : 1)ω7c and/or C(18 : 1)ω6c, C(16 : 0), C(18 : 0) and 11-methyl C(18 : 1)ω7c. The major polar lipids of ZH114(T) were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified lipids. The major respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content of strain ZH114(T) was 63.8 mol%. Based on this phenotypic, chemotaxonomic and phylogenetic analysis, strain ZH114(T) should be classified as a representative of a novel species of the genus Salipiger , for which the name Salipiger nanhaiensis sp. nov. is proposed. The type strain is ZH114(T) ( = JCM 19383(T) = KCTC 32468(T)). PMID:25589735

  18. Halomonas salicampi sp. nov., a halotolerant and alkalitolerant bacterium isolated from a saltern soil.

    PubMed

    Lee, Jae-Chan; Kim, Young-Sook; Yun, Bong-Sik; Whang, Kyung-Sook

    2015-12-01

    A Gram-stain-negative, halotolerant and alkalitolerant bacterium, designated strain BH103T, was isolated from saltern soil in Gomso, Korea. Cells of strain BH103T were strictly aerobic, motile, straight rods and grew at pH 7.0-10.8 (optimum, pH 8.5), at 10-55 °C (optimum, 28 °C) and at salinities of 0-23 % (w/v) NaCl (optimum, 14 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BH103T belongs to the genus Halomonas, showing highest sequence similarity to Halomonas boliviensis LC1T (97.7 %), Halomonas neptunia Eplume1T (97.7 %), Halomonas variabilis IIIT (97.7 %), Halomonas alkaliantarctica CRSST (97.7 %), Halomonas olivaria TYRC17T (97.5 %), Halomonas titanicae BH1T (97.2 %) and Halomonas sulfidaeris Esulfide1T (96.2 %). The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1ω7c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C12 : 0 3-OH. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown phospholipid. The DNA G+C content of this novel isolate was 54.7 mol%. DNA-DNA relatedness between strain BH103T and H. boliviensis KACC 16615T, H. neptunia KCTC 2888T, H. variabilis KCTC 2889T, H. alkaliantarctica KCTC 22844T, H. olivaria DSM 19074T, H. titanicae JCM 16411T and H. sulfidaeris DSM 15722T was 45, 41, 39, 32, 38, 45 and 35 %, respectively. On the basis of polyphasic analysis from this study, strain BH103T represents a novel species of the genus Halomonas, for which the name Halomonas salicampi sp. nov. is proposed. The type strain is BH103T ( = KACC 17609T = NBRC 109914T = NCAIM B 02528T). PMID:26431725

  19. Halomonas heilongjiangensis sp. nov., a novel moderately halophilic bacterium isolated from saline and alkaline soil.

    PubMed

    Dou, Guiming; He, Wei; Liu, Hongcan; Ma, Yuchao

    2015-08-01

    A moderately halophilic bacterium, designated strain 9-2(T), was isolated from saline and alkaline soil collected in Lindian county, Heilongjiang province, China. The strain was observed to be strictly aerobic, Gram-negative, rod-shaped, oxidase-positive, catalase-positive and motile. It was found to require NaCl for growth and to grow at NaCl concentrations of 0.5-14 % (w/v) (optimum, 7-10 %, w/v), at temperatures of 10-45 °C (optimum 25-30 °C) and at pH 5.0-10.0 (optimum pH 8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 9-2(T) is a member of the genus Halomonas and is closely related to Halomonas desiderata DSM 9502(T) (96.68 %), Halomonas campaniensis DSM 1293(T) (96.46 %), Halomonas ventosae DSM 15911(T) (96.27 %) and Halomonas kenyensis DSM 17331(T) (96.27 %). The DNA-DNA hybridization value was 38.9 ± 0.66 % between the novel isolate 9-2(T) and H. desiderata DSM 9502(T). The predominant ubiquinones were identified as Q9 (75.1 %) and Q8 (24.9 %). The major fatty acids were identified as C16:0 (22.0 %), Summed feature 8 (C18:1 ω6c/C18:1 ω7c, 19.6 %), Summed feature 3 (C16:1 ω6c/C16:1 ω7c, 12.6 %), C12:0 3-OH (12.0 %) and C10:0 (11.7 %). The DNA G+C content was determined to be 69.7 mol%. On the basis of the evidence presented in this study, strain 9-2(T) is considered to represent a novel species of the genus Halomonas, for which the name Halomonas heilongjiangensis sp. nov. is proposed. The type strain is 9-2(T) (=DSM 26881(T) = CGMCC 1.12467(T)). PMID:26036672

  20. Lysinibacillus alkaliphilus sp. nov., an extremely alkaliphilic bacterium, and emended description of genus Lysinibacillus.

    PubMed

    Zhao, Fei; Feng, Youzhi; Chen, Ruirui; Zhang, Jianwei; Lin, Xiangui

    2015-08-01

    A novel aerobic, alkaliphilic, Gram-staining-positive, endospore-forming bacterium, strain OMN17T, was isolated from a typical sandy loam soil under long-term OMN fertilization (half organic manure N plus half mineral N fertilizer) in northern China and was subjected to a polyphasic taxonomic study. The best growth was achieved at 30 °C and pH 8-10 in medium containing 0.5% (w/v) NaCl. The cell-wall peptidoglycan of strain OMN17T was type A4α; (l-Lys-Gly-d-Asp) and the cell-wall sugars were ribose, traces of galactose and arabinose. The only respiratory quinone found in strain OMN17T was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of strain OMN17T based on the 16S rRNA gene sequence showed that the strain was most closely related to Lysinibacillus halotolerans (97.8%), Lysinibacillus sinduriensis (97.5%), Lysinibacillus chungkukjangi (97.4%) and Lysinibacillus xylanilyticus (97.0%). The DNA-DNA hybridization results indicated that this strain was distinct from other species of the genus Lysinibacillus, the degree of relatedness being 21.8 ± 0.2% with L. halotolerans, 45.6 ± 1.8% with L. sinduriensis, 33.7 ± 1.2% with L. chungkukjangi and 23.7 ± 0.7% with L. xylanilyticus. The DNA G+C content of strain OMN17T was 38.1 mol%. The phenotypic, chemotaxonomic and genetic analyses identified strain OMN17T as a novel species of the genus Lysinibacillus, for which the name Lysinibacillus alkaliphilus sp. nov. is proposed. The type strain is OMN17T ( = DSM 28019T = CCTCC AB 2014073T). An emended description of the genus Lysinibacillus is also provided. PMID:25908711

  1. Vibrio xiamenensis sp. nov., a cellulase-producing bacterium isolated from mangrove soil.

    PubMed

    Gao, Zhao-Ming; Xiao, Jing; Wang, Xing-Na; Ruan, Ling-Wei; Chen, Xiu-Lan; Zhang, Yu-Zhong

    2012-08-01

    A taxonomic study was carried out on a cellulase-producing bacterium, strain G21(T), isolated from mangrove soil in Xiamen, Fujian province, China. Cells were Gram-negative, slightly curved rods, motile with a single polar flagellum. The strain grew at 15-40 °C and in 0.5-10% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G21(T) belonged to the genus Vibrio and formed a clade with Vibrio furnissii ATCC 350116(T) (97.4% sequence similarity), V. fluvialis LMG 7894(T) (97.1%) and V. ponticus CECT 5869(T) (96.1%). However, multilocus sequence analysis (using rpoA, recA, mreB, gapA, gyrB and pyrH sequences) and DNA-DNA hybridization experiments indicated that the strain was distinct from the closest related Vibrio species. Additionally, strain G21(T) could be differentiated from them phenotypically by the ability to grow in 10% NaCl but not on TCBS plates, its enzyme activity spectrum, citrate utilization, oxidization of various carbon sources, hydrolysis of several substrates and its cellular fatty acid profile. The G+C content of the genomic DNA was 46.0 mol%. The major cellular fatty acids were summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH), C(16:0) and C(18:1)ω7c. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol, with trace amounts of diphosphatidylglycerol. The predominant quinones were Q-8 and Q-7. Based on phylogenetic, phenotypic and chemotaxonomic characteristics and DNA-DNA hybridization analysis, it is concluded that strain G21(T) represents a novel species of the genus Vibrio, for which the name Vibrio xiamenensis sp. nov. is proposed. The type strain is G21(T) ( = DSM 22851(T)  = CGMCC 1.10228(T)). PMID:22039001

  2. Caulobacter flavus sp. nov., a stalked bacterium isolated from rhizosphere soil.

    PubMed

    Sun, Le-Ni; Yang, En-Dong; Wei, Jie-Chao; Tang, Xin-Yun; Cao, Yuan-Yuan; Han, Guo-Min

    2015-12-01

    A Gram-stain-negative, aerobic, yellow-pigmented and rod-shaped bacterium with a single polar flagellum or a stalk, designated strain RHGG3T, was isolated from rhizosphere soil of cultivated watermelon (Citrullus lanatus) collected from Hefei, China. Optimal growth of strain RHGG3T was observed at pH 7.0 and 28-30 °C. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RHGG3T belonged to the genus Caulobacter and showed the highest 16S rRNA gene sequence similarities to Caulobacter segnis ATCC 21756T (98.6 %), Caulobacter vibrioides CB51T (98.3 %) and Caulobacter henricii ATCC 15253T (97.2 %). The G+C content of the genomic DNA was 70 mol%. Strain RHGG3T contained Q-10 as the sole ubiquinone and the major fatty acids (>8 %) were 11-methyl C18 : 1ω7c, C18 : 1ω7c, C16 : 0, C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipids were various unknown glycolipids, phosphatidylglycerol and phosphoglycolipids. DNA-DNA relatedness of strain RHGG3T to type strains of the most closely related species (Caulobacter segnis ATCC 21756T, Caulobacter vibrioides DSM 4738 and Caulobacter henricii ATCC 15253T) was 32.4-40.9 %. Based on polyphasic taxonomy analysis (phylogenetic, unique phenotypic traits, chemotaxonomic and DNA-DNA hybridizations), strain RHGG3T represents a novel species of the genus Caulobacter, for which the name Caulobacter flavus sp. nov. is proposed. The type strain is RHGG3T ( = CGMCC 1.15093T = KCTC 42581T = JCM 30763T). PMID:26354335

  3. Tumebacillus flagellatus sp. nov., an α-amylase/pullulanase-producing bacterium isolated from cassava wastewater.

    PubMed

    Wang, Qingyan; Xie, Nengzhong; Qin, Yan; Shen, Naikun; Zhu, Jing; Mi, Huizhi; Huang, Ribo

    2013-09-01

    A novel α-amylase/pullulanase-producing bacterium, designated strain GST4(T), was isolated from samples collected from the wastewater of a cassava starch factory in Nanning, Guangxi Autonomous Region, southern China. Cells of strain GST4(T) were rod-shaped bacilli containing ellipsoidal terminal spores and found to be Gram-reaction-positive, aerobic, motile, oxidase-positive, catalase-negative and formed light yellow colonies on agar plates. Strain GST4(T) was able to grow at pH 4.5-8.5 (optimum at pH 5.5), temperatures ranging from 20 to 42 °C (optimum at 37 °C) and salt concentrations of 0-1% (w/v) NaCl (optimum at 0.5%, w/v) on R2A medium. Strain GST4(T) grew heterotrophically on complex carbon substrates and chemolithoautotrophically on inorganic sulfur compounds, as demonstrated by growth on sodium thiosulfate and sulfite as sole electron donors. It can reduce nitrate and nitrite. Strain GST4(T) contained iso-C(15:0) and anteiso-C(15:0) as the major cellular fatty acids and menaquinone 7 (MK-7) as the major respiratory quinone. The cell-wall peptidoglycan was of type A1γ. The genomic DNA G+C content of strain GST4(T) was 53.7 mol%. Physiological and chemotaxonomic characteristics combined with phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GST4(T) was a member of the genus Tumebacillus and most closely related to Tumebacillus permanentifrigoris DSM 18773(T) and Tumebacillus ginsengisoli DSM 18389(T) with 97.3 and 94.5% sequence similarity, respectively. The DNA-DNA relatedness values between strain GST4(T) and T. permanentifrigoris DSM 18773(T), and strain GST4(T) and T. ginsengisoli DSM 18389(T) were 44.0 and 60.4%, respectively. The new isolate differed from those species of the genus Tumebacillus in that it has peritrichous flagella for motility. Based on the evidence obtained from this study, strain GST4(T) represents a novel species of the genus Tumebacillus, for which the name Tumebacillus flagellatus sp. nov. is proposed

  4. Caloramator quimbayensis sp. nov., an anaerobic, moderately thermophilic bacterium isolated from a terrestrial hot spring.

    PubMed

    Rubiano-Labrador, Carolina; Baena, Sandra; Díaz-Cárdenas, Carolina; Patel, Bharat K C

    2013-04-01

    An anaerobic, moderately thermophilic, terminal-spore-forming bacterium, designated strain USBA A(T), was isolated from a terrestrial hot spring located at an altitude of 2683 m in the Andean region of Colombia (04° 50' 14.0″ N 75° 32' 53.4″ W). Cells of strain USBA A(T) were Gram-stain-positive, straight to slightly curved rods (0.9×2.5 µm), that were arranged singly or in pairs, and were motile by means of flagella. Growth occurred at 37-55 °C and pH 6.0-8.0, with a doubling time of 2 h under the optimal conditions (50 °C and pH 7.0). Glucose fermentation in strain USBA A(T) required yeast extract or peptone (each at 0.2 %, w/v). The novel strain fermented sugars, amino acids, Casamino acids, propanol, propionate, starch and dextrin, but no growth was observed on galactose, lactose, xylose, histidine, serine, threonine, benzoate, butyrate, lactate, pyruvate, succinate, methanol, ethanol, glycerol, casein, gelatin or xylan. The end products of glucose fermentation were formate, acetate, ethanol and lactate. Strain USBA A(T) did not grow autotrophically (with CO2 as carbon source and H2 as electron donor) and did not reduce thiosulfate, sulfate, elemental sulfur, sulfite, vanadium (V) or Fe (III) citrate. Growth of strain USBA A(T) was inhibited by ampicillin, chloramphenicol, kanamycin, penicillin and streptomycin (each at 10 µg ml(-1)). The predominant fatty acids were iso-C15 : 0, C16 : 0 and iso-C17 : 0 and the genomic DNA G+C content was 32.6 mol%. 16S rRNA gene sequence analysis indicated that strain USBA A(T) belonged in the phylum Firmicutes and that its closest relative was Caloramator viterbiensis JW/MS-VS5(T) (95.0 % sequence similarity). A DNA-DNA relatedness value of only 30 % was recorded in hybridization experiments between strain USBA A(T) and Caloramator viterbiensis DSM 13723(T). Based on the phenotypic, chemotaxonomic and phylogenetic evidence and the results of the DNA-DNA hybridization experiments, strain USBA A

  5. Anoxybacillus calidus sp. nov., a thermophilic bacterium isolated from soil near a thermal power plant.

    PubMed

    Cihan, Arzu Coleri; Cokmus, Cumhur; Koc, Melih; Ozcan, Birgul

    2014-01-01

    A novel thermophilic, Gram-stain-positive, facultatively anaerobic, endospore-forming, motile, rod-shaped bacterium, strain C161ab(T), was isolated from a soil sample collected near Kizildere, Saraykoy-Buharkent power plant in Denizli. The isolate could grow at temperatures between 35 and 70 °C (optimum 55 °C), at pH 6.5-9.0 (optimum pH 8.0-8.5) and with 0-2.5 % NaCl (optimum 0.5 %, w/v). The strain formed cream-coloured, circular colonies and tolerated up to 70 mM boron. Its DNA G+C content was 37.8 mol%. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. Strain C161ab(T) contained menaquinones MK-7 (96 %) and MK-6 (4 %). The major cellular fatty acids were iso-branched fatty acids: iso-C15 : 0 (52.2 %) and iso-C17 : 0 (28.0 %,) with small amounts of C16 : 0 (7.4 %). Phylogenetic analysis based on the 16S rRNA gene revealed 94.6-96.8 % sequence similarity with all recognized species of the genus Anoxybacillus. Strain C161ab(T) showed the greatest sequence similarity to Anoxybacillus rupiensis DSM 17127(T) and Anoxybacillus voinovskiensis DSM 17075(T), both had 96.8 % similarity to strain C161ab(T), as well as to Anoxybacillus caldiproteolyticus DSM 15730(T) (96.6 %). DNA-DNA hybridization revealed low levels of relatedness with the closest relatives of strain C161ab(T), A. rupiensis (21.2 %) and A. voinovskiensis (16.5 %). On the basis of the results obtained from phenotypic, chemotaxonomic, genomic fingerprinting, phylogenetic and hybridization analyses, the isolate is proposed to represent a novel species, Anoxybacillus calidus sp. nov. (type strain C161ab(T) = DSM 25520(T) = NCIMB 14851(T)). PMID:24052627

  6. Marinobacter halophilus sp. nov., a halophilic bacterium isolated from a salt lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Liu, Hong-Can; Wang, Fang; Zhou, Yu-Guang; Liu, Zhi-Pei

    2015-09-01

    A Gram-staining-negative bacterium, strain XCD-X12(T), was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9%, w/w) in Qaidam basin, Qinghai Province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X12(T) were non-spore-forming rods, 0.4-0.7 μm wide, 2.1-3.2 μm long and motile with a single polar flagellum. Strain XCD-X12(T) was strictly aerobic and catalase- and oxidase-positive. Growth was observed in the presence of 0-20.0% (w/v) NaCl (optimum, 4.0-8.0%), at 4-35 °C (optimum, 30 °C) and at pH 6.5-10.5 (optimum, pH 8.5). It contained Q-9 as the predominant respiratory quinone. The major fatty acids (>10.0%) were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unknown phospholipids and an uncharacterized aminophospholipid. The DNA G+C content was 55.6 mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X12(T) was associated with the genus Marinobacter, and showed the highest 16S rRNA gene sequence similarity to Marinobacter hydrocarbonoclasticus ATCC 49840(T) (97.4%), M. vinifirmus FB1(T) (96.8%), M. excellens KMM 3809(T) (96.8%) and M. antarcticus ZS2-30(T) (96.7%). DNA-DNA relatedness of strain XCD-X12(T) to M. hydrocarbonoclasticus CGMCC 1.7683(T) was 34 ± 5%. Based on these data, it is concluded that strain XCD-X12(T) represents a novel species of the genus Marinobacter, for which the name Marinobacter halophilus sp. nov. is proposed. The type strain is XCD-X12(T) ( = CGMCC 1.12481(T)= JCM 30472(T)). PMID:25985830

  7. [Rhodobaculum claviforme gen. nov., sp. nov., a New Alkaliphilic Nonsulfur Purple Bacterium].

    PubMed

    Bryantseva, I A; Gaisin, V A; Gorlenko, V M

    2015-01-01

    Two alkaliphilic strains of nonsulfur purple bacteria (NPB), B7-4 and B8-2, were isolated from southeast Siberia moderately saline alkaline steppe lakes with pH values above 9.0. The isolates were motile, polymorphous cells (from short rods to long spindly cells) 2.0-3.2 x 9.6-20.0 μm. Intracellular membranes of vesicular type were mostly located at the cell periphery. The microorganisms contained bacteriochlorophyll a and carotenoids of the spheroidene and spirilloxanthin series. The photosynthetic apparatus was represented by LH2 and LH1 light-harvesting complexes. In the presence of organic compounds, the strains grew aerobically in the dark or anaerobically in the light. Capacity for photo- and chemoautotrophic growth was not detected. The cbbl gene encoding RuBisCO was not revealed. Optimal growth of both strains occurred at 2% NaCl (range from 0.5 to 4%), pH 8.0-8.8 (range from 7.5 to 9.7), and 25-35 degrees C. The DNA G+C content was 67.6-69.8 mol %. Pairwise comparison of the nucleotides of the 16S rRNA genes revealed that strains B7-4 and B8-2 belonged to the same species (99.9% homology) and were most closely related to the aerobic alkaliphilic bacteriochlorophyll a-containing anoxygenic phototrophic bacterium (APB) Roseibacula alcaliphilum De (95.2%) and to NPB strains Rhodobaca barguzinensis VKM B-2406(T) (94.2%) and Rbc. bogoriensis LBB1(T) (93.9%). The isolates were closely related to the NPB Rhodobacter veldkampii DSM 11550(T) (94.8%) and to aerobic bacteriochlorophyll a-containing bacteria Roseinatronobacter monicus ROS 35(T) and Roseicitreum antarcticul ZS2-28(T) (93.5 and 93.9%, respectively). New strains were described as a new NPB genus and species of the family Rhodobacteriaceae, Rhodobaculum claviforme gen. nov., sp. nov., with B7-4(T) (VKM B-2708, LMG 28126) as the type strain. PMID:26263629

  8. Photobacterium kishitanii sp. nov., a luminous marine bacterium symbiotic with deep-sea fishes.

    PubMed

    Ast, Jennifer C; Cleenwerck, Ilse; Engelbeen, Katrien; Urbanczyk, Henryk; Thompson, Fabiano L; De Vos, Paul; Dunlap, Paul V

    2007-09-01

    Six representatives of a luminous bacterium commonly found in association with deep, cold-dwelling marine fishes were isolated from the light organs and skin of different fish species. These bacteria were Gram-negative, catalase-positive, and weakly oxidase-positive or oxidase-negative. Morphologically, cells of these strains were coccoid or coccoid-rods, occurring singly or in pairs, and motile by means of polar flagellation. After growth on seawater-based agar medium at 22 degrees C for 18 h, colonies were small, round and white, with an intense cerulean blue luminescence. Analysis of 16S rRNA gene sequence similarity placed these bacteria in the genus Photobacterium. Phylogenetic analysis based on seven housekeeping gene sequences (16S rRNA gene, gapA, gyrB, pyrH, recA, rpoA and rpoD), seven gene sequences of the lux operon (luxC, luxD, luxA, luxB, luxF, luxE and luxG) and four gene sequences of the rib operon (ribE, ribB, ribH and ribA), resolved the six strains as members of the genus Photobacterium and as a clade distinct from other species of Photobacterium. These strains were most closely related to Photobacterium phosphoreum and Photobacterium iliopiscarium. DNA-DNA hybridization values between the designated type strain, Photobacterium kishitanii pjapo.1.1(T), and P. phosphoreum LMG 4233(T), P. iliopiscarium LMG 19543(T) and Photobacterium indicum LMG 22857(T) were 51, 43 and 19 %, respectively. In AFLP analysis, the six strains clustered together, forming a group distinct from other analysed species. The fatty acid C(17 : 0) cyclo was present in these bacteria, but not in P. phosphoreum, P. iliopiscarium or P. indicum. A combination of biochemical tests (arginine dihydrolase and lysine decarboxylase) differentiates these strains from P. phosphoreum and P. indicum. The DNA G+C content of P. kishitanii pjapo.1.1(T) is 40.2 %, and the genome size is approximately 4.2 Mbp, in the form of two circular chromosomes. These strains represent a novel species, for

  9. Erythrobacter atlanticus sp. nov., a bacterium from ocean sediment able to degrade polycyclic aromatic hydrocarbons.

    PubMed

    Zhuang, Lingping; Liu, Yang; Wang, Lin; Wang, Wanpeng; Shao, Zongze

    2015-10-01

    A Gram-stain-negative, motile, rod-shaped, orange-pigmented bacterium able to degrade polycyclic aromatic hydrocarbons was isolated from deep-sea sediment of the Atlantic Ocean and subjected to a polyphasic taxonomic study. The strain, designated s21-N3T, could grow at 4–37 °C (optimum 28 °C), at pH 5–10 (optimum pH 7–8) and with 1–7 % (w/v) NaCl (optimum 2–3 %). Strain s21-N3T was positive for nitrate reduction, denitrification, aesculin hydrolysis, oxidase and catalase, but negative for indole production and urease. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain s21-N3T formed a distinct branch within the genus Erythrobacter, sharing high similarities with three closely related strains, Erythrobacter marinus HWDM-33T (98.67 %), ‘Erythrobacter luteus’ KA37 (97.80 %) and Erythrobacter gangjinensis K7-2T (97.59 %). The similarities between strain s21-N3T and other type strains of recognized species within the genus Erythrobacter ranged from 95.00 to 96.47 %. The digital DNA–DNA hybridization values and average nucleotide identity (ANI) values between strain s21-N3T and the three closely related strains Erythrobacter marinus HWDM-33T, ‘Erythrobacter luteus’ KA37 and Erythrobacter gangjinensis K7-2T were 18.60, 18.00 and 18.50 % and 74.24, 72.49 and 72.54 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1ω7c/ω6c) and summed feature 3 (C16 : 1ω7c/ω6c). The respiratory lipoquinone was identified as Q-10. The major polar lipids comprised sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. The G+C content of the chromosomal DNA was determined to be 58.18 mol%. The combined genotypic and phenotypic distinctiveness demonstrated that strain s21-N3T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter atlanticus sp. nov. is proposed, with the type strain s21-N3T (

  10. Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments.

    PubMed

    Florentino, Anna P; Brienza, Claudio; Stams, Alfons J M; Sánchez-Andrea, Irene

    2016-03-01

    A novel acidotolerant and moderately thermophilic sulfur-reducing bacterium was isolated from sediments of the Tinto River (Spain), an extremely acidic environment. Strain TR1T stained Gram-negative, and was obligately anaerobic, non-spore-forming and motile. Cells were short rods (1.5-2 × 0.5-0.7 μm), appearing singly or in pairs. Strain TR1T was catalase-negative and slightly oxidase-positive. Urease activity and indole formation were absent, but gelatin hydrolysis was present. Growth was observed at 20-52 °C with an optimum close to 50 °C, and a pH range of 3-7 with optimum between pH 6 and 6.5. Yeast extract was essential for growth, but extra vitamins were not required. In the presence of sulfur, strain TR1T grew with acetate, formate, lactate, pyruvate, stearate, arginine and H2/CO2. All substrates were completely oxidized and H2S and CO2 were the only metabolic products detected. Besides elemental sulfur, thiosulfate was used as an electron acceptor. The isolate also grew by disproportionation of elemental sulfur. The predominant cellular fatty acids were saturated components: C16 : 0, anteiso-C17 : 0 and C18 : 0. The only quinone component detected was menaquinone MK-7(H2). The G+C content of the genomic DNA was 34 mol%. The isolate is affiliated to the genus Desulfurella of the class Deltaproteobacteria, sharing 97 % 16S rRNA gene sequence similarity with the four species described in the genus Desulfurella. Considering the distinct physiological and phylogenetic characteristics, strain TR1T represents a novel species within the genus Desulfurella, for which the name Desulfurella amilsii sp. nov. is proposed. The type strain is TR1T ( = DSM 29984T = JCM 30680T). PMID:26704766

  11. Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment.

    PubMed

    Tsubouchi, Taishi; Shimane, Yasuhiro; Usui, Keiko; Shimamura, Shigeru; Mori, Kozue; Hiraki, Toshiki; Tame, Akihiro; Uematsu, Katsuyuki; Maruyama, Tadashi; Hatada, Yuji

    2013-06-01

    A novel Gram-negative, aerobic, psychrotolerant, alkali-tolerant, heterotrophic and dimorphic prosthecate bacterium, designated strain TAR-001(T), was isolated from deep-sea floor sediment in Japan. Cells of this strain had a dimorphic life cycle and developed an adhesive stalk at a site not coincident with the centre of the cell pole, and the other type of cell, a swarm cell, had a polar flagellum. Colonies were glossy, viscous and yellowish-white in colour. The temperature, pH and salt concentration range for growth were 2-41 °C, pH 6.5-10.0 and 1-4% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-001(T) belongs to the family Caulobacteraceae of the class Alphaproteobacteria, and lies between the genus Brevundimonas and the genus Caulobacter. Levels of similarity between the 16S rRNA gene sequence of strain TAR-001(T) and those of the type strains of Brevundimonas species were 93.3-95.7%; highest sequence similarity was with the type strain of Brevundimonas diminuta. Levels of sequence similarity between those of the type strains of Caulobacter species were 94.9-96.0%; highest sequence similarity was with the type strain of Caulobacter mirabilis. The G+C content of strain TAR-001(T) was 67.6 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18:1ω7c and C16:0, and the presence of 1,2-di-O-acyl-3-O-[D-glucopyranosyl-(1→4)-α-D-glucopyranuronosyl]glycerol suggests strain TAR-001(T) is more closely to the genus Brevundimonas than to the genus Caulobacter. The mean DNA-DNA hybridization levels between strain TAR-001(T) and the type strains of two species of the genus Brevundimonas were higher than that of the genus Caulobacter. On the basis of polyphasic biological features and the 16S rRNA gene sequence comparison presented here, strain TAR-001(T) is considered to represent a novel species of the genus Brevundimonas, for which the name Brevundimonas abyssalis sp. nov. is proposed; the

  12. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    PubMed

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene

  13. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock.

    PubMed

    Fukuda, Wakao; Chino, Yohzo; Araki, Shigeo; Kondo, Yuka; Imanaka, Hiroyuki; Kanai, Tamotsu; Atomi, Haruyuki; Imanaka, Tadayuki

    2014-06-01

    A Gram-stain-negative, non-spore-forming, aerobic, oligotrophic bacterium (strain 262-7(T)) was isolated from a crack of white rock collected in the Skallen region of Antarctica. Strain 262-7(T) grew at temperatures between -4 and 30 °C, with optimal growth at 25 °C. The pH range for growth was between pH 6.0 and 9.0, with optimal growth at approximately pH 7.0. The NaCl concentration range allowing growth was between 0.0 and 1.0%, with an optimum of 0.5%. Strain 262-7(T) showed an unprecedented range of morphological diversity in response to growth conditions. Cells grown in liquid medium were circular or ovoid with smooth surfaces in the lag phase. In the exponential phase, ovoid cells with short projections were observed. Cells in the stationary phase possessed long tentacle-like projections intertwined intricately. By contrast, cells grown on agar plate medium or in liquid media containing organic compounds at low concentration exhibited short- and long-rod-shaped morphology. These projections and morphological variations clearly differ from those of previously described bacteria. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C(17 : 1)ω6c (28.2%), C(16 : 1)ω7c (22.6%), C(18 : 1)ω7c (12.9%) and C(15 : 0) 2-OH (12.3%). The G+C content of genomic DNA was 68.0 mol%. Carotenoids were detected from the cells. Comparative analyses of 16S rRNA gene sequences indicated that strain 262-7(T) belongs to the family Sphingomonadaceae, and that 262-7(T) should be distinguished from known genera in the family Sphingomonadaceae. According to the phylogenetic position, physiological characteristics and unique morphology variations, strain 262-7(T) should be classified as a representative of a novel genus of the family Sphingomonadaceae. Here, a novel genus and species with the name Polymorphobacter multimanifer gen. nov., sp. nov. is proposed (type strain 262-7(T) = JCM 18140(T) = ATCC BAA-2413(T)). The novel species was

  14. Marinobacter aromaticivorans sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from sea sediment.

    PubMed

    Cui, Zhisong; Gao, Wei; Xu, Guangfei; Luan, Xiao; Li, Qian; Yin, Xiaofei; Huang, Deming; Zheng, Li

    2016-01-01

    A rod-shaped, Gram-stain-negative, slightly halotolerant bacterium, designated strain D15-8PT, was isolated from a sediment sample from the South China Sea. The strain could grow in NaCl concentrations ranging from 0.5 % to 10 % (w/v) (optimum 0.5-1.5 %), and could be cultivated at 10-40 °C (optimum 25 °C) and pH 5.5-9.5 (optimum pH 7.0-8.0). The strain was positive for catalase, oxidase, and hydrolysis of Tween 80, but negative for hydrolysis of DNA and gelatin, nitrite reduction, indole production, Voges-Proskauer reaction, and methyl red test. Strain D15-8PT could biodegrade naphthalene, phenanthrene, and anthracene. The major respiratory quinone was Q-9. The main cellular fatty acids were C12 : 0 (11.5 %), C14 : 0 3-methyl (22.0 %), C16 : 0 (19.2 %), C16 : 1ω9c (22.9 %), and C18 : 1ω9c (6.7 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified phospholipid. The DNA G+C content was 56.8 mol%. Phylogenetic analyses based on 16S rRNA genes showed that strain D15-8PT was most closely related to Marinobacter maritimus JCM 12521T (98.5 % 16S rRNA gene sequence similarity), Marinobacter antarcticus CGMCC 1.10835T (98.1 %), Marinobacter lipolyticus DSM 15157T (97.1 %), and Marinobacter guineae CECT 7243T (97.0 %). Results of the gyrB gene analysis and DNA-DNA hybridization were both less than the cut-off values (90 % for gyrB gene sequence similarity and 70 % for DNA-DNA hybridization). On the basis of this taxonomic study using a polyphasic approach, strain D15-8PT represents a novel species of the genus Marinobacter, for which the name Marinobacter aromaticivorans sp. nov. is proposed. The type strain is D15-8PT ( = CGMCC 1.11015T = KCTC 23781T). PMID:26518711

  15. Revision of the taxonomic position of the xylanolytic Bacillus sp. MIR32 reidentified as Bacillus halodurans and plasmid-mediated transformation of B. halodurans.

    PubMed

    Martínez, M Alejandra; Delgado, Osvaldo D; Breccia, Javier D; Baigorí, Mario D; Siñeriz, Faustino

    2002-10-01

    Bacillus sp. MIR32 has been isolated using xylan as the only carbon source, and one of its xylanolytic enzymes has been extensively studied. Biochemical analysis first related this strain to Bacillus amyloliquefaciens, but further studies based on a comparison of 16S rDNA sequences, G+C content, and DNA-DNA hybridization showed that strain MIR32 should be classified as a member of the species Bacillus halodurans. This change is also supported by the typical phenotype observed and by the results of PCR amplification directed toward spacers in rDNA and tDNA genes, which were assayed and compared with those of B. halodurans DSM 497(T). Although among alkaliphilic bacilli competence development has not been experimentally demonstrated, in this work both B. halodurans MIR32 and DSM 497(T) were transformed according to a simple procedure developed in our laboratory, reaching 10(2)-10(3) stable transformants per microgram of plasmid DNA. PMID:12382115

  16. Fractionation of Natural Organic Matter Upon Adsorption to the Bacterium, Bacillus subtilis

    NASA Astrophysics Data System (ADS)

    Manecki, M.; Maurice, P. A.; Fein, J. B.

    2001-12-01

    High pressure size exclusion chromatography (HPSEC) was used to measure changes in molecular weight distribution and average molecular weight upon adsorption of fulvic acid onto Bacillus subtilis at pH 3-7. The FA was an XAD-8 extract from a stream in the New Jersey Pine Barrens (USA), and had a weight average molecular weight of 1890 Da. Adsorption of aqueous FA onto B.subtilis was relatively fast, with steady state attained within 2 hours. An adsorption isotherm at pH 4.5 revealed a strong affinity of FA for the B.subtilis surface. The maximum adsorption capacity of a 20g bacteria/L suspension was greater than 9 mg C/L of FA at pH 4.5. Adsorption of FA onto B.subtilis was strongly pH dependent, increasing markedly with decreasing pH over the pH range 3-7. Comparison of HPSEC analysis of control (FA not reacted with bacteria) versus reacted samples showed that in all experiments, the weight average molecular weight (Mw) of FA remaining in solution decreased by several hundred Da. The observed decrease in solution Mw upon adsorption indicated that the higher molecular weight FA components adsorbed preferentially to the bacterial surfaces, at all studied pH values (3-7). Additionally, there was a low molecular weight FA fraction that did not adsorb, even at low pH. Our results suggest that hydrophobic interactions may be important for FA sorption to B.subtilis and that low molecular weight, more hydrophilic components may thus be less likely to adsorb than higher molecular weight, more hydrophobic components.

  17. Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium

    PubMed Central

    Cassir, Nadim; Croce, Olivier; Pagnier, Isabelle; Benamar, Samia; Couderc, Carine; Robert, Catherine; Raoult, Didier; La Scola, Bernard

    2014-01-01

    Bacteroides neonati strain MS4T, is the type strain of Bacteroides neonati sp. nov., a new species within the genus Bacteroides. This strain, whose genome is described here, was isolated from a premature neonate stool sample. B. neonati strain MS4T is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes. PMID:25197464

  18. Genome Sequence of Sphingomonas sp. Strain PAMC 26621, an Arctic-Lichen-Associated Bacterium Isolated from a Cetraria sp.

    PubMed Central

    Lee, Hyoungseok; Shin, Seung Chul; Lee, Jungeun; Kim, Su Jin; Kim, Bum-Keun; Hong, Soon Gyu; Kim, Eun Hye

    2012-01-01

    The lichen-associated bacterial strain Sphingomonas sp. PAMC 26621 was isolated from an Arctic lichen Cetraria sp. on Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide novel insights into the molecular principles of lichen-microbe interactions. PMID:22582384

  19. Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.

    PubMed

    Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

    2014-01-01

    Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

  20. Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah

    PubMed Central

    Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

    2014-01-01

    Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

  1. IAA production by Bacillus sp. JH 2-2 promotes Indian mustard growth in the presence of hexavalent chromium.

    PubMed

    Shim, Jaehong; Kim, Jin-Won; Shea, Patrick J; Oh, Byung-Taek

    2015-05-01

    Bacillus sp. strain JH 2-2, isolated from the rhizosphere of plants at a multi-metal contaminated mine site, has the potential to reduce Cr(VI) to Cr(III) and promote plant growth by reducing Cr toxicity and producing IAA. The minimum inhibitory concentration of Cr(VI) to Bacillus sp. JH 2-2 was 1000 mg L(-1) and the strain reduced 99% of 10 mg Cr(VI) L(-1) to Cr(IV) within 24 h. Lower Cr(VI) stress (10 mg L(-1) ) stimulated IAA production, but much less IAA was produced at 30 or 50 mg Cr(VI) L(-1) . Inoculation with Bacillus sp. JH 2-2 increased the length of Brassica juncea L. roots by 364% and stems by 735% in the presence of 10 mg Cr(VI) L(-1) from those of uninoculated control plants. These findings suggest potential use of Bacillus sp. JH 2-2 to promote phytoremediation of soil contaminated with Cr(VI). PMID:25283159

  2. Isolation, purification and spectrometric analysis of PSP toxins from moraxella sp., a bacterium associated with a toxic dinoflagellate

    SciTech Connect

    Boyce, S.D.; Doucette, G.J.

    1994-12-31

    Paralytic shellfish poisoning (PSP) is a seafood intoxication syndrome caused by the injestion of shellfish contaminated with toxins produced by algae known as dinoflagellates. The PSP toxins, saxitoxin and its derivatives, act to block voltage-dependent sodium channels and can cause paralysis and even death at higher doses. It is well documented that bacteria coexist with many harmful or toxic algal species, though the exact nature of the association in relation to toxin production is unknown. Recently, the bacterium Moraxella sp. was isolated from the PSP toxin producing dinoflagellate Alexandrium tamarense. Through HPLC analysis and saxitoxin receptor binding assays performed on crude bacterial extracts, it appears that Moraxella sp. is capable of producing saxitoxin and several of its derivatives. However, physical confirmation (e.g. mass spectrometry) of these results is still needed.

  3. Inhibitory activity of an extract from a marine bacterium Halomonas sp. HSB07 against the red-tide microalga Gymnodinium sp. (Pyrrophyta)

    NASA Astrophysics Data System (ADS)

    Liu, Juan; Li, Fuchao; Liu, Ling; Jiang, Peng; Liu, Zhaopu

    2013-11-01

    In recent years, red tides occurred frequently in coastal areas worldwide. Various methods based on the use of clay, copper sulfate, and bacteria have been successful in controlling red tides to some extent. As a new defensive agent, marine microorganisms are important sources of compounds with potent inhibitory bioactivities against red-tide microalgae, such as Gymnodinium sp. (Pyrrophyta). In this study, we isolated a marine bacterium, HSB07, from seawater collected from Hongsha Bay, Sanya, South China Sea. Based on its 16S rRNA gene sequence and biochemical characteristics, the isolated strain HSB07 was identified as a member of the genus Halomonas. A crude ethyl acetate extract of strain HSB07 showed moderate inhibition activity against Gymnodinium sp. in a bioactive prescreening experiment. The extract was further separated into fractions A, B, and C by silica gel column chromatography. Fractions B and C showed strong inhibition activities against Gymnodinium. This is the first report of inhibitory activity of secondary metabolites of a Halomonas bacterium against a red-tide-causing microalga.

  4. A thermo-halo-tolerant and proteinase-resistant endoxylanase from Bacillus sp. HJ14.

    PubMed

    Zhou, Junpei; Wu, Qian; Zhang, Rui; Mo, Minghe; Tang, Xianghua; Li, Junjun; Xu, Bo; Ding, Junmei; Lu, Qian; Huang, Zunxi

    2014-09-01

    A glycosyl hydrolase family 10 endoxylanase from Bacillus sp. HJ14 was grouped in a separated cluster with another six Bacillus endoxylanases which have not been characterized. These Bacillus endoxylanases showed less than 52% amino acid sequence identity with other endoxylanases and far distance with endoxylanases from most microorganisms. Signal peptide was not detected in the endoxylanase. The endoxylanase was expressed in Escherichia coli BL21 (DE3), and the purified recombinant enzyme (rXynAHJ14) was characterized. rXynAHJ14 was apparent optimal at 62.5 °C and pH 6.5 and retained more than 55% of the maximum activity when assayed at 40-75 °C, 23% at 20 °C, 16% at 85 °C, and even 8% at 0 °C. Half-lives of the enzyme were more than 60 min, approximately 25 and 4 min at 70, 75, and 80 °C, respectively. The enzyme exhibited more than 62% xylanase activity and stability at the concentration of 3-30% (w/v) NaCl. No xylanase activity was lost after incubation of the purified rXynAHJ14 with trypsin and proteinase K at 37 °C for 60 min. Different components of oligosaccharides were detected in the time-course hydrolysis of beechwood xylan by the enzyme. During the simulated intestinal digestion phase in vitro, 11.5-19.0, 15.3-19.0, 21.9-27.7, and 28.2-31.2 μmol/mL reducing sugar were released by the purified rXynAHJ14 from soybean meal, wheat bran, beechwood xylan, and rapeseed meal, respectively. The endoxylanase might be an alternative for potential applications in the processing of sea food and saline food and in aquaculture as agastric fish feed additive. PMID:24728834

  5. Studies on cultivation kinetics for elastase production by Bacillus sp. EL31410.

    PubMed

    Chen, Qi-He; He, Guo-Qing; Schwarz, Paul

    2004-06-01

    It was the first time to study elastase batch cultivation kinetics. This paper discusses the growth kinetics, elastase production, and substrate consumption kinetics model of Bacillus sp. EL31410 in batch cultivation. A simple model was proposed using a logistic equation for growth, the Luedeking-Piret equation for elastase production, and the Luedeking-Piret-like equation for glucose consumption. The model appeared to provide a reasonable description for each parameter during the growth phase. This study could provide some support for studying elastase fermentation kinetics, especially for studying its singular growth phenomenon. However, the model for elastase production is not good for explaining the real process and is still up to research. PMID:15161197

  6. Genomic and functional features of the biosurfactant producing Bacillus sp. AM13.

    PubMed

    Shaligram, Shraddha; Kumbhare, Shreyas V; Dhotre, Dhiraj P; Muddeshwar, Manohar G; Kapley, Atya; Joseph, Neetha; Purohit, Hemant P; Shouche, Yogesh S; Pawar, Shrikant P

    2016-09-01

    Genomic studies provide deeper insights into secondary metabolites produced by diverse bacterial communities, residing in various environmental niches. This study aims to understand the potential of a biosurfactant producing Bacillus sp. AM13, isolated from soil. An integrated approach of genomic and chemical analysis was employed to characterize the antibacterial lipopeptide produced by the strain AM13. Genome analysis revealed that strain AM13 harbors a nonribosomal peptide synthetase (NRPS) cluster; highly similar with known biosynthetic gene clusters from surfactin family: lichenysin (85 %) and surfactin (78 %). These findings were substantiated with supplementary experiments of oil displacement assay and surface tension measurements, confirming the biosurfactant production. Further investigation using LCMS approach exhibited similarity of the biomolecule with biosurfactants of the surfactin family. Our consolidated effort of functional genomics provided chemical as well as genetic leads for understanding the biochemical characteristics of the bioactive compound. PMID:27492417

  7. Efficient proteolysis and application of an alkaline protease from halophilic Bacillus sp. EMB9.

    PubMed

    Sinha, Rajeshwari; Srivastava, A K; Khare, S K

    2014-10-01

    A salt-stable alkaline protease from moderately halophilic Bacillus sp. EMB9, isolated from the western coast of India, is described. This protease was capable of efficiently removing silver from used/waste X-Ray films, as well as hydrolyzing defatted soy flour with 31% degree of hydrolysis (DH). Production of the protease was optimized by using response surface methodology. Ca(2+) and NaCl were the most critical factors in enhancing the yield. Under optimized culture conditions, a maximum of 369 U protease/mL was obtained, which is quite comparable to the yields of commercial proteases. The elevated production level coupled with ability to efficiently hydrolyze protein-laden soy flour and complete recovery of silver from used X-Ray films makes it a prospective industrial enzyme. PMID:24905047

  8. Biosurfactant production through Bacillus sp. MTCC 5877 and its multifarious applications in food industry.

    PubMed

    Anjum, Farhan; Gautam, Gunjan; Edgard, Gnansounou; Negi, Sangeeta

    2016-08-01

    In this study Bacillus sp. MTCC5877 was explored for the production of biosurfactant (BSs) and various carbon sources 1% (w/v), 0.5% (w/v) nitrogen sources were tested at different pH, and temperature. Yield was measured in terms of Emulsification index (EI), Oil Displacement Area (ODA) and Drop Collapse Area (DCA) and maximum emulsification activities of BSs were found (E24) 50%, 76% and 46%, respectively, and maximum ODA of 5.0, 6.2 and 4.7cm, were shown respectively. The BS was able to reduce the surface tension of water from 72 to 30mN/m and 72 to 32mN/m. Structural compositions of BS were confirmed by FTIR, GC-MS and NMR. Anti-adhesive property of BS was determined and found effective against biofilm formation. It could remove 73% Cd from vegetable which confirms its application in food industry. PMID:27013189

  9. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

    PubMed Central

    Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

    2016-01-01

    Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX. PMID:27124467

  10. Identification and catalytic residues of the arsenite methyltransferase from a sulfate-reducing bacterium, Clostridium sp. BXM.

    PubMed

    Wang, Pei-Pei; Bao, Peng; Sun, Guo-Xin

    2015-01-01

    Arsenic methylation is an important process frequently occurring in anaerobic environments. Anaerobic microorganisms have been implicated as the major contributors for As methylation. However, very little information is available regarding the enzymatic mechanism of As methylation by anaerobes. In this study, one novel sulfate-reducing bacterium isolate, Clostridium sp. BXM, which was isolated from a paddy soil in our laboratory, was demonstrated to have the ability of methylating As. One putative arsenite S-Adenosyl-Methionine methyltransferase (ArsM) gene, CsarsM was cloned from Clostridium sp. BXM. Heterologous expression of CsarsM conferred As resistance and the ability of methylating As to an As-sensitive strain of Escherichia coli. Purified methyltransferase CsArsM catalyzed the formation of methylated products from arsenite, further confirming its function of As methylation. Site-directed mutagenesis studies demonstrated that three conserved cysteine residues at positions 65, 153 and 203 in CsArsM are necessary for arsenite methylation, but only Cysteine 153 and Cysteine 203 are required for the methylation of monomethylarsenic to dimethylarsenic. These results provided the characterization of arsenic methyltransferase from anaerobic sulfate-reducing bacterium. Given that sulfate-reducing bacteria are ubiquitous in various wetlands including paddy soils, enzymatic methylation mediated by these anaerobes is proposed to contribute to the arsenic biogeochemical cycling. PMID:25790486

  11. Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser, Iceland.

    PubMed

    Gaisin, Vasil A; Ivanov, Timophey M; Kuznetsov, Boris B; Gorlenko, Vladimir M; Grouzdev, Denis S

    2016-01-01

    We report here the draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain isl-2, which was isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C content of 59.65%. The annotated genome sequence offers the genetic basis for understanding the strain's ecological role as a phototrophic bacterium within the bacterial community. PMID:27445390

  12. Draft Genome Sequence of Chloroflexus sp. Strain isl-2, a Thermophilic Filamentous Anoxygenic Phototrophic Bacterium Isolated from the Strokkur Geyser, Iceland

    PubMed Central

    Gaisin, Vasil A.; Ivanov, Timophey M.; Kuznetsov, Boris B.; Gorlenko, Vladimir M.

    2016-01-01

    We report here the draft genome sequence of the thermophilic filamentous anoxygenic phototrophic bacterium Chloroflexus sp. strain isl-2, which was isolated from the Strokkur geyser, Iceland, and contains 5,222,563 bp with a G+C content of 59.65%. The annotated genome sequence offers the genetic basis for understanding the strain’s ecological role as a phototrophic bacterium within the bacterial community. PMID:27445390

  13. Draft Genome Sequence of Triclosan-Degrading Bacterium Sphingomonas sp. Strain YL-JM2C, Isolated from a Wastewater Treatment Plant in China

    PubMed Central

    Mulla, Sikandar I.; Xu, Haili

    2015-01-01

    Sphingomonas sp. strain YL-JM2C was isolated from a wastewater treatment plant in Xiamen, China, by enrichment on triclosan. The bacterium is of special interest because of its ability to degrade triclosan. Here, we present a draft genome sequence of the microorganism and its functional annotation. To our best knowledge, this is the first report of a draft genome sequence of a triclosan-degrading bacterium PMID:26044437

  14. Characterization of a Bioflocculant (MBF-UFH) Produced by Bacillus sp. AEMREG7

    PubMed Central

    Okaiyeto, Kunle; Nwodo, Uchechukwu U.; Mabinya, Leonard V.; Okoli, Arinze S.; Okoh, Anthony I.

    2015-01-01

    A bioflocculant named MBF-UFH produced by a Bacillus species isolated from sediment samples of Algoa Bay of the Eastern Cape Province of South Africa was characterized. The bacterial identification was through 16S rDNA sequencing; nucleotide sequences were deposited in GenBank as Bacillus sp. AEMREG7 with Accession Number KP659187. The production of the bioflocculant was observed to be closely associated with cell growth. The bioflocculant had the highest flocculating activity of 83.2% after 72 h of cultivation, and approximately 1.6 g of purified MBF-UFH was recovered from 1 L of fermentation broth. Its chemical analyses indicated that it is a glycoprotein composed of polysaccharide (76%) and protein (14%). Fourier transform infrared spectroscopy (FTIR) revealed that it consisted of hydroxyl, amide, carboxyl and methoxyl as the functional moieties. Scanning electron microscopy (SEM) revealed the amorphous structure of MBF-UFH and flocculated kaolin clay particles. The maximum flocculating activity of 92.6% against kaolin clay suspension was achieved at 0.3 mg/mL over pH ranges of 3–11 with the peak flocculating rate at pH 8 in the presence of MgCl2. The bioflocculant retained high flocculating activity of 90% after heating at 100 °C for 1 h. MBF-UFH appears to have immense potential as an alternative to conventional chemical flocculants. PMID:26062133

  15. Root Associated Bacillus sp. Improves Growth, Yield and Zinc Translocation for Basmati Rice (Oryza sativa) Varieties

    PubMed Central

    Shakeel, Muhammad; Rais, Afroz; Hassan, Muhammad Nadeem; Hafeez, Fauzia Yusuf

    2015-01-01

    Plant associated rhizobacteria prevailing in different agro-ecosystems exhibit multiple traits which could be utilized in various aspect of sustainable agriculture. Two hundred thirty four isolates were obtained from the roots of basmati-385 and basmati super rice varieties growing in clay loam and saline soil at different locations of Punjab (Pakistan). Out of 234 isolates, 27 were able to solubilize zinc (Zn) from different Zn ores like zinc phosphate [Zn3 (PO4)2], zinc carbonate (ZnCO3) and zinc oxide (ZnO). The strain SH-10 with maximum Zn solubilization zone of 24 mm on Zn3 (PO4)2ore and strain SH-17 with maximum Zn solubilization zone of 14–15 mm on ZnO and ZnCO3ores were selected for further studies. These two strains solubilized phosphorous (P) and potassium (K) in vitro with a solubilization zone of 38–46 mm and 47–55 mm respectively. The strains also suppressed economically important rice pathogens Pyricularia oryzae and Fusarium moniliforme by 22–29% and produced various biocontrol determinants in vitro. The strains enhanced Zn translocation toward grains and increased yield of basmati-385 and super basmati rice varieties by 22–49% and 18–47% respectively. The Zn solubilizing strains were identified as Bacillus sp. and Bacillus cereus by 16S rRNA gene analysis. PMID:26635754

  16. Root Associated Bacillus sp. Improves Growth, Yield and Zinc Translocation for Basmati Rice (Oryza sativa) Varieties.

    PubMed

    Shakeel, Muhammad; Rais, Afroz; Hassan, Muhammad Nadeem; Hafeez, Fauzia Yusuf

    2015-01-01

    Plant associated rhizobacteria prevailing in different agro-ecosystems exhibit multiple traits which could be utilized in various aspect of sustainable agriculture. Two hundred thirty four isolates were obtained from the roots of basmati-385 and basmati super rice varieties growing in clay loam and saline soil at different locations of Punjab (Pakistan). Out of 234 isolates, 27 were able to solubilize zinc (Zn) from different Zn ores like zinc phosphate [Zn3 (PO4)2], zinc carbonate (ZnCO3) and zinc oxide (ZnO). The strain SH-10 with maximum Zn solubilization zone of 24 mm on Zn3 (PO4)2ore and strain SH-17 with maximum Zn solubilization zone of 14-15 mm on ZnO and ZnCO3ores were selected for further studies. These two strains solubilized phosphorous (P) and potassium (K) in vitro with a solubilization zone of 38-46 mm and 47-55 mm respectively. The strains also suppressed economically important rice pathogens Pyricularia oryzae and Fusarium moniliforme by 22-29% and produced various biocontrol determinants in vitro. The strains enhanced Zn translocation toward grains and increased yield of basmati-385 and super basmati rice varieties by 22-49% and 18-47% respectively. The Zn solubilizing strains were identified as Bacillus sp. and Bacillus cereus by 16S rRNA gene analysis. PMID:26635754

  17. Bioflocculant production by Bacillus sp. Gilbert isolated from a marine environment in South Africa.

    PubMed

    Ugbenyen, A M; Cosa, S; Mabinya, L V; Okoh, A I

    2014-01-01

    In our previous study we reported on the bioflocculant production by a Bacillus species isolated from sediment samples of Algoa Bay in the Eastern Cape Province of South Africa. In current study we carried out further evaluation on the effect of different culture conditions on the bioflocculant production, as well as characterised the bioflocculant produced in detail. The bacteria produced bioflocculant optimally under the following conditions: using sodium carbonate (95.2% flocculating activity) and potassium nitrate (76.6% flocculating activity) as carbon and nitrogen sources, respectively; inoculum size of 3% (v/v); initial pH 9.0; and Al3+ as coagulant aid. The crude bioflocculant retained 44.2% residual flocculating activity after heating at 100 degrees C for 15 min. Chemical analysis of the Bacillus sp. Gilbert purified bioflocculant demonstrated that it was composed mainly of polysaccharide. Fourier transform infrared spectroscopy analysis revealed the presence of hydroxyl, carboxyl and methylene groups in the bioflocculant and energy-dispersive X-ray analysis detected the elemental composition in mass proportion (% w/w) of C, N, O, S and P as 4.12 : 7.40: 39.92: 3.00: 13.91. Scanning electron micrograph image of the bioflocculant revealed an amorphous compound. PMID:25272753

  18. Chromium reduction, plant growth-promoting potentials, and metal solubilizatrion by Bacillus sp. isolated from alluvial soil.

    PubMed

    Wani, Parvaze Ahmad; Khan, Mohammad Saghir; Zaidi, Almas

    2007-03-01

    The plant growth-promoting potentials, production of siderophore and solubilization of insoluble phosphorus (P) and zinc and lead by the chromium (vi) -reducing Bacillus species, PSB 1, PSB 7, and PSB 10, was assessed both in the presence and absence of chromium under in vitro conditions. The Bacillus strains tolerated chromium up to the concentration of 500 (PSB1), 400 (PSB7), and 550 microg ml(-1) (PSB10), respectively, on nutrient agar plates. Bacillus sp. PSB 10 reduced Cr (vi) by 87% at pH 7, which was followed by Bacillus sp. PSB 1 (83%) and PSB 7 (74%) in nutrient broth after 120 h of incubation. A concentration of 50 microg ml(-1) of Cr (vi) was completely reduced by Bacillus sp. PSB 1 and PSB 10 (after 100 h) and PSB 7 (after 120 h). The Bacillus strains PSB 1, PSB 7, and PSB 10 produced 19.3, 17.7, and 17.4 microg ml(-1) of indole acetic acid, respectively, in luria bertani broth at 100 microg ml(-1) of tryptophan, which consistently decreased with an increase in chromium concentration. The Bacillus strains were positive for siderophore, HCN, and ammonia both in the absence and presence of chromium. The Bacillus strains solubilized 375 (PSB 1), 340 (PSB 7), and 379 (PSB 10) microg ml(-1) P, respectively, in Pikovskaya broth devoid of chromium. In contrast, chromium at 150 microg ml(-1) reduced the amount of P solubilized by 17 (PSB 1), 15 (PSB 7), and 9% (PSB 10) compared to control. The tested bacterial strains solubilized a considerable amount of zinc and lead in nutrient broth both in the absence and presence of chromium. Generally, the chromium reduction and the plant growth-promoting potentials of chromium-reducing Bacillus were strongly correlated at the tested concentration of chromium. The present observations demonstrated that the chromium-reducing, metal-solubilizing, and plant growth-promoting potentials of the Bacillus strains PSB1, PSB 7, and PSB10 were not adversely affected by the chromium application and, hence, may be applied for raising

  19. Initial Reactions in Anaerobic Oxidation of m-Xylene by the Denitrifying Bacterium Azoarcus sp. Strain T

    PubMed Central

    Krieger, Cynthia J.; Beller, Harry R.; Reinhard, Martin; Spormann, Alfred M.

    1999-01-01

    The initial enzymatic steps in anaerobic m-xylene oxidation were studied in Azoarcus sp. strain T, a denitrifying bacterium capable of mineralizing m-xylene via 3-methylbenzoate. Permeabilized cells of m-xylene-grown Azoarcus sp. strain T catalyzed the addition of m-xylene to fumarate to form (3-methylbenzyl)succinate. In the presence of succinyl coenzyme A (CoA) and nitrate, (3-methylbenzyl)succinate was oxidized to E-(3-methylphenyl)itaconate (or a closely related isomer) and 3-methylbenzoate. Kinetic studies conducted with permeabilized cells and whole-cell suspensions of m-xylene-grown Azoarcus sp. strain T demonstrated that the specific rate of in vitro (3-methylbenzyl)succinate formation accounts for at least 15% of the specific rate of in vivo m-xylene consumption. Based on these findings, we propose that Azoarcus sp. strain T anaerobically oxidizes m-xylene to 3-methylbenzoate (or its CoA thioester) via (3-methylbenzyl)succinate and E-(3-methylphenyl)itaconate (or its CoA thioester) in a series of reactions that are analogous to those recently proposed for anaerobic toluene oxidation to benzoyl-CoA. A deuterium kinetic isotope effect was observed in the (3-methylbenzyl)succinate synthase reaction (and the benzylsuccinate synthase reaction), suggesting that a rate-determining step in this novel fumarate addition reaction involves breaking a C-H bond. PMID:10515931

  20. Optimization of antifungal lipopeptide production from Bacillus sp. BH072 by response surface methodology.

    PubMed

    Zhao, Xin; Han, Ye; Tan, Xi-qian; Wang, Jin; Zhou, Zhi-jiang

    2014-04-01

    Antifungal lipopeptide produced by Bacillus sp. BH072 was extracted from fermentation liquor and determined as iturin A by liquid chromatography-mass spectrometry (LC-MS). For industrial-scale production, the yield of iturin A was improved by optimizing medium components and fermentation conditions. A one-factor test was conducted; fermentation conditions were then optimized by response surface methodology (RSM) to obtain the following: temperature, 29.5°C; pH 6.45; inoculation quantity, 6.7%; loading volume, 100 ml (in 500 ml flasks); and rotary speed, 150 rpm. Under these conditions, the mass concentration of iturin A was increased from 45.30 mg/ml to 47.87 mg/ml. The following components of the medium were determined: carbon sources (glucose, fructose, sucrose, xylose, rhamnose, and soluble starch); nitrogen sources (peptone, soybean meal, NH4Cl, urea, and ammonium citrate); and metal ions (Zn(2+), Fe(3+), Mg(2+), Mn(2+), Ca(2+), and K(+)). The effects of these components on iturin A production were observed in LB medium. We selected sucrose, soybean meal, and Mg(2+) for RSM to optimize the conditions because of several advantages, including maximum iturin A production, high antifungal activity, and low cost. The optimum concentrations of these components were 0.98% sucrose, 0.94% soybean meal, and 0.93% Mg(2+). After iturin A production was optimized by RSM, the mass concentration reached 52.21 mg/ml. The antifungal specific activity was enhanced from 350.11 AU/mg to 513.92 AU/mg, which was 46.8% higher than the previous result. The present study provides an important experimental basis for the industrial-scale production of iturin A and the agricultural applications of Bacillus sp. BH072. PMID:24535741

  1. Complete genome sequence of deoxynivalenol-degrading bacterium Devosia sp. strain A16.

    PubMed

    Yin, Xianchao; Zhu, Ziwei; Zhou, Yidong; Ji, Fang; Yao, Zhenyu; Shi, Jianrong; Xu, Jianhong

    2016-01-20

    The strain A16, capable of degrading deoxynivalenol was isolated from a wheat field and identified preliminarily as Devosia sp. Here, we present the genome sequence of the Devosia sp. A16, which has a size of 5,032,994 bp, with 4913 coding sequences (CDSs). The annotated full genome sequence of the Devosia sp. A16 strain might shed light on the function of its degradation. PMID:26630999

  2. Draft Genome Sequence of Rhodovulum sp. Strain NI22, a Naphthalene-Degrading Marine Bacterium

    PubMed Central

    Brown, Lisa M.; Gunasekera, Thusitha S.; Bowen, Loryn L.

    2015-01-01

    Rhodovulum sp. strain NI22 is a hydrocarbon-degrading member of the genus Rhodovulum. The draft genome of Rhodovulum sp. NI22 is 3.8 Mb in size, with 3,756 coding sequences and 64.4% G+C content. The catechol and gentisate pathways for naphthalene degradation are predicted to be present in Rhodovulum sp. NI22. PMID:25614575

  3. Genome Sequence of Paenibacillus sp. Strain FJAT-28004 for the Genome Sequencing Project for Genomic Taxonomy and Phylogenomics of Bacillus-Like Bacteria

    PubMed Central

    Liu, Guo-hong; Wang, Jie-ping; Che, Jian-Mei; Zhu, Yu-Jing; Chen, Qian-Qian; Ruan, Chuan-Qing

    2015-01-01

    Paenibacillus sp. strain FJAT-28004 is a spore forming and strictly aerobic bacterium. Here, we report the draft 7,479,858-bp genome sequence of Paenibacillus sp. FJAT-28004, which will provide useful information for genomic taxonomy and phylogenomics of the genus Paenibacillus, as well as for the functional gene mining and application of Paenibacillus sp. FJAT-28004. PMID:26494657

  4. Studies on the toxicity of an aqueous suspension of C60 nanoparticles using a bacterium (gen. Bacillus) and an aquatic plant (Lemna gibba) as in vitro model systems.

    PubMed

    Santos, Sandra M A; Dinis, Augusto M; Rodrigues, David M F; Peixoto, Francisco; Videira, Romeu A; Jurado, Amália S

    2013-10-15

    The increasing use of C60 nanoparticles and the diversity of their applications in industry and medicine has led to their production in a large scale. C60 release into wastewaters and the possible accumulation in the environment has raised concerns about their ecotoxicological impact. In the present study, an aqueous suspension of C60 nanoparticles was prepared and its potential toxicity studied in laboratory, using a bacterium (Bacillus stearothermophilus) and an aquatic plant (Lemna gibba) as model systems. C60 nanoparticles inhibited the growth of L. gibba, in contrast to that of the bacterium. Consistently, the ultrastructure and respiratory activity of bacterial cells were not affected by C60, but the contents of chlorophylls a and b and chloroplast oxygen production decreased considerably in L. gibba. Altogether, our results suggest that C60 aqueous dispersions must be viewed as an environmental pollutant, potentially endangering the equilibrium of aquatic ecosystems. PMID:24084257

  5. Expression of Bacillus protease (Protease BYA) from Bacillus sp. Y in Bacillus subtilis and enhancement of its specific activity by site-directed mutagenesis-improvement in productivity of detergent enzyme-.

    PubMed

    Tobe, Seiichi; Shimogaki, Hisao; Ohdera, Motoyasu; Asai, Yoshio; Oba, Kenkichi; Iwama, Masanori; Irie, Masachika

    2006-01-01

    An attempt was made to express protease BYA produced by an alkalophilic Bacillus sp. Y in Bacillus subtilis by gene engineering methods. The gene encoding protease BYA was cloned from Bacillus sp. Y, and expression vector pTA71 was constructed from the amylase promoter of Bacillus licheniformis, DNA fragments encoding the open reading frame of protease BYA, and pUB110. Protease BYA was secreted at an activity level of 5100 APU/ml in the common industrial culture medium of Bacillus subtilis transformed with pTA71. We then attempted to increase the specific activity of protease BYA by site-directed mutagenesis. Amino acid residue Ala29 next to catalytic Asp30 was replaced by one of three uncharged amino acid residues (Val29, Leu29, Ile29), and each mutant enzyme was expressed and isolated from the culture medium. Val29 mutant enzyme was secreted at an activity level of greater than 7000 APU/ml in culture medium, and its specific activity was 1.5-fold higher than that of the wild-type enzyme. Other mutant enzymes had specific activity similar to that of the original one and were less stabile than the wild-type enzyme. It can be thought that the substitution at amino acid residue 29 affects the level of activity and stability of protease BYA. PMID:16394504

  6. Bacillus sp. BS061 Suppresses Gray Mold and Powdery Mildew through the Secretion of Different Bioactive Substances.

    PubMed

    Kim, Young-Sook; Song, Ja-Gyeong; Lee, In-Kyoung; Yeo, Woon-Hyung; Yun, Bong-Sik

    2013-09-01

    A Bacillus sp. BS061 significantly reduced disease incidence of gray mold and powdery mildew. To identify the active principle, the culture filtrate was partitioned between butanol and water. The antifungal activity against B. cinerea was evident in the butanol-soluble portion, and active substances were identified as cyclic lipopeptides, iturin A series, by nuclear magnetic resonance spectrometry (NMR) and mass analysis. Interestingly, antifungal activity against powdery mildew was observed in the water-soluble portion, suggesting that cyclic lipopeptides have no responsibility to suppress powdery mildew. This finding reveals that biocontrol agents of Bacillus origin suppress gray mold and powdery mildew through the secretion of different bioactive substances. PMID:24198673

  7. A Novel Erythromycin Resistance Plasmid from Bacillus Sp. Strain HS24, Isolated from the Marine Sponge Haliclona Simulans

    PubMed Central

    Leong, Dara; Morrissey, John P.; Adams, Claire; Dobson, Alan D. W.; O’Gara, Fergal

    2014-01-01

    A better understanding of the origin and natural reservoirs of resistance determinants is fundamental to efficiently tackle antibiotic resistance. This paper reports the identification of a novel 5.8 kb erythromycin resistance plasmid, from Bacillus sp. HS24 isolated from the marine sponge Haliclona simulans. pBHS24B has a mosaic structure and carries the erythromycin resistance gene erm(T). This is the first report of an erythromycin resistance plasmid from a sponge associated bacteria and of the Erm(T) determinant in the genus Bacillus. PMID:25548909

  8. Complete genome sequence of Chelatococcus sp. CO-6, a crude-oil-degrading bacterium.

    PubMed

    Wang, Yingning; Cui, Di; Li, Ang; Yang, Jixian; Ma, Fang

    2016-02-10

    Chelatococcus sp. CO-6 is a crude-oil-degrading strain, which was isolated from Shengli Oilfield. However, little genetic information is known about this species. We present the complete genome sequence analysis of Chelatococcus sp. CO-6 in this study. It could provide further insight into its genetic basis for membrane transport and immune system against bacteriophage in strain CO-6. PMID:26712476

  9. Halobacterium saccharovorum sp. nov., a carbohydrate-metabolizing, extremely halophilic bacterium

    NASA Technical Reports Server (NTRS)

    Tomlinson, G. A.; Hochstein, L. I.

    1976-01-01

    The previously described extremely halophilic bacterium, strain M6, metabolizes a variety of carbohydrates with the production of acid. In addition, the organism produces nitrite (but no gas) from nitrate, is motile, and grows most rapidly at about 50 C. These characteristics distinguish it from all previously described halophilic bacteria in the genus Halobacterium. It is suggested that it be designated as a new species, Halobacterium saccharovorum.

  10. Genome Sequence of Vibrio sp. Strain EJY3, an Agarolytic Marine Bacterium Metabolizing 3,6-Anhydro-l-Galactose as a Sole Carbon Source

    PubMed Central

    Roh, Hanseong; Yun, Eun Ju; Lee, Saeyoung; Ko, Hyeok-Jin; Kim, Sujin; Kim, Byung-Yong; Song, Heesang; Lim, Kwang-il

    2012-01-01

    The metabolic fate of 3,6-anhydro-l-galactose (l-AHG) is unknown in the global marine carbon cycle. Vibrio sp. strain EJY3 is an agarolytic marine bacterium that can utilize l-AHG as a sole carbon source. To elucidate the metabolic pathways of l-AHG, we have sequenced the complete genome of Vibrio sp. strain EJY3. PMID:22535948

  11. Crystal structures of complexes of NAD{sup +}-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    SciTech Connect

    Filippova, E. V. Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-15

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI{sub 2} with the coupled reduction of nicotinamide adenine dinucleotide (NAD{sup +}). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD{sup +}-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  12. Fourier transform Raman spectroscopic characterisation of cells of the plant-associated soil bacterium Azospirillum brasilense Sp7

    NASA Astrophysics Data System (ADS)

    Kamnev, A. A.; Tarantilis, P. A.; Antonyuk, L. P.; Bespalova, L. A.; Polissiou, M. G.; Colina, M.; Gardiner, P. H. E.; Ignatov, V. V.

    2001-05-01

    Structural and compositional features of bacterial cell samples and of lipopolysaccharide-protein complex isolated from the cell surface of the plant-growth-promoting rhizobacterium Azospirillum brasilense (wild-type strain Sp7) were characterised using Fourier transform (FT) Raman spectroscopy. The structural spectroscopic information obtained is analysed and considered together with analytical data on the content of metal cations (Co 2+, Cu 2+ and Zn 2+) in the bacterial cells grown in a standard medium as well as in the presence of each of the cations (0.2 mM). The latter, being taken up by bacterial cells from the culture medium in significant amounts, were shown to induce certain metabolic changes in the bacterium revealed in FT-Raman spectra, which is discussed from the viewpoint of bacterial response to environmental stresses.

  13. Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway

    PubMed Central

    Yu, Fang-Bo; Li, Xiao-Dan; Ali, Shinawar Waseem; Shan, Sheng-Dao; Luo, Lin-Ping; Guan, Li-Bo

    2014-01-01

    A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation. PMID:25763034

  14. Noncontiguous finished genome sequence and description of Virgibacillus massiliensis sp. nov., a moderately halophilic bacterium isolated from human gut

    PubMed Central

    Khelaifia, S.; Croce, O.; Lagier, J.-C.; Robert, C.; Couderc, C.; Di Pinto, F.; Davoust, B.; Djossou, F.; Raoult, D.; Fournier, P.-E.

    2015-01-01

    Strain Vm-5T was isolated from the stool specimen of a 10-year-old Amazonian boy. This bacterium is a Gram-positive, strictly aerobic rod, motile by a polar flagellum. Here we describe its phenotypic characteristics and complete genome sequence. The 4 353 177 bp long genome exhibits a G + C content of 36.87% and contains 4394 protein-coding and 125 predicted RNA genes. Phylogenetically and genetically, strain Vm-c is a member of the genus Virgibacillus but is distinct enough to be classified as a new species. We propose the creation of V. massiliensis sp. nov., whose type strain is strain Vm-5T (CSUR P971 = DSM 28587). PMID:26649181

  15. Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator.

    PubMed

    Vancanneyt, Marc; Nedashkovskaya, Olga I; Snauwaert, Cindy; Mortier, Stefanie; Vandemeulebroecke, Katrien; Hoste, Bart; Dawyndt, Peter; Frolova, Galina M; Janssens, Danielle; Swings, Jean

    2006-01-01

    A Gram-negative bacterium, designated strain LMG 22510T, was isolated from water of a pharmaceutical company steam generator. The cells had a ring-like and horseshoe-shaped morphology and possessed gliding motility. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain was a member of the Flexibacter group within the phylum 'Bacteroidetes'; its nearest neighbour was Spirosoma linguale (88.8 % sequence similarity). DNA base content, fatty acid composition and biochemical characteristics were determined. Genotypic and phenotypic data indicated that strain LMG 22510T could not be assigned to any recognized genus; therefore, a novel genus and species is proposed, Larkinella insperata gen. nov., sp. nov., with LMG 22510T (= NCIMB 14103T) as the type strain. PMID:16403892

  16. Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium.

    PubMed

    Tang, M; Chen, C; Li, J; Xiang, W; Wu, H; Wu, J; Dai, S; Wu, H; Li, T; Wang, G

    2016-02-01

    A Gram-stain-negative, red, non-spore-forming, strictly aerobic bacterium, designated strain A4T, was isolated from culture broth of a marine cyanobacterium. Cells were flexible rods with gliding motility. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain A4T formed a coherent cluster with members of the genera Roseivirga and Fabibacter, and represents a distinct lineage in the family Flammeovirgaceae. Thermotolerance and a distinctive cellular fatty acid profile could readily distinguish this isolate from any bacteria of the genera Roseivirga and Fabibacter with a validly published name. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain A4T is suggested to represent a novel species in a novel genus, for which the name Fabivirga thermotolerans gen. nov., sp. nov. is proposed. The type strain is A4T ( = KCTC 42507T = CGMCC 1.15111T). PMID:26652750

  17. Study on human intestinal bacterium Blautia sp. AUH-JLD56 for the conversion of arctigenin to (-)-3'-desmethylarctigenin.

    PubMed

    Liu, Ming-Yue; Li, Meng; Wang, Xiu-Ling; Liu, Peng; Hao, Qing-Hong; Yu, Xiu-Mei

    2013-12-11

    Arctium lappa L. (A. lappa) is a popularly used vegetable as well as herbal medicine. Human intestinal microflora was reported to convert arctiin, the lignan compound with highest content in the dried fruits of Arctium lappa, to a series of metabolites. However, the specific bacterium responsible for the formation of 3'-desmethylarctigenin (3'-DMAG), the most predominant metabolite of arctiin by rat or human intestinal microflora, has not been isolated yet. In the present study, we isolated one single bacterium, which we named Blautia sp. AUH-JLD56, capable of solely biotransforming arctiin or arctigenin to (-)-3'-DMAG. The structure of the metabolite 3'-DMAG was elucidated by electrospray ionization mass spectrometry (ESI-MS) and (1)H and (13)C nuclear magnetic resonance spectroscopy. The biotransforming kinetics and maximum biotransforming capacity of strain AUH-JLD56 was investigated. In addition, the metabolite 3'-DMAG showed significantly higher 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity than that of the substrate arctigenin at the concentrations tested. PMID:24236649

  18. The death mechanism of the harmful algal bloom species Alexandrium tamarense induced by algicidal bacterium Deinococcus sp. Y35

    PubMed Central

    Li, Yi; Zhu, Hong; Lei, Xueqian; Zhang, Huajun; Cai, Guanjing; Chen, Zhangran; Fu, Lijun; Xu, Hong; Zheng, Tianling

    2015-01-01

    Harmful algal blooms (HABs) cause a variety of deleterious effects on aquatic ecosystems, especially the toxic dinoflagellate Alexandrium tamarense, which poses a serious threat to marine economic and human health based on releasing paralytic shellfish poison into the environment. The algicidal bacterium Deinococcus sp. Y35 which can induce growth inhibition on A. tamarense was used to investigate the functional mechanism. The growth status, reactive oxygen species (ROS) content, photosynthetic system and the nuclear system of algal cells were determined under algicidal activity. A culture of strain Y35 not only induced overproduction of ROS in algal cells within only 0.5 h of treatment, also decrease the total protein content as well as the response of the antioxidant enzyme. Meanwhile, lipid peroxidation was induced and cell membrane integrity was lost. Photosynthetic pigments including chlorophyll a and carotenoid decreased along with the photosynthetic efficiency being significantly inhibited. At the same time, photosynthesis-related gene expression showed down-regulation. More than, the destruction of cell nuclear structure and inhibition of proliferating cell nuclear antigen (PCNA) related gene expression were confirmed. The potential functional mechanism of the algicidal bacterium on A. tamarense was investigated and provided a novel viewpoint which could be used in HABs control. PMID:26441921

  19. Impact resistance of different factors on ammonia removal by heterotrophic nitrification-aerobic denitrification bacterium Aeromonas sp. HN-02.

    PubMed

    Chen, Maoxia; Wang, Wenchao; Feng, Ye; Zhu, Xiaohua; Zhou, Houzhen; Tan, Zhouliang; Li, Xudong

    2014-09-01

    To give reference for the application of heterotrophic nitrification-aerobic denitrification bacteria in actual wastewater treatment, the impact resistance of extreme pH, low temperature, heavy metals and high salinity on ammonia removal by a typical heterotrophic nitrifying-aerobic denitrifying bacterium Aeromonas sp. HN-02 was investigated. The results showed that HN-02 demonstrated strong acid- and alkali-resistance. In addition, it remained active at 5°C, and the removal rates of ammonia and COD were 0.90 mg L(-1)h(-1) and 22.34 mg L(-1)h(-1), respectively. Under the same extent of immediate temperature drop, the temperature correction coefficients of ammonia, COD removal rates and cell growth rate were close. Moreover, HN-02 could survive in the solution containing 0.5 mg L(-1) Cu(2+) or 8 mg L(-1) Zn(2+), or 0.5 mg L(-1) of equivalent Cu(2+)-Zn(2+). Furthermore, efficient ammonia removal was retained at salinity below 20 g L(-1), thus it could be identified as a halotolerant bacterium. At last, stronger stress resulted in higher ΔCOD/ΔTN ratio. PMID:25006021

  20. Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4

    SciTech Connect

    Roh, Yul; Gao, Haichun; Vali, Hojatollah; Kennedy, David W.; Yang, Zamin; Gao, Weimin; Dohnalkova, Alice; Stapleton, Raymond D.; Moon, Ji-Won; Phelps, T. J.; Fredrickson, Jim K.; Zhou, Jizhong

    2006-05-01

    A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation.

  1. Metal Reduction and Iron Biomineralization by a Psychrotolerant Fe(III)-Reducing Bacterium, Shewanella sp. Strain PV-4

    SciTech Connect

    Roh, Yul; Gao, Haichun; Vali, Hojatollah; Kennedy, David W.; Yang, Zamin; Gao, Weimin; Dohnalkova, Alice; Stapleton, Raymond D.; Moon, Ji-Won; Phelps, Tommy J.; Fredrickson, Jim K.; Zhou, Jizhong

    2006-09-01

    A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37 C, with an optimum growth temperature of 18 C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37 C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation.

  2. Molecular cloning of an endoglucanase gene from an alkalophilic bacillus sp. and its expression in escherichia coli

    SciTech Connect

    Kim, J.M.; Kong, I.S.; Yu, J.H.

    1987-11-01

    One of the cellulase genes from alkalophilic Bacillus sp. strain N-4 was cloned in pBR322. A recombinant plasmid, pYBC107, expressing carboxymethyl cellulase (CMCase) was isolated, and the size of the cloned HindIII fragment was found to be 5.5 kilobases. The restriction map of pYBC107 showed a different pattern from those of pNKI and pNKII. When the HindIII fragment from pYBC107 was subcloned into pYEJ001, there was a 3.8-fold increase in CMCase activity over that observed with pYBC107. Plasmid pYBC108 constructed by treatment of pYBC107 with HindIII and ECORI expressed the CMCase activity, although to a limited extend. To verify the originality of cloned pYBC107 from Bacillus sp;, the authors analyzed the restriction digest by Southern blotting.

  3. Endophytic Colonization of Vitis vinifera L. by Plant Growth-Promoting Bacterium Burkholderia sp. Strain PsJN

    PubMed Central

    Compant, Stéphane; Reiter, Birgit; Sessitsch, Angela; Nowak, Jerzy; Clément, Christophe; Ait Barka, Essaïd

    2005-01-01

    Patterns of colonization of Vitis vinifera L. cv. Chardonnay plantlets by a plant growth-promoting bacterium, Burkholderia sp. strain PsJN, were studied under gnotobiotic conditions. Wild-type strain PsJN and genetically engineered derivatives of this strain tagged with gfp (PsJN::gfp2x) or gusA (PsJN::gusA11) genes were used to enumerate and visualize tissue colonization. The rhizospheres of 4- to 5-week-old plantlets with five developed leaves were inoculated with bacterial suspensions. Epiphytic and endophytic colonization patterns were then monitored by dilution plating assays and microscopic observation of organ sections. Bacteria were chronologically detected first on root surfaces, then in root internal tissues, and finally in the fifth internode and the tissues of the fifth leaf. Analysis of the PsJN colonization patterns showed that this strain colonizes grapevine root surfaces, as well as cell walls and the whole surface of some rhizodermal cells. Cells were also abundant at lateral root emergence sites and root tips. Furthermore, cell wall-degrading endoglucanase and endopolygalacturonase secreted by PsJN explained how the bacterium gains entry into root internal tissues. Host defense reactions were observed in the exodermis and in several cortical cell layers. Bacteria were not observed on stem and leaf surfaces but were found in xylem vessels of the fifth internode and the fifth leaf of plantlets. Moreover, bacteria were more abundant in the fifth leaf than in the fifth internode and were found in substomatal chambers. Thus, it seems that Burkholderia sp. strain PsJN induces a local host defense reaction and systemically spreads to aerial parts through the transpiration stream. PMID:15811990

  4. Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.

    PubMed

    Hwang, C; Copeland, A; Lucas, S; Lapidus, A; Barry, K; Glavina Del Rio, T; Dalin, E; Tice, H; Pitluck, S; Sims, D; Brettin, T; Bruce, D C; Detter, J C; Han, C S; Schmutz, J; Larimer, F W; Land, M L; Hauser, L J; Kyrpides, N; Lykidis, A; Richardson, P; Belieav, A; Sanford, R A; Löeffler, F E; Fields, M W

    2015-01-01

    We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium's genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation. PMID:25614562

  5. Draft Genome Sequence of Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China

    PubMed Central

    Mu, Dashuai; Zhao, Jinxin; Wang, Zongjie; Chen, Guanjun

    2016-01-01

    Algoriphagus sp. NH1 is a multidrug-resistant bacterium isolated from coastal sediments of the northern Yellow Sea in China. Here, we report the draft genome sequence of NH1, with a size of 6,131,579 bp, average G+C content of 42.68%, and 5,746 predicted protein-coding sequences. PMID:26769940

  6. Degradation of dimethylphthalate by cells of Bacillus sp. immobilized in calcium alginate and polyurethane foam.

    PubMed

    Niazi, J H; Karegoudar, T B

    2001-01-01

    A Bacillus sp. which is capable of degrading dimethylphthalate (DMP) was immobilized in calcium alginate and polyurethane foam for efficient and long term degradation of DMP. Freely suspended cells (10(12) cfu ml-1) degraded a maximum of 20 mM DMP. Whereas, alginate-(10(12)cfu g-1 beads) and polyurethane foam-entrapped (0.34 x 10(6-9) cfu g-1 foam cubes) cells degraded a maximum of 40 mM DMP within 12-15 days of incubation. Polyurethane foam-entrapped cells degraded 30 mM of DMP at 4 days and alginate-entrapped cells degraded within 10 to 12 days of incubation irrespective of the cell population. When the initial concentration of DMP increased to 50 mM, the DMP degrading ability of the immobilized cells was not increased even after 20 days. Repeated batch cultures by alginate-entrapped cells with initial 35 mM DMP loading could be reused for a maximum of 20 cycles. However, the degradation rate was gradually decreased when the beads were reused for more than 15 cycles. On the other hand, the foam-entrapped cells, with the same initial DMP loading there was no decrease in DMP degrading ability and could be reused for more than 20 cycles. The packed bed reactor with alginate-entrapped cells (1 x 10(10-12) cfu g-1 bead) could be continuously operated for 7-8 days with an initial 25 mM DMP at a flow rate of 50 ml h-1. Whereas, the polyurethane foam-entrapped cells (1 x 10(6-9) cfu g-1 foam cubes) could be operated continuously for more than 90 days with the same initial DMP loading at a flow rate of 100 ml h-1. Thus the enhanced degradation of DMP could be achieved by immobilizing the cells of Bacillus sp. in calcium alginate and polyurethane foam as compared to that of freely suspended cells. PMID:11501311

  7. Draft Genome Sequence of an Industrially Important Bacillus sp. from Mandarmani Coastal Waters in Midnapur District, West Bengal, India

    PubMed Central

    2016-01-01

    Reported here is the draft genome sequence of an amylase-, protease-, DNase-, oxidase-, gelatinase-, and catalase-producing, Gram-positive diplobacillus (Bacillus sp. SM1 strain MCC2138), which was isolated from marine coastal waters and has the ability to degum raw silk fabric as well as Ramie fiber. The genome comprises 1.76 Mb with a GC content of 34.5%. PMID:27540077

  8. Haloanaerobium salsugo sp. nov., a moderately halophilic, anaerobic bacterium from a subterranean brine

    SciTech Connect

    Bhupathiraju, V.K.; Sharma, P.K.; Tanner, R.S.; McInerney, M.J.; Oren, A.; Woese, C.R.

    1994-07-01

    A strictly anaerobic, moderately halophilic, gram-negative bacterium was isolated from a highly saline oil field brine. The bacterium was a non-spore-forming, nonmotile rod, appearing singly, in pairs, or occasionally as long chains, and measured 0.3 to 0.4 by 2.6 to 4 {micro}m. The bacterium had a specific requirement for NaCl and grew at NaCl concentrations of between 6 and 24%, with optimal growth at 9% NaCl. The isolate grew at temperatures of between 22 and 51 C and pH values of between 5.6 and 8.0. The doubling time in a complex medium containing 10% NaCl was 9 h. Growth was inhibited by chloramphenicol, tetracycline, and penicillin but not by cycloheximide or azide. Fermentable substrates were predominantly carbohydrates. The end products of glucose fermentation were acetate, ethanol, CO{sub 2}, and H{sub 2}. The major components of the cellular fatty acids were C{sub 14:0}, C{sub 16:0}, C{sub 16:1}, and C{sub 17:0 cyc} acids. The DNA base composition of the isolate was 34 mol% G+C. Oligonucleotide catalog and sequence analyses of the 16S rRNA showed that strain VS-752{sup T} was most closely related to Haloanaerobium praevalens GSL{sup T} (ATCC 33744), the sole member of the genus Haloanaerobium. The authors propose that strain VS-752 (ATCC 51327) by established as the type strain of a new species, Haloanaerobium salsugo, in the genus Haloanaerobium. 40 refs., 3 figs, 5 tabs.

  9. Depolymerization and decolorization of kraft lignin by bacterium Comamonas sp. B-9.

    PubMed

    Chai, Li-yuan; Chen, Yue-hui; Tang, Chong-jian; Yang, Zhi-hui; Zheng, Yu; Shi, Yan

    2014-02-01

    There is no commercial or industrial-scale process for the remediation of black liquor using microorganisms to date. One of the most important causes is that most microorganisms are not able to use lignin as their principal metabolic carbon or energy source. The bacterial strain Comamonas sp. B-9 has shown remarkable ability to degrade kraft lignin and decolorize black liquor using lignin as its principal metabolic carbon and energy source. This report looks at the depolymerization and decolorization of kraft lignin by Comamonas sp. B-9. The degradation, decolorization, and total carbon removal reached 45, 54, and 47.3%, respectively, after 7 days treatment. Comamonas sp. B-9 was capable of depolymerizing kraft lignin effectively as analyzed by gel permeation chromatography and decolorization via degrading benzene ring structures as shown using Fourier transform infrared spectroscopy analysis. PMID:23948726

  10. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22.

    PubMed

    Kanaly, Robert A; Micheletto, Ruggero; Matsuda, Tomonari; Utsuno, Youko; Ozeki, Yasuhiro; Hamamura, Natsuko

    2015-10-01

    Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2'-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H](+) > [M + H - 116](+) transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work. PMID:26305056

  11. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22

    PubMed Central

    Kanaly, Robert A; Micheletto, Ruggero; Matsuda, Tomonari; Utsuno, Youko; Ozeki, Yasuhiro; Hamamura, Natsuko

    2015-01-01

    Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2′-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H]+ > [M + H − 116]+ transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2′-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work. PMID:26305056

  12. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage

    PubMed Central

    Mehboob, Farrakh; van Gelder, Antonie H.; Rijpstra, W. Irene C.; Damsté, Jaap S. Sinninghe; Stams, Alfons J. M.

    2010-01-01

    A mesophilic bacterium, strain An4, was isolated from an underground gas storage reservoir with methanol as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5–0.8 μm in diameter, and 2–8 μm in length, growing as single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H2/CO2 to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO2. The G+C content of the DNA was 42.6 mol%. Based on the 16S rRNA gene sequence analysis, strain An4 was most closely related to Sporomusa ovata (98% similarity). The bacterium reduced perchlorate and chlorate completely to chloride. Key enzymes, perchlorate reductase and chlorite dismutase, were detected in cell-free extracts. PMID:20680263

  13. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002.

    PubMed

    Weber, Karrie A; Hedrick, David B; Peacock, Aaron D; Thrash, J Cameron; White, David C; Achenbach, Laurie A; Coates, John D

    2009-06-01

    A lithoautotrophic, Fe(II) oxidizing, nitrate-reducing bacterium, strain 2002 (ATCC BAA-1479; =DSM 18807), was isolated as part of a study on nitrate-dependent Fe(II) oxidation in freshwater lake sediments. Here we provide an in-depth phenotypic and phylogenetic description of the isolate. Strain 2002 is a gram-negative, non-spore forming, motile, rod-shaped bacterium which tested positive for oxidase, catalase, and urease. Analysis of the complete 16S rRNA gene sequence placed strain 2002 in a clade within the family Neisseriaceae in the order Nessieriales of the Betaproteobacteria 99.3% similar to Pseudogulbenkiania subflava. Similar to P. sublfava, predominant whole cell fatty acids were identified as 16:17c, 42.4%, and 16:0, 34.1%. Whole cell difference spectra of the Fe(II) reduced minus nitrate oxidized cyctochrome content revealed a possible role of c-type cytochromes in nitrate-dependent Fe(II) oxidation. Strain 2002 was unable to oxidize aqueous or solid-phase Mn(II) with nitrate as the electron acceptor. In addition to lithotrophic growth with Fe(II), strain 2002 could alternatively grow heterotrophically with long-chain fatty acids, simple organic acids, carbohydrates, yeast extract, or casamino acids. Nitrate, nitrite, nitrous oxide, and oxygen also served as terminal electron acceptors with acetate as the electron donor. PMID:19333599

  14. Enzymatic Properties of an Alkaline and Chelator Resistant Proportional to alpha-Amylase from the Alkaliphilic Bacillus sp. Isolate L1711

    NASA Technical Reports Server (NTRS)

    Bernhardsdotter, Eva C. M. J.; Pusey, Marc L.; Ng, Joseph D.; Garriott, Owen K.

    2004-01-01

    An alkaliphilic amylase producing bacterium, Bacillus sp. strain L1711, was selected among 13 soda lakes isolates. When grown at pH 10.5 and 370 C, strain L1711 produced multiple forms of amylases in the culture broth. One of these, BAA, was purified from the culture supernatant by QAE column chromatography and preparative native gel electrophoresis. The molecular weight of BAA was determined to be 51 kDa by denaturing gel electrophoresis. The pH optima for activity below and above 40 C were 9.5-10.0 and 7.0-7.5 respectively. BAA was stable in the pH range 6-11 and was completely inactivated at 55?C. The thermostability was not increased in the presence of Ca(2+). The enzyme was strongly inhibited by Ca(2+), Zn(2+), Mg(2+), Mn(2+), Ba(2+) and Cu(2+), whereas the presence of Na(+), Co2+ and EDTA (10 mM) enhanced enzymatic activity. The K(sub m) and specific activity of BAA on soluble starch were 1.9 mg/ml and 18.5 U/mg respectively. The main end products of hydrolysis were maltotetraose, maltose and glucose .

  15. Study of optimization of wastewater contaminant removal along with extracellular polymeric substances (EPS) production by a thermotolerant Bacillus sp. ISTVK1 isolated from heat shocked sewage sludge.

    PubMed

    Gupta, Asmita; Thakur, Indu Shekhar

    2016-08-01

    The present work involved study of wastewater contaminant removal along with EPS production by a thermotolerant bacterium Bacillus sp. ISTVK1, isolated from heat shocked sewage sludge. EPS production in basal and mineral medium containing 50% filter sterilized wastewater and 0.5% sucrose was found to be 0.83±0.12gL(-1) and 0.31±0.10gL(-1) culture, respectively. GC-MS analysis of EPS revealed the presence of β-d-glucose, α-d-galactose and β-d-arabinose. FT-IR spectrum confirmed the presence carbohydrates. Box-Behnken design was used to optimize process parameters for enhanced EPS production along with % COD reduction of wastewater. The optimised conditions when used in a 1.5L bioreactor showed EPS production of 1.67±0.06gL(-1) culture and 93.0±0.21 % COD removal. PMID:26906445

  16. Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13

    PubMed Central

    Kwon, Yong Min

    2016-01-01

    Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we present the first complete genome sequence of this genus, which consists of 3,569,807 bp with 39.4% GC content. This strain contains proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize sunlight as an energy source. PMID:26823585

  17. Genome Sequence of the Mycorrhiza Helper Bacterium Streptomyces sp. Strain AcH 505

    PubMed Central

    Feldhahn, L.; Buscot, F.; Wubet, T.

    2015-01-01

    A draft genome sequence of Streptomyces sp. strain AcH 505 is presented here. The genome encodes 22 secondary metabolite gene clusters and a large arsenal of secreted proteins, and their comparative and functional analyses will help to advance our knowledge of symbiotic interactions and fungal and plant biomass degradation. PMID:25838498

  18. Complete genome sequence of the crude oil-degrading thermophilic bacterium Geobacillus sp. JS12.

    PubMed

    Jeon, Sung-Jong; Park, Ae Kyung; Kim, Bum-Keun; Park, Hyun; Lee, Jun Hyuck; Kim, Han-Woo; Shin, Seung Chul

    2016-07-20

    Here, we report the complete genome sequence of Geobacillus sp. JS12, isolated from composts located in Namhae, Korea, which shows extracellular lipolytic activities at high temperatures. An array of genes related to the utilization of lipids was identified by whole genome analysis. The genome sequence of the strain JS12 provides basic information for wider exploitation of thermostable industrial lipases. PMID:27184431

  19. Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13.

    PubMed

    Kwon, Yong Min; Kim, Sang-Jin

    2016-01-01

    Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we present the first complete genome sequence of this genus, which consists of 3,569,807 bp with 39.4% GC content. This strain contains proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize sunlight as an energy source. PMID:26823585

  20. Characterization of a fluoride-resistant bacterium Acinetobacter sp. RH5 towards assessment of its water defluoridation capability

    NASA Astrophysics Data System (ADS)

    Mukherjee, Shraboni; Yadav, Vaibhav; Mondal, Madhumanti; Banerjee, Soumya; Halder, Gopinath

    2015-12-01

    The present study investigates the defluoridation capability of fluoride-resistant bacteria from contaminated groundwater collected from Asanjola and Madhabpur, West Bengal, India. Seven strains of fluoride-resistant bacteria were isolated employing culture media containing 10-250 mg/L of fluoride to evaluate their ability in reducing fluoride concentration in water. Five isolates exhibited significant amount of reduction in fluoride. Isolate RH5 achieved a maximum fluoride removal of 25.7 % from the media at 30 °C and pH 7 after 8 days of incubation. Based on morphological, physiological characteristics and analysis of 16S rDNA gene sequence, isolate RH5 was identified as Acinetobacter sp. RH5. Growth of RH5 was analysed at a diverse pH range, and it could thrive at pH 5-10. The present investigation revealed that the selective pressure of fluoride results in growth of fluoride-resistant bacteria capable of secreting high-affinity anion-binding compounds. This bacterium played a dominant bioremediative role by concentrating the anions so that they become less available. Hence, the fluoride-resistant bacteria, Acinetobacter sp. RH5, could be used as a promising strain for application in water defluoridation from contaminated sites.

  1. Spongiimicrobium salis gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae isolated from a marine sponge.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2016-09-01

    A Gram-stain-negative, strictly aerobic, pale-yellow pigmented, rod-shaped, chemoheterotrophic bacterium, designated A6F-11(T), was isolated from a marine sponge collected in Japan. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (92.9 %) sequence similarity with Arenibacter palladensis LMG 21972(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. The major fatty acids of strain A6F-11(T) were iso-C15:1 G, iso-C15:0, C16:1 ω6c and/or C16:1 ω7c and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 34.7 mol%, and the major respiratory quinone was menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel taxon in the family Flavobacteriaceae, for which the name Spongiimicrobium salis gen. nov., sp. nov. is proposed. The type strain of S. salis gen. nov., sp. nov. is A6F-11(T) (= KCTC 42753(T) = NBRC 111401(T)). PMID:27125652

  2. Expression and enzymatic characterization of a cold-adapted β-agarase from Antarctic bacterium Pseudoalteromonas sp. NJ21

    NASA Astrophysics Data System (ADS)

    Li, Jiang; Sha, Yujie

    2015-03-01

    An agar-degrading bacterium, designated as Pseudoalteromonas sp. NJ21, was isolated from an Antarctic sediment sample. The agarase gene aga1161 from Pseudoalteromonas sp. NJ21 consisting of a 2 382-bp coding region was cloned. The gene encodes a 793-amino acids protein and was found to possess characteristic features of the Glyco_hydro_42 family. The recombinant agarase (rAga1161) was overexpressed in Escherichia coli and purified as a fusion protein. Enzyme activity analysis revealed that the optimum temperature and pH for the purified recombinant agarase were 30-40°C and 8.0, respectively. rAga1161 was found to maintain as much as 80% of its maximum activity at 10°C, which is typical of a coldadapted enzyme. The pattern of agar hydrolysis demonstrated that the enzyme is an β-agarase, producing neoagarobiose (NA2) as the final main product. Furthermore, this work is the first proof of an agarolytic activity in Antarctic bacteria and these results indicate the potential for the Antarctic agarase as a catalyst in medicine, food and cosmetic industries.

  3. Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.

    PubMed

    Koeck, Daniela E; Ludwig, Wolfgang; Wanner, Gerhard; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

    2015-08-01

    Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9% 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1%) were 16 : 0 dimethyl acetal, 16 : 0 fatty acid methyl ester and 16 : 0 aldehyde. The DNA G+C content was 36.6 mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T ( = DSM 29228T = CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov., sp. nov. PMID:25872956

  4. Quorum quenching bacteria Bacillus sp. QSI-1 protect zebrafish (Danio rerio) from Aeromonas hydrophila infection.

    PubMed

    Chu, Weihua; Zhou, Shuxin; Zhu, Wei; Zhuang, Xiyi

    2014-01-01

    Quorum Sensing (QS) is a bacterial regulatory mechanism, which is responsible for controlling the expression of various biological macromolecules such as the virulence factors in a cell density-dependent manner. Disruption of the QS system of pathogens has been proposed as a new anti-infective strategy. Biodegradation of AHLs proves to be an efficient way to interrupt QS, since AHLs are the main family of QS autoinducers used in Gram negative bacteria. In this study, the effect of Bacillus sp. QSI-1 as an efficient quorum quencher on virulence factors production and biofilm formation of fish pathogen Aeromonas hydrophila was investigated. QSI-1 reduced the accumulation of AHLs but did not affect the growth of A. hydrophila YJ-1 when cocultured. In the result, the supernatant of QSI-1 showed significant inhibition of protease production (83.9%), hemolytic activity (77.6%) and biofilm formation (77.3%) in YJ-1. In biocontrol experiment, QSI-1 significantly reduced the pathogenicity of A. hydrophila strain YJ-1 in zebrafish (Danio rerio). The fish fed with QSI-1 was observed to have a relative percentage survival of 80.8%. Our results indicate that AHLs degrading bacteria should be considered as an alternative for antibiotics in aquaculture for the biocontrol of bacterial fish diseases. PMID:24962441

  5. Kinetic modeling of thermal inactivation of the Bacillus sp. protease P7.

    PubMed

    Sant'Anna, Voltaire; Corrêa, Ana Paula Folmer; Daroit, Daniel Joner; Brandelli, Adriano

    2013-07-01

    Data from thermal stability of a keratinolytic protease produced by the Amazon isolate Bacillus sp. P7 was fitted to various mathematical models. Kinetic modeling showed that Weibull distribution was the best equation to describe the residual activity of protease P7 after heat treatment. The effects of temperature on equation parameters and on characteristics of the inactivation curves were evaluated. As expected, faster inactivation was observed at higher temperatures. The critical temperature to accelerate protease decomposition was about 70 °C. The reliable life (t(R)) of the enzyme, analogous to the D value, ranged from 1,824 to 8 min at 45-65 °C. Within these temperatures, an increase of 8.81 °C was needed to lower enzyme t(R) in one-log unit. Protease P7 is a potentially useful biocatalyst for various industrial bioprocesses, and therefore, kinetic modeling of thermal inactivation addresses an important topic aiming enzyme characterization and applications. PMID:23076433

  6. Microwave Accelerated Transglycosylation of Rutin by Cyclodextrin Glucanotransferase from Bacillus sp. SK13.002

    PubMed Central

    Sun, Tao; Jiang, Bo; Pan, Beilei

    2011-01-01

    Rutin was subjected to intermolecular transglycosylation assisted with microwave irradiation using cyclodextrin glucanotransferase (CGTase) produced from Bacillus sp. SK13.002. Compared with the conventional enzymatic method for rutin transglycosylation (without microwave irradiation), microwave-assisted reaction (MAR) was much faster and thus more efficient. While the conventional reaction took dozens of hours to reach the highest conversion rate of rutin and yield of transglycosylated rutin, MAR of rutin transglycosylation completed within only 6 min providing almost the same conversion rate of rutin and yield of products consisting of mono-, di-, tri-, tetra-, penta-glucosylated rutins. The optimum transglycosylation conditions for microwave irradiation were 40 °C and 60 W with the reaction system consisting mainly of the mixture of 0.3 g rutin (0.49 mmol) pre-dissolved in 15 mL methanol, 1.8 g maltodextrin in 15 mL of 0.2 M sodium acetate buffer (pH 5.5) and CGTase (900 U). Results from this study indicated that MAR could be a potentially useful and economical technique for a faster and more efficient transglycosylation of rutin. PMID:21747706

  7. Production of cyclodextrin glycosyltransferase by immobilized Bacillus sp. on chitosan matrix.

    PubMed

    Eş, Ismail; Ribeiro, Maycon Carvalho; Dos Santos Júnior, Samuel Rodrigues; Khaneghah, Amin Mousavi; Rodriguez, Armando Garcia; Amaral, André Corrêa

    2016-10-01

    The whole-cell immobilization on chitosan matrix was evaluated. Bacillus sp., as producer of CGTase, was grown in solid-state and batch cultivation using three types of starches (cassava, potato and cornstarch). Biomass growth and substrate consumption were assessed by flow cytometry and modified phenol-sulfuric acid assays, respectively. Qualitative analysis of CGTase production was determined by colorless area formation on solid culture containing phenolphthalein. Scanning electron microscopy (SEM) analysis demonstrated that bacterial cells were immobilized on chitosan matrix efficiently. Free cells reached very high numbers during batch culture while immobilized cells maintained initial inoculum concentration. The maximum enzyme activity achieved by free cells was 58.15 U ml(-1) (36 h), 47.50 U ml(-1) (36 h) and 68.36 U ml(-1) (36 h) on cassava, potato and cornstarch, respectively. CGTase activities for immobilized cells were 82.15 U ml(-1) (18 h) on cassava, 79.17 U ml(-1) (12 h) on potato and 55.37 U ml(-1) (in 6 h and max 77.75 U ml(-1) in 36 h) on cornstarch. Application of immobilization technique increased CGTase activity significantly. The immobilized cells produced CGTase with higher activity in a shorter fermentation time comparing to free cells. PMID:27194141

  8. Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp.

    PubMed

    Wang, Guangli; Xu, Dayong; Xiong, Minghua; Zhang, Hui; Li, Feng; Liu, Yuan

    2016-09-15

    Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments. PMID:27208995

  9. Isolation of a Bacillus sp. capable of transforming isoeugenol to vanillin.

    PubMed

    Shimoni, E; Ravid, U; Shoham, Y

    2000-02-28

    Natural aroma compounds are of major interest to the flavor and fragrance industry. Due to the limited sources for natural aromas, there is a growing interest in developing alternative sources for natural aroma compounds, and in particular aromatic aldehydes. In several microbial species aromatic aldehydes are detected as intermediates in the degradation pathway of phenylpropanoids. Thus, bioconversion of phenylpropanoids is one possible route for the production of these aroma compounds. The present work describes the isolation of microbial strains, capable of producing vanillin from isoeugenol. Bacterial strains isolated from soil, were screened for their ability to transform isoeugenol to vanillin. One of these strains, strain B2, was found to produce high amounts of vanillin when grown in the presence of isoeugenol, and was also capable of growing on isoeugenol as the sole carbon source. Based on its fatty acids profile, strain B2 was identified as a Bacillus subtilis sp. The bioconversion capabilities of strain B2 were tested in growing cultures and cell free extracts. In the presence of isoeugenol, a growing cultures of B. subtilis B2 produced 0.61 g l-1 vanillin (molar yield of 12.4%), whereas cell free extracts resulted in 0.9 g l-1 vanillin (molar yield of 14%). PMID:10702906

  10. Algicidal metabolites produced by Bacillus sp. strain B1 against Phaeocystis globosa.

    PubMed

    Zhao, Ling; Chen, Lina; Yin, Pinghe

    2014-03-01

    The bloom of Phaeocystis globosa has broken out frequently in the coastal areas of China in recent years, which has led to substantial economic losses. This study shows that Bacillus sp. strain B1, which was previously identified by our group, is effective in regulating P. globosa by excreting active metabolites. Heat stability, pH stability and molecular weight range of the algicidal compounds from strain B1 were measured and the results demonstrated that the algicidal activities of these compounds were not affected by pH or temperature variation. The algicidal compounds extracted with methanol were isolated and purified by ODS-A column chromatography and HPLC. The algicidal compounds corresponding to peaks 2-5 eluted from HPLC were further analysed by quadrupole time-of-flight mass spectrometry (Q-TOF-MS). PeakView™ Software determined the compounds corresponding to peaks 2-5 to be L-histidine, o-tyrosine, N-acetylhistamine and urocanic acid on the basis of the accurate mass information, the isotopic pattern and MS-MS spectra. Furthermore, these compounds were also able to eliminate Skeletonema costatum, Prorocentrum donghaiense and Heterosigma akashiwo. This is the first report of bacteria-derived algicidal compounds being identified only by Q-TOF-MS and PeakView™ Software, and these compounds may be used as the constituents of algicides in the future. PMID:24370882

  11. Production and Purification of Extracellular D-Xylose Isomerase from an Alkaliphilic, Thermophilic Bacillus sp. †

    PubMed Central

    Chauthaiwale, Jyoti; Rao, Mala

    1994-01-01

    An alkaliphilic, thermophilic Bacillus sp. (NCIM 59) produced extracellular xylose isomerase at pH 10 and 50°C by using xylose or wheat bran as the carbon source. The distribution of xylose isomerase as a function of growth in comparison with distributions of extra- and intracellular marker enzymes such as xylanase and β-galactosidase revealed that xylose isomerase was truly secreted as an extracellular enzyme and was not released because of sporulation or lysis. The enzyme was purified to homogeneity by ammonium sulfate precipitation followed by gel filtration, preparative polyacrylamide gel electrophoresis, and ion-exchange chromatography. The molecular weight of xylose isomerase was estimated to be 160,000 by gel filtration and 50,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating the presence of three subunits. The enzyme is most active at pH 8.0 and with incubation at 85°C for 20 min. Divalent metal ions Mg2+, Co2+, and Mn2+ were required for maximum activity of the enzyme. The Km values for D-xylose and D-glucose at 80°C and pH 7.5 were 6.66 and 142 mM, respectively, while Kcat values were 2.3 × 102 s-1 and 0.5 × 102 s-1, respectively. Images PMID:16349464

  12. Antiviral activity of a Bacillus sp. P34 peptide against pathogenic viruses of domestic animals

    PubMed Central

    Silva, Débora Scopel e; de Castro, Clarissa Caetano; Silva, Fábio da Silva e; Sant’anna, Voltaire; Vargas, Gilberto D’Avila; de Lima, Marcelo; Fischer, Geferson; Brandelli, Adriano; da Motta, Amanda de Souza; Hübner, Silvia de Oliveira

    2014-01-01

    P34 is an antimicrobial peptide produced by a Bacillus sp. strain isolated from the intestinal contents of a fish in the Brazilian Amazon basin with reported antibacterial activity. The aim of this work was to evaluate the peptide P34 for its in vitro antiviral properties against canine adenovirus type 2 (CAV-2), canine coronavirus (CCoV), canine distemper virus (CDV), canine parvovirus type 2 (CPV-2), equine arteritis virus (EAV), equine influenza virus (EIV), feline calicivirus (FCV) and feline herpesvirus type 1 (FHV-1). The results showed that the peptide P34 exhibited antiviral activity against EAV and FHV-1. The peptide P34 inhibited the replication of EAV by 99.9% and FHV-1 by 94.4%. Virucidal activity was detected only against EAV. When P34 and EAV were incubated for 6 h at 37 °C the viral titer reduced from 104.5 TCID50 to 102.75 TCID50, showing a percent of inhibition of 98.6%. In conclusion, our results demonstrated that P34 inhibited EAV and FHV-1 replication in infected cell cultures and it showed virucidal activity against EAV. Since there is documented resistance to the current drugs used against herpesviruses and there is no treatment for equine viral arteritis, it is advisable to search for new antiviral compounds to overcome these infections. PMID:25477947

  13. Highly thermostable and alkaline α-amylase from a halotolerant-alkaliphilic Bacillus sp. AB68

    PubMed Central

    Aygan, Ashabil; Arikan, Burhan; Korkmaz, Hatice; Dinçer, Sadik; Çolak, Ömer

    2008-01-01

    An alkaliphilic and highly thermostable α-amylase producing Bacillus sp. was isolated from Van soda lake. Enzyme synthesis occurred at temperatures between 25°C and 40°C. Analysis of the enzyme by SDS-PAGE revealed a single band which was estimated to be 66 kDa. The enzyme was active in a broad temperature range, between 20°C and 90°C, with an optimum at 50°C; and maximum activity was at pH 10.5. The enzyme was almost completely stable up to 80°C with a remaining activity over 90% after 30 min pre-incubation. Thermostability was not increased in the presence of Ca2+. An average of 75% and 60°C of remaining activity was observed when the enzyme was incubated between pH 5 and 9 for 1 h and for 2 h, respectively. The activity of the enzyme was inhibited by SDS and EDTA by 38% and 34%, respectively. PMID:24031264

  14. Enzymatic dehairing of goat skins using alkaline protease from Bacillus sp. SB12.

    PubMed

    Briki, Selmen; Hamdi, Olfa; Landoulsi, Ahmed

    2016-05-01

    The present paper reports the production, purification and biochemical characterization of an extracellular alkaline protease from Bacillus sp. SB12. The enzyme has been used as an alternative to conventional chemicals treatment for dehairing of goat skins. The protease was optimally active at 37 °C and pH 9. Starch at 2% (w/v) was used as the best carbon source and the addition of yeast extract and peptone at 1% each supported the maximum level of protease production in the presence of 5 mM Ca(2+). Protease purification was performed with ammonium sulphate precipitation at 70% saturated fraction followed by dialysis and gel filtration chromatography using Sephadex G-100. The purified enzyme was homogeneous on non-denaturing PAGE and appeared as a single band with an apparent molecular weight of 41 kDa. This enzyme was moderately thermostable and has a wide pH stability range extending from pH 7 to 11. It showed high tolerance toward surfactants agents and organic solvents while it was completely inhibited by PMSF indicating the serine protease type. Purified protease was used to remove hair from goat skin proving its potential application in leather processing industry. The results revealed that the protease has enhanced the quality and physico-chemical properties of the skins while reducing the pollution. PMID:26763763

  15. Bacteriophage SP82G Inhibition of an Intracellular Deoxyribonucleic Acid Inactivation Process in Bacillus subtilis1

    PubMed Central

    McAllister, William T.; Green, D. MacDonald

    1972-01-01

    The stability of SP82G bacteriophage deoxyribonucleic acid (DNA) after its uptake by competent Bacillus subtilis was examined by determining the ability of superinfecting phage particles to rescue genetic markers carried by the infective DNA. These experiments show that a DNA inactivation process within the cell is inhibited after infection of the cell by intact phage particles. The inhibition is maximally expressed 6 min after phage infection and is completely prevented by the addition of chloramphenicol at the time of infection. The protective effect of this function extends even to infective DNA which was present in the cell before the addition of intact phage. Continued protein synthesis does not appear to be a requirement for the maintenance of the inhibition. In an analogous situation, if infectious centers resulting from singly infecting phage particles are exposed to chloramphenicol shortly after the time of infection, an exponential decrease in the survival of infectious centers with time held in chloramphenicol is observed. If the addition of chloramphenicol is delayed until 6 min after infection, the infectious centers are resistant to chloramphenicol. The sensitivity of infectious centers treated with chloramphenicol at early times after infection is strongly dependent upon the multiplicity of infection and is consistent with a model of multiplicity reactivation. These results indicate that injected DNA is also susceptible to the intracellular inactivation process and suggest that the inhibition of this system is necessary for the successful establishment of an infectious center. PMID:4625174

  16. Haloarcula marismortui (Volcani) sp. nov., nom. rev., an extremely halophilic bacterium from the Dead Sea

    NASA Technical Reports Server (NTRS)

    Oren, A.; Ginzburg, M.; Ginzburg, B. Z.; Hochstein, L. I.; Volcani, B. E.

    1990-01-01

    An extremely halophilic red archaebacterium isolated from the Dead Sea (Ginzburg et al., J. Gen. Physiol. 55: 187-207, 1970) belongs to the genus Haloarcula and differs sufficiently from the previously described species of the genus to be designated a new species; we propose the name Haloarcula marismortui (Volcani) sp. nov., nom. rev. because of the close resemblance of this organism to "Halobacterium marismortui," which was first described by Volcani in 1940. The type strain is strain ATCC 43049.

  17. Genome Sequence of the Agar-Degrading Marine Bacterium Alteromonadaceae sp. Strain G7

    PubMed Central

    Kwak, Min-Jung; Song, Ju Yeon; Kim, Byung Kwon; Chi, Won-Jae; Kwon, Soon-Kyeong; Choi, Soobeom; Chang, Yong-Keun

    2012-01-01

    Here, we present the high-quality draft genome sequence of the agar-degrading marine gammaproteobacterium Alteromonadaceae sp. strain G7, which was isolated from coastal seawater to be utilized as a bioresource for production of agar-derived biofuels. The 3.91-Mb genome contains a number of genes encoding algal polysaccharide-degrading enzymes such as agarases and sulfatases. PMID:23209220

  18. Draft Genome Sequence of Thermoanaerobacter sp. Strain YS13, a Novel Thermophilic Bacterium.

    PubMed

    Peng, Tingting; Pan, Siyi; Christopher, Lew; Sparling, Richard; Levin, David B

    2015-01-01

    Here, we report the draft genome sequence of Thermoanerobacter sp. YS13, isolated from a geothermal hot spring in Yellowstone National Park, which consists of 2,713,030 bp with a mean G+C content of 34.05%. A total of 2,779 genes, including 2,707 protein-coding genes, 12 rRNAs, and 59 tRNAs were identified. PMID:26044430

  19. Genome Sequence of the Petroleum Hydrocarbon-Degrading Bacterium Alcanivorax sp. Strain 97CO-5

    PubMed Central

    Luan, Xiao; Gao, Wei; Li, Qian; Yin, Xiaofei; Zheng, Li

    2014-01-01

    Alcanivorax sp. strain 97CO-5 was isolated from a crude-oil-degrading consortium, enriched from Yellow Sea sediment of China. Here, we present the draft genome of strain 97CO-5, which comprises 3,251,558 bp with a G+C content of 54.54% and contains 2,962 protein-coding genes and 42 tRNAs. PMID:25502673

  20. Novel thermostable endo-xylanase cloned and expressed from bacterium Geobacillus sp. WSUCF1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A gene encoding a GH10 endo-xylanase from Geobacillus sp. WSUCF1 was cloned and expressed in Escherichia coli. Recombinant endo-xylanase (37 kDa) exhibited high specific activity of 461.0 U/ mg of protein. Endo-xylanase was optimally active on birchwood xylan at 70°C and pH 6.5. Zn2+ and Ca2+ ions i...

  1. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2

    PubMed Central

    2014-01-01

    In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M. PMID:25566348

  2. Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis.

    PubMed

    Gatson, Joshua W; Benz, Bruce F; Chandrasekaran, Chitra; Satomi, Masataka; Venkateswaran, Kasthuri; Hart, Mark E

    2006-07-01

    A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate as Bacillus subtilis. DNA isolated from the tomb isolate, strain 10b(T), and closely related species was used to amplify a Bacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodA(int)). Trees derived from maximum-likelihood methods applied to the sodA(int) sequences yielded non-zero branch lengths between strain 10b(T) and its closest relative, whereas a comparison of a Bacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity with B. subtilis. Although the 16S rRNA gene sequences of strain 10b(T) and B. subtilis were 99 % similar, PFGE of NotI-digested DNA of strain 10b(T) revealed a restriction profile that was considerably different from those of B. subtilis and other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10b(T) and each of the other closely related Bacillus species examined. In addition, DNA-DNA hybridization studies demonstrated that strain 10b(T) had a relatedness value of less than 70 % with B. subtilis and other closely related species. Evidence from the sodA(int) sequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA-DNA hybridization studies, justify the classification of strain 10b(T) as representing a distinct species, for which the name Bacillus tequilensis sp. nov. is proposed. The type strain is 10b(T) (=ATCC BAA-819(T)=NCTC 13306(T)). PMID:16825615

  3. Porticoccus hydrocarbonoclasticus sp. nov., an aromatic hydrocarbon-degrading bacterium identified in laboratory cultures of marine phytoplankton.

    PubMed

    Gutierrez, Tony; Nichols, Peter D; Whitman, William B; Aitken, Michael D

    2012-02-01

    A marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellate Lingulodinium polyedrum CCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to Porticoccus litoralis IMCC2115(T) (96.5%) and to members of the genera Microbulbifer (91.4 to 93.7%) and Marinimicrobium (90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the class Gammaproteobacteria for which P. litoralis is presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C(16:1ω7c), C(18:1ω7c), and C(16:0). DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species of Porticoccus, for which the name Porticoccus hydrocarbonoclasticus sp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean. PMID:22139001

  4. Alicyclobacillus dauci sp. nov., a slightly thermophilic, acidophilic bacterium isolated from a spoiled mixed vegetable and fruit juice product.

    PubMed

    Nakano, Chisa; Takahashi, Naoto; Tanaka, Naoto; Okada, Sanae

    2015-02-01

    A novel, moderately thermophilic, acidophilic, Gram-variable, rod-shaped, endospore-forming bacterium was isolated from a spoiled mixed vegetable and fruit juice product that had the off-flavour of guaiacol. The bacterium, strain 4F(T), grew aerobically at 20-50 °C (optimum 40 °C) and pH 3.0-6.0 (optimum pH 4.0) and produced acid from glycerol, d-galactose and d-glucose. It contained menaquinone-7 (MK-7) as the major isoprenoid quinone and the DNA G+C content was 49.6 mol%. The predominant cellular fatty acids of strain 4F(T) were ω-alicyclic (ω-cyclohexane fatty acids), which are characteristic of the genus Alicyclobacillus. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belongs to the Alicyclobacillus cluster, and is related most closely to the type strains of Alicyclobacillus acidoterrestris (97.4 % similarity) and Alicyclobacillus fastidiosus (97.3 %). Strain 4F(T) produced guaiacol from vanillic acid. It can be distinguished from related species by its acid production type and guaiacol production. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness values, it can be concluded that the strain represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus dauci sp. nov. is proposed; the type strain is 4F(T) ( = DSM 28700(T) = NBRC 108949(T) = NRIC 0938(T)). PMID:25505343

  5. Biosynthetic gene cluster of cetoniacytone A, an unusual aminocyclitol from the endosymbiotic Bacterium Actinomyces sp. Lu 9419.

    PubMed

    Wu, Xiumei; Flatt, Patricia M; Xu, Hui; Mahmud, Taifo

    2009-01-26

    A gene cluster responsible for the biosynthesis of the antitumor agent cetoniacytone A was identified in Actinomyces sp. strain Lu 9419, an endosymbiotic bacterium isolated from the intestines of the rose chafer beetle (Cetonia aurata). The nucleotide sequence analysis of the 46 kb DNA region revealed the presence of 31 complete ORFs, including genes predicted to encode a 2-epi-5-epi-valiolone synthase (CetA), a glyoxalase/bleomycin resistance protein (CetB), an acyltransferase (CetD), an FAD-dependent dehydrogenase (CetF2), two oxidoreductases (CetF1 and CetG), two aminotransferases (CetH and CetM), and a pyranose oxidase (CetL). CetA has previously been demonstrated to catalyze the cyclization of sedoheptulose 7-phosphate to the cyclic intermediate, 2-epi-5-epi-valiolone. In this report, the glyoxalase/bleomycin resistance protein homolog CetB was identified as a 2-epi-5-epi-valiolone epimerase (EVE), a new member of the vicinal oxygen chelate (VOC) superfamily. The 24 kDa recombinant histidine-tagged CetB was found to form a homodimer; each monomer contains two betaalphabetabetabeta scaffolds that form a metal binding site with two histidine and two glutamic acid residues. A BLAST search using the newly isolated cet biosynthetic genes revealed an analogous suite of genes in the genome of Frankia alni ACN14a, suggesting that this plant symbiotic nitrogen-fixing bacterium is capable of producing a secondary metabolite related to the cetoniacytones. PMID:19101977

  6. Carboxydothermus siderophilus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic, dissimilatory Fe(III)-reducing bacterium from a Kamchatka hot spring.

    PubMed

    Slepova, Tatiana V; Sokolova, Tatyana G; Kolganova, Tatyana V; Tourova, Tatyana P; Bonch-Osmolovskaya, Elizaveta A

    2009-02-01

    A novel anaerobic, thermophilic, Fe(III)-reducing, CO-utilizing bacterium, strain 1315(T), was isolated from a hot spring of Geyser Valley on the Kamchatka Peninsula. Cells of the new isolate were Gram-positive, short rods. Growth was observed at 52-70 degrees C, with an optimum at 65 degrees C, and at pH 5.5-8.5, with an optimum at pH 6.5-7.2. In the presence of Fe(III) or 9,10-anthraquinone 2,6-disulfonate (AQDS), the bacterium was capable of growth with CO and yeast extract (0.2 g l(-1)); during growth under these conditions, strain 1315(T) produced H(2) and CO(2) and Fe(II) or AQDSH(2), respectively. Strain 1315(T) also grew by oxidation of yeast extract, glucose, xylose or lactate under a N(2) atmosphere, reducing Fe(III) or AQDS. Yeast extract (0.2 g l(-1)) was required for growth. Isolate 1315(T) grew exclusively with Fe(III) or AQDS as an electron acceptor. The generation time under optimal conditions with CO as growth substrate was 9.3 h. The G+C content of the DNA was 41.5+/-0.5 mol%. 16S rRNA gene sequence analysis placed the organism in the genus Carboxydothermus (97.8 % similarity with the closest relative). On the basis of physiological features and phylogenetic analysis, it is proposed that strain 1315(T) should be assigned to a novel species, Carboxydothermus siderophilus sp. nov., with the type strain 1315(T) (=VKPM 9905B(T) =VKM B-2474(T) =DSM 21278(T)). PMID:19196756

  7. From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov.

    PubMed Central

    León, María José; Fernández, Ana B.; Ghai, Rohit; Sánchez-Porro, Cristina; Rodriguez-Valera, Francisco

    2014-01-01

    Recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40T, isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40T has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40T (= CECT 8282T = IBRC-M 10768T = LMG 27464T) being the type strain. PMID:24747894

  8. From metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium Spiribacter salinus gen. nov., sp. nov.

    PubMed

    León, María José; Fernández, Ana B; Ghai, Rohit; Sánchez-Porro, Cristina; Rodriguez-Valera, Francisco; Ventosa, Antonio

    2014-07-01

    Recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both Euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera Alkalilimnicola and Arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. Here we used several strategies and culture media in order to isolate this organism in pure culture. We report the isolation and taxonomic characterization of this new, never before cultured microorganism, designated M19-40(T), isolated from a saltern located in Isla Cristina, Spain, using a medium with a mixture of 15% salts, yeast extract, and pyruvic acid as the carbon source. Morphologically small curved cells (young cultures) with a tendency to form long spiral cells in older cultures were observed in pure cultures. The organism is a Gram-negative, nonmotile bacterium that is strictly aerobic, non-endospore forming, heterotrophic, and moderately halophilic, and it is able to grow at 10 to 25% (wt/vol) NaCl, with optimal growth occurring at 15% (wt/vol) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that strain M19-40(T) has a low similarity with other previously described bacteria and shows the closest phylogenetic similarity with species of the genera Alkalilimnicola (94.9 to 94.5%), Alkalispirillum (94.3%), and Arhodomonas (93.9%) within the family Ectothiorhodospiraceae. The phenotypic, genotypic, and chemotaxonomic features of this new bacterium showed that it constitutes a new genus and species, for which the name Spiribacter salinus gen. nov., sp. nov., is proposed, with strain M19-40(T) (= CECT 8282(T) = IBRC-M 10768(T) = LMG 27464(T)) being the type strain. PMID:24747894

  9. Does S-Metolachlor Affect the Performance of Pseudomonas sp. Strain ADP as Bioaugmentation Bacterium for Atrazine-Contaminated Soils?

    PubMed Central

    Viegas, Cristina A.; Costa, Catarina; André, Sandra; Viana, Paula; Ribeiro, Rui; Moreira-Santos, Matilde

    2012-01-01

    Atrazine (ATZ) and S-metolachlor (S-MET) are two herbicides widely used, often as mixtures. The present work examined whether the presence of S-MET affects the ATZ-biodegradation activity of the bioaugmentation bacterium Pseudomonas sp. strain ADP in a crop soil. S-MET concentrations were selected for their relevance in worst-case scenarios of soil contamination by a commercial formulation containing both herbicides. At concentrations representative of application of high doses of the formulation (up to 50 µg g−1 of soil, corresponding to a dose approximately 50× higher than the recommended field dose (RD)), the presence of pure S-MET significantly affected neither bacteria survival (∼107 initial viable cells g−1 of soil) nor its ATZ-mineralization activity. Consistently, biodegradation experiments, in larger soil microcosms spiked with 20× or 50×RD of the double formulation and inoculated with the bacterium, revealed ATZ to be rapidly (in up to 5 days) and extensively (>96%) removed from the soil. During the 5 days, concentration of S-MET decreased moderately to about 60% of the initial, both in inoculated and non-inoculated microcosms. Concomitantly, an accumulation of the two metabolites S-MET ethanesulfonic acid and S-MET oxanilic acid was found. Despite the dissipation of almost all the ATZ from the treated soils, the respective eluates were still highly toxic to an aquatic microalgae species, being as toxic as those from the untreated soil. We suggest that this high toxicity may be due to the S-MET and/or its metabolites remaining in the soil. PMID:22615921

  10. Porticoccus hydrocarbonoclasticus sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium Identified in Laboratory Cultures of Marine Phytoplankton

    PubMed Central

    Nichols, Peter D.; Whitman, William B.; Aitken, Michael D.

    2012-01-01

    A marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellate Lingulodinium polyedrum CCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related to Porticoccus litoralis IMCC2115T (96.5%) and to members of the genera Microbulbifer (91.4 to 93.7%) and Marinimicrobium (90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the class Gammaproteobacteria for which P. litoralis is presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C16:1ω7c, C18:1ω7c, and C16:0. DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species of Porticoccus, for which the name Porticoccus hydrocarbonoclasticus sp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean. PMID:22139001

  11. Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.

    PubMed

    Han, Song-Ih; Kim, Ju-Ok; Lee, Ye-Rim; Ekpeghere, Kalu I; Koh, Sung-Cheol; Whang, Kyung-Sook

    2016-06-01

    A denitrifying bacterium, designated strain E4-1(T), was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1(T), a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1(T) forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1(T) is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1(T) (=KACC 17565(T) = NCAIM B 025327(T)). PMID:27108138

  12. Nucleotide sequence of a chromosomal mercury resistance determinant from a Bacillus sp. with broad-spectrum mercury resistance. [Mercury reductase

    SciTech Connect

    Wang, Y.; Levinson, H.S.; Mahler, I. ); Moore, M.; Walsh, C. ); Silver, S. )

    1989-01-01

    A 13.5-kilobase HindIII fragment, bearing an intact mercury resistance (mer) operon, was isolated from chromosomal DNA of broad-spectrum mercury-resistant Bacillus sp. strain RC607 by using as a probe a clone containing the mercury reductase (merA) gene. The new clone, pYW33, expressed broad-spectrum mercury resistance both in Escherichia coli and in Bacillus subtilis, but only in B. subtilis was the mercuric reductase activity inducible. Sequencing of a 1.8-kilobase mercury hypersensitivity-producing fragment revealed four open reading frames (ORFs). ORF1 may code for a regulatory protein (MerR). ORF2 and ORF4 were associated with cellular transport function and the hypersensitivity phenotype. DNA fragments encompassing the merA and the merB genes were sequenced. The predicted Bacillus sp. strain RC607 MerA (mercuric reductase) and MerB (organomercurial lyase) were similar to those predicted from Staphylococcus aureus plasmid pI258 (67 and 73% amino acid identities, respectively); however, only 40% of the amino acid residues of RC607 MerA were identical to those of the mercuric reductase from gram-negative bacteria. A 69-kilodalton polypeptide was isolated and identified as the merA gene product by examination of its amino-terminal sequence.

  13. Characterization of antimicrobial lipopeptides produced by Bacillus sp. LM7 isolated from chungkookjang, a Korean traditional fermented soybean food.

    PubMed

    Lee, Mi-Hwa; Lee, Jiyeon; Nam, Young-Do; Lee, Jong Suk; Seo, Myung-Ji; Yi, Sung-Hun

    2016-03-16

    A wild-type microorganism exhibiting antimicrobial activities was isolated from the Korean traditional fermented soybean food Chungkookjang and identified as Bacillus sp. LM7. During its stationary growth phase, the microorganism secreted an antimicrobial substance, which we partially purified using a simple two-step procedure involving ammonium sulfate precipitation and heat treatment. The partially purified antimicrobial substance, Anti-LM7, was stable over a broad pH range (4.0-9.0) and at temperatures up to 80 °C for 30 min, and was resistant to most proteolytic enzymes and maintained its activity in 30% (v/v) organic solvents. Anti-LM7 inhibited the growth of a broad range of Gram-positive bacteria, including Bacillus cereus and Listeria monocytogenes, but it did not inhibit lactic acid bacteria such as Lactobacillus plantarum and Lactococcus lactis subsp. Lactis. Moreover, unlike commercially available nisin and polymyxin B, Anti-LM7 inhibited certain fungal strains. Lastly, liquid chromatography-mass spectrometry analysis of Anti-LM7 revealed that it contained eight lipopeptides belonging to two families: four bacillomycin D and four surfactin analogs. These Bacillus sp. LM7-produced heterogeneous lipopeptides exhibiting extremely high stability and a broad antimicrobial spectrum are likely to be closely related to the antimicrobial activity of Chungkookjang, and their identification presents an opportunity for application of the peptides in environmental bioremediation, pharmaceutical, cosmetic, and food industries. PMID:26803269

  14. Enterobacter sacchari sp. nov., a nitrogen-fixing bacterium associated with sugar cane (Saccharum officinarum L.).

    PubMed

    Zhu, Bo; Zhou, Qing; Lin, Li; Hu, Chunjin; Shen, Ping; Yang, Litao; An, Qianli; Xie, Guanlin; Li, Yangrui

    2013-07-01

    Five nitrogen-fixing bacterial strains (SP1(T), NN143, NN144, NN208 and HX148) were isolated from stem, root or rhizosphere soil of sugar cane (Saccharum officinarum L.) plants. Cells were Gram-negative, motile, rods with peritrichous flagella. DNA G+C content was 55.0 ± 0.5 mol%. Sequence determinations and phylogenetic analysis of 16S rRNA gene and rpoB indicated that the strains were affiliated with the genus Enterobacter and most closely related to E. radicincitans DSM 16656(T) and E. oryzae LMG 24251(T). Fluorimetric determination of thermal denaturation temperatures after DNA-DNA hybridization, enterobacterial repetitive intergenic consensus PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiated the whole-genome, genotype and protein profiles from those of E. radicincitans and E. oryzae. The strains' cell fatty acid composition differentiated them from E. radicincitans and E. oryzae by containing a higher level of summed feature 2 (C16 : 1ω7c and/or C16 : 1ω6c) and a lower level of C17 : 0 cyclo. Their physiological and biochemical profiles differentiated them from E. radicincitans by being positive for methyl red test, ornithine decarboxylase and utilization of putrescine, D-arabitol, L-fucose and methyl α-D-glucoside and being negative for arginine dihydrolase, and differentiated them from E. oryzae by being positive for aesculin hydrolysis and utilization of putrescine, D-arabitol and L-rhamnose and being negative for arginine dihydrolase, lysine decarboxylase and utilization of mucate. The five strains therefore represent a novel species, for which the name Enterobacter sacchari sp. nov. is proposed, with the type strain SP1(T) ( = CGMCC 1.12102(T) = LMG 26783(T)). PMID:23291881

  15. Platinum and rhenium extraction from a spent refinery catalyst using Bacillus megaterium as a cyanogenic bacterium: statistical modeling and process optimization.

    PubMed

    Motaghed, M; Mousavi, S M; Rastegar, S O; Shojaosadati, S A

    2014-11-01

    The present study evaluated the potential of Bacillus megaterium as a cyanogenic bacterium to produce cyanide for solubilization of platinum and rhenium from a spent refinery catalyst. Response surface methodology was applied to study the effects and interaction between two main effective parameters including initial glycine concentration and pulp density. Maximum Pt and Re recovery was obtained 15.7% and 98%, respectively, under optimum conditions of 12.8 g/l initial glycine concentration and 4% (w/v) pulp density after 7 days. Increasing the free cyanide concentration to 3.6 mg/l, varying the pH from 6.7 to 9, and increasing the dissolved oxygen from 2 to 5mg/l demonstrated the growth characteristics of B. megaterium during bioleaching process. The modified shrinking core model was used to determine the rate limiting step of the process. It was found that diffusion through the product layer is the rate controlling step. PMID:25226056

  16. Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

    SciTech Connect

    Vishnivetskaya, T.; Lucas, Susan; Copeland, A; Lapidus, Alla L.; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Saunders, Elizabeth H; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Larimer, Frank W; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ovchinnikova, Galina; Kathariou, Sophia; Ramaley, Robert F.; Rodrigues, Debora F.; Hendrix, Christie; Richardson, Paul; Tiedje, James M.

    2011-01-01

    Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physico-chemical gradient. This genome was sequenced to be a comparative resource for study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

  17. Complete Genome Sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

    SciTech Connect

    Vishnivetskaya, T.; Lucas, Susan; Copeland, A; Lapidus, Alla L; Glavina Del Rio, Tijana; Dalin, Eileen; Tice, Hope; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Saunders, Elizabeth H; Brettin, Tom; Detter, J. Chris; Han, Cliff; Larimer, Frank W; Land, Miriam L; Hauser, Loren John; Kyrpides, Nikos C; Ovchinnikova, Galina; Kathariou, Sophia; Ramaley, Robert F.; Rodrigues, Debora F.; Hendrix, Christie; Richardson, Paul; Tiedje, James M.

    2011-01-01

    Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy s (DOE s) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).

  18. Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant

    NASA Technical Reports Server (NTRS)

    Venkateswaran, Kasthuri; Kempf, Michael; Chen, Fei; Satomi, Masataka; Nicholson, Wayne; Kern, Roger

    2003-01-01

    One of the spore-formers isolated from a spacecraft-assembly facility, belonging to the genus Bacillus, is described on the basis of phenotypic characterization, 16S rDNA sequence analysis and DNA-DNA hybridization studies. It is a Gram-positive, facultatively anaerobic, rod-shaped eubacterium that produces endospores. The spores of this novel bacterial species exhibited resistance to UV, gamma-radiation, H2O2 and desiccation. The 18S rDNA sequence analysis revealed a clear affiliation between this strain and members of the low G+C Firmicutes. High 16S rDNA sequence similarity values were found with members of the genus Bacillus and this was supported by fatty acid profiles. The 16S rDNA sequence similarity between strain FO-92T and Bacillus benzoevorans DSM 5391T was very high. However, molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in this genus, but DNA-DNA hybridization data support the proposal of FO-92T as Bacillus nealsonii sp. nov. (type strain is FO-92T =ATCC BAAM-519T =DSM 15077T).

  19. Bacillus nealsonii sp. nov., isolated from a spacecraft-assembly facility, whose spores are gamma-radiation resistant.

    PubMed

    Venkateswaran, Kasthuri; Kempf, Michael; Chen, Fei; Satomi, Masataka; Nicholson, Wayne; Kern, Roger

    2003-01-01

    One of the spore-formers isolated from a spacecraft-assembly facility, belonging to the genus Bacillus, is described on the basis of phenotypic characterization, 16S rDNA sequence analysis and DNA-DNA hybridization studies. It is a Gram-positive, facultatively anaerobic, rod-shaped eubacterium that produces endospores. The spores of this novel bacterial species exhibited resistance to UV, gamma-radiation, H2O2 and desiccation. The 18S rDNA sequence analysis revealed a clear affiliation between this strain and members of the low G+C Firmicutes. High 16S rDNA sequence similarity values were found with members of the genus Bacillus and this was supported by fatty acid profiles. The 16S rDNA sequence similarity between strain FO-92T and Bacillus benzoevorans DSM 5391T was very high. However, molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in this genus, but DNA-DNA hybridization data support the proposal of FO-92T as Bacillus nealsonii sp. nov. (type strain is FO-92T =ATCC BAAM-519T =DSM 15077T). PMID:12656168

  20. Characterization of a Facultatively Psychrophilic Bacterium, Vibrio rumoiensis sp. nov., That Exhibits High Catalase Activity

    PubMed Central

    Yumoto, Isao; Iwata, Hideaki; Sawabe, Tomoo; Ueno, Keisuke; Ichise, Nobutoshi; Matsuyama, Hidetoshi; Okuyama, Hidetoshi; Kawasaki, Kosei

    1999-01-01

    A novel facultatively psychrophilic bacterium, strain S-1, which exhibits extraordinarily high catalase activity was isolated from the drain pool of a fish product processing plant that uses H2O2 as a bleaching and microbicidal agent. The catalase activity of the isolate was 1 or 2 orders of magnitude higher than those of Corynebacterium glutamicum, Staphylococcus aureus, Pseudomonas fluorescens, and five other species tested in this study. The strain seemed to possess only one kind of catalase, according to the results of polyacrylamide gel electrophoresis of the cell extract. The optimum temperature for catalase activity was about 30°C, which was about 20°C lower than that for bovine catalase activity. Electron microscopic observation revealed that the surface of the microorganism was covered by blebs. Although the isolate was nonflagellated, its taxonomic position on the basis of physiological and biochemical characteristics and analysis of 16S rRNA sequence and DNA-DNA relatedness data indicated that strain S-1 is a new species belonging to the genus Vibrio. Accordingly, we propose the name Vibrio rumoiensis. The type strain is S-1 (FERM P-14531). PMID:9872761

  1. Rhodoferax antarcticus sp. nov., a moderately psychrophilic purple nonsulfur bacterium isolated from an Antarctic microbial mat

    NASA Technical Reports Server (NTRS)

    Madigan, M. T.; Jung, D. O.; Woese, C. R.; Achenbach, L. A.

    2000-01-01

    A new species of purple nonsulfur bacteria isolated from an Antarctic microbial mat is described. The organism, designated strain ANT.BR, was mildly psychrophilic, growing optimally at 15-18 degrees C with a growth temperature range of 0-25 degrees C. Cells of strain ANT.BR were highly motile curved rods and spirals, contained bacteriochlorophyll a, and showed a multicomponent in vivo absorption spectrum. A specific phylogenetic relationship was observed between strain ANT.BR and the purple bacterium Rhodoferax fermentans FR2T, and the two organisms shared several physiological and other phenotypic properties, with the notable exception of growth temperature optimum. Tests of genomic DNA hybridization, however, showed Rfx. fermentans FR2T and strain ANT.BR to be genetically distinct bacteria. Because of its unique set of properties, especially its requirement for low growth temperatures, we propose to recognize strain ANT.BR as a new species of the genus Rhodoferax, Rhodoferax antarcticus, named for its known habitat, the Antarctic.

  2. Haloanaerobium kushneri sp. nov., an obligately halophilic, anaerobic bacterium from an oil brine

    NASA Technical Reports Server (NTRS)

    Bhupathiraju, V. K.; McInerney, M. J.; Woese, C. R.; Tanner, R. S.

    1999-01-01

    Three strains, designated VS-751T, VS-511 and VS-732, of a strictly anaerobic, moderately halophilic, Gram-negative, rod-shaped bacterium were isolated from a highly saline (15-20%) brine from an oil reservoir in central Oklahoma, USA. The optimal concentration of NaCl for growth of these three strains was 2 M (12%), and the strains also grew in the presence of an additional 1 M MgCl2. The strains were mesophilic and grew at a pH range of 6-8. Carbohydrates used by all three strains included glucose, fructose, arabinose, galactose, maltose, mannose, cellobiose, sucrose and inulin. Glucose fermentation products included ethanol, acetate, H2 and CO2, with formate produced by two of the three strains. Differences were noted among strains in the optimal temperature and pH for growth, the maximum and minimum NaCl concentration that supported growth, substrate utilization and cellular fatty acid composition. Despite the phenotypic differences among the three strains, analysis of the 16S rRNA gene sequences and DNA-DNA hybridizations showed that these three strains were members of the same genospecies which belonged to the genus Haloanaerobium. The phenotypic and genotypic characteristics of strains VS-751T, VS-511 and VS-732 are different from those of previously described species of Haloanaerobium. It is proposed that strain VS-751T (ATCC 700103T) be established as the type strain of a new species, Haloanaerobium kushneri.

  3. A polysaccharide-degrading marine bacterium Flammeovirga sp. MY04 and its extracellular agarase system

    NASA Astrophysics Data System (ADS)

    Han, Wenjun; Gu, Jingyan; Yan, Qiujie; Li, Jungang; Wu, Zhihong; Gu, Qianqun; Li, Yuezhong

    2012-09-01

    Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported regarding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L-1 ± 18.2 mg L-1 liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These proteins have an activity of 310 U mg-1 ± 9.6 U mg-1 proteins. The extracellular agarase system (EAS) in the crude extracellular enzymes contains at least four agarose depolymerases, which are with molecular masses of approximately 30-70 kDa. The EAS is stable at a wide range of pH values (6.0-11.0), temperatures (0-50°C), and sodium chloride (NaCl) concentrations (0-0.9 mol L-1). Two major degradation products generated from agarose by the EAS are identified to be neoagarotetraose and neoagarohexaose, suggesting that β-agarases are the major constituents of the MY04 EAS. These results suggest that the Flammeovirga strain MY04 and its polysaccharide-degradation system hold great promise in industrial applications.

  4. Prevention of aflatoxin contamination by a soil bacterium of Stenotrophomonas sp. that produces aflatoxin production inhibitors.

    PubMed

    Jermnak, Usuma; Chinaphuti, Amara; Poapolathep, Amnart; Kawai, Ryo; Nagasawa, Hiromichi; Sakuda, Shohei

    2013-05-01

    A soil bacterium, designated strain no. 27, was found to produce aflatoxin-production inhibitors. The strain was identified as a species of the genus Stenotrophomonas, and was found to be closely related to Stenotrophomonas rhizophila. Two diketopiperazines, cyclo(L-Ala-L-Pro) and cyclo(L-Val-L-Pro), were isolated from the bacterial culture filtrate as main active components. These compounds inhibited aflatoxin production of Aspergillus parasiticus and Aspergillus flavus in liquid medium at concentrations of several hundred µM without affecting fungal growth. Both inhibitors inhibited production of norsorolinic acid, a biosynthetic intermediate involved in an early step of the aflatoxin biosynthetic pathway, and reduced the mRNA level of aflR, which is a gene encoding a key regulatory protein necessary for the expression of aflatoxin-biosynthetic enzymes. These results indicated that the inhibitors targets are present in early regulatory steps leading to AflR expression. Co-culture of strain no. 27 with aflatoxigenic fungi in liquid medium effectively suppressed aflatoxin production of the fungus without affecting fungal growth. Furthermore, application of the bacterial cells to peanuts in laboratory experiments and at a farmer's warehouse in Thailand by dipping peanuts in the bacterial cell suspension strongly inhibited aflatoxin accumulation. The inhibitory effect was dependent on bacterial cell numbers. These results indicated that strain no. 27 may be a practically effective biocontrol agent for aflatoxin control. PMID:23449921

  5. Desulfuromonas thiophila sp. nov., a new obligately sulfur-reducing bacterium from anoxic freshwater sediment

    USGS Publications Warehouse

    Finster, K.; Coates, J.D.; Liesack, W.; Pfennig, N.

    1997-01-01

    A mesophilic, acetate-oxidizing, sulfur-reducing bacterium, strain NZ27(T), was isolated from anoxic mud from a freshwater sulfur spring. The cells were ovoid, motile, and gram negative. In addition to acetate, the strain oxidized pyruvate, succinate, and fumarate. Sulfur flower could be replaced by polysulfide as an electron acceptor. Ferric nitrilotriacetic acid was reduced in the presence of pyruvate; however, this reduction did not sustain growth. These phenotypic characteristics suggested that strain NZ27(T) is affiliated with the genus Desulfuromonas. A phylogenetic analysis based on the results of comparative 16S ribosomal DNA sequencing confirmed that strain NZ27(T) belongs to the Desulfuromonas cluster in the recently proposed family 'Geobacteraceae' in the delta subgroup of the Proteobacteria. In addition, the results of DNA-DNA hybridization studies confirmed that strain NZ27(T) represents a novel species. Desulfuromonas thiophila, a name tentatively used in previous publications, is the name proposed for strain NZ27(T) in this paper.

  6. Growth and metabolic profiling of the novel thermophilic bacterium Thermoanaerobacter sp. strain YS13.

    PubMed

    Peng, Tingting; Pan, Siyi; Christopher, Lew P; Sparling, Richard; Levin, David B

    2016-09-01

    A strictly anaerobic, thermophilic bacterium, designated strain YS13, was isolated from a geothermal hot spring. Phylogenetic analysis using the 16S rRNA genes and cpn60 UT genes suggested strain YS13 as a species of Thermoanaerobacter. Using cellobiose or xylose as carbon source, YS13 was able to grow over a wide range of temperatures (45-70 °C), and pHs (pH 5.0-9.0), with optimum growth at 65 °C and pH 7.0. Metabolic profiling on cellobiose, glucose, or xylose in 1191 medium showed that H2, CO2, ethanol, acetate, and lactate were the major metabolites. Lactate was the predominant end product from glucose or cellobiose fermentations, whereas H2 and acetate were the dominant end products from xylose fermentation. The metabolic balance shifted away from ethanol to H2, acetate, and lactate when YS13 was grown on cellobiose as temperatures increased from 45 to 70 °C. When YS13 was grown on xylose, a metabolic shift from lactate to H2, CO2, and acetate was observed in cultures as the temperature of incubation increased from 45 to 65 °C, whereas a shift from ethanol and CO2 to H2, acetate, and lactate was observed in cultures incubated at 70 °C. PMID:27569998

  7. Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea.

    PubMed

    Machado, Henrique; Giubergia, Sonia; Mateiu, Ramona Valentina; Gram, Lone

    2015-12-01

    A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T). PMID:26374506

  8. Physiological factors affecting carbon tetrachloride dehalogenation by the denitrifying bacterium Pseudomonas sp. strain KC.

    PubMed Central

    Lewis, T A; Crawford, R L

    1993-01-01

    Pseudomonas sp. strain KC was grown on a medium with a low content of transition metals in order to examine the conditions for carbon tetrachloride (CT) transformation. Several carbon sources, including acetate, glucose, glycerol, and glutamate, were able to support CT transformation. The chelators 2,2'-dipyridyl and 1,10-phenanthroline stimulated CT transformation in a rich medium that otherwise did not support this activity. Low (< 10 microM) additions of dissolved iron(II), iron(III), and cobalt(II), as well as an insoluble iron(III) compound, ferric oxyhydroxide, inhibited CT transformation. The addition of 50 microM iron to actively growing cultures resulted in delayed inhibition of CT transformation. CT transformation was seen in aerobic cultures of KC, but with reduced efficiency compared with denitrifying cultures. Inhibition of CT transformation by iron was also seen in aerobically grown cultures. Optimal conditions were used in searching for effective CT transformation activity among denitrifying enrichments grown from samples of aquifer material. No activity comparable to that of Pseudomonas sp. strain KC was found among 16 samples tested. PMID:8517754

  9. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

    DOE PAGESBeta

    Billings, Andrew F.; Fortney, Julian L.; Hazen, Terry C.; Simmons, Blake; Davenport, Karen W.; Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanja; et al

    2015-11-19

    Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involvedmore » in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. Finally, by characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.« less

  10. Asaia krungthepensis sp. nov., an acetic acid bacterium in the alpha-Proteobacteria.

    PubMed

    Yukphan, Pattaraporn; Potacharoen, Wanchern; Tanasupawat, Somboon; Tanticharoen, Morakot; Yamada, Yuzo

    2004-03-01

    Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60.2-60.5 mol% G+C, with a range of 0.3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA-DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q(10). On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08(T) (=BCC 12978(T)=TISTR 1524(T)=NBRC 100057(T)=NRIC 0535(T)), which had a DNA G+C content of 60.3 mol% and was isolated from a heliconia flower ('paksaasawan' in Thai; Heliconia sp.) collected in Bangkok, Thailand. PMID:15023938

  11. Polyphasic Characterization of Lysobacter maris sp. nov., a Bacterium Isolated from Seawater.

    PubMed

    Yoon, Jaewoo

    2016-03-01

    A strictly aerobic, Gram-negative, apricot-pigmented, non-motile, rod-shaped strain designated KMU-14(T) was isolated from seawater collected from the coastal zone of Yokji Island, Gyeongsangnam-do, Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the genus Lysobacter within the class Gammaproteobacteria and that it showed the highest sequence similarity (97.1 %) to Lysobacter concretionis Ko07(T). The hybridization value for DNA-DNA relatedness between the strains of KMU-14(T) and L. concretionis Ko07(T) was 34.8 %, which was lower than 70 %, the recommended delineation value for differentiation of species. The DNA G+C content of strain KMU-14(T) was 64.9 mol%. The major respiratory quinone was ubiquinone 8 (Q-8), and iso-C15:0, iso-C16:0, and 10-methyl C16:0 and/or iso-C17:1 ω9c were the major (>10 %) cellular fatty acids. A polar lipid profile was present consisting of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoglycolipid, two unidentified aminophospholipids, and two unidentified phospholipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species for which the name Lysobacter maris sp. nov. is proposed. The type strain of L. maris sp. nov. is KMU-14(T) (=KCTC 42381(T) =NBRC 110750(T)). PMID:26616671

  12. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

    PubMed

    Billings, Andrew F; Fortney, Julian L; Hazen, Terry C; Simmons, Blake; Davenport, Karen W; Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos C; Mavromatis, Konstantinos; Woyke, Tanja; DeAngelis, Kristen M

    2015-01-01

    Tolumonas lignolytica BRL6-1(T) sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1(T) are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. By characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material. PMID:26594307

  13. Pelagitalea pacifica gen. nov., sp. nov., a new marine bacterium isolated from seawater.

    PubMed

    Lee, Hyunsang; Yoshizawa, Susumu; Kogure, Kazuhiro; Kim, Hyun Soo; Yoon, Jaewoo

    2015-04-01

    A strictly aerobic, Gram-negative, beige-pigmented, short-rod-shaped, non-motile and chemoheterotrophic bacteria, designated K2-48(T) was isolated from seawater collected in the Western North Pacific Ocean near Japan. Preliminary analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Oceanospirillaceae within the class Gammaproteobacteria and that it showed the highest sequence similarity (93.7 %) to Neptunomonas qingdaonensis P10-2-4(T). The strain could be differentiated phenotypically from recognized members of the family Oceanospirillaceae. The major fatty acids of strain K2-48(T) were identified as summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and C16:0 as defined by the MIDI system. The DNA G+C content was determined to be 43.2 mol%, the major respiratory quinone was identified as ubiquinone 9 and a polar lipid profile was present consisting of phosphatidylethanolamine, a phosphatidylglycerol and an unidentified phospolipid. On the basis of polyphasic taxonomic studies, it was concluded that strain K2-48(T) represents a novel genus sp. We propose the name Pelagitalea pacifica gen. nov., sp. nov. for this strain; its type strain is K2-48(T) (=KCCM 90119(T)). PMID:25487119

  14. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

    SciTech Connect

    Billings, Andrew F.; Fortney, Julian L.; Hazen, Terry C.; Simmons, Blake; Davenport, Karen W.; Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanja; DeAngelis, Kristen M.

    2015-11-19

    Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. Finally, by characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.

  15. Cyclodextrin glycosyltransferase production by new Bacillus sp. strains isolated from brazilian soil

    PubMed Central

    Menocci, Vivian; Goulart, Antonio José; Adalberto, Paulo Roberto; Tavano, Olga Luisa; Marques, Daniela Parreira; Contiero, Jonas; Monti, Rubens

    2008-01-01

    Three strains of Bacillus sp. (BACRP, BACNC-1 and BACAR) were isolated from soil adhered to cassava husk. CGTase specific activity for the three isolated strains was higher when cultivated at 40°C. Potato starch, cassava starch, maltodextrin and glucose were used as carbon source and growth temperatures varied from 25 to 55°C. The three isolates presented higher CGTase specific activity when cultivated with potato starch at 40°C. Isolated BACRP and BACAR presented specific activity of 4.0×10–3 and 2.2×10–3 U/mg prot at pH 7.0, respectively, when cultivated in mediums added with NaCl 2%; at pH 10,0 their activities were of 3.4×10–3 and 3.0×10–3 U/mg prot, respectively, in the same concentration of NaCl. On the other hand, the isolated BACNC-1 presented activity specific of 2.4×10–3 U/mg prot when cultivated at pH 7.0 added of NaCl 1%, and at pH 10.0 the specific activity was of 3.4×10–3 U/mg prot without NaCl addition. This work also showed the presence of cyclodextrins formed during fermentation process and that precipitation with acetone or lyophilization followed by dialysis was efficient at removing CDs (cyclodextrins), thus, eliminating interference in the activity assays. The enzyme produced by the BACAR strain was partially purified and β-CD was liberated as a reaction product. PMID:24031289

  16. Characterization of a novel lipase from Bacillus sp. isolated from tannery wastes

    PubMed Central

    Ghori, M. I.; Iqbal, M. J.; Hameed, A.

    2011-01-01

    Kinetics of a lipase isolated from Bacillus sp. was studied. The enzyme showed maximum activity at pH 9 and temperature 60°C. The Michaelis constant (KM 0.31 mM) obtained from three different plots i.e., Lineweaver-Burk, Hanes-Wolf and Hofstee, was found to be lower than already reported lipases that confirmed higher affinity of the enzyme for its substrate p-NPL (p-nitrophenyl laurate). Vmax of the enzyme was found to be 7.6 µM/mL/min. Energy of activation calculated from Arrhenius plot was found to be 20.607 kJmol−1. Activation enthalpy (ΔH*) had negative trend and the value for the hydrolysis of p-NPL by the enzyme at optimum temperature was −2.748 kJmol−1. Activation entropy (ΔS*) and free energy of activation (ΔG*) of the enzyme were found to be 1.468 Jmol−1K−1 and −3.237 kJmol−1, respectively at optimum temperature. Low value of Q10 (0.04788) shows high catalytic activity of the enzyme. Mn2+, Fe2+ and Mg2+ enhanced the lipase activity whereas Cu2+, Na+ and Co2+ inhibited the enzyme activity. However, the enzyme activity was not affected significantly by K+ ions. EDTA and SDS also significantly inhibited the lipase activity. Activity of the enzyme was increased in n-hexane while decreased with increase in concentration of acetone, chloroform, ethanol and isopropanol. PMID:24031600

  17. Hyperstabilization of Tetrameric Bacillus sp. TB-90 Urate Oxidase by Introducing Disulfide Bonds through Structural Plasticity.

    PubMed

    Hibi, Takao; Kume, Asami; Kawamura, Akie; Itoh, Takafumi; Fukada, Harumi; Nishiya, Yoshiaki

    2016-02-01

    Bacillus sp. TB-90 urate oxidase (BTUO) is one of the most thermostable homotetrameric enzymes. We previously reported [Hibi, T., et al. (2014) Biochemistry 53, 3879-3888] that specific binding of a sulfate anion induced thermostabilization of the enzyme, because the bound sulfate formed a salt bridge with two Arg298 residues, which stabilized the packing between two β-barrel dimers. To extensively characterize the sulfate-binding site, Arg298 was substituted with cysteine by site-directed mutagenesis. This substitution markedly increased the protein melting temperature by ∼ 20 °C compared with that of the wild-type enzyme, which was canceled by reduction with dithiothreitol. Calorimetric analysis of the thermal denaturation suggested that the hyperstabilization resulted from suppression of the dissociation of the tetramer into the two homodimers. The crystal structure of R298C at 2.05 Å resolution revealed distinct disulfide bond formation between the symmetrically related subunits via Cys298, although the Cβ distance between Arg298 residues of the wild-type enzyme (5.4 Å apart) was too large to predict stable formation of an engineered disulfide cross-link. Disulfide bonding was associated with local disordering of interface loop II (residues 277-300), which suggested that the structural plasticity of the loop allowed hyperstabilization by disulfide formation. Another conformational change in the C-terminal region led to intersubunit hydrogen bonding between Arg7 and Asp312, which probably promoted mutant thermostability. Knowledge of the disulfide linkage of flexible loops at the subunit interface will help in the development of new strategies for enhancing the thermostabilization of multimeric proteins. PMID:26739254

  18. Chromium isotopic fractionation during Cr(VI) reduction by Bacillus sp. under aerobic conditions.

    PubMed

    Xu, Fen; Ma, Teng; Zhou, Lian; Hu, Zhifang; Shi, Liu

    2015-07-01

    This study investigated the fractionation of chromium isotopes during chromium reduction by Bacillus sp. under aerobic condition, variable carbon source (glucose) concentration (0, 0.1, 1, 2.5 and 10mM), and incubation temperatures (4, 15, 25 and 37°C). The results revealed that the δ(53)Cr values in the residual Cr(VI) increased with the degree of Cr reduction, and followed a Rayleigh fractionation model. The addition of glucose only slightly affected cell-specific Cr(VI) reduction rates (cSRR). However, the value of ε (2.00±0.21‰) in the experiments with different concentrations of glucose (0.1, 1, 2.5 and 10mM) was smaller than that from the experiment without glucose (3.74±0.16‰). The results indicated that the cell-specific reduction rate is not the sole control on the degree of isotopic fractionation, and different metabolic pathways would result in differing degrees of Cr isotopic fractionation. The cSRR decreased with decreasing temperature, showing that the values of ε were 7.62±0.36‰, 4.59±0.28‰, 3.09±0.16‰ and 1.99±0.23‰ at temperatures of 4, 15, 25 and 37°C, respectively. It shown that increasing cSRR linked to decreasing fractionations has been associated with increasing temperatures. Overall, our results revealed that temperature is a primary factor affecting Cr isotopic fractionation under microbial actions. PMID:25777078

  19. Horizontal transmission of the symbiotic bacterium Asaia sp. in the leafhopper Scaphoideus titanus Ball (Hemiptera: Cicadellidae)

    PubMed Central

    2012-01-01

    Background Bacteria of the genus Asaia have been recently recognized as secondary symbionts of different sugar-feeding insects, including the leafhopper Scaphoideus titanus, vector of Flavescence dorée phytoplasmas. Asaia has been shown to be localized in S. titanus gut, salivary glands and gonoducts and to be maternally transmitted to the progeny by an egg smearing mechanism. It is currently not known whether Asaia in S. titanus is transmitted by additional routes. We performed a study to evaluate if Asaia infection is capable of horizontal transmission via co-feeding and venereal routes. Results A Gfp-tagged strain of Asaia was provided to S. titanus individuals to trace the transmission pathways of the symbiotic bacterium. Co-feeding trials showed a regular transfer of bacterial cells from donors to recipients, with a peak of frequency after 72 hours of exposure, and with concentrations of the administrated strain growing over time. Venereal transmission experiments were first carried out using infected males paired with uninfected females. In this case, female individuals acquired Gfp-labelled Asaia, with highest infection rates 72-96 hours after mating and with increasing abundance of the tagged symbiont over time. When crosses between infected females and uninfected males were conducted, the occurrence of “female to male” transmission was observed, even though the transfer occurred unevenly. Conclusions The data presented demonstrate that the acetic acid bacterial symbiont Asaia is horizontally transmitted among S. titanus individuals both by co-feeding and venereal transmission, providing one of the few direct demonstrations of such a symbiotic transfer in Hemiptera. This study contributes to the understanding of the bacterial ecology in the insect host, and indicates that Asaia evolved multiple pathways for the colonization of S. titanus body. PMID:22376056

  20. A novel compound from the marine bacterium Bacillus pumilus S6-15 inhibits biofilm formation in gram-positive and gram-negative species.

    PubMed

    Nithya, Chari; Devi, Muthu Gokila; Karutha Pandian, Shunmugiah

    2011-05-01

    Biofilm formation is a critical problem in nosocomial infections and in the aquaculture industries and biofilms show high resistance to antibiotics. The aim of the present study was to reveal a novel anti-biofilm compound from marine bacteria against antibiotic resistant gram-positive and gram-negative biofilms. The bacterial extract (50 μg ml(-1)) of S6-01 (Bacillus indicus = MTCC 5559) showed 80-90% biofilm inhibition against Escherichia coli, Shigella flexneri, Proteus mirabilis and S6-15 (Bacillus pumilus = MTCC 5560) showed 80-95% biofilm inhibition against all the 10 tested organisms. Furthermore, they also reduced the hydrophobicity index and extracellular polymeric substances (EPS) production. Structural elucidation of the active principle in S6-15 using GC-MS, (1)H NMR, and (13)C NMR spectral data revealed it to be 4-phenylbutanoic acid. This is the first report of 4-phenylbutanoic acid as a natural product. The purified compound (10-15 μg ml(-1)) showed potential activity against a wide range of biofilms. This study for the first time, reports a novel anti-biofilm compound from a marine bacterium with wide application in medicine and the aquaculture industry. PMID:21614700