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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).

  2. 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.

  3. Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium.

    PubMed

    Manickam, Natesan; Singh, Nitin Kumar; Bajaj, Abhay; Kumar, Rajendran Mathan; Kaur, Gurwinder; Kaur, Navjot; Bala, Monu; Kumar, Anand; Mayilraj, Shanmugam

    2014-07-01

    The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01% yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54T differs from all other species of Bacillus by at least 2.1% at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9%) followed by Bacillus infantis (97.7%), Bacillus firmus (97.4%), Bacillus drentensis (97.3%), Bacillus circulans (97.2%), Bacillus soli (97.1%), Bacillus horneckiae (97.1%), Bacillus pocheonensis (97.1%) and Bacillus bataviensis (97.1%), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4%) and anteiso-C15:0 (27.4%). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54T with its phylogenetic relatives and suggest that the strain IITR-54T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54T (=MTCC 11060T=JCM 19208T).

  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.

  5. Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains L-lysine in its cell wall.

    PubMed

    Lee, Jae-Chan; Lim, Jee-Min; Park, Dong-Jin; Jeon, Che Ok; Li, Wen-Jun; Kim, Chang-Jin

    2006-08-01

    A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724(T), was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724(T) grew at salinities of 0-10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15-50 degrees C with an optimum of 40 degrees C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724(T) belonged to the genus Bacillus and that Bacillus aquimaris TF-12(T), Bacillus marisflavi TF-11(T) and Bacillus vietnamensis JCM 11124(T) were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(16 : 0) and iso-C(14 : 0). The peptidoglycan type was A1alpha, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724(T) represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724(T) (=KCTC 3913(T)=DSM 16464(T)).

  6. Bacillus thermotolerans sp. nov., a thermophilic bacterium capable of reducing humus.

    PubMed

    Yang, Guiqin; Zhou, Xuemei; Zhou, Shungui; Yang, Dehui; Wang, Yueqiang; Wang, Dingmei

    2013-10-01

    A novel thermotolerant bacterium, designated SgZ-8(T), was isolated from a compost sample. Cells were non-motile, endospore-forming, Gram-staining positive, oxidase-negative and catalase-positive. The isolate was able to grow at 20-65 °C (optimum 50 °C) and pH 6.0-9.0 (optimum 6.5-7.0), and tolerate up to 9.0 % NaCl (w/v) under aerobic conditions. Anaerobic growth occurred with anthraquinone-2,6-disulphonate (AQDS), fumarate and NO3(-) as electron acceptors. Phylogenetic analysis based on the16S rRNA and gyrB genes grouped strain SgZ-8(T) into the genus Bacillus, with the highest similarity to Bacillus badius JCM 12228(T) (96.2 % for 16S rRNA gene sequence and 83.5 % for gyrB gene sequence) among all recognized species in the genus Bacillus. The G+C content of the genomic DNA was 49.3 mol%. The major isoprenoid quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The major cellular fatty acid was iso-C16 : 0. On the basis of its phenotypic and phylogenetic properties, chemotaxonomic analysis and the results of physiological and biochemical tests, strain SgZ-8(T) ( = CCTCC AB 2012108(T) = KACC 16706(T)) was designated the type strain of a novel species of the genus Bacillus, for which the name Bacillus thermotolerans sp. nov. is proposed.

  7. Bacillus salitolerans sp. nov., a novel bacterium isolated from a salt mine in Xinjiang province, China.

    PubMed

    Zhang, Wei-Yan; Hu, Jing; Zhang, Xin-Qi; Zhu, Xu-Fen; Wu, Min

    2015-08-01

    A novel aerobic bacterium, KC1(T), was isolated from a salt mine in Kuche county, Xinjiang province, China. Cells were observed to be Gram-positive, rod-shaped, endospore-forming and motile with flagella. Strain KC1(T) was found to grow at 25-45 °C (optimum 37 °C), pH 6.5-9.0 (optimum 8.0) and NaCl 0-10 % (v/v) (optimum 4 %). The major fatty acids were identified as anteiso-C15:0 and anteiso-C17:0. Menaquinone-7 (MK-7) was found to be the predominant isoprenoid quinone. The cell-wall diamino acid was found to be meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol and a glycolipid. The 16S rRNA gene sequence of strain KC1(T) showed low similarity (<96 %) to other validly named species. The phylogenetic trees showed that strain KC1(T) is closely related to Bacillus azotoformans DSM 1046(T) and Bacillus methanolicus DSM 16454(T). Both these type strains showed 95.4 % 16S rRNA gene sequence similarity to strain KC1(T). The DNA G+C content of strain KC1(T) was determined to be 39.0 mol%. On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain KC1(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus salitolerans sp. nov. is proposed. The type strain is KC1(T) (=JCM 19760(T) = CGMCC 1.12810(T)).

  8. 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)).

  9. "Bacillus hackensackii" sp. nov., a novel carbon dioxide sensitive bacterium isolated from blood culture.

    PubMed

    Hong, Tao; Heibler, Nueda; Tang, Y i-Wei

    2003-02-01

    An endospore-forming, gram-positive bacillus was isolated from a patient's blood culture. This bacillus did not grow in the presence of 5% carbon dioxide although it grew well in ambient air at 37 degrees C. Although the organism thus is an aerobic bacterium, its sensitivity to increased carbon dioxide concentration places it in a distinct category of gaseous atmospheric requirement: capnophobic. Based on its morphology, growth characteristics, biochemical reactions and a complete 16S rRNA gene nucleotide sequence analysis, this microorganism represents a novel Bacillus species. The clinical significance of this isolate is unknown. It is proposed that the bacterium be classified in the genus Bacillus as "Bacillus hackensackii".

  10. 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)).

  11. 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.

  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. Rapid aggregation of biofuel-producing algae by the bacterium Bacillus sp. strain RP1137.

    PubMed

    Powell, Ryan J; Hill, Russell T

    2013-10-01

    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.

  14. 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

  15. Genome sequence of the aerobic bacterium Bacillus sp. strain FJAT-13831.

    PubMed

    Liu, Guohong; Liu, Bo; Lin, Naiquan; Tang, Weiqi; Tang, Jianyang; Lin, Yingzhi

    2012-12-01

    Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's Terracotta Warriors in Xi'an City, People's Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%.

  16. Genome Sequence of the Aerobic Bacterium Bacillus sp. Strain FJAT-13831

    PubMed Central

    Liu, Guohong; Lin, Naiquan; Tang, Weiqi; Tang, Jianyang; Lin, Yingzhi

    2012-01-01

    Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's Terracotta Warriors in Xi'an City, People's Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%. PMID:23144388

  17. 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.

  18. 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.

  19. 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)).

  20. Bacillus methylotrophicus sp. nov., a methanol-utilizing, plant-growth-promoting bacterium isolated from rice rhizosphere soil.

    PubMed

    Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Kwon, Soon-Wo; Sa, Tong-Min

    2010-10-01

    A Gram-positive bacterium, designated strain CBMB205(T), was isolated from the rhizosphere soil of traditionally cultivated, field-grown rice. Cells were strictly aerobic, motile, rod-shaped and formed endospores. The best growth was achieved at 30°C and pH 7.0 in ammonium mineral salts (AMS) medium containing 600 mM methanol. A comparative 16S rRNA gene sequence-based phylogenetic analysis placed strain CBMB205(T) in a clade with the species Bacillus amyloliquefaciens, Bacillus vallismortis, Bacillus subtilis, Bacillus atrophaeus, Bacillus mojavensis and Bacillus licheniformis and revealed pairwise similarities ranging from 98.2 to 99.2 %. DNA-DNA hybridization experiments revealed a low level (<36 %) of DNA-DNA relatedness between strain CBMB205(T) and its closest relatives. The major components of the fatty acid profile were C₁₅:₀ anteiso, C₁₅:₀ iso, C₁₆:₀ iso and C₁₇:₀ anteiso. The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 45.0 mol%. The lipids present in strain CBMB205(T) were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. The 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 enabled strain CBMB205(T) to be described as representing a novel species of the genus Bacillus, for which the name Bacillus methylotrophicus sp. nov. is proposed. The type strain is CBMB205(T) (=KACC 13105(T)=NCCB 100236(T)).

  1. Bacillus sp. strain DJ-1, potent arsenic hypertolerant bacterium isolated from the industrial effluent of India.

    PubMed

    Joshi, Dhaval N; Flora, S J S; Kalia, Kiran

    2009-07-30

    Arsenic hypertolerant bacterial cells were isolated from the common industrial effluent treatment plant, Vapi, India. Strain DJ-1 sustaining 400 mM, As (V) out of 16 bacterial strains was identified as Bacillus sp. strain DJ-1 through 16S rRNA ribotyping. The maximum arsenic accumulation of 9.8+/-0.5 mg g(-1) (dry weight) was observed during stationary phase of growth. Intracellular compartmentalization has shown 80% of arsenic accumulation in cytoplasm. The lack of arsC gene and arsenate reductase activity indicated that Bacillus sp. strain DJ-1 may lack classical ars operon and detoxification may be mediated through some novel mechanism. The arsenite binding protein was purified by affinity chromatography and characterized as DNA protection during starvation (DPS) protein by electrospray ionization mass spectrometry. The induction of DPS showed the adaptation of bacteria in arsenic stress condition and/or in detoxification mechanism, relies on its ability to bind with arsenic. These results indicate the hypertolerance with higher intracellular accumulation of arsenic by Bacillus sp. strain DJ-1, which could be mediated by DPS protein thus signifying this organism is a potential candidate for the removal of arsenic from industrial wastewater, which needs further study.

  2. 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)).

  3. 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.

  4. 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)).

  5. Bacillus caseinilyticus sp. nov., an alkali- and thermotolerant bacterium isolated from a soda lake.

    PubMed

    Vishnuvardhan Reddy, Sultanpuram; Thirumala, Mothe; Farooq, Mohammed

    2015-08-01

    A novel Gram-stain-positive, rod-shaped, motile, endospore-forming and proteolytic bacterial strain, SPT, was isolated from Lonar soda lake, in India. On the basis of 16S rRNA gene sequence analysis it was identified as belonging to the class Firmibacteria and was most closely related to Bacillus cellulosilyticus DSM 2522T (96.7%) and other members of the genus Bacillus ( < 95.9%). Strain SPT was catalase- and oxidase-positive. The cell-wall peptidoglycan of strain SPT contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three phospholipids, two aminolipids and two unknown lipids. The predominant isoprenoid quinone was MK-7. Anteiso-C15 : 0 (26.8%) was the predominant fatty acid and significant proportions (>5%) of iso-C15 : 0 (20.9%), C16 : 1ω7c alcohol (6.3%), iso-C16 : 0 (6.3%) and anteiso-C17 : 0 (5.3  %) were also detected in strain SPT. The DNA G+C content of strain SPT was 38.9 mol%. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain SPT from all other members of the genus Bacillus. Strain SPT represents a novel member of the genus Bacillus, for which the name Bacilluscaseinilyticus sp. nov. is proposed. The type strain is SPT ( = MCC 2612T = JCM 30246T).

  6. Bacillus dabaoshanensis sp. nov., a Cr(VI)-tolerant bacterium isolated from heavy-metal-contaminated soil.

    PubMed

    Cui, Xiaowen; Wang, Yueqiang; Liu, Jing; Chang, Ming; Zhao, Yong; Zhou, Shungui; Zhuang, Li

    2015-05-01

    A Cr(VI)-tolerant, Gram-staining-positive, rod-shaped, endospore-forming and facultative anaerobic bacterium, designated as GSS04(T), was isolated from a heavy-metal-contaminated soil. Strain GSS04(T) was Cr(VI)-tolerant with a minimum inhibitory concentration of 600 mg l(-1) and was capable of reducing Cr(VI) under both aerobic and anaerobic conditions. Growth occurred with presence of 0-3 % (w/v) NaCl (optimum 1 %), at pH 5.5-10.0 (optimum pH 7.0) and 15-50 °C (optimum 30-37 °C). The main respiratory quinone was MK-7 and the major fatty acids were anteiso-C15:0 and iso-C15:0. The DNA G+C content was 41.1 mol%. The predominant polar lipid was diphosphatidylglycerol. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relative was Bacillus shackletonii DSM 18868(T) (97.6 %). The DNA-DNA hybridization between GSS04(T) and its closest relatives revealed low relatedness (<70 %). The results of phenotypic, chemotaxonomic and genotypic analyses clearly indicated that strain GSS04(T) represents a novel species of the genus Bacillus, for which the name Bacillus dabaoshanensis sp. nov. is proposed. The type strain is GSS04(T) (=CCTCC AB 2013260(T) = KCTC 33191(T)).

  7. 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)).

  8. Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni.

    PubMed

    Lee, Jae-Bong; Jeon, Seon Hwa; Choi, Seok-Gwan; Jung, Hee-Young; Kim, Myung Kyum; Srinivasan, Sathiyaraj

    2016-12-01

    In this paper, a new bacterial strain designated as 16MFT21(T) is isolated from the muscle of a fish caught in the Antarctic Ocean. Strain 16MFT21(T) is a Gram-staining-positive, catalase-oxidase-positive, rod-shaped facultative-aerobic bacterium. The phylogenetic analysis that is based on the 16S-rRNA gene sequence of strain 16MFT21(T) revealed that it belongs to the genus Bacillus in the family Bacillaceae in the class Bacilli. The highest degrees of the sequence similarity of the strain 16MFT21(T) is with Bacillus licheniformis ATCC 14580(T) (96.6%) and Bacillus sonorensis NBRC 101234(T) (96.6%). The isolate formed a pale-yellow pigment, and it grew in the presence of 0% to 10% (w/v) NaCl (optimum at 2% NaCl), a pH of 6.0 to 10.0 (optimum pH from 7.0 to 8.0), and from 4°C to 30°C (optimum at 30°C). The major polar lipids consist of diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG). The predominant fatty acids are iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The main respiratory quinone is menaquinone-7 (MK-7), and based on the use of the meso-diaminopimelic acid as the diagnostic diamino acid, the peptidoglycan cell-wall type is A1γ. Based on the phylogenetic, phenotypic, and chemotaxonomic data, strain 16MFT21(T) (=KCTC 18866(T) =JCM 31664(T)) for which the name Bacillus piscis sp. nov. is proposed should be classified as a new species.

  9. 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).

  10. Bacillus eiseniae sp. nov., a swarming, moderately halotolerant bacterium isolated from the intestinal tract of an earthworm (Eisenia fetida L.).

    PubMed

    Hong, Sung Wook; Park, Jung Min; Kim, Soo-Jin; Chung, Kun Sub

    2012-09-01

    A swarming and moderately halotolerant bacterium, designated strain A1-2(T), was isolated from the intestinal tract of the earthworm Eisenia fetida L. Cells were endospore-forming rods that were facultatively anaerobic, catalase-positive, oxidase-negative and motile by peritrichous flagella. The isolate grew optimally at 30 °C and pH 7.0, and could grow with up to 9 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain A1-2(T) belonged to the genus Bacillus and exhibited 16S rRNA gene sequence similarities of 96.8, 96.0, 96.0, 96.4 and 96.7 % with Bacillus drentensis LMG 21831(T), B. horneckiae PT-45(T), B. niacini BAC 1015, B. infantis SMC 4352-1(T) and B. shackletonii LMG 18435(T), respectively. DNA-DNA relatedness values between the isolate and the reference strains were ≤ 38.3 %. The DNA G+C content of strain A1-2(T) was 38.5 mol%. The predominant menaquinone was MK-7 and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C(15 : 0) (51.5 %) and anteiso-C(15 : 0) (29.6 %) and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and phenotypic characteristics, it is concluded that strain A1-2(T) represents a novel species of the genus Bacillus, for which we propose the name Bacillus eiseniae sp. nov. The type strain is A1-2(T) (= KCCM 90092(T) = JCM 16993(T)).

  11. Characterization and Potential Applications of a Selenium Nanoparticle Producing and Nitrate Reducing Bacterium Bacillus oryziterrae sp. nov.

    NASA Astrophysics Data System (ADS)

    Bao, Peng; Xiao, Ke-Qing; Wang, Hui-Jiao; Xu, Hao; Xu, Peng-Peng; Jia, Yan; Häggblom, Max M.; Zhu, Yong-Guan

    2016-09-01

    A novel nitrate- and selenite reducing bacterium strain ZYKT was isolated from a rice paddy soil in Dehong, Yunnan, China. Strain ZYKT is a facultative anaerobe and grows in up to 150, 000 ppm O2. The comparative genomics analysis of strain ZYKT implies that it shares more orthologues with B. subtilis subsp. subtilis NCIB 3610T (ANIm values, 85.4–86.7%) than with B. azotoformans NBRC 15712T (ANIm values, 84.4–84.7%), although B. azotoformans NBRC 15712T (96.3% 16S rRNA gene sequence similarity) is the closest Bacillus species according to 16S rRNA gene comparison. The major cellular fatty acids of strain ZYKT were iso-C14:0 (17.8%), iso-C15:0 (17.8%), and C16:0 (32.0%). The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. Based on physiological, biochemical and genotypic properties, the strain was considered to represent a novel species of the genus Bacillus, for which the name Bacillus oryziterrae sp. nov. is proposed. The type strain is ZYKT (=DSM 26460T =CGMCC 1.5179T). Strain ZYKT can reduce nitrate to nitrite and ammonium and possesses metabolic genes for nitrate reduction including nar, nap and nrf. Biogenic selenium nanoparticles of strain ZYKT show a narrow size distribution and agree with the gaussian distribution. These selenium nanoparticles show significant dose-dependent inhibition of the lung cancer cell line H157, which suggests potential for application in cancer therapy.

  12. Characterization and Potential Applications of a Selenium Nanoparticle Producing and Nitrate Reducing Bacterium Bacillus oryziterrae sp. nov.

    PubMed Central

    Bao, Peng; Xiao, Ke-Qing; Wang, Hui-Jiao; Xu, Hao; Xu, Peng-Peng; Jia, Yan; Häggblom, Max M.; Zhu, Yong-Guan

    2016-01-01

    A novel nitrate- and selenite reducing bacterium strain ZYKT was isolated from a rice paddy soil in Dehong, Yunnan, China. Strain ZYKT is a facultative anaerobe and grows in up to 150, 000 ppm O2. The comparative genomics analysis of strain ZYKT implies that it shares more orthologues with B. subtilis subsp. subtilis NCIB 3610T (ANIm values, 85.4–86.7%) than with B. azotoformans NBRC 15712T (ANIm values, 84.4–84.7%), although B. azotoformans NBRC 15712T (96.3% 16S rRNA gene sequence similarity) is the closest Bacillus species according to 16S rRNA gene comparison. The major cellular fatty acids of strain ZYKT were iso-C14:0 (17.8%), iso-C15:0 (17.8%), and C16:0 (32.0%). The polar lipid profile consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. Based on physiological, biochemical and genotypic properties, the strain was considered to represent a novel species of the genus Bacillus, for which the name Bacillus oryziterrae sp. nov. is proposed. The type strain is ZYKT (=DSM 26460T =CGMCC 1.5179T). Strain ZYKT can reduce nitrate to nitrite and ammonium and possesses metabolic genes for nitrate reduction including nar, nap and nrf. Biogenic selenium nanoparticles of strain ZYKT show a narrow size distribution and agree with the gaussian distribution. These selenium nanoparticles show significant dose-dependent inhibition of the lung cancer cell line H157, which suggests potential for application in cancer therapy. PMID:27677458

  13. NMR structural study of fructans produced by Bacillus sp. 3B6, bacterium isolated in cloud water.

    PubMed

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

    2011-03-01

    Bacillus sp. 3B6, bacterium isolated from cloud water, was incubated on sucrose for exopolysaccharide production. Dialysis of the obtained mixture (MWCO 500) afforded dialyzate (DIM) and retentate (RIM). Both were separated by size exclusion chromatography. RIM afforded eight fractions: levan exopolysaccharide (EPS), fructooligosaccharides (FOSs) of levan and inulin types with different degrees of polymerization (dp 2-7) and monosaccharides fructose:glucose=9:1. Levan was composed of two components with molecular mass ~3500 and ~100kDa in the ratio 2.3:1. Disaccharide fraction contained difructose anhydride DFA IV. 1-Kestose, 6-kestose, and neokestose were identified as trisaccharides in the ratio 2:1:3. Fractions with dp 4-7 were mixtures of FOSs of levan (2,6-βFruf) and inulin (1,2-βFruf) type. DIM separation afforded two dominant fractions: monosaccharides with fructose: glucose ratio 1:3; disaccharide fraction contained sucrose only. DIM trisaccharide fraction contained 1-kestose, 6-kestose, and neokestose in the ratio1.5:1:2, penta and hexasaccharide fractions contained FOSs of levan type (2,6-βFruf) containing α-glucose. In the pentasaccharide fraction also the presence of a homopentasaccharide composed of 2,6-linked βFruf units only was identified. Nystose, inulin (1,2-βFruf) type, was identified as DIM tetrasaccharide. Identification of levan 2,6-βFruf and inulin 1,2-βFruf type oligosaccharides in the incubation medium suggests both levansucrase and inulosucrase enzymes activity in Bacillus sp. 3B6.

  14. Draft Genome Sequence of a Polydroxyalkanoate-Synthesizing Bacterium, Bacillus sp. Strain PJC48, Isolated from Activated Sludge

    PubMed Central

    Gu, Jin-Jin; Zhou, Ying; Lu, Jian-Jiang

    2017-01-01

    ABSTRACT The genome sequence of a Bacillus strain is capable of synthesizing polyhydroxyalkanoates, and Bacillus sp. is considered a platform strain for the production of many biodegradable materials. Here, we present the sequence of the PJC48 strain genome, which is composed of three chromatin structures, an extracellular structure, and a cytoskeleton. PMID:28280031

  15. Laboratory-scale continuous reactor for soluble selenium removal using selenate-reducing bacterium, Bacillus sp. SF-1.

    PubMed

    Fujita, Masanori; Ike, Michihiko; Kashiwa, Masami; Hashimoto, Ryoko; Soda, Satoshi

    2002-12-30

    A model continuous flow bioreactor (volume 0.5 L) was constructed for removing toxic soluble selenium (selenate/selenite) of high concentrations using a selenate-reducing bacterium, Bacillus sp. SF-1, which transforms selenate into elemental selenium via selenite for anaerobic respiration. Model wastewater contained 41.8 mg-Se/L selenate and excess lactate as the carbon and energy source; the bioreactor was operated as an anoxic, completely mixed chemostat with cell retention time between 2.2-95.2 h. At short cell retention times selenate was removed by the bioreactor, but accumulation of selenite was observed. At long cell retention times soluble selenium, both selenate and selenite, was successfully reduced into nontoxic elemental selenium. A simple mathematical model is proposed to evaluate Se reduction ability of strain SF-1. First-order kinetic constants for selenate and selenite reduction were estimated to be 2.9 x 10(-11) L/cells/h and 5.5 x 10(-13) L/cells/h, respectively. The yield of the bacterial cells by selenate reduction was estimated to be 2.2 x 10(9) cells/mg-Se.

  16. 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) ).

  17. Dimethyl disulfide produced by the naturally associated bacterium bacillus sp B55 promotes Nicotiana attenuata growth by enhancing sulfur nutrition.

    PubMed

    Meldau, Dorothea G; Meldau, Stefan; Hoang, Long H; Underberg, Stefanie; Wünsche, Hendrik; Baldwin, Ian T

    2013-07-01

    Bacillus sp B55, a bacterium naturally associated with Nicotiana attenuata roots, promotes growth and survival of wild-type and, particularly, ethylene (ET)-insensitive (35)S-ethylene response1 (etr1) N. attenuata plants, which heterologously express the mutant Arabidopsis thaliana receptor ETR1-1. We found that the volatile organic compound (VOC) blend emitted by B55 promotes seedling growth, which is dominated by the S-containing compound dimethyl disulfide (DMDS). DMDS was depleted from the headspace during cocultivation with seedlings in bipartite Petri dishes, and (35)S was assimilated from the bacterial VOC bouquet and incorporated into plant proteins. In wild-type and (35)S-etr1 seedlings grown under different sulfate (SO(4)(-2)) supply conditions, exposure to synthetic DMDS led to genotype-dependent plant growth promotion effects. For the wild type, only S-starved seedlings benefited from DMDS exposure. By contrast, growth of (35)S-etr1 seedlings, which we demonstrate to have an unregulated S metabolism, increased at all SO(4)(-2) supply rates. Exposure to B55 VOCs and DMDS rescued many of the growth phenotypes exhibited by ET-insensitive plants, including the lack of root hairs, poor lateral root growth, and low chlorophyll content. DMDS supplementation significantly reduced the expression of S assimilation genes, as well as Met biosynthesis and recycling. We conclude that DMDS by B55 production is a plant growth promotion mechanism that likely enhances the availability of reduced S, which is particularly beneficial for wild-type plants growing in S-deficient soils and for (35)S-etr1 plants due to their impaired S uptake/assimilation/metabolism.

  18. Genome sequence of the leaf-colonizing Bacterium Bacillus sp. strain 5B6, isolated from a cherry tree.

    PubMed

    Kim, Byung Kwon; Chung, Joon-hui; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kwon, Soon-Kyeong; Lee, Choong Hoon; Song, Ju Yeon; Yu, Dong Su; Ryu, Choong-Min; Kim, Jihyun F

    2012-07-01

    Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb genome uncovers its potential for understanding the nature of leaf colonization as well as antibiosis against plant pathogens.

  19. Isolation, Identification, and Optimization of Culture Conditions of a Bioflocculant-Producing Bacterium Bacillus megaterium SP1 and Its Application in Aquaculture Wastewater Treatment.

    PubMed

    Luo, Liang; Zhao, Zhigang; Huang, Xiaoli; Du, Xue; Wang, Chang'an; Li, Jinnan; Wang, Liansheng; Xu, Qiyou

    2016-01-01

    A bioflocculant-producing bacterium, Bacillus megaterium SP1, was isolated from biofloc in pond water and identified by using both 16S rDNA sequencing analysis and a Biolog GEN III MicroStation System. The optimal carbon and nitrogen sources for Bacillus megaterium SP1 were 20 g L(-1) of glucose and 0.5 g L(-1) of beef extract at 30°C and pH 7. The bioflocculant produced by strain SP1 under optimal culture conditions was applied into aquaculture wastewater treatment. The removal rates of chemical oxygen demand (COD), total ammonia nitrogen (TAN), and suspended solids (SS) in aquaculture wastewater reached 64, 63.61, and 83.8%, respectively. The volume of biofloc (FV) increased from 4.93 to 25.97 mL L(-1). The addition of Bacillus megaterium SP1 in aquaculture wastewater could effectively improve aquaculture water quality, promote the formation of biofloc, and then form an efficient and healthy aquaculture model based on biofloc technology.

  20. Isolation, Identification, and Optimization of Culture Conditions of a Bioflocculant-Producing Bacterium Bacillus megaterium SP1 and Its Application in Aquaculture Wastewater Treatment

    PubMed Central

    Luo, Liang; Huang, Xiaoli; Du, Xue; Wang, Chang'an; Li, Jinnan; Wang, Liansheng

    2016-01-01

    A bioflocculant-producing bacterium, Bacillus megaterium SP1, was isolated from biofloc in pond water and identified by using both 16S rDNA sequencing analysis and a Biolog GEN III MicroStation System. The optimal carbon and nitrogen sources for Bacillus megaterium SP1 were 20 g L−1 of glucose and 0.5 g L−1 of beef extract at 30°C and pH 7. The bioflocculant produced by strain SP1 under optimal culture conditions was applied into aquaculture wastewater treatment. The removal rates of chemical oxygen demand (COD), total ammonia nitrogen (TAN), and suspended solids (SS) in aquaculture wastewater reached 64, 63.61, and 83.8%, respectively. The volume of biofloc (FV) increased from 4.93 to 25.97 mL L−1. The addition of Bacillus megaterium SP1 in aquaculture wastewater could effectively improve aquaculture water quality, promote the formation of biofloc, and then form an efficient and healthy aquaculture model based on biofloc technology. PMID:27840823

  1. Assessment of bioflocculant production by Bacillus sp. Gilbert, a marine bacterium isolated from the bottom sediment of Algoa Bay.

    PubMed

    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.

  2. 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

  3. 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

  4. 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)).

  5. Reuse of red seaweed waste by a novel bacterium, Bacillus sp. SYR4 isolated from a sandbar.

    PubMed

    Kang, Soyeon; Kim, Joong Kyun

    2015-01-01

    A potent bacterial strain was isolated from a sandbar and identified as Bacillus sp. SYR4 for the reuse of red seaweed waste. The isolate possessed both agarase and carrageenase activities. The optimal pH and temperature for the degradation of both agar and carrageenan by the isolate were found to be pH 7.5 and 30 °C, respectively. The effects of cations on cell growth and degradation ability of the isolate were significant in comparison with controls. The isolate produced 0.27 and 0.29 g l(-1) of reducing sugars from 1 g l(-1) of agar and carrageenan, respectively. When the isolate was cultivated in red seaweed powder medium for 10 days, the yield of reducing sugars was 24 %. As a result, the eco-friendly reuse of red seaweed waste by this isolate appears to be feasible for the production of reducing sugars and could be a valuable resource. To the best of our knowledge, this is the first study to directly demonstrate the ability of Bacillus sp. SYR4 to degrade both agar and carrageenan.

  6. 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)).

  7. Salipaludibacillus aurantiacus gen. nov., sp. nov. a novel alkali tolerant bacterium, reclassification of Bacillus agaradhaerens as Salipaludibacillus agaradhaerens comb. nov. and Bacillus neizhouensis as Salipaludibacillus neizhouensis comb. nov.

    PubMed

    Sultanpuram, Vishnuvardhan Reddy; Mothe, Thirumala

    2016-04-26

    Two novel (S9T and S12) Gram-stain-positive, rod shaped, non-motile and endospore forming bacteria were isolated from Narayan sarovar Lake, in India. The high 16S rRNA gene sequence similarity (99.9 %) and DNA-DNA relatedness (86 + 2 %) indicated that strains S9T and S12 were members of a single species. Based on the 16S rRNA gene sequence analysis these strains were identified as belonging to the class Firmibacteria and were most closely related to Bacillus agaradhaerens PN-105T (96.8 % sequence similarity), Bacillus neizhouensis JSM 071004T (96.5%) and Bacillus luteus JC167T (96.1%). However, these strains shared only 90.3 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that they might not be members of the genus Bacillus. The cell-wall peptidoglycan contains meso-diaminopimelic acid. Polar lipids include diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), one unknown phospholipid (PL1) and an unknown lipid (L1). The predominant isoprenoid quinone was MK-7. Major fatty acids (>5 %) include anteiso-C15:0, C16:0, iso-C15:0, anteiso- C17:0, iso-C16:0 and summed feature 3. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S9T and S12 from all other members of the family Bacillaceae, which represents a novel member of a new genus from the family Bacillaceae,, for which the name Salipaludibacillus aurantiacus gen. nov., sp. nov. is proposed. The type strain is S9T (= KCTC 33633T = LMG 28644T). Based on the present study, it is also proposed the transfer of Bacillus agaradhaerens and Bacillus neizhouensis to this new genus.

  8. A Sequential Statistical Approach towards an Optimized Production of a Broad Spectrum Bacteriocin Substance from a Soil Bacterium Bacillus sp. YAS 1 Strain

    PubMed Central

    Embaby, Amira M.; Heshmat, Yasmin; Hussein, Ahmed; Marey, Heba S.

    2014-01-01

    Bacteriocins, ribosomally synthesized antimicrobial peptides, display potential applications in agriculture, medicine, and industry. The present study highlights integral statistical optimization and partial characterization of a bacteriocin substance from a soil bacterium taxonomically affiliated as Bacillus sp. YAS 1 after biochemical and molecular identifications. A sequential statistical approach (Plackett-Burman and Box-Behnken) was employed to optimize bacteriocin (BAC YAS 1) production. Using optimal levels of three key determinants (yeast extract (0.48% (w/v), incubation time (62 hrs), and agitation speed (207 rpm)) in peptone yeast beef based production medium resulted in 1.6-fold enhancement in BAC YAS 1 level (470 AU/mL arbitrary units against Erwinia amylovora). BAC YAS 1 showed activity over a wide range of pH (1–13) and temperature (45–80°C). A wide spectrum antimicrobial activity of BAC YAS 1 against the human pathogens (Clostridium perfringens, Staphylococcus epidermidis, Campylobacter jejuni, Enterobacter aerogenes, Enterococcus sp., Proteus sp., Klebsiella sp., and Salmonella typhimurium), the plant pathogen (E. amylovora), and the food spoiler (Listeria innocua) was demonstrated. On top and above, BAC YAS 1 showed no antimicrobial activity towards lactic acid bacteria (Lactobacillus bulgaricus, L. casei, L. lactis, and L. reuteri). Promising characteristics of BAC YAS 1 prompt its commercialization for efficient utilization in several industries. PMID:25614886

  9. A sequential statistical approach towards an optimized production of a broad spectrum bacteriocin substance from a soil bacterium Bacillus sp. YAS 1 strain.

    PubMed

    Embaby, Amira M; Heshmat, Yasmin; Hussein, Ahmed; Marey, Heba S

    2014-01-01

    Bacteriocins, ribosomally synthesized antimicrobial peptides, display potential applications in agriculture, medicine, and industry. The present study highlights integral statistical optimization and partial characterization of a bacteriocin substance from a soil bacterium taxonomically affiliated as Bacillus sp. YAS 1 after biochemical and molecular identifications. A sequential statistical approach (Plackett-Burman and Box-Behnken) was employed to optimize bacteriocin (BAC YAS 1) production. Using optimal levels of three key determinants (yeast extract (0.48% (w/v), incubation time (62 hrs), and agitation speed (207 rpm)) in peptone yeast beef based production medium resulted in 1.6-fold enhancement in BAC YAS 1 level (470 AU/mL arbitrary units against Erwinia amylovora). BAC YAS 1 showed activity over a wide range of pH (1-13) and temperature (45-80 °C). A wide spectrum antimicrobial activity of BAC YAS 1 against the human pathogens (Clostridium perfringens, Staphylococcus epidermidis, Campylobacter jejuni, Enterobacter aerogenes, Enterococcus sp., Proteus sp., Klebsiella sp., and Salmonella typhimurium), the plant pathogen (E. amylovora), and the food spoiler (Listeria innocua) was demonstrated. On top and above, BAC YAS 1 showed no antimicrobial activity towards lactic acid bacteria (Lactobacillus bulgaricus, L. casei, L. lactis, and L. reuteri). Promising characteristics of BAC YAS 1 prompt its commercialization for efficient utilization in several industries.

  10. A native plant growth promoting bacterium, Bacillus sp. B55, rescues growth performance of an ethylene-insensitive plant genotype in nature

    PubMed Central

    Meldau, Dorothea G.; Long, Hoang H.; Baldwin, Ian T.

    2012-01-01

    Many plants have intimate relationships with soil microbes, which improve the plant’s growth and fitness through a variety of mechanisms. Bacillus sp. isolates are natural root-associated bacteria, isolated from Nicotiana attenuata plant roots growing in native soils. A particular isolate B55, was found to have dramatic plant growth promotion (PGP) effects on wild type (WT) and transgenic plants impaired in ethylene (ET) perception (35S-etr1), the genotype from which this bacterium was first isolated. B55 not only improves N. attenuata growth under in vitro, glasshouse, and field conditions, but it also “rescues” many of the deleterious phenotypes associated with ET insensitivity. Most notably, B55 dramatically increases the growth and survival of 35S-etr1 plants under field conditions. To our knowledge, this is the first demonstration of a PGP effect in a native plant–microbe association under natural conditions. Our study demonstrates that this facultative mutualistic plant–microbe interaction should be viewed as part of the plant’s extended phenotype. Possible modalities of recruitment and mechanisms of PGP are discussed. PMID:22701461

  11. Dimethyl Disulfide Produced by the Naturally Associated Bacterium Bacillus sp B55 Promotes Nicotiana attenuata Growth by Enhancing Sulfur Nutrition[W

    PubMed Central

    Meldau, Dorothea G.; Meldau, Stefan; Hoang, Long H.; Underberg, Stefanie; Wünsche, Hendrik; Baldwin, Ian T.

    2013-01-01

    Bacillus sp B55, a bacterium naturally associated with Nicotiana attenuata roots, promotes growth and survival of wild-type and, particularly, ethylene (ET)–insensitive 35S-ethylene response1 (etr1) N. attenuata plants, which heterologously express the mutant Arabidopsis thaliana receptor ETR1-1. We found that the volatile organic compound (VOC) blend emitted by B55 promotes seedling growth, which is dominated by the S-containing compound dimethyl disulfide (DMDS). DMDS was depleted from the headspace during cocultivation with seedlings in bipartite Petri dishes, and 35S was assimilated from the bacterial VOC bouquet and incorporated into plant proteins. In wild-type and 35S-etr1 seedlings grown under different sulfate (SO4−2) supply conditions, exposure to synthetic DMDS led to genotype-dependent plant growth promotion effects. For the wild type, only S-starved seedlings benefited from DMDS exposure. By contrast, growth of 35S-etr1 seedlings, which we demonstrate to have an unregulated S metabolism, increased at all SO4−2 supply rates. Exposure to B55 VOCs and DMDS rescued many of the growth phenotypes exhibited by ET-insensitive plants, including the lack of root hairs, poor lateral root growth, and low chlorophyll content. DMDS supplementation significantly reduced the expression of S assimilation genes, as well as Met biosynthesis and recycling. We conclude that DMDS by B55 production is a plant growth promotion mechanism that likely enhances the availability of reduced S, which is particularly beneficial for wild-type plants growing in S-deficient soils and for 35S-etr1 plants due to their impaired S uptake/assimilation/metabolism. PMID:23903320

  12. 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

  13. Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands.

    PubMed

    Heyrman, Jeroen; Vanparys, Bram; Logan, Niall A; Balcaen, An; Rodríguez-Díaz, Marina; Felske, Andreas; De Vos, Paul

    2004-01-01

    A group of 42 isolates were isolated from the soil of several disused hay fields, in the Drentse A agricultural research area (The Netherlands), that were taken out of production at different times. The group represents hitherto-uncultured Bacillus lineages that have previously been found, by a non-cultural method, to be predominant in soil. The strains were subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA sequence analysis, DNA-DNA hybridizations, DNA base-ratio determination, fatty acid analysis and morphological and biochemical characterization. By comparing the groupings obtained by (GTG)5-PCR and 16S rDNA sequence analysis, six clusters of similar strains could be recognized. A DNA-DNA relatedness study showed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus, namely Bacillus novalis sp. nov. (type strain IDA3307T=R-15439T=LMG 21837T=DSM 15603T), Bacillus vireti sp. nov. (type strain IDA3632T=R-15447T=LMG 21834T=DSM 15602T), Bacillus soli sp. nov. (type strain IDA0086T=R-16300T=LMG 21838T=DSM 15604T), Bacillus bataviensis sp. nov. (type strain IDA1115T=R-16315T=LMG 21833T=DSM 15601T) and Bacillus drentensis sp. nov. (type strain IDA1967T=R-16337T=LMG 21831T=DSM 15600T).

  14. Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov.

    PubMed

    Banat, Ibrahim M; Marchant, Roger; Rahman, Thahira J

    2004-11-01

    Several aerobic, motile, rod-shaped, thermophilic, spore-forming Geobacillus bacteria predominantly giving a Gram-positive staining reaction were isolated from a cool soil environment in Northern Ireland and taxonomically investigated. Two isolates, F10 and Tf(T), showed low 16S rRNA gene sequence similarity to recognized members of the genus Geobacillus. Phylogenetic tree investigation using neighbour-joining, maximum-likelihood and parsimony methods indicated that strains F10 and Tf(T) represent a single novel species, for which the name Geobacillus debilis sp. nov. is proposed, with type strain Tf(T) (=DSM 16016(T)=NCIMB 13995(T)) and which belongs to a subgroup of the genus Geobacillus comprising Geobacillus toebii and Geobacillus caldoxylosilyticus. However, G. debilis showed closest affinities to Bacillus pallidus, which we propose should become Geobacillus pallidus comb. nov.

  15. Salibacterium halotolerans gen. nov., sp. nov., a bacterium isolated from a salt pan, reclassification of Bacillus qingdaonensis as Salibacterium qingdaonense comb. nov. and Bacillus halochares as Salibacterium halochares comb. nov.

    PubMed

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

    2015-11-01

    Two novel Gram-stain-positive, rod-shaped, non-motile, non-endospore-forming bacterial strains, S7T and IB5, were isolated from Khavda, India. Based on 16S rRNA gene sequence analysis they were identified as belonging to the class Bacilli, order Bacillales, family Bacillaceae, and were most closely related to Bacillus qingdaonensis CGMCC 1.6134T (97.3 %, sequence similarity), Bacillus halochares LMG 24571T (96.9 %), Bacillus salarius KCTC 3912T (95.6 %) and Bacillus aidingensis DSM 18341T (95.3 %). However, these strains shared only 88.2 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strains S7T and IB5 might not be members of the genus Bacillus. The DNA-DNA relatedness of these strains with B. qingdaonensis CGMCC 1.6134T was 42.9 ± 0.8. The cell-wall peptidoglycan of strains S7T and IB5 contained meso-diaminopimelic acid, while the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and three unknown lipids. The predominant isoprenoid quinone was MK-7. anteiso-C15 : 0 was the predominant fatty acid. The results of the phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strains S7T and IB5, suggesting that they represent a novel member of the family Bacillaceae, for which the name Salibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of Salibacterium halotolerans is S7T ( = KCTC 33658T = CGMCC 1.15324T). Based on the results of the present study, it is also suggested that B. qingdaonensis and B. halochares should be transferred to this novel genus, as Salibacterium qingdaonense comb. nov. and Salibacterium halochares comb. nov., respectively.

  16. 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

    Zhou, Cheng; Ye, Jintong; Xue, Yanfen; Ma, Yanhe

    2015-09-01

    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 Ca(2+). 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.

  17. Role of two amino acid residues' insertion on thermal stability of thermophilic α-amylase AMY121 from a deep sea bacterium Bacillus sp. SCSIO 15121.

    PubMed

    Li, Lizhen; Yang, Jian; Li, Jie; Long, Lijuan; Xiao, Yunzhu; Tian, Xinpeng; Wang, Fazuo; Zhang, Si

    2015-05-01

    α-Amylases from Bacillus licheniformis (BLA) and Bacillus amyloliquefaciens (BAA) are both important industrial enzymes with high similarity in structure but significant differences in thermostability. The mechanisms underlying this discrepancy are still poorly understood. Here, we investigated the role of two amino acids' insertion on the thermostability of these two group amylases. A newly obtained thermophilic amylase AMY121 was found much closer to BLA in both primary structure and enzymological properties. Two amino acids' insertion widespread among BAA group α-amylases was identified as one of the key factors leading to the thermostability differences, since thermostability of insertion mutants (AMY121-EG and AMY121-AA) from AMY121 significantly decreased, while that of deletion mutant from BAA increased. Moreover, we proposed that conformational disturbance caused by insertion mutation might weaken the calcium-binding affinity and consequently decrease the enzyme thermostability.

  18. Bacillus paraflexus sp. nov., isolated from compost.

    PubMed

    Chandna, Piyush; Mayilraj, Shanmugam; Kuhad, Ramesh Chander

    2013-12-01

    A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium capable of growing at 15-42 °C (optimum 30 °C) and at pH 5-11 (optimum pH 7) was isolated from compost. Its taxonomic position was deduced using a polyphasic approach and the strain was designated RC2(T). 16S rRNA gene sequence analysis showed that the isolate belongs to the division Firmicutes, forming a clade within the cluster containing Bacillus flexus IFO 15715(T), and showed highest similarity to B. flexus IFO 15715(T) (98.1 %). The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids of the novel strain were iso-C15:0 (36.83 %), anteiso-C15:0 (49.19 %) and C16:0 (5.19 %). DNA-DNA hybridization between strain RC2(T) and B. flexus DSM 1320(T) showed a level of relatedness of 54.5 %. The polar lipid profile of strain RC2(T) showed the presence of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was MK-7 and the G+C content of strain RC2(T) was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain RC2(T) was clearly distinguished from closely related members of the genus, and the strain is assigned to a novel species, for which the name Bacillus paraflexus sp. nov. is proposed. The type strain is RC2(T) ( = MTCC 9831(T) = MCC 2100(T) = KCTC 13724(T) = CCM 7754(T)).

  19. Bacillus oryzisoli sp. nov., isolated from rice rhizosphere.

    PubMed

    Zhang, Xiao-Xia; Gao, Ju-Sheng; Zhang, Lei; Zhang, Cai-Wen; Ma, Xiao-Tong; Zhang, Jun

    2016-09-01

    The taxonomy of strain 1DS3-10T, a Gram-staining-positive, endospore-forming bacterium isolated from rice rhizosphere, was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel strain was grouped with established members of the genus Bacillus and appeared to be closely related to the type strains Bacillus benzoevorans DSM 5391T (97.9 %), Bacillus circulans DSM 11T (97.7 %), Bacillus novalis JCM 21709T (97.3 %), Bacillus soli JCM 21710T (97.3 %), Bacillus oceanisediminis CGMCC 1.10115T (97.3 %) and BacillusnealsoniiFO-92T (97.1 %). The fatty acid profile of strain 1DS3-10T, which showed a predominance of iso-C15 : 0 and anteiso-C15 : 0, supported the allocation of the strain to the genus Bacillus. The predominant menaquinone was MK-7 (100 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unknown aminolipids. Cell-wall peptidoglycan contained meso-diaminopimelic acid. DNA-DNA hybridization values between strain 1DS3-10T and the type strains of closely related species were 25-33 %, which supported that 1DS3-10T represented a novel species in the genus Bacillus. The results of some physiological and biochemical tests also allowed the phenotypic differentiation of strain 1DS3-10T from the most closely related recognized species. On the basis of the phylogenetic and phenotypic evidence, strain 1DS3-10T represents a novel species of the genus Bacillus, for which the name Bacillus oryzisoli sp. nov. is proposed. The type strain of the novel species is 1DS3-10T (=ACCC 19781T=DSM 29761T).

  20. Reductive transformation of parathion and methyl parathion by Bacillus sp.

    PubMed

    Yang, Chao; Dong, Ming; Yuan, Yulan; Huang, Yao; Guo, Xinmin; Qiao, Chuanling

    2007-03-01

    Based on the results of phenotypic features, phylogenetic similarity of 16S rRNA gene sequences and BIOLOG test, a soil bacterium was identified as Bacillus sp. DM-1. Using either growing cells or a cell-free extract, it transformed parathion and methyl parathion to amino derivatives by reducing the nitro group. Pesticide transformation by a cell-free extract was specifically inhibited by three nitroreductase inhibitors, indicating the presence of nitroreductase activity. The nitroreductase activity was NAD(P)H-dependent, O(2)-insensitive, and exhibited the substrate specificity for parathion and methyl parathion. Reductive transformation significantly decreased the toxicity of pesticides.

  1. Draft Genome Sequence of Multitrait Plant Growth-Promoting Bacillus sp. Strain RZ2MS9

    PubMed Central

    Batista, Bruna Durante; Taniguti, Lucas Mitsuo; Almeida, Jaqueline Raquel; Azevedo, João Lúcio

    2016-01-01

    Bacillus sp. strain RZ2MS9 is a multitrait soybean and maize growth-promoting bacterium isolated in Brazil from guarana’s rhizosphere. Here, we present the draft genome sequence of RZ2MS9 and its genes involved in many features related to plant growth promotion. PMID:28007854

  2. Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain JS.

    PubMed

    Song, Ju Yeon; Kim, Hyun A; Kim, Ji-Seoung; Kim, Seon-Young; Jeong, Haeyoung; Kang, Sung Gyun; Kim, Byung Kwon; Kwon, Soon-Kyeong; Lee, Choong Hoon; Yu, Dong Su; Kim, Beom Seok; Kim, Sun-Hyung; Kwon, Suk Yoon; Kim, Jihyun F

    2012-07-01

    Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.

  3. 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).

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

    PubMed

    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).

  5. Whole-Genome Sequence and Fosfomycin Resistance of Bacillus sp. Strain G3(2015) Isolated from Seawater off the Coast of Malaysia

    PubMed Central

    Chan, Xin-Yue; Chen, Jian-Woon; Adrian, Tan-Guan-Sheng; Hong, Kar-Wai; Chang, Chien-Yi; Yin, Wai-Fong

    2017-01-01

    ABSTRACT Bacillus sp. is a Gram-positive bacterium that is commonly found in seawater. In this study, the genome of marine Bacillus sp. strain G3(2015) was sequenced using MiSeq. The fosfomycin resistant gene fosB was identified upon bacterial genome annotation. PMID:28360153

  6. 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.

  7. 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).

  8. Bacillus chungangensis sp. nov., a halophilic species isolated from sea sand.

    PubMed

    Cho, Sung-Lim; Jung, Min Young; Park, Mi-Hak; Kim, Wonyong

    2010-06-01

    The taxonomic position of a Gram-stain-positive, endospore-forming, halophilic strain, designated CAU 348(T), isolated from sea sand was investigated using a polyphasic approach. Colony morphology, biochemical tests and chemotaxonomic investigations revealed that strain CAU 348(T) had the characteristics of the genus Bacillus. Comparative 16S rRNA gene sequence analysis showed that the organism formed a hitherto unknown subline within the genus Bacillus. Sequence divergence values of more than 4.3 % from other described Bacillus species, together with phenotypic differences, showed that the unidentified bacterium represents a previously unrecognized member of this genus. The genotypic and phenotypic data indicated that strain CAU 348(T) represents a novel species of the genus Bacillus, for which the name Bacillus chungangensis sp. nov. is proposed. The type strain is CAU 348(T) (=KCTC 13566(T) =CCUG 57835(T)).

  9. Bacillus endolithicus sp. nov., isolated from pebbles.

    PubMed

    Parag, B; Sasikala, Ch; Ramana, Ch V

    2015-12-01

    Strain JC267T was isolated from pebbles collected from Pingleshwar beach, Gujarat, India. Cells are Gram-stain-positive, facultatively anaerobic, non-motile rods forming sub-terminal endospores in swollen ellipsoidal to oval sporangia. Strain JC267T contains anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as major (>5 %) cellular fatty acids. Polar lipids include phosphatidylglycerol, phospholipids (PL1-3), glycolipids (GL1-2) and an unidentified lipid. Cell-wall amino acids are composed of diagnostic meso-diaminopimelic acid, dl-alanine and a small amount of d-glutamic acid. The genomic DNA G+C content of strain JC267T is 45.5 mol%. The 16S rRNA gene sequence of strain JC267T showed highest sequence similarities of < 98.41 % with all species of the genus Bacillus when subjected to EzTaxon-e blast analysis. The reassociation values based on DNA-DNA hybridization of strain JC267T with Bacillus halosaccharovorans IBRC-M 10095T and Bacillus niabensis JCM 16399T were 26 ± 1 % and 34 ± 3 %, respectively. Based on taxonomic data obtained using a polyphasic approach, strain JC267T represents a novel species of the genus Bacillus, for which the name Bacillus endolithicus sp. nov. is proposed. The type strain is JC267T ( = IBRC-M 10914T = KCTC 33579T).

  10. 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).

  11. Complete Genome Sequence of the Mosquitocidal Bacterium Bacillus sphaericus C3-41 and Comparison with Those of Closely Related Bacillus Species▿ †

    PubMed Central

    Hu, Xiaomin; Fan, Wei; Han, Bei; Liu, Haizhou; Zheng, Dasheng; Li, Qibin; Dong, Wei; Yan, Jianping; Gao, Meiying; Berry, Colin; Yuan, Zhiming

    2008-01-01

    Bacillus sphaericus strain C3-41 is an aerobic, mesophilic, spore-forming bacterium that has been used with great success in mosquito control programs worldwide. Genome sequencing revealed that the complete genome of this entomopathogenic bacterium is composed of a chromosomal replicon of 4,639,821 bp and a plasmid replicon of 177,642 bp, containing 4,786 and 186 potential protein-coding sequences, respectively. Comparison of the genome with other published sequences indicated that the B. sphaericus C3-41 chromosome is most similar to that of Bacillus sp. strain NRRL B-14905, a marine species that, like B. sphaericus, is unable to metabolize polysaccharides. The lack of key enzymes and sugar transport systems in the two bacteria appears to be the main reason for this inability, and the abundance of proteolytic enzymes and transport systems may endow these bacteria with exclusive metabolic pathways for a wide variety of organic compounds and amino acids. The genes shared between B. sphaericus C3-41 and Bacillus sp. strain NRRL B-14905, including mobile genetic elements, membrane-associated proteins, and transport systems, demonstrated that these two species are a biologically and phylogenetically divergent group. Knowledge of the genome sequence of B. sphaericus C3-41 thus increases our understanding of the bacilli and may also offer prospects for future genetic improvement of this important biological control agent. PMID:18296527

  12. 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).

  13. 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

    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; Maeng, Jin-Soo

    2012-12-01

    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).

  14. 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.

  15. Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6.

    PubMed

    Zhang, Jianli; Wang, Jiewei; Song, Fei; Fang, Caiyuan; Xin, Yuhua; Zhang, Yabo

    2011-05-01

    A Gram-stain-positive, rod-shaped bacterium, designated strain NH3(T), was isolated from a sediment sample from the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew optimally at 37 °C and pH 9. Strain NH3(T) had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The cellular fatty acid profile included significant amounts of iso-C(15 : 0) and iso-C(14 : 0). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NH3(T) was 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NH3(T) was a member of rRNA group 6 of the genus Bacillus, which includes alkalitolerant, alkaliphilic and halotolerant species. The closest phylogenetic relatives were Bacillus akibai 1139(T) (96.82 % 16S rRNA gene sequence similarity), B. pseudofirmus DSM 8715(T) (96.76 %), B. okhensis Kh10-101(T) (96.76 %) and B. alkalidiazotrophicus MS 6(T) (96.47 %). Strain NH3(T) could be distinguished from these phylogenetically close neighbours based on a number of phenotypic properties. On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, we conclude that strain NH3(T) ( = CGMCC 1.10116(T)  = JCM 16507(T)) merits classification as the type strain of a novel species, for which the name Bacillus nanhaiisediminis sp. nov. is proposed.

  16. 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

    2013-11-07

    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.

  17. 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.

  18. Bacillus nakamurai sp. nov., a black pigment producing strain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two isolates of a Gram-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 da...

  19. Bacillus thiaminolyticus sp. nov., nom. rev.

    PubMed

    Nakamura, L K

    1990-07-01

    The name "Bacillus thiaminolyticus" Kuno 1951 was not included on the Approved Lists of Bacterial Names and has lost standing in bacteriological nomenclature. The genetic homogeneity of "Bacillus thiaminolyticus" was assessed by determining guanine-plus-cytosine contents by the buoyant density method and by measuring DNA relatedness by using spectrophotometric reassociation procedures. Of the 26 strains which I studied, 24 had guanine-plus-cytosine contents in the range from 52 to 54 mol%. The consistently high DNA relatedness values of 60 to 100% of these 24 strains to the type strain indicated that the "B. thiaminolyticus" group is genetically homogeneous. Low DNA relatedness values of 20 to 31% showed that "B. thiaminolyticus" is genetically unrelated to Bacillus alvei, "Bacillus aneurinolyticus," "Bacillus apiarius," Bacillus larvae, Bacillus laterosporus, Bacillus macerans, and Bacillus stearothermophilus. In general, the "B. thiaminolyticus" group was highly homogeneous for 49 phenotypic characteristics and clearly distinguishable from B. alvei, with which it was allegedly synonymous. On the basis of these findings, revival of the name Bacillus thiaminolyticus is proposed.

  20. Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus.

    PubMed

    Glaeser, Stefanie P; Dott, Wolfgang; Busse, Hans-Jürgen; Kämpfer, Peter

    2013-08-01

    A Gram-positive-staining, aerobic, endospore-forming bacterium (Ca7(T)) was isolated from a bioreactor showing extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strain Ca7(T) was grouped in the genus Bacillus, most closely related to Bacillus nanhaiensis JSM 082006(T) (100 %), Bacillus barbaricus V2-BIII-A2(T) (99.2 %) and Bacillus arsenicus Con a/3(T) (97.7 %). Moderate 16S rRNA gene sequence similarities were found to the type strains of the species Bacillus gelatini and Bacillus rigui (96.4 %), Bacillus macauensis (95.1 %) and Bacillus solisalsi (96.1 %). All these species were grouped into a monophyletic cluster and showed very low sequence similarities (<94 %) to the type species of the genus Bacillus, Bacillus subtilis. The quinone system of strain Ca7(T) consists predominantly of menaquinone MK-7. The polar lipid profile exhibited the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, minor compounds of an unidentified phospholipid and an aminophospholipid were detected. No glycolipids were found in strain Ca7(T), which was consistent with the lipid profiles of B. nanhaiensis, B. barbaricus, B. arsenicus, B. rigui, B. solisalsi, B. macauensis and B. gelatini, but in contrast to B. subtilis. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid and the polyamine pattern contained predominantly spermidine and spermine. The major fatty acids, which were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0, supported the grouping of strain Ca7(T) in the family Bacillaceae. The strain showed DNA-DNA similarities of 48 % (reciprocal 47 %) to B. nanhaiensis DSM 23009(T), 31 % (reciprocal 36 %) to B. barbaricus V2-BIII-A2(T) and 29 % (reciprocal 39 %) to B. arsenicus DSM 15822(T), respectively. These results clearly demonstrate that strain Ca7(T) is a representative of a novel species, which can be differentiated from its closest relatives by physiological and

  1. Hydrogen production of a salt tolerant strain Bacillus sp. B2 from marine intertidal sludge.

    PubMed

    Liu, Hongyan; Wang, Guangce

    2012-01-01

    To isolate a salt tolerant hydrogen-producing bacterium, we used the sludge from the intertidal zone of a bathing beach in Tianjin as inoculum to enrich hydrogen-producing bacteria. The sludge was treated by heat-shock pretreatment with three different temperature (80, 100 and 121°C) respectively. A hydrogen-producing bacterium was isolated from the sludge pretreated at 80°C by sandwich plate technique and identified using microscopic examination and 16S rDNA gene sequence analysis. The isolated bacterium was named as Bacillus sp. B2. The present study examined the hydrogen-producing ability of Bacillus sp. B2. The strain was able to produce hydrogen over a wide range of initial pH from 5.0 to 10.0, with an optimum at pH 7.0. The level of hydrogen production was also affected by the salt concentration. Strain B2 has unique capability to adapt high salt concentration. It could produce hydrogen at the salt concentration from 4 to 60‰. The maximum of hydrogen-producing yield of strain B2 was 1.65 ± 0.04 mol H(2)/mol glucose (mean ± SE) at an initial pH value of 7.0 in marine culture conditions. Hydrogen production under fresh culture conditions reached a higher level than that in marine ones. As a result, it is likely that Bacillus sp. B2 could be applied to biohydrogen production using both marine and fresh organic waste.

  2. Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes.

    PubMed

    Shivaji, S; Chaturvedi, P; Suresh, K; Reddy, G S N; Dutt, C B S; Wainwright, M; Narlikar, J V; Bhargava, P M

    2006-07-01

    Four novel bacterial strains were isolated from cryogenic tubes used to collect air samples at altitudes of 24, 28 and 41 km. The four strains, 24K(T), 28K(T), 41KF2a(T) and 41KF2b(T), were identified as members of the genus Bacillus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that three of the strains, 24K(T), 28K(T) and 41KF2a(T), are very similar to one another (>98 % sequence similarity) and show a similarity of 98-99 % with Bacillus licheniformis and 98 % with Bacillus sonorensis. DNA-DNA hybridization studies showed that strains 24K(T), 28K(T) and 41KF2a(T) exhibit <70 % similarity with each other and with B. licheniformis and B. sonorensis. Differences in phenotypic and chemotaxonomic characteristics between the novel strains and B. licheniformis and B. sonorensis further confirmed that these three isolates are representatives of three separate novel species. Strain 41KF2b(T) showed 100 % 16S rRNA gene sequence similarity to Bacillus pumilus, but differed from its nearest phylogenetic neighbour in a number of phenotypic and chemotaxonomic characteristics and showed only 55 % DNA-DNA relatedness. Therefore, the four isolates represent four novel species for which the names Bacillus aerius sp. nov. (type strain, 24K(T)=MTCC 7303(T)=JCM 13348(T)), Bacillus aerophilus sp. nov. (type strain, 28K(T)=MTCC 7304(T)=JCM 13347(T)), Bacillus stratosphericus sp. nov. (type strain, 41KF2a(T)=MTCC 7305(T)=JCM 13349(T)) and Bacillus altitudinis sp. nov. (type strain, 41KF2b(T)=MTCC 7306(T)=JCM 13350(T)) are proposed.

  3. Bacillus cellulasensis sp. nov., isolated from marine sediment.

    PubMed

    Mawlankar, Rahul; Thorat, Meghana N; Krishnamurthi, Srinivasan; Dastager, Syed G

    2016-01-01

    A novel bacterial strain NIO-1130(T) was isolated from sediment sample taken from Chorao Island, Goa Province, India, and subjected to a taxonomic investigation. The strain was Gram-positive, aerobic, and motile. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate within the genus Bacillus and strain NIO-1130(T) showed highest sequence similarity with Bacillus halosaccharovorans DSM 25387(T) (98.4%) and Bacillus niabensis CIP 109816(T) (98.1%), whereas other Bacillus species showed <97.0% similarity. Tree based on gyrB gene sequence revealed that strain bacillus group. The major menaquinone was MK-7 and the predominant cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0. The strain showed a DNA G+C content of 39.9 mol%. DNA-DNA hybridization studies revealed that strain NIO-1130(T) exhibits 70% similarity with Bacillus halosaccharovorans DSM 25387(T) and Bacillus niabensis CIP 109816(T). On the basis of physiological, biochemical, chemotaxonomic and phylogenetic analyses, we consider the isolate to represent a novel species of the genus Bacillus, for which the name Bacillus cellulasensis sp. nov., is proposed. The type strain is NIO-1130(T) (=NCIM 5461(T)=CCTCC AB 2011126(T)).

  4. Antifungal activity of Bacillus coagulans against Fusarium sp.

    PubMed

    Czaczyk, Katarzyna; Trojanowska, Krystyna; Mueller, Anna

    2002-01-01

    The antifungal activity of Bacillus coagulans against three pathogenic species of Fusarium was examined. Fungal growth was determined by colony forming units, dry matter and ergosterol level. Biosynthesis of Fusarium mycotoxins was also investigated. The strongest inhibition of fungal growth was noticed when Bacillus coagulans was co-inoculated at the beginning of culture. Estimation of ergosterol level as a determinant of fungal growth showed the greatest degree of Fusarium sp. inhibition. Addition of Bacillus coagulans to Fusarium culmorum culture inhibits the DON (deoxynivalenol) production.

  5. 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.

  6. Induced adaptation of Bacillus sp. to antimicrobial nanosilver.

    PubMed

    Gunawan, Cindy; Teoh, Wey Yang; Marquis, Christopher P; Amal, Rose

    2013-11-11

    The natural ability of Bacillus sp. to adapt to nanosilver cytotoxicity upon prolonged exposure is reported for the first time. The combined adaptive effects of nanosilver resistance and enhanced growth are induced under various intensities of nanosilver-stimulated cellular oxidative stress, ranging from only minimal cellular redox imbalance to the lethal levels of cellular ROS stimulation. An important implication of the present work is that such adaptive effects lead to the ultimate domination of nanosilver-resistant Bacillus sp. in the microbiota, to which nanosilver cytotoxicity is continuously applied.

  7. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov.

    PubMed

    Bittar, Fadi; Bibi, Fehmida; Ramasamy, Dhamodharan; Lagier, Jean-Christophe; Azhar, Esam I; Jiman-Fatani, Asif A; Al-Ghamdi, Ahmed K; Nguyen, Ti Thien; Yasir, Muhammad; Fournier, Pierre-Edouard; Raoult, Didier

    2015-01-01

    Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).

  8. 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

  9. 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

  10. Chlorxanthomycin, a Fluorescent, Chlorinated, Pentacyclic Pyrene from a Bacillus sp.†

    PubMed Central

    Magyarosy, Andrew; Ho, Jonathan Z.; Rapoport, Henry; Dawson, Scott; Hancock, Joe; Keasling, Jay D.

    2002-01-01

    A gram-positive Bacillus sp. that fluoresces yellow under long-wavelength UV light on several common culture media was isolated from soil samples. On the basis of carbon source utilization studies, fatty acid methyl ester analysis, and 16S ribosomal DNA analysis, this bacterium was most similar to Bacillus megaterium. Chemical extraction yielded a yellow-orange fluorescent pigment, which was characterized by X-ray crystallography, mass spectrometry, and nuclear magnetic resonance spectroscopy. The fluorescent compound, chlorxanthomycin, is a pentacyclic, chlorinated molecule with the molecular formula C22H15O6Cl and a molecular weight of 409.7865. Chlorxanthomycin appears to be located in the cytoplasm, does not diffuse out of the cells into the culture medium, and has selective antibiotic activity. PMID:12147512

  11. Biosurfactant production by a CO2 sequestering Bacillus sp. strain ISTS2.

    PubMed

    Sundaram, Smita; Thakur, Indu Shekhar

    2015-01-01

    A chemolithotrophic bacterium, Bacillus sp. strain ISTS2, produced biosurfactant when enriched in the chemostat in presence of sodium bicarbonate as carbon source was evaluated for carbon dioxide (CO2) sequestration and biosurfactant production. CO2 sequestration efficiency of the bacterium was determined by enzymatic activity of carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Biosurfactant production ability at 100 mM NHCO3 and 5% CO2 was screened by surface and interfacial tension measurement, emulsification stability test, hydrophobicity test, contact angle measurement, bacterial adhesion to hydrocarbon and purified by silica gel column (60-120 mesh). Thin layer chromatography (TLC) and gas chromatography-mass spectrometry (GC-MS) showed that the crude biosurfactant of ISTS2 were composed of lipopeptides and free fatty acids (FA) and its hydrophobic fraction contained five kinds of fatty acids (FA) with chain lengths of C14-C19. Thus Bacillus sp. strain IST2 can be used as a cleaner bioprocess for the utilization of industrial CO2 as alternate substrate.

  12. Biodegradation of 2-hydroxyquinoxaline (2-HQ) by Bacillus sp.

    PubMed

    Reddy, G V Subba; Reddy, B R; Tlou, M G

    2014-08-15

    An aerobic Gram +ve bacterial strain capable of utilizing 2-Hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Chrysanthemum indicum Indian agricultural soil and named as HQ2. On the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis, strain HQ2 was identified as Bacillus sp. The generation time of Bacillus sp. in log phase during growth on 2-HQ is 0.79 h or 47.4 min. The optimal conditions for 2-HQ degradation by Bacillus sp. were inoculum density of 1.0 OD, pH of 6-8, temperature of 37-45 °C and 2-HQ concentration of 500 ppm. Among the additional carbon and nitrogen sources, carbon sources did not influence the degradation rate of 2-HQ, but nitrogen sources-yeast extract marginally enhanced the rate of degradation of 2-HQ. GC-MS analysis of the culture Bacillus sp. grown on 2-HQ indicated the formation of dimers from 2 molecules of 2-hydroxyquinoxaline. The formation of dimer for degradation of 2-HQ by the culture appears to be the first report to our scientific knowledge.

  13. 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)).

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

    PubMed

    Masuda, Hisako; Shiwa, Yuh; Yoshikawa, Hirofumi; Zylstra, Gerben J

    2014-12-04

    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.

  15. 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)).

  16. Expression of the Bacillus thuringiensis mosquitocidal toxin Cry11Aa in the aquatic bacterium Asticcacaulis excentricus.

    PubMed

    Armengol, Gemma; Guevara, Oscar Enrique; Orduz, Sergio; Crickmore, Neil

    2005-12-01

    A mosquitocidal aquatic bacterium has been developed by introducing an operon containing the cry11Aa, and p20 genes from Bacillus thuringiensis subsp. israelensis (Bti) into the gram-negative aquatic bacterium Asticcacaulis excentricus. After transformation, the cry11Aa gene was successfully expressed in recombinant A. excentricus under the tac promoter, at the level of 0.04 pg/cell. The recombinant bacteria were toxic to Aedes aegypti larvae with an LC(50) of 6.83 x 10(5) cells/mL. We believe that these bacteria may have potential as genetically engineered microorganisms for the control of mosquito larvae.

  17. Genome of Bacillus macauensis ZFHKF-1, a long-chain-forming bacterium.

    PubMed

    Cai, Lin; Zhang, Tong

    2012-09-01

    Here, we report the draft genome sequence of Bacillus macauensis ZFHKF-1, a novel long-chain bacterium previously isolated and identified by us (Zhang T, Fan XJ, Hanada S, Kamagata Y, Fang HHP, J. Syst. Evol. Microbiol. 56:349-353, 2006). The genome provides basic genetic information to understand this particular species and explore the potential mechanism of long-chain formation. The type strain is ZFHKF-1 (= JCM 13285 = DSM 17262).

  18. 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

  19. 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.

  20. 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.

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

    PubMed

    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

    2011-12-31

    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.

  2. Synergism between Phyllobacterium sp. (N(2)-fixer) and Bacillus licheniformis (P-solubilizer), both from a semiarid mangrove rhizosphere.

    PubMed

    Rojas, A; Holguin, G; Glick, B R.; Bashan, Y

    2001-04-01

    Mangrove seedlings were treated with a mixture of two bacterial species, the slow-growing, N(2)-fixing bacterium Phyllobacterium sp. and the fast-growing, phosphate-solubilizing bacterium Bacillus licheniformis, both isolated from the rhizosphere from black, white, and red mangroves of a semiarid zone. Nitrogen fixation and phosphate solubilization increased when the mixture was used compared to the effects observed when adding individual cultures, notwithstanding that there was no increase in bacterial multiplication under these conditions. Inoculation of black mangrove seedlings in artificial seawater showed the mixture performed somewhat better than inoculation of the individual bacterium; more leaves were developed and higher levels of (15)N were incorporated into the leaves, although the total nitrogen level decreased. This study demonstrates that interactions between individual components of the rhizosphere of mangroves should be considered when evaluating these bacteria as plant growth promoters.

  3. Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis).

    PubMed

    Chen, Jin-Hua; Tian, Xiang-Rong; Ruan, Ying; Yang, Ling-Ling; He, Ze-Qiang; Tang, Shu-Kun; Li, Wen-Jun; Shi, Huazhong; Chen, Yi-Guang

    2015-05-01

    A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118(T), was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118(T) was able to grow with 0-13% (w/v) NaCl (optimum 2-5%), at pH 5.5-10.0 (optimum pH 7.5) and at 5-50 °C (optimum 30-35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118(T) belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211(T) (98.9% 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33(T) (98.3%), Bacillus niabensis 4T19(T) (97.8%) and Bacillus herbersteinensis D-1,5a(T) (97.1%). The combination of results from the phylogenetic analysis, DNA-DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118(T) represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118(T) ( = CTCC AB 2010452(T) =DSM 24486(T) =JCM 17523(T)).

  4. 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

  5. Kinetics of molybdenum reduction to molybdenum blue by Bacillus sp. strain A.rzi.

    PubMed

    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 p max, K(s), S(m), 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.

  6. 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).

  7. The sponge-associated bacterium Bacillus licheniformis SAB1: a source of antimicrobial compounds.

    PubMed

    Devi, Prabha; Wahidullah, Solimabi; Rodrigues, Cheryl; Souza, Lisette D

    2010-04-09

    Several bacterial cultures were isolated from sponge Halichondria sp., collected from the Gujarat coast of the Indo Pacific region. These bacterial cultures were fermented in the laboratory (100 mL) and the culture filtrate was assayed for antibiotic activity against 16 strains of clinical pathogens. Bacillus sp. (SAB1), the most potent of them and antagonistic to several clinically pathogenic Gram-positive, Gram-negative bacteria and the fungus Aspergillus fumigatus was chosen for further investigation. Analysis of the nucleotide sequence of the 16S rDNA gene of Bacillus sp. SAB1 showed a strong similarity (100%) with the 16S rDNA gene of Bacillus licheniformis HNL09. The bioactive compounds produced by Bacillus licheniformis SAB1 (GenBank accession number: DQ071568) were identified as indole (1), 3-phenylpropionic acid (2) and a dimer 4,4'-oxybis[3-phenylpropionic acid] (3) on the basis of their Fourier Transform Infrared (FTIR), Nuclear Magnetic Resonance (NMR) and Electrospray Ionization Mass Spectrometer (ESI-MS) data. There is a single reference on the natural occurrence of compound 3 from the leaves of a terrestrial herb Aptenia cordifolia in the literature, so to the best of our knowledge, this is a first report of its natural occurrence from a marine source. The recovery of bacterial strains with antimicrobial activity suggests that marine-invertebrates remain a rich source for the isolation of culturable isolates capable of producing novel bioactive secondary metabolites.

  8. Bacillus axarquiensis sp. nov. and Bacillus malacitensis sp. nov., isolated from river-mouth sediments in southern Spain.

    PubMed

    Ruiz-García, Cristina; Quesada, Emilia; Martínez-Checa, Fernando; Llamas, Inmaculada; Urdaci, Maria C; Béjar, Victoria

    2005-05-01

    Two Gram-positive, rod-shaped, endospore-forming bacteria (strains CR-119(T) and CR-95(T)) were isolated from brackish sediments in the mouth of the river Velez in Malaga, southern Spain, and subjected to a polyphasic taxonomic study. Phenotypic tests showed that these strains were related to other Bacillus species at a similarity level of less than 87.6 %. Both strains are halotolerant, aerobic, chemoheterotrophic, motile with peritrichous flagella and biosurfactant producers. Their endospores are oval, subterminal and non-deforming structures. The predominant menaquinone in both strains is MK-7. The fatty-acid profiles of both strains contain large quantities of branched and saturated fatty acids. The major fatty acids (%) are 15 : 0 anteiso (32.4), 15 : 0 iso (16.8), 17 : 0 iso (13.4), 16 : 0 (11.5) and 17 : 0 anteiso (10.2) in strain CR-119(T) and 15 : 0 anteiso (37.5), 17 : 0 iso (16.0) and 17 : 0 anteiso (15.8) in strain CR-95(T). The G + C contents of strains CR-119(T) and CR-95(T) are 41.0 and 42.5 mol%, respectively. RAPD analysis confirmed the low degree of similarity between the two strains and also amongst other Bacillus species. 16S rRNA gene analysis of strain CR-119(T) showed the highest sequence similarity to be 97.4 %, with Bacillus mojavensis and Bacillus subtilis subsp. spizizenii. In the case of strain CR-95(T), the maximum similarity value was 99.5 %, with B. mojavensis. DNA-DNA hybridization of strains CR-119(T) and CR-95(T) with the above species produced values lower than 46.9 %. Therefore, on the basis of phenotypic characteristics, phylogenetic data and genomic distinctiveness, we conclude that these Bacillus strains merit classification as novel species, for which we propose the names Bacillus axarquiensis sp. nov. (type strain CR-119(T) = CECT 5688(T) = LMG 22476(T)) and Bacillus malacitensis sp. nov. (type strain CR-95(T) = CECT 5687(T) = LMG 22477(T)).

  9. Bacillus amyloliquefaciens: a mosquitocidal bacterium from mangrove forests of Andaman & Nicobar islands, India.

    PubMed

    Geetha, I; Manonmani, A M; Prabakaran, G

    2011-12-01

    Samples collected from the mangrove forests of Andaman & Nicobar islands yielded a mosquitocidal bacterium, whose extracellular metabolite(s) exhibited mosquito larvicidal and pupicidal activity. The bacterium was isolated using standard microbiological methods and identified using classical biochemical tests and rpoB gene sequences. The mosquitocidal bacterium was identified as Bacillus amyloliquefaciens. Mosquitocidal metabolite(s) was separated from the culture supernatant of the bacterium and its efficacy against the larval and pupal stages of different species of mosquitoes was determined in terms of LC(50) and LC(90). Mosquito larvicidal activity in terms of LC(50) against Anopheles stephensi, Culex quinquefasciatus and Aedes aegypti was respectively, 26.4μg, 22.2μg and 20.5μg/ml and its pupicidal activity was 4.4μg, 8.2μg and 14.5μg/ml respectively. The mosquitocidal metabolite(s) was found to be a biosurfactant. This is the first report of the mosquitocidal activity of B. amyloliquefaciens and it is a new weapon which can be added to the array of microbial agents for use against mosquitoes.

  10. Genome Sequence of the Boron-Tolerant and -Requiring Bacterium Bacillus boroniphilus

    PubMed Central

    Çöl, Bekir; Özkeserli, Zeynep; Kumar, Dibyendu; Özdağ, Hilal

    2014-01-01

    Bacillus boroniphilus is a highly boron-tolerant bacterium that also requires this element for its growth. The complete genome sequence of B. boroniphilus was determined by a combination of shotgun sequencing and paired-end sequencing using 454 pyrosequencing technology. A total of 84,872,624 reads from shotgun sequencing and a total of 194,092,510 reads from paired-end sequencing were assembled using Newbler 2.3. The estimated size of the draft genome is 5.2 Mb. PMID:24385571

  11. 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.

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

    PubMed

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

    1991-07-11

    Several hundred million tons of toxic mercurials are dispersed in the biosphere. Microbes can detoxify organo-mercurials and mercury salts through sequential action of two enzymes, organomercury lyase and mercuric ion reductase (MerA). The latter, a homodimer with homology to the FAD-dependent disulphide oxidoreductases, catalyses the reaction NADPH + Hg(II)----NADP+ + H+ + Hg(0), one of the very rare enzymic reactions with metal substrates. Human glutathione reductase serves as a reference molecule for FAD-dependent disulphide reductases and between its primary structure and that of MerA from Tn501 (Pseudomonas), Tn21 (Shigella), p1258 (Staphylococcus) and Bacillus, 25-30% of the residues have been conserved. 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 Tn501 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 operon. These domains can be proteolytically cleaved off without changing the catalytic efficiency. 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.

  13. 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.

  14. 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

  15. Characterization of a novel feather-degrading Bacillus sp. strain.

    PubMed

    Werlang, Patricia Orosco; Brandelli, Adriano

    2005-01-01

    Feather waste is generated in large amounts as a byproduct of commercial poultry processing. This residue is almost pure keratin, which is not easily degradable by common proteolytic enzymes. A feather-degrading bacterium was isolated from poultry feathers in decomposition. The strain identified as kr16 showed important feather-degrading activity when grown on basal medium containing 10 g/L of native feather as the source of energy, carbon, and nitrogen. The isolate was characterized according to the phenotypical characteristics and biochemical profiling that belong to the Bacillus genus. Keratinolytic activity of this isolate was monitored during cultivation of the bacterium on raw feathers at different temperatures. Maximum growth and feather-degrading activity were observed at 30-37 degrees C. The keratinolytic enzyme had a pH optimum ranging from 8.0 to 11.0 and a temperature optimum of 45-65 degrees C. The keratinase was strongly inhibited by EDTA and the metal ions Hg2+ and Sn2+.

  16. Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain 916.

    PubMed

    Wang, Xiaoyu; Luo, Chuping; Chen, Zhiyi

    2012-10-01

    Bacillus sp. strain 916, isolated from the soil, showed strong activity against Rhizoctonia solani. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 916. Its 3.9-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.

  17. 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...

  18. Permanent draft genome of acetaldehyde degradation bacterium, Shewanella sp. YQH10.

    PubMed

    Liu, Yang; Shang, Xiexie; Zeng, Runying

    2015-02-01

    Shewanella sp. YQH10 isolated from mangrove sediment, was a novel species of Shewanella, which has the ability to degrade acetaldehyde. Here, we present an annotated draft genome sequence of Shewanella sp. YQH10, which contains 4,215,794 bp with a G + C content of 48.1%. This information regarding the genetic basis of this bacterium can greatly advance our understanding of the physiology of this species.

  19. Bacillus terrae sp. nov. isolated from Cistus ladanifer rhizosphere soil.

    PubMed

    Díez-Méndez, Alexandra; Rivas, Raúl; Mateos, Pedro F; Martínez-Molina, Eustoquio; Santín, Primitivo Julio; Sánchez-Rodríguez, Juan Antonio; Velázquez, Encarna

    2016-12-15

    A bacterial strain designated RA9T was isolated from a root of Cistus ladanifer in Spain. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Bacillus with its closest relatives being B. fortis R-6514T and B. fordii R-7190T with 98.2% similarity in both cases. DNA-DNA hybridization studies showed averages of 29 and 30%, respectively, between the strain RA9T and the type strains of B. fortis and B. fordii. The isolate was Gram-stain positive, motile and sporulating rod. Catalase and oxidase were positive. Gelatin, starch and casein were not hydrolysed. MK-7 was the only menaquinone detected and iso-C15:0 and anteiso-C15:0 were the major fatty acids. The polar lipids profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, one unidentifed glycolipid and one unidentified lipid. Mesodiaminopimelic acid was detected in peptidoglycan. The G+C content was 43.1 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RA9T should be considered as a new species of genus Bacillus, for which the name Bacillus terrae sp. nov. is proposed. The type strain is RA9T (=LMG 29736T= CECT 9170T).

  20. 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

  1. 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

  2. Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

    PubMed Central

    Liu, Jin-liang; Hu, Xiao-min

    2013-01-01

    Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

  3. Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9.

    PubMed

    Jiang, Bin-Hui; Liu, Jin-Liang; Hu, Xiao-Min

    2013-04-25

    Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus.

  4. 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.

  5. Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1

    PubMed Central

    Lai, Qiliang; Li, Weiwei; Wang, Baojiang; Yu, Zhiwei

    2012-01-01

    Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation. PMID:23144416

  6. 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

  7. 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

  8. Bacillus rigui sp. nov., isolated from wetland fresh water.

    PubMed

    Baik, Keun Sik; Lim, Chae Hong; Park, Seong Chan; Kim, Eun Mi; Rhee, Moon Soo; Seong, Chi Nam

    2010-09-01

    Two Gram-stain-positive strains, WPCB074(T) and WPCB165, were isolated from fresh water collected from the Woopo wetland (Republic of Korea). Both strains were strictly aerobic, motile, endospore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WPCB074(T) and WPCB165 belonged to the genus Bacillus and that strain WPCB074(T) was most closely related to Bacillus solisalsi YC1(T) (98.4 % sequence similarity), B. barbaricus V2-BIII-A2(T) (97.7 %), B. macauensis ZFHKF-1(T) (96.9 %), B. arsenicus Con a/3(T) (96.4 %) and B. gelatini LMG 21880(T) (95.1 %). The 16S rRNA gene sequences of strains WPCB074(T) and WPCB165 differed at one position (99.9 % similarity), suggesting that these two strains constitute a single species. DNA-DNA relatedness between strain WPCB074(T) and the type strains of B. solisalsi, B. barbaricus, B. macauensis, B. arsenicus and B. gelatini were 26, 17, 20, 14 and 7 %, respectively. Strain WPCB074(T) was characterized by having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C(15 : 0) and anteiso-C(15 : 0) as the major fatty acids. The DNA G+C content of strain WPCB074(T) was 41.9 mol%. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain WPCB074(T) represents a novel species of the genus Bacillus for which the name Bacillus rigui sp. nov. is proposed. The type strain is WPCB074(T) (=KCTC 13278(T) =JCM 16348(T)).

  9. 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))].

  10. Bacillus flexus strain As-12, a new arsenic transformer bacterium isolated from contaminated water resources.

    PubMed

    Jebeli, Mohammad Ahmadi; Maleki, Afshin; Amoozegar, Mohammad Ali; Kalantar, Enayatollah; Izanloo, Hassan; Gharibi, Fardin

    2017-02-01

    A total of 14 arsenic-resistant bacteria were isolated from an arsenic-contaminated travertine spring water in the central district of Qorveh county, Kurdistan Province, Iran. One of strains designated As-12 was selected for further investigation because of its ability to transform arsenic. The strain was identified by cultural, morphological and biochemical tests, and 16S rRNA gene sequencing. Finally, the growth characteristics of the isolate were investigated in a chemically defined medium which included varied ranges of environmental factors such as pH, temperature and salinity. Moreover, the resistance of this strain to some heavy metals was evaluated. The bacterium was a Gram-positive, endospore-forming with all other characteristics of the genus Bacillus. It revealed maximum similarity at the 16S rRNA gene level with Bacillus flexus. The optimum growth of the strain was observed at 38 °C, pH 9 and 2% salinity. This strain was resistant to heavy metals such as zinc, chromium, lead, nickel, copper, mercuric and cadmium at concentrations of 15 mM, 15.5 mM, 11.5 mM, 12 mM, 11 mM, 5.5 mM, and 1 mM, respectively. The isolated bacterium was able to reduce As (V) to As (III) (about 28%) and oxidize As (III) to As (V) (about 45%) after 48 h of incubation at 37 °C. In conclusion, Bacillus flexus strain As-12, was identified as an arsenic transformer, for the first time.

  11. 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

  12. 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.

  13. Biodegradation of kraft-lignin by Bacillus sp. isolated from sludge of pulp and paper mill.

    PubMed

    Raj, Abhay; Reddy, M M Krishna; Chandra, Ram; Purohit, Hemant J; Kapley, Atya

    2007-12-01

    Eight bacterial strains were isolated on kraft lignin (KL) containing mineral salt medium (L-MSM) agar with glucose and peptone from the sludge of pulp and paper mill. Out of these, ITRC-S8 was selected for KL degradation, because of its fast growth at highest tested KL concentration and use of various lignin-related low molecular weight aromatic compounds (LMWACs) as sole source of carbon and energy. The bacterium was identified by biochemical tests as Gram-positive, rod-shaped and non-motile. Subsequent 16S rRNA gene sequencing showed 95% base sequence homology and it was identified as Bacillus sp. In batch experiments, a decrease in pH was observed initially followed by an increase till it reached an alkaline pH, which did not alter the culture growth significantly. The bacterium reduced the colour and KL content of 500 mg l(-1 )KL in MSM, in the presence of glucose and peptone, at pH 7.6, temperature 30 degrees C, agitation of 120 rpm and 6 days of incubation by 65 and 37% respectively. Significant reduction in colour and KL content in subsequent incubations is indicative of a co-metabolism mechanism, possibly due to initial utilization of added co-substrates for energy followed by utilization of KL as a co-metabolic. The degradation of KL by bacterium was confirmed by GC-MS analysis indicating formation of several LMWACs such as t-cinnamic acid, 3, 4, 5-trimethoxy benzaldehyde and ferulic acid as degradation products, which were not present in the control (uninoculated) sample. This favours the idea of biochemical modification of the KL polymer to a single monomer unit.

  14. Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel–Degrading and Plant Growth–Promoting Phyllospheric Bacterium

    PubMed Central

    Stevens, Vincent; Thijs, Sofie; McAmmond, Breanne; Langill, Tori; Van Hamme, Jonathan; Weyens, Nele

    2017-01-01

    ABSTRACT We report here the 4.19-Mb draft genome sequence of Bacillus licheniformis VSD4, a Gram-positive bacterium of the Bacillaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. Knowledge about its genome will help to evaluate its potential as an inoculant in phylloremediation applications. PMID:28302775

  15. Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel-Degrading and Plant Growth-Promoting Phyllospheric Bacterium.

    PubMed

    Stevens, Vincent; Thijs, Sofie; McAmmond, Breanne; Langill, Tori; Van Hamme, Jonathan; Weyens, Nele; Vangronsveld, Jaco

    2017-03-16

    We report here the 4.19-Mb draft genome sequence of Bacillus licheniformis VSD4, a Gram-positive bacterium of the Bacillaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. Knowledge about its genome will help to evaluate its potential as an inoculant in phylloremediation applications.

  16. Production and characterization of a novel protease from Bacillus sp. RRM1 under solid state fermentation.

    PubMed

    Rajkumar, Renganathan; Kothilmozhian, Jayappriyan; Ramasamy, Rengasamy

    2011-06-01

    A commercially important alkaline protease, produced by Bacillus sp. RRM1 isolated from the red seaweed Kappaphycus alvarezii (Doty) Doty ex Silva, was first recognized and characterized in the present study. Identification of the isolated bacterium was done using both biochemical characterization as well as 16S rRNA gene sequencing. The bacterial strain, Bacillus sp. RRM1, produced a high level of protease using easily available, inexpensive agricultural residues solid-state fermentation (SSF). Among them, wheat bran was found to be the best substrate. Influences of process parameters such as moistening agents, moisture level, temperature, inoculum concentration, and co-carbon and co-nitrogen sources on the fermentation were also evaluated. Under optimized conditions, maximum protease production (i.e., 2081 U/g) was obtained from wheat bran, which is about 2-fold greater than the initial conditions. The protease enzyme was stable over a temperature range of 30-60 degrees C and pH 6-12, with maximum activity at 50 degrees C and pH 9.0. Whereas the metal ions Na+, Ca2+, and K+ enhanced the activity of the enzyme, others such as Hg2+, Cu2+, Fe2+, Co2+, and Zn2+ had rendered negative effects. The activity of the enzyme was inhibited by EDTA and enhanced by Cu2+ ions, thus indicating the nature of the enzyme as a metalloprotease. The enzyme showed extreme stability and activity even in the presence of detergents, surfactants, and organic solvents. Moreover, the present findings opened new vistas in the utilization of wheat bran, a cheap, abundantly available, and effective waste as a substrate for SSF.

  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. Characteristics of Bacillus sp. PZ-1 and its biosorption to Pb(II).

    PubMed

    Ren, Guangming; Jin, Yu; Zhang, Chunmiao; Gu, Haidong; Qu, Juanjuan

    2015-07-01

    During the long and cold winter season in northern area of China, wastewater treatment is often inefficient which causes the substandard discharge. In this study, a lead-resistant psychrotrophilic bacterium was isolated and used as an adsorbent to remove Pb(II) from aqueous solution at 15 °C. The strain was identified and designated as Bacillus sp. PZ-1 based on the morphology, physiological-biochemical experiments and 16S rDNA sequence analysis. The minimal inhibitory concentration and antibiotic experiments revealed that PZ-1 had high resistance to 1500 mg L(-1) of Zn(II), 800 mg L(-1) of Cu(II), 400 mg L(-1) of Ni(II), 15 µg mL(-1) of chloramphenicol and 50 µg mL(-1) of streptomycin, but susceptibility to 200 mg L(-1) of Co(II). Scanning electron microscopy, energy dispersive X-ray spectroscopy and atomic force microscopy analyses showed that biosorption of Bacillus sp. PZ-1 to Pb(II) involved surface adsorption, ion exchange and micro-precipitate. Fourier transform infrared spectroscopy analyses indicated that hydroxyl, carbonyl and carboxyl on cells may play vital roles in Pb(II) adsorption. Besides, siderophore secreted by PZ-1 had beneficial impacts on the Pb(II) removal. Biosorption experiments were carried out as a function of initial Pb(II) concentration (50-500 mg L(-1)), pH (3.0-7.0), biomass concentration (5-50 g L(-1)) and contact time (5-40 min). Biosorption rate of 93.01% with adsorption capacity of 9.30 mg g(-1) was obtained under the initial Pb(II) concentration of 400 mg (-1), pH of 5.0, contact time of 20 min, biomass concentration of 40 g L(-1) and the temperature of 15 °C. The equilibrium data were well fitted with Langmuir model, which indicated the adsorption process of Pb(II) is monolayer adsorption. Bacillus sp. PZ-1 appeared to be an efficient biosorbent for removing Pb(II) from wastewater at low temperature.

  19. 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.

  20. 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

  1. Biodegradation of nitrobenzene in a lysogeny broth medium by a novel halophilic bacterium Bacillus licheniformis.

    PubMed

    Li, Tian; Deng, Xinping; Wang, Jinjun; Chen, Yucheng; He, Lin; Sun, Yuchuan; Song, Caixia; Zhou, Zhifeng

    2014-12-15

    The Bacillus licheniformis strain YX2, a novel nitrobenzene-degrading halophilic bacterium, was isolated from active sludge obtained from a pesticide factory. Strain YX2 can withstand highly acidic and alkaline conditions and high temperatures. Degradation of nitrobenzene (200mgL(-1)) by YX2 exceeded 70% after 72h in lysogeny broth medium (pH 4-9). Under optimal degradation conditions (33°C, pH 7 in LB medium) YX2 degraded 50, 100, 200, and 600mgL(-1) nitrobenzene within 36, 36, 72, and 156h, respectively. Even in the presence of benzene, phenol or aniline, strain YX2 efficiently degraded nitrobenzene. Furthermore, strain YX2 completely degraded 600mgL(-1) nitrobenzene in 7% NaCl (w/w). Thus, our data show that strain YX2 may have promise for removing nitrobenzene from complex wastewaters with high salinity and variable pH.

  2. Characterization and a point mutational approach of a psychrophilic lipase from an arctic bacterium, Bacillus pumilus.

    PubMed

    Wi, Ah Ram; Jeon, Sung-Jong; Kim, Sunghui; Park, Ha Ju; Kim, Dockyu; Han, Se Jong; Yim, Joung Han; Kim, Han-Woo

    2014-06-01

    A bacterium with lipolytic activity was isolated from the Chukchi Sea within the Arctic Ocean. The lipase BpL5 from the isolate, Bacillus pumilus ArcL5, belongs to subfamily 4 of lipase family I. The optimum pH and temperature of the recombinant enzyme BpL5, as expressed in Escherichia coli, were 9.0 and 20 °C, respectively. The enzyme retained 85 % of its activity at 5 °C. There was a significant difference between temperatures for maximal activity (20 °C) and for protein denaturation (approx. 45 °C). The enzyme preferred middle-chain (C8) p-nitrophenyl substrates. Two mutants, S139A and S139Y, were rationally designed based on the 3D-structure model, and their activities were compared with that of the wild type. The both mutants showed significantly improved activity against tricaprylin.

  3. Klebsiella singaporensis sp. nov., a novel isomaltulose-producing bacterium.

    PubMed

    Li, Xianzhen; Zhang, Daohai; Chen, Feng; Ma, Jie; Dong, Yihu; Zhang, Lianhui

    2004-11-01

    Cells of strain LX3(T), isolated from soil, were Gram-negative, facultatively anaerobic, non-motile, capsulated and non-endospore-forming straight rods, able to grow at 10 degrees C, unable to produce gas from lactose at 45 degrees C and unable to produce indole. The isolate converted sucrose to isomaltulose and did not produce detectable glucose by-products. The G+C content of the DNA was 56.4 mol%. Furthermore, comparison of 16S rRNA and rpoB gene sequences showed that the isolate clearly belongs to the genus Klebsiella. The closest phylogenetic relative was Klebsiella pneumoniae, there being 99.3 and 97.5 % similarity in 16S rRNA and rpoB gene sequences, respectively. DNA-DNA hybridization analysis demonstrated a very low level of relatedness to other members of the genus Klebsiella, indicating that the isolated strain and other species in the genus Klebsiella were not related at the species level. The isolate could be differentiated from other previously described members of the genus Klebsiella on the basis of phenotypic differences and 16S rRNA and rpoB gene sequence divergence, together with DNA-DNA reassociation data. Therefore, it is proposed that strain LX3(T) (=DSM 16265(T)=JCM 12419(T)) should be classified as the type strain of a novel species of genus Klebsiella, Klebsiella singaporensis sp. nov.

  4. Paenibacillus susongensis sp. nov., a mineral-weathering bacterium.

    PubMed

    Guo, Xin-Qi; Gu, Jia-Yu; Yu, Ya-Jun; Zhang, Wen-Bin; He, Lin-Yan; Sheng, Xia-Fang

    2014-12-01

    A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated M327(T), was isolated from the weathered surfaces of rock (mica schist) from Susong, Anhui Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M327(T) belonged to the genus Paenibacillus and was related most closely to Paenibacillus terrigena A35(T) (98.6 % similarity) and Paenibacillus selenitireducens ES3-24(T) (98.3 %). Strain M327(T) contained meso-diaminopimelic acid in the cell wall and MK-7 as the major menaquinone. The main fatty acids of strain M327(T) were anteiso-C15 : 0 and iso-C16 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown aminophospholipids and an unknown lipid. The total DNA G+C content of strain M327(T) was 48.6 mol%. Based on the low level of DNA-DNA relatedness (ranging from 26.6 to 33.1 %) to these type strains of species of the genus Paenibacillus and unique phenotypic characteristics, it is suggested that strain M327(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus susongensis sp. nov. is proposed. The type strain is M327(T) ( = CCTCC AB 2014058(T) = LMG 28236(T) = JCM 19951(T)).

  5. Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

    PubMed

    Liu, Yang; Wang, Runping; Zeng, Runying

    2014-12-01

    Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate.

  6. Rhizobium yantingense sp. nov., a mineral-weathering bacterium.

    PubMed

    Chen, Wei; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi

    2015-02-01

    A Gram-stain-negative, rod-shaped bacterial strain, H66(T), was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66(T) were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66(T) belongs to the genus Rhizobium. It is closely related to Rhizobium huautlense SO2(T) (98.1 %), Rhizobium alkalisoli CCBAU 01393(T) (98.0 %) and Rhizobium cellulosilyticum ALA10B2(T) (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (<92.0 %) between strain H66(T) and other recognized species of the genus Rhizobium. The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66(T) was 60.3 mol%. Strain H66(T) is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA-DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66(T) ( = CCTCC AB 2014007(T) = LMG 28229(T)).

  7. 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)).

  8. 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)).

  9. Draft Genome Sequence of the Anaerobic Ammonium-Oxidizing Bacterium “Candidatus Brocadia sp. 40”

    PubMed Central

    Ali, Muhammad; Haroon, Mohamed Fauzi; Narita, Yuko; Zhang, Lei; Rangel Shaw, Dario; Okabe, Satoshi

    2016-01-01

    The anaerobic ammonium-oxidizing (anammox) bacterium “Candidatus Brocadia sp. 40” demonstrated the fastest growth rate compared to others in this taxon. Here, we report the 2.93-Mb draft genome sequence of this bacterium, which has 2,565 gene-coding regions, 41 tRNAs, and a single rrn operon. PMID:27932661

  10. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris.

    PubMed

    Valverde, Angel; Igual, José M; Peix, Alvaro; Cervantes, Emilio; Velázquez, Encarna

    2006-11-01

    the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).

  11. Draft Genome Sequence of Bacillus sp. FMQ74, a Dairy-Contaminating Isolate from Raw Milk

    PubMed Central

    Okshevsky, Mira; Regina, Viduthalai R.; Marshall, Ian P. G.; Schreiber, Lars

    2017-01-01

    ABSTRACT Representatives of the genus Bacillus are common milk contaminants that cause spoilage and flavor alterations of dairy products. Bacillus sp. FMQ74 was isolated from raw milk on a Danish dairy farm. To elucidate the genomic basis of this strain’s survival in the dairy industry, a high-quality draft genome was produced. PMID:28126940

  12. 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 ~3.97 Mb in 55 contigs with the G+C content of 39.9%, and a total of 3740 protein-coding genes were obtained.

  13. Bacillusurumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake.

    PubMed

    Zhang, Shanshan; Li, Zhaojun; Yan, Yanchun; Zhang, Chuanlun; Li, Jun; Zhao, Baisuo

    2016-06-01

    A Gram-stain-positive, rod-shaped, aerobic and moderately haloalkaliphilic bacterium, designated BZ-SZ-XJ18T, was isolated from the mixed water and sediment of a saline-alkaline lake located in the Xinjiang Uyghur Autonomous Region of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BZ-SZ-XJ18T was a member of the genus Bacillus. The closest phylogenetic relatives were Bacillus saliphilus 6AGT (96.7 % 16S rRNA gene sequence similarity), 'Bacillusdaqingensis' X10-1 (96.6 %), Bacillus luteus JC167T (96.5 %), Bacillus daliensis DLS13T (96.2 %), Bacillus chagannorensis CG-15T (95.2 %) and Bacillus polygoni YN-1T (95.0 %). DNA-DNA relatedness between strain BZ-SZ-XJ18T and the reference type strains of the related species of the genus Bacillus was lower than 27 %. The isolate formed yellow pigment and grew in the presence of 0.22-4.32 M Na+ (equivalent to 1.3-25.3 %, w/v, NaCl) (optimum 1.08 M Na+, equivalent to 6.3 %, w/v, NaCl), at pH 6.5-10.0 (optimum pH 8.5-9.5) and at 8-41 ºC (optimum 37 ºC). The major cellular fatty acids were anteiso-C15:0 (43.0 %), C16:0 (18.1 %), iso-C15:0 (11.3 %), anteiso-C17:0 (8.0 %) and iso-C16:0 (7.0 %). The major polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The main respiratory quinone was menaquinone-7 (MK-7), and the peptidoglycan type of the cell wall was A1γ based on meso-diaminopimelic acid as the diagnostic diamino acid. The genomic DNA G+C content was 42.3 mol% (HPLC) or 41.4 mol% (Tm). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BZ-SZ-XJ18T is proposed to represent a novel species, Bacillusurumqiensis within the genus Bacillus. The type strain is BZ-SZ-XJ18T (=DSM 29145T=JCM 30195T).

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

    SciTech Connect

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

    1986-10-01

    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 ..mu..mol/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.

  15. Production and characteristics of a bioflocculant produced by Bacillus sp. F19.

    PubMed

    Zheng, Yan; Ye, Zhi-Long; Fang, Xu-Liang; Li, Ya-Hong; Cai, Wei-Min

    2008-11-01

    A bioflocculant-producing bacterium isolated from soil was identified as Bacillus sp. and the bioflocculant produced was named MBFF19. Effects of physico-chemical conditions including pH, carbon sources and nitrogen sources on MBFF19 production were studied. Chemical analyses of the purified bioflocculant MBFF19 indicated that it was a sugar-protein derivative, composed of neutral sugar (3.6%, w/w), uronic acid (37.0%, w/w), amino sugars (0.5%, w/w) and protein (16.4%, w/w). The two neutral sugar components were mannose and glucose and the molar ratio was 1.2:1. Infrared spectrophotometry analysis revealed that MBFF19 contained carboxyl, hydroxyl and methoxyl groups in its structural. Flocculating properties of bioflocculant MBFF19 was examined using kaolin, activated carbon and fly coal suspension. Cation supplement had no positive effects on the flocculating activity whereas the presence of Fe3+ inhibited flocculation. Influences of pH and bioflocculant dosage on the flocculation were also examined.

  16. 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.

  17. 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

  18. 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.

  19. Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea.

    PubMed

    Jung, Min Young; Jung, Min-Young; Paek, Woon Kee; Park, In-Soon; Han, Jeong-Ran; Sin, Yeseul; Paek, Jayoung; Rhee, Moon-Soo; Kim, Hongik; Song, Hong Seok; Chang, Young-Hyo

    2010-12-01

    A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6(T), was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereus group, and is closely related to Bacillus mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), Bacillus weihenstephanensis (99.0%), Bacillus cereus (98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides (98.1%). The phylogenetic distance from any validly described Bacillus species outside the Bacillus cereus group was less than 95.6%. The DNA G+C content of the strain was 39.4 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C(14:0) (17.8%), iso-C(16:0) (15.8%), and iso-C(12:0) (11.3%). The diagnostic amino acid of the cell wall was meso-diaminopimelic acid and the major cell wall sugar was galactose. The results of DNA-DNA hybridization (<55.6%) and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain BL3-6(T) from the published Bacillus species. BL3-6(T) therefore represents a new species, for which the name Bacillus gaemokensis sp. nov. is proposed, with the type strain BL3-6(T) (=KCTC 13318(T) =JCM 15801(T)).

  20. 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

    2016-05-19

    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.

  1. 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

  2. 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

  3. Metabolism of 4-chloro-2-nitrophenol in a Gram-positive bacterium, Exiguobacterium sp. PMA

    PubMed Central

    2012-01-01

    Background Chloronitrophenols (CNPs) are widely used in the synthesis of dyes, drugs and pesticides, and constitute a major group of environmental pollutants. 4-Chloro-2-nitrophenol (4C2NP) is an isomer of CNPs that has been detected in various industrial effluents. A number of physicochemical methods have been used for treatment of wastewater containing 4C2NP. These methods are not as effective as microbial degradation, however. Results A 4C2NP-degrading bacterium, Exiguobacterium sp. PMA, which uses 4C2NP as the sole carbon and energy source was isolated from a chemically-contaminated site in India. Exiguobacterium sp. PMA degraded 4C2NP with the release of stoichiometeric amounts of chloride and ammonium ions. The effects of different substrate concentrations and various inoculum sizes on degradation of 4C2NP were investigated. Exiguobacterium sp. PMA degraded 4C2NP up to a concentration of 0.6 mM. High performance liquid chromatography and gas chromatography–mass spectrometry identified 4-chloro-2-aminophenol (4C2AP) and 2-aminophenol (2AP) as possible metabolites of the 4C2NP degradation pathway. The crude extract of 4C2NP-induced PMA cells contained enzymatic activity for 4C2NP reductase and 4C2AP dehalogenase, suggesting the involvement of these enzymes in the degradation of 4C2NP. Microcosm studies using sterile and non-sterile soils spiked with 4C2NP were carried out to monitor the bioremediation potential of Exiguobacterium sp. PMA. The bioremediation of 4C2NP by Exiguobacterium sp. PMA was faster in non-sterilized soil than sterilized soil. Conclusions Our studies indicate that Exiguobacterium sp. PMA may be useful for the bioremediation of 4C2NP-contaminated sites. This is the first report of (i) the formation of 2AP in the 4C2NP degradation pathway by any bacterium and (iii) the bioremediation of 4C2NP by any bacterium. PMID:23171039

  4. 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).

  5. 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

  6. 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.

  7. Degradation of 3-phenoxybenzoic acid by a Bacillus sp.

    PubMed

    Chen, Shaohua; Hu, Wei; Xiao, Ying; Deng, Yinyue; Jia, Jianwen; Hu, Meiying

    2012-01-01

    3-Phenoxybenzoic acid (3-PBA) is of great environmental concern with regards to endocrine disrupting activity and widespread occurrence in water and soil, yet little is known about microbial degradation in contaminated regions. We report here that a new bacterial strain isolated from soil, designated DG-02, was shown to degrade 95.6% of 50 mg·L(-1) 3-PBA within 72 h in mineral salt medium (MSM). Strain DG-02 was identified as Bacillus sp. based on the morphology, physio-biochemical tests and 16S rRNA sequence. The optimum conditions for 3-PBA degradation were determined to be 30.9°C and pH 7.7 using response surface methodology (RSM). The isolate converted 3-PBA to produce 3-(2-methoxyphenoxy) benzoic acid, protocatechuate, phenol, and 3,4-dihydroxy phenol, and subsequently transformed these compounds with a q(max), K(s) and K(i) of 0.8615 h(-1), 626.7842 mg·L(-1) and 6.7586 mg·L(-1), respectively. A novel microbial metabolic pathway for 3-PBA was proposed on the basis of these metabolites. Inoculation of strain DG-02 resulted in a higher degradation rate on 3-PBA than that observed in the non-inoculated soil. Moreover, the degradation process followed the first-order kinetics, and the half-life (t(1/2)) for 3-PBA was greatly reduced as compared to the non-inoculated control. This study highlights an important potential application of strain DG-02 for the in situ bioremediation of 3-PBA contaminated environments.

  8. Interrelationships between Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144 in the induced systemic resistance against Sclerotium rolfsii and symbiosis on peanut plants.

    PubMed

    Figueredo, Maria Soledad; Tonelli, Maria Laura; Taurian, Tania; Angelini, Jorge; Ibanez, Fernando; Valetti, Lucio; Munoz, Vanina; Anzuay, Maria Soledad; Luduena, Liliana; Fabra, Adriana

    2014-12-01

    Plant-growth-promoting bacteria are often used to enhance crop yield and for biological control of phytopathogens. Bacillus sp. CHEP5 is a biocontrol agent that induces systemic resistance (ISR) in Arachis hypogaea L. (peanut) against Sclerotium rolfsii, the causal agent of root and stem wilt. In this work, the effect of the co-inoculation of Bacillus sp. CHEP5 and the peanut nodulating strain Bradyrhizobium sp. SEMIA 6144 was studied on induction of both systemic resistance and nodulation processes. Bradyrhizobium sp. SEMIA 6144 did not affect the ability of Bacillus sp. CHEP5 to protect peanut plants from S. rolfsii by ISR and the priming in challenged-plants, as evidenced by an increment in phenylalanine ammonia-lyase enzyme activity. Additionally, the capacity of Bradyrhizobium sp. SEMIA 6144 to induce nodule formation in pathogen-challenged plants was improved by the presence of Bacillus sp. CHEP5.

  9. Identification and Production of Bioflocculants by Enterobacter sp. and Bacillus sp. and their Characterization Studies.

    PubMed

    Muthulakshmi, L; Nellaiah, H; Kathiresan, T; Rajini, N; Christopher, Fenila

    2017-02-16

    In this work, two bioflocculants, namely, EB-EPS and B1-EPS were derived from Enterobacter sp. and Bacillus sp., respectively and analyzed with regard to their production and characterization. About 0.9 g and 0.16 g of purified EB and B1 were obtained from I L of fermentation broth. Chemical analysis showed the contents of purified EB and B1 mainly as 88.7% and 92.8% (w/w) of carbohydrate, and 11.3% and 21.8% (w/w) protein, respectively. Fourier-transform infrared (FTIR) spectrometry analysis revealed the presence of hydroxyl, amide and carboxyl groups in the identified bioflocculant. TGA results exhibited enhanced thermal stability with a minimum mass loss of 50% while 25% were found to have occurred at higher temperatures (>400 °C) for microbial-derived compounds EB, B1 leading to the possibility of using these compounds as fillers or for fabricating composite films for high-temperature applications. Further, the compounds from both the bacteria exhibited good antibacterial characteristics against pathogenic E.coli. Degradability study of bioflocculant embedded composite films show the possibility of attaining eco-friendly bioremediation. Accordingly, experimental results revealed the suitability of developed composite films as a suitable alternative for food packaging and biomedical applications.

  10. Isolation and characterization of bacterial strains Paenibacillus sp. and Bacillus sp. for kraft lignin decolorization from pulp paper mill waste.

    PubMed

    Chandra, Ram; Singh, Shail; Krishna Reddy, M M; Patel, D K; Purohit, Hemant J; Kapley, Atya

    2008-12-01

    Eight aerobic bacterial strains were isolated from pulp paper mill waste and screened for tolerance of kraft lignin (KL) using the nutrient enrichment technique in mineral salt media (MSM) agar plate (15 g/L) amended with different concentrations of KL (100, 200, 300, 400, 500, 600 ppm) along with 1% glucose and 0.5% peptone (w/v) as additional carbon and nitrogen sources. The strains ITRC S6 and ITRC S8 were found to have the most potential for tolerance of the highest concentration of KL. These organisms were characterized by biochemical tests and further 16S rRNA gene (rDNA) sequencing, which showed 96.5% and 95% sequence similarity of ITRC S(6) and ITRC S(8) and confirmed them as Paenibacillus sp. and Bacillus sp., respectively. KL decolorization was routinely monitored with a spectrophotometer and further confirmed by HPLC analysis. Among eight strains, ITRC S(6) and ITRC S(8) were found to degrade 500 mg/L of KL up to 47.97% and 65.58%, respectively, within 144 h of incubation in the presence of 1% glucose and 0.5% (w/v) peptone as a supplementary source of carbon and nitrogen. In the absence of glucose and peptone, these bacteria were unable to utilize KL. The analysis of lignin degradation products by GC-MS analysis revealed the formation of various acids as lignin monomers which resulted in a decrease in pH and a major change in the chromatographic profile of the bacterial degraded sample as compared to the control clear indications of biochemical modification of KL due to the bacterial ligninolytic system by ITRC S(6), namely, acetic acid, propanoic acid, butanoic acid, guaiacol, hexanoic acid, and ITRC S(8), namely acetic acid, propanoic acid, ethanedioic acid, furan carboxylic acid, 2-propanoic acid, butanoic acid, 3-acetoxybutyric acid, propanedioic acid, acetoguiacone, 1,2,3-thiadiazole, 5-carboxaldixime, 4-hydroxy-3,5-dimethoxyphenol, and dibutyl phthalate, indicating the bacterium characteristic to degrade G and S units of lignin polymer.

  11. 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.

  12. Utilization of Phenylpropanoids by Newly Isolated Bacterium Pseudomonas sp. TRMK1.

    PubMed

    T R, Monisha; I, Mukram; B, Kirankumar; Reddy, Pooja V; Nayak, Anand S; Karegoudar, T B

    2017-01-25

    A bacterium Pseudomonas sp. TRMK1 capable of utilizing various phenylpropanoids was isolated from agro-industrial waste by enrichment culture technique. It is gram-negative, motile, aerobic, and able to utilize three different phenolic acids such as p-coumaric, ferulic, and caffeic acids at concentrations of 5, 10, and 15 mM in 18 h of incubation. The residual concentration of phenolic acids was analyzed by HPLC. The catabolic pathway of p-coumaric, ferulic, and caffeic acids is suggested based on the characterization of metabolic intermediates by GC, GC-HRMS, and different enzymatic assays. Further, Pseudomonas sp. TRMK1 utilizes a wide range of mixture of phenolic acids present in the synthetic effluent.

  13. 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.

  14. 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

  15. Rhodococcus sp. Q5, a novel agarolytic bacterium isolated from printing and dyeing wastewater.

    PubMed

    Feng, Zehua; Peng, Lin; Chen, Mei; Li, Mengying

    2012-09-01

    An agar-degrading bacterium, Rhodococcus sp. Q5, was isolated from printing and dyeing wastewater using a mineral salts agar plate containing agar as the sole carbon source. The bacterium grew from pH 4.0 to 9.0, from 15 to 35°C, and in NaCl concentrations of 0-5 %; optimal values were pH 6.0, 30°C, and 1 % NaCl. Maximal agarase production was observed at pH 6.0 and 30°C. The bacterium did not require NaCl for growth or agarase production. The agarase secreted by Q5 was inducible by agar and was repressed by all simple sugars tested except lactose. Strain Q5 could hydrolyze starch but not cellulose or carboxymethyl cellulose. Agarase activity could also be detected in the medium when lactose or starch was the sole source of carbon and energy. Strain Q5 could grow in nitrogen-free mineral media; an organic nitrogen source was more effective than inorganic carbon sources for growth and agarase production. Addition of more organic nitrogen (peptone) to the medium corresponded with reduced agarase activity.

  16. Anaerobranca zavarzinii sp. nov., an anaerobic, alkalithermophilic bacterium isolated from Kamchatka thermal fields.

    PubMed

    Kevbrin, Vadim; Boltyanskaya, Yulia; Garnova, Elena; Wiegel, Juergen

    2008-06-01

    A novel obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from a small and very shallow geothermally heated pool at Pushino (Kamchatka, Far East Russia). The bacterium, designated strain JW/VK-KS5Y(T), was a Gram staining negative, Gram type positive rod. The cells were sometimes branched, with a tendency to grow in long chains, and were non-sporulating and non-motile. The shortest observed doubling time was 28 min when the novel strain was grown at 54-60 degrees C in 120 mM sodium carbonate-containing medium at pH(25 degrees C) 8.5-9.0. The novel bacterium grew on yeast extract and soytone as sole carbon and energy sources but could also use fumarate, thiosulfate and sulfur as electron acceptors. The DNA G+C content was 32.5 mol%. Based on phylogenetic, DNA-DNA hybridization and phenotypic data, it was concluded that isolate JW/VK-KS5Y(T) (=VKM B-2436(T)=DSM 18970(T)) represents the type strain of a novel species, Anaerobranca zavarzinii sp. nov.

  17. 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.

  18. Isolation and Characterization of a Novel Electrogenic Bacterium, Dietzia sp. RNV-4

    PubMed Central

    Sacco, Natalia J.; Bonetto, M. Celina; Cortón, Eduardo

    2017-01-01

    Electrogenic bacteria are organisms that can transfer electrons to extracellular electron acceptors and have the potential to be used in devices such as bioelectrochemical systems (BES). In this study, Dietzia sp. RNV-4 bacterium has been isolated and identified based on its biochemical, physiological and morphological characteristics, as well as by its 16S rRNA sequence analysis. Furthermore, the current density production and electron transfer mechanisms were investigated using bioelectrochemical methods. The chronoamperometric data showed that the biofilm of Dietzia sp. RNV-4 grew as the current increased with time, reaching a maximum of 176.6 ± 66.1 mA/m2 at the end of the experiment (7 d); this highly suggests that the current was generated by the biofilm. The main electron transfer mechanism, indicated by the cyclic voltammograms, was due to secreted redox mediators. By high performance liquid chromatography, canthaxanthin was identified as the main compound involved in charge transfer between the bacteria and the solid electrodes. Dietzia sp. RNV-4 was used as biological material in a microbial fuel cell (MFC) and the current density production was 299.4 ± 40.2 mA/m2. This is the first time that Dietzia sp. RNV-4 has been electrochemically characterized and identified as a new electrogenic strain. PMID:28192491

  19. Endoglucanase and Xylanase Production by Bacillus sp. AR03 in Co-Culture Glycosyl Hydrolases by Bacillus sp. AR03 in Co-Culture.

    PubMed

    Hero, Johan S; Pisa, José H; Perotti, Nora I; Romero, Cintia M; Martínez, María A

    2017-01-20

    The behaviour of three isolates retrieved from different cellulolytic consortia, Bacillus sp. AR03, Paenibacillus sp. AR247 and Achromobacter sp. AR476-2, were examined individually and as co-cultures in order evaluate their ability to produce extracellular cellulases and xylanases. Utilizing a peptone-based medium supplemented with carboxymethyl cellulose (CMC), an increase estimated of 1.30 and 1.50 times was obtained by the co-culture containing the strains AR03 and AR247, with respect to enzyme titles registered by their individual cultivation. On the contrary, the extracellular enzymatic production decreased during the co-cultivation of strain AR03 with the non-cellulolytic Achromobacter sp. AR476-2. The synergistic behaviour observed through the combined cultivation of the strains AR03 and AR247 might be a consequence of the consumption by Paenibacillus sp. AR247 of the products of the CMC hydrolysis (i.e., cellobiose and/or cello- oligosaccharides), which were mostly generated by the cellulase producer Bacillus sp. AR03. The effect observed could be driven by the requirement to fulfil the nutritional supply from both strains on the substrate evaluated. These results would contribute to a better description of the degradation of the cellulose fraction of the plant cell walls in nature, expected to an efficient utilization of renewable sources.

  20. Draft genome of Bacillus sp. A053 isolated from the Arctic seawater with antimicrobial activity.

    PubMed

    Guo, Wenbin; Chen, Zhiteng; Cui, Pengfei; Chen, Xinhua

    2015-08-01

    Bacillus sp. A053, isolated from the Arctic seawater, shows strong antifungal activity against plant pathogenic fungi. Here, we report the draft sequence of the approximately 4.1-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Bacillus strain isolated from the Arctic seawater with antifungal activity. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compound in this strain.

  1. Co-inoculation with Bacillus sp. CECT 450 improves nodulation in Phaseolus vulgaris L.

    PubMed

    Camacho, M; Santamaría, C; Temprano, F; Rodriguez-Navarro, D N; Daza, A

    2001-11-01

    The strain Bacillus sp. CECT 450 increased nodulation on bean (Phaseolus vulgaris L.) when co-inoculated with Rhizobium tropici CIAT 899. This positive effect occured under controlled conditions on perlite-vermiculite, sand, or in a mixture of soil and sand. This increase was also observed in a field assay. Nodulation kinetic studies suggested that the synergistic effect is pronounced during the latter stages of cultivation. In contrast, the same bacteria co-inoculated with Bradyrhizobium japonicum USDA 110 reduced nodulation on soybean (Glycine max (L.) Merr.). Inoculation with Bacillus sp. CECT 450 alone had no effect on bean plants, but reduced root growth in soybean. The survival of Bacillus sp. CECT 450 on inoculated seeds was high, even when inoculated seeds were maintained for several months at room temperature.

  2. Fibrinolytic enzyme from newly isolated marine bacterium Bacillus subtilis ICTF-1: media optimization, purification and characterization.

    PubMed

    Mahajan, Prafulla M; Nayak, Shubhada; Lele, Smita S

    2012-03-01

    Fibrinolytic enzymes are important in treatment of cardiovascular diseases. The present work reports isolation, screening and identification of marine cultures for production of fibrinolytic enzymes. A potent fibrinolytic enzyme-producing bacterium was isolated from marine niches and identified as Bacillus subtilis ICTF-1 on the basis of the 16S rRNA gene sequencing and biochemical properties. Further, media optimization using L(18)-orthogonal array method resulted in enhanced production of fibrinolytic enzyme (8814 U/mL) which was 2.6 fold higher than in unoptimized medium (3420 U/mL). In vitro assays revealed that the enzyme could catalyze blood clot lysis effectively, indicating that this enzyme could be a useful thrombolytic agent. A fibrinolytic enzyme was purified from the culture supernatant to homogeneity by three step procedures with a 34.42-fold increase in specific activity and 7.5% recovery. This purified fibrinolytic enzyme had molecular mass of 28 kDa, optimal temperature and pH at 50 °C and 9, respectively. It was stable at pH 5.0-11.0 and temperature of 25-37 °C. The enzyme activity was activated by Ca(2+) and obviously inhibited by Zn(2+), Fe(3)(+), Hg(2+) and PMSF. The purified fibrinolytic enzyme showed high stability towards various surfactants and was relatively stable towards oxidizing agent. Considering these properties purified fibrinolytic enzyme also finds potential application in laundry detergents in addition to thrombolytic agent. The gene encoding fibrinolytic enzyme was isolated and its DNA sequence was determined. Compared the full DNA sequence with those in NCBI, it was considered to be a subtilisin like serine-protease.

  3. 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.

  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. Complete Genome Sequence of a Potential Novel Bacillus sp. Strain, FJAT-18017, Isolated from a Potato Field

    PubMed Central

    Liu, Guo-Hong; Wang, Jie-Ping; Che, Jian-Mei; Chen, Qian-Qian

    2017-01-01

    ABSTRACT Bacillus sp. strain FJAT-18017 was isolated from a potato field in Xinjiang, China. This paper is the first report, to our knowledge, to demonstrate the fully sequenced and completely annotated genome of Bacillus sp. FJAT-18017. The genome size is 5,265,521 bp. The average G+C content was 42.42%. PMID:28104649

  6. Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga.

    PubMed

    Verma, Ashish; Ojha, Anup Kumar; Kumari, Parveen; Sundharam, Shiva S; Mayilraj, Shanmugam; Krishnamurthi, Srinivasan

    2016-12-01

    A Gram-stain-negative, rod-shaped bacterium, forming yellow colonies and designated CDR SL 15T, was isolated from the surface of Padina sp., a brown macroalga, which grows in the Western coastal regions of the state of Goa, India. The 16S rRNA gene sequence phylogeny placed the strain in the genus Luteimonas and it showed closest sequence similarity to Luteimonas terricola BZ92rT (97.6 %) and <97.0 % to other species of the genus Luteimonas. Chemotaxonomic features, such as having iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl/iso-C17 : 1ω9c) as the major fatty acids and Q-8 as the only ubiquinone further supported its placement within this genus. There were some critical differences in phenotypic properties between Luteimonas padinae sp. nov. CDR SL 15T and L. terricola DSM 22344T i.e. temperature range for growth and salinity range and optimum for growth (L. terricola is a psychrotolerant bacterium with a lower optimum temperature for growth), acid production and assimilation of substrates, enzyme activities and resistance to certain antibiotics. The DNA-DNA relatedness value of the novel strain with its closest phylogenetic relative was only 40 %, below the 70 % threshold value recommended for species delineation. All these characteristics are consistent with strain CDR SL 15T representing a novel species of the genus Luteimonas, for which the name Luteimonas padinae sp. nov. is proposed. The type strain is CDR SL 15T (=DSM 101536T=KCTC 52403T).

  7. Oceanobacillus caeni sp. nov., isolated from a Bacillus-dominated wastewater treatment system in Korea.

    PubMed

    Nam, Ji-Hyun; Bae, Wookeun; Lee, Dong-Hun

    2008-05-01

    A Gram-positive, rod-shaped, spore-forming bacterium, strain S-11T, was isolated from the activated sludge of a Bacillus-dominated wastewater treatment system in South Korea and was characterized using a polyphasic approach in order to determine its taxonomic position. Cells (0.5-0.6 x 2.0-2.2 microm) were motile by means of a single subpolar flagellum. They bore ellipsoidal endospores that lay in a central position in swollen sporangia. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S-11T was a member of the genus Oceanobacillus. 16S rRNA gene sequence similarity values and DNA-DNA relatedness of strain S-11T to the type strains of other Oceanobacillus species were less than 96.2 and 66.0 %, respectively. Strain S-11T showed distinct differences in the G+C content of the genomic DNA (33.6 mol%). The major cellular fatty acids were iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. There were also some physiological differences in comparison with the type strains of Oceanobacillus species: tests for production of acetoin and acid production from dulcitol, erythritol, myo-inositol and sorbitol were positive. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain S-11T from the six Oceanobacillus species and subspecies with validly published names. Strain S-11T therefore represents a novel species, for which the name Oceanobacillus caeni sp. nov. is proposed, with the type strain S-11T (=KCTC 13061T =CCUG 53534T =CIP 109363T).

  8. 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

  9. 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

    2016-01-04

    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.

  10. Kordia ulvae sp. nov., a bacterium isolated from the surface of green marine algae Ulva sp.

    PubMed

    Qi, Feng; Huang, Zhaobin; Lai, Qiliang; Li, Dengfeng; Shao, Zongze

    2016-04-20

    A novel bacterial strain SC2T was isolated from Ulva sp. a green marine algae. Strain SC2T was Gram-negative, aerobic, rod-shaped and had no flagellum. Oxidase and catalase were positive. Strain SC2T can degrade skim milk, agar, soluble starch, Tween 20 and Tween 80. The optimal salinity and temperature of strain SC2T were 2% and 30 °C, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that strain SC2T was affiliated to the genus Kordia, with highest sequence similarity to Kordia algicida OT-1T (97.23%), Kordia antarctica IMCC3317T (97.23%) and Kordia jejudonensis SSK3-3T (97.02%); other species of the genus Kordia shared 93.98%-95.78% sequence similarity. The ANI value and the DNA-DNA hybridization estimated value between strain SC2T and three type strains (K. algicida OT-1T, K. antarctica IMCC3317T and K. jejudonensis SSK3-3T) were found to be 79.4%-82.4% and 24.2%-27.0%, respectively. The predominant fatty acids (>5.0%) were C16:0, iso-C15:0, iso-C15:0 3-OH, iso-C17:0 3-OH, summed feature 3 (comprised C16:1 ω7c/C16:1 ω6c), summed feature 8 (comprised C18:1 ω7c/C18:1 ω6c) and summed feature 9 (comprised iso-C17:1 ω9c/C16:0 10-methyl). The respiratory quinone was Menaquinone-6 (MK-6). The polar lipid profile consisted of four unknown lipids, three unidentified phospholipids, one unidentified aminolipid and one phosphatidylethanolamine. The G+C content of the genomic DNA was 34.5 mol%. The combined genotypic and phenotypic data showed that strain SC2T represents a novel species within the genus Kordia, for which the name Kordia ulvae sp. nov. is proposed, with the type strain SC2T (= KCTC 42872T = MCCC 1A01772T = LMG 29123T).

  11. 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

  12. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

    PubMed

    Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

    2004-09-01

    The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T).

  13. Shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the Alboran Sea.

    PubMed

    Makemson, J C; Fulayfil, N R; Landry, W; Van Ert, L M; Wimpee, C F; Widder, E A; Case, J F

    1997-10-01

    Thirty-four strains of nonfermentative, respiratory, luminous bacteria were isolated from samples of squid ink and seawater from depths of 200 to 300 m in the Alboran Sea. Although these strains had a few properties similar to properties of Shewanella (Alteromonas) hanedai, they did not cluster phenotypically with any previously described bacterium. The nucleotide sequence of a 740-bp segment of luxA was not homologous with other known luxA sequences but clustered with the luxA sequences of Shewanella hanedai, Vibrio logei, Vibrio fischeri, and Photobacterium species. The 16S RNA gene from two strains was sequenced and was found to be most closely related to the S. hanedai 16S RNA gene. Based on the differences observed, we describe the new isolates as members of new species, Shewanella woodyi sp. nov. Strain ATCC 51908 (= MS32) is the type strain of this new species.

  14. Exopolysaccharide of Antarctic bacterium Pseudoaltermonas sp. S-5 induces apoptosis in K562 cells.

    PubMed

    Chen, Guochuang; Qian, Wen; Li, Jing; Xu, Yanghui; Chen, Kaoshan

    2015-05-05

    The aim of this study was to investigate the anticancer activity of exopolysaccharide (PEP) of Antarctic bacterium Pseudoaltermonas sp. S-5 and elucidate the underlying molecular mechanisms. PEP significantly inhibited the growth of human leukemia K562 cells. Results of morphological characterization showed that PEP-treated cells displayed typical morphological characteristics of apoptosis such as condensation of chromatin and formation of apoptotic bodies. Flow cytometry analyses and colorimetric assay demonstrated that PEP induced collapse of mitochondrial membrane potential and activation of caspase-9, which indicated that intrinsic apoptotic signaling pathway was involved in apoptosis induced by PEP in K562 cells. Western blot analysis showed that PEP increased the ratio of Bax/Bcl-2. In addition, calcium signal might contribute to the cytotoxicity of PEP against K562 cells. These findings suggest that PEP may be potentially effective drug against human leukemia.

  15. [Isolation, identification and degradation characteristics of a quinoline-degrading bacterium Rhodococcus sp QL2].

    PubMed

    Zhu, Shun-ni; Liu, Dong-qi; Fan, Li; Ni, Jin-ren

    2008-02-01

    A quinoline-degrading bacterium QL2, which utilizes quinoline as sole source of carbon, nitrogen and energy, was isolated from activated sludge in a coke-plant wastewater biological treatment system. According to the morphological characteristics, physiological and biochemical characteristics, and sequence analysis of 16S rRNA, the strain was identified as Rhodococcus sp.. The optimal temperature, initial pH, and shaker rotary speed for strain QL2 utilizing quinoline are 35-42 degrees C, pH 8-9, and 150 r/min, respectively. Extra nitrogen sources stimulate the isolate growth on quinoline, and inorganic nitrogen better than organic nitrogen, NH4+ -N better than NO3(-) -N. The degradation reaction of quinoline by strain QL2 can be described with zero order kinetic equation within the initial quinoline concentrations of 60-680 mg/L. When the initial concentration was 150 mg/L, quinoline was degraded completely in 8 hours and TOC removal efficiency was 70% in 14 hours. This bacterium produced pigmented compounds, and ring nitrogen was released into the growth medium as ammonium. The main intermediate in the degradation pathway was 2-hydroxyquinoline by the analysis of HPLC and GC/MS. With a broad range of substrate utilization, the strain can degrade phenol, naphthalene, pyridine, and some other kinds of aromatic compounds.

  16. Thiorhodococcus mannitoliphagus sp. nov., a purple sulfur bacterium from the White Sea.

    PubMed

    Rabold, Sandra; Gorlenko, Vladimir M; Imhoff, Johannes F

    2006-08-01

    A novel purple sulfur bacterium, strain WS(T), was isolated from a microbial mat from an estuary of the White Sea. Individual cells are coccoid shaped, motile by flagella and do not contain gas vesicles. The mean cell diameter is 1.85 mum (range 1.5-2.0 mum). Cell suspensions exhibit a purple-violet colour. They contain bacteriochlorophyll a and carotenoids of the rhodopinal series as photosynthetic pigments. The novel bacterium is an anoxygenic photoautotroph, using sulfide, thiosulfate, sulfite and elemental sulfur as electron donors for photosynthesis and is capable of photoassimilating several organic carbon sources in the presence of carbonate and a reduced sulfur source (sulfide and/or thiosulfate). Sulfur globules, formed during oxidation of sulfide, are stored transiently inside the cells. Optimal salinity and pH for growth are at 0.5-2.0 % NaCl and pH 7.0-7.5. The DNA base composition of strain WS(T) is 61.8 mol% G+C. 16S rRNA gene sequence analysis showed that the new isolate belongs to the genus Thiorhodococcus, with Thiorhodococcus minor CE2203(T) as the nearest relative (sequence similarity of 97.3 %). Several distinct differences from described species necessitate the description of a novel species. Thiorhodococcus mannitoliphagus sp. nov. is the proposed name, with strain WS(T) (=ATCC BAA-1228(T)=VKM B-2393(T)) as the type strain.

  17. Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil.

    PubMed

    Vasilyeva, Lina V; Omelchenko, Marina V; Berestovskaya, Yulia Y; Lysenko, Anatolii M; Abraham, Wolf-Rainer; Dedysh, Svetlana N; Zavarzin, George A

    2006-09-01

    A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023(T). Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023(T) was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 degrees Celsius (optimum 15-20 degrees Celsius) and between pH 4.5 and 8.0 (optimum 5.6-6.0). The major phospholipid fatty acid was 18 : 1omega7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023(T) was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA-DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023(T) (=DSM 16100(T)=ATCC BAA-896(T)).

  18. Isolation and characterization of an anaerobic, cellulolytic bacterium, Clostridium cellulovorans sp. nov

    SciTech Connect

    Sleat, R.; Mah, R.A.; Robinson, R.

    1984-07-01

    A new anaerobic, mesophilic, spore-forming cellulolytic bacterium is described. Cellulose is cleared within 24 to 48 h around colonies formed in cellulose agar roll tubes. Cells stain gram negative and are nonmotile rods which form oblong spores either centrally or subterminally in a clostridial swelling. Colonies are irregular with an opaque edge and a center devoid of both vegetative cells and spores. Cellulose, xylan, pectin, cellubiose, glucose, maltose, galactose, sucrose, lactose, and mannose serve as substrates for growth. H/sub 2/, CO/sub 2/, acetate, butyrate, formate, and lactate are produced during fermentation of cellulose or cellobiose. The temperature and pH for optimum growth are 37/sup 0/C and 7.0, respectively. The DNA composition is 26 to 27 mol% guanine plus cytosine. This bacterium resembles Clostridium lochhheadii in morphological and some biochemical characteristics but is not identical to it. The name Clostridium cellulovorans sp. nov. is proposed. The type strain is 743B (ATCC 35296).

  19. 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).

  20. Identification of 4″-isovaleryl-spiramycin III produced by Bacillus sp. fmbJ.

    PubMed

    Deng, Yang; Ju, Yanjuan; Lu, Zhaoxin; Lu, Fengxia; Yan, Dong; Bie, Xiaomei

    2014-02-01

    The production of secondary metabolites with antibiotic properties is a common characteristic to Bacillus spp. These metabolites not only have diverse chemical structures but also have a wide range of bioactivities with medicinal and agricultural interests such as antibiotic. Bacillus sp. fmbJ has been found to produce lipopeptides fengycin and surfactin in accordance with our previous report. In this study, another antimicrobial substance was separated and purified from the culture supernatant of strain fmbJ using the silica gel column chromatography and preparative reversed-phase high-performance liquid chromatography. By means of electrospray ionization mass spectroscopy, infrared spectroscopy, and nuclear magnetic resonance, the antagonistic compound was determined to be 4″-isovaleryl-spiramycin III with the molecular weight of 982 Da. This report is the first to introduce the finding of spiramycin produced from Bacillus sp. The study provides a novel source for the production of spiramycin in pharmaceutical industries.

  1. Complete genome of Bacillus sp. Pc3 isolated from the Antarctic seawater with antimicrobial activity.

    PubMed

    Guo, Wenbin; Cui, Pengfei; Chen, Xinhua

    2015-04-01

    Bacillus sp. Pc3 was isolated from the Antarctic seawater with strong antifungal activity against several plant pathogenic fungi. Here, we report the complete sequence of the 3.9-Mbp genome of this strain. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of antimicrobial compounds in this strain.

  2. 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

  3. 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...

  4. 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 ...

  5. 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...

  6. Draft Genome Sequence of Enterobacter sp. Sa187, an Endophytic Bacterium Isolated from the Desert Plant Indigofera argentea

    PubMed Central

    Lafi, Feras F.; Alam, Intikhab; Geurts, Rene; Bisseling, Ton; Bajic, Vladimir B.

    2017-01-01

    ABSTRACT Enterobacter sp. Sa187 is a plant endophytic bacterium, isolated from root nodules of the desert plant Indigofera argentea, collected from the Jizan region of Saudi Arabia. Here, we report the genome sequence of Sa187, highlighting several genes involved in plant growth–promoting activity and environmental adaption. PMID:28209831

  7. Genome Sequence of the Facultative Anaerobic Arsenite-Oxidizing and Nitrate-Reducing Bacterium Acidovorax sp. Strain NO1

    PubMed Central

    Huang, Yinyan; Li, Hang; Rensing, Christopher; Zhao, Kai; Johnstone, Laurel

    2012-01-01

    Acidovorax sp. strain NO1, isolated from gold mine soil, was shown to be a facultative anaerobic arsenite-oxidizing and nitrate-reducing bacterium. The reported draft genome predicts the presence of genes involved in arsenic metabolism, nitrate reduction, phosphate transport, and multiple metal resistances and indicates putative horizontal gene transfer events. PMID:22374962

  8. Bacillus gossypii sp. nov., isolated from the stem of Gossypium hirsutum.

    PubMed

    Kämpfer, Peter; Busse, Hans-Jürgen; McInroy, John A; Glaeser, Stefanie P

    2015-11-01

    A Gram-stain-positive, facultatively anaerobic, endospore-forming organism, isolated from the stem of Gossypium hirsutum, was studied to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity comparisons, strain JM-267T was grouped in the genus Bacillus, related most closely to the type strains of Bacillus simplex and Bacillus huizhouensis (both 97.8%), Bacillus muralis (97.7%), Bacillus butanolivorans and Bacillus psychrosaccharolyticus (both 97.3%). 16S rRNA gene sequence similarity to the sequences of the type strains of other Bacillus species was < 97.0%. The fatty acid profile supported the grouping of the strain to the genus Bacillus. As major fatty acids, anteiso-C15:0, iso-C15:0, iso-C14:0 and iso-C16:0 were detected. The polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major quinone was menaquinone 7 (MK-7). DNA-DNA hybridizations with B. simplex DSM 1321T, B. huizhouensis GSS03T, B. muralis LMG 20238T, B. butanolivorans LMG 23974T and B. psychrosaccharolyticus DSM 6T resulted in values clearly below 70%. In addition, physiological and biochemical test results allowed the clear phenotypic differentiation of strain JM-267T from the most closely related species. Hence, strain JM-267T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus gossypii sp. nov. is proposed. The type strain is JM-267T ( = DSM 100034T = LMG 28742T).

  9. Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant.

    PubMed

    Vaz-Moreira, Ivone; Figueira, Vânia; Lopes, Ana R; Lobo-da-Cunha, Alexandre; Spröer, Cathrin; Schumann, Peter; Nunes, Olga C; Manaia, Célia M

    2012-01-01

    A Gram-positive, aerobic, non-motile, endospore-forming rod, designated DS22(T), was isolated from a drinking-water treatment plant. Cells were catalase- and oxidase-positive. Growth occurred at 15-37 °C, at pH 7-10 and with <8% (w/v) NaCl (optimum growth: 30 °C, pH 7-8 and 1-3% NaCl). The major respiratory quinone was menaquinone 7, the G+C content of the genomic DNA was 36.5 mol% and the cell wall contained meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis, strain DS22(T) was a member of the genus Bacillus. Its closest phylogenetic neighbours were Bacillus horneckiae NRRL B-59162(T) (98.5% 16S rRNA gene sequence similarity), Bacillus oceanisediminis H2(T) (97.9%), Bacillus infantis SMC 4352-1(T) (97.4%), Bacillus firmus IAM 12464(T) (96.8%) and Bacillus muralis LMG 20238(T) (96.8%). DNA-DNA hybridization, and biochemical and physiological characterization allowed the differentiation of strain DS22(T) from its closest phylogenetic neighbours. The data supports the proposal of a novel species, Bacillus purgationiresistans sp. nov.; the type strain is DS22(T) (=DSM 23494(T)=NRRL B-59432(T)=LMG 25783(T)).

  10. 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

  11. 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

  12. Draft genome sequence of the plant growth-promoting bacterium Bacillus siamensis KCTC 13613T.

    PubMed

    Jeong, Haeyoung; Jeong, Da-Eun; Kim, Sun Hong; Song, Geun Cheol; Park, Soo-Young; Ryu, Choong-Min; Park, Seung-Hwan; Choi, Soo-Keun

    2012-08-01

    Bacillus siamensis KCTC 13613(T), a novel halophilic Bacillus species isolated from a salted Thai food, produced antimicrobial compounds against plant pathogens and promoted plant growth by volatile emission. We determined the 3.8-Mb genome sequence of B. siamensis KCTC 13613(T) to reveal the plant-beneficial effect at the genomic level.

  13. Lacinutrix gracilariae sp. nov., a bacterium isolated from the surface of a marine red alga Gracilaria sp.

    PubMed

    Huang, Zhaobin; Li, Guizhen; Lai, Qiliang; Gu, Li; Shao, Zongze

    2015-11-09

    A Gram-negative, aerobic, non-flagellated, rod-shaped bacterium, designated as strain Lxc1T, was isolated from the surface of a marine red alga, Gracilaria sp., which was collected from the coastal regions in Jinjiang, Fujian Province, China. The colony of the strain was orange-yellow, circular and smooth. The 16S rRNA gene of Lxc1T had maximum sequence similarity with Lacinutrix himadriensis E4-9aT (97.1%), followed by L. jangbogonensis PAMC 27137T, L. copepodicola DJ3T, L. algicola AKS293T, and L. mariniflava AKS 432T (similarities <96.4%). Phylogenetic analysis showed strain Lxc1T formed a tight cluster with L. himadriensis E4-9aT and L. copepodicola DJ3T, but represented a novel lineage belonging to the genus Lacinutrix. The predominant fatty acids were iso-C15:1 G (18.3%), iso-C15:0 (16.7%), iso-C17:0-3OH (10.6%), and iso-C15:0-3OH (8.6%). Menaquinone-6 (MK-6) was the only respiratory quinone present. The DNA G+C content of Lxc1T was 31.7 mol%. Combining the results above, it was ascertained that the strain Lxc1T represented a novel species of the genus Lacinutrix, for which the name Lacinutrix gracilariae sp. nov. is proposed. The type strain is Lxc1T (=MCCC 1A01567T=KCTC 42808T).

  14. Aurantibacter crassamenti gen. nov., sp. nov., a bacterium isolated from marine sediment.

    PubMed

    Yoon, Jaewoo; Kasai, Hiroaki

    2017-01-01

    A Gram-stain-negative, strictly aerobic, orange-colored, rod-shaped, chemoheterotrophic bacterium, designated HG732(T), was isolated from marine sediment 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 (94.1 %) sequence similarity with Kriegella aquimaris KMM 3665(T). The strain could be differentiated phenotypically from related members of the family Flavobacteriaceae. Major fatty acids of strain HG732(T) were iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, three unidentidied aminolipids and two unidentified lipids. The DNA G+C content of the strain was determined to be 35.2 mol%, and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Aurantibacter crassamenti gen. nov., sp. nov. is proposed. The type strain of A. crassamenti gen. nov., sp. nov. is HG732(T) (= KCTC 52207(T) = NBRC 112211(T)).

  15. Propionate-degrading bacterium, Syntrophobacter wolinii sp. nov. gen. nov. , from methanogenic ecosystems

    SciTech Connect

    Boone, D.R.; Bryant, M.P.

    1980-09-01

    A new genus and species of a nonmotile gram-negative rod, Syntrophobacter wolinii, is the first bacterium described which degrades propionate only in coculture with an H/sub 2/-using organism and in the absence of light or exogenous electron acceptors such as O/sub 2/, sulfate, or nitrate. It was isolated from methanogenic enrichments from an anaerobic municipal sewage digestor, using anaerobic roll tubes containing a medium with propionate as the energy source in association with an H/sub 2/-using, sulfate-reducing Desulfovibrio sp. which cannot utilize fatty acids other than formate. S. wolinii produced acetate and, presumably, CO/sub 2/ and H/sub 2/ (or formate) from propionate. In media without sulfate and with Methanospirillum hungatei, a methanogen that uses only H/sub 2/-CO/sub 2/ or formate as an energy source, acetate, methane, and, presumably, CO/sub 2/ were produced from propionate and only small amounts of Desulfovibrio sp. were present. Isolation in coculture with the methanogen was not successful. S. wolinii does not use other saturated fatty acids as energy sources. 2 figures, 3 tables.

  16. 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

  17. Adenosine deaminase production by an endophytic bacterium (Lysinibacillus sp.) from Avicennia marina.

    PubMed

    Kathiresan, Kandasamy; Saravanakumar, Kandasamy; Sahu, Sunil Kumar; Sivasankaran, Muthu

    2014-06-01

    The present study was carried out with the following objectives: (1) to isolate the endophytic bacilli strains from the leaves of mangrove plant Avicennia marina, (2) to screen the potential strains for the production of adenosine deaminase, (3) to statistically optimize the factors that influence the enzyme activity in the potent strain, and (4) to identify the potent strain using 16S rRNA sequence and construct its phylogenetic tree. The bacterial strains isolated from the fresh leaves of a mangrove A. marina were assessed for adenosine deaminase activity by plating method. Optimization of reaction process was carried out using response surface methodology of central composite design. The potent strain was identified based on 16S rRNA sequencing and phylogeny. Of five endophytic strains, EMLK1 showed a significant deaminase activity over other four strains. The conditions for maximum activity of the isolated adenosine deaminase are described. The potent strain EMLK1 was identified as Lysinibacillus sp. (JQ710723) being the first report as a mangrove endophyte. Mangrove-derived endophytic bacillus strain Lysinibacillus sp. EMLK1 is proved to be a promising source for the production of adenosine deaminase and this enzyme deserves further studies for purification and its application in disease diagnosis.

  18. 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

  19. 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.

  20. Bacillus cytotoxicus sp. nov. is a novel thermotolerant species of the Bacillus cereus Group occasionally associated with food poisoning.

    PubMed

    Guinebretière, Marie-Hélène; Auger, Sandrine; Galleron, Nathalie; Contzen, Matthias; De Sarrau, Benoit; De Buyser, Marie-Laure; Lamberet, Gilles; Fagerlund, Annette; Granum, Per Einar; Lereclus, Didier; De Vos, Paul; Nguyen-The, Christophe; Sorokin, Alexei

    2013-01-01

    An aerobic endospore-forming bacillus (NVH 391-98(T)) was isolated during a severe food poisoning outbreak in France in 1998, and four other similar strains have since been isolated, also mostly from food poisoning cases. Based on 16S rRNA gene sequence similarity, these strains were shown to belong to the Bacillus cereus Group (over 97% similarity with the current Group species) and phylogenetic distance from other validly described species of the genus Bacillus was less than 95%. Based on 16S rRNA gene sequence similarity and MLST data, these novel strains were shown to form a robust and well-separated cluster in the B. cereus Group, and constituted the most distant cluster from species of this Group. Major fatty acids (iso-C(15:0), C(16:0), iso-C(17:0), anteiso-C(15 : 0), iso-C(16:0), iso-C(13:0)) supported the affiliation of these strains to the genus Bacillus, and more specifically to the B. cereus Group. NVH 391-98(T) taxon was more specifically characterized by an abundance of iso-C(15:0) and low amounts of iso-C(13:0) compared with other members of the B. cereus Group. Genome similarity together with DNA-DNA hybridization values and physiological and biochemical tests made it possible to genotypically and phenotypically differentiate NVH 391-98(T) taxon from the six current B. cereus Group species. NVH 391-98(T) therefore represents a novel species, for which the name Bacillus cytotoxicus sp. nov. is proposed, with the type strain NVH 391-98(T) (= DSM 22905(T) = CIP 110041(T)).

  1. 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).

  2. Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir.

    PubMed

    Feio, Maria J; Zinkevich, Vitaly; Beech, Iwona B; Llobet-Brossa, Enric; Eaton, Peter; Schmitt, Jürgen; Guezennec, Jean

    2004-09-01

    A novel sulphate-reducing bacterium (Al1T) was recovered from a soured oil well in Purdu Bay, Alaska. Light and atomic force microscopy observations revealed that cells were Gram-negative, vibrio-shaped and motile by means of a single polar flagellum. The carbon and energy sources used by the isolate and the salinity, temperature and pH ranges facilitating its growth proved to be typical of a partial lactate-oxidizing, moderately halophilic, mesophilic, sulphate-reducing bacterium. Analysis of the fatty acid profile revealed that C(18 : 0), isoC(15 : 0) and isoC(17 : 1)omega7c were the predominant species. Fatty acid profile and complete 16S rRNA gene sequencing demonstrated the similarity between strain Al1T and members of the genus Desulfovibrio. The position of strain Al1T within the phylogenetic tree indicated that it clustered closely with Desulfovibrio vietnamensis DSM 10520T (98.9 % sequence similarity), a strain recovered from a similar habitat. However, whole-cell protein profiles, Fourier-transform infrared studies and DNA-DNA hybridization demonstrated that, in spite of the high level of 16S rRNA gene sequence similarity, there is sufficient dissimilarity at the DNA sequence level between D. vietnamensis DSM 10520T and strain Al1T (10.2 % similarity) to propose that strain Al1T belongs to a separate species within the genus Desulfovibrio. Based on the results obtained, the name Desulfovibrio alaskensis sp. nov. is therefore proposed, with Al1T (= NCIMB 13491T = DSM 16109T) as the type strain.

  3. 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

    2016-01-04

    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.

  4. Geobacter luticola sp. nov., an Fe(III)-reducing bacterium isolated from lotus field mud.

    PubMed

    Viulu, Samson; Nakamura, Kohei; Okada, Yurina; Saitou, Sakiko; Takamizawa, Kazuhiro

    2013-02-01

    A novel species of Fe(III)-reducing bacterium, designated strain OSK6(T), belonging to the genus Geobacter, was isolated from lotus field mud in Japan. Strain OSK6(T) was isolated using a solid medium containing acetate, Fe(III)-nitrilotriacetate (NTA) and gellan gum. The isolate is a strictly anaerobic, gram-negative, motile, straight rod-shaped bacterium, 0.6-1.9 µm long and 0.2-0.4 µm wide. The growth of the isolate occurred at 20-40 °C with optima of 30-37 °C and pH 6.5-7.5 in the presence of up to 0.5 g NaCl l(-1). The G+C content of the genomic DNA was determined by HPLC to be 59.7 mol%. The major respiratory quinone was MK-8. The major fatty acids were 16 : 1ω7c and 16 : 0. Strain OSK6(T) was able to grow with Fe(III)-NTA, ferric citrate, amorphous iron (III) hydroxide and nitrate, but not with fumarate, malate or sulfate as electron acceptors. Among examined substrates grown with Fe(III)-NTA, the isolate grew on acetate, lactate, pyruvate and succinate. Analysis of the near full-length 16S rRNA gene sequence revealed that strain OSK6(T) is closely related to Geobacter daltonii and Geobacter toluenoxydans with 95.6 % similarity to the type strains of these species. On the basis of phylogenetic analysis and physiological tests, strain OSK6(T) is described as a representative of a novel species, Geobacter luticola sp. nov.; the type strain is OSK6(T) ( = DSM 24905(T) = JCM 17780(T)).

  5. Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment.

    PubMed

    Urakawa, Hidetoshi; Garcia, Juan C; Nielsen, Jeppe L; Le, Vang Q; Kozlowski, Jessica A; Stein, Lisa Y; Lim, Chee Kent; Pommerening-Röser, Andreas; Martens-Habbena, Willm; Stahl, David A; Klotz, Martin G

    2015-01-01

    A Gram-negative, spiral-shaped, chemolithotrophic, ammonia-oxidizing bacterium, designated APG3(T), was isolated into pure culture from sandy lake sediment collected from Green Lake, Seattle, WA, USA. Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain APG3(T) belongs to cluster 0 of the genus Nitrosospira, which is presently not represented by described species, with Nitrosospira multiformis (cluster 3) as the closest species with a validly published name (identity of 98.6 % to the type strain). Strain APG3(T) grew at 4 °C but could not grow at 35 °C, indicating that this bacterium is psychrotolerant. Remarkably, the strain was able to grow over a wide range of pH (pH 5-9), which was greater than the pH range of any studied ammonia-oxidizing bacteria in pure culture. The DNA G+C content of the APG3(T) genome is 53.5 %, which is similar to that of Nitrosospira multiformis ATCC 25196(T) (53.9 %) but higher than that of Nitrosomonas europaea ATCC 19718 (50.7 %) and Nitrosomonas eutropha C71 (48.5 %). The average nucleotide identity (ANI) calculated for the genomes of strain APG3(T) and Nitrosospira multiformis ATCC 25196(T) was 75.45 %, significantly lower than the value of 95 % ANI that corresponds to the 70 % species-level cut-off based on DNA-DNA hybridization. Overall polyphasic taxonomy study indicated that strain APG3(T) represents a novel species in the genus Nitrosospira, for which the name Nitrosospira lacus sp. nov. is proposed (type strain APG3(T) = NCIMB 14869(T) = LMG 27536(T) = ATCC BAA-2542(T)).

  6. Psychrobacter fjordensis sp. nov., a psychrotolerant bacterium isolated from an Arctic fjord in Svalbard.

    PubMed

    Zeng, Yin-Xin; Yu, Yong; Li, Hui-Rong; Luo, Wei

    2015-12-01

    A Gram-negative, non-motile, non-spore-forming, psychrotolerant and halotolerant bacterium designated BSw21516B(T), was obtained from seawater in Kongsfjorden, a glacial fjord in the Arctic Svalbard and subjected to taxonomic analysis using a polyphasic approach. This bacterium was observed to optimally grow at 25-29 °C; between at 4 and 34 °C, but not at >35 °C; and in the presence of 0-8 % (w/v) NaCl at an optimum concentration of 2-5 % (w/v) NaCl. Strain BSw21516B(T) was found to contain Ubiquinone-8 (Q-8) as a predominant respiratory lipoquinone and C18:1 ω9c and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as predominant cellular fatty acids. Phylogenetic analysis of 16S rRNA and gyrB gene sequences showed that this isolate belongs to the genus Psychrobacter and is closely related to Psychrobacter fozii LMG 21280(T), which was isolated from a sediment sample in Antarctica. DNA hybridization experiments revealed a low level of DNA-DNA relatedness (less than 58.6 %) between strain BSw21516B(T) and its closest relatives. Based on these results a new species Psychrobacter fjordensis sp. nov. is proposed (type strain BSw21516B(T) = KCTC 42279(T) = CCTCC AB 2014020(T)).

  7. Flavobacterium arsenitoxidans sp. nov., an arsenite-oxidizing bacterium from Thai soil.

    PubMed

    Khianngam, Saowapar; Akaracharanya, Ancharida; Lee, Jung-Sook; Lee, Keun Chul; Kim, Kyoung-Woong; Tanasupawat, Somboon

    2014-12-01

    An arsenite-oxidizing bacterium, strain S2-3H(T), was isolated from arsenic-contaminated soil sample collected from Dantchaeng district, Suphanburi province, Thailand and was characterized based on polyphasic taxonomic study. The strain was observed to be a Gram-stain negative, aerobic, yellow pigmented, non-spore forming and rod-shaped bacterium. Major menaquinone was MK-6. Iso-C15:0, iso-C15:0 3OH, C16:1 ω7c/C16:1 ω6c, C16:0, iso-C17:0 3OH, and C16:0 3OH were the predominant cellular fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, unidentified phospholipids and unidentified aminophospholipids. The DNA G+C content was 37.0 mol%. Phylogenetic analysis using 16S rRNA sequence showed that strain S2-3H(T) is affiliated to the genus Flavobacterium, and is closely related to F. defluvii KCTC 12612(T) (97.0 %) and F. johnsoniae NBRC 14942(T) (97.0 %). The strain S2-3H(T) could be clearly distinguished from the related Flavobacterium species by its physiological and biochemical characteristics as well as its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Flavobacterium, for which the name Flavobacterium arsenitoxidans sp. nov. (type strain S2-3H(T) = KCTC 22507(T) = NBRC 109607(T) = PCU 331(T) = TISTR 2238(T)) is proposed.

  8. 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

  9. Crystal structure of the inactive state of the receiver domain of Spo0A from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier.

    PubMed

    Lee, Chang Woo; Park, Sun-Ha; Lee, Sung Gu; Shin, Seung Chul; Han, Se Jong; Kim, Han-Woo; Park, Hyun Ho; Kim, Sunghwan; Kim, Hak Jun; Park, Hyun; Park, HaJeung; Lee, Jun Hyuck

    2017-03-09

    The two-component phosphorelay system is the most prevalent mechanism for sensing and transducing environmental signals in bacteria. Spore formation, which relies on the two-component phosphorelay system, enables the longterm survival of the glacial bacterium Paenisporosarcina sp. TG-14 in the extreme cold environment. Spo0A is a key response regulator of the phosphorelay system in the early stage of spore formation. The protein is composed of a regulatory N-terminal phospho-receiver domain and a DNAbinding C-terminal activator domain. We solved the threedimensional structure of the unphosphorylated (inactive) form of the receiver domain of Spo0A (PaSpo0A-R) from Paenisporosarcina sp. TG-14. A structural comparison with phosphorylated (active form) Spo0A from Bacillus stearothermophilus (BsSpo0A) showed minor notable differences. A molecular dynamics study of a model of the active form and the crystal structures revealed significant differences in the α4 helix and the preceding loop region where phosphorylation occurs. Although an oligomerization study of PaSpo0A-R by analytical ultracentrifugation (AUC) has shown that the protein is in a monomeric state in solution, both crosslinking and crystal-packing analyses indicate the possibility of weak dimer formation by a previously undocumented mechanism. Collectively, these observations provide insight into the mechanism of phosphorylation-dependent activation unique to Spo0A.

  10. 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).

  11. 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.

  12. 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.

  13. 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....

  14. Complete Genome Sequence of Bacillus pumilus PDSLzg-1, a Hydrocarbon-Degrading Bacterium Isolated from Oil-Contaminated Soil in China

    PubMed Central

    Hao, Kun; Li, Hongna; Li, Feng

    2016-01-01

    Bacillus pumilus strain PDSLzg-1, an efficient hydrocarbon-degrading bacterium, was isolated from oil-contaminated soil. Here, we present the complete sequence of its circular chromosome and circular plasmid. The genomic information is essential for the study of degradation of oil by B. pumilus PDSLzg-1. PMID:27795249

  15. [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.

  16. Marinomonas arctica sp. nov., a psychrotolerant bacterium isolated from the Arctic.

    PubMed

    Zhang, De-Chao; Li, Hui-Rong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Chi, Zhen-Ming; Zhou, Pei-Jin; Yu, Yong

    2008-07-01

    A novel psychrotolerant, Gram-negative, motile bacterium, designated strain 328(T), was isolated from sea-ice samples collected off the Canadian Basin of the Arctic Ocean (7 degrees 23' 14'' N 14 degrees 06' 55'' W). Strain 328(T) was able to grow at 0-37 degrees C, with optimum growth at 25-27 degrees C. It possessed phosphatidylethanolamine and phosphatidylglycerol as major phospholipids and C(10 : 0) 3-OH (31.78 %), C(18 : 1)omega7c (27.50 %) and iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c (19.22 %) as predominant cellular fatty acids. The DNA G+C content of strain 328(T) was 45.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 328(T) was a member of the genus Marinomonas (92.7-96.0 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain 328(T) was considered to represent a novel species of the genus Marinomonas. The name Marinomonas arctica sp. nov. is proposed, with strain 328(T) (=CGMCC 1.6498(T)=JCM 14976(T)) as the type strain.

  17. 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)).

  18. Genome shuffling of marine derived bacterium Nocardia sp. ALAA 2000 for improved ayamycin production.

    PubMed

    El-Gendy, Mervat M A; El-Bondkly, Ahmed M A

    2011-05-01

    Genome shuffling is a recent development in microbiology. The advantage of this technique is that genetic changes can be made in a microorganism without knowing its genetic background. Genome shuffling was applied to the marine derived bacterium Nocardia sp. ALAA 2000 to achieve rapid improvement of ayamycin production. The initial mutant population was generated by treatment with ethyl methane sulfonate (EMS) combined with UV irradiation of the spores, resulting in an improved population (AL/11, AL/136, AL/213 and AL/277) producing tenfold (150 μg/ml) more ayamycin than the original strain. These mutants were used as the starting strains for three rounds of genome shuffling and after each round improved strains were screened and selected based on their ayamycin productivity. The population after three rounds of genome shuffling exhibited an improved ayamycin yield. Strain F3/22 yielded 285 μg/ml of ayamycin, which was 19-fold higher than that of the initial strain and 1.9-fold higher than the mutants used as the starting point for genome shuffling. We evaluated the genetic effect of UV + EMS-mutagenesis and three rounds of genome shuffling on the nucleotide sequence by random amplified polymorphic DNA (RAPD) analysis. Many differences were noticed in mutant and recombinant strains compared to the wild type strain. These differences in RAPD profiles confirmed the presence of genetic variations in the Nocardia genome after mutagenesis and genome shuffling.

  19. Enterobacter siamensis sp. nov., a transglutaminase-producing bacterium isolated from seafood processing wastewater in Thailand.

    PubMed

    Khunthongpan, Suwannee; Bourneow, Chaiwut; H-Kittikun, Aran; Tanasupawat, Somboon; Benjakul, Soottawat; Sumpavapol, Punnanee

    2013-01-01

    A novel strain of Enterobacter, C2361(T), a Gram-negative, non-spore-forming, rod-shaped and facultative anaerobic bacterium with the capability to produce transglutaminase, was isolated from seafood processing wastewater collected from a treatment pond of a seafood factory in Songkhla Province, Thailand. Phylogenetic analyses and phenotypic characteristics, including chemotaxonomic characteristics, showed that the strain was a member of the genus Enterobacter. The 16S rRNA gene sequence similarities between strain C2361(T) and Enterobacter cloacae subsp. cloacae ATCC 13047(T) and Enterobacter cloacae subsp. dissolvens LMG 2683(T) were 97.5 and 97.5%, respectively. Strain C2361(T) showed a low DNA-DNA relatedness with the above-mentioned species. The major fatty acids were C16:0, C17:0cyclo and C14:0. The DNA G+C content was 53.0 mol%. On the basis of the polyphasic evidence gathered in this study, it should be classified as a novel species of the genus Enterobacter for which the name Enterobacter siamensis sp. nov. is proposed. The type strain is C2361(T) (= KCTC 23282(T) = NBRC 107138(T)).

  20. Asticcacaulis taihuensis sp. nov., a novel stalked bacterium isolated from Taihu Lake, China.

    PubMed

    Liu, Zhi-Pei; Wang, Bao-Jun; Liu, Shuang-Jiang; Liu, Ying-Hao

    2005-05-01

    A novel stalked bacterium, designated strain T3-B7(T), was isolated from sediment of Taihu Lake, Jiangsu Province, China, and its taxonomy was studied by using a polyphasic approach. Cell morphology, physiological and biochemical properties, and polar lipids indicated that strain T3-B7(T) represented a member of the genus Asticcacaulis. Based on 16S rRNA gene sequence similarity analysis, strain T3-B7(T) was found to be phylogenetically related to Asticcacaulis biprosthecium DSM 4723(T) (98.5 %) and Asticcacaulis excentricus DSM 4724(T) (95.0 %), but could be differentiated from these two species on the basis of the number and position of prosthecae, assimilation of sugars, nitrate reduction and tolerance to NaCl. Levels of DNA-DNA relatedness of strain T3-B7(T) to A. biprosthecium DSM 4723(T) and A. excentricus DSM 4724(T) were 37.1 and 18.0 %, respectively. The G + C content of strain T3-B7(T) was 59 mol% (T(m)). It is concluded that strain T3-B7(T) represents a novel species of the genus Asticcacaulis, for which the name of Asticcacaulis taihuensis sp. nov. is proposed. The type strain is T3-B7(T) (=AS 1.3431(T) = JCM 12463(T)).

  1. Lysinibacillus tabacifolii sp. nov., a novel endophytic bacterium isolated from Nicotiana tabacum leaves.

    PubMed

    Duan, Yan-Qing; He, Song-Tao; Li, Qing-Qing; Wang, Ming-Feng; Wang, Wen-Yuan; Zhe, Wei; Cao, Yong-Hong; Mo, Ming-He; Zhai, Yu-Long; Li, Wen-Jun

    2013-06-01

    A Gram-positive, catalase- and oxidase-positive, strictly aerobic, endospore-forming rod bacterium, designated K3514(T), was isolated from the leaves of Nicotiana tabacum. The strain was able to grow at temperatures of 8-40°C, pH 5.0-10.0 and NaCl concentrations of 0-7%. The predominant quinones (>30%) of this strain were MK-7(H2) and MK-7. Phylogenetic analysis of 16S rRNA gene sequence showed that strain K3514(T) was affiliated to the genus Lysinibacillus, with its closest relatives being Lysinibacillus mangiferihumi (98.3% sequence similarity), Lysinibacillus sphaericus (97.9% sequence similarity), Lysinibacillus fusiformis (97.4% sequence similarity), and Lysinibacillus xylanilyticus (97.3% sequence similarity). However, low levels of DNA-DNA relatedness values suggested that the isolate was distinct from the other closest Lysinibacillus species. Additionally, based on analysis of morphological, physiological, and biochemical characteristics, the isolate could be differentiated from the closest known relatives. Therefore, based on polyphasic taxonomic data, the novel isolate likely represents a novel species, for which the name Lysinibacillus tabacifolii sp. nov. and the type strain K3514(T) (=KCTC 33042(T) =CCTCC AB 2012050(T)) are proposed.

  2. Purification and Characterization of a New Alginate Lyase from Marine Bacterium Vibrio sp. SY08

    PubMed Central

    Li, Shangyong; Wang, Linna; Hao, Jianhua; Xing, Mengxin; Sun, Jingjing; Sun, Mi

    2016-01-01

    Unsaturated alginate disaccharides (UADs), enzymatically derived from the degradation of alginate polymers, are considered powerful antioxidants. In this study, a new high UAD-producing alginate lyase, AlySY08, has been purified from the marine bacterium Vibrio sp. SY08. AlySY08, with a molecular weight of about 33 kDa and a specific activity of 1070.2 U/mg, showed the highest activity at 40 °C in phosphate buffer at pH 7.6. The enzyme was stable over a broad pH range (6.0–9.0) and retained about 75% activity after incubation at 40 °C for 2 h. Moreover, the enzyme was active in the absence of salt ions and its activity was enhanced by the addition of NaCl and KCl. AlySY08 resulted in an endo-type alginate lyase that degrades both polyM and polyG blocks, yielding UADs as the main product (81.4% of total products). All these features made AlySY08 a promising candidate for industrial applications in the production of antioxidants from alginate polysaccharides. PMID:28025527

  3. 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.

  4. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora.

    PubMed

    Kim, Byung-Chun; Lee, Kang Hyun; Kim, Mi Na; Kim, Eun-Mi; Rhee, Moon-Soo; Kwon, O-Yu; Shin, Kee-Sun

    2009-10-01

    A novel cellulolytic bacterium, strain S23(T), was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, alpha-galactosidase, and beta-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C(15:0) (51.9%), iso-C(16:0) (14.7%), and iso-C(15:0) (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23(T) and other Paenibacillus species were between 89.9% and 95.9%, and S23(T) was most closely related to Paenibacillus tarimensis SA-7-6(T). On the basis of phylogenetic and phenotypic properties of strain S23(T), the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23(T) (=KCTC 13695(T) =KACC 14199(T) =JCM 16419(T)).

  5. Paenibacillus puernese sp. nov., a β-glucosidase-producing bacterium isolated from Pu'er tea.

    PubMed

    Wang, Dan-Dan; Kim, Yeon-Ju; Hoang, Van-An; Nguyen, Ngoc-Lan; Singh, Priyanka; Wang, Chao; Chun-Yang, Deok

    2016-04-01

    A Gram-staining-positive, endospore-forming, aerobic, rod-shaped bacterium, designated as DCY97(T), was isolated from ripened Pu'er tea and was identified by using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain DCY97(T) was closely related to Paenibacillus dongdonensis KUDC0114(T) (98.0 %), Paenibacillus oceanisediminis L10(T) (97.7 %), and Paenibacillus barcinonensis BP-23(T) (97.2 %). The phenotypic and chemotaxonomic characteristics of strain DCY97(T) matched with the characteristics of members belonging to the genus Paenibacillus. The major identified polar lipids included phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant quinone was MK-7. The major fatty acids were anteiso-C15:0 (35.1 %), anteiso-C16:0 (19.0 %), and iso-C16:0 (13.9 %). The peptidoglycan cell wall was composed of meso-diaminopimelic acids, alanine, and D-glutamic acid. The genomic DNA G + C content was determined to be 46.7 mol%. The DNA-DNA relatedness between strain DCY97(T) and Paenibacillus dongdonensis KCTC 33221(T), Paenibacillus oceanisediminis KACC 16023(T), Paenibacillus barcinonensis KCTC 13019(T) were 27, 19, and 10 %, respectively. Based on the genotypic, phenotypic, and chemotaxonomic characteristics, strain DCY97(T) is considered as a novel species of the genus Paenibacillus, for which the name Paenibacillus puernese sp. nov. is proposed. The type strain is DCY97(T) (=KCTC 33596(T) = JCM 140369(T)).

  6. 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)).

  7. 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)).

  8. Brassicibacter thermophilus sp. nov., a thermophilic bacterium isolated from coastal sediment.

    PubMed

    Wang, Bing; Ji, Shi-Qi; Tian, Xin-Xin; Qu, Ling-Yun; Li, Fu-Li

    2015-09-01

    A novel thermophilic, obligately anaerobic bacterium, strain Cel2f(T), was isolated from a cellulolytic community enriched from coastal marine sediment. Cells were Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Optimal growth temperature and pH of strain Cel2f(T) were 55 °C and pH 7.0, respectively. NaCl was essential for the growth of strain Cel2f(T) and the strain showed enhanced growth in the presence of sea salt; the optimum sea salt concentration for growth was 7% (w/v). Thiosulfate, sulfate and sulfite were potential electron acceptors. The major fatty acids of strain Cel2f(T) were iso-C15 : 0, C16 : 0, and C18 : 0. Polar lipid analysis indicated the presence of phosphatidylethanolamine and phosphatidylglycerol. Strain Cel2f(T) contained menaquinone MK-7 as the isoprenoid quinone, and the DNA G+C content was 31.3 mol%. Phylogenetic analysis revealed that the nearest relative of strain Cel2f(T) was Brassicibacter mesophilus BM(T) with 93.8% 16S rRNA gene sequence similarity. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain Cel2f(T) represents a novel species of genus Brassicibacter, for which the name Brassicibacter thermophilus sp. nov. is proposed. The type strain is Cel2f(T) ( = JCM 30480(T) = CGMCC 1.5200(T)).

  9. 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)).

  10. Arthrobacter nitrophenolicus sp. nov. a new 2-chloro-4-nitrophenol degrading bacterium isolated from contaminated soil.

    PubMed

    Arora, Pankaj Kumar; Jain, Rakesh Kumar

    2013-02-01

    Strain SJCon(T), a 2-chloro-4-nitrophenol (2C4NP) degrading bacterium, was isolated from soil collected from a pesticide-contaminated site in Punjab, India. The strain, which stained Gram positive, displayed a rod-coccus life cycle, and possessed a type A3α peptidoglycan (L-Lys-L-Ala3), MK-9(H2) as the major menaquinone, anteiso-C15 and iso-C15:0 as the major cellular fatty acids, and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and a glycolipid as the major polar lipids, showed morphological and chemotaxonomic properties consistent with those reported for members of the genus Arthrobacter. Phylogenetic analysis of the 16S rRNA gene sequence of strain SJCon(T) confirmed that it was a member of this genus with Arthrobacter globiformis DSM 20124(T) being the closest relative (sequence similarity of 97 %). The DNA G + C content of strain SJCon(T) was 69 ± 1 mol% and DNA homology with A. globiformis DSM 20124(T) was 45 %, suggesting that strain SJCon(T) represented a novel species of the genus Arthrobacter, which we have named Arthrobacter nitrophenolicus sp. nov The type strain is SJCon(T) (=MTCC 10104(T) =DSM 23165(T)).

  11. Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Baek, Sang-Hoon; Im, Wan-Taek; Oh, Hyun Woo; Lee, Jung-Sook; Oh, Hee-Mock; Lee, Sung-Taik

    2006-11-01

    A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088T was shown to belong to the family Paenibacillaceae, being related to Brevibacillus centrosporus (96.6%), Brevibacillus borstelensis (96.3%), Brevibacillus parabrevis (96.1%), Brevibacillus formosus (96.1%), Brevibacillus brevis (96.1%) and Brevibacillus laterosporus (96.0%). The phylogenetic distances from other validly described species within the genus Brevibacillus were greater than 4.0% (i.e. there was less than 96.0% similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15:0, iso-C14:0 and anteiso-C15:0) supported the affiliation of strain Gsoil 3088T to the genus Brevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3088T (=KCTC 13938T=LMG 23403T).

  12. 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

  13. 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)).

  14. Flavobacterium noncentrifugens sp. nov., a psychrotolerant bacterium isolated from glacier meltwater.

    PubMed

    Zhu, Lang; Liu, Qing; Liu, Hongcan; Zhang, Jianli; Dong, Xiuzhu; Zhou, Yuguang; Xin, Yuhua

    2013-06-01

    A non-motile, Gram-stain-negative bacterium, designated R-HLS-17(T), was isolated from the meltwater of Hailuogou Glacier located in Sichuan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Flavobacterium, with the closest relatives being Flavobacterium antarcticum JCM 12383(T) (95.5% 16S rRNA gene sequence similarity), F. omnivorum JCM 11313(T) (95.0%) and F. fryxellicola LMG 22022(T) (95.2%). Growth occurred at 0-29 °C (optimum, 10-20 °C) and pH 6.0-8.5 (optimum, 7.0-8.0). The DNA G+C content was 46.5 mol%. The major cellular fatty acids were iso-C15:0, iso-C15:1 G, summed feature 9 (comprising iso-C17:1ω9c and/or 10-methyl C16:0), iso-C17:0 3-OH and iso-C15:0 3-OH. The predominant menaquinone was MK-6. Based on the genotypic and phenotypic characteristics, we propose that strain R-HLS-17(T) represents a novel species of the genus Flavobacterium, Flavobacterium noncentrifugens sp. nov. The type strain is R-HLS-17(T) (=CGMCC 1.10076(T)=NBRC 108844(T)).

  15. Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field.

    PubMed

    Im, Wan-Taek; Liu, Qing-Mei; Lee, Kang-Jin; Kim, Se-Young; Lee, Sung-Taik; Yi, Tae-Hoo

    2010-07-01

    A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165(T)) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165(T) was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165(T) and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165(T) was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C(16 : 0) and C(17 : 0) cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165(T) to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165(T) from recognized Variovorax species. Gsoil 3165(T) is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165(T) (=KCTC 12583(T) =LMG 23392(T)).

  16. Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.

    PubMed

    Miwa, Hiroki; Ahmed, Iftikhar; Yoon, Jaewoo; Yokota, Akira; Fujiwara, Toru

    2008-01-01

    A non-spore-forming, Gram-negative, motile, rod-shaped, boron-accumulating bacterium isolated from soil was characterized by polyphasic taxonomy. The strain, designated BAM-48(T), was positive for catalase and oxidase activities and grew at 4-37 degrees C, 0-1% NaCl and pH 5-9. Comparative analysis of the 16S rRNA gene sequence demonstrated that the novel isolate BAM-48(T) was closely related to Variovorax paradoxus IAM 12373(T) (99.3% sequence similarity), Variovorax soli GH9-3(T) (98.3%) and Variovorax dokdonensis DS-43(T) (97.0%). DNA-DNA hybridization values between strain BAM-48(T) and V. paradoxus NBRC 15149(T), V. soli KACC 11579(T) and V. dokdonensis KCTC 12544(T) were only 49.1, 25.4 and 24.6%, respectively. The major respiratory quinone was ubiquinone 8 (Q-8). The DNA G+C content was 71.2 mol%. Strain BAM-48(T) contained C(16:0) (36.1%), C(16:1)omega7c (21.4%) and C(17:0) cyclo (19.0%) as the major fatty acids. Based on phenotypic, chemotaxonomic and phylogenetic data, strain BAM-48(T) should be classified as a member of a novel species in the genus Variovorax, for which the name Variovorax boronicumulans sp. nov. is proposed. The type strain is BAM-48(T) (=NBRC 103145(T) =KCTC 22010(T)).

  17. Prosthecochloris indica sp. nov., a novel green sulfur bacterium from a marine aquaculture pond, Kakinada, India.

    PubMed

    Anil Kumar, Pinnaka; Naga Radha Srinivas, Tanuku; Sasikala, Chintalapati; Venkata Ramana, Chintalapati; Süling, Jorg; Imhoff, Johannes

    2009-04-01

    A green sulfur bacterium, strain JAGS6T was isolated from a marine aquaculture pond located near Kakinada on the east coast of India. Cells of strain JAGS6T were Gram-negative, non-motile, coccoid, 1-1.2 microm in diameter, with prosthecae. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JAGS6T clusters with members of the genus Prosthecochloris and the sequence similarity with the nearest relative, Prosthecochloris vibrioformis, is 96.7%. Cultures of strain JAGS6T are green in color and the cells contain bacteriochlorophyll c and most likely carotenoids of the chlorobactene series as photosynthetic pigments. Strain JAGS6T is mesophilic, halotolerant (up to 7% NaCl) and is obligately phototrophic, utilizing sulfide but not thiosulfate as a photosynthetic electron donor. Sulfur globules are deposited outside the cells during oxidation of sulfide. On the basis of 16S rRNA gene sequence analysis and its morphological and physiological characteristics, strain JAGS6T is distinct from described species of the genus Prosthecochloris and we propose to describe it as a new species, Prosthecochloris indica, sp. nov. The type strain is JAGS6T (=JCM 13299T=ATCC BAA1214T).

  18. 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).

  19. 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.

  20. A New Diketopiperazine, Cyclo(D-trans-Hyp-L-Leu) from a Kenyan Bacterium Bacillus licheniformis LB 8CT.

    PubMed

    Lee, Seoung Rak; Beemelmanns, Christine; Tsuma, Leah M M; Clardy, Jon; Cao, Shugeng; Kim, Ki Hyun

    2016-04-01

    Bacterially-produced small molecules demonstrate a wide range of structural and functional diversity. A new diketopiperazine, cyclo(D-trans-Hyp-L-Leu) (1), and five other known diketopiperazines (2-6), were isolated and purified from the fermented broth of a Kenyan bacterium Bacillus licheniformis LB 8CT. The structure of 1 was elucidated by a combination of extensive spectroscopic analyses, including 2D NMR and HR-MS, and the absolute configuration was determined by a combination of NOESY analysis and Marfey's method. The known compounds were identified as cyclo(D-cis-Hyp-L-Leu) (2), cyclo(D-cis-Hyp-L-Phe) (3), cyclo(D-Pro-L-Tyr) (4), cyclo-(D-Trp-L-Leu) (5), and cyclo(L-Tyr-Gly) (6) by comparison of their spectroscopic and physical data with reported values. Compounds 1-6 were tested for antifungal and antimicrobial properties.

  1. 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

  2. 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

  3. Development of plasmid vector and electroporation condition for gene transfer in sporogenic lactic acid bacterium, Bacillus coagulans.

    PubMed

    Rhee, Mun Su; Kim, Jin-Woo; Qian, Yilei; Ingram, L O; Shanmugam, K T

    2007-07-01

    Bacillus coagulans is a sporogenic lactic acid bacterium that ferments glucose and xylose, major components of plant biomass, a potential feedstock for cellulosic ethanol. The temperature and pH for optimum rate of growth of B. coagulans (50 to 55 degrees C, pH 5.0) are very similar to that of commercially developed fungal cellulases (50 degrees C; pH 4.8). Due to this match, simultaneous saccharification and fermentation (SSF) of cellulose to products by B. coagulans is expected to require less cellulase than needed if the SSF is conducted at a sub-optimal temperature, such as 30 degrees C, the optimum for yeast, the main biocatalyst used by the ethanol industry. To fully exploit B. coagulans as a platform organism, we have developed an electroporation method to transfer plasmid DNA into this genetically recalcitrant bacterium. We also constructed a B. coagulans/E. coli shuttle vector, plasmid pMSR10 that contains the rep region from a native plasmid (pMSR0) present in B. coagulans strain P4-102B. The native plasmid, pMSR0 (6823bp), has 9 ORFs, and replicates by rolling-circle mode of replication. Plasmid pNW33N, developed for Geobacillus stearothermophilus, was also transformed into this host and stably maintained while several other Bacillus/Escherichia coli shuttle vector plasmids were not transformed into B. coagulans. The transformation efficiency of B. coagulans strain P4-102B using the plasmids pNW33N or pMSR10 was about 1.5x10(16) per mole of DNA. The availability of shuttle vectors and an electroporation method is expected to aid in genetic and metabolic engineering of B. coagulans.

  4. Bacillus shackletonii sp. nov., from volcanic soil on Candlemas Island, South Sandwich archipelago.

    PubMed

    Logan, Niall A; Lebbe, Liesbeth; Verhelst, An; Goris, Johan; Forsyth, Gillian; Rodríguez-Díaz, Marina; Heyndrickx, Marc; De Vos, Paul

    2004-03-01

    A sample of mossy soil taken from the eastern lava flow of northern Candlemas Island, South Sandwich archipelago, yielded six isolates of aerobic, endospore-forming bacteria. Miniaturized routine phenotypic tests and other observations, amplified rDNA restriction analysis and SDS-PAGE analysis suggested that the strains represent a novel taxon. 16S rDNA sequence comparisons support the proposal of a novel species, Bacillus shackletonii sp. nov., the type strain of which is LMG 18435(T) (=CIP 107762(T)).

  5. Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009

    PubMed Central

    DebRoy, Shreya; Mukherjee, Pallavi; Roy, Sujata; Thakur, Ashoke Ranjan

    2013-01-01

    The draft genome sequence (5,868,741 bp) of a nitrate- and phosphate-removing Bacillus sp., WBUNB009, isolated from a raw sewage canal in nitrate broth (Himedia M439) with a G+C content of 34.9% is reported. It removes 60.23% nitrate and 96% phosphate within 16 h at 37°C. PMID:23469363

  6. Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004

    PubMed Central

    DebRoy, Shreya; Mukherjee, Pallavi; Roy, Sujata; Thakur, Ashoke Ranjan

    2013-01-01

    The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive Bacillus sp. with optimum growth at 37°C and pH 7 in nitrate broth (HiMedia M439) isolated from rhizosphere of a water lily, with a genome size of 5,465,157 bp and a G+C content of 35.0%, is reported here. PMID:23469361

  7. Influence of heavy metals on the activity of antioxidant enzymes in the metal resistant strains of Ochrobactrum and Bacillus sp.

    PubMed

    Pandey, Sanjeev; Barai, Prabir Kumar; Maiti, Tushar K

    2013-11-01

    Three bacterial strains, a cadmium resistant Ochrobactrum sp. designated as CdSP9 and two strains of Bacillus sp. named PbSP6 and AsSP9 resistant to lead and arsenate, respectively were characterized here with respect to their oxidative enzyme activities. The bacterial strains were grown in basal medium supplemented with 50 microg ml(-1) of respective elements to determine the changes in the level of oxidative enzymes. The superoxide dismutase activity increased in all three isolates, but the catalase activity and malondialdehyde concentration were relatively more in CdSP9 than PbSP6 and AsSP9. The glutathione peroxidase, however, remained almost uninduced in CdSP9 but was enhanced in PbSP6 and AsSP9. A possible role of these enzymes in metal tolerance is evident from these results.

  8. 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.

  9. Labrenzia sp. BM1: A Quorum Quenching Bacterium That Degrades N-acyl Homoserine Lactones via Lactonase Activity

    PubMed Central

    Ghani, Norshazliza Ab; Norizan, Siti Nur Maisarah; Chan, Xin Yue; Yin, Wai-Fong; Chan, Kok-Gan

    2014-01-01

    We report the degradation of quorum sensing N-acylhomoserine lactone molecules by a bacterium isolated from a Malaysian marine water sample. MALDI-TOF and phylogenetic analysis indicated this isolate BM1 clustered closely to Labrenzia sp. The quorum quenching activity of this isolate was confirmed by using a series of bioassays and rapid resolution liquid chromatography analysis. Labrenzia sp. degraded a wide range of N-acylhomoserine lactones namely N-(3-hexanoyl)-l-homoserine lactone (C6-HSL), N-(3-oxohexanoyl)-l-homoserine lactone (3-oxo-C6-HSL) and N-(3-hydroxyhexanoyl)-l-homoserine lactone (3-hydroxy-C6-HSL). Re-lactonisation bioassays confirmed Labrenzia sp. BM1 degraded these signalling molecules efficiently via lactonase activity. To the best of our knowledge, this is the first documentation of a Labrenzia sp. capable of degrading N-acylhomoserine lactones and confirmation of its lactonase-based mechanism of action. PMID:24995373

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

    PubMed Central

    Bollmann, Annette; Sedlacek, Christopher J.; Norton, Jeanette; Laanbroek, Hendrikus J.; Suwa, Yuichi; Stein, Lisa Y.; Klotz, Martin G.; Arp, Daniel; Sayavedra-Soto, Luis; Lu, Megan; Bruce, David; Detter, Chris; Tapia, Roxanne; Han, James; Woyke, Tanja; Lucas, Susan M.; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L.; Huntemann, Marcel; Deshpande, Shweta; Han, Cliff; Chen, Amy; Kyrpides, Nikos; Mavromatis, Konstantinos; Markowitz, Victor; Szeto, Ernest; Ivanova, Natalia; 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. PMID:24019993

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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).

  18. Utilization of Bacillus sp. strain TAT105 as a biological additive to reduce ammonia emissions during composting of swine feces.

    PubMed

    Kuroda, Kazutaka; Waki, Miyoko; Yasuda, Tomoko; Fukumoto, Yasuyuki; Tanaka, Akihiro; Nakasaki, Kiyohiko

    2015-01-01

    Bacillus sp. strain TAT105 is a thermophilic, ammonium-tolerant bacterium that grows assimilating ammonium nitrogen and reduces ammonia emission during composting of swine feces. To develop a practical use of TAT105, a dried solid culture of TAT105 (5.3 × 10(9) CFU/g of dry matter) was prepared as an additive. It could be stored for one year without significant reduction of TAT105. Laboratory-scale composting of swine feces was conducted by mixing the additive. When the additive, mixed with an equal weight of water one day before use, was added to obtain a TAT105 concentration of above 10(7) CFU/g of dry matter in the initial material, the ammonia concentration emitted was lower and nitrogen loss was approximately 22% lower in the treatment with the additive than in the control treatment without the additive. The colony formation on an agar medium containing high ammonium could be used for enumeration of TAT105 in the composted materials.

  19. Semiquinone glucoside derivative (SQGD) isolated from Bacillus sp. INM-1 protects against gamma radiation-induced oxidative stress.

    PubMed

    Mishra, Saurabh; Malhotra, Poonam; Gupta, Ashutosh K; Singh, Praveen K; Javed, Saleem; Kumar, Raj

    2014-03-01

    In the present study, radioprotective potential of Semiquinone glucoside derivative (SQGD) isolated from radioresistant bacterium Bacillus sp. INM-1 was evaluated. γ-Radiation induced protein carbonylation, plasmid DNA damage, enzyme functional impairment, lipid peroxidation, HO radicals generation and their protection by SQGD was assessed. As a result of SQGD treatment, significant inhibition (p<0.05) in protein carbonylation was observed with BSA. SQGD treatment was found to restore supercoiled (~70±3.21%) form of irradiated plasmid DNA against γ-irradiation. SQGD protects enzymes (EcoR1 and BamH1) against radiation-induced dysfunctioning. SQGD significantly inhibited (p<0.05) lipid peroxidation in liposomes, brain and liver homogenate. Higher HO(•) radicals-averting activity of SQGD was observed in the serum and liver homogenate of C57BL/6 mice against H2O2-induced oxidative stress. In conclusion, SQGD demonstrates excellent radical-scavenging activity towards bio-macromolecules in irradiated environment and can be developed as an ideal radioprotector against radiation-induced oxidative stress in future.

  20. Properties of a Newly Identified Esterase from Bacillus sp. K91 and Its Novel Function in Diisobutyl Phthalate Degradation

    PubMed Central

    Xie, Zhenrong; Li, Junjun; Yang, Yunjuan; Mu, Yuelin; Tang, Xianghua; Xu, Bo; Zhou, Junpei; Huang, Zunxi

    2015-01-01

    The widely used plasticizer phthalate esters (PAEs) have become a public concern because of their effects on environmental contamination and toxicity on mammals. However, the biodegradation of PAEs, especially diisobutyl phthalate (DiBP), remains poorly understood. In particular, genes involved in the hydrolysis of these compounds were not conclusively identified. In this study, the CarEW gene, which encodes an enzyme that is capable of hydrolyzing ρ-nitrophenyl esters of fatty acids, was cloned from a thermophilic bacterium Bacillus sp. K91 and heterologously expressed in Escherichia coli BL21 using the pEASY-E2 expression system. The enzyme showed a monomeric structure with a molecular mass of approximately 53.76 kDa and pI of 4.88. The enzyme exhibited maximal activity at pH 7.5 and 45°C, with ρ-NP butyrate as the best substrate. The enzyme was fairly stable within the pH range from 7.0 to 8.5. High-pressure liquid chromatography (HPLC) and electrospray ionization mass spectrometry (ESI-MS) were employed to detect the catabolic pathway of DiBP. Two intermediate products were identified, and a potential biodegradation pathway was proposed. Altogether, our findings present a novel DiBP degradation enzyme and indicate that the purified enzyme may be a promising candidate for DiBP detoxification and for environmental protection. PMID:25746227

  1. Degradation of the seaweed wakame (Undaria pinnatifida) by a composting process with the inoculation of Bacillus sp. HR6.

    PubMed

    Tang, Jing-Chun; Wei, Jian-He; Maeda, Kenji; Kawai, Hiroshi; Zhou, Qixing; Hosoi-Tanabe, Shoko; Nagata, Shinichi

    2007-06-01

    Disposal of the seaweed wakame (Undaria pinnatifida) by inoculating the halotolerant bacterium Bacillus sp. HR6 was examined in an experimental scale composting system. Strain HR6 was effective in initiating the composting process of wakame, and there was a rapid increase in temperature to over 54.9-55.7 degrees C after 18-20 h. The composting process of wakame could be carried out despite a high NaCl content, 28.2 mg/g, although lower salinity resulted in a shorter lag time and higher weight reduction. In a larger scale composting process with aeration, two peaks of temperature change were found which corresponded well to oxygen consumption and CO2 emission during the process. The pH increased to 8.83 and organic materials were reduced to 93.4% after 72 h. The initial N and C contents were 3.9 and 34.0%, respectively, both of which decreased during the composting process. The changes in the viable cell numbers suggested that strain HR6 predominated before 24 h and other microorganisms including HR6 were present in a mixed state during the later period of composting. The total content of alginate (TA), 32.2% in the initial stage, decreased to 29.2% after 72 h, while water soluble alginate (WSA) increased, indicating that the solubilization and decomposition of alginate had occurred during the composting process.

  2. 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.

  3. A Halotolerant Bacterium Bacillus licheniformis HSW-16 Augments Induced Systemic Tolerance to Salt Stress in Wheat Plant (Triticum aestivum)

    PubMed Central

    Singh, Rajnish P.; Jha, Prabhat N.

    2016-01-01

    Certain plant growth promoting bacteria can protect associated plants from harmful effects of salinity. We report the isolation and characterization of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase bacterium Bacillus licheniformis HSW-16 capable of ameliorating salt (NaCl) stress in wheat plants. The bacterium was isolated from the water of Sambhar salt lake, Rajasthan, India. The presence of ACC deaminase activity was confirmed by enzyme assay and analysis of AcdS gene, a structural gene for ACC deaminase. Inoculation of B. licheniformis HSW-16 protected wheat plants from growth inhibition caused by NaCl and increased plant growth (6-38%) in terms of root length, shoot length, fresh weight, and dry weight. Ionic analysis of plant samples showed that the bacterial inoculation decreased the accumulation of Na+ content (51%), and increased K+ (68%), and Ca2+ content (32%) in plants at different concentration of NaCl. It suggested that bacterial inoculation protected plants from the effect of NaCl by decreasing the level of Na+ in plants. Production of exopolysaccharide by the B. licheniformis HSW-16 can also protect from Na+ by binding this ion. Moreover, application of test isolate resulted in an increase in certain osmolytes such as total soluble sugar, total protein content, and a decrease in malondialdehyde content, illustrating their role in the protection of plants. The ability of B. licheniformis HSW-16 to colonize plant root surface was examined by staining the bacterium with acridine orange followed by fluorescence microscopy and polymerase chain reaction-based DNA finger printing analysis. These results suggested that B. licheniformis HSW-16 could be used as a bioinoculant to improve the productivity of plants growing under salt stress. PMID:28018415

  4. Genome Sequence of “Candidatus Arthromitus” sp. Strain SFB-Mouse-NL, a Commensal Bacterium with a Key Role in Postnatal Maturation of Gut Immune Functions

    PubMed Central

    Bolotin, Alexander; de Wouters, Tomas; Schnupf, Pamela; Bouchier, Christiane; Loux, Valentin; Rhimi, Moez; Jamet, Alexandre; Dervyn, Rozenn; Boudebbouze, Samira; Blottière, Hervé M.; Sorokin, Alexei; Snel, Johannes; Cerf-Bensussan, Nadine; Gaboriau-Routhiau, Valérie; van de Guchte, Maarten

    2014-01-01

    “Candidatus Arthromitus” sp. strain SFB-mouse-NL (SFB, segmented filamentous bacteria) is a commensal bacterium necessary for inducing the postnatal maturation of homeostatic innate and adaptive immune responses in the mouse gut. Here, we report the genome sequence of this bacterium, which sets it apart from earlier sequenced mouse SFB isolates. PMID:25035333

  5. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity

    PubMed Central

    Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A.

    2013-01-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645T was isolated from human subgingival dental plaque. Bacterial cells were 4–40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30–42 °C and 4.9–7.5, respectively. Major fatty acids were C14 : 0, C14 : 0 DMA (dimethyl aldehyde), C16 : 0, C16 : 1ω7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645T formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645T represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645T ( = HM-480T; deposited in BEI Resources, an NIH collection managed by the ATCC). PMID:22843721

  6. Stomatobaculum longum gen. nov., sp. nov., an obligately anaerobic bacterium from the human oral cavity.

    PubMed

    Sizova, Maria V; Muller, Paul; Panikov, Nicolai; Mandalakis, Manolis; Hohmann, Tine; Hazen, Amanda; Fowle, William; Prozorov, Tanya; Bazylinski, Dennis A; Epstein, Slava S

    2013-04-01

    A strictly anaerobic Gram-stain-variable but positive by structure, non-spore-forming bacterium designated Lachnospiraceae bacterium ACC2 strain DSM 24645(T) was isolated from human subgingival dental plaque. Bacterial cells were 4-40 µm long non-motile rods, often swollen and forming curved filaments up to 200 µm. Cells contained intracellular, poorly crystalline, nanometre-sized iron- and sulfur-rich particles. The micro-organism was able to grow on yeast extract, trypticase peptone, milk, some sugars and organic acids. The major metabolic end-products of glucose fermentation were butyrate, lactate, isovalerate and acetate. The growth temperature and pH ranges were 30-42 °C and 4.9-7.5, respectively. Major fatty acids were C14 : 0, C14 : 0 DMA (dimethyl aldehyde), C16 : 0, C16 : 1ω7c DMA. The whole-cell hydrolysate contained meso-diaminopimelic acid, indicating peptidoglycan type A1γ. The DNA G+C content was calculated to be 55.05 mol% from the whole-genome sequence and 55.3 mol% as determined by HPLC. There were no predicted genes responsible for biosynthesis of respiratory lipoquinones, mycolic acids and lipopolysaccharides. Genes associated with synthesis of teichoic and lipoteichoic acids, diaminopimelic acid, polar lipids and polyamines were present. According to the 16S rRNA gene sequence phylogeny, strain DSM 24645(T) formed, together with several uncultured oral clones, a separate branch within the family Lachnospiraceae, with the highest sequence similarity to the type strain of Moryella indoligenes at 94.2 %. Based on distinct phenotypic and genotypic characteristics, we suggest that strain DSM 24645(T) represents a novel species in a new genus, for which the name Stomatobaculum longum gen. nov., sp. nov. is proposed. The type strain of Stomatobaculum longum is DSM 24645(T) ( = HM-480(T); deposited in BEI Resources, an NIH collection managed by the ATCC).

  7. Genetic tool development for a new host for biotechnology, the thermotolerant bacterium Bacillus coagulans.

    PubMed

    Kovács, Akos T; van Hartskamp, Mariska; Kuipers, Oscar P; van Kranenburg, Richard

    2010-06-01

    Bacillus coagulans has good potential as an industrial production organism for platform chemicals from renewable resources but has limited genetic tools available. Here, we present a targeted gene disruption system using the Cre-lox system, development of a LacZ reporter assay for monitoring gene transcription, and heterologous d-lactate dehydrogenase expression.

  8. 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.

  9. Isolation and Characterisation of a Molybdenum-reducing and Metanil Yellow Dye-decolourising Bacillus sp. strain Neni-10 in Soils from West Sumatera, Indonesia

    PubMed Central

    Mansur, Rusnam; Gusmanizar, Neni; Roslan, Muhamad Akhmal Hakim; Ahmad, Siti Aqlima; Shukor, Mohd Yunus

    2017-01-01

    A molybdenum reducing bacterium with the novel ability to decolorise the azo dye Metanil Yellow is reported. Optimal conditions for molybdenum reduction were pH 6.3 and at 34°C. Glucose was the best electron donor. Another requirement includes a narrow phosphate concentration between 2.5 and 7.5 mM. A time profile of Mo-blue production shows a lag period of approximately 12 hours, a maximum amount of Mo-blue produced at a molybdate concentration of 20 mM, and a peak production at 52 h of incubation. The heavy metals mercury, silver, copper and chromium inhibited reduction by 91.9, 82.7, 45.5 and 17.4%, respectively. A complete decolourisation of the dye Metanil Yellow at 100 and 150 mg/L occurred at day three and day six of incubations, respectively. Higher concentrations show partial degradation, with an approximately 20% decolourisation observed at 400 mg/L. The bacterium is partially identified based on biochemical analysis as Bacillus sp. strain Neni-10. The absorption spectrum of the Mo-blue suggested the compound is a reduced phosphomolybdate. The isolation of this bacterium, which shows heavy metal reduction and dye-decolorising ability, is sought after, particularly for bioremediation. PMID:28228917

  10. 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.

  11. Anoxybacillus sp. Strain UARK-01, a New Thermophilic Soil Bacterium with Hyperthermostable Alkaline Laccase Activity.

    PubMed

    Al-Kahem Al-Balawi, Thamir H; Wood, Adam L; Solis, Alexis; Cooper, Ted; Barabote, Ravi D

    2017-04-08

    We describe the isolation and characteristics of a novel thermophilic bacterium from soil. The organism is a member of the Anoxybacillus genus based on phylogenetic analysis of the 16S rRNA gene. The 16S rRNA of the organism shares >99% sequence identity with those of two species, Anoxybacillus rupiensis and A. geothermalis. We named this isolate as Anoxybacillus sp. strain UARK-01. UARK-01 grows optimally in the presence of oxygen at 55 °C and pH 8. It grew excellently in the presence of lignin as the sole carbon source. Culture supernatant from UARK-01 grown on lignin was rich in laccase activity. The laccase activity was optimal at 90 °C and pH 9, and there was comparable activity at 80 and 100 °C. The crude laccase decolorized approximately 75% of Congo Red in 7 h under optimal conditions. A single laccase gene was identified from the draft genome sequence of Anoxybacillus sp. UARK-01. The UARK-01 laccase (Anox_Lacc) was cloned and overexpressed in Escherichia coli and was partially purified. The partially purified Anox_Lacc decolorized approximately 1.64+/0.21 nanomoles of Congo Red per microgram protein in 30 min at 90 °C and pH 9. Anox_Lacc is a member of the multicopper polyphenol oxidoreductase laccase family (pfam02578 Cu-oxidase_4) and has novel characteristics. Multiple sequence analysis of Anox_Lacc with six homologs from the family revealed four conserved copper ligands and several new residues that are fully conserved. Anox_Lacc is enriched in leucine, glutamine, and lysine, and it contains fewer alanine, arginine, glycine, and serine residues. Skewed amino acid composition of Anox_Lacc likely contributes to the exceptional thermochemical properties of the laccase activity from UARK-01. Both lignin utilization and production of hyperthermostable alkaline laccase are new findings in the Anoxybacillus genus.

  12. Algoriella xinjiangensis gen. nov., sp. nov., a new psychrotolerant bacterium of the family Flavobacteriaceae.

    PubMed

    Yang, Na; Zhang, Lixin; Sun, Chaomin

    2015-11-01

    An aerobic, Gram-stain negative, non-spore-forming and psychrotolerant bacterium, designated strain XJ109(T), was isolated from a sewage water sample collected from Xinjiang Uigur Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XJ109(T) represents a novel member of the family Flavobacteriaceae. The strain showed 95.5 % similarity with the 16S rRNA gene sequence of Empedobacter brevis LMG 4011(T), 95.4% with Chishuiella changwenlii BY4(T), 95.3% with Empedobacter falsenii NF 993(T) and 92.3% with Weeksella virosa DSM 16922(T). Strain XJ109(T) showed the common phenotypic and chemotaxonomic characteristics of the family Flavobacteriaceae, containing menaquinone-6 (MK-6) as the predominant respiratory quinone and iso-C17:0 3OH and iso-C15:0 as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one unidentified phospholipid and two unidentified lipids. The genomic DNA G+C content was 38.0 mol%. Strain XJ109(T) was positive for catalase and oxidase activities, and it was observed to grow at 4-30 °C (optimal 16-20 °C), pH 6.5-10.0 (optimal 7.0-7.5) and in media containing 0-2.0% (w/v) NaCl (optimal 0.5 %). On the basis of the polyphasic evidence presented, strain XJ109(T) is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Algoriella xinjiangensis gen. nov., sp. nov. is proposed. The type strain is XJ109(T) (=CGMCC 1.10229(T)=JCM 16590(T)).

  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)).

  14. Akkermansia glycaniphila sp. nov., an anaerobic mucin-degrading bacterium isolated from reticulated python faeces.

    PubMed

    Ouwerkerk, Janneke P; Aalvink, Steven; Belzer, Clara; de Vos, Willem M

    2016-11-01

    A Gram-stain-negative, non-motile, strictly anaerobic, oval-shaped, non-spore-forming bacterium (strain PytT) was isolated from reticulated python faeces. Strain PytT was capable of using mucin as sole carbon, energy and nitrogen source. Cells could grow singly, in pairs, and were also found to aggregate. Scanning electron microscopy revealed the presence of filamentous structures connecting individual bacterial cells. Strain PytT could grow on a limited number of single sugars, including N-acetylglucosamine, N-acetylgalactosamine, glucose, lactose and galactose, but only when a plentiful protein source was provided. Phylogenetic analysis based on 16S rRNA gene sequencing showed strain PytT to belong to the Verrucomicrobiae class I, family Akkermansiaceae, genus Akkermansia, with Akkermansia muciniphila MucT as the closest relative (94.4 % sequence similarity). DNA-DNA hybridization revealed low relatedness of 28.3 % with A. muciniphila MucT. The G+C content of DNA from strain PytT was 58.2 mol%. The average nucleotide identity (ANI) of the genome of strain PytT compared to the genome of strain MucT was 79.7 %. Chemotaxonomic data supported the affiliation of strain PytT to the genus Akkermansia. Based on phenotypic, phylogenetic and genetic characteristics, strain PytT represents a novel species of the genus Akkermansia, for which the name Akkermansia glycaniphila sp. nov. is proposed. The type strain is PytT (=DSM 100705T=CIP 110913T).

  15. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine.

    PubMed

    Kläring, Karoline; Hanske, Laura; Bui, Nam; Charrier, Cédric; Blaut, Michael; Haller, Dirk; Plugge, Caroline M; Clavel, Thomas

    2013-12-01

    A Gram-positive, spore-forming, non-motile, strictly anaerobic rod-shaped bacterium was isolated from the caecal content of a TNF(deltaARE) mouse. The isolate, referred to as strain SRB-521-5-I(T), was originally cultured on a reduced agar medium containing yeast extract, rumen fluid and lactic acid as main energy and carbon sources. Phylogenetic analysis of partial 16S rRNA genes revealed that the species most closely related to strain SRB-521-5-I(T) were Flavonifractor plautii and Pseudoflavonifractor capillosus (<95 % sequence similarity; 1436 bp). In contrast to F. plautii and P. capillosus, strain SRB-521-5-I(T) contained a substantial amount of C18 : 0 dimethylacetal. Additional major fatty acids were C14 : 0 methyl ester, C16 : 0 dimethylacetal and C18 : 0 aldehyde. Strain SRB-521-5-I(T) differed in its enzyme profile from F. plautii and P. capillosus by being positive for dextrin, maltotriose, turanose, dl-lactic acid and d-lactic acid methyl ester but negative for d-fructose. In reduced Wilkins-Chalgren-Anaerobe broth, strain SRB-521-5-I(T) produced approximately 8 mM butyrate and 4 mM acetate. In contrast to F. plautii, the strain did not metabolize flavonoids. It showed intermediate resistance towards the antibiotics ciprofloxacin, colistin and tetracycline. Based on genotypic and phenotypic characteristics, we propose the name Intestinimonas butyriciproducens gen. nov., sp. nov. to accommodate strain SRB-521-5-I(T) ( = DSM 26588(T) = CCUG 63529(T)) as the type strain.

  16. 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).

  17. Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

    PubMed

    Yan, Jun; Yan, Hui; Liu, Li Xue; Chen, Wen Feng; Zhang, Xiao Xia; Verástegui-Valdés, Myrthala M; Wang, En Tao; Han, Xiao Zeng

    2017-01-01

    One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14(T), was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14(T) within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14(T) contained summed feature 8 (C18:1 ω6c/C18:1 ω7c, 59.96 %), C16:0 (10.6 %) and summed feature 2 (C12:0 aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14(T) from the type strains for the related species. The genome size and DNA G+C content of FH14(T) were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14(T) (=HAMBI 3636(T) = LMG 29288(T)) as the type strain.

  18. Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove.

    PubMed

    Vashist, Poonam; Nogi, Yuichi; Ghadi, Sanjeev C; Verma, Pankaj; Shouche, Yogesh S

    2013-07-01

    A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13(T), was isolated from the mangrove ecosystem of Goa, India. Strain DD-13(T) degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13(T) was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13(T) formed a coherent cluster with species of the genus Microbulbifer. Strain DD-13(T) exhibited 16S rRNA gene sequence similarity levels of 98.9-97.1 % with Microbulbifer hydrolyticus IRE-31(T), Microbulbifer salipaludis JCM 11542(T), Microbulbifer agarilyticus JAMB A3(T), Microbulbifer celer KCTC 12973(T) and Microbulbifer elongatus DSM 6810(T). However, the level of DNA-DNA relatedness between strain DD-13(T) and the five type strains of these species of the genus Microbulbifer were in the range of 26-33 %. Additionally, strain DD-13(T) demonstrates several phenotypic differences from these type strains of species of the genus Microbulbifer. Thus strain DD-13(T) represents a novel species of the genus Microbulbifer, for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13(T) ( = KCTC 23483(T) = JCM 17729(T)).

  19. 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)).

  20. Halobacillus mangrovi sp. nov., a moderately halophilic bacterium isolated from the black mangrove Avicennia germinans.

    PubMed

    Soto-Ramírez, Nelís; Sánchez-Porro, Cristina; Rosas-Padilla, Soniris; Almodóvar, Karinna; Jiménez, Gina; Machado-Rodríguez, Marlene; Zapata, Magaly; Ventosa, Antonio; Montalvo-Rodríguez, Rafael

    2008-01-01

    A moderately halophilic, spore-forming, Gram-positive, short-rod-shaped bacterium, designated strain MS10(T), was isolated from the surface of leaves of the black mangrove Avicennia germinans and was subjected to a polyphasic taxonomic study. Strain MS10(T) was able to grow at NaCl concentrations in the range 5-20% (w/v) with optimum growth at 10% (w/v) NaCl. Growth occurred at temperatures of 10-50 degrees C (optimal growth at 33-35 degrees C) and pH 6.0-9.0 (optimal growth at pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain MS10(T) fell within the branch encompassing members of the genus Halobacillus and was most closely related to Halobacillus dabanensis JCM 12772(T) (99.2% 16S rRNA gene sequence similarity). The DNA G+C content of strain MS10(T) was 45.7 mol%, the major respiratory isoprenoid quinone was MK-7 and the cell-wall peptidoglycan was of the L-Orn-D-Asp type, characteristics consistent with its affiliation to the genus Halobacillus. Strain MS10(T) showed a level of DNA-DNA hybridization with H. dabanensis JCM 12772(T) of 29% and levels below 70% were also obtained with respect to other recognized members of the genus Halobacillus. The major fatty acids of strain MS10(T) were iso-C(16:0), anteiso-C(15:0), iso-C(14:0) and iso-C(15:0). Overall, the phenotypic, genotypic and phylogenetic results presented in this study demonstrate that strain MS10(T) represents a novel species of the genus Halobacillus, for which the name Halobacillus mangrovi sp. nov. is proposed. The type strain is MS10(T) (=CECT 7206(T)=CCM 7397(T)).

  1. Haloimpatiens lingqiaonensis gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater.

    PubMed

    Wu, Dildar; Zhang, Nai-Fang; Sun, Cong; Zhang, Wen-Wu; Han, Shuai-Bo; Pan, Jie; Wu, Min; Th, Dilbar; Zhu, Xu-Fen

    2015-11-11

    An anaerobic bacterium, strain ZC-CMC3T, was isolated from a wastewater sample in Zhejiang, China. Cells were Gram-positive, peritrichous, non-spore-forming and rod-shaped (0.6-1.2 × 2.9-5.1 μm). Strain ZC-CMC3T was able to grow at 25-48 °C (optimum 43 °C), and pH 5.5-8.0 (optimum pH 7.0). NaCl concentration range of growth was 0-3 % (w/v) with the optimum 0 %. Catalase- and Oxidase- negative. The major polar lipids of the isolate were diphosphatidylglycerol, phosphatidylglycerol, several phospholipids and glycolipids. Main fermentation products from PYG medium were formate, acetate, lactate and ethanol. Substrates which could be utilized were peptone, tryptone, yeast extract and beef extract. No respiratory quinone was detected. The mainly fatty acids were C14:0, C16:0, C16:1 cis 7 and C16:1 cis 9. The DNA G+C content was 30.0 mol%. The 16S rRNA gene sequence analysis revealed that the isolate belonged to the family Clostridiaceae. The most closely phylogenetic related species was Oceanirhabdus sediminicola NH-JN4T (with 92.8 % sequence similarity) and Clostridium tepidiprofundi SG 508T (with 92.6 % sequence similarity). On the basis of phylogenetic, chemotaxonomic and phenotypic characteristics, we propose that strain ZC-CMC3T as a novel species of a novel genus in the family Clostridiaceae, for which the name Haloimpatiens lingqiaonensis gen. nov., sp. nov. is proposed. The type strain of type species is ZC-CMC3T (KCTC 15321T = JCM 19210T= CCTCC AB 2013104T).

  2. Halomonas huangheensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil.

    PubMed

    Miao, Chaohua; Jia, Fangfang; Wan, Yusong; Zhang, Wei; Lin, Min; Jin, Wujun

    2014-03-01

    A novel, Gram-stain-negative, aerobic, rod-shaped, non-motile and moderately halophilic bacterium, designated strain BJGMM-B45(T), was isolated from a saline-alkali soil collected from Shandong Province, China. Growth of strain BJGMM-B45(T) occurred at 10-45 °C (optimum, 30 °C) and pH 5.0-12.0 (optimum, pH 7.0) on Luria-Bertani agar medium with 1-20 % (w/v) NaCl (optimum, 7-10 %). The predominant respiratory quinone was Q-9. The major cellular fatty acids (>5 %) were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3, C12 : 0 3-OH and C12 : 0. The genomic DNA G+C content was 57.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BJGMM-B45(T) belonged to the genus Halomonas in the class Gammaproteobacteria. The closest relatives were Halomonas cupida DSM 4740(T) (98.2 % 16S rRNA gene sequence similarity) and Halomonas denitrificans M29(T) (97.8 %). Levels of DNA-DNA relatedness between strain BJGMM-B45(T) and Halomonas cupida CGMCC 1.2312(T) and Halomonas denitrificans DSM 18045(T) were 57.0 and 58.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BJGMM-B45(T) is considered to represent a novel species of the genus Halomonas, for which the name Halomonas huangheensis sp. nov. is proposed. The type strain is BJGMM-B45(T) ( = ACCC 05850(T) = KCTC 32409(T)).

  3. Marinospirillum celere sp. nov., a novel haloalkaliphilic, helical bacterium isolated from Mono Lake.

    PubMed

    Namsaraev, Zorigto; Akimov, Vladimir; Tsapin, Alexandre; Barinova, Ekaterina; Nealson, Kenneth; Gorlenko, Vladimir

    2009-09-01

    Two strains of a Gram-negative, helical, haloalkaliphilic bacterium were isolated from Mono Lake (USA). Both strains were mesophilic and grew between 13 and 55 degrees C, with optimum growth at 35-45 degrees C. The optimum pH for growth was 9.5. Growth was observed at NaCl concentrations of 0.5-12% (w/v), with optimum growth at 2% NaCl. Both isolates were motile by means of bipolar tuft flagella, coccoid body-forming and strictly aerobic. It was concluded that they belong to the same species, based on DNA-DNA hybridization values (95% DNA relatedness). DNA G+C contents of the novel strains were 52.1 and 52.3 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were shown to be related closely to the members of the genus Marinospirillum (family Oceanospirillaceae, class Gammaproteobacteria). Sequence similarity of strain v1c_Sn-redT to the type strains of Marinospirillum alkaliphilum, Marinospirillum minutulum, Marinospirillum megaterium and Marinospirillum insulare was 95.0, 92.7, 91.8 and 91.8%, respectively. Chemotaxonomic data [major ubiquinone, Q8; major fatty acids, C18:1(n-7) and C16:0] and physiological and biochemical tests supported the affiliation of the novel strains to the genus Marinospirillum as members of a novel species, for which the name Marinospirillum celere sp. nov. is proposed, with the type strain v1c_Sn-redT (=LMG 24610T=VKM 2416T).

  4. 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)).

  5. Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family 'Saccharospirillaceae'.

    PubMed

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Fazeli, Seyed Abolhassan Shahzadeh; Schumann, Peter; Ventosa, Antonio

    2014-11-01

    A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1(T), was isolated from water of the coastal-marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1-10% (w/v) and optimal growth was achieved at 3% (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5-10 and 4-40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class Gammaproteobacteria as a separate deep branch, with 92.1% or lower sequence similarity to representatives of the genera Saccharospirillum and Reinekea and less than 91.0% sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C(18 : 1)ω7c, C(16:0) and C(17 : 0), and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1(T) contained the isoprenoid quinones Q-9 and Q-8 (81% and 2%, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1(T) represents a novel species in a new genus in the family 'Saccharospirillaceae', order Oceanospirillales, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1(T) ( = IBRC-M 10765(T) =CECT 8342(T)).

  6. Cyclobacterium halophilum sp. nov., a marine bacterium isolated from a coastal-marine wetland.

    PubMed

    Shahinpei, Azadeh; Amoozegar, Mohammad Ali; Sepahy, Abbas Akhavan; Schumann, Peter; Ventosa, Antonio

    2014-03-01

    A novel Gram-stain-negative, slightly halophilic bacterium, designated strain GASx41(T), was isolated from soil of the coastal-marine wetland Gomishan in Iran. Cells of strain GASx41(T) were curved, ring-like or horseshoe-shaped rods and non-motile. Strain GASx41(T) was strictly aerobic, and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 1-10% (w/v), with optimum growth occurring at 2.5-3% (w/v) NaCl. The optimum temperature and pH for growth were 25-30 °C and pH 7.5-8.0. On the basis of 16S rRNA gene sequence analysis, strain GASx41(T) was shown to belong to the genus Cyclobacterium within the phylum Bacteroidetes and showed closest phylogenetic similarity to 'Cyclobacterium jeungdonense' HMD3055 (98.0%). The DNA G+C content of strain GASx41(T) was 48.1 mol%. The major cellular fatty acids of strain GASx41(T) were iso-C15 : 0, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0 2-OH, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and its polar lipid pattern consisted of phosphatidylethanolamine, phosphatidylcholine and 12 unknown lipids. The only quinone present was menaquinone 7 (MK-7). All these features confirmed the placement of isolate GASx41(T) within the genus Cyclobacterium. On the basis of evidence from this study, a novel species of the genus Cyclobacterium, Cyclobacterium halophilum sp. nov., is proposed, with strain GASx41(T) ( = IBRC-M 10761(T) = CECT 8341(T)) as the type strain.

  7. Metabolism of 2-methylpropene (isobutylene) by the aerobic bacterium Mycobacterium sp. strain ELW1.

    PubMed

    Kottegoda, Samanthi; Waligora, Elizabeth; Hyman, Michael

    2015-03-01

    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.

  8. 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)).

  9. Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil.

    PubMed

    Ahmed, Iftikhar; Yokota, Akira; Fujiwara, Toru

    2007-04-01

    A motile, Gram-positive, boron-tolerant and moderately halotolerant rod-shaped bacterium was isolated from a soil naturally high in boron minerals found in the Hisarcik area of Turkey. The novel isolate, designated T-16X(T), produced spherical or ellipsoidal endospores in a non-bulging or slightly swollen sporangium in a terminal position and survived in a medium containing up to 450 mM boron. Whereas it tolerated 11 % (w/v) NaCl, it also grew without NaCl or boron. The temperature range for growth was 16-37 degrees C (optimum 25-28 degrees C) and the pH range for growth was 6.0-10.0 (optimum pH 7.5-8.5). The DNA G+C content was 35.8 mol% and the major cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) at 18.2 and 45.7 % of the total fatty acids, respectively. MK-7 (90 %) was the predominant respiratory quinone system and meso-diaminopimelic acid was the predominant diamino acid of the cell-wall peptidoglycan. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the novel strain is closely related to the type strains of Gracilibacillus orientalis (96.7 % similarity), G. halotolerans (95.5 %) and G. dipsosauri (95.4 %). However, the maximum DNA hybridization value for this strain with these closely related strains was less than 26.2 %. On the basis of 16S rRNA gene sequence data and chemotaxonomic and physiological features, the organism T-16X(T) (=DSM 17256(T)=IAM 15263(T)=ATCC BAA-1190(T)) is proposed to be a member of the genus Gracilibacillus as the type strain of the novel species Gracilibacillus boraciitolerans sp. nov.

  10. Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.

    PubMed

    Song, Geun Cheol; Yasir, Muhammad; Bibi, Fehmida; Chung, Eu Jin; Jeon, Che Ok; Chung, Young Ryun

    2011-01-01

    A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903(T), was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903(T) grew optimally at 30 °C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903(T) was related most closely to Nocardioides pyridinolyticus OS4(T) (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436(T) (96.6 %), Nocardioides aquiterrae GW-9(T) (96.6 %) and Nocardioides hankookensis DS-30(T) (96.6 %). The cell-wall peptidoglycan contained LL-diaminopimelic acid and MK-8(H(4)) was the major respiratory quinone. The mean (±SD) level of DNA-DNA relatedness between strain YC6903(T) and N. pyridinolyticus OS4(T) was 53.5±5.5 %. The predominant cellular fatty acid of strain YC6903(T) was iso-C(16 : 0) (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903(T) (=KACC 13778(T) =DSM 22177(T)).

  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)).

  12. Demethylation of Polymethoxyflavones by Human Gut Bacterium, Blautia sp. MRG-PMF1.

    PubMed

    Burapan, Supawadee; Kim, Mihyang; Han, Jaehong

    2017-03-01

    Polymethoxyflavones (PMFs) were biotransformed to various demethylated metabolites in the human intestine by the PMF-metabolizing bacterium, Blautia sp. MRG-PMF1. Because the newly formed metabolites can have different biological activities, the pathways and regioselectivity of PMF bioconversion were investigated. Using an anaerobic in vitro study, 12 PMFs, 5,7-dimethoxyflavone (5,7-DMF), 5-hydroxy-7-methoxyflavone (5-OH-7-MF), 3,5,7-trimethoxyflavone (3,5,7-TMF), 5-hydroxy-3,7-dimethoxyflavone (5-OH-3,7-DMF), 5,7,4'-trimethoxyflavone (5,7,4'-TMF), 5-hydroxy-7,4'-dimethoxyflavone (5-OH-7,4'-DMF), 3,5,7,4'-tetramethoxyflavone (3,5,7,4'-TMF), 5-hydroxy-3,7,4'-trimethoxyflavone (5-OH-3,7,4'-TMF), 5,7,3',4'-tetramethoxyflavone (5,7,3',4'-TMF), 3,5,7,3',4'-pentamethoxyflavone (3,5,7,3',4'-PMF), 5-hydroxy-3,7,3',4'-tetramethoxyflavone (5-OH-3,7,3',4'-TMF), and 5,3'-dihydroxy-3,7,4'-trimethoxyflavone (5,3'-diOH-3,7,4'-TMF), were converted to chrysin, apigenin, galangin, kaempferol, luteolin, and quercetin after complete demethylation. The time-course monitoring of PMF biotransformations elucidated bioconversion pathways, including the identification of metabolic intermediates. As a robust flavonoid demethylase, regioselectivity of PMF demethylation generally followed the order C-7 > C-4' ≈ C-3' > C-5 > C-3. PMF demethylase in the MRG-PMF1 strain was suggested as a Co-corrinoid methyltransferase system, and this was supported by the experiments utilizing other methyl aryl ether substrates and inhibitors.

  13. Hoeflea suaedae sp. nov., an endophytic bacterium isolated from the root of the halophyte Suaeda maritima.

    PubMed

    Chung, Eu Jin; Park, Jeong Ae; Pramanik, Prabhat; Bibi, Fehmida; Jeon, Che Ok; Chung, Young Ryun

    2013-06-01

    A Gram-negative, aerobic, short rod-shaped bacterium, designated strain YC6898(T), was isolated from the surface-sterilized root of a halophyte (Suaeda maritima) inhabiting tidal flat of Namhae Island, Korea. Strain YC6898(T) grew optimally at 30-37 °C and pH 6.5-7.5. The strain inhibited mycelial growth of Pythium ultimum and Phytophthora capsici. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YC6898(T) belongs to the genus Hoeflea in the family Phyllobacteriaceae. Its closest relatives were Hoeflea alexandrii AM1V30(T) (96.7% 16S rRNA gene sequence similarity), Hoeflea anabaenae WH2K(T) (95.7%), Hoeflea phototrophica DFL-43(T) (95.5%) and Hoeflea marina LMG 128(T) (94.8%). Strain YC6898(T) contained Q-10 as the major ubiquinone. The major fatty acids of strain YC6898(T) were C18:1ω7c (61.1%), C16:0 (11.9%), 11-methyl C18:1ω7c (9.6%) and C19:0 cyclo ω8c (8.0%). The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unknown lipids and an unknown glycolipid. The total genomic DNA G+C content was 53.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain YC6898(T) represents a novel species of the genus Hoeflea, for which the name Hoeflea suaedae sp. nov. is proposed. The type strain is YC6898(T) (=KACC 14911(T)=NBRC 107700(T)).

  14. Mobilisporobacter senegalensis gen. nov., sp. nov., an anaerobic bacterium isolated from tropical shea cake.

    PubMed

    Mbengue, Malick; Thioye, Abdoulaye; Labat, Marc; Casalot, Laurence; Joseph, Manon; Samb, Abdoulaye; Ben Ali Gam, Zouhaier

    2016-01-08

    A new Gram-stain positive, endospore-forming, strictly anaerobic bacterium, designated strain Gal1T was isolated from shea cake, a waste material from the production of shea-butter originating from Saraya, Senegal. The cells were rod-shaped slightly curved, motile with peritrichous flagella. The strain is oxidase negative and catalase-negative. Growth was observed at temperatures ranging from 15 to 45 °C (optimum 30 °C) and at pH 6.5-9.3 (optimum pH 7.8). The salinity range for growth was 0-3.5% of NaCl (optimum 1%). Yeast extract is required for growth. Strain Gal1T fermented various carbohydrates such as mannose, mannitol, arabinose, cellobiose, fructose, glucose, maltose, sucrose, trehalose and lactose as positive reactions and the major end products were ethanol and acetate. The only major cellular fatty acid was C16:0 (19.5%). The DNA base G+C content of strain Gal1T was 33.8 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that this strain was related respectively to Mobilitalea sibirica DSM 26468T with 94.27% similarity, Clostridium populeti ATTC 3225T with 93.94%, Clostridium aminovalericum DSM 1283T and Anaerosporobacter mobilis DSM 15930T with 93.63%. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain Gal1T was clearly distinguished from closely related genera, and the strain Gal1T can be assigned to a new genus for which the name Mobilisporobacter senegalensis gen. nov., sp. nov. is proposed. The type strain is Gal1T (= DSM 26537T, = JCM 18753T).

  15. 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

  16. 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.

  17. 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)).

  18. Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from geyser Strokkur (Iceland).

    PubMed

    Gaisin, Vasil A; Kalashnikov, Alexander M; Grouzdev, Denis S; Sukhacheva, Marina V; Kuznetsov, Boris B; Gorlenko, Vladimir M

    2017-01-23

    A novel, thermophilic filamentous anoxygenic phototrophic bacterium, strain isl-2T, was isolated from the Strokkur Geyser, Iceland. Strain isl-2T formed unbranched multicellular filaments with gliding motility. The cells formed no spores and stained Gram-negative. The existence of pili was described in Chloroflexus spp. for the first time. Optimal growth occurred in a pH range of 7.5-7.7 and at a temperature of 55°C. Strain isl-2T grew photoheterotrophically under anaerobic conditions in the light and chemoheterotrophically under aerobic conditions in the dark. The major cellular fatty acids were C18:1ω9, C16:0, C18:0, and C18:0-OH. The major quinone was menaquinone-10. The photosynthetic pigments were bacteriochlorophylls c and a as well as β- and γ-carotenes. Phylogenetic analysis of the 16S rRNA gene sequences placed strain isl-2T into the genus Chloroflexus of the phylum Chloroflexi with Chloroflexus aggregans DSM 9485T as the closest relative (97.0% identity). The whole-genome sequence of strain isl-2T was determined. Average nucleotide identity values obtained for strain isl-2T in comparison to available genomic sequences of other strains of Chloroflexus spp. were ≤81.4% and digital DNA-DNA hybridisation values ≤ 22.8%. Additional phylogenetic analysis of the PufLM and BchG amino acid sequences supported the separate position of the isl-2T phylotype from other Chloroflexus phylotypes. Based on physiological and phylogenetic data as well as on genomic data, it was suggested that strain isl-2T represents a novel species within the genus Chloroflexus, with the proposed name Chloroflexus islandicus sp. nov. The type strain of the species is isl-2T (=VKM B-2978T, =DSM 29225T, =JCM 30533T).

  19. Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil.

    PubMed

    Lin, Shih-Yao; Hameed, Asif; Liu, You-Cheng; Hsu, Yi-Han; Lai, Wei-An; Chen, Wen-Ming; Shen, Fo-Ting; Young, Chiu-Chung

    2013-07-01

    An aerobic, Gram-stain-negative, rod-shaped bacterium with a single polar flagellum, designated CC-OPY-1(T), was isolated from an oil-contaminated site in Taiwan. CC-OPY-1(T) produces siderophores, and can grow at temperatures of 25-37 °C and pH 5.0-9.0 and tolerate <5 % (w/v) NaCl. The 16S rRNA gene sequence analysis of CC-OPY-1(T) showed high pairwise sequence similarity to Pseudomonas alcaligenes BCRC 11893(T) (97.1 %), Pseudomonas. alcaliphila DSM 17744(T) (97.1 %), Pseudomonas tuomuerensis JCM 14085(T) (97.1 %), Pseudomonas toyotomiensis JCM 15604(T) (96.9 %) and lower sequence similarity to remaining species of the genus Pseudomonas. The phylogenetic trees reconstructed based on gyrB and rpoB gene sequences supported the classification of CC-OPY-1(T) as a novel member of the genus Pseudomonas. The predominant quinone system of strain CC-OPY-1T was ubiquinone (Q-9) and the DNA G+C content was 68.4 ± 0.3 mol%. The major fatty acids were C12 : 0, C16 : 0, C17 : 0 cyclo and summed features 3 and 8 consisting of C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c, respectively. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC) and two unknown phospholipids (PL1-2). Due to distinct phylogenetic, phenotypic and chemotaxonomic features, CC-OPY-1(T) is proposed to represent a novel species within the genus Pseudomonas for which the name Pseudomonas sagittaria sp. nov. is proposed. The type strain is CC-OPY-1(T) ( = BCRC 80399(T) = JCM 18195(T)).

  20. Cecembia rubra sp. nov., a thermophilic bacterium isolated from a hot spring sediment.

    PubMed

    Duan, Yan-Yan; Ming, Hong; Dong, Lei; Yin, Yi-Rui; Meng, Xiao-Lin; Zhou, En-Min; Zhang, Jian-Xin; Nie, Guo-Xing; Li, Wen-Jun

    2015-07-01

    A Gram-staining negative, rod-shaped bacterium, designated strain YIM 78110(T), was isolated from a sediment sample collected from Hehua hot spring in Tengchong, Yunnan province, south-west China. The taxonomic status of strain YIM 78110(T) was confirmed by a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain YIM 78110(T) belongs to the genus Cecembia, displaying 96.8% and 94.7% sequence similarity with the two most closely related type strains, Cecembia calidifontis RQ-33(T) and Cecembia lonarensis LW9T, respectively. The low value of DNA-DNA hybridization (52.3 ± 2.3%) between strain YIM 78110(T) and its closest neighbour, Cecembia calidifontis RQ-33(T), indicated that this new isolate represented a different genomic species in the genus Cecembia. The temperature for growth ranged from 30 to 50 °C. The pH for growth ranged from pH 4.0 to 10.0, with NaCl tolerance of 0.5-6.0% (w/v). The predominant menaquinone of strain YIM 78110(T) was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were iso-C15:0 and C15:0. The DNA G+C content was 47.1 mol%. On the basis of physiological, biochemical and phylogenetic analyses, it is proposed that strain YIM 78110(T) represents a novel species of the genus Cecembia, for which the name Cecembia rubra sp. nov. is proposed. The type strain is YIM 78110(T) ( = CCTCC AB2013287(T) = DSM 28057(T)).

  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).

  2. Chitinivorax tropicus gen. nov., sp. nov., a chitinolytic bacterium isolated from a freshwater lake.

    PubMed

    Chen, Wen-Ming; Yang, Shwu-Harn; Huang, Wei-Cheng; Cheng, Chih-Yu; Sheu, Shih-Yi

    2012-05-01

    A facultatively anaerobic, chitinolytic bacterium, strain KL-9(T), was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9(T) were gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15-40 °C (optimum, 30-37 °C), at pH 7.0-9.0 (optimum, pH 8.0) and with 0-1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9(T) was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9(T) formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria, being most closely related to members of the genera Leeia, Chitinimonas, Silvimonas and Andreprevotia. Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9(T) is thus considered to represent a novel species of a new genus within the class Betaproteobacteria, for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9(T) ( = BCRC 80168(T) = LMG 25530(T)).

  3. Burkholderia susongensis sp. nov., a mineral-weathering bacterium isolated from weathered rock surface.

    PubMed

    Gu, Jia-Yu; Zang, Sheng-Gang; Sheng, Xia-Fang; He, Lin-Yan; Huang, Zhi; Wang, Qi

    2015-03-01

    A novel type of mineral-weathering bacterium was isolated from the weathered surface of rock (mica schist) collected from Susong (Anhui, China). Cells of strain L226(T) were Gram-stain-negative. The strain grew optimally at 30 °C, with 1 % (w/v) NaCl and at pH 7.0 in trypticase soy broth. On the basis of 16S rRNA gene phylogeny, strain L226(T) was shown to belong to the genus Burkholderia and the closest phylogenetic relatives were Burkholderia sprentiae WSM5005(T) (98.3 %), Burkholderia acidipaludis NBRC 101816(T) (98.2 %), Burkholderia tuberum STM678(T) (97.2 %) and Burkholderia diazotrophica JPY461(T) (97.1 %). The DNA G+C content was 63.5 mol% and the respiratory quinone was Q-8. The major fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The polar lipid profile of strain L226(T) consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, unknown lipids and unidentified aminophospholipids. Based on the low level of DNA-DNA relatedness (ranging from 25.8 % to 34.4 %) to the tested type strains of species of the genus Burkholderia and unique phenotypic characteristics, it is suggested that strain L226(T) represents a novel species of the genus Burkholderia, for which the name Burkholderia susongensis sp. nov., is proposed. The type strain is L226(T) ( = CCTCC AB2014142(T) = JCM 30231(T)).

  4. Anaeromicrobium sediminis gen. nov., sp. nov., a fermentative bacterium isolated from deep-sea sediment.

    PubMed

    Zhang, Xiaobo; Zeng, Xiang; Li, Xi; Alain, Karine; Jebbar, Mohamed; Shao, Zongze

    2016-12-14

    A novel anaerobic, mesophilic,heterotrophic bacterium, designated strain DY2726DT, was isolated from West Pacific Ocean sediments. Cells were long rods (0.5-0.8 μm wide,4-15 μm long),Gram-positive and motile by means of flagella. The temperature and pH ranges for growth were 25-40 °C and pH 6.5-9.0,while optimal growth occurred at 37 °C and pH 7.5, with a generation time 76 minutes. The strain required sea salts for growth from 10 to 30 g L-1 (optimum at 20 g L-1). Substrates used as carbon sources were yeast extract, tryptone, glucose, cellobiose, starch, gelatin, dextrin, fructose, fucose, galactose, galacturonic acid, gentiobiose, glucosaminic acid, mannose, melibiose, palatinose and rhamnose. Products of fermentation were carbon dioxide, acetic acid and butyric acid. Strain DY2726DT was able to reduce amorphous iron hydroxide, goethite, amorphous iron oxides, AQDS and crotonate, but did not reduce sulfur, sulfate, thiosulfate, sulfite and nitrate. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain DY2726DT was affiliated to the family Clostridiaceae and is most closely related to Alkaliphilus transvaalensis (90.0% similarity), Alkaliphilus oremlandii (89.6%). The genomic DNA G + C content, was 33.4 mol%. The major cellular fatty acids of strain DY2726DT were C16:1, C14:0 and C16:0. On the basis of its phenotypic and genotypic properties, strain DY2726DT is suggested to represent a novel species of a new genus in the family Clostridiaceae, for which the name Anaeromicrobium sediminis gen. nov., sp. nov. is proposed. The type strain of Anaeromicrobium sediminis is DY2726DT (=JCM 30224T =MCCC 1A00776T).

  5. Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater.

    PubMed

    Bhumika, V; Srinivas, T N R; Kumar, P Anil

    2013-07-01

    A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1(T), was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate reduction and ornithine decarboxylase activities and negative for citrate utilization, urease, oxidase, catalase and DNase activities. The predominant fatty acids were C16 : 0 3-OH, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, anteiso-C15 : 0, C16 : 0, C15 : 0 3-OH, and C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3). Strain N1(T) contained menaquinone 6 (MK-6) as the sole respiratory quinone. The only polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine (PE), three unidentified aminolipids (AL1-AL3) and two unidentified lipids (L1, L2). The DNA G+C content of the strain was 36.3 mol%. 16S rRNA gene sequence analysis indicated that strain N1(T) was a member of the genus Flavobacterium and closely related to Flavobacterium resistens with pairwise sequence similarity of 96.5 %. Phylogenetic analysis showed that strain N1(T) clustered with Flavobacterium glycines and Flavobacterium daejeonense with a distance of 4.8 and 6.0 % (95.2 and 94.0 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, strain N1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium nitratireducens sp. nov. is proposed. The type strain is N1(T) ( = MTCC 11155(T) = JCM 17678(T)).

  6. 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).

  7. Desulfonatronum thiodismutans sp. nov., a novel alkaliphilic, sulfate-reducing bacterium capable of lithoautotrophic growth.

    PubMed

    Pikuta, Elena V; Hoover, Richard B; Bej, Asim K; Marsic, Damien; Whitman, William B; Cleland, David; Krader, Paul

    2003-09-01

    A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7x1.2-2.7 micro m in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 degrees C (optimum, 37 degrees C), >1-7 % NaCl, 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(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(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(T), exhibited 51 % homology. Also, the genome size (1.6x10(9) Da) and T(m) value of the genomic DNA (71+/-2 degrees C) for strain MLF1(T) were significantly different from the genome size (2.1x10(9) Da) and T(m) value (63+/-2 degrees C) for Desulfonatronum lacustre Z-7951(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(T)=ATCC BAA-395(T)=DSM 14708(T)).

  8. Saccharofermentans acetigenes gen. nov., sp. nov., an anaerobic bacterium isolated from sludge treating brewery wastewater.

    PubMed

    Chen, Shuangya; Niu, Lili; Zhang, Yongxiang

    2010-12-01

    A spore-forming anaerobic bacterium, designated strain P6(T), was isolated from the sludge of an up-flow anaerobic sludge blanket reactor treating brewery wastewater. Cells were Gram-positive, oval and 0.6-0.9 μm by 1.2-1.8 μm in size. Growth was observed at 20-42 °C and at pH 5.0-7.5. It fermented several hexoses, polysaccharides and alcohols. Sucrose and aesculin could also be fermented. The main end products of fermentation from glucose were acetate, lactate and fumarate; trace CO(2) and H(2) were also produced. The DNA G+C content of strain P6(T) was 55.6 mol%. The major cellular fatty acids were iso-C(15 : 0), anteiso-C(15 : 0) and iso-C(14 : 0) 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain P6(T) represented a novel phyletic sublineage in clostridial cluster III, and showed <91 % similarity to the type strains of recognized species in this cluster. Phenotypically, the new isolate was distinguished from its phylogenetic relatives (e.g. Clostridium straminisolvens, Clostridium thermocellum, Acetivibrio cellulolyticus and Clostridium aldrichii) by producing acid from glucose and its inability to degrade cellulose. On the basis of evidence from this polyphasic study, strain P6(T) is considered to represent a novel species of a new genus, for which the name Saccharofermentans acetigenes gen. nov., sp. nov. is proposed. The type strain of Saccharofermentans acetigenes is P6(T) (=JCM 14006(T) =AS 1.5064(T)).

  9. 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).

  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)).

  11. Brassicibacter mesophilus gen. nov., sp. nov., a strictly anaerobic bacterium isolated from food industry wastewater.

    PubMed

    Fang, Ming-Xu; Zhang, Wen-Wu; Zhang, Yan-Zhou; Tan, Hai-Qin; Zhang, Xin-Qi; Wu, Min; Zhu, Xu-Fen

    2012-12-01

    A novel mesophilic, strictly anaerobic bacterium, strain BM(T), was isolated from food industry wastewater. The cells were motile, non-spore-forming rods and stained Gram-negative. Growth of strain BM(T) was observed at 16-44 °C (optimum 37 °C) and pH 6.0-9.0 (optimum pH 7.5). The NaCl concentration range for growth was 0-8% (optimum 1.5%, w/v). Strain BM(T) was chemo-organotrophic, using a few sugars and amino acids as sole carbon and energy sources. The fermentation products from peptone-yeast extract broth were propionate, formate, acetate, ethanol and isovalerate. Indole, NH(3) and H(2)S were produced from peptone. No respiratory quinones could be detected. The major fatty acids were iso-C(15:0) (39.3%), iso-C(15:0) dimethyl acetal (10.1%), anteiso-C(15:0) (7.6%), C(14:0) (6.1%) and C(16:0) (5.6%). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol and a number of unidentified aminoglycolipids, glycolipids and phospholipids. The DNA G+C content was 28.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain BM(T) was related to various genera of the family Clostridiaceae, and its closest relatives were Sporosalibacterium faouarense SOL3f37(T) (94.3% 16S rRNA gene sequence similarity), Proteiniborus ethanoligenes GW(T) (92.1%) and Clostridiisalibacter paucivorans 37HS60(T) (92.0%). In recognition of its distinct phenotypic and genotypic characteristics, isolate BM(T) is proposed to represent a novel species of a new genus, Brassicibacter mesophilus gen. nov., sp. nov. The type strain of Brassicibacter mesophilus is BM(T) ( = JCM 16868(T)  = DSM 24659(T)).

  12. Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment.

    PubMed

    Zavarzina, Daria G; Zhilina, Tatyana N; Kuznetsov, Boris B; Kolganova, Tatyana V; Osipov, Georgy A; Kotelev, Mikhail S; Zavarzin, Georgy A

    2013-12-01

    An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001(T). Cells of strain Z-1001(T) were straight, Gram-positive rods, slowly motile. Strain Z-1001(T) was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25-9.5 (at 40 °C), a temperature range from 20 to 57 °C with an optimum at 45-50 °C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2-1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001(T). Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001(T) reduced S(2)O(3)(2-), NO(-)(3), AsO(3-)(4), Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l(-1). The main fatty acids were C16 : 0, C16 : 1ω7c, C18 : 0 and C18 : 1ω9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001(T) is a member of family Natranaerobiaceae, clustering with the type strain of Natranaerobius thermophilus (95.8-96.0 % sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001(T) ( = DSM 24923(T) = VKM B-2666(T)) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov.

  13. Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge.

    PubMed

    Liu, Yi; Qiao, Jiang-Tao; Yuan, Xian-Zheng; Guo, Rong-Bo; Qiu, Yan-Ling

    2014-05-01

    An anaerobic, spore-forming, ethanol-hydrogen-coproducing bacterium, designated LX-BT, was isolated from an anaerobic sludge treating herbicide wastewater. Cells of strain LX-BT were non-motile rods (0.3-0.5×3.0-18.0 µm). Spores were terminal with a bulged sporangium. Growth occurred at 20-50 °C (optimum 37-45 °C), pH 5.0-8.0 (optimum pH 6.0-7.7) and 0-2.5% (w/v) NaCl. The strain could grow fermentatively on glucose, maltose, arabinose, fructose, xylose, ribose, galactose, mannose, raffinose, sucrose, pectin, starch, glycerol, fumarate, tryptone and yeast extract. The major end-products of glucose fermentation were acetate, ethanol and hydrogen. Yeast extract was not required but stimulated growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, anthraquinone-2,6-disulfonate, fumarate and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 56.1 mol%. The major cellular fatty acids were anteiso-C15:0, iso-C14:0 and C16:0. The most abundant polar lipids of strain LX-BT were diphosphatidylglycerol and phosphatidylglycerol. 16S rRNA gene sequence analysis revealed that it belongs to an as-yet-unidentified taxon at the order- or class-level (OPB54) within the phylum Firmicutes, showing 86.5% sequence similarity to previously described species of the Desulfotomaculum cluster. The name Hydrogenispora ethanolica gen. nov., sp. nov. is proposed to accommodate strain LX-BT (=DSM 25471T=JCM 18117T=CGMCC 1.5175T) as the type strain.

  14. Caloramator boliviensis sp. nov., a thermophilic, ethanol-producing bacterium isolated from a hot spring.

    PubMed

    Crespo, Carla; Pozzo, Tania; Karlsson, Eva Nordberg; Alvarez, Maria Teresa; Mattiasson, Bo

    2012-07-01

    A novel moderately thermophilic, anaerobic, ethanol-producing bacterial strain, 45B(T), was isolated from a mixed sediment water sample collected from a hot spring at Potosi, Bolivia. The cells were straight to slightly curved rods approximately 2.5 µm long and 0.5 µm wide. The strain was Gram-stain-variable, spore-forming and monotrichously flagellated. Growth of the strain was observed at 45-65 °C and pH 5.5-8.0, with optima of 60 °C and pH 6.5. The substrates utilized by strain 45B(T) were xylose, cellobiose, glucose, arabinose, sucrose, lactose, maltose, fructose, galactose, mannose, glycerol, xylan, carboxymethylcellulose and yeast extract. The main fermentation product from xylose and cellobiose was ethanol (0.70 and 0.45 g ethanol per gram of consumed sugar, respectively). Acetate, lactate, propionate, carbon dioxide and hydrogen were also produced in minor quantities. 1,3-Propanediol was produced when glycerol-containing medium was supplemented with yeast extract. The major cellular fatty acids were anteiso-C(15:0), C(16:0), iso-C(16:0), C(15:1), iso-C(14:0), C(13:0) and C(14:0). The polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminoglycolipid and 15 other unidentified lipids were predominant. The DNA G+C content of strain 45B(T) was 32.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain 45B(T) is located within the Gram-type positive Bacillus-Clostridium branch of the phylogenetic tree. On the basis of morphological and physiological properties and phylogenetic analysis, strain 45B(T) represents a novel species, for which the name Caloramator boliviensis sp. nov. is proposed; the type strain is 45B(T) (=DSM 22065(T)=CCUG 57396(T)).

  15. 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.

  16. Bacillus horneckiae sp. nov., isolated from a spacecraft-assembly clean room.

    PubMed

    Vaishampayan, Parag; Probst, Alexander; Krishnamurthi, Srinivasan; Ghosh, Sudeshna; Osman, Shariff; McDowall, Alasdair; Ruckmani, Arunachalam; Mayilraj, Shanmugam; Venkateswaran, Kasthuri

    2010-05-01

    Five Gram-stain-positive, motile, aerobic strains were isolated from a clean room of the Kennedy Space Center where the Phoenix spacecraft was assembled. All strains are rod-shaped, spore-forming bacteria, whose spores were resistant to UV radiation up to 1000 J m(-2). The spores were subterminally positioned and produced an external layer. A polyphasic taxonomic study including traditional biochemical tests, fatty acid analysis, cell-wall typing, lipid analyses, 16S rRNA gene sequencing and DNA-DNA hybridization studies was performed to characterize these novel strains. 16S rRNA gene sequencing and lipid analyses convincingly grouped these novel strains within the genus Bacillus as a cluster separate from already described species. The similarity of 16S rRNA gene sequences among the novel strains was >99 %, but the similarity was only about 97 % with their nearest neighbours Bacillus pocheonensis, Bacillus firmus and Bacillus bataviensis. DNA-DNA hybridization dissociation values were <24 % to the closest related type strains. The novel strains had a G+C content 35.6+/-0.5 mol% and could liquefy gelatin but did not utilize or produce acids from any of the carbon substrates tested. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0) and the cell-wall diamino acid was meso-diaminopimelic acid. Based on phylogenetic and phenotypic results, it is concluded that these strains represent a novel species of the genus Bacillus, for which the name Bacillus horneckiae sp. nov. is proposed. The type strain is 1P01SC(T) (=NRRL B-59162(T) =MTCC 9535(T)).

  17. High-yield fermentative preparation of tetramethylpyrazine by Bacillus sp. using an endogenous precursor approach.

    PubMed

    Zhu, Bing-Feng; Xu, Yan; Fan, Wen-Lai

    2010-02-01

    A spore-forming Bacillus sp. was isolated from a high-temperature Daqu, a starter culture of Chinese Maotai-flavor liquor, using an endogenous precursor screening strategy. The Bacillus sp. was capable of producing a high level of 2,3,5,6-tetramethylpyrazine (TTMP) via a precursor of 3-hydroxy-2-butanone (HB). The strain was characterized as Bacillus subtilis based on morphological, physiological, and biochemical properties as well as on partial 16S rRNA gene sequences. Different carbon and nitrogen sources as well as fermentation conditions were investigated. Optimization tests showed that oxygen supply and fermentation temperature were the most important parameters determining the production process. The production of >4.08 g/l TTMP was achieved together with a high level of endogenous precursor HB accumulation (>20 g/l) in both flask and fermentor cultures when the optimized medium and cultivation conditions were applied. Our data demonstrates the effectiveness of the endogenous precursor strategy for screening microorganisms that produce flavor compounds with structure-related precursors. The high yield of TTMP and the inexpensiveness of the agro-industrial product used as the substrate (soybean meal) indicate the potential of this process for industrial application.

  18. Acute toxicity evaluation of explosive wastewater by bacterial bioluminescence assays using a freshwater luminescent bacterium, Vibrio qinghaiensis sp. Nov.

    PubMed

    Ye, Zhengfang; Zhao, Quanlin; Zhang, Mohe; Gao, Yuchen

    2011-02-28

    The compositions of explosive wastewater generated from TNT (2,4,6-trinitrotoluene) purification stage were characterized by using UV-vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), high performance liquid chromatograph (HPLC) and gas chromatograph/mass spectroscopy (GC/MS). The acute toxicity was evaluated by bacterium bioluminescence assay using a freshwater luminescent bacterium (Vibrio qinghaiensis sp. Nov.) and a marine luminescent bacterium (Photobacterium phosphoreum). The results showed that the wastewater's biodegradability was poor due to the high amount of chemical oxygen demand (COD). The main organic components were dinitrotoluene sulfonates (DNTS) with small amount of TNT, dinitrotoluene (DNT), mononitrotoluene (MNT) and other derivatives of nitrobenzene. It was highly toxic to luminescent bacteria P. phosphoreum and V. qinghaiensis sp. Nov. After reaction time of 15 min, the relative concentration of toxic pollutants (expressed as reciprocal of dilution ratio of wastewater) at 50% of luminescence inhibition ratio was 5.32×10(-4) for P. phosphoreu, while that was 4.34×10(-4) for V. qinghaiensis. V. qinghaiensis is more sensitive and suitable for evaluating the wastewater's acute toxicity than P. phosphoreum. After adsorption by resin, the acute toxicity can be greatly reduced, which is helpful for further treatment by biological methods.

  19. 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

    2016-09-02

    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.

  20. Genome sequence of Desulfovibrio sp. A2, a highly copper resistant, sulfate-reducing bacterium isolated from effluents of a zinc smelter at the Urals.

    PubMed

    Mancini, Stefano; Abicht, Helge K; Karnachuk, Olga V; Solioz, Marc

    2011-12-01

    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.

  1. Genome sequence of Vibrio sp. strain EJY3, an agarolytic marine bacterium metabolizing 3,6-anhydro-L-galactose as a sole carbon source.

    PubMed

    Roh, Hanseong; Yun, Eun Ju; Lee, Saeyoung; Ko, Hyeok-Jin; Kim, Sujin; Kim, Byung-Yong; Song, Heesang; Lim, Kwang-il; Kim, Kyoung Heon; Choi, In-Geol

    2012-05-01

    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.

  2. Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil.

    PubMed

    Liu, Xu-Yun; Li, Chun-Xiu; Luo, Xiao-Jing; Lai, Qi-Liang; Xu, Jian-He

    2014-09-01

    A methyl parathion (MP) degrading bacterial strain, designated MP-1(T), was isolated from a waste land where pesticides were formerly manufactured in Jiangsu province, China. Polyphasic taxonomic studies showed that MP-1(T) is a Gram-stain-negative, non-spore-forming, rod-shaped and motile bacterium. The bacterium could grow at salinities of 0-1 % (w/v) and temperatures of 15-40 °C. Strain MP-1(T) could reduce nitrate to nitrite, utilize d-glucose and l-arabinose, but not produce indole, or hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that MP-1(T) belongs to the genus Burkholderia, showing highest sequence similarity to Burkholderia grimmiae DSM 25160(T) (98.5 %), and similar strains including Burkholderia zhejiangensis OP-1(T) (98.2 %), Burkholderia choica LMG 22940(T) (97.5 %), Burkholderia glathei DSM 50014(T) (97.4 %), Burkholderia terrestris LMG 22937(T) (97.2 %) and Burkholderia telluris LMG 22936(T) (97.0 %). In addition, the gyrB and recA gene segments of strain MP-1(T) exhibited less than 89.0 % and 95.1 % similarities with the most highly-related type strains indicated above. The G+C content of strain MP-1(T) was 62.6 mol%. The major isoprenoid quinone was ubiquinone Q-8. The predominant polar lipids comprised phosphatidyl ethanolamine, phosphatidyl glycerol, aminolipid and phospholipid. The principal fatty acids in strain MP-1(T) were C18 : 1ω7c/C18 : 1ω6c (23.3 %), C16 : 0 (16.8 %), cyclo-C17 : 0 (15.0 %), C16 : 1ω7c/C16 : 1ω6 (8.5 %), cyclo-C19 : 0ω8c (8.1 %), C16 : 1 iso I/C14 : 0 3-OH (5.7 %), C16 : 0 3-OH (5.6 %) and C16 : 02-OH (5.1 %). The DNA-DNA relatedness values between strain MP-1(T) and the three type strains (B. grimmiae DSM 25160(T), B. zhejiangensis OP-1(T) and B. glathei DSM 50014(T)) ranged from 24.6 % to 37.4 %. In accordance with phenotypic and genotypic characteristics, strain MP-1(T) represents a novel

  3. 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.

  4. Characterization and site-directed mutagenesis of an α-galactosidase from the deep-sea bacterium Bacillus megaterium.

    PubMed

    Xu, Haibo; Qin, Yongjun; Huang, Zongqing; Liu, Ziduo

    2014-03-05

    A novel gene (BmelA) (1323bp) encoding an α-galactosidase of 440 amino acids was cloned from the deep-sea bacterium Bacillus megaterium and the protein was expressed in Escherichia coli BL21 (DE3) with an estimated molecular mass of about 45 kDa by SDS-PAGE. The enzyme belongs to glycoside hydrolase family 4, with the highest identity (74%) to α-galactosidase Mel4A from Bacillus halodurans among the characterized α-galactosidases. The recombinant BmelA displayed its maximum activity at 35 °C and pH 8.5-9.0 in 50 mM Tris-HCl buffer, and could hydrolyze different substrates with the Km values against p-nitrophenyl-α-D-galactopyranoside (pNP-α-Gal), raffinose and stachyose being 1.02±0.02, 2.24±0.11 and 3.42±0.17 mM, respectively. Besides, 4 mutants (I38 V, I38A, I38F and Q84A) were obtained by site-directed mutagenesis based on molecular modeling and sequence alignment. The kinetic analysis indicated that mutants I38 V and I38A exhibited a 1.7- and 1.4-fold increase over the wild type enzyme in catalytic efficiency (k(cat)/K(m)) against pNP-α-Gal, respectively, while mutant I38F showed a 3.5-fold decrease against pNP-α-Gal and mutant Q84A almost completely lost its activity. All the results suggest that I38 and Q84 sites play a vital role in enzyme activity probably due to their steric and polar effects on the predicted "tunnel" structure and NAD+ binding to the enzyme.

  5. Bacillus amyloliquefaciens G1: A Potential Antagonistic Bacterium against Eel-Pathogenic Aeromonas hydrophila

    PubMed Central

    Cao, Haipeng; He, Shan; Wei, Ruopeng; Diong, Marek; Lu, Liqun

    2011-01-01

    Recent studies have revealed that the use of probiotics is an alternative to control marine aeromonas. However, few probiotics are available against Aeromonas hydrophila infections in eels. In the present study, a potential antagonistic strain G1 against the eel-pathogenic A. hydrophila was isolated from sediment underlying brackish water. Its extracellular products with antibacterial activities were shown to be stable under wide range of pH, temperature, and proteinase K. It was initially identified as Bacillus amyloliquefaciens using API identification kits and confirmed to be B. amyloliquefaciens strain (GenBank accession number DQ422953) by phylogenetic analysis. In addition, it was shown to be safe for mammalians, had a wide anti-A. hydrophila spectrum, and exhibited significant effects on inhibiting the growth of the eel-pathogenic A. hydrophila both in vitro and in vivo. To the best of our knowledge, this is the first report on a promising antagonistic Bacillus amyloliquefaciens strain from brackish water sediment against eel-pathogenic A. hydrophila. PMID:21754944

  6. Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin.

    PubMed

    Albert, Richard A; Archambault, Julieta; Rosselló-Mora, Ramón; Tindall, Brian J; Matheny, Mike

    2005-09-01

    A mesophilic, acidophilic, spore-forming bacterium, strain 105-2(T), was isolated from an acidic Sphagnum peat bog in Wisconsin, USA. Strain 105-2(T) has 16S rRNA gene sequence similarity to Bacillus sporothermodurans DSM 10599(T) and Bacillus oleronius DSM 9356(T) of 97.4 and 97.8%, respectively. The primary lipoquinone is MK-7 and the major fatty acids are 15:0 iso, 15:0 anteiso and 17:0 anteiso. The predominant polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a glycolipid. The DNA G+C content was found to be 43.2 mol%. The phenotypic, chemotaxonomic and molecular analyses identified strain 105-2(T) as a novel Bacillus species, for which the name Bacillus acidicola is proposed. The type strain is 105-2(T) (=DSM 14745(T)=ATCC BAA-366(T)=NRRL B-23453(T)).

  7. 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)).

  8. Larsenimonas suaedae sp. nov., a moderately halophilic, endophytic bacterium isolated from the euhalophyte Suaeda salsa.

    PubMed

    Xia, Zhi-Jie; Wu, Hong-Zhen; Cui, Chun-Xiao; Chen, Qi; Zhao, Guo-Yan; Wang, Hai-Xia; Dai, Mei-Xue

    2016-08-01

    A moderately halophilic, Gram-stain-negative, non-endospore-forming endophytic bacterium designated strain ST307T was isolated from the euhalophyte Suaeda salsa in Dongying, China. Strain ST307T was aerobic, rod-shaped, motile and orange-yellow-pigmented. The organism grew at NaCl concentrations of 0.6-20 % (w/v) (optimum 5-6 %, w/v), at temperatures of 5-45 °C (optimum 35 °C) and at pH 5-9 (optimum pH 7-8). It accumulated poly-β-hydroxybutyric acid and produced exopolysaccharides. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The predominant lipoquinone was ubiquinone Q-9. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, a glycoaminolipid and a phosphoglycoaminolipid. The DNA G+C content was 60.5 mol%. Phylogenetic analyses of 16S rRNA gene sequences and concatenated atpA, rpoD and secA gene sequences revealed that the strain represents a member of the genus Larsenimonas. The closest related type strain was Larsenimonas salina M1-18T. Mean DNA-DNA relatedness values between strain ST307T and the related species L. salina M1-18T, Chromohalobacter beijerinckii DSM 7218T, C. canadensis DSM 6769T, C. israelensis DSM 6768T, C. marismortui CGMCC 1.2321T, C. nigrandesensis DSM 14323T, C. salexigens DSM 3043T and C. sarecensis DSM 15547T were 15±2-45±1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain ST307T clearly represents a novel species of the genus Larsenimonas. The name Larsenimonassuaedae sp. nov. is proposed, with ST307T (=CGMCC 1.8902T=DSM 22428T) as the type strain.

  9. Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica.

    PubMed

    Rozahon, Manziram; Ismayil, Nurimangul; Hamood, Buayshem; Erkin, Raziya; Abdurahman, Mehfuzem; Mamtimin, Hormathan; Abdukerim, Muhtar; Lal, Rup; Rahman, Erkin

    2014-09-01

    An endophytic bacterium, designated K-38(T), was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38(T) was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38(T) grew at temperatures of 25-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, pH 7.5) and in the presence of 0-3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38(T) was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3(T), followed by Rhizobium nepotum 39/7(T) (96.5 %) and Rhizobium borbori DN316(T) (96.2 %). Phylogenetic analysis of strain K-38(T) based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium. The DNA G+C content was determined to be 63.5 mol%. DNA-DNA relatedness between K-38(T) and R. rosettiformans W3(T) was 48.4 %, indicating genetic separation of strain K-38(T) from the latter strain. The major components of the cellular fatty acids in strain K-38(T) were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38(T) include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38(T). Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38(T) represents a novel species of the genus Rhizobium, for which the name Rhizobium populi sp. nov. is proposed

  10. [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.

  11. Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh.

    PubMed

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

    2016-12-01

    A novel Gram-stain-positive, coccoid-shaped, facultative anaerobic, motile and halophilic bacterium strain 5M(T) was isolated from Surajbari in India. Based on the 16S rRNA gene sequence analysis, it was identified as belonging to the genus Marinococcus and was most closely related to Marinococcus luteus KCTC 13214(T) (99.3 %, sequence similarity), Marinococcus halotolerans KCTC 19045(T) (99.0 %), Marinococcus halophilus LMG 17439(T) (98.8 %) and Marinococcus tarijensis LMG 26930(T) (98.7 %). However, the DNA-DNA relatedness of strain 5M(T) with M. luteus KCTC 13214(T), M. halotolerans KCTC 19045(T), M. halophilus LMG 17439(T) and M. tarijensis LMG 26930(T) was 42.6 ± 0.8, 48.6 ± 0.8, 40.9 ± 0.8 and 39.8 ± 0.9 %, respectively. Strain 5M(T) grows optimally at 5 % (w/v) NaCl, pH 7.5-8.5 and 37 °C. The cell-wall peptidoglycan of strain 5M(T) contains meso-diaminopimelic acid. Polar lipids of the strain 5M(T) include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and two unknown lipids. The predominant isoprenoid quinone was MK-7. DNA G+C content was 48.9 mol%, and anteiso-C15:0 (40.9 %) was the predominant fatty acid. The results of phylogenetic, biochemical tests and chemotaxonomic allowed a clear differentiation of strain 5M(T) from all of its nearest phylogenetic neighbours, which represents a novel member of the genus Marinococcus, for which the name Marinococcus salis sp., nov., is proposed. The type strain is 5M(T) (=KCTC 33743(T) = LMG 29101(T) = CGMCC 1.15385(T)).

  12. Oceanobacillus limi sp. nov., a moderately halophilic bacterium from a salt lake.

    PubMed

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Makhdoumi-Kakhki, Ali; Didari, Maryam; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-04-01

    A Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, moderately halophilic bacterium, designated strain H9B(T), was isolated from a mud sample of the hypersaline lake Aran-Bidgol in Iran. Cells of strain H9B(T) were motile and produced colonies with a yellowish-grey pigment. Growth occurred between 2.5 and 10 % (w/v) NaCl and the isolate grew optimally at 7.5 % (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of pH 6-10 and 25-45 °C, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H9B(T) is a member of the genus Oceanobacillus. The closest relative to this strain was Oceanobacillus profundus CL-MP28(T) with 97.1 % 16S rRNA gene sequences similarity. The level of DNA-DNA relatedness between the novel isolate and this phylogenetically related species was 17 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The polar lipid pattern of strain H9B(T) consisted of phosphatidylglycerol, diphosphatidylglycerol, four phospholipids and an aminolipid. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 37.1 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus limi sp. nov. is proposed. The type strain of Oceanobacillus limi is strain H9B(T) ( = IBRC-M 10780(T) = KCTC 13823(T) = CECT 7997(T)).

  13. 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

  14. Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment.

    PubMed

    Shivaji, S; Reddy, P Vishnu Vardhan; Rao, S S S Nageshwara; Begum, Zareena; Manasa, Poorna; Srinivas, T N R

    2012-09-01

    A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11B(T), was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C(15 : 0) (14.9 %), anteiso-C(15 : 0) (11.4 %), iso-C(15 : 1) G (13.1 %), C(15 : 1)ω6c (5.4 %), C(17 : 1)ω6c (6.7 %), summed feature 3 (C(16 : 1)ω7c and/or C(16 : 1)ω6c; 9.3 %) and summed feature 9 (10-methyl C(16 : 0) and/or iso-C(17 : 1)ω9c; 5.9 %). Strain M12-11B(T) contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense, Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11B(T) with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA-DNA hybridization with Cyclobacterium amurskyense KCTC 12363(T) and Cyclobacterium marinum DSM 745(T) showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11B(T). Based on the results of DNA-DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11B(T) represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11B(T) (= KCTC 23011(T) = NBRC 106168(T)) and it has a DNA G+C content of 40.5 mol%.

  15. 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.

  16. Halobacillus sediminis 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

    2015-12-01

    A Gram-staining-positive, moderately halophilic bacterium, designated strain NGS-2T, was isolated from sediment of a solar saltern pond located in Shinan, Korea. Strain NGS-2T was a strictly aerobic, non-motile rod that grew at pH 5.0-10.0 (optimum, pH 8.0), at 10-30 °C (optimum, 28 °C) and in the presence of 1-20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain NGS-2T belonged to the genus Halobacillus, with sequence similarity of 98.4-95.8 % to existing type strains, showing the highest sequence similarity to Halobacillus dabanensis D-8T (98.4 %), H. litoralis SL-4T (98.4 %), H. trueperi SL-5T (98.2 %), H. faecis IGA7-4T (98.2 %), H. profundi IS-Hb4T (98.1 %) and H. mangrovi MS10T (98.0 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methylethanolamine and an unknown glycolipid. The cell-wall peptidoglycan was based on l-Orn-d-Asp, the predominant isoprenoid quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C15: 0 and anteiso-C17: 0. The DNA G+C content of the novel isolate was 45.0 mol%. Levels of DNA-DNA relatedness between strain NGS-2T and the type strains of 12 other species of the genus ranged from 32 to 3 %. On the basis of the polyphasic analysis conducted in this study, strain NGS-2T represents a novel species of the genus Halobacillus, for which the name Halobacillus sediminis sp. nov. is proposed. The type strain is NGS-2T ( = KACC 18263T = NBRC 110639T).

  17. 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

  18. Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome

    PubMed Central

    Schmidt, Johanna; Taipale, Sami J.; Doolittle, W. Ford; Koll, Ulrike

    2014-01-01

    A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8T is noticeable due to its unusually low values of cell size (0.05 µm3), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8T is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8T and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8T was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8T ( = DSM 23834T = LMG 26932T). PMID:24984700

  19. Salimesophilobacter vulgaris gen. nov., sp. nov., an anaerobic bacterium isolated from paper-mill wastewater.

    PubMed

    Zhang, Yan-Zhou; Fang, Ming-Xu; Zhang, Wen-Wu; Li, Tian-Tian; Wu, Min; Zhu, Xu-Fen

    2013-04-01

    A novel anaerobic, heterotrophic bacterium, designated strain Zn2(T), was isolated from the wastewater of a paper mill in Zhejiang, China. Cells were gram-type-positive rods, 0.5-0.8 µm wide and 2-4 µm long, and were motile by a lateral flagellum. The ranges of temperature and pH for growth were 10-50 °C and pH 6.0-9.5. Optimal growth occurred at 35 °C and pH 7.3-7.5. The strain did not require NaCl for growth, but its inclusion in the medium improved growth (optimum concentration 6 %). Substrates utilized as sole carbon sources were peptone, tryptone, Casamino acids, D-xylose, salicin, glycerol, formate, acetate and propionate. The main products of carbohydrate fermentation were acetate, formate, propionate and lactate. Elemental sulfur, thiosulfate and Fe(III) were used as electron acceptors, but sulfate, sulfite, nitrate, nitrite and Mn(IV) were not. Growth was inhibited by the addition of 10 µg ampicillin, penicillin, tetracycline or chloramphenicol ml(-1). iso-C15 : 0, C14 : 0, C16 : 0, C16 : 1 cis9 and C18 : 1 cis9 were the major fatty acids. Strain Zn2(T) did not contain any detectable menaquinones or ubiquinones. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, two unknown phospholipids and four unknown glycolipids. The genomic DNA G+C content was 37 mol%, as determined by HPLC. 16S rRNA gene sequence analysis revealed that strain Zn2(T) was a member of family Clostridiaceae, and was most closely related to the type strains of Geosporobacter subterraneus, Thermotalea metallivorans and Caminicella sporogenes, showing 91.2, 90.3 and 91.1 % sequence similarity, respectively. On the basis of its phenotypic and genotypic properties, strain Zn2(T) is suggested to represent a novel species of a new genus, for which the name Salimesophilobacter vulgaris gen. nov., sp. nov. is proposed. The type strain of Salimesophilobacter vulgaris is Zn2(T) ( = DSM 24770(T)

  20. Oceanirhabdus sediminicola gen. nov., sp. nov., an anaerobic bacterium isolated from sea sediment.

    PubMed

    Pi, Ruo-Xi; Zhang, Wen-Wu; Fang, Ming-Xu; Zhang, Yan-Zhou; Li, Tian-Tian; Wu, Min; Zhu, Xu-Fen

    2013-11-01

    A novel anaerobic bacterium, designated NH-JN4(T) was isolated from a sediment sample collected in the South China Sea. Cells were Gram-stain-positive, spore-forming, peritrichous and rod-shaped (0.5-1.2×2.2-7 µm). The temperature and pH ranges for growth were 22-42 °C and pH 6.0-8.5. Optimal growth occurred at 34-38 °C and pH 6.5-7.0. The NaCl concentration range for growth was 0.5-6 % (w/v) with an optimum of 2.5 %. Catalase and oxidase were not produced. Substrates which could be utilized were peptone, tryptone, yeast extract, beef extract and glycine. Main fermentation products from PYG medium were formate, acetate, butyrate and ethanol. Strain NH-JN4(T) could utilize sodium sulfite as an electron acceptor. No respiratory quinone was detected. The predominant fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0 DMA. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The DNA G+C content was 35.8 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain NH-JN4(T) was a member of family Clostridiaceae, and was most closely related to Clostridium limosum ATCC 25620(T), Clostridium proteolyticum DSM 3090(T), Clostridium histolyticum ATCC 19401(T) and Clostridium tepidiprofundi SG 508(T), showing 94.0, 93.0, 92.9 and 92.3 % sequence similarity, respectively. On the basis of phenotypic, genotypic and chemotaxonomic properties, strain NH-JN4(T) represents a novel species of a new genus in the family Clostridiaceae, for which the name Oceanirhabdus sediminicola gen. nov., sp. nov. is proposed. The type strain of the type species is NH-JN4(T) ( = JCM 18501(T) = CCTCC AB 2013103(T) = KCTC 15322(T)).

  1. 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

  2. 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

  3. Naphthalecin, a novel antibiotic produced by the anaerobic bacterium, Sporotalea colonica sp. nov.

    PubMed

    Ezaki, Masami; Muramatsu, Hideyuki; Takase, Shigehiro; Hashimoto, Michizane; Nagai, Koji

    2008-04-01

    A novel antibiotic naphthalecin was purified and isolated from the cells of an anaerobic bacterium isolated from a soil sample. This antibiotic contained a naphthalene moiety, so named as naphthalecin, and showed antibacterial activity against gram positive species. The producing strain, an obligate anaerobe, was identified as a new species of the genus Sporotalea. Identification of the bacterium, cultivation, purification, structure determination, and antibacterial activity are shown.

  4. Genome sequence of Sphingomonas sp. strain PAMC 26621, an Arctic-lichen-associated bacterium isolated from a Cetraria sp.

    PubMed

    Lee, Hyoungseok; Shin, Seung Chul; Lee, Jungeun; Kim, Su Jin; Kim, Bum-Keun; Hong, Soon Gyu; Kim, Eun Hye; Park, Hyun

    2012-06-01

    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.

  5. 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.

  6. Genome sequence of Nitrosomonas sp. strain AL212, an ammonia-oxidizing bacterium sensitive to high levels of ammonia.

    PubMed

    Suwa, Yuichi; Yuichi, Suwa; Norton, Jeanette M; Bollmann, Annette; Klotz, Martin G; Stein, Lisa Y; Laanbroek, Hendrikus J; Arp, Daniel J; Goodwin, Lynne A; Chertkov, Olga; Held, Brittany; Bruce, David; Detter, J Chris; Detter, Janine C; Tapia, Roxanne; Han, Cliff S

    2011-09-01

    Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower K(m)), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide.

  7. Chromopeptide A, a highly cytotoxic depsipeptide from the marine sediment-derived bacterium Chromobacterium sp. HS-13-94

    PubMed Central

    Zhou, Zhenfang; Wang, Xin; Zhang, Hui; Sun, Jingya; Zheng, Linghui; Liu, Hongchun; Wang, Jidong; Shen, Aijun; Geng, Meiyu; Guo, Yuewei

    2015-01-01

    A bicyclic depsipeptide, chromopeptide A (1), was isolated from a deep-sea-derived bacterium Chromobacterium sp. HS-13-94. Its structure was determined by extensive spectroscopic analysis and by comparison with a related known compound. The absolute configuration of chromopeptide A was established by X-ray diffraction analysis employing graphite monochromated Mo Kα radiation (λ=0.71073 Å) with small Flack parameter 0.03. Chromopeptide A suppressed the proliferation of HL-60, K-562, and Ramos cells with average IC50 values of 7.7, 7.0, and 16.5 nmol/L, respectively. PMID:26579426

  8. 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.

  9. Characteristics of extracellular proteases produced by Bacillus laterosporus and Flavobacterium sp. isolated from gelatinfactory effluents.

    PubMed

    Sharma, A; Rao, C L; Ball, B K; Hasija, S K

    1996-11-01

    Forty bacterial isolates from the effluents of a gelatin factory (Jabalpur, India) were screened for protease activity and the two most potent producers were identified as Bacillus laterosporus and a Flavobacterium sp. The enzymes of both isolates were optimal at pH 8 and 60°C, with maximum activity after 90 min. The enzyme activity of B. laterosporus was suppressed by Fe(2+), Mg(2+), Mn(2+) and Zn(2+) ions but was enhanced by Ba(2+) and Ca(2+). That of Flavobacterium sp. was suppressed by Mg(2+) and Mn(2+) ions but enhanced by Ba(2+), Ca(2+) and Fe(2+). The enzyme activity of the former was strongly inhibited by KCN, whereas that of the latter was only slightly inhibited by 8-hydroxyquinoline.

  10. 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.

  11. Production of Optically Pure D-Lactic Acid by the Combined use of Weissella sp. S26 and Bacillus sp. ADS3.

    PubMed

    Li, Qingxin; Hudari, Mohammad Sufian Bin; Wu, Jin Chuan

    2016-01-01

    Optically pure D-lactic acid was produced from glucose, xylose, or starch by the combined use of Weissella sp. S26 and Bacillus sp. ADS3, two native bacterial strains isolated from Singapore environment. Weissella sp. S26 was used to ferment various sugars to lactic acid rich in D-isomer followed by sterilization of the broth and inoculation of Bacillus sp. ADS3 cells to selectively degrade acetic acid (if any) and L-lactic acid. In a simultaneous saccharification and fermentation of starch by Weissella sp. S26 in 1 L of modified MRS medium containing 50 g/L starch at 30 °C, lactic acid reached 24.2 g/L (23.6 g/L of D-isomers and 0.6 g/L of L-isomers), and acetic acid was 11.8 g/L at 37 h. The fermentation broth was sterilized at 100 °C for 20 min and cooled down to 30 °C followed by inoculation of Bacillus sp. ADS3 (10 %, v/v), and the mixture was kept at 30 °C for 115 h. Acetic acid was completely removed, and L-lactic acid was largely removed giving an optical purity of D-lactic acid as high as 99.5 %.

  12. Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with a "Geospirillum" sp. strain.

    PubMed

    Heising, S; Richter, L; Ludwig, W; Schink, B

    1999-08-01

    A green phototrophic bacterium was enriched with ferrous iron as sole electron donor and was isolated in defined coculture with a spirilloid chemoheterotrophic bacterium. The coculture oxidized ferrous iron to ferric iron with stoichiometric formation of cell mass from carbon dioxide. Sulfide, thiosulfate, or elemental sulfur was not used as electron donor in the light. Hydrogen or acetate in the presence of ferrous iron increased the cell yield of the phototrophic partner, and hydrogen could also be used as sole electron source. Complexed ferric iron was slowly reduced to ferrous iron in the dark, with hydrogen as electron source. Similar to Chlorobium limicola, the phototrophic bacterium contained bacteriochlorophyll c and chlorobactene as photosynthetic pigments, and also resembled representatives of this species morphologically. On the basis of 16S rRNA sequence comparisons, this organism clusters with Chlorobium, Prosthecochloris, and Pelodictyon species within the green sulfur bacteria phylum. Since the phototrophic partner in the coculture KoFox is only moderately related to the other members of the cluster, it is proposed as a new species, Chlorobium ferrooxidans. The chemoheterotrophic partner bacterium, strain KoFum, was isolated in pure culture with fumarate as sole substrate. The strain was identified as a member of the epsilon-subclass of the Proteobacteria closely related to "Geospirillum arsenophilum" on the basis of physiological properties and 16S rRNA sequence comparison. The "Geospirillum" strain was present in the coculture only in low numbers. It fermented fumarate, aspartate, malate, or pyruvate to acetate, succinate, and carbon dioxide, and could reduce nitrate to dinitrogen gas. It was not involved in ferrous iron oxidation but possibly provided a thus far unidentified growth factor to the phototrophic partner.

  13. 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.

  14. Bacillus kochii sp. nov., isolated from foods and a pharmaceuticals manufacturing site.

    PubMed

    Seiler, Herbert; Schmidt, Verena; Wenning, Mareike; Scherer, Siegfried

    2012-05-01

    Three Gram-staining-positive, strictly aerobic, motile, catalase-positive, endospore-forming rods, designated WCC 4582(T), WCC 4581 and WCC 4583, were isolated from two different food sources and a pharmaceuticals production site. The three isolates were highly similar in their 16S rRNA gene sequences (100 % similarity) and groEL sequences (99.2-100 % similarity), Fourier-transform infrared spectroscopic fingerprints and other features tested. The isolates were most closely related to Bacillus horneckiae; the isolates and the type strain of B. horneckiae shared 97.6 % and 89.6 % 16S rRNA gene and groEL sequence similarities, respectively. The organisms grew optimally at 30 °C, at pH 7 and in the presence of 0.5 % (w/v) NaCl. The cell-wall peptidoglycan of WCC 4582(T) contained meso-diaminopimelic acid (A1γ) and the genomic DNA G+C content was 36.4 mol%. DNA-DNA relatedness between strain WCC 4582(T) and B. horneckiae NRRL B-59162(T) was 17 %. The three isolates are considered to represent a novel species of the genus Bacillus, for which the name Bacillus kochii sp. nov. is proposed. The type strain is WCC 4582(T) ( = DSM 23667(T) = CCUG 59877(T) = LMG 25855(T)).

  15. Effects of Bacterial Community Members on the Proteome of the Ammonia-Oxidizing Bacterium Nitrosomonas sp. Strain Is79

    PubMed Central

    Sedlacek, Christopher J.; Nielsen, Susanne; Greis, Kenneth D.; Haffey, Wendy D.; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J.

    2016-01-01

    ABSTRACT Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study, we investigated how the presence of a nitrite-oxidizing bacterium (NOB) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (AOB) Nitrosomonas sp. strain Is79. We investigated Nitrosomonas sp. Is79 in co-culture with Nitrobacter winogradskyi, in co-cultures with selected heterotrophic bacteria, and as a member of the nitrifying enrichment culture G5-7. In batch culture, N. winogradskyi and heterotrophic bacteria had positive effects on the growth of Nitrosomonas sp. Is79. An isobaric tag for relative and absolute quantification (iTRAQ) liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was used to investigate the effect of N. winogradskyi and the co-cultured heterotrophic bacteria from G5-7 on the proteome of Nitrosomonas sp. Is79. In co-culture with N. winogradskyi, several Nitrosomonas sp. Is79 oxidative stress response proteins changed in abundance, with periplasmic proteins increasing and cytoplasmic proteins decreasing in abundance. In the presence of heterotrophic bacteria, the abundance of proteins directly related to the ammonia oxidation pathway increased, while the abundance of proteins related to amino acid synthesis and metabolism decreased. In summary, the proteome of Nitrosomonas sp. Is79 was differentially influenced by the presence of either N. winogradskyi or heterotrophic bacteria. Together, N. winogradskyi and heterotrophic bacteria reduced the oxidative stress for Nitrosomonas sp. Is79, which resulted in more efficient metabolism. IMPORTANCE Aerobic ammonia-oxidizing microorganisms play an important role in the global nitrogen cycle, converting ammonia to

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor

    PubMed Central

    Wei, Yuli; Cao, Junwei; Kato, Chiaki; Cui, Weicheng

    2017-01-01

    ABSTRACT Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic bacterium isolated from coal-bearing sediment down to ~2.4 km below the ocean floor in the northwestern Pacific. The strain is a Gram-positive spore-forming bacterium, closely related to Bacillus subtilis within the phylum Firmicutes. This is the first complete genome sequence of a Bacillus subtilis strain from the deep biosphere. The genome sequence will provide a valuable resource for comparative studies of microorganisms from the surface and subsurface environments. PMID:28232436

  1. Biosurfactant and Degradative Enzymes Mediated Crude Oil Degradation by Bacterium Bacillus subtilis A1.

    PubMed

    Parthipan, Punniyakotti; Preetham, Elumalai; Machuca, Laura L; Rahman, Pattanathu K S M; Murugan, Kadarkarai; Rajasekar, Aruliah

    2017-01-01

    In this work, the biodegradation of the crude oil by the potential biosurfactant producing Bacillus subtilis A1 was investigated. The isolate had the ability to synthesize degradative enzymes such as alkane hydroxylase and alcohol dehydrogenase at the time of biodegradation of hydrocarbon. The biosurfactant producing conditions were optimized as pH 7.0, temperature 40°C, 2% sucrose and 3% of yeast extract as best carbon and nitrogen sources for maximum production of biosurfactant (4.85 g l(-1)). Specifically, the low molecular weight compounds, i.e., C10-C14 were completely degraded, while C15-C19 were degraded up to 97% from the total hydrocarbon pools. Overall crude oil degradation efficiency of the strain A1 was about 87% within a short period of time (7 days). The accumulated biosurfactant from the biodegradation medium was characterized to be lipopeptide in nature. The strain A1 was found to be more robust than other reported biosurfactant producing bacteria in degradation efficiency of crude oil due to their enzyme production capability and therefore can be used to remove the hydrocarbon pollutants from contaminated environment.

  2. 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+).

  3. Biosurfactant and Degradative Enzymes Mediated Crude Oil Degradation by Bacterium Bacillus subtilis A1

    PubMed Central

    Parthipan, Punniyakotti; Preetham, Elumalai; Machuca, Laura L.; Rahman, Pattanathu K. S. M.; Murugan, Kadarkarai; Rajasekar, Aruliah

    2017-01-01

    In this work, the biodegradation of the crude oil by the potential biosurfactant producing Bacillus subtilis A1 was investigated. The isolate had the ability to synthesize degradative enzymes such as alkane hydroxylase and alcohol dehydrogenase at the time of biodegradation of hydrocarbon. The biosurfactant producing conditions were optimized as pH 7.0, temperature 40°C, 2% sucrose and 3% of yeast extract as best carbon and nitrogen sources for maximum production of biosurfactant (4.85 g l-1). Specifically, the low molecular weight compounds, i.e., C10–C14 were completely degraded, while C15–C19 were degraded up to 97% from the total hydrocarbon pools. Overall crude oil degradation efficiency of the strain A1 was about 87% within a short period of time (7 days). The accumulated biosurfactant from the biodegradation medium was characterized to be lipopeptide in nature. The strain A1 was found to be more robust than other reported biosurfactant producing bacteria in degradation efficiency of crude oil due to their enzyme production capability and therefore can be used to remove the hydrocarbon pollutants from contaminated environment. PMID:28232826

  4. Respiratory chain of the alkalophilic bacterium Bacillus firmus RAB and its non-alkalophilic mutant derivative

    SciTech Connect

    Kitada, M.; Lewis, R.J.; Krulwich, T.A.

    1983-04-01

    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 derivate 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. 13 references, 7 figures.

  5. Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach.

    PubMed

    Handtke, Stefan; Volland, Sonja; Methling, Karen; Albrecht, Dirk; Becher, Dörte; Nehls, Jenny; Bongaerts, Johannes; Maurer, Karl-Heinz; Lalk, Michael; Liesegang, Heiko; Voigt, Birgit; Daniel, Rolf; Hecker, Michael

    2014-12-20

    Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.

  6. Purification and characterization of a liquefying α-amylase from alkalophilic thermophilic Bacillus sp. AAH-31.

    PubMed

    Kim, Dae Hoon; Morimoto, Naoki; Saburi, Wataru; Mukai, Atsushi; Imoto, Koji; Takehana, Toshihiko; Koike, Seiji; Mori, Haruhide; Matsui, Hirokazu

    2012-01-01

    α-Amylase (EC 3.2.1.1) hydrolyzes an internal α-1,4-glucosidic linkage of starch and related glucans. Alkalophilic liquefying enzymes from Bacillus species are utilized as additives in dishwashing and laundry detergents. In this study, we found that Bacillus sp. AAH-31, isolated from soil, produced an alkalophilic liquefying α-amylase with high thermostability. Extracellular α-amylase from Bacillus sp. AAH-31 (AmyL) was purified in seven steps. The purified enzyme showed a single band of 91 kDa on SDS-PAGE. Its specific activity of hydrolysis of 0.5% soluble starch was 16.7 U/mg. Its optimum pH and temperature were 8.5 and 70 °C respectively. It was stable in a pH range of 6.4-10.3 and below 60 °C. The calcium ion did not affect its thermostability, unlike typical α-amylases. It showed 84.9% of residual activity after incubation in the presence of 0.1% w/v of EDTA at 60 °C for 1 h. Other chelating reagents (nitrilotriacetic acid and tripolyphosphate) did not affect the activity at all. AmyL was fully stable in 1% w/v of Tween 20, Tween 80, and Triton X-100, and 0.1% w/v of SDS and commercial detergents. It showed higher activity towards amylose than towards amylopectin or glycogen. Its hydrolytic activity towards γ-cyclodextin was as high as towards short-chain amylose. Maltotriose was its minimum substrate, and maltose and maltotriose accumulated in the hydrolysis of maltooligosaccharides longer than maltotriose and soluble starch.

  7. 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

  8. Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

    PubMed

    Lee, Sang-Yeop; Kim, Gun-Hwa; 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.

  9. Polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from Antarctica.

    PubMed

    Irgens, R L; Gosink, J J; Staley, J T

    1996-07-01

    Several strains of a novel heterotrophic gas vacuolate bacterium were isolated from antarctic marine waters. The results of phylogenetic analyses in which 16S ribosomal DAN sequencing was used, coupled with phenotypic tests, indicated that strain 34-P(T) (T = type strain) belongs to a new genus and species of the beta subgroup of the Proteobacteria, for which the name Polaromonas vacuolata is proposed. Although the other four strains studied probably belong to this new species, DNA-DNA hybridization tests were not conducted. The closest phylogenetic relatives of P. vacuolata are the photosynthetic nonsulfur purple bacterium Rhodoferax fermentans and the hydrogen autotroph Variovorax paradoxus.

  10. Bacillus butanolivorans sp. nov., a species with industrial application for the remediation of n-butanol.

    PubMed

    Kuisiene, Nomeda; Raugalas, Juozas; Spröer, Cathrin; Kroppenstedt, Reiner M; Chitavichius, Donaldas

    2008-02-01

    Four bacterial strains, designated K9(T), K105, K1012A and K101, were isolated from soil in Lithuania. All these strains could use n-butanol as a sole carbon source. The strains grew in a medium containing 12-120 mM n-butanol. The strains were strictly aerobic, Gram-positive endospore-formers. The best growth was achieved at 25 degrees C and pH 7.0 in medium containing 1 % (w/v) NaCl. The strains showed identical profiles of 16S-23S rRNA internal transcribed spacer PCR and nearly identical 16S rRNA gene PCR-RFLP electrophoretic patterns and physiological characteristics, demonstrating their relationship at the species level. The cellular fatty acid profile of K9(T) consisted of significant amounts of the C(15) branched-chain fatty acids iso-C(15 : 0) (16.78 %) and anteiso-C(15 : 0) (45.80 %). The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The 16S rRNA gene sequence of K9(T) showed the highest similarity to the sequences of Bacillus simplex DSM 1321(T) and Bacillus muralis LMG 20238(T) (98.3 and 97.7 %, respectively). The DNA G+C content was 37.4 mol%. Studies of DNA-DNA relatedness, morphological, physiological and chemotaxonomic analyses and phylogenetic data based on 16S rRNA gene sequencing allowed strains K9(T), K105, K1012A and K101 to be described as members of a novel species of the genus Bacillus, for which the name Bacillus butanolivorans sp. nov. is proposed. The type strain is K9(T) (=DSM 18926(T) =LMG 23974(T)).

  11. Caloramator australicus sp. nov., a thermophilic, anaerobic bacterium from the Great Artesian Basin of Australia.

    PubMed

    Ogg, Christopher D; Patel, Bharat K C

    2009-01-01

    A strictly anaerobic, thermophilic bacterium, designated strain RC3T, was isolated from microbial mats colonizing thermal waters of a run-off channel formed by free-flowing waters from a bore well (registered no. 17263) of the Great Artesian Basin, Australia. The slightly curved rods (2.5-4.2x0.8-1.0 microm) of strain RC3T stained Gram-positive and grew optimally in tryptone-yeast extract-glucose medium at 60 degrees C (range 45-70 degrees C) and pH 7 (range pH 5-9). Strain RC3T grew poorly on yeast extract (0.2 %) but did not grow on tryptone (0.2 %) as a sole carbon source; yeast extract was required for growth on other energy sources, which included glucose, fructose, galactose, xylose, maltose, sucrose, raffinose, mannose, cellobiose, cellulose, starch, amylopectin, xylan, peptone, amyl media (Research Achievement), threonine and pyruvate but did not include arabinose, ribose, lactose, CM-cellulose, myo-inositol, mannitol, chitin, casein, formate, acetate, succinate, propionate, lactate, benzoate, glycerol, ethanol, Casamino acids, arginine, alanine, serine, glycine, glutamine, leucine, isoleucine, methionine or aspartate. The end products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but not sulfate, sulfite, thiosulfate, nitrate or nitrite. Iron(III) was also reduced in the presence of peptone, tryptone, amyl media, threonine and glycerol but not chitin, xylan, pectin, starch, pyruvate, acetate, benzoate, lactate, propionate, succinate, inositol, ethanol, mannitol, arginine, glutamine or serine. Strain RC3T was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). In the presence of iron(III) and glycerol, increased concentrations of Fe(II) corresponded to increased cell numbers, demonstrating that strain RC3(T) was able to conserve energy to support growth from the reduction of Fe(III) to Fe

  12. 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

  13. 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

    2016-07-21

    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.

  14. 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

  15. Effect of feeding Bacillus sp. as probiotic bacteria on growth of giant freshwater prawn (Macrobrachium rosenbergii de Man).

    PubMed

    Deeseenthum, Sirirat; Leelavatcharamas, Vichai; Brookes, John D

    2007-05-01

    The effects of feeding two Bacillus spp. isolated from the intestine of the giant freshwater prawn on the growth of Giant Freshwater Prawns (Macrobrachium rosenbergii de Man) was examined. The isolated Bacillus KKU02 and Bacillus KKU03 (approximately 10(7) CFU mL(-1)) were mixed into commercial prawn feed (200 mL kg(-1)). After rearing shrimp with the bacteria in four feed treatments, (Bacillus KKU03, Bacillus KKU02, mixed culture and control groups) for 120 days, body length and weight of the prawns in mixed culture tanks were significantly higher (p = 0.05) than in the control tanks (7.48 cm and 3.32 g, vs 6.6 cm and 2.1 g, respectively). Both isolates were found to produce amylase and protease. The stabilities of the single Bacillus sp., mixed culture and commercial probiotic in the feeds were examined during storage at 4 degrees C and room temperature. The percentage viability of Bacillus KKU02, Bacillus KKU03 and mixed culture stored at room temperature declined dramatically to 2.54, 21.88 and 10.92% within 2 weeks, respectively. At 4 degrees C however, the percentage viability of the tested probiotics reduced slowly. The survival of the commercial probiotics was the same at both temperatures about 50% after 70 days' storage.

  16. 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.

  17. 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.

  18. Spectral characterization of a pteridine derivative from cyanide-utilizing bacterium Bacillus subtilis - JN989651.

    PubMed

    Durairaju Nisshanthini, S; Teresa Infanta S, Antony K; Raja, Duraisamy Senthil; Natarajan, Karuppannan; Palaniswamy, M; Angayarkanni, Jayaraman

    2015-04-01

    Soil and water samples were collected from various regions of SIPCOT and nearby Vanappadi Lake, Ranipet, Tamilnadu, India. Based on their colony morphology and their stability during subculturing, 72 bacteria were isolated, of which 14 isolates were actinomycetes. Preliminary selection was carried out to exploit the ability of the microorganisms to utilize sodium cyanate as nitrogen source. Those organisms that were able to utilize cyanate were subjected to secondary screening viz., utilization of sodium cyanide as the nitrogen source. The oxygenolytic cleavage of cyanide is dependent on cyanide monooxygenase which obligately requires pterin cofactor for its activity. Based on this, the organisms capable of utilizing sodium cyanide were tested for the presence of pterin. Thin layer chromatography (TLC) of the cell extracts using n-butanol: 5 N glacial acetic acid (4:1) revealed that 10 out of 12 organisms that were able to utilize cyanide had the pterin-related blue fluorescent compound in the cell extract. The cell extracts of these 10 organisms were subjected to high performance thin layer chromatography (HPTLC) for further confirmation using a pterin standard. Based on the incubation period, cell biomass yield, peak height and area, strain VPW3 was selected and was identified as Bacillus subtilis. The Rf value of the cell extract was 0.73 which was consistent with the 0.74 Rf value of the pterin standard when scanned at 254 nm. The compound was extracted and purified by preparative High Performance Liquid Chromatography (HPLC). Characterization of the compound was performed by ultraviolet spectrum, fluorescence spectrum, Electrospray Ionization-Mass Spectrometry (ESI-MS), and Nuclear Magnetic Resonance spectroscopy (NMR). The compound is proposed to be 6-propionyl pterin (2-amino-6-propionyl-3H-pteridin-4-one).

  19. Cloning, expression, and isolation of the mannitol transport protein from the thermophilic bacterium Bacillus stearothermophilus.

    PubMed Central

    Henstra, S A; Tolner, B; ten Hoeve Duurkens, R H; Konings, W N; Robillard, G T

    1996-01-01

    A mannitol phosphotransferase system (PTS) was identified in Bacillus stearothermophilus by in vitro complementation with Escherichia coli EI, HPr, and IIA(Mtl). Degenerate primers based on regions of high amino acid similarity in the E. coli and Staphylococcus carnosus EII(Mt1) were used to develop a digoxigenin-labeled probe by PCR. Using this probe, we isolated three overlapping DNA fragments totaling 7.2 kb which contain the genes mtlA, mtlR, mtlF, and mtlD, encoding the mannitol IICB,a regulator, IIA, and a mannitol-1-phosphate dehydrogenase, respectively. The mtl4 gene consists of 1,413 bp coding for a 471-amino-acid protein with a calculated mass of 50.1 kDa. The amino acid sequence shows high similarity with the sequence of IICB(Mtl) of S. carnosus and the IICB part of the IICBA(Mtl)s of E. coli and B. subtilis. The enzyme could be functionally expressed in E. coli by placing it behind the strong tac promoter. The rate of thermal inactivation at 60 degrees C of B. stearothermophilus HCB(Mt1) expressed in E. coli was two times lower than that of E. coli IICB(Mtl). IICB(Mtl) in B. stearothermophilus is maximally active at 85 degrees C and thus very thermostable. The enzyme was purified on Ni-nitrilotriacetic acid resin to greater than 95% purity after six histidines were fused to the C-terminal part of the transporter. PMID:8824601

  20. O-heterocyclic derivatives with antibacterial properties from marine bacterium Bacillus subtilis associated with seaweed, Sargassum myriocystum.

    PubMed

    Chakraborty, Kajal; Thilakan, Bini; Chakraborty, Rekha Devi; Raola, Vamshi Krishna; Joy, Minju

    2017-01-01

    The brown seaweed, Sargassum myriocystum associated with heterotrophic bacterium, Bacillus subtilis MTCC 10407 (JF834075) exhibited broad-spectra of potent antibacterial activities against pathogenic bacteria Aeromonas hydrophila, Vibrio vulnificus, and Vibrio parahaemolyticus. B. subtilis MTCC 10407 was found to be positive for polyketide synthetase (pks) gene, and therefore, was considered to characterize secondary metabolites bearing polyketide backbone. Using bioassay-guided fractionation, two new antibacterial O-heterocyclic compounds belonging to pyranyl benzoate analogs of polyketide origin, with activity against pathogenic bacteria, have been isolated from the ethyl acetate extract of B. subtilis MTCC 10407. In the present study, the secondary metabolites of B. subtilis MTCC 10407 with potent antibacterial action against bacterial pathogens was recognized to represent the platform of pks-1 gene-encoded products. Two homologous compounds 3 (3-(methoxycarbonyl)-4-(5-(2-ethylbutyl)-5,6-dihydro-3-methyl-2H-pyran-2-yl)-butyl benzoate) and 4 [2-(8-butyl-3-ethyl-3,4,4a,5,6,8a-hexahydro-2H-chromen-6-yl)-ethyl benzoate] also have been isolated from the ethyl acetate extract of host seaweed S. myriocystum. The two compounds isolated from ethyl acetate extract of S. myriocystum with lesser antibacterial properties shared similar structures with the compounds purified from B. subtilis that suggested the ecological and metabolic relationship between these compounds in seaweed-bacterial relationship. Tetrahydropyran-2-one moiety of the tetrahydropyrano-[3,2b]-pyran-2(3H)-one system of 1 might be cleaved by the metabolic pool of seaweeds to afford methyl 3-(dihydro-3-methyl-2H-pyranyl)-propanoate moiety of 3, which was found to have no significant antibacterial activity. It is therefore imperative that the presence of dihydro-methyl-2H-pyran-2-yl propanoate system is essentially required to impart the greater activity. The direct involvement of polarisability (Pl) with

  1. Complete genome sequence of Oceanimonas sp. GK1, a halotolerant bacterium from Gavkhouni Wetland in Iran.

    PubMed

    Yeganeh, Laleh Parsa; Azarbaijani, Reza; Sarikhan, Sajjad; Mousavi, Hossein; Ramezani, Mohadeseh; Amoozegar, Mohammad Ali; Fazeli, Abolhassan Shahzadeh; Salekdeh, Ghasem Hosseini

    2012-04-01

    Oceanimonas sp. GK1 (IBRC-M 10197) is a marine halotolerant gammaproteobacterium which was characterized as producing large amounts of poly-β-hydroxybutyrate. Here we present the whole-genome sequence of Oceanimonas sp. GK1, which consists of a single circular chromosome of 3,514,537 bp and two plasmids 8,462 and 4,245 bp in length.

  2. 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.

  3. 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).

  4. Genome Sequence of Bacillus sp. Strain UMTAT18 Isolated from the Dinoflagellate Alexandrium tamiyavanichii Found in the Straits of Malacca

    PubMed Central

    Ming, Gan Han; Mohd Noor, Mohd Ezhar; Sung, Yeong Yik; Usup, Gires

    2016-01-01

    Bacillus sp. strain UMTAT18 was isolated from the harmful dinoflagellate Alexandrium tamiyavanichii. Its genome consists of 5,479,367 bp with 5,546 open reading frames, 102 tRNAs, and 29 rRNAs. Gene clusters for biosynthesis of nonribosomal peptides, bacteriocin, and lantipeptide were identified. It also contains siderophore and genes related to stress tolerance. PMID:27795265

  5. 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.

  6. Cloning and characterization of a novel oligoalginate lyase from a newly isolated bacterium Sphingomonas sp. MJ-3.

    PubMed

    Park, Hwan Hee; Kam, Natania; Lee, Eun Yeol; Kim, Hee Sook

    2012-04-01

    A bacterium possessing alginate-degrading activity was isolated from marine brown seaweed soup liquefied by salted and fermented anchovy. The isolated strain was designated as Sphingomonas sp. MJ-3 based on the analyses of 16S ribosomal DNA sequences, 16S-23S internal transcribed spacer region sequences, biochemical characteristics, and cellular fatty acid composition. A novel alginate lyase gene was cloned from genomic DNA library and then expressed in Escherichia coli. When the deduced amino acid sequence was compared with the sequences on the databases, interestingly, the cloned gene product was predicted to consist of AlgL (alginate lyase L)-like and heparinase-like protein domain. The MJ-3 alginate lyase gene shared below 27.0% sequence identity with exolytic alginate lyase of Sphingomonas sp. A1. The optimal pH and temperature for the recombinant MJ-3 alginate lyase were 6.5 and 50°C, respectively. The final degradation products of alginate oligosaccharides were analyzed by electrospray ionization mass spectrometry and proved to be alginate monosaccharides. Based on the results, the recombinant alginate lyase from Sphingomonas sp. MJ-3 is regarded as an oligoalginate lyase that can degrade oligoalginate and alginate into alginate monosaccharides.

  7. An extremely thermophilic anaerobic bacterium Caldicellulosiruptor sp. F32 exhibits distinctive properties in growth and xylanases during xylan hydrolysis.

    PubMed

    Ying, Yu; Meng, Dongdong; Chen, Xiaohua; Li, Fuli

    2013-08-15

    An anaerobic, extremely thermophilic, and cellulose- and xylan-degrading bacterium F32 was isolated from biocompost. Sequence analysis of the 16S rRNA gene of this strain showed that it was closely related to Caldicellulosiruptor saccharolyticus DSM 8903 (99.0% identity). Physiological and biochemical data also supported that identification of strain F32 as a Caldicellulosiruptor species. The proteins secreted by Caldicellulosiruptor sp. F32 grown on xylan showed a xylanase activity of 7.74U/mg, which was 2.5 times higher than that of C. saccharolyticus DSM 8903. Based on the genomic sequencing data, 2 xylanase genes, JX030400 and JX030401, were identified in Caldicellulosiruptor sp. F32. The xylanase encoded by JX030401 shared 97% identity with Csac_0696 of C. saccharolyticus DSM 8903, while that encoded by JX030400 shared 94% identity with Athe_0089 of C. bescii DSM 6725, which was not found in the genome of strain DSM 8903. Xylanse encoded by JX030400 had 9-fold higher specific activity than JX030401. Our results indicated that although the 2 strains shared high identity, the xylanase system in Caldicellulosiruptor sp. F32 was more efficient than that in C. saccharolyticus DSM 8903.

  8. Nitrate removal efficiency of bacterial consortium (Pseudomonas sp. KW1 and Bacillus sp. YW4) in synthetic nitrate-rich water.

    PubMed

    Rajakumar, Sundaram; Ayyasamy, Pudukadu Munusamy; Shanthi, Kuppusamy; Thavamani, Palanisami; Velmurugan, Palanivel; Song, Young Chae; Lakshmanaperumalsamy, Perumalsamy

    2008-09-15

    The efficiency of bacterial isolates to reduce nitrate from synthetic nitrate-rich water was tested using a batch scale process. Two efficient nitrate reducing bacterial species were isolated from water samples collected from Kodaikanal and Yercaud lakes. Bacterial analysis of the samples revealed the presence of nitrate reducing bacteria belonging to the genera Pseudomonas, Bacillus, Micrococcus and Alcaligenes. Among the isolates, the consortium of Pseudomonas sp. KW1 and Bacillus sp. YW4 was found to be efficient in nitrate reduction. Influences of various carbon sources, incubation temperature and pH on nitrate reduction from synthetic wastewater were also studied. The results showed a rapid and efficient process of nitrate removal (99.4%) from synthetic wastewater supplemented with starch (1%), inoculated by bacterial consortium (Pseudomonas sp. KW1 and Bacillus sp. YW4) at incubation temperature of 30 degrees C at pH 7. This observation has led to the conclusion that the bacterial consortium was responsible for nitrate removal from synthetic nitrate-rich wastewater.

  9. Cloning of the maltose phosphorylase gene from Bacillus sp. strain RK-1 and efficient production of the cloned gene and the trehalose phosphorylase gene from Bacillus stearothermophilus SK-1 in Bacillus subtilis.

    PubMed

    Inoue, Yasushi; Yasutake, Nozomu; Oshima, Yoshie; Yamamoto, Yoshie; Tomita, Tetsuji; Miyoshi, Shinsuke; Yatake, Tsuneya

    2002-12-01

    The maltose phosphorylase (MPase) gene of Bacillus sp. strain RK-1 was cloned by PCR with oligonucleotide primers designed on the basis of a partial N-terminal amino acid sequence of the purified enzyme. The MPase gene consisted of 2,655 bp encoding a theoretical protein with a Mr of 88,460, and had no secretion signal sequence, although most of the MPase activity was detected in the culture supernatant of RK-1. This cloned MPase gene and the trehalose phosphorylase (TPase) gene from Bacillus stearothermophilus SK-1 were efficiently expressed intracellularly under the control of the Bacillus amyloliquefaciens alpha-amylase promoter in Bacillus subtilis. The production yields were estimated to be more than 2 g of enzyme per liter of medium, about 250 times the production of the original strains, in a simple shake flask. About 60% of maltose was converted into trehalose by the simultaneous action of both enzymes produced in B. subtilis.

  10. Biological denitration of propylene glycol dinitrate by Bacillus sp. ATCC 51912.

    PubMed

    Sun, W Q; Meng, M; Kumar, G; Geelhaar, L A; Payne, G F; Speedie, M K; Stacy, J R

    1996-05-01

    In previous studies, bacterial cultures were isolated that had the ability to degrade the nitrate ester glyceryl trinitrate (i.e., nitroglycerin). The goal of the present study was to examine the ability of resting cells and cell-free extracts of the isolate Bacillus sp. ATCC 51912 to degrade the more recalcitrant nitrate ester propylene glycol dinitrate (PGDN). It was observed that the PGDN-denitrating activity was expressed during growth even when cells were cultured in the absence of nitrate esters. This indicates that nitrate esters are not required for expression of denitration activity. Using cell-free extracts, PGDN was observed to be sequentially denitrated to propylene glycol mononitrate (PGMN) and propylene glycol with the second denitration step proceeding more slowly than the first. Also it was observed that dialysis of the cell-free extracts did not affect denitration activity indicating that regenerable cofactors [e.g., NAD(P)H or ATP] are not required for denitration.

  11. Efficient proteolysis and application of an alkaline protease from halophilic Bacillus sp. EMB9.

    PubMed

    Sinha, Rajeshwari; Srivastava, A K; Khare, S K

    2014-10-03

    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.

  12. Identification and characterization of a library of surfactins and fengycins from a marine endophytic Bacillus sp.

    PubMed

    Nair, Divya; Vanuopadath, Muralidharan; Nair, Bipin G; Pai, Jayashree Gopalakrishna; Nair, Sudarslal Sadasivan

    2016-11-01

    An endophytic bacterial strain from a marine green alga, Ulva lactuca, was isolated and identified by 16S rRNA gene sequencing method. The bacterial isolate was found to secrete two major families of cyclic depsilipopeptides, surfactins, and fengycins. Sequencing of the isolated lipopeptides was carried out using the MS(n) data obtained from an electrospray ionization (ESI) ion trap mass spectrometer coupled to an HPLC system. The assigned sequences were confirmed by a chemical derivatization approach involving esterification followed by mass spectrometric analysis. Distinction of leucine residues from isoleucine was established through a combined electron transfer dissociation-collision-induced dissociation (ETD-CID) method. The fengycins described in this study were found to cause significant delay of growth of two plants, Vigna radiata (mung bean) and Oryza sativa (rice). To the best of our knowledge, this is the first study describing identification and characterization of cyclic peptides from an endophytic Bacillus sp. isolated from marine algae.

  13. Early Extracellular Events in Infection of Competent Bacillus subtilis by DNA of Bacteriophage SP82G

    PubMed Central

    Williams, Gordon L.; Green, D. Macdonald

    1972-01-01

    Analysis, by the recovery of specific genetic “markers,” of the effects of DNase I, physical shear, and temperature shock on DNA-cell complexes demonstrates that sequential attachment of both ends of bacteriophage SP82G DNA to Bacillus subtilis precedes entry of the DNA molecule into the cell, and that each attachment is end-and time-specific. The first attachment involves an initial reversible phase, followed by irreversible binding. After a latent period, the second end then attaches to the cell. Entry of the molecule begins immediately after binding of the second end has occurred, and entry is complete within 3 min. The polarity of entry, as judged by attainment of resistance to DNase I, is the reverse of that observed in normal phage injection. PMID:4624760

  14. 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

  15. Characterization of a Bioflocculant (MBF-UFH) Produced by Bacillus sp. AEMREG7.

    PubMed

    Okaiyeto, Kunle; Nwodo, Uchechukwu U; Mabinya, Leonard V; Okoli, Arinze S; Okoh, Anthony I

    2015-06-08

    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.

  16. 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.

  17. Directed evolution of a maltogenic alpha-amylase from Bacillus sp. TS-25.

    PubMed

    Jones, Aubrey; Lamsa, Michael; Frandsen, Torben P; Spendler, Tina; Harris, Paul; Sloma, Alan; Xu, Feng; Nielsen, Jack Bech; Cherry, Joel R

    2008-04-30

    Directed evolution coupled with a high-throughput robotic screen was employed to broaden the industrial use of the maltogenic alpha-amylase Novamyl from Bacillus sp. TS-25. Wild-type Novamyl is currently used in the baking industry as an anti-staling agent in breads baked at neutral or near neutral pH. However, the enzyme is rapidly inactivated during the baking process of bread made with low pH recipes and Novamyl thus has very limited beneficial effect for this particular application. In an effort to improve the performance of Novamyl for low pH bread applications such as sourdough and rye, two error-prone PCR libraries were generated, expressed in Bacillus subtilis and screened for variants with improved thermal stability and activity under low pH conditions. Variants exhibiting improved performance were iteratively recombined using DNA shuffling to create two generations of libraries. Relative to wild-type Novamyl, a number of the resulting variants exhibited more than 10 degrees C increase in thermal stability at pH 4.5, one of which demonstrated substantial anti-staling properties in low pH breads.

  18. 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

  19. 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

  20. Bacillus amyloliquefaciens Q-426 as a potential biocontrol agent against Fusarium oxysporum f. sp. spinaciae.

    PubMed

    Zhao, Pengchao; Quan, Chunshan; Wang, Yingguo; Wang, Jianhua; Fan, Shengdi

    2014-05-01

    In recent years, Bacillus species have received considerable attention for the biological control of many fungal diseases. In this study, Bacillus amyloliquefaciens Q-426 was tested for its potential use against a variety of plant pathogens. Our screen for genes involved in the biosynthesis of antifungal agents revealed that the fen and bmy gene clusters are present in the Q-426 genome. Lipopeptides such as bacillomycin D, fengycin A, and fengycin B were purified from the bacterial culture broth and subsequently identified by ESI-mass spectrometry. The minimal inhibitory concentration of fengycin A against Fusarium oxysporum f. sp. spinaciae W.C. Snyder & H.N. Hansen O-27 was determined to be 31.25 μg ml(-1) . However, exposure of fungal cells to 50 μg ml(-1) of fengycin A did not allow permeation of fluorescein diacetate into the cytoplasm through the cell membrane. Moreover, leakage of intracellular inorganic cations, nucleic acid and protein were also not detected, indicating that the fungal cell membrane is not the primary target of action for fengycin A. Profound morphological changes were observed in the F. oxysporum strain and spore germination was completely inhibited, suggesting that 50 μg ml(-1) of fengycin A acts, at least, as a fungistatic agent.

  1. TEMPERATURE-SENSITIVE MUTANTS OF BACILLUS SUBTILIS BACTERIOPHAGE SP3 II.

    PubMed Central

    Nishihara, Mutsuko; Romig, W. R.

    1964-01-01

    Nishihara, Mutsuko (University of California, Los Angeles), and W. R. Romig. Temperature-sensitive mutants of Bacillus subtilis bacteriophage SP3. II. In vivo complementation studies. J. Bacteriol. 88:1230–1239. 1964.—A plate-spotting procedure was used in initial attempts to group the temperature-sensitive Bacillus subtilis phage SP3 mutants by complementation. The results obtained did not show any clear patterns of reactions among the mutants. Crosses were, therefore, repeated in broth at a temperature of 49 C, which greatly reduced the extent of replication of each mutant type alone. The data on mixed infections indicated that there was a minimum of six complementation groups. Of the 12 isolates, 7 did not seem to complement with each other; the rest complemented with each other and with the seven noncomplementing mutants. There was a positive correlation between the complementation reaction of a pair and the recovery of wild-phenotype phages from a 49 C broth lysate. The relative proportion of phages capable of forming wild-phenotype plaques on plates incubated at 46 C to the total number of plaque-forming units was higher in a lysate of a mixed infection with two mutants than in lysates of each mutant alone. Moreover, this frequency was higher for a mixed lysate made at 49 C than for a lysate of the same two mutants made at 37 C. These observations suggested that genetic recombination might occur at 49 C, and that the increased recovery of wild-phenotype phages in lysates made at this temperature might be due to a selective advantage for these phages. Recombination experiments at 37 C with some complementing pairs gave frequencies of 2.0 to 4.8%. The ratio of wild-phenotype revertants to total phages in the stock lysates used for these crosses at 37 C was less than 10−6. The noncomplementing mutants were not conclusively shown to be nonidentical. PMID:14234775

  2. Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway.

    PubMed

    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.

  3. Klebsiella sp. FIRD 2, a TBT-resistant bacterium isolated from contaminated surface sediment along Strait of Johor Malaysia.

    PubMed

    Abubakar, Abdussamad; Mustafa, Muskhazli B; Johari, Wan Lutfi Wan; Zulkifli, Syaizwan Zahmir; Ismail, Ahmad; Mohamat-Yusuff, Ferdaus Binti

    2015-12-15

    A possible tributyltin (TBT)-degrading bacterium isolated from contaminated surface sediment was successfully identified as Klebsiella sp. FIRD 2. It was found to be the best isolate capable of resisting TBT at a concentration of 1000 μg L(-1). This was a concentration above the reported contaminated level at the sampling station, 790 μg L(-1). Further studies revealed that the isolate was Gram negative and resisted TBT concentrations of up to 1500 μg L(-1) in a Minimal Salt Broth without the addition of any carbon source within the first 48 h of incubation. It is expected that additional work could be conducted to check the degradation activity of this new isolate and possibly improve the degradation capacity in order to contribute to finding a safe and sustainable remediation solution of TBT contamination.

  4. 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

  5. The effects of K+ growth conditions on the accumulation of cesium by the bacterium Thermus sp. TibetanG6.

    PubMed

    Wang, Hailei; Kong, Fanjing; Zheng, Mianping

    2006-04-01

    The accumulation of cesium by the bacterium Thermus sp. TibetanG6 was examined under different K+ growth conditions. The effects of external pH and Na+ on the accumulation of cesium were also studied, and the mechanism involved was discussed. K+ regimes played an important role in the accumulation of cesium by the strain TibetanG6. The quantity of cesium accumulated (24 h) was much higher in K+-deficient regime than that in K+-sufficient regime. The pH and Na+ had different effects on the accumulation of cesium in the two K+ regimes. IR spectra analyses indicated that the biosorption is a process of homeostasis with cesium initially accumulated on the cell wall.

  6. 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.

  7. 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

  8. Isolation and characterization of a thermotolerant ammonia-oxidizing bacterium Nitrosomonas sp. JPCCT2 from a thermal power station.

    PubMed

    Itoh, Yoshikane; Sakagami, Keiko; Uchino, Yoshihito; Boonmak, Chanita; Oriyama, Tetsuro; Tojo, Fuyumi; Matsumoto, Mitsufumi; Morikawa, Masaaki

    2013-01-01

    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48 °C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL(-1). This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C.

  9. Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake.

    PubMed

    Gorlenko, Vladimir; Tsapin, Alexandre; Namsaraev, Zorigto; Teal, Tracy; Tourova, Tatyana; Engler, Diane; Mielke, Randy; Nealson, Kenneth

    2004-05-01

    A novel, obligately anaerobic, alkalithermophilic, chemo-organotrophic bacterium was isolated from the sediment of an alkaline hot spring located on Paoha Island in Mono Lake, California, USA. This rod-shaped bacterium was motile via peritrichous flagella. Isolated strains grew optimally in 5-25 g NaCl l(-1), at pH 9.0-9.5 and at a temperature of 58 degrees C and were fermentative and mainly proteolytic, utilizing peptone, Casamino acids and yeast extract. Optimal growth was seen in the presence of elemental sulfur, polysulfide or thiosulfate with concomitant reduction to hydrogen sulfide. Sulfite was also formed in an equal ratio to sulfide during reduction of thiosulfate. The novel isolate could also reduce Fe(III) and Se(IV) in the presence of organic matter. On the basis of physiological properties, 16S rRNA gene sequence and DNA-DNA hybridization data, strain PAOHA-1(T) (=DSM 14826(T)=UNIQEM 227(T)) belongs to the genus Anaerobranca and represents a novel species, Anaerobranca californiensis sp. nov.

  10. Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an offshore oil well in Congo.

    PubMed

    Miranda-Tello, Elizabeth; Fardeau, Marie-Laure; Joulian, Catherine; Magot, Michel; Thomas, Pierre; Tholozan, Jean-Luc; Ollivier, Bernard

    2007-01-01

    A novel thermophilic, moderately halophilic, rod-shaped bacterium, strain MET-B(T), with a sheath-like outer structure (toga) was isolated from an offshore oil-producing well in Congo, West Africa. Strain MET-B(T) was a Gram-negative bacterium with the ability to reduce elemental sulfur, but not sulfate, thiosulfate or sulfite into sulfide. The optimum growth conditions were 60 degrees C, pH 6.7-7.2 and 4-6 % NaCl. The DNA G+C content was 34.6 mol%. Strain MET-B(T) was phylogenetically related to members of the genus Petrotoga; Petrotoga miotherma, Petrotoga olearia and Petrotoga mexicana were the closest relatives, with type strains exhibiting more than 99 % identity in an analysis of small-subunit rRNA gene sequences. The values for DNA-DNA relatedness between the type strains of these three species and strain MET-B(T) were less than 42 %. As MET-B(T) was found to be genetically and physiologically different from other species of the genus Petrotoga, this strain is proposed as representing a novel species, for which the name Petrotoga halophila sp. nov. is proposed. The type strain is MET-B(T) (=DSM 16923(T)=CCUG 50214(T)).

  11. The death mechanism of the harmful algal bloom species Alexandrium tamarense induced by algicidal bacterium Deinococcus sp. Y35.

    PubMed

    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.

  12. 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.

  13. Clostridium tunisiense sp. nov., a new proteolytic, sulfur-reducing bacterium isolated from an olive mill wastewater contaminated by phosphogypse.

    PubMed

    Thabet, Olfa Ben Dhia; Fardeau, Marie-Laure; Joulian, Catherine; Thomas, Pierre; Hamdi, Moktar; Garcia, Jean-Louis; Ollivier, Bernard

    2004-06-01

    A new sporulated fermentative bacterium designated strain E1(T) (T=type strain), was isolated from an anaerobic mud of an olive mill wastewater basin contaminated by phosphogypse produced by a Tunisian factory. Strain E1(T) was a motile Gram-positive slightly curved rod with spherical terminal spore swelling the cell. It grew between 18 degrees C and 43 degrees C with an optimum at 37 degrees C and pH 7.8 (range 5.5-8.7), without NaCl (range 0-3%). Strain E1(T) was a chemoorganotrophic anaerobic bacterium fermenting only proteins and amino acids. Yeast extract was required for growth. Elemental sulfur was used as terminal electron acceptor. The G+C content of the DNA was 32.6 mol%. The closest phylogenetical relatives of strain E1(T) were Clostridium thiosulfatireducens and C. subterminale (97.3% similarity for partial rRNA gene sequences). DNA-DNA hybridization values between strain E1(T) and both species were 17% and 20.8%, respectively. On the basis of differences in genotypic and phenotypic characteristics, strain E1(T) (DSM 15206(T), CIP 107666(T)) is proposed as the type strain of a new species, C. tunisiense sp. nov. GenBank accession number for the 16S rRNA gene sequence of strain E1(T) is AY187622.

  14. Isolation and Characterization of a Thermotolerant Ammonia-Oxidizing Bacterium Nitrosomonas sp. JPCCT2 from a Thermal Power Station

    PubMed Central

    Itoh, Yoshikane; Sakagami, Keiko; Uchino, Yoshihito; Boonmak, Chanita; Oriyama, Tetsuro; Tojo, Fuyumi; Matsumoto, Mitsufumi; Morikawa, Masaaki

    2013-01-01

    A thermotolerant ammonia-oxidizing bacterium strain JPCCT2 was isolated from activated sludge in a thermal power station. Cells of JPCCT2 are short non-motile rods or ellipsoidal. Molecular phylogenetic analysis of 16S rRNA gene sequences demonstrated that JPCCT2 belongs to the genus Nitrosomonas with the highest similarity to Nitrosomonas nitrosa Nm90 (100%), Nitrosomonas sp. Nm148 (99.7%), and Nitrosomonas communis Nm2 (97.7%). However, G+C content of JPCCT2 DNA was 49.1 mol% and clearly different from N. nitrosa Nm90, 47.9%. JPCCT2 was capable of growing at temperatures up to 48°C, while N. nitrosa Nm90 and N. communis Nm2 could not grow at 42°C. Moreover, JPCCT2 grew similarly at concentrations of carbonate 0 and 5 gL−1. This is the first report that Nitrosomonas bacterium is capable of growing at temperatures higher than 37°C. PMID:24256971

  15. Endophytic colonization of Vitis vinifera L. by plant growth-promoting bacterium Burkholderia sp. strain PsJN.

    PubMed

    Compant, Stéphane; Reiter, Birgit; Sessitsch, Angela; Nowak, Jerzy; Clément, Christophe; Ait Barka, Essaïd

    2005-04-01

    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.

  16. Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent.

    PubMed

    Slobodkina, G B; Kolganova, T V; Chernyh, N A; Querellou, J; Bonch-Osmolovskaya, E A; Slobodkin, A I

    2009-06-01

    A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50(T)) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) at a depth of 4100 m. Cells of strain SL50(T) were motile, straight to bent rods with one polar flagellum, 0.5-0.6 mum in width and 3.0-3.5 mum in length. The temperature range for growth was 25-75 degrees C, with an optimum at 60 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.5. Growth of strain SL50(T) was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50(T) was 60 min. Strain SL50(T) used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50(T) was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50(T) was Deferribacter abyssi JR(T) (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50(T) (=DSM 21529(T)=VKPM B-10097(T)). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO(2) as the carbon source.

  17. 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.

  18. Newly isolated bacterial strains belonging to Bacillaceae (Bacillus sp.) and Micrococcaceae accelerate death of the honey bee mite, Varroa destructor (V. jacobsoni), in laboratory assays.

    PubMed

    Tsagou, Vasiliki; Lianou, Alexandra; Lazarakis, Dimitrios; Emmanouel, Nikolaos; Aggelis, George

    2004-03-01

    Newly isolated bacterial strains belonging to Bacillaceae (Bacillus sp.), Micrococcaceae and three unidentified strains were tested for their pathogenicity against the mite, Varroa destructor. The Bacillus sp. strain and two of the strains belonging to the Micrococcaceae family significantly decreased the time for 50% mortality of the mite population (up to 57%) and hence may be potential control agents. In in vitro bioassay whole cells, extracellular broth and cellular extract of the Bacillus sp. strain effectively killed the mites, suggesting that both endotoxins and exotoxins contributed to the killing.

  19. Bacillus stamsii sp. nov., a facultatively anaerobic sugar degrader that is numerically dominant in freshwater lake sediment.

    PubMed

    Müller, Nicolai; Scherag, Frank D; Pester, Michael; Schink, Bernhard

    2015-09-01

    A novel type of anaerobic bacteria was previously isolated from profundal lake sediment by direct dilution of the sediment in mineral agar medium containing glucose and a background lawn of Methanospirillum hungatei as a syntrophic partner. The isolated bacteria grouped with aerobic Bacillus spp. according to their 16S rRNA gene sequence, and the most closely related species is Bacillus thioparans. Fermentative growth of the novel strain with glucose was possible only in the presence of syntrophic partners, and cocultures produced acetate and methane, in some cases also lactate and traces of succinate as fermentation products. In contrast, the closely related strains Bacillus jeotgali and Bacillus sp. strain PeC11 are able to grow with glucose axenically by mixed acid fermentation yielding lactate, acetate, formate, succinate, and ethanol as fermentation products. Alternatively, the isolated strain grew anaerobically in pure culture if pyruvate was added to glucose-containing media, and lactate, acetate and formate were the major fermentation products, but the strain never produced ethanol. Aerobic growth was found with a variety of organic substrates in the presence of partly reduced sulfur compounds. In the absence of sulfide and oxygen, nitrate served as an electron acceptor. Strain BoGlc83 was characterized as the type strain of a new species for which the name Bacillus stamsii sp. nov. (DSM 19598=JCM 30025) is proposed.

  20. Orally administered thermostable N-acyl homoserine lactonase from Bacillus sp. strain AI96 attenuates Aeromonas hydrophila infection in zebrafish.

    PubMed

    Cao, Yanan; He, Suxu; Zhou, Zhigang; Zhang, Meichao; Mao, Wei; Zhang, Huitu; Yao, Bin

    2012-03-01

    N-Acylated homoserine lactone (AHL) lactonases are capable of degrading signal molecules involved in bacterial quorum sensing and therefore represent a new approach to control bacterial infection. Here a gene responsible for the AHL lactonase activity of Bacillus sp. strain AI96, 753 bp in length, was cloned and then expressed in Escherichia coli. The deduced amino acid sequence of Bacillus sp. AI96 AiiA (AiiA(AI96)) is most similar to those of other Bacillus sp. AHL lactonases (~80% sequence identity) and was consequently categorized as a member of the metallo-β-lactamase superfamily. AiiA(AI96) maintains ~100% of its activity at 10°C to 40°C at pH 8.0, and it is very stable at 70°C at pH 8.0 for at least 1 h; no other Bacillus AHL lactonase has been found to be stable under these conditions. AiiA(AI96) resists digestion by proteases and carp intestinal juice, and it has broad-spectrum substrate specificity. The supplementation of AiiA(AI96) into fish feed by oral administration significantly attenuated Aeromonas hydrophila infection in zebrafish. This is the first report of the oral administration of an AHL lactonase for the efficient control of A. hydrophila.

  1. 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

  2. Acinetobacter sp. strain Ths, a novel psychrotolerant and alkalitolerant bacterium that utilizes hydrocarbon.

    PubMed

    Yamahira, Keiko; Hirota, Kikue; Nakajima, Kenji; Morita, Naoki; Nodasaka, Yoshinobu; Yumoto, Isao

    2008-09-01

    A novel psychrotolerant, alkalitolerant bacterium, strain Ths, was isolated from a soil sample immersed in hot spring water containing hydrocarbons and grown on a chemically defined medium containing n-tetradecane as the sole carbon source. The isolate grew at 0 degrees C but not at temperatures higher than 45 degrees C; its optimum growth temperature was 27 degrees C. It grew in the pH range of 7-9. The strain utilized C(13)-C(30) n-alkane and fluorene at pH 9 and 4 degrees C. To our knowledge, this is the first report on the bacterium that utilizes a wide range of hydrocarbons at a high pH and a low temperature. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ths is closely related to genomic species 6 ATCC 17979 (99.1% similarity), genomic species BJ13/TU14 ATCC 17905 (97.8% similarity), genomic species 9 ATCC 9957 (97.6% similarity) belonging to the genus Acinetobacter and to Acinetobacter calcoaceticus JCM 6842(T) (97.5% similarity). DNA-DNA hybridization revealed that the isolate has 62, 25, 18 and 19% relatedness, respectively, to genomic species 6 ATCC 17979, genomic species BJ13/TU14 ATCC 17905, genomic species 9 ATCC 9957 and A. calcoaceticus, respectively.

  3. (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

  4. (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage.

    PubMed

    Balk, Melike; Mehboob, Farrakh; van Gelder, Antonie H; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; Stams, Alfons J M

    2010-09-01

    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 microm in diameter, and 2-8 microm in length, growing as single cells or in pairs. The cells grew optimally at 37 degrees C, and the pH optimum was around 7. Strain An4 converted various alcohols, organic acids, fructose, acetoin, and H(2)/CO(2) to acetate, usually as the only product. Succinate was decarboxylated to propionate. The isolate was able to respire with (per)chlorate, nitrate, and CO(2). 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.

  5. SP10 infectivity is aborted after bacteriophage SP10 infection induces nonA transcription on the prophage SPβ region of the Bacillus subtilis genome.

    PubMed

    Yamamoto, Tatsuya; Obana, Nozomu; Yee, Lii Mien; Asai, Kei; Nomura, Nobuhiko; Nakamura, Kouji

    2014-02-01

    Bacteria have developed various strategies for phage resistance. Infection with phage induces the transcription of part of the phage resistance gene, but the regulatory mechanisms of such transcription remain largely unknown. The phage resistance gene nonA is located on the SPβ prophage region of the Bacillus subtilis Marburg strain genome. The nonA transcript was detected at the late stage of SP10 infection but is undetectable in noninfected cells. The nonA transcript was detected after the induction of the sigma factor Orf199-Orf200 (σ(Orf199-200)), when sigma factors encoded in the SP10 genome were expressed from a xylose-inducible plasmid. Thus, the SP10 sigma factor is an activator of a set of SP10 genes and nonA. The nonA gene encodes a 72-amino-acid protein with a transmembrane motif and has no significant homology with any protein in any database. NonA overexpression halted cell growth and reduced the efficiency of B. subtilis colony formation and respiration activity. In addition, SP10 virion protein synthesis was inhibited in the nonA(+) strain, and SP10 virion particles were scarce in it. These results indicate that NonA is a novel protein that can abort SP10 infection, and its transcription was regulated by SP10 sigma factor.

  6. SP10 Infectivity Is Aborted after Bacteriophage SP10 Infection Induces nonA Transcription on the Prophage SPβ Region of the Bacillus subtilis Genome

    PubMed Central

    Yamamoto, Tatsuya; Obana, Nozomu; Yee, Lii Mien; Asai, Kei; Nomura, Nobuhiko

    2014-01-01

    Bacteria have developed various strategies for phage resistance. Infection with phage induces the transcription of part of the phage resistance gene, but the regulatory mechanisms of such transcription remain largely unknown. The phage resistance gene nonA is located on the SPβ prophage region of the Bacillus subtilis Marburg strain genome. The nonA transcript was detected at the late stage of SP10 infection but is undetectable in noninfected cells. The nonA transcript was detected after the induction of the sigma factor Orf199-Orf200 (σOrf199-200), when sigma factors encoded in the SP10 genome were expressed from a xylose-inducible plasmid. Thus, the SP10 sigma factor is an activator of a set of SP10 genes and nonA. The nonA gene encodes a 72-amino-acid protein with a transmembrane motif and has no significant homology with any protein in any database. NonA overexpression halted cell growth and reduced the efficiency of B. subtilis colony formation and respiration activity. In addition, SP10 virion protein synthesis was inhibited in the nonA+ strain, and SP10 virion particles were scarce in it. These results indicate that NonA is a novel protein that can abort SP10 infection, and its transcription was regulated by SP10 sigma factor. PMID:24272782

  7. Effects of nitrogen and carbon sources on the production of inulinase from strain Bacillus sp. SG113

    NASA Astrophysics Data System (ADS)

    Gavrailov, Simeon; Ivanova, Viara

    2016-03-01

    The effects of the carbon and nitrogen substrates on the growth of Bacillus sp. SG113 strain were studied. The use of organic nitrogen sources (peptone, beef extract, yeast extract, casein) leads to rapid cellular growth and the best results for the Bacillus strain were obtained with casein hydrolysate. From the inorganic nitrogen sources studied, the (NH4) 2SO4 proved to be the best nitrogen source. Casein hydrolysate and (NH4) 2SO4 stimulated the invertase synthesis. In the presence of Jerusalem artichoke, onion and garlic extracts as carbon sources the strain synthesized from 6 to 10 times more inulinase.

  8. 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

  9. 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.

  10. Complete Genome Sequence of Enterobacter sp. Strain ODB01, a Bacterium That Degrades Crude Oil

    PubMed Central

    Lan, Hui; Yang, Hui; Li, Peiwang; Wang, Chong; Zhou, Haiyan; Zhou, Hui; Pan, Hu; Yu, Ye

    2017-01-01

    ABSTRACT Enterobacter sp. strain ODB01, which was isolated from the Changqing oil field, can degrade crude oil efficiently and use crude oil as its sole source of carbon and energy. We report the complete genome sequence of ODB01. The results promote its application in the remediation of petroleum contaminants. PMID:28280034

  11. Draft Genome Sequence for Caulobacter sp. Strain OR37, a Bacterium Tolerant to Heavy Metals

    PubMed Central

    Utturkar, Sagar M.; Brzoska, Ryann M.; Klingeman, Dawn M.; Epstein, Slava E.; Palumbo, Anthony V.

    2013-01-01

    Caulobacter sp. strain OR37 belongs to the class Alphaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here. PMID:23792749

  12. Draft Genome Sequence for Ralstonia sp. Strain OR214, a Bacterium with Potential for Bioremediation

    PubMed Central

    Utturkar, Sagar M.; Brzoska, Ryann M.; Klingeman, Dawn M.; Epstein, Slava E.; Palumbo, Anthony V.

    2013-01-01

    Ralstonia sp. strain OR214 belongs to the class Betaproteobacteria and was isolated from subsurface sediments in Oak Ridge, TN. A member of this genus has been described as a potential bioremediation agent. Strain OR214 is tolerant to various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present its draft genome sequence here. PMID:23792748

  13. Draft Genome Sequence of Pseudoalteromonas sp. Strain PLSV, an Ulvan-Degrading Bacterium

    PubMed Central

    Kopel, Moran; Helbert, William; Henrissat, Bernard; Doniger, Tirza

    2014-01-01

    We present the draft genome sequence of Pseudoalteromonas sp. strain PLSV, isolated from the feces of an Aplysia sea slug. The addition of the PLSV genome to the existing genomes of three other ulvan-degrading bacterial species will enhance our understanding of ulvan utilization. PMID:25502665

  14. 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

  15. 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)).

  16. Mitigation of Membrane Biofouling in MBR Using a Cellulolytic Bacterium, Undibacterium sp. DM-1, Isolated from Activated Sludge.

    PubMed

    Nahm, Chang Hyun; Lee, Seonki; Lee, Sang Hyun; Lee, Kibaek; Lee, Jaewoo; Kwon, Hyeokpil; Choo, Kwang-Ho; Lee, Jung-Kee; Jang, Jae Young; Lee, Chung-Hak; Park, Pyung-Kyu

    2017-03-28

    Biofilm formation on the membrane surface results in the loss of permeability in membrane bioreactors (MBRs) for wastewater treatment. Studies have revealed that cellulose is not only produced by a number of bacterial species but also plays a key role during formation of their biofilm. Hence, in this study, cellulase was introduced to a MBR as a cellulose-induced biofilm control strategy. For practical application of cellulase to MBR, a cellulolytic (i.e., cellulase-producing) bacterium, Undibacterium sp. DM-1, was isolated from a lab-scale MBR for wastewater treatment. Prior to its application to MBR, it was confirmed that the cell-free supernatant of DM-1 was capable of inhibiting biofilm formation and of detaching the mature biofilm of activated sludge and cellulose-producing bacteria. This suggested that cellulase could be an effective anti-biofouling agent for MBRs used in wastewater treatment. Undibacterium sp. DM-1-entrapping beads (i.e., cellulolytic-beads) were applied to a continuous MBR to mitigate membrane biofouling 2.2-fold, compared with an MBR with vacant-beads as a control. Subsequent analysis of the cellulose content in the biofilm formed on the membrane surface revealed that this mitigation was associated with an approximately 30% reduction in cellulose by cellulolytic-beads in MBR.

  17. 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.

  18. Aerobic-heterotrophic nitrogen removal through nitrate reduction and ammonium assimilation by marine bacterium Vibrio sp. Y1-5.

    PubMed

    Li, Yating; Wang, Yanru; Fu, Lin; Gao, Yizhan; Zhao, Haixia; Zhou, Weizhi

    2017-04-01

    An aerobic marine bacterium Vibrio sp. Y1-5 was screened to achieve efficient nitrate and ammonium removal simultaneously and fix nitrogen in cells without N loss. Approximately 98.0% of nitrate (100mg/L) was removed in 48h through assimilatory nitrate reduction and nitrate reductase was detected in the cytoplasm. Instead of nitrification, the strain assimilated ammonium directly, and it could tolerate as high as 1600mg/L ammonium concentration while removing 844.6mg/L. In addition, ammonium assimilation occurred preferentially in the medium containing nitrate and ammonium with a total nitrogen (TN) removal efficiency of 80.4%. The results of nitrogen balance and Fourier infrared spectra illustrated that the removed nitrogen was all transformed to protein or stored as organic nitrogen substances in cells and no N was lost in the process. Toxicological studies with the brine shrimp species Artemia naupliia indicated that Vibrio sp. Y1-5 can be applied in aquatic ecosystems safely.

  19. 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.

  20. Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments.

    PubMed

    Lakhal, Raja; Pradel, Nathalie; Postec, Anne; Ollivier, Bernard; Cayol, Jean-Luc; Godfroy, Anne; Fardeau, Marie-Laure; Galés, Grégoire

    2015-09-01

    A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766H(T), was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002  m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766H(T) grew at temperatures of 25-45 °C (optimum 30 °C), pH 6.7-8.1 (optimum 7.5) and in a salinity of 5-60 g l(-1) NaCl (optimum 30 g l(-1)). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766H(T) was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766H(T) was Geosporobacter subterraneus (94.2% 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766H(T) ( = DSM 27501(T) = JCM 19377(T)) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

  1. Bile acids are new products of a marine bacterium, Myroides sp. strain SM1.

    PubMed

    Maneerat, Suppasil; Nitoda, Teruhiko; Kanzaki, Hiroshi; Kawai, Fusako

    2005-06-01

    Strain SM1 was isolated as a biosurfactant-producing microorganism from seawater and presumptively identified as Myroides sp., based on morphology, biochemical characteristics and 16S rDNA sequence. The strain produced surface-active compounds in marine broth, which were purified, using emulsification activity for n-hexadecane as an indicator. The purified compounds were identified by thin-layer chromatography, (1)H- and (13)C-NMR spectra and fast atom bombardment mass spectrometry as cholic acid, deoxycholic acid and their glycine conjugates. Type strains of the genus Myroides, M. odoratus JCM7458 and M. odoramitimus JCM7460, also produced these compounds. Myroides sp. strain SM1 possessed a biosynthetic route to cholic acid from cholesterol. Thus, bile acids were found as new products of prokaryotic cells, genus Myroides.

  2. 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.

  3. 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

  4. Identification and characterization of salt-inducible polypeptide in Paenibacillus sp., a moderately halophilic bacterium.

    PubMed

    Sokhansanj, Ashrafaddin; Karkhane, Ali Asghar; Jazii, Ferdous Rastgar

    2005-11-01

    In response to salt, Paenibacillus sp. strain XII expresses a 21.4 kDa polypeptide. N-terminal sequencing and sequence homology analysis indicate homology between the N-terminal sequence of the polypeptide and a segment of the N-terminus of the spore coat associated protein CotN of Oceanobacillus iheyensis, an extremely halotolerant bacteria of the deep-sea.

  5. 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...

  6. 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

  7. Isolation and identification of N-butyl-tetrahydro-5-oxofuran-2-carboxamide produced by Bacillus sp. L60 and its antifungal activity.

    PubMed

    Lee, Yong-Seong; Cho, Jeong-Yong; Moon, Jae-Hak; Kim, Kil-Yong

    2017-03-01

    Rhizoctonia solani is the cause of substantial economic loss in many crops. The aim of this study is to investigate biocontrol potential of Bacillus sp. L60 against R. solani and to purify an antifungal compound. In this study, Bacillus sp. L60 demonstrated significant antagonism toward R. solani with the dual culture assay. The antifungal compound was extracted from Bacillus sp. L60 culture supernatant with n-butanol, and identified as N-butyl-tetrahydro-5-oxofuran-2-carboxamide (BT-5O-2C) having molecular weights of 185.1052 Da with the formula C9 H15 NO3 using NMR and HR-ESI-MS analysis. The minimum inhibitory concentration (MIC) value of the antifungal compound was 256 µg ml(-1) against R. solani. Therefore, our results clearly demonstrated BT-5O-2C as well as Bacillus sp. L60 as potential biological control agents for the management of R. solani.

  8. Semiquinone fraction isolated from Bacillus sp. INM-1 protects hepatic tissues against γ-radiation induced toxicity.

    PubMed

    Mishra, Saurabh; Bansal, Deen Dayal; Malhotra, Poonam; K Reddy, D Sudheer; Jamwal, Vishawdeep S; Patel, Dev Dutt; Gupta, Ashutosh Kumar; Singh, Praveen Kumar; Javed, Saleem; Kumar, Raj

    2014-12-01

    Present study was focused on evaluation of a semiquinone glucoside derivative (SQGD) isolated from radioresistant bacterium Bacillus sp. INM-1 for its ability against γ radiation induced oxidative stress in irradiated mice. Animals were divided into four group, i.e., (i) untreated control mice; (ii) SQGD treated (50 mg/kg b. wt. i.p.) mice; (iii) irradiated (10 Gy) mice; and (iv) irradiated mice which were pre-treated (-2 h) with SQGD (50 mg/kg b. wt. i.p.). Following treatment, liver homogenates of the treated mice were subjected to endogenous antioxidant enzymes estimation. Result indicated that SQGD pre-treatment, significantly (P < 0.05) induced superoxide dismutase (SOD) (19.84 ± 2.18% at 72 h), catalase (CAT) (26.47 ± 3.11% at 12 h), glutathione (33.81 ± 1.99% at 24 h), and glutathione-S-transferase (24.40 ± 2.65% at 6 h) activities in the liver of mice as compared with untreated control. Significant (P < 0.05) induction in SOD (50.04 ± 5.59% at 12 h), CAT (62.22 ± 7.50 at 72 h), glutathione (42.92 ± 2.28% at 24 h), and glutathione-S-transferase (46.65 ± 3.25 at 12 h) was observed in irradiated mice which were pre-treated with SQGD compared with only irradiated mice. Further, significant induction in ABTS(+) radicals (directly proportional to decrease mM Trolox equivalent) was observed in liver homogenate of H2 O2 treated mice which were found to be significantly inhibited in H2 O2 treated mice pre-treated with SQGD. Thus, it can be concluded that SQGD treatment neutralizes oxidative stress caused by irradiation not only by enhancing endogenous antioxidant enzymes but also by improving total antioxidant status of cellular system and thus cumulative effect of the phenomenon may contributes to radioprotection.

  9. Purification and characterization of solvent tolerant lipase from Bacillus sp. for methyl ester production from algal oil.

    PubMed

    Sivaramakrishnan, Ramachandran; Incharoensakdi, Aran

    2016-05-01

    Lipase from Bacillus sp. isolated from the oil contaminated soil was purified by ammonium sulphate precipitation and ion-exchange chromatography with a 5.1-fold purification and 10.5% yield. SDS-PAGE analysis of the enzyme revealed the molecular mass of 24 kDa. The optimum pH and temperature for lipase activity were 6.5 and 37°C, respectively. The isolated lipase was stimulated by pretreatment with methanol and ethanol as well as by divalent metal ions Ca(2+), Mg(2+) and Mn(2+). The enzyme showed high activity towards oleic rich oils. The enzyme immobilized on celite could retain 90% lipase activity after eight cycles. Transesterification of Botryococcus sp. oil using the immobilized enzyme for 40 h resulted in 80% yield of fatty acid methyl esters which had good properties for use as biodiesel. Overall results suggested that the solvent tolerant Bacillus lipase can be a potential biocatalyst for methyl ester production.

  10. 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)).

  11. 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.

  12. 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

  13. 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)).

  14. Physiology and biochemistry of a lignin degrading bacterium Erwinia sp. Cu 3614

    SciTech Connect

    Rajan, J.S.

    1992-01-01

    Previous researchers have reported the isolation of a diphenylether cleaving organism, Erwinia sp., using an enrichment medium containing lignin. A copper and dinitrophenol resistant mutant of this organism, Erwinia sp. Cu3614, has also been reported. To assess the effect of copper on the growth and biochemistry of this organism, continuous cultivation was used employing an apparently optimized medium containing ethanol as carbon source. Upon increasing the concentration of copper sulfate in the medium from 5 [mu]g/ml to 10 [mu]g/ml increases in maximum specific growth rate and growth yield were seen. Also decrease in the values for doubling time and the coefficient for maintenance energy were seen. At higher levels of copper sulfate a [open quotes]non competitive[close quotes] inhibition of growth was seen as indicated by the values calculated for substrate affinity constant, and inhibition constant. To assess this organism's ligninolytic ability, an assay for residual lignin was developed. The assay measured a reaction between diazotized sulfanilic acid and lignin in alkaline solution by spectrophotometric monitoring of the resulting adduct. Use of this technique indicated that Erwinia sp. Cu3614 could degrade up to 80% of lignin in batch cultures. Further evidence about the ligninolytic ability of this organism was provided by examination of electron micrographs of lignocellulosic substrates incubated with cell suspensions. An assay for monitoring diphenylether cleaving abilities was also developed using resazurin, a redox dye. In vivo assays with cells obtained from continuous culture studies indicated a linear relationship between the rates of reaction with resazurin and the amount of copper associated with cells. In vitro assays, employing cell free extracts and resazurin, were used to obtain a fraction enriched in diphenylether cleaving activity by a heat treatment procedure.

  15. 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)).

  16. Vibrio psychroerythrus sp. n.: Classification of the Psychrophilic Marine Bacterium, NRC 1004

    PubMed Central

    D'aoust, J. Y.; Kushner, D. J.

    1972-01-01

    A red-pigmented organism, formerly known as marine psychrophile NRC 1004, has been classified as Vibrio psychroerythrus sp. n. Classification was mainly based on morphology, the ability of the organism to oxidize and ferment glucose, its sensitivity to vibriostat 0/129, and its deoxyribonucleic acid base composition of 40.0 moles% guanine plus cytosine, determined by thermal denaturation. The organism gave positive reactions for catalase, oxidase, and starch hydrolysis and produced acid from maltose and dextrin but not from arabinose. It was indole- and citrate-negative and reduced nitrate to nitrite without producing gas. PMID:5053463

  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. 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/).

  19. Use of Bacillus pumilus CBMAI 0008 and Paenibacillus sp. CBMAI 868 for colour removal from paper mill effluent

    PubMed Central

    de Oliveira, Patrícia Lopes; Duarte, Marta Cristina Teixeira; Ponezi, Alexandre Nunes; Durrant, Lúcia Regina

    2009-01-01

    Bacillus pumilus and Paenibacillus sp. were applied on the paper mill effluent to investigate the colour remotion. Inocula were individually applied in effluent at pH 7.0, 9.0 and 11.0. The real colour and COD remotion after 48h at pH 9.0 were, respectively, 41.87% and 22.08% for B. pumilus treatment and 42.30% and 22.89% for Paenibacillus sp. Gel permeation chromatography was used to verify the molar masses of compounds in the non-treated and treated effluent, showing a decrease in the compounds responsible for the paper mill effluent colour. PMID:24031372

  20. Use of Bacillus pumilus CBMAI 0008 and Paenibacillus sp. CBMAI 868 for colour removal from paper mill effluent.

    PubMed

    de Oliveira, Patrícia Lopes; Duarte, Marta Cristina Teixeira; Ponezi, Alexandre Nunes; Durrant, Lúcia Regina

    2009-04-01

    Bacillus pumilus and Paenibacillus sp. were applied on the paper mill effluent to investigate the colour remotion. Inocula were individually applied in effluent at pH 7.0, 9.0 and 11.0. The real colour and COD remotion after 48h at pH 9.0 were, respectively, 41.87% and 22.08% for B. pumilus treatment and 42.30% and 22.89% for Paenibacillus sp. Gel permeation chromatography was used to verify the molar masses of compounds in the non-treated and treated effluent, showing a decrease in the compounds responsible for the paper mill effluent colour.

  1. Sporosarcina antarctica sp. nov., a psychrophilic bacterium isolated from the Antarctic.

    PubMed

    Yu, Yong; Xin, Yu-Hua; Liu, Hong-Can; Chen, Bo; Sheng, Jun; Chi, Zhen-Ming; Zhou, Pei-Jin; Zhang, De-Chao

    2008-09-01

    A Gram-positive, psychrophilic, rod-shaped bacterium, designated strain N-05(T), was isolated from soil samples collected off King George Island, west Antarctica (6 degrees 13' 31'' S 5 degrees 57' 08'' W). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N-05(T) was related to members of the genus Sporosarcina and had highest 16S rRNA gene sequence similarity with the type strain of Sporosarcina macmurdoensis (98.0%). The temperature range for growth of strain N-05(T) was 0-23 degrees C, with optimum growth occurring at 17-18 degrees C and approximately pH 6.0-8.0. Strain N-05(T) had MK-7 as the major menaquinone and anteiso-C(15:0) and C(16:1)omega7c alcohol as major fatty acids. The genomic DNA G+C content was 39.2 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, strain N-05(T) is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina antarctica is proposed. The type strain is N-05(T) (=CGMCC 1.6503(T)=JCM 14646(T)).

  2. 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.

  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. 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).

  5. 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.

  6. 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.

  7. Isolation and characterization of comprehensive polychlorinated biphenyl degrading bacterium, Enterobacter sp. LY402.

    PubMed

    Jia, Ling-Yun; Zheng, Ai-Ping; Xu, Li; Huang, Xiao-Dong; Zhang, Qing; Yang, Feng-Lin

    2008-05-01

    A Gram-negative bacterium, named LY402, was isolated from contaminated soil. 16S rDNA sequencing and measurement of the physiological and biochemical characteristics identified it as belonging to the genus Enterobacter. Degradation experiments showed that LY402 had the ability to aerobically transform 79 of the 91 major congeners of Aroclor 1242, 1254, and 1260. However, more interestingly, the strain readily degraded certain highly chlorinated and recalcitrant polychlorinated biphenyls (PCBs). Almost all the tri- and tetra-chlorobiphenyls (CBs), except for 3,4,3',4'-CB, were degraded in 3 days, whereas 73% of 3,4,3',4'-, 92% of the penta-, 76% of the hexa-, and 37% of the hepta-CBs were transformed after 6 days. In addition, among 12 octa-CBs, 2,2',3,3',5,5',6,6- CB was obviously degraded, and 2,2',3,3',4,5,6,6'- and 2,2',3,3',4,5,5',6'-CB were slightly transformed. In a metabolite analysis, mono- and di-chlorobenzoic acids (CBAs) were identified, and parts of them were also transformed by strain LY402. Analysis of PCB degradation indicated that strain LY402 could effectively degrade PCB congeners with chlorine substitutions in both ortho- and para-positions. Consequently, this is the first report of an Enterobacteria that can efficiently degrade both low and highly chlorinated PCBs under aerobic conditions.

  8. Streptococcus danieliae sp. nov., a novel bacterium isolated from the caecum of a mouse.

    PubMed

    Clavel, Thomas; Charrier, Cédric; Haller, Dirk

    2013-01-01

    We report the characterization of one novel bacterium, strain ERD01G(T), isolated from the cecum of a TNF(deltaARE) mouse. The strain was found to belong to the genus Streptococcus based on phylogenetic analysis of partial 16S rRNA gene sequences. The bacterial species with standing name in nomenclature that was most closely related to our isolate was Streptococcus alactolyticus (97 %). The two bacteria were characterized by a DNA-DNA hybridization similarity value of 35 %, demonstrating that they belong to different species. The new isolate was negative for acetoin production, esculin hydrolysis, urease, α-galactosidase and β-glucosidase, was able to produce acid from starch and trehalose, grew as beta-hemolytic coccobacilli on blood agar, did not grow at >40 °C, did not survive heat treatment at 60 °C for 20 min and showed negative agglutination in Lancefield tests. On the basis of these characteristics, strain ERD01G(T) differed from the most closely related species S. alactolyticus, Streptococcus gordonii, Streptococcus intermedius and Streptococcus sanguinis. Thus, based on genotypic and phenotypic evidence, we propose that the isolate belongs to a novel bacterial taxon within the genus Streptococcus, for which the name Streptococcus danieliae is proposed. The type strain is ERD01G(T) (= DSM 22233(T) = CCUG 57647(T)).

  9. 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.

  10. Genome sequence of Bacillus sp. strain HYC-10, isolated from intestinal tract contents from a marine fish (Mugil cephalus).

    PubMed

    Lai, Qiliang; Liu, Yang; Shao, Zongze

    2012-12-01

    Bacillus sp. strain HYC-10 was isolated with intestinal tract content of a fish, Mugil cephalus, captured from the sea close to Xiamen Island, China. Here, we present the draft genome of strain HYC-10, which contains 3,611,918 bp with a G+C content of 41.30% and contains 3,687 protein-coding genes and 33 tRNA genes.

  11. [Isolation, charcaterization of an anthracene degrading bacterium Martelella sp. AD-3 and cloning of dioxygenase gene].

    PubMed

    Cui, Chang-Zheng; Feng, Tian-Cai; Yu, Ya-Qi; Dong, Fei; Yang, Xin-Mei; Feng, Yao-Yu; Liu, Yong-Di; Lin, Han-Ping

    2012-11-01

    Anthracene, among the 16 US EPA polycyclic aromatic hydrocarbons (PAHs), is a typical low molecular weight environmental contaminant, which gains concern on its biodegradation under hypersaline condition. In this study, an anthracene-degrading bacterial strain was isolated from highly saline petroleum-contaminated soil. Based on its physiological, biochemical characteristics and 16S rDNA sequence analysis, the bacteria was preliminary identified and named as Martelella sp. AD-3. The strain was able to utilize anthracene as sole carbon source for growth and the degradation occurred under broad salinities (0.1% to 10%) and varying pHs (6.0 to 10.0). The optimized degradation conditions were initial concentration 25 mg x L(-1), culture temperature 30 degrees C, pH 9.0 and salinity 3%. And 94.6% of anthracene was degraded by strain AD-3 under the optimal conditions within 6 days. Degenerate primers design was performed with a reported dioxygenase alpha subunit homologous gene. A length of 307 bp fragment of the partial dioxygenase gene sequences (GenBank accession: JF823991.1) was amplified by nested PCR. The clones amino acid sequence from strain AD-3 showed 95% identity to that of the partial naphthalene dioxygenase large-subunit from Marinobacter sp. NCE312 (AF295033). The results lay a foundation for the further study of molecular mechanism involved in the PAHs biodegradation by strain AD-3.

  12. 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

  13. Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.

    DOE PAGES

    Billings, Andrew F.; Fortney, Julian L.; Hazen, Terry C.; ...

    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

  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. 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.

  16. Purification and Characterization of Chitosanase from Bacillus sp. Strain KCTC 0377BP and Its Application for the Production of Chitosan Oligosaccharides

    PubMed Central

    Choi, Yeon Jin; Kim, Eun Jung; Piao, Zhe; Yun, Young Chul; Shin, Yong Chul

    2004-01-01

    For the enzymatic production of chitosan oligosaccharides from chitosan, a chitosanase-producing bacterium, Bacillus sp. strain KCTC 0377BP, was isolated from soil. The bacterium constitutively produced chitosanase in a culture medium without chitosan as an inducer. The production of chitosanase was increased from 1.2 U/ml in a minimal chitosan medium to 100 U/ml by optimizing the culture conditions. The chitosanase was purified from a culture supernatant by using CM-Toyopearl column chromatography and a Superose 12HR column for fast-performance liquid chromatography and was characterized according to its enzyme properties. The molecular mass of the enzyme was estimated to be 45 kDa by means of sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme demonstrated bifunctional chitosanase-glucanase activities, although it showed very low glucanase activity, with less than 3% of the chitosanase activity. Activity of the enzyme increased with an increase of the degrees of deacetylation (DDA) of the chitosan substrate. However, the enzyme still retained 72% of its relative activity toward the 39% DDA of chitosan, compared with the activity of the 94% DDA of chitosan. The enzyme produced chitosan oligosaccharides from chitosan, ranging mainly from chitotriose to chitooctaose. By controlling the reaction time and by monitoring the reaction products with gel filtration high-performance liquid chromatography, chitosan oligosaccharides with a desired oligosaccharide content and composition were obtained. In addition, the enzyme was efficiently used for the production of low-molecular-weight chitosan and highly acetylated chitosan oligosaccharides. A gene (csn45) encoding chitosanase was cloned, sequenced, and compared with other functionally related genes. The deduced amino acid sequence of csn45 was dissimilar to those of the classical chitosanase belonging to glycoside hydrolase family 46 but was similar to glucanases classified with glycoside hydrolase

  17. Proteolytic system of Bacillus sp. CL18 is capable of extensive feather degradation and hydrolysis of diverse protein substrates.

    PubMed

    Rieger, T J; de Oliveira, C T; Pereira, J Q; Brandelli, A; Daroit, D J

    2017-03-17

    1. Feathers are recalcitrant protein-rich wastes produced in huge amounts by poultry processing for meat production. Hence, feather bioconversion and protease production by Bacillus sp. CL18 were investigated. 2. Bacillus sp. CL18 demonstrated a remarkable feather-degrading potential. Through cultivations on feather broth (10 g l(-1) feathers), 94.5% ± 3% of whole feathers were degraded after 4 d. Increases in soluble protein contents were observed and protease production was maximal also at d 4. This strain produced diverse proteolytic enzymes during growth. 3. Crude protease displayed optimal activity at 55°C (50-62°C), pH 8.0 (7.0-9.0) and a low thermal stability. Proteolytic activity increased in the presence of Ca(2+), Mg(2+), Triton X-100, Tween 20 and dimethyl sulphoxide. Inhibition profile indicated that crude protease contains, mainly, serine proteases. Enzyme preparation hydrolysed mainly casein and soy protein isolate. 4. The keratinolytic capacity of Bacillus sp. CL18 at moderate temperatures (30°C) might be appropriate for feather conversion, resulting in protein hydrolysates and proteolytic enzymes. Proteases are postulated to be added-value products that can be obtained from such a bioprocess.

  18. A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding.

    PubMed

    Zhou, Zhanping; Zhao, Shuangzhi; Liu, Yang; Chang, Zhengying; Ma, Yanhe; Li, Jian; Song, Jiangning

    2016-11-01

    The chitosanase from Bacillus sp. TS (CsnTS) is an enzyme belonging to the glycoside hydrolase family 8. The sequence of CsnTS shares 98 % identity with the chitosanase from Bacillus sp. K17. Crystallography analysis and site-direct mutagenesis of the chitosanase from Bacillus sp. K17 identified the important residues involved in the catalytic interaction and substrate binding. However, despite progress in understanding the catalytic mechanism of the chitosanase from the famil