Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics

PubMed Central

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-01-01

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains. PMID:26691589

Stable coexistence of five bacterial strains as a cellulose-degrading community.

PubMed

Kato, Souichiro; Haruta, Shin; Cui, Zong Jun; Ishii, Masaharu; Igarashi, Yasuo

2005-11-01

A cellulose-degrading defined mixed culture (designated SF356) consisting of five bacterial strains (Clostridium straminisolvens CSK1, Clostridium sp. strain FG4, Pseudoxanthomonas sp. strain M1-3, Brevibacillus sp. strain M1-5, and Bordetella sp. strain M1-6) exhibited both functional and structural stability; namely, no change in cellulose-degrading efficiency was observed, and all members stably coexisted through 20 subcultures. In order to investigate the mechanisms responsible for the observed stability, "knockout communities" in which one of the members was eliminated from SF356 were constructed. The dynamics of the community structure and the cellulose degradation profiles of these mixed cultures were determined in order to evaluate the roles played by each eliminated member in situ and its impact on the other members of the community. Integration of each result gave the following estimates of the bacterial relationships. Synergistic relationships between an anaerobic cellulolytic bacterium (C. straminisolvens CSK1) and two strains of aerobic bacteria (Pseudoxanthomonas sp. strain M1-3 and Brevibacillus sp. strain M1-5) were observed; the aerobes introduced anaerobic conditions, and C. straminisolvens CSK1 supplied metabolites (acetate and glucose). In addition, there were negative relationships, such as the inhibition of cellulose degradation by producing excess amounts of acetic acid by Clostridium sp. strain FG4, and growth suppression of Bordetella sp. strain M1-6 by Brevibacillus sp. strain M1-5. The balance of the various types of relationships (both positive and negative) is thus considered to be essential for the stable coexistence of the members of this mixed culture.

High concentrations of intracellular Ap4A and/or Ap5A in developing Myxococcus xanthus cells inhibit sporulation.

PubMed

Kimura, Yoshio; Tanaka, Chihiro; Sasaki, Katsuho; Sasaki, Masashi

2017-01-01

Diadenosine polyphosphates (ApnA) are thought to act as signalling molecules regulating stress responses and biofilm formation in prokaryotes. However, ApnA function in Myxococcus xanthus remains unknown. Here, we investigated the role of ApnA in M. xanthus, using the wild-type and ApnA hydrolase (apaH) mutant strains exposed to various stress conditions. In both wild-type and apaH mutant cells cultured on starvation medium (CF agar), the levels of intracellular diadenosine tetraphosphate (Ap4A) and pentaphosphate (Ap5A) increased several fold during the first 16 h of development and decreased gradually thereafter. The levels of Ap4A and Ap5A in the apaH mutant were about 5- and 11-fold higher than those in the wild-type strain at 16 h, respectively. ApnA hydrolase activity of the wild-type strain increased 1.5-fold during the first 8 h of development, and it then gradually decreased. The apaH mutant formed spores 1-2 days after the wild-type strain did, and the yield of viable spores was 5.5 % of that in the wild-type strain 5 days after inoculation onto CF agar. These results suggest the possibility that high intracellular levels of Ap4A and/or Ap5A may inhibit M. xanthus sporulation at the early stage of development and that the bacteria reduce intracellular Ap4A and Ap5A accumulation through ApnA hydrolase activity.

Antiviral activity of acidic polysaccharides from Coccomyxa gloeobotrydiformi, a green alga, against an in vitro human influenza A virus infection.

PubMed

Komatsu, Takayuki; Kido, Nobuo; Sugiyama, Tsuyoshi; Yokochi, Takashi

2013-02-01

The extracts prepared from green algae are reported to possess a variety of biological activities including antioxidant, antitumor and antiviral activities. The acidic polysaccharide fraction from a green alga Coccomyxa gloeobotrydiformi (CmAPS) was isolated and the antiviral action on an in vitro infection of influenza A virus was examined. CmAPS inhibited the growth and yield of all influenza A virus strains tested, such as A/H1N1, A/H2N2, A/H3N2 and A/H1N1 pandemic strains. The 50% inhibitory concentration of CmAPS on the infection of human influenza A virus strains ranged from 26 to 70 µg/mL and the antiviral activity of CmAPS against influenza A/USSR90/77 (H1N1) was the strongest. The antiviral activity of CmAPS was not due to the cytotoxicity against host cells. The antiviral activity of CmAPS required its presence in the inoculation of virus onto MDCK cells. Pretreatment and post-treatment with CmAPS was ineffective for the antiviral activity. CmAPS inhibited influenza A virus-induced erythrocyte hemagglutination and hemolysis. Taken together, CmAPS was suggested to exhibit the anti-influenza virus activity through preventing the interaction of virus and host cells. The detailed antiviral activity of CmAPS is discussed.

Growth in coculture stimulates metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2.

PubMed

Sørensen, Sebastian R; Ronen, Zeev; Aamand, Jens

2002-07-01

Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene, strain SRS1 was assigned to the beta-subdivision of the proteobacteria and probably represents a new genus. Strain SRS1 was unable to degrade either isoproturon or its known metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, or 4-isopropyl-aniline. Pure culture studies indicate that Sphingomonas sp. SRS2 is auxotrophic and requires components supplied by association with other soil bacteria. A specific mixture of amino acids appeared to meet these requirements, and it was shown that methionine was essential for Sphingomonas sp. SRS2. This suggests that strain SRS1 supplies amino acids to Sphingomonas sp. SRS2, thereby leading to rapid metabolism of (14)C-labeled isoproturon to (14)CO(2) and corresponding growth of strain SRS2. Proliferation of strain SRS1 suggests that isoproturon metabolism by Sphingomonas sp. SRS2 provides unknown metabolites or cell debris that supports growth of strain SRS1. The role of strain SRS1 in the consortium was not ubiquitous among soil bacteria; however, the indigenous soil microflora and some strains from culture collections also stimulate isoproturon metabolism by Sphingomonas sp. strain SRS2 to a similar extent.

Growth in Coculture Stimulates Metabolism of the Phenylurea Herbicide Isoproturon by Sphingomonas sp. Strain SRS2

PubMed Central

Sørensen, Sebastian R.; Ronen, Zeev; Aamand, Jens

2002-01-01

Metabolism of the phenylurea herbicide isoproturon by Sphingomonas sp. strain SRS2 was significantly enhanced when the strain was grown in coculture with a soil bacterium (designated strain SRS1). Both members of this consortium were isolated from a highly enriched isoproturon-degrading culture derived from an agricultural soil previously treated regularly with the herbicide. Based on analysis of the 16S rRNA gene, strain SRS1 was assigned to the β-subdivision of the proteobacteria and probably represents a new genus. Strain SRS1 was unable to degrade either isoproturon or its known metabolites 3-(4-isopropylphenyl)-1-methylurea, 3-(4-isopropylphenyl)-urea, or 4-isopropyl-aniline. Pure culture studies indicate that Sphingomonas sp. SRS2 is auxotrophic and requires components supplied by association with other soil bacteria. A specific mixture of amino acids appeared to meet these requirements, and it was shown that methionine was essential for Sphingomonas sp. SRS2. This suggests that strain SRS1 supplies amino acids to Sphingomonas sp. SRS2, thereby leading to rapid metabolism of 14C-labeled isoproturon to 14CO2 and corresponding growth of strain SRS2. Proliferation of strain SRS1 suggests that isoproturon metabolism by Sphingomonas sp. SRS2 provides unknown metabolites or cell debris that supports growth of strain SRS1. The role of strain SRS1 in the consortium was not ubiquitous among soil bacteria; however, the indigenous soil microflora and some strains from culture collections also stimulate isoproturon metabolism by Sphingomonas sp. strain SRS2 to a similar extent. PMID:12089031

Two synthetic Sp1-binding sites functionally substitute for the 21-base-pair repeat region to activate simian virus 40 growth in CV-1 cells.

PubMed Central

Lednicky, J; Folk, W R

1992-01-01

The 21-bp repeat region of simian virus 40 (SV40) activates viral transcription and DNA replication and contains binding sites for many cellular proteins, including Sp1, LSF, ETF, Ap2, Ap4, GT-1B, H16, and p53, and for the SV40 large tumor antigen. We have attempted to reduce the complexity of this region while maintaining its growth-promoting capacity. Deletion of the 21-bp repeat region from the SV40 genome delays the expression of viral early proteins and DNA replication and reduces virus production in CV-1 cells. Replacement of the 21-bp repeat region with two copies of DNA sequence motifs bound with high affinities by Sp1 promotes SV40 growth in CV-1 cells to nearly wild-type levels, but substitution by motifs bound less avidly by Sp1 or bound by other activator proteins does not restore growth. This indicates that Sp1 or a protein with similar sequence specificity is primarily responsible for the function of the 21-bp repeat region. We speculate about how Sp1 activates both SV40 transcription and DNA replication. Images PMID:1328672

Mesoporous silica nanoparticles for efficient rivastigmine hydrogen tartrate delivery into SY5Y cells.

PubMed

Karimzadeh, Mahmonir; Rashidi, Ladan; Ganji, Fariba

2017-04-01

Rivastigmine hydrogen tartrate (RT) is a molecule with both hydrophilic and hydrophobic properties used for the treatment of the Alzheimer's disease. In this work, the larger pore size of mesoporous silica nanoparticles (P1-MSN) was synthesized and then, P1-MSN were functionalized by succinic anhydride (S-P1-MSN) and 3-aminopropyltriethoxysilane (APTES) (AP-CO-P1-MSN) using the grafting and co-condensation methods, respectively. A new method was used for the functionalization of P1-MSN by succinic anhydride at room temperature. Nanoparticles were characterized by special instrumental analysis and loaded by RT. Maximum entrapment efficiency and RT loading percentage into P1-MSN, AP-CO-P1-MSN and S-P1-MSN were respectively obtained as 21.26 and 25.5%, 41.5 and 49.8%, and 11.9 and 14.28% for 24 h. In the simulated gastric and body fluids, the release rate of RT-loaded AP-CO-P1-MSN (AP-CO-P1-MSN-RT) was lower than that of other RT-loaded nanoparticles. In oral pathway, the sustained release of RT was observed in AP-CO-P1-MSN-RT. Moreover, no cytotoxicity effect was observed for P1-MSN, but the cells treated by AP-CO-P1-MSN showed a reduction in SY5Y cell viability due to easy entrance of these nanoparticles and their accumulation in different parts of the cell as observed by TEM.

A novel spotted fever group Rickettsia infecting Amblyomma parvitarsum (Acari: Ixodidae) in highlands of Argentina and Chile.

PubMed

Ogrzewalska, Maria; Nieri-Bastos, Fernanda A; Marcili, Arlei; Nava, Santiago; González-Acuña, Daniel; Muñoz-Leal, Sebastián; Ruiz-Arrondo, Ignacio; Venzal, José M; Mangold, Atilio; Labruna, Marcelo B

2016-04-01

The tick Amblyomma parvitarsum (Acari: Ixodidae) has established populations in Andean and Patagonic environments of South America. For the present study, adults of A. parvitarsum were collected in highland areas (elevation >3500 m) of Argentina and Chile during 2009-2013, and tested by PCR for rickettsial infection in the laboratory, and isolation of rickettsiae in Vero cell culture by the shell vial technique. Overall, 51 (62.2%) out of 82 A. parvitarsum adult ticks were infected by spotted fever group (SFG) rickettsiae, which generated DNA sequences 100% identical to each other, and when submitted to BLAST analysis, they were 99.3% identical to corresponding sequence of the ompA gene of Rickettsia sp. strain Atlantic rainforest. Rickettsiae were successfully isolated in Vero cell culture from two ticks, one from Argentina and one from Chile. DNA extracted from the third passage of the isolates of Argentina and Chile were processed by PCR, resulting in partial sequences for three rickettsial genes (gltA, ompB, ompA). These sequences were concatenated and aligned with rickettsial corresponding sequences available in GenBank. Phylogenetic analysis revealed that the A. pavitarsum rickettsial agent grouped under high bootstrap support in a clade composed by the SFG pathogens R. sibirica, R. africae, R. parkeri, Rickettsia sp. strain Atlantic rainforest, and two unnamed SFG agents of unknown pathogenicty, Rickettsia sp. strain NOD, and Rickettsia sp. strain ApPR. The pathogenic role of this A. parvitarsum rickettsia cannot be discarded, since several species of tick-borne rickettsiae that were considered nonpathogenic for decades are now associated with human infections. Copyright © 2016. Published by Elsevier GmbH.

Metagenome-Assembled Genome Sequences of Acetobacterium sp. Strain MES1 and Desulfovibrio sp. Strain MES5 from a Cathode-Associated Acetogenic Microbial Community.

PubMed

Ross, Daniel E; Marshall, Christopher W; May, Harold D; Norman, R Sean

2017-09-07

Draft genome sequences of Acetobacterium sp. strain MES1 and Desulfovibrio sp. strain MES5 were obtained from the metagenome of a cathode-associated community enriched within a microbial electrosynthesis system (MES). The draft genome sequences provide insight into the functional potential of these microorganisms within an MES and a foundation for future comparative analyses. Copyright © 2017 Ross et al.

Advantages of Environmental Scanning Electron Microscopy in Studies of Microorganisms

DTIC Science & Technology

1993-01-01

external structures, cultures of Aspergillus sp. and Cunninghamella sp. but details of cytoplasmic organization were lacking were maintained on corn meal ... agar . (Fig. 7). Uncoated, freeze-dried Euglena sp. cells exam- ined with either ESD or BSE detectors did not exhibit Specimen Preparation for ESEM...approximately Agar plugs from sporulating cultures of Cunning- 1.0 pLm in diameter (Fig. 23). Many of the vesicles ap- hamella sp., Mucor sp., and Aspergillus

Structural determination of the acidic exopolysaccharide produced by a Pseudomonas sp. strain 1.15.

PubMed

Cescutti, P; Toffanin, R; Pollesello, P; Sutherland, I W

1999-01-31

Pseudomonas strain 1.15 was isolated from a freshwater biofilm and shown to produce considerable amounts of an acidic polysaccharide which was investigated by methylation analysis, NMR spectroscopy and ionspray mass spectrometry (ISMS). The polysaccharide was depolymerised by a bacteriophage-associated endoglucosidase and by autohydrolysis, and the resulting oligosaccharides were investigated by NMR spectroscopy and mass spectrometry. The resulting data showed that the parent repeating unit of the 1.15 exopolysaccharide (EPS) is a branched hexasaccharide. The main chain is constituted of the trisaccharide -->4)-alpha-L-Fucp-(1-->4)-alpha-L-Fucp-(1-->3)-beta-D-Glcp- (1--> and the side chain alpha-D-Galp-(1-->4)-beta-D-GlcAp-(1-->3)-alpha-D-Galp-(1-->is linked to O-3 of the first Fuc residue. The terminal non-reducing Gal carries a 1-carboxyethylidene acetal in the R configuration at the positions 4 and 6. Of the four different O-acetyl groups present in non-stoichiometric amounts, two were established to be on O-2 of the 3-linked Gal and on O-2 of the 4-linked Fuc.

Two Anaplasma phagocytophilum Strains in Ixodes scapularis Ticks, Canada

PubMed Central

Krakowetz, Chantel N.; Dibernardo, Antonia; Lindsay, L. Robbin

2014-01-01

We developed PCR-based assays to distinguish a human pathogenic strain of Anaplasma phagocytophilum, Ap-ha, from Ap-variant 1, a strain not associated with human infection. The assays were validated on A. phagocytophilum-infected blacklegged ticks (Ixodes scapularis) collected in Canada. The relative prevalence of these 2 strains in I. scapularis ticks differed among geographic regions. PMID:25417645

The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia

PubMed Central

Constable, Fiona E.; Nancarrow, Narelle; Rodoni, Brendan

2018-01-01

Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries. PMID:29562672

Exopolysaccharide-producing lactic acid bacteria strains from traditional Thai fermented foods: isolation, identification and exopolysaccharide characterization.

PubMed

Smitinont, T; Tansakul, C; Tanasupawat, S; Keeratipibul, S; Navarini, L; Bosco, M; Cescutti, P

1999-10-15

Lactic Acid Bacteria (LAB) isolated from various traditional Thai fermented foods were screened for exopolysaccharides (EPS) production. From 104 isolates, two rod-shaped and five coccal-shaped LAB were able to produce EPS from sucrose on solid media. However, only the cocci were capable of producing EPS in liquid media and these were identified as Pediococcus pentosaceus. Pediococcus pentosaceus strains AP-1 and AP-3 produced EPS in high yield. In liquid media containing sucrose as carbon source, the amount of EPS produced by AP-1 and AP-3 strains was 6.0 and 2.5 g/L, respectively. The isolated and purified EPSs were chemically characterized. On the basis of sugar composition, methylation analysis and nuclear magnetic resonance spectroscopy, both the EPSs were shown to belong to the same dextran class. In particular, both EPSs differed from linear dextran by branching through 3,6-di-Osubstituted alpha-D-glucopyranosyl residues. The EPS from P. pentosaceus AP-3 was characterized by a relatively higher degree of branching and by a higher molecular weight than that from P. pentosaceus AP-1.

Draft Genome Sequence of Pedobacter sp. Strain Hv1, an Isolate from Medicinal Leech Mucosal Castings

PubMed Central

Ott, Brittany M.; Beka, Lidia; Graf, Joerg

2015-01-01

The Pedobacter sp. Hv1 strain was isolated from the medicinal leech, Hirudo verbana, mucosal castings. These mucosal sheds have been demonstrated to play a role in horizontal symbiont transmission. Here, we report the draft 4.9 Mbp genome sequence of Pedobacter sp. strain Hv1. PMID:26679583

Plant growth promoting rhizobacteria reduce aphid population and enhance the productivity of bread wheat.

PubMed

Naeem, Muhammad; Aslam, Zubair; Khaliq, Abdul; Ahmed, Jam Nazir; Nawaz, Ahmad; Hussain, Mubshar

2018-04-24

Plant growth promoting rhizobacteria increase plant growth and give protection against insect pests and pathogens. Due to the negative impact of chemical pesticides on environment, alternatives to these chemicals are needed. In this scenario, the biological methods of pest control offer an eco-friendly and an attractive option. In this study, the effect of two plant growth promoting rhizobacterial strains (Bacillus sp. strain 6 and Pseudomonas sp. strain 6K) on aphid population and wheat productivity was evaluated in an aphid susceptible (Pasban-90) and resistant (Inqlab-91) wheat cultivar. The seeds were inoculated with each PGPR strain, separately or the combination of both. The lowest aphid population (2.1tiller -1 ), and highest plant height (85.8cm), number of spikelets per spike (18), grains per spike (44), productive tillers (320m -2 ), straw yield (8.6Mgha -1 ), and grain yield (4.8Mgha -1 ) were achieved when seeds were inoculated with Bacillus sp. strain 6+Pseudomonas sp. strain 6K. The grain yield of both varieties was enhanced by 35.5-38.9% with seed inoculation with both bacterial strains. Thus, the combine use of both PGPR strains viz. Bacillus sp. strain 6+Pseudomonas sp. strain 6K offers an attractive option to reduce aphid population tied with better wheat productivity. Copyright © 2018 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Local bioprospecting for high-lipid producing microalgal strains to be grown on concentrated municipal wastewater for biofuel production.

PubMed

Zhou, Wenguang; Li, Yecong; Min, Min; Hu, Bing; Chen, Paul; Ruan, Roger

2011-07-01

Mass cultivation of microalgae for biofuel production depends heavily on the performance of the microalgae strains used. In this study, 60 algae-like microorganisms collected from different sampling sites in Minnesota were examined using multi-step screening and acclimation procedures to select high-lipid producing facultative heterotrophic microalgae strains capable of growing on concentrated municipal wastewater (CMW) for simultaneous energy crop production and wastewater treatment. Twenty-seven facultative heterotrophic microalgae strains were found, among which 17 strains were proved to be tolerant to CMW. These 17 top-performing strains were identified through morphological observation and DNA sequencing as Chlorella sp., Heynigia sp., Hindakia sp., Micractinium sp., and Scenedesmus sp. Five strains were chosen for other studies because of their ability to adapt to CMW, high growth rates (0.455-0.498 d(-1)) and higher lipid productivities (74.5-77.8 mg L(-1)d(-1)). These strains are considered highly promising compared with other strains reported in the literature. Copyright © 2011 Elsevier Ltd. All rights reserved.

Additional conformer observed in the microwave spectrum of methyl vinyl ketone

NASA Astrophysics Data System (ADS)

Wilcox, David S.; Shirar, Amanda J.; Williams, Owen L.; Dian, Brian C.

2011-05-01

A chirped-pulse Fourier transform microwave spectrometer was used to record the rotational spectrum of methyl vinyl ketone (MVK, 3-butene-2-one). Two stable conformations were identified: the previously documented antiperiplanar (ap) conformer and synperiplanar (sp), which is reported for the first time in this microwave study. Methyl torsional analysis resulted in V3 barrier heights of 433.8(1) and 376.6(2) cm-1 for ap- and sp-MVK, respectively. Heavy atom isotopic species of both conformers were detected in natural abundance allowing bond lengths and angles of the molecular frames to be calculated through Kraitchman analysis. A comparison with ab initio calculations is included.

Biological removal of arsenic pollution by soil fungi.

PubMed

Srivastava, Pankaj Kumar; Vaish, Aradhana; Dwivedi, Sanjay; Chakrabarty, Debasis; Singh, Nandita; Tripathi, Rudra Deo

2011-05-15

Fifteen fungal strains were isolated from arsenic contaminated (range 9.45-15.63 mg kg(-1)) agricultural soils from the state of West Bengal, India. Five fungal strains were belonged to the Aspergillus and Trichoderma group each, however, remaining five were identified as the Neocosmospora, Sordaria, Rhizopus, Penicillium and sterile mycelial strain. All these fungal strains were cultivated on medium supplemented with 100, 500, 1000, 5000 and 10,000 mg l(-1) of sodium arsenate. After 30-day cultivation under laboratory conditions, radial growth of these strains was determined and compared with control. Toxicity and tolerance of these strains to arsenate were evaluated on the basis of tolerance index. Out of fifteen, only five fungal strains were found resistant and survived with tolerance index pattern as 0.956 (sterile mycelial strain)>0.311 (Rhizopus sp.)>0.306 (Neocosmospora sp.)>0.212 (Penicillium sp.)>0.189 (Aspergillus sp.) at 10,000 mg l(-1) of arsenate. The arsenic removal efficacy of ten fungal strains, tolerant to 5000 mg l(-1) arsenate, was also assayed under laboratory conditions for 21 days. All these strains were cultivated individually on mycological broth enriched with 10 mg l(-1) of arsenic. The initial and final pH of cultivating medium, fungal biomass and removal of arsenic by each fungal strain were evaluated. Fungal biomass of ten strains removed arsenic biologically from the medium which were ranged from 10.92 to 65.81% depending on fungal species. The flux of biovolatilized arsenic was determined indirectly by estimating the sum of arsenic content in fungal biomass and medium. The mean percent removal as flux of biovolatilized arsenic ranged from 3.71 to 29.86%. The most effective removal of arsenic was observed in the Trichoderma sp., sterile mycelial strain, Neocosmospora sp. and Rhizopus sp. fungal strains. These fungal strains can be effectively used for the bioremediation of arsenic-contaminated agricultural soils. Copyright © 2011 Elsevier B.V. All rights reserved.

Nanoparticles modulate surfactant protein A and D mediated protection against influenza A infection in vitro

PubMed Central

McKenzie, Zofi; Kendall, Michaela; Mackay, Rose-Marie; Tetley, Teresa D.; Morgan, Cliff; Griffiths, Mark; Clark, Howard W.; Madsen, Jens

2015-01-01

Numerous epidemiological and toxicological studies have indicated that respiratory infections are exacerbated following enhanced exposure to airborne particulates. Surfactant protein A (SP-A) and SP-D form an important part of the innate immune response in the lung and can interact with nanoparticles to modulate the cellular uptake of these particles. We hypothesize that this interaction will also affect the ability of these proteins to combat infections. TT1, A549 and differentiated THP-1 cells, representing the predominant cell types found in the alveolus namely alveolar type I (ATI) epithelial cells, ATII cells and macrophages, were used to examine the effect of two model nanoparticles, 100 nm amine modified (A-PS) and unmodified polystyrene (U-PS), on the ability of SP-A and SP-D to neutralize influenza A infections in vitro. Pre-incubation of low concentrations of U-PS with SP-A resulted in a reduction of SP-A anti-influenza activity in A549 cells, whereas at higher concentrations there was an increase in SP-A antiviral activity. This differential pattern of U-PS concentration on surfactant protein mediated protection against IAV was also shown with SP-D in TT1 cells. On the other hand, low concentrations of A-PS particles resulted in a reduction of SP-A activity in TT1 cells and a reduction in SP-D activity in A549 cells. These results indicate that nanoparticles can modulate the ability of SP-A and SP-D to combat viral challenges. Furthermore, the nanoparticle concentration, surface chemistry and cell type under investigation are important factors in determining the extent of these modulations. PMID:25533100

Carbon Monoxide, Hydrogen, and Formate Metabolism during Methanogenesis from Acetate by Thermophilic Cultures of Methanosarcina and Methanothrix Strains

PubMed Central

Zinder, S. H.; Anguish, T.

1992-01-01

CO and H2 have been implicated in methanogenesis from acetate, but it is unclear whether they are directly involved in methanogenesis or electron transfer in acetotrophic methanogens. We compared metabolism of H2, CO, and formate by cultures of the thermophilic acetotrophic methanogens Methanosarcina thermophila TM-1 and Methanothrix sp. strain CALS-1. M. thermophila accumulated H2 to partial pressures of 40 to 70 Pa (1 Pa = 0.987 × 10-5 atm), as has been previously reported for this and other Methanosarcina cultures. In contrast, Methanothrix sp. strain CALS-1 accumulated H2 to maximum partial pressures near 1 Pa. Growing cultures of Methanothrix sp. strain CALS-1 initially accumulated CO, which reached partial pressures near 0.6 Pa (some CO came from the rubber stopper) during the middle of methanogenesis; this was followed by a decrease in CO partial pressures to less than 0.01 Pa by the end of methanogenesis. Accumulation or consumption of CO by cultures of M. thermophila growing on acetate was not detected. Late-exponential-phase cultures of Methanothrix sp. strain CALS-1, in which the CO partial pressure was decreased by flushing with N2-CO2, accumulated CO to 0.16 Pa, whereas cultures to which ca. 0.5 Pa of CO was added consumed CO until it reached this partial pressure. Cyanide (1 mM) blocked CO consumption but not production. High partial pressures of H2 (40 kPa) inhibited methanogenesis from acetate by M. thermophila but not by Methanothrix sp. strain CALS-1, and 2 kPa of CO was not inhibitory to M. thermophila but was inhibitory to Methanothrix sp. strain CALS-1. Levels of CO dehydrogenase, hydrogenase, and formate dehydrogenase in Methanothrix sp. strain CALS-1 were 9.1, 0.045, and 5.8 μmol of viologen reduced min-1 mg of protein-1. These results suggest that CO plays a role in Methanothrix sp. strain CALS-1 similar to that of H2 in M. thermophila and are consistent with the conclusion that CO is an intermediate in a catabolic or anabolic pathway in Methanothrix sp. strain CALS-1; however, they could also be explained by passive equilibration of CO with a metabolic intermediate. PMID:16348788

The Saccharomyces cerevisiae ETH1 Gene, an Inducible Homolog of Exonuclease III That Provides Resistance to DNA-Damaging Agents and Limits Spontaneous Mutagenesis

PubMed Central

Bennett, Richard A. O.

1999-01-01

The recently sequenced Saccharomyces cerevisiae genome was searched for a gene with homology to the gene encoding the major human AP endonuclease, a component of the highly conserved DNA base excision repair pathway. An open reading frame was found to encode a putative protein (34% identical to the Schizosaccharomyces pombe eth1+ [open reading frame SPBC3D6.10] gene product) with a 347-residue segment homologous to the exonuclease III family of AP endonucleases. Synthesis of mRNA from ETH1 in wild-type cells was induced sixfold relative to that in untreated cells after exposure to the alkylating agent methyl methanesulfonate (MMS). To investigate the function of ETH1, deletions of the open reading frame were made in a wild-type strain and a strain deficient in the known yeast AP endonuclease encoded by APN1. eth1 strains were not more sensitive to killing by MMS, hydrogen peroxide, or phleomycin D1, whereas apn1 strains were ∼3-fold more sensitive to MMS and ∼10-fold more sensitive to hydrogen peroxide than was the wild type. Double-mutant strains (apn1 eth1) were ∼15-fold more sensitive to MMS and ∼2- to 3-fold more sensitive to hydrogen peroxide and phleomycin D1 than were apn1 strains. Elimination of ETH1 in apn1 strains also increased spontaneous mutation rates 9- or 31-fold compared to the wild type as determined by reversion to adenine or lysine prototrophy, respectively. Transformation of apn1 eth1 cells with an expression vector containing ETH1 reversed the hypersensitivity to MMS and limited the rate of spontaneous mutagenesis. Expression of ETH1 in a dut-1 xthA3 Escherichia coli strain demonstrated that the gene product functionally complements the missing AP endonuclease activity. Thus, in apn1 cells where the major AP endonuclease activity is missing, ETH1 offers an alternate capacity for repair of spontaneous or induced damage to DNA that is normally repaired by Apn1 protein. PMID:10022867

Carbon Monoxide, Hydrogen, and Formate Metabolism during Methanogenesis from Acetate by Thermophilic Cultures of Methanosarcina and Methanothrix Strains.

PubMed

Zinder, S H; Anguish, T

1992-10-01

CO and H(2) have been implicated in methanogenesis from acetate, but it is unclear whether they are directly involved in methanogenesis or electron transfer in acetotrophic methanogens. We compared metabolism of H(2), CO, and formate by cultures of the thermophilic acetotrophic methanogens Methanosarcina thermophila TM-1 and Methanothrix sp. strain CALS-1. M. thermophila accumulated H(2) to partial pressures of 40 to 70 Pa (1 Pa = 0.987 x 10 atm), as has been previously reported for this and other Methanosarcina cultures. In contrast, Methanothrix sp. strain CALS-1 accumulated H(2) to maximum partial pressures near 1 Pa. Growing cultures of Methanothrix sp. strain CALS-1 initially accumulated CO, which reached partial pressures near 0.6 Pa (some CO came from the rubber stopper) during the middle of methanogenesis; this was followed by a decrease in CO partial pressures to less than 0.01 Pa by the end of methanogenesis. Accumulation or consumption of CO by cultures of M. thermophila growing on acetate was not detected. Late-exponential-phase cultures of Methanothrix sp. strain CALS-1, in which the CO partial pressure was decreased by flushing with N(2)-CO(2), accumulated CO to 0.16 Pa, whereas cultures to which ca. 0.5 Pa of CO was added consumed CO until it reached this partial pressure. Cyanide (1 mM) blocked CO consumption but not production. High partial pressures of H(2) (40 kPa) inhibited methanogenesis from acetate by M. thermophila but not by Methanothrix sp. strain CALS-1, and 2 kPa of CO was not inhibitory to M. thermophila but was inhibitory to Methanothrix sp. strain CALS-1. Levels of CO dehydrogenase, hydrogenase, and formate dehydrogenase in Methanothrix sp. strain CALS-1 were 9.1, 0.045, and 5.8 mumol of viologen reduced min mg of protein. These results suggest that CO plays a role in Methanothrix sp. strain CALS-1 similar to that of H(2) in M. thermophila and are consistent with the conclusion that CO is an intermediate in a catabolic or anabolic pathway in Methanothrix sp. strain CALS-1; however, they could also be explained by passive equilibration of CO with a metabolic intermediate.

Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern.

PubMed

León, María José; Rodríguez-Olmos, Angel; Sánchez-Porro, Cristina; López-Pérez, Mario; Rodríguez-Valera, Francisco; Soliveri, Juan; Ventosa, Antonio; Copa-Patiño, José Luis

2015-12-01

A novel pink-pigmented bacterial strain, UAH-SP71T, was isolated from a saltern located in Santa Pola, Alicante (Spain) and the complete genome sequence was analysed and compared with that of Spiribacter salinus M19-40T, suggesting that the two strains constituted two separate species, with a 77.3% ANI value. In this paper, strain UAH-SP71T was investigated in a taxonomic study using a polyphasic approach. Strain UAH-SP71T was a Gram-stain-negative, strictly aerobic, non-motile curved rod that grew in media containing 5-20% (w/v) NaCl (optimum 10% NaCl), at 5-40 °C (optimum 37 °C) and at pH 5-10 (optimum pH 8). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed thatstrain UAH-SP71T is a member of the genus Spiribacter, showing a sequence similarity of 96.5% with Spiribacter salinus M19-40T. Other related species are also members of the family Ectothiorhodospiraceae, including Arhodomonas recens RS91T (95.5% 16S rRNA gene sequence similarity), Arhodomonas aquaeolei ATCC 49307T (95.4 %) and Alkalilimnicola ehrlichii MLHE-1T (94.9 %). DNA-DNA hybridization between strain UAH-SP71T and Spiribacter salinus M19-40T was 39 %. The major cellular fatty acids of strain UAH-SP71T were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c, C10 : 0 3-OH and C12 : 0, a pattern similar to that of Spiribacter salinus M19-40T. Phylogenetic, phenotypic and genotypic differences between strain UAH-SP71T and Spiribacter salinus M19-40T indicate that strainUAH-SP71T represents a novel species of the genus Spiribacter, for which the name Spiribacter curvatus sp. nov. is proposed. The type strain is UAH-SP71T (5CECT8396T5DSM 28542T).

Isolation and evaluation of potent Pseudomonas species for bioremediation of phorate in amended soil.

PubMed

Jariyal, Monu; Gupta, V K; Jindal, Vikas; Mandal, Kousik

2015-12-01

Use of phorate as a broad spectrum pesticide in agricultural crops is finding disfavor due to persistence of both the principal compound as well as its toxic residues in soil. Three phorate utilizing bacterial species (Pseudomonas sp. strain Imbl 4.3, Pseudomonas sp. strain Imbl 5.1, Pseudomonas sp. strain Imbl 5.2) were isolated from field soils. Comparative phorate degradation analysis of these species in liquid cultures identified Pseudomonas sp. strain Imbl 5.1 to cause complete metabolization of phorate during seven days as compared to the other two species in 13 days. In soils amended with phorate at different levels (100, 200, 300 mg kg(-1) soil), Pseudomonas sp. strain Imbl 5.1 resulted in active metabolization of phorate by between 94.66% and 95.62% establishing the same to be a potent bacterium for significantly relieving soil from phorate residues. Metabolization of phorate to these phorate residues did not follow the first order kinetics. This study proves that Pseudomonas sp. strain Imbl 5.1 has huge potential for active bioremediation of phorate both in liquid cultures and agricultural soils. Copyright © 2015 Elsevier Inc. All rights reserved.

Draft genome sequence of Pseudomonas sp. strain M47T1, carried by Bursaphelenchus xylophilus isolated from Pinus pinaster.

PubMed

Proença, Diogo Neves; Espírito Santo, Christophe; Grass, Gregor; Morais, Paula V

2012-09-01

The draft genome sequence of Pseudomonas sp. strain M47T1, carried by the Bursaphelenchus xylophilus pinewood nematode, the causative agent of pine wilt disease, is presented. In Pseudomonas sp. strain M47T1, genes that make this a plant growth-promoting bacterium, as well as genes potentially involved in nematotoxicity, were identified.

Mobile chemical detector (AP2C+SP4E) as an aid for medical decision making in the battlefield.

PubMed

Eisenkraft, Arik; Markel, Gal; Simovich, Shirley; Layish, Ido; Hoffman, Azik; Finkelstein, Arseny; Rotman, Eran; Dushnitsky, Tsvika; Krivoy, Amir

2007-09-01

The combination of the AP2C unit with the SP4E kit composes a lightweight mobile detector of chemical warfare agents (CWA), such as nerve and mustard agents, with both vapor- and liquid-sampling capabilities. This apparatus was recently introduced into our military medical units as an aid for detection of CWA on casualties. Importantly, critical information regarding the applicability in the battlefield was absent. In view of the serious consequences that might follow a proclamation of CWA recognition in battlefield, a high false-positive rate positions the utilization of this apparatus as a medical decision tool in question. We have therefore conducted a field experiment to test the false-positive rate as well as analyze possible factors leading to false-positive readings with this device. The experiment was carried out before and after a 4-day army field exercise, using a standard AP2C device, a SP4E surface sampling kit, and a specially designed medical sampling kit for casualties, intended for medical teams. Soldiers were examined at rest, after mild exercise, and after 4 days in the field. The readings with AP2C alone were compared to the combination of AP2C and SP4E and to the medical sampling kit. Various body fluids served as negative controls. Remarkably, we found a false-positive rate of 57% at rest and after mild exercise, and an even higher rate of 64% after the 4-day field exercise with the AP2C detector alone, as compared to almost no false-positive readings with the combination of AP2C and SP4E. Strikingly, the medical sampling kit has yielded numerous false-positive readings, even in normal body fluids such as blood, urine, and saliva. We therefore see no place for using the medical sampling kit due to an unaccepted high rate of false-positive readings. Finally, we have designed an algorithm that uses the entire apparatus of AP2C and SP4E as a reliable validation tool for medical triage in the setting of exposure to nerve agents in the battlefield.

Bifidobacterium reuteri sp. nov., Bifidobacterium callitrichos sp. nov., Bifidobacterium saguini sp. nov., Bifidobacterium stellenboschense sp. nov. and Bifidobacterium biavatii sp. nov. isolated from faeces of common marmoset (Callithrix jacchus) and red-handed tamarin (Saguinus midas).

PubMed

Endo, Akihito; Futagawa-Endo, Yuka; Schumann, Peter; Pukall, Rüdiger; Dicks, Leon M T

2012-03-01

Five strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic group of the genus Bifidobacterium but did not show high sequence similarities between the isolates and to known species in the genus by phylogenetic analysis based on 16S rRNA gene sequences. Sequence analyses of dnaJ1 and hsp60 also indicated their independent phylogenetic positions to each other in the Bifidobacterium cluster. DNA G+C contents of the species ranged from 57.3 to 66.3 mol%, which is within the values recorded for Bifidobacterium species. All isolates showed fructose-6-phosphate phosphoketolase activity. Based on the data provided, the five isolates represent five novel species, for which the names Bifidobacterium reuteri sp. nov. (type strain: AFB22-1(T) = JCM 17295(T) = DSM 23975(T)), Bifidobacterium callitrichos sp. nov. (type strain: AFB22-5(T) = JCM 17296(T) = DSM 23973(T)), Bifidobacterium saguini sp. nov. (type strain: AFB23-1(T) = JCM 17297(T) = DSM 23967(T)), Bifidobacterium stellenboschense sp. nov. (type strain: AFB23-3(T) = JCM 17298(T) = DSM 23968(T)) and Bifidobacterium biavatii sp. nov. (type strain: AFB23-4(T) = JCM 17299(T) = DSM 23969(T)) are proposed. Copyright © 2011 Elsevier GmbH. All rights reserved.

Candida asparagi sp. nov., Candida diospyri sp. nov. and Candida qinlingensis sp. nov., novel anamorphic, ascomycetous yeast species.

PubMed

Lu, Hui-Zhong; Jia, Jian-Hua; Wang, Qi-Ming; Bai, Feng-Yan

2004-07-01

Among ascomycetous yeasts that were isolated from several nature reserve areas in China, three anamorphic strains isolated from soil (QL 5-5T) and fruit (QL 21-2T and SN 15-1T) were revealed, by conventional characterization and molecular phylogenetic analysis based on internal transcribed spacer and large subunit (26S) rRNA gene D1/D2 region sequencing, to represent three novel species in the genus Candida. Candida qinlingensis sp. nov. (type strain, QL 5-5T=AS 2.2524T=CBS 9768T) was related closely to a teleomorphic species, Williopsis pratensis. The close relatives of Candida diospyri sp. nov. (type strain, QL 21-2T=AS 2.2525T=CBS 9769T) are Candida friedrichii and Candida membranifaciens. Candida asparagi sp. nov. (type strain, SN 15-1T=AS 2.2526T=CBS 9770T) forms a clade with Candida fructus.

Comparison of Thraustochytrids Aurantiochytrium sp., Schizochytrium sp., Thraustochytrium sp., and Ulkenia sp. for production of biodiesel, long-chain omega-3 oils, and exopolysaccharide.

PubMed

Lee Chang, Kim Jye; Nichols, Carol Mancuso; Blackburn, Susan I; Dunstan, Graeme A; Koutoulis, Anthony; Nichols, Peter D

2014-08-01

Heterotrophic growth of thraustochytrids has potential in coproducing biodiesel for transportation, as well as producing a feedstock for omega-3 long-chain (≥C20) polyunsaturated fatty acids (LC-PUFA), especially docosahexaenoic acid (DHA) for use in nutraceuticals. In this study, we compared eight new endemic Australian thraustochytrid strains from the genera Aurantiochytrium, Schizochytrium, Thraustochytrium, and Ulkenia for the synthesis of exopolysaccharide (EPS), in addition to biodiesel and LC-PUFA. Aurantiochytrium sp. strains readily utilized glucose for biomass production, and increasing glucose from 2 to 4 % w/v of the culture medium resulted in increased biomass yield by an average factor of 1.7. Ulkenia sp. strain TC 010 and Thraustochytrium sp. strain TC 033 did not utilize glucose, while Schizochytrium sp. strain TC 002 utilized less than half the glucose available by day 14, and Thraustochytrium sp. strain TC 004 utilized glucose at 4 % w/v but not 2 % w/v of the culture suggesting a threshold requirement between these values. Across all strains, increasing glucose from 2 to 4 % w/v of the culture medium resulted in increased total fatty acid methyl ester content by an average factor of 1.9. Despite an increasing literature demonstrating the capacity of thraustochytrids for DHA synthesis, the production of EPS from these organisms is not well documented. A broad range of EPS yields was observed. The maximum yield of EPS was observed for Schizochytrium sp. strain TC 002 (299 mg/L). High biomass-producing strains that also have high lipid and high EPS yield may be better candidates for commercial production of biofuels and other coproducts.

Three anamorphic yeast species Candida sanitii sp. nov., Candida sekii sp. nov. and Candida suwanaritii, three novel yeasts in the Saturnispora clade isolated in Thailand.

PubMed

Limtong, Savitree; Kaewwichian, Rungluk; Am-In, Somjit; Boonmak, Chanita; Jindamorakot, Sasitorn; Yongmanitchai, Wichien; Srisuk, Natana; Kawasaki, Hiroko; Nakase, Takashi

2010-02-01

Nine strains of three novel anamorphic yeast species were obtained from samples collected in Thailand including six strains (RV96, RV152, R14, RS9, RS58 and EA1) obtained from estuarine waters collected from two mangrove forests, one strain (ST84) from insect frass and two strains (SR16 and UB13) from forest soils. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analysis of the D1/D2 domain of the large subunit rRNA gene, the nine strains were found to represent three novel Candida species in the Saturnispora clade. Five strains (RV96, RV152, R14, RS9 and RS58) were assigned as a single novel species, which was named Candida sanitii sp. nov. The type strain is RV152(T) (BCC 25967(T)=NBRC 103864(T)=CBS 10864(T)). Strain EA1 was named as Candida suwanaritii sp. nov. The type strain is EA1(T) (BCC 29900(T)=NBRC 104877(T)=CBS 11021(T)). Three strains (ST84, SR16 and UB13) represented another novel species, for which Candida sekii sp. nov. is proposed. The type strain is ST84(T) (BCC 8320(T)=NBRC 105671(T)=CBS 10931(T)).

Torulaspora quercuum sp. nov. and Candida pseudohumilis sp. nov., novel yeasts from human and forest habitats.

PubMed

Wang, Qi-Ming; Xu, Jianping; Wang, Huamin; Li, Juan; Bai, Feng-Yan

2009-12-01

Strains XZ-46A, XZ-105, XZ-129 and XZ-281(T) isolated from the oral cavities of healthy Tibetan volunteers were revealed to represent two novel ascomycetous yeast species by molecular taxonomic characterizations. Strain XZ-281(T) was most closely related to Candida humilis, but differed from the type strain of the species by eight (1.2%) substitutions in the 26S rRNA gene D1/D2 domain and by >100 (>20%) mismatches in the internal transcribed spacer (ITS) region. Strains XZ-46A, XZ-105 and XZ-129 had identical or similar D1/D2 and ITS sequences with each other and with strain 17YF(T) isolated from a leaf of an oak tree (Quercus sp.). The closest relative of this group was Torulaspora microellipsoides. They differed from the type strain of the species by five (0.9%) substitutions in the D1/D2 domain and >70 (>15%) mismatches in the ITS region. A sexual state was observed in strain 17YF(T), but not in the other four oral strains. An anamorphic name Candida pseudohumilis sp. nov. is proposed for strain XZ-281(T) (=AS 2.3956(T)=CBS 11404(T)) and a teleomorphic name Torulaspora quercuum sp. nov. is proposed for strain 17YF(T) (=AS 2.3768(T)=CBS 11403(T)) and the other three oral strains.

The Microwave Spectrum of Methyl Vinyl Ketone Revisited

NASA Astrophysics Data System (ADS)

Wilcox, David S.; Shirar, Amanda J.; Williams, Owen L.; Dian, Brian C.

2011-06-01

A chirped-pulse Fourier transform microwave spectrometer was used to record the rotational spectrum of methyl vinyl ketone (MVK, 3-butene-2-one) from 6 to 18.9 GHz. Two stable conformations were identified: the previously documented antiperiplanar (ap) conformer and synperiplanar (sp), which is reported for the first time in this microwave study. Methyl torsional analysis with XIAM resulted in V3 barrier heights of 433.8(1) and 376.6(2) Cm-1 for ap- and sp-MVK, respectively. Heavy atom isotopic species were detected in natural abundance allowing bond lengths and angles of the molecular frames to be calculated through Kraitchman analysis. A comparison with ab initio calculations is included.

Three novel species of d-xylose-assimilating yeasts, Barnettozyma xylosiphila sp. nov., Barnettozyma xylosica sp. nov. and Wickerhamomyces xylosivorus f.a., sp. nov.

PubMed

Kobayashi, Ryuichi; Kanti, Atit; Kawasaki, Hiroko

2017-10-01

This study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces. The morphological, biochemical and physiological characteristics indicated that the strains were distinct from other closely related species. Strains 13Y206 T and 14Y196 T belonging to the Barnettozyma clade are described as the type strains of Barnettozyma xylosiphila sp. nov. (type strain 13Y206 T =NBRC 110202 T =InaCC Y726 T ; MycoBank MB808598) and Barnettozyma xylosica sp. nov. (type strain 14Y196 T =NBRC 111558 T =InaCC Y1030 T ; MycoBank MB819485). Strain 14Y125 T belonging to the Wickerhamomyces clade is described as the type strain of Wickerhamomyces xylosivorus f.a., sp. nov. (type strain 14Y125 T =NBRC 111553 T =InaCC Y1026 T ; MycoBank MB819484).

Molecular profiles of Venezuelan isolates of Trypanosoma sp. by random amplified polymorphic DNA method.

PubMed

Perrone, T M; Gonzatti, M I; Villamizar, G; Escalante, A; Aso, P M

2009-05-12

Nine Trypanosoma sp. Venezuelan isolates, initially presumed to be T. evansi, were collected from three different hosts, capybara (Apure state), horse (Apure state) and donkey (Guarico state) and compared by the random amplification polymorphic DNA technique (RAPD). Thirty-one to 46 reproducible fragments were obtained with 12 of the 40 primers that were used. Most of the primers detected molecular profiles with few polymorphisms between the seven horse, capybara and donkey isolates. Quantitative analyses of the RAPD profiles of these isolates revealed a high degree of genetic conservation with similarity coefficients between 85.7% and 98.5%. Ten of the primers generated polymorphic RAPD profiles with two of the three Trypanosoma sp. horse isolates, namely TeAp-N/D1 and TeGu-N/D1. The similarity coefficient between these two isolates and the rest, ranged from 57.9% to 68.4% and the corresponding dendrogram clustered TeAp-N/D1 and Te Gu-N/D1 in a genetically distinct group.

Identification and characterization of Vibrio harveyi associated with diseased abalone Haliotis diversicolor.

PubMed

Jiang, Qingru; Shi, Liuyang; Ke, Caihuan; You, Weiwei; Zhao, Jing

2013-03-26

Mass mortality of farmed small abalone Haliotis diversicolor occurred in Fujian, China, from 2009 to 2011. Among isolates obtained from moribund abalones, the dominant species AP37 exhibited the strongest virulence. After immersion challenge with 106 CFU ml-1 of AP37, abalone mortalities of 0, 53 and 67% were induced at water temperatures of 20°C, 24°C, and 28°C, respectively. Following intramuscular injection, AP37 showed a low LD50 (median lethal concentration) value of 2.9 × 102 CFU g-1 (colony forming units per gram abalone wet body weight). The LT50 (median lethal time) values were 5.2 h for 1 × 106 CFU abalone-1, 8.4 h for 1 × 105 CFU abalone-1, and 21.5 h for 1 × 104 CFU abalone-1. For further analysis of virulence, AP37 was screened for the production of extracellular factors. The results showed that various factors including presence of flagella and production of extracellular enzymes, such as lipase, phospholipase and haemolysin, could be responsible for pathogenesis. Based on its 16S rRNA gene sequence, strain AP37 showed >98.8% similarity to Vibrio harveyi, V. campbellii, V. parahaemolyticus, V. alginolyticus, V. natriegens and V. rotiferianus, so it could not be identified by this method. However, multi-locus sequence analysis (MLSA) of concatenated sequences, including the rpoD, rctB, gyrB, toxR and pyrH genes, identified strain AP37 as V. harveyi. Phenotypic characters of AP37 were identified by API 20E. In antibiotic susceptibility tests, strain AP37 exhibited susceptibility to 7 antibiotics and resistance to 13. This is the first report of a V. harveyi-related species being linked with the mass mortality of adult abalone H. diversicolor in southern China.

In-planta Sporulation Capacity Enhances Infectivity and Rhizospheric Competitiveness of Frankia Strains.

PubMed

Cotin-Galvan, Laetitia; Pozzi, Adrien C; Schwob, Guillaume; Fournier, Pascale; Fernandez, Maria P; Herrera-Belaroussi, Aude

2016-01-01

Frankia Sp+ strains maintain their ability to sporulate in symbiosis with actinorhizal plants, producing abundant sporangia inside host plant cells, in contrast to Sp- strains, which are unable to perform in-planta sporulation. We herein examined the role of in-planta sporulation in Frankia infectivity and competitiveness for root infection. Fifteen strains belonging to different Sp+ and Sp- phylogenetic lineages were inoculated on seedlings of Alnus glutinosa (Ag) and A. incana (Ai). Strain competitiveness was investigated by performing Sp-/Sp+ co-inoculations. Plant inoculations were standardized using crushed nodules obtained under laboratory-controlled conditions (same plant species, age, and environmental factors). Specific oligonucleotide primers were developed to identify Frankia Sp+ and/or Sp- strains in the resulting nodules. Single inoculation experiments showed that (i) infectivity by Sp+ strains was significantly greater than that by Sp- strains, (ii) genetically divergent Sp+ strains exhibited different infective abilities, and (iii) Sp+ and Sp- strains showed different host preferences according to the origin (host species) of the inocula. Co-inoculations of Sp+ and Sp- strains revealed the greater competitiveness of Sp+ strains (98.3 to 100% of Sp+ nodules, with up to 15.6% nodules containing both Sp+ and Sp- strains). The results of the present study highlight differences in Sp+/Sp- strain ecological behaviors and provide new insights to strengthen the obligate symbiont hypothesis for Sp+ strains.

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

DOE PAGES

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui; ...

2015-06-04

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agriculturalmore » relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.« less

High-quality permanent draft genome sequence of the Parapiptadenia rigida-nodulating Burkholderia sp. strain UYPR1.413

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Fabiano, Elena; Tian, Rui

We report that Burkholderia sp. strain UYPR1.413 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Parapiptadenia rigida collected at the Angico plantation, Mandiyu, Uruguay, in December 2006. A survey of symbionts of P. rigida in Uruguay demonstrated that this species is nodulated predominantly by Burkholderia microsymbionts. Moreover, Burkholderia sp. strain UYPR1.413 is a highly efficient nitrogen fixing symbiont with this host. Currently, the only other sequenced isolate to fix with this host is Cupriavidus sp. UYPR2.512. Therefore, Burkholderia sp. strain UYPR1.413 was selected for sequencing on the basis of its environmental and agriculturalmore » relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the GEBA-RNB project. Here we describe the features of Burkholderia sp. strain UYPR1.413, together with sequence and annotation. The 10,373,764 bp high-quality permanent draft genome is arranged in 336 scaffolds of 342 contigs, contains 9759 protein-coding genes and 77 RNA-only encoding genes.« less

Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria)

PubMed Central

Koenigsaecker, Tynisha M.; Coil, David A.

2016-01-01

Here, we present the draft genome of Gordonia sp. strain UCD-TK1. The assembly contains 5,470,576 bp in 98 contigs. This strain was isolated from a disinfected ambulatory surgery center. PMID:27738036

Molecular characterization of hot spring cyanobacteria and evaluation of their photoprotective compounds.

PubMed

Rastogi, Rajesh P; Kumari, Sunita; Richa; Han, Taejun; Sinha, Rajeshwar P

2012-06-01

Phylogenetic analysis of 4 cyanobacterial strains isolated from hot springs in Rajgir, India, was carried out using the 16S rRNA gene (1400 bp). These strains were identified as members of Chroococcales ( Cyanothece sp. strain HKAR-1) and Nostocales ( Nostoc sp. strain HKAR-2, Scytonema sp. strain HKAR-3, and Rivularia sp. strain HKAR-4). Furthermore, we evaluated the presence of ultraviolet-screening and (or) photoprotective compounds, such as mycosporine-like amino acids (MAAs) and scytonemin, in these cyanobacteria by using high-performance liquid chromatography. Well-characterized MAAs, including the critical and highly polar compounds shinorine, porphyra-334, and mycosporine-glycine, as well as several unknown MAAs, were found in these hot-spring-inhabiting microorganisms. The presence of scytonemin was detected only in Scytonema sp. strain HKAR-3 and Rivularia sp. strain HKAR-4. The results indicate that hot spring cyanobacteria, namely Cyanothece, Nostoc, Scytonema, and Rivularia, belonging to different groups possess various photoprotective compounds to cope up with the negative impacts of damaging radiations.

Aerosol optical properties at SORPES in Nanjing, east China

NASA Astrophysics Data System (ADS)

Shen, Yicheng; Virkkula, Aki; Ding, Aijun; Wang, Jiaping; Chi, Xuguang; Nie, Wei; Qi, Ximeng; Huang, Xin; Liu, Qiang; Zheng, Longfei; Xu, Zheng; Petäjä, Tuukka; Aalto, Pasi P.; Fu, Congbin; Kulmala, Markku

2018-04-01

Aerosol optical properties (AOPs) and supporting parameters - particle number size distributions, PM2.5 mass concentrations, and the concentrations of trace gases (NOx and NOy) - were measured at SORPES, a regional background station in Nanjing, China from June 2013 to May 2015. The aerosol was highly scattering: the average scattering coefficient was σsp = 403 ± 314 Mm-1, the absorption coefficient σap = 26 ± 19 Mm-1, and the single-scattering albedo SSA = 0.93 ± 0.03 for green light. The SSA in Nanjing appears to be slightly higher than published values from several other sites in China and elsewhere. The average Ångström exponent of absorption (AAE) for the wavelength range 370-950 nm was 1.04 and the AAE range was 0.7-1.4. These AAE values can be explained with different amounts of non-absorbing coating on pure black carbon (BC) cores and different core sizes rather than contribution by brown carbon. The AOPs had typical seasonal cycles with high σsp and σap in winter and low ones in summer: the averages were σsp = 544 ± 422 and σap = 36 ± 24 Mm-1 in winter and σsp = 342 ± 281 and σap = 20 ± 13 Mm-1 in summer. The intensive AOPs had no clear seasonal cycles, the variations in them were rather related to the evolution of pollution episodes. The diurnal cycles of the intensive AOPs were clear and in agreement with the cycle of the particle number size distribution. The diurnal cycle of SSA was similar to that of the air photochemical age, suggesting that the darkest aerosol originated from fresh traffic emissions. A Lagrangian retroplume analysis showed that the potential source areas of high σsp and σap are mainly in eastern China. Synoptic weather phenomena dominated the cycle of AOPs on a temporal scale of 3-7 days. During pollution episodes, modeled boundary layer height decreased, whereas PM2.5 concentrations and σsp and σap typically increased gradually and remained high during several days but decreased faster, sometimes by even more than an order of magnitude within some hours. During the growth phase of the pollution episodes the intensive AOPs evolved clearly. The mass scattering efficiency MSE of PM2.5 grew during the extended pollution episodes from ˜ 4 to ˜ 6 m2 g-1 and the mass fraction of BCe decreased from ˜ 10 to ˜ 3 % during the growth phase of the episodes. Particle growth resulted in the backscatter fraction decreasing from more than 0.16 to less than 0.10, SSA growing from less than 0.9 to more than 0.95, and radiative forcing efficiency (RFE) changing from less than -26 W m-2 to more than -24 W m-2, which means that the magnitude of RFE decreased. The RFE probability distribution at SORPES was clearly narrower than at a clean background site which is in agreement with a published RFE climatology.

Draft Whole-Genome Sequence of Serratia sp. Strain TEL, Associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae) Isolated from a Grassland in South Africa.

PubMed

Lephoto, Tiisetso E; Featherston, Jonathan; Gray, Vincent M

2015-07-09

Here, we report on the draft genome sequence of Serratia sp. strain TEL, associated with Oscheius sp. TEL-2014 (Nematoda: Rhabditidae, KM492926) isolated from a grassland in Suikerbosrand Nature Reserve near Johannesburg in South Africa. Serratia sp. strain TEL has a genome size of 5,000,541 bp with 4,647 genes and a G+C content of 59.1%. Copyright © 2015 Lephoto et al.

Candida alocasiicola sp. nov., Candida hainanensis sp. nov., Candida heveicola sp. nov. and Candida musiphila sp. nov., novel anamorphic, ascomycetous yeast species isolated from plants.

PubMed

Wang, Shi-An; Jia, Jian-Hua; Bai, Feng-Yan

2008-08-01

In a taxonomic study on the ascomycetous yeasts isolated from plant materials collected in tropical forests in Yunnan and Hainan Provinces, southern China, four strains isolated from tree sap (YJ2E(T)) and flowers (YF9E(T), YWZH3C(T) and YYF2A(T)) were revealed to represent four undescribed yeast species. Molecular phylogenetic analysis based on the large subunit (26S) rRNA gene D1/D2 domain sequences showed that strain YJ2E(T) was located in a clade together with Candida haemulonii and C. pseudohaemulonii. Strain YF9E(T) was most closely related to C. azyma and strain YWZH3C(T) to C. sorbophila and C. spandovensis. Strain YYF2A(T) was clustered in a clade containing small-spored Metschnikowia species and related anamorphic Candida species. The new strains differed from their closely related described species by more than 10% mismatches in the D1/D2 domain. No sexual states were observed for the four strains on various sporulation media. The new species are therefore assigned to the genus Candida and described as Candida alocasiicola sp. nov. (type strain, YF9E(T) = AS 2.3484(T) = CBS 10702(T)), Candida hainanensis sp. nov. (type strain, YYF2A(T) = AS 2.3478(T) = CBS 10696(T)), Candida heveicola sp. nov. (type strain, YJ2E(T) = AS 2.3483(T) = CBS 10701(T)) and Candida musiphila sp. nov. (type strain, YWZH3C(T) = AS 2.3479(T) = CBS 10697(T)).

Bioremediation of heavy metal-contaminated effluent using optimized activated sludge bacteria

NASA Astrophysics Data System (ADS)

Bestawy, Ebtesam El.; Helmy, Shacker; Hussien, Hany; Fahmy, Mohamed; Amer, Ranya

2013-03-01

Removal of heavy metals from contaminated domestic-industrial effluent using eight resistant indigenous bacteria isolated from acclimatized activated sludge was investigated. Molecular identification using 16S rDNA amplification revealed that all strains were Gram-negative among which two were resistant to each of copper, cadmium and cobalt while one was resistant to each of chromium and the heavy metal mixture. They were identified as Enterobacter sp. (Cu1), Enterobacter sp. (Cu2), Stenotrophomonas sp. (Cd1), Providencia sp. (Cd2), Chryseobacterium sp. (Co1), Comamonas sp. (Co2), Ochrobactrum sp. (Cr) and Delftia sp. (M1) according to their resistance pattern. Strains Cu1, Cd1, Co2 and Cr were able to resist 275 mg Cu/l, 320 mg Cd/l, 140 mg Co/l and 29 mg Cr/l respectively. The four resistant strains were used as a mixture to remove heavy metals (elevated concentrations) and reduce the organic load of wastewater effluent. Results revealed that using the proposed activated sludge with the resistant bacterial mixture was more efficient for heavy metal removal compared to the activated sludge alone. It is therefore recommended that the proposed activated sludge system augmented with the acclimatized strains is the best choice to ensure high treatment efficiency and performance under metal stresses especially when industrial effluents are involved.

Streptomyces sp. ASBV-1 reduces aflatoxin accumulation by Aspergillus parasiticus in peanut grains.

PubMed

Zucchi, T D; de Moraes, L A B; de Melo, I S

2008-12-01

To evaluate the ability of Streptomyces sp. (strain ASBV-1) to restrict aflatoxin accumulation in peanut grains. In the control of many phytopathogenic fungi the Streptomyces sp. ASBV-1 strain showed promise. An inhibitory test using this strain and A. parasiticus was conducted in peanut grains to evaluate the effects of this interaction on spore viability and aflatoxin accumulation. In some treatments the Streptomyces sp ASBV-1 strain reduced the viability of A. parasiticus spores by c. 85%, and inhibited aflatoxin accumulation in peanut grains. The values of these reductions ranged from 63 to 98% and from 67% to 96% for aflatoxins B(1) and G(1), respectively. It was demonstrated that Streptomyces sp. ASBV-1 is able to colonize peanut grains and thus inhibit the spore viability of A. parasiticus, as well as reducing aflatoxin production. The positive finding for aflatoxin accumulation reduction in peanut grains seems promising and suggests a wider use of this actinobacteria in biological control programmes.

Human acylphosphatase cannot replace phosphoglycerate kinase in Saccharomyces cerevisiae.

PubMed

Van Hoek, P; Modesti, A; Ramponi, G; Kötter, P; van Dijken, J P; Pron, J T

2001-10-01

Human acylphosphatase (h-AP, EC 3.6.1.7) has been reported to catalyse the hydrolysis of the 1-phosphate group of 1,3-diphosphoglycerate. In vivo operation of this reaction in the yeast Saccharomyces cerevisiae would bypass phosphoglycerate kinase and thus reduce the ATP yield from glycolysis. To investigate whether h-AP can indeed replace the S. cerevisiae phosphoglycerate kinase, a multi-copy plasmid carrying the h-AP gene under control of the yeast TDH3 promoter was introduced into a pgk1 delta mutant of S. cerevisiae. A strain carrying the expression vector without the h-AP cassette was used as a reference. For both strains, steady-state carbon- and energy-limited chemostat cultures were obtained at a dilution rate of 0.10 h(-1) on a medium containing a mixture of glucose and ethanol (15% and 85% on a carbon basis, respectively). Although the h-AP strain exhibited a high acylphosphatase activity in cell extracts, switching to glucose as sole carbon and energy source resulted in a complete arrest of glucose consumption and growth. The lack of a functional glycolytic pathway was further evident from the absence of ethanol formation in the presence of excess glucose in the culture. As h-AP cannot replace yeast phosphoglycerate kinase in vivo, the enzyme is not a useful tool to modify the ATP yield of glycolysis in S. cerevisiae.

Complete Genome Sequence of the Diesel-Degrading Acinetobacter sp. Strain DR1 ▿

PubMed Central

Jung, Jaejoon; Baek, Jeong-Hun; Park, Woojun

2010-01-01

The genus Acinetobacter is ubiquitous in soil, aquatic, and sediment environments and includes pathogenic strains, such as A. baumannii. Many Acinetobacter species isolated from various environments have biotechnological potential since they are capable of degrading a variety of pollutants. Acinetobacter sp. strain DR1 has been identified as a diesel degrader. Here we report the complete genome sequence of Acinetobacter sp. DR1 isolated from the soil of a rice paddy. PMID:20639327

Biodegradation of phthalate esters by newly isolated Rhizobium sp. LMB-1 and its biochemical pathway of di-n-butyl phthalate.

PubMed

Tang, W-J; Zhang, L-S; Fang, Y; Zhou, Y; Ye, B-C

2016-07-01

To isolate a novel strain that could degrade many kinds PAEs efficiently and investigate the DBP-degrading pathway in this strain. Based on its 16S rRNA gene sequence, the strain was identified as Rhizobium sp. This strain, named LMB-1, can also utilize phthalates, such as DEHP, DMP, DBP and DEP. During the degradation of DBP, six possible metabolites, diethyl phthalate, mono-ethyl phthalate, di-methyl phthalate, mono-methyl phthalate, phthalic acid and tartaric acid, were identified by gas chromatography-mass spectrometry (GC-MS) analysis, and the degradation pathway of DBP was also identified in this study. In summary, strain LMB-1, identified as Rhizobium sp., was found to be capable of efficiently degrading PAEs, and it was determined that the strain degraded DMP completely within 45 h. DEP, DMP, MEP, MMP, PA and tartaric acid were detected during the course of DBP degradation by LMB-1. We propose that this strain could completely degrade DBP or other PAEs. Our results offer a novel and potential candidate, Rhizobium sp. LMB-1, for use in the bioremediation of cultivated soil contaminated by PAEs. This is the first report concerning the complete degradation of phthalate esters by Rhizobium sp. © 2016 The Society for Applied Microbiology.

Isolation and complementation analysis of 10 methanol oxidation mutant classes and identification of the methanol dehydrogenase structural gene of Methylobacterium sp. strain AM1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nunn, D.N.; Lidstrom, M.E.

A method has been developed for the direct selection of methanol oxidation mutants of the facultative methylotroph Methylobacterium sp. strain AM1 (formerly Pseudomonas sp. strain AM1). Using this direct selection technique, we have isolated mutants of Methylobacterium sp. strain AM1 that are no longer capable of growth on methanol but retain the ability to grow on methylamine. These methanol oxidation (Mox) mutants were complemented with a genomic clone bank of this organism constructed in the broad-host-range cosmid pVK100, and subcloning and Tn5 mutagenesis experiments have assigned the Mox mutants to 10 distinct complementation groups. Using an open reading frame beta-galactosidasemore » fusion vector and antibodies specific for Methylobacterium sp. strain AM1 methanol dehydrogenase, we have identified the methanol dehydrogenase structural gene and determined the direction of transcription. The results suggest that the synthesis and utilization of an active methanol dehydrogenase in this organism requires at least 10 different gene functions.« less

Self-propulsion against a moving membrane: Enhanced accumulation and drag force

NASA Astrophysics Data System (ADS)

Marini Bettolo Marconi, U.; Sarracino, A.; Maggi, C.; Puglisi, A.

2017-09-01

Self-propulsion (SP) is a main feature of active particles (AP), such as bacteria or biological micromotors, distinguishing them from passive colloids. A renowned consequence of SP is accumulation at static interfaces, even in the absence of hydrodynamic interactions. Here we address the role of SP in the interaction between AP and a moving semipermeable membrane. In particular, we implement a model of noninteracting AP in a channel crossed by a partially penetrable wall, moving at a constant velocity c . With respect to both the cases of passive colloids with c >0 and AP with c =0 , the AP with finite c show enhancement of accumulation in front of the obstacle and experience a largely increased drag force. This effect is understood in terms of an effective potential localised at the interface between particles and membrane, of height proportional to c τ /ξ , where τ is the AP's reorientation time and ξ the width characterizing the surface's smoothness (ξ →0 for hard core obstacles). An approximate analytical scheme is able to reproduce the observed density profiles and the measured drag force, in very good agreement with numerical simulations. The effects discussed here can be exploited for automatic selection and filtering of AP with desired parameters.

Field and experimental evidence of Vibrio parahaemolyticus as the causative agent of acute hepatopancreatic necrosis disease of cultured shrimp (Litopenaeus vannamei) in Northwestern Mexico.

PubMed

Soto-Rodriguez, Sonia A; Gomez-Gil, Bruno; Lozano-Olvera, Rodolfo; Betancourt-Lozano, Miguel; Morales-Covarrubias, Maria Soledad

2015-03-01

Moribund shrimp affected by acute hepatopancreatic necrosis disease (AHPND) from farms in northwestern Mexico were sampled for bacteriological and histological analysis. Bacterial isolates were molecularly identified as Vibrio parahaemolyticus by the presence of the tlh gene. The tdh-negative, trh-negative, and tlh-positive V. parahaemolyticus strains were further characterized by repetitive extragenic palindromic element-PCR (rep-PCR), and primers AP1, AP2, AP3, and AP and an ems2 IQ2000 detection kit (GeneReach, Taiwan) were used in the diagnostic tests for AHPND. The V. parahaemolyticus strains were used in immersion challenges with shrimp, and farmed and challenged shrimp presented the same clinical and pathological symptoms: lethargy, empty gut, pale and aqueous hepatopancreas, and expanded chromatophores. Using histological analysis and bacterial density count, three stages of AHNPD (initial, acute, and terminal) were identified in the affected shrimp. The pathognomonic lesions indicating severe desquamation of tubular epithelial cells of the hepatopancreas were observed in both challenged and pond-infected shrimp. The results showed that different V. parahaemolyticus strains have different virulences; some of the less virulent strains do not induce 100% mortality, and mortality rates also rise more slowly than they do for the more virulent strains. The virulence of V. parahaemolyticus strains was dose dependent, where the threshold infective density was 10(4) CFU ml(-1); below that density, no mortality was observed. The AP3 primer set had the best sensitivity and specificity. Field and experimental results showed that the V. parahaemolyticus strain that causes AHPND acts as a primary pathogen for shrimp in Mexico compared with the V. parahaemolyticus strains reported to date. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Field and Experimental Evidence of Vibrio parahaemolyticus as the Causative Agent of Acute Hepatopancreatic Necrosis Disease of Cultured Shrimp (Litopenaeus vannamei) in Northwestern Mexico

PubMed Central

Gomez-Gil, Bruno; Lozano-Olvera, Rodolfo; Betancourt-Lozano, Miguel; Morales-Covarrubias, Maria Soledad

2014-01-01

Moribund shrimp affected by acute hepatopancreatic necrosis disease (AHPND) from farms in northwestern Mexico were sampled for bacteriological and histological analysis. Bacterial isolates were molecularly identified as Vibrio parahaemolyticus by the presence of the tlh gene. The tdh-negative, trh-negative, and tlh-positive V. parahaemolyticus strains were further characterized by repetitive extragenic palindromic element-PCR (rep-PCR), and primers AP1, AP2, AP3, and AP and an ems2 IQ2000 detection kit (GeneReach, Taiwan) were used in the diagnostic tests for AHPND. The V. parahaemolyticus strains were used in immersion challenges with shrimp, and farmed and challenged shrimp presented the same clinical and pathological symptoms: lethargy, empty gut, pale and aqueous hepatopancreas, and expanded chromatophores. Using histological analysis and bacterial density count, three stages of AHNPD (initial, acute, and terminal) were identified in the affected shrimp. The pathognomonic lesions indicating severe desquamation of tubular epithelial cells of the hepatopancreas were observed in both challenged and pond-infected shrimp. The results showed that different V. parahaemolyticus strains have different virulences; some of the less virulent strains do not induce 100% mortality, and mortality rates also rise more slowly than they do for the more virulent strains. The virulence of V. parahaemolyticus strains was dose dependent, where the threshold infective density was 104 CFU ml−1; below that density, no mortality was observed. The AP3 primer set had the best sensitivity and specificity. Field and experimental results showed that the V. parahaemolyticus strain that causes AHPND acts as a primary pathogen for shrimp in Mexico compared with the V. parahaemolyticus strains reported to date. PMID:25548045

Non contiguous-finished genome sequence and description of Peptoniphilus obesi sp. nov.

PubMed Central

Mishra, Ajay Kumar; Hugon, Perrine; Lagier, Jean-Christophe; Nguyen, Thi-Thien; Robert, Catherine; Couderc, Carine; Raoult, Didier

2013-01-01

Peptoniphilus obesi strain ph1T sp. nov., is the type strain of P. obesi sp. nov., a new species within the genus Peptoniphilus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. P. obesi strain ph1T is a Gram-positive, obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,774,150 bp long genome (1 chromosome but no plasmid) contains 1,689 protein-coding and 29 RNA genes, including 5 rRNA genes. PMID:24019985

Copper tolerance in Frankia sp. strain EuI1c involves surface binding and copper transport.

PubMed

Rehan, Medhat; Furnholm, Teal; Finethy, Ryan H; Chu, Feixia; El-Fadly, Gomaah; Tisa, Louis S

2014-09-01

Several Frankia strains have been shown to be copper-tolerant. The mechanism of their copper tolerance was investigated for Frankia sp. strain EuI1c. Copper binding was shown by binding studies. Unusual globular structures were observed on the surface of the bacterium. These globular structures were composed of aggregates containing many relatively smaller "leaf-like" structures. Scanning electron microscopy with energy-dispersive X-ray (SEM-EDAX) analysis of these structures indicated elevated copper and phosphate levels compared to the control cells. Fourier transform infrared spectroscopy (FTIR) analysis indicated an increase in extracellular phosphate on the cell surface of copper-stressed cells. Bioinformatics' analysis of the Frankia sp. strain EuI1c genome revealed five potential cop genes: copA, copZ, copC, copCD, and copD. Experiments with Frankia sp. strain EuI1c using qRT-PCR indicated an increase in messenger RNA (mRNA) levels of the five cop genes upon Cu(2+) stress. After 5 days of Cu(2+) stress, the copA, copZ, copC, copCD, and copD mRNA levels increased 25-, 8-, 18-, 18-, and 25-fold, respectively. The protein profile of Cu(2+)-stressed Frankia sp. strain EuI1c cells revealed the upregulation of a 36.7 kDa protein that was identified as FraEuI1c_1092 (sulfate-binding periplasmic transport protein). Homologues of this gene were only present in the genomes of the Cu(2+)-resistant Frankia strains (EuI1c, DC12, and CN3). These data indicate that copper tolerance by Frankia sp. strain EuI1c involved the binding of copper to the cell surface and transport proteins.

[Biofilm Formation by the Nonflagellated flhB1 Mutant of Azospirillum brasilense Sp245].

PubMed

Shelud'ko, A V; Filip'echeva, Yu A; Shumiliva, E M; Khlebtsov, B N; Burov, A M; Petrova, L P; Katsy, E I

2015-01-01

Azospirillum brasilense Sp245 with mixed flagellation are able to form biofilms on various surfaces. A nonflagellated mutant of this strain with inactivated chromosomal copy of the flhB gene (flhB1) was shown to exhibit specific traits at the later stages of biofilm formation on a hydrophilic (glass) surface. Mature biofilms of the flhB1::Omegon-Km mutant Sp245.1063 were considerably thinner than those of the parent strain Sp245. The biofilms of the mutant were more susceptible to the forces of hydrodynamic shear. A. brasilense Sp245 cells in biofilms were not found to possess lateral flagella. Cells with polar flagella were, however, revealed by atomic force microscopy of mature native biofilms of strain Sp245. Preservation of a polar flagellum (probably nonmotile) on the cells of A. brasilense Sp245 may enhance the biofilm stability.

Candida adriatica sp. nov. and Candida molendinolei sp. nov., two yeast species isolated from olive oil and its by-products.

PubMed

Čadež, Neža; Raspor, Peter; Turchetti, Benedetta; Cardinali, Gianluigi; Ciafardini, Gino; Veneziani, Gianluca; Péter, Gábor

2012-09-01

Thirteen strains isolated from virgin olive oil or its by-products in several Mediterranean countries were found to be phenotypically and genetically divergent from currently recognized yeast species. Sequence analysis of the large subunit (LSU) rDNA D1/D2 domain and internal transcribed spacer regions/5.8S rDNA revealed that the strains represented two novel species described as Candida adriatica sp. nov. (type strain ZIM 2334(T) = CBS 12504(T) = NCAIM Y.02001(T)) and Candida molendinolei sp. nov. (type strain DBVPG 5508(T) = CBS 12508(T) = NCAIM Y.02000(T)). Phylogenetic analysis based on concatenated sequences of the small subunit rRNA gene, the D1/D2 region of the LSU rDNA and the translation elongation factor-1α gene suggested that C. adriatica sp. nov. and C. molendinolei sp. nov. should be placed within the Lindnera and Nakazawaea clades, respectively.

Characterization and application of monoclonal antibodies against Shewanella marisflavi, a novel pathogen of Apostichopus japonicus

USDA-ARS?s Scientific Manuscript database

Shewanella marisflavi strain AP629 was certified as a novel pathogen of the sea cucumber Apostichopus japonicus. In this study, four monoclonal antibodies (MAbs) (3C1, 3D9, 2F2, 2A8) against strain AP629 were developed by immunizing Balb/C mice. 3C1 and 3D9 recognized S. marisflavi only, showing no ...

Benomyl Tolerance of Ten Fungi Antagonistic to Plant-parasitic Nematodes.

PubMed

Meyer, S L; Sayre, R M; Huettel, R N

1991-10-01

Ten strains of fungi were tested for tolerance to the fungicide benomyl. Verticillium chlamydosporium strain 2 did not grow in the presence of benomyl; Drechraeria coniospora strains 1 and 2 and Chaetomium sp. tolerated only 0.1 mug benomyl/ml medium; Acremonium bacillisporum, an unidentified fungus, and Phoma chrysanthemicola uniformly grew at 1 mug/ml, but some hyphae grew at higher benomyl concentrations; Fusarium sp. tolerated 475 mug/ml, but some hyphae grew on medium amended with 1,000 mug/ml; Verticillium lecanii and V. chlamydosporium strain 1 routinely tolerated 1,000 mug/ml. Fungi generally grew more slowly at higher than at lower benomyl concentrations. Strains with elevated tolerance to benomyl were selected from Acremonium bacillisporum, Drechmeria coniospora, Fusarium sp., and an unidentified fungus. These strains retained the increased tolerance after repeated transfers on unamended medium.

Isolation of Toxigenic Nocardiopsis Strains from Indoor Environments and Description of Two New Nocardiopsis Species, N. exhalans sp. nov. and N. umidischolae sp. nov.

PubMed Central

Peltola, Joanna S. P.; Andersson, Maria A.; Kämpfer, Peter; Auling, Georg; Kroppenstedt, Reiner M.; Busse, Hans-Jürgen; Salkinoja-Salonen, Mirja S.; Rainey, Frederick A.

2001-01-01

Nocardiopsis strains were isolated from water-damaged indoor environments. Two strains (N. alba subsp. alba 704a and a strain representing a novel species, ES10.1) as well as strains of N. prasina, N. lucentensis, and N. tropica produced methanol-soluble toxins that paralyzed the motility of boar spermatozoa at <30 μg of crude extract (dry weight) ml−1. N. prasina, N. lucentensis, N. tropica, and strain ES10.1 caused cessation of motility by dissipating the mitochondrial membrane potential, Δψ, of the boar spermatozoa. Indoor strain 704a produced a substance that destroyed cell membrane barrier function and depleted the sperm cells of ATP. Indoor strain 64/93 was antagonistic towards Corynebacterium renale. Two indoor Nocardiopsis strains were xerotolerant, and all five utilized a wide range of substrates. This combined with the production of toxic substances suggests good survival and potential hazard to human health in water-damaged indoor environments. Two new species, Nocardiopsis exhalans sp. nov. (ES10.1T) and Nocardiopsis umidischolae sp. nov. (66/93T), are proposed based on morphology, chemotaxonomic and physiological characters, phylogenetic analysis, and DNA-DNA reassociations. PMID:11526036

Draft Genome Sequence of Thalassotalea sp. Strain ND16A Isolated from Eastern Mediterranean Sea Water Collected from a Depth of 1,055 Meters

DOE PAGES

Stelling, Savannah C.; Techtmann, Stephen M.; Utturkar, Sagar M.; ...

2014-11-26

Thalassotalea sp. strain ND16A belongs to the family Colwelliaceae and was isolated from eastern Mediterranean Sea water at a depth of 1,055 m. Members of Colwelliaceae are ubiquitous marine heterotrophs. Lastly, here we report the draft genome sequence of Thalassotalea sp. strain ND16A, a member of the newly described genus Thalassotalea.

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

PubMed

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

2006-11-01

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

Characterization of a novel Pseudomonas sp. that mineralizes high concentrations of pentachlorophenol.

PubMed Central

Radehaus, P M; Schmidt, S K

1992-01-01

A pentachlorophenol (PCP)-mineralizing bacterium was isolated from polluted soil and identified as Pseudomonas sp. strain RA2. In batch cultures, Pseudomonas sp. strain RA2 used PCP as its sole source of carbon and energy and was capable of completely degrading this compound as indicated by radiotracer studies, stoichiometric release of chloride, and biomass formation. Pseudomonas sp. strain RA2 was able to mineralize a higher concentration of PCP (160 mg liter-1) than any previously reported PCP-degrading pseudomonad. At a PCP concentration of 200 mg liter-1, cell growth was completely inhibited and PCP was not degraded, although an active population of Pseudomonas sp. RA2 was still present in these cultures after 2 weeks. The inhibitory effect of PCP was partially attributable to its effect on the growth rate of Pseudomonas sp. strain RA2. The highest specific growth rate (mu = 0.09 h-1) was reached at a PCP concentration of 40 mg liter-1 but decreased at higher or lower PCP concentrations, with the lowest mu (0.05 h-1) occurring at 150 mg liter-1. Despite this reduction in growth rate, total biomass production was proportional to PCP concentration at all PCP concentrations degraded by Pseudomonas sp. RA2. In contrast, final cell density was reduced to below expected values at PCP concentrations greater than 100 mg liter-1. These results indicate that, in addition to its effect as an uncoupler of oxidative phosphorylation, PCP may also inhibit cell division in Pseudomonas sp. strain RA2.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1444401

Haloplanus salinarum sp. nov., an extremely halophilic archaeon isolated from a solar saltern.

PubMed

Hwang, Han-Bit; Kim, Ye-Eun; Koh, Hyeon-Woo; Song, Hye Seon; Roh, Seong Woon; Kim, So-Jeong; Nam, Seung Won; Park, Soo-Je

2017-11-01

An extremely halophilic archaeal strain SP28 T was isolated from the Gomso solar saltern, Republic of Korea. Cells of the new strain SP28 T were pleomorphic and Gram stain negative, and produced red-pigmented colonies. These grew in medium with 2.5-4.5 M NaCl (optimum 3.1 M) and 0.05-0.5 M MgCl2 (optimum 0.1 M), at 25-50 °C (optimum 37 °C) and at a pH of 6.5-8.5 (optimum pH 8.0). Mg 2+ was required for growth. A concentration of at least 2 M NaCl was required to prevent cell lysis. Polar lipids included phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one glycolipid chromatographically identical to sulfated mannosyl glucosyl diether. 16S rRNA and rpoB' gene sequence analyses showed that strain SP28 T is closely related to Haloplanus ruber R35 T (97.3 and 94.1 %, 16S rRNA and rpoB' gene sequence similarity, respectively), Haloplanus litoreus GX21 T (97.0 and 92.1 %), Haloplanus salinus YGH66 T (96.0 and 91.9 %), Haloplanus vescus RO5-8 T (95.9 and 90.9 %), Haloplanus aerogenes TBN37 T (95.6 and 90.3 %) and Haloplanus natans RE-101 T (95.3 and 89.8 %). The DNA G+C content of the novel strain SP28 T was 66.2 mol%, which is slightly higher than that of Hpn.litoreus GX21 T (65.8 mol%) and Hpn.ruber R35 T (66.0 mol%). DNA-DNA hybridization values betweenHpn.ruber R35 T and strain SP28 T and between Hpn.litoreus GX21 T and strain SP28 T were about 24.8 and 20.7 %, respectively. We conclude that strain SP28 T represents a novel species of the genus Haloplanus and propose the name Haloplanus salinarum sp. nov. The type strain is SP28 T (=JCM 31424 T =KCCM 43210 T ).

Biodegradation of phenol and benzene by endophytic bacterial strains isolated from refinery wastewater-fed Cannabis sativa.

PubMed

Iqbal, Aneela; Arshad, Muhammad; Hashmi, Imran; Karthikeyan, Raghupathy; Gentry, Terry J; Schwab, Arthur Paul

2017-06-13

The presence of benzene and phenol in the environment can lead to serious health effects in humans and warrant development of efficient cleanup strategies. The aim of the present work was to assess the potential of indigenous endophytic bacterial strains to degrade benzene and phenol. Seven strains were successfully isolated from Cannabis sativa plants irrigated with oil refinery wastewater. Molecular characterization was performed by 16S rRNA gene sequencing. Phenol was biodegraded almost completely with Achromobacter sp. (AIEB-7), Pseudomonas sp. (AIEB-4), and Alcaligenes sp. (AIEB-6) at 250, 500, and 750 mg L -1 ; however, the degradation was only 81%, 72%, and 69%, respectively, when exposed to 1000 mg L -1 . Bacillus sp. (AIEB-1), Enterobacter sp. (AIEB-3), and Acinetobacter sp. (AIEB-2) degraded benzene significantly at 250, 500, and 750 mg L -1 . However, these strains showed 80%, 72%, and 68% benzene removal at 1000 mg L -1 exposure, respectively. Rates of degradation could be modeled with first-order kinetics with rate constant values of 1.86 × 10 -2 for Pseudomonas sp. (AIEB-4) and 1.80 × 10 -2  h -1 for Bacillus sp. (AIEB-1) and half-lives of 1.5 and 1.6 days, respectively. These results establish a foundation for further testing of the phytoremediation of hydrocarbon-contaminated soils in the presence of these endophytic bacteria.

Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments

USGS Publications Warehouse

McDonald, I.R.; Kampfer, P.; Topp, E.; Warner, K.L.; Cox, M.J.; Connell, Hancock T.L.; Miller, L.G.; Larkin, M.J.; Ducrocq, V.; Coulter, C.; Harper, D.B.; Murrell, J.C.; Oremland, R.S.

2005-01-01

The bacterial strains IMB-1T and CC495T, which are capable of growth on methyl chloride (CH3Cl, chloromethane) and methyl bromide (CH3Br, bromomethane), were isolated from agricultural soil in California fumigated with CH3Br, and woodland soil in Northern Ireland, respectively. Two pesticide- /herbicide-degrading bacteria, strains ER2 and C147, were isolated from agricultural soil in Canada. Strain ER2 degrades N-methyl carbamate insecticides, and strain C147 degrades triazine herbicides widely used in agriculture. On the basis of their morphological, physiological and genotypic characteristics, these four strains are considered to represent two novel species of the genus Aminobacter, for which the names Aminobacter ciceronei sp. nov. (type strain IMB-1T=ATCC 202197T=CIP 108660T=CCUG 50580T; strains ER2 and C147) and Aminobacter lissarensis sp. nov. (type strain CC495T=NCIMB 13798T=CIP 108661T=CCUG 50579T) are proposed. ?? 2005 IUMS.

Randomized controlled trial of accelerated rehabilitation versus standard protocol following surgical repair of ruptured Achilles tendon.

PubMed

Porter, Mark D; Shadbolt, Bruce

2015-05-01

There is no consensus regarding the optimal management of the acutely ruptured Achilles tendon (TA). Functional bracing alone achieves outcomes similar to those of surgical repair. Surgical repair combined with immediate mobilization may improve the clinical outcome further. The purpose of our study was to determine if an accelerated rehabilitation programme following surgical repair of the ruptured TA could improve clinical outcome, relative to the standard protocol. Patients with an acutely ruptured TA were randomly allocated to undergo an accelerated programme (AP) or standard programme (SP), following surgery. Outcome was assessed at 12 months post-surgery using the Achilles tendon Total Rupture Score (ATRS), the heel-raise height and the time taken to return to running. Fifty-one patients completed the study, 25 in the AP group and 26 in the SP group. At 12 months post-surgery, the ATRS results were similar in the two treatment groups (87.46 in AP with standard error (SE) of 0.735 versus 87.12 in SP with SE of 0.75) while the AP group had less lengthening of the TA (0.385 cm, SE 0.166 versus 1.00 cm, SE 0.169) and a more rapid return to running (17.231 weeks, SE 0.401 versus 21.08 weeks, SE 0.409), than the SP group. The accelerated rehabilitation programme resulted in less tendon lengthening, more rapid return to running, but similar ATRS relative to the standard rehabilitation. Immobilization following TA repair may prolong recovery. © 2014 Royal Australasian College of Surgeons.

Isolation and Molecular Characterization of Novel Chlorpyrifos and 3,5,6-trichloro-2-pyridinol-degrading Bacteria from Sugarcane Farm Soils

PubMed Central

Rayu, Smriti; Nielsen, Uffe N.; Nazaries, Loïc; Singh, Brajesh K.

2017-01-01

Chlorpyrifos (CP) is one of the most widely used organophosphate pesticides in agriculture worldwide, but its extensive use has led to the contamination of various soil and water systems. Microbial bioremediation is considered to be one of the most viable options for the removal of CP from the environment; however, little is known about the soil bacterial diversity that degrade CP. Sequential soil and liquid culture enrichments enabled the isolation of bacterial CP degraders with sequence homologies to Xanthomonas sp., Pseudomonas sp., and Rhizobium sp. The efficacy of the three isolated strains: Xanthomonas sp. 4R3-M1, Pseudomonas sp. 4H1-M3, and Rhizobium sp. 4H1-M1 was further investigated for biodegradation of CP and its primary metabolic product, 3,5,6-trichloro-2-pyridinol (TCP). The results indicate that all three bacterial strains almost completely metabolized CP (10 mg/L) and TCP, occurring as a metabolic degradation product, in mineral salt media as a sole source of carbon and nitrogen. The isolated bacterial strains Xanthomonas sp. 4R3-M1 and Pseudomonas sp. 4H1-M3 could also degrade TCP (10 mg/L) as a sole carbon and nitrogen source, when provided externally. Thus, these bacterial strains may be effective in practical application of bioremediation of both CP and TCP. PMID:28421040

Molecular Characterization of Lactobacillus plantarum DMDL 9010, a Strain with Efficient Nitrite Degradation Capacity

PubMed Central

Fei, Yong-tao; Liu, Dong-mei; Luo, Tong-hui; Chen, Gu; Wu, Hui; Li, Li; Yu, Yi-gang

2014-01-01

Nitrites commonly found in food, especially in fermented vegetables, are potential carcinogens. Therefore, limiting nitrites in food is critically important for food safety. A Lactobacillus strain (Lactobacillus sp. DMDL 9010) was previously isolated from fermented vegetables by our group, and is not yet fully characterized. A number of phenotypical and genotypical approaches were employed to characterize Lactobacillus sp. DMDL 9010. Its nitrite degradation capacity was compared with four other Lactobacillus strains, including Lactobacillus casei subsp. rhamnosus 719, Lactobacillus delbrueckii subsp. bulgaricu 1.83, Streptococcus thermophilus 1.204, and lactobacillus plantarum 8140, on MRS medium. Compared to these four Lactobacillus strains, Lactobacillus sp. DMDL 9010 had a significantly higher nitrite degradation capacity (P<0.001). Based on 16S rDNA sequencing and sequence comparison, Lactobacillus sp. DMDL 9010 was identified as either Lactobacillus plantarum or Lactobacillus pentosus. To further identify this strain, the flanking regions (922 bp and 806 bp upstream and downstream, respectively) of the L-lactate dehydrogenase 1 (L-ldh1) gene were amplified and sequenced. Lactobacillus sp. DMDL 9010 had 98.92 and 76.98% sequence identity in the upstream region with L. plantarum WCFS1 and L. pentosus IG1, respectively, suggesting that Lactobacillu sp. DMDL 9010 is an L. plantarum strain. It was therefore named L. plantarum DMDL 9010. Our study provides a platform for genetic engineering of L. plantarum DMDL 9010, in order to further improve its nitrite degradation capacity. PMID:25423449

Molecular characterization of Lactobacillus plantarum DMDL 9010, a strain with efficient nitrite degradation capacity.

PubMed

Fei, Yong-tao; Liu, Dong-mei; Luo, Tong-hui; Chen, Gu; Wu, Hui; Li, Li; Yu, Yi-gang

2014-01-01

Nitrites commonly found in food, especially in fermented vegetables, are potential carcinogens. Therefore, limiting nitrites in food is critically important for food safety. A Lactobacillus strain (Lactobacillus sp. DMDL 9010) was previously isolated from fermented vegetables by our group, and is not yet fully characterized. A number of phenotypical and genotypical approaches were employed to characterize Lactobacillus sp. DMDL 9010. Its nitrite degradation capacity was compared with four other Lactobacillus strains, including Lactobacillus casei subsp. rhamnosus 719, Lactobacillus delbrueckii subsp. bulgaricu 1.83, Streptococcus thermophilus 1.204, and lactobacillus plantarum 8140, on MRS medium. Compared to these four Lactobacillus strains, Lactobacillus sp. DMDL 9010 had a significantly higher nitrite degradation capacity (P<0.001). Based on 16S rDNA sequencing and sequence comparison, Lactobacillus sp. DMDL 9010 was identified as either Lactobacillus plantarum or Lactobacillus pentosus. To further identify this strain, the flanking regions (922 bp and 806 bp upstream and downstream, respectively) of the L-lactate dehydrogenase 1 (L-ldh1) gene were amplified and sequenced. Lactobacillus sp. DMDL 9010 had 98.92 and 76.98% sequence identity in the upstream region with L. plantarum WCFS1 and L. pentosus IG1, respectively, suggesting that Lactobacillu sp. DMDL 9010 is an L. plantarum strain. It was therefore named L. plantarum DMDL 9010. Our study provides a platform for genetic engineering of L. plantarum DMDL 9010, in order to further improve its nitrite degradation capacity.

Synergistic Degradation of Linuron by a Bacterial Consortium and Isolation of a Single Linuron-Degrading Variovorax Strain

PubMed Central

Dejonghe, Winnie; Berteloot, Ellen; Goris, Johan; Boon, Nico; Crul, Katrien; Maertens, Siska; Höfte, Monica; De Vos, Paul; Verstraete, Willy; Top, Eva M.

2003-01-01

The bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16S rRNA gene pool, isolation and identification of strains, and biodegradation assays. Three strains, Variovorax sp. strain WDL1, Delftia acidovorans WDL34, and Pseudomonas sp. strain WDL5, were isolated directly from the linuron-degrading culture. In addition, subculture of this enrichment culture on potential intermediates in the degradation pathway of linuron (i.e., N,O-dimethylhydroxylamine and 3-chloroaniline) resulted in the isolation of, respectively, Hyphomicrobium sulfonivorans WDL6 and Comamonas testosteroni WDL7. Of these five strains, only Variovorax sp. strain WDL1 was able to use linuron as the sole source of C, N, and energy. WDL1 first converted linuron to 3,4-dichloroaniline (3,4-DCA), which transiently accumulated in the medium but was subsequently degraded. To the best of our knowledge, this is the first report of a strain that degrades linuron further than the aromatic intermediates. Interestingly, the rate of linuron degradation by strain WDL1 was lower than that for the consortium, but was clearly increased when WDL1 was coinoculated with each of the other four strains. D. acidovorans WDL34 and C. testosteroni WDL7 were found to be responsible for degradation of the intermediate 3,4-DCA, and H. sulfonivorans WDL6 was the only strain able to degrade N,O-dimethylhydroxylamine. The role of Pseudomonas sp. strain WDL5 needs to be further elucidated. The degradation of linuron can thus be performed by a single isolate, Variovorax sp. strain WDL1, but is stimulated by a synergistic interaction with the other strains isolated from the same linuron-degrading culture. PMID:12620840

Cryobacterium flavum sp. nov. and Cryobacterium luteum sp. nov., isolated from glacier ice.

PubMed

Liu, Qing; Liu, Hongcan; Wen, Ying; Zhou, Yuguang; Xin, Yuhua

2012-06-01

Gram-positive, rod-shaped bacteria, strains Hh8(T), Hh15(T) and Hh40-2, were isolated from the No. 1 glacier in Xinjiang, north-west China. Colonies of strain Hh8(T) were orange-yellow, convex and round on PYG plates. Strain Hh8(T) grew at 0-19 °C and pH 5.5-10.5. Colonies of strain Hh15(T), which was able to grow at 0-20 °C and pH 5.5-12, were lemon yellow, convex and round on PYG plates. Phylogenetic analysis based on 16S rRNA gene sequences showed that these three strains were related to members of the genus Cryobacterium. The major cellular fatty acids of the novel strains were anteiso-C(15:0), iso-C(16:0), iso-C(15:0) and anteiso-C(15:1) A. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, two novel species, Cryobacterium flavum sp. nov. (type strain Hh8(T) = CGMCC 1.11215(T) = NBRC 107879(T)) and Cryobacterium luteum sp. nov. (type strain Hh15(T) = CGMCC 1.11210(T) = NBRC 107880(T)), are proposed.

Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp. nov., Kazachstaniaserrabonitensis sp. nov. and Kazachstania australis sp. nov. Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov. and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov.

PubMed

Jacques, Noémie; Sarilar, Véronique; Urien, Charlotte; Lopes, Mariana R; Morais, Camila G; Uetanabaro, Ana Paula T; Tinsley, Colin R; Rosa, Carlos A; Sicard, Delphine; Casaregola, Serge

2016-12-01

Five ascosporogenous yeast strains related to the genus Kazachstania were isolated. Two strains (CLIB 1764T and CLIB 1780) were isolated from French sourdoughs; three others (UFMG-CM-Y273T, UFMG-CM-Y451 and UFMG-CM-Y452) were from rotting wood in Brazil. The sequences of the French and Brazilian strains differed by one and three substitutions, respectively, in the D1/D2 large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS). The D1/D2 LSU rRNA sequence of these strains differed by 0.5 and 0.7 % from Kazachstania exigua, but their ITS sequences diverged by 8.1 and 8.3 %, respectively, from that of the closest described species Kazachstania barnettii. Analysis of protein coding sequences of RPB1, RPB2 and EF-1α distinguished the French from the Brazilian strains, with respectively 3.3, 6 and 11.7 % substitutions. Two novel species are described to accommodate these newly isolated strains: Kazachstania saulgeensis sp. nov. (type strain CLIB 1764T=CBS 14374T) and Kazachstania serrabonitensis sp. nov. (type strain UFMG-CM-Y273T=CLIB 1783T=CBS 14236T). Further analysis of culture collections revealed a strain previously assigned to the K. exigua species, but having 3.8 % difference (22 substitutions and 2 indels) in its ITS with respect to K. exigua. Hence, we describe a new taxon, Kazachstania australis sp. nov. (type strain CLIB 162T=CBS 2141T), to accommodate this strain. Finally, Candida humilis and Candida pseudohumilis are reassigned to the genus Kazachstania as new combinations. On the basis of sequence analysis, we also propose that Candida milleri and Kazachstania humilis comb. nov. are conspecific.

'Enterococcus timonensis' sp. nov., 'Actinomyces marseillensis' sp. nov., 'Leptotrichia massiliensis' sp. nov., 'Actinomyces pacaensis' sp. nov., 'Actinomyces oralis' sp. nov., 'Actinomyces culturomici' sp. nov. and 'Gemella massiliensis' sp. nov., new bacterial species isolated from the human respiratory microbiome.

PubMed

Fonkou, M D Mbogning; Bilen, M; Cadoret, F; Fournier, P-E; Dubourg, G; Raoult, D

2018-03-01

We report the main characteristics of 'Enterococcus timonensis' strain Marseille-P2817 T (CSUR P2817), 'Leptotrichia massiliensis' sp. nov., strain Marseille-P3007 T (CSUR P3007), 'Actinomyces marseillensis' sp. nov., strain Marseille-P2818 T (CSUR P2818), 'Actinomyces pacaensis' sp. nov., strain Marseille-P2985 T (CSUR P2985), 'Actinomyces oralis' sp. nov., strain Marseille-P3109 T (CSUR P3109), 'Actinomyces culturomici' sp. nov., strain Marseille-P3561 T (CSUR P3561) and 'Gemella massiliensis' sp. nov., strain Marseille-P3249 T (CSUR P3249) which were isolated from human sputum samples.

Candida laoshanensis sp. nov. and Candida qingdaonensis sp. nov., anamorphic, ascomycetous yeast species isolated from decayed wood.

PubMed

Wang, Shi-An; Li, Fu-Li; Bai, Feng-Yan

2010-07-01

During a study of newly isolated yeast strains utilizing d-xylose as sole carbon source, eight strains, isolated from decayed wood, were found to represent two novel anamorphic, ascomycetous yeast species based on sequence analysis of the 26S rDNA D1/D2 domain and internal transcribed spacer region, and phenotypic characterization. The names Candida laoshanensis sp. nov. (type strain MLRW 6-2(T)=AS 2.4030(T)=CBS 11389(T)) and Candida qingdaonensis sp. nov. (type strain MLRW 7-1(T)=AS 2.4031(T)=CBS 11390(T)) are proposed for these two novel species; the closest relatives of the two novel species are Candida pomicola and Candida marilandica, respectively.

Degradation of car engine base oil by Rhodococcus sp. NDKK48 and Gordonia sp. NDKY76A.

PubMed

Koma, Daisuke; Sakashita, Yuichi; Kubota, Kenzo; Fujii, Yoshihide; Hasumi, Fumihiko; Chung, Seon-Yong; Kubo, Motoki

2003-07-01

Two microorganisms (NDKK48 and NDKY76A) that degrade long-chain cyclic alkanes (c-alkanes) were isolated from soil samples. Strains NDKK48 and NDKY76A were identified as Rhodococcus sp. and Gordonia sp., respectively. Both strains used not only normal alkane (n-alkane) but also c-alkane as a sole carbon and energy source, and the strains degraded more than 27% of car engine base oil (1% addition).

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

PubMed Central

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

2016-01-01

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

Genomic and Functional Analyses of the 2-Aminophenol Catabolic Pathway and Partial Conversion of Its Substrate into Picolinic Acid in Burkholderia xenovorans LB400

PubMed Central

Agulló, Loreine; González, Myriam; Seeger, Michael

2013-01-01

2-aminophenol (2-AP) is a toxic nitrogen-containing aromatic pollutant. Burkholderia xenovorans LB400 possess an amn gene cluster that encodes the 2-AP catabolic pathway. In this report, the functionality of the 2-aminophenol pathway of B. xenovorans strain LB400 was analyzed. The amnRJBACDFEHG cluster located at chromosome 1 encodes the enzymes for the degradation of 2-aminophenol. The absence of habA and habB genes in LB400 genome correlates with its no growth on nitrobenzene. RT-PCR analyses in strain LB400 showed the co-expression of amnJB, amnBAC, amnACD, amnDFE and amnEHG genes, suggesting that the amn cluster is an operon. RT-qPCR showed that the amnB gene expression was highly induced by 2-AP, whereas a basal constitutive expression was observed in glucose, indicating that these amn genes are regulated. We propose that the predicted MarR-type transcriptional regulator encoded by the amnR gene acts as repressor of the amn gene cluster using a MarR-type regulatory binding sequence. This report showed that LB400 resting cells degrade completely 2-AP. The amn gene cluster from strain LB400 is highly identical to the amn gene cluster from P. knackmussi strain B13, which could not grow on 2-AP. However, we demonstrate that B. xenovorans LB400 is able to grow using 2-AP as sole nitrogen source and glucose as sole carbon source. An amnBA − mutant of strain LB400 was unable to grow with 2-AP as nitrogen source and glucose as carbon source and to degrade 2-AP. This study showed that during LB400 growth on 2-AP this substrate was partially converted into picolinic acid (PA), a well-known antibiotic. The addition of PA at lag or mid-exponential phase inhibited LB400 growth. The MIC of PA for strain LB400 is 2 mM. Overall, these results demonstrate that B. xenovorans strain LB400 posses a functional 2-AP catabolic central pathway, which could lead to the production of picolinic acid. PMID:24124510

Specificity of monoclonal antibodies to strains of Dickeya sp. that cause bacterial heart rot of pineapple.

PubMed

Peckham, Gabriel D; Kaneshiro, Wendy S; Luu, Van; Berestecky, John M; Alvarez, Anne M

2010-10-01

During a severe outbreak of bacterial heart rot that occurred in pineapple plantations on Oahu, Hawaii, in 2003 and years following, 43 bacterial strains were isolated from diseased plants or irrigation water and identified as Erwinia chrysanthemi (now Dickeya sp.) by phenotypic, molecular, and pathogenicity assays. Rep-PCR fingerprint patterns grouped strains from pineapple plants and irrigation water into five genotypes (A-E) that differed from representatives of other Dickeya species, Pectobacterium carotovorum and other enteric saprophytes isolated from pineapple. Monoclonal antibodies produced following immunization of mice with virulent type C Dickeya sp. showed only two specificities. MAb Pine-1 (2D11G1, IgG1 with kappa light chain) reacted to all 43 pineapple/water strains and some reference strains (D. dianthicola, D. chrysanthemi, D. paradisiaca, some D. dadantii, and uncharacterized Dickeya sp.) but did not react to reference strains of D. dieffenbachiae, D. zeae, or one of the two Malaysian pineapple strains. MAb Pine-2 (2A7F2, IgG3 with kappa light chain) reacted to all type B, C, and D strains but not to any A or E strains or any reference strains except Dickeya sp. isolated from Malaysian pineapple. Pathogenicity tests showed that type C strains were more aggressive than type A strains when inoculated during cool months. Therefore, MAb Pine-2 distinguishes the more virulent type C strains from less virulent type A pineapple strains and type E water strains. MAbs with these two specificities enable development of rapid diagnostic tests that will distinguish the systemic heart rot pathogen from opportunistic bacteria associated with rotted tissues. Use of the two MAbs in field assays also permits the monitoring of a known subpopulation and provides additional decision tools for disease containment and management practices.

Discovery of Rare and Highly Toxic Microcystins from Lichen-Associated Cyanobacterium Nostoc sp. Strain IO-102-I

PubMed Central

Oksanen, Ilona; Jokela, Jouni; Fewer, David P.; Wahlsten, Matti; Rikkinen, Jouko; Sivonen, Kaarina

2004-01-01

The production of hepatotoxic cyclic heptapeptides, microcystins, is almost exclusively reported from planktonic cyanobacteria. Here we show that a terrestrial cyanobacterium Nostoc sp. strain IO-102-I isolated from a lichen association produces six different microcystins. Microcystins were identified with liquid chromatography-UV mass spectrometry by their retention times, UV spectra, mass fragmentation, and comparison to microcystins from the aquatic Nostoc sp. strain 152. The dominant microcystin produced by Nostoc sp. strain IO-102-I was the highly toxic [ADMAdda5]microcystin-LR, which accounted for ca. 80% of the total microcystins. We assigned a structure of [DMAdda5]microcystin-LR and [d-Asp3,ADMAdda5]microcystin-LR and a partial structure of three new [ADMAdda5]-XR type of microcystin variants. Interestingly, Nostoc spp. strains IO-102-I and 152 synthesized only the rare ADMAdda and DMAdda subfamilies of microcystin variants. Phylogenetic analyses demonstrated congruence between genes involved directly in microcystin biosynthesis and the 16S rRNA and rpoC1 genes of Nostoc sp. strain IO-102-I. Nostoc sp. strain 152 and the Nostoc sp. strain IO-102-I are distantly related, revealing a sporadic distribution of toxin production in the genus Nostoc. Nostoc sp. strain IO-102-I is closely related to Nostoc punctiforme PCC 73102 and other symbiotic Nostoc strains and most likely belongs to this species. Together, this suggests that other terrestrial and aquatic strains of the genus Nostoc may have retained the genes necessary for microcystin biosynthesis. PMID:15466511

Isolation and characterization of Dehalobacter sp. strain UNSWDHB capable of chloroform and chlorinated ethane respiration.

PubMed

Wong, Yie K; Holland, Sophie I; Ertan, Haluk; Manefield, Mike; Lee, Matthew

2016-09-01

Dehalobacter sp. strain UNSWDHB can dechlorinate up to 4 mM trichloromethane at a rate of 0.1 mM per day to dichloromethane and 1,1,2-trichloroethane (1 mM, 0.1 mM per day) with the unprecedented product profile of 1,2-dichloroethane and vinyl chloride. 1,1,1-trichloroethane and 1,1-dichloroethane were slowly utilized by strain UNSWDHB and were not completely removed, with minimum threshold concentrations of 0.12 mM and 0.07 mM respectively under growth conditions. Enzyme kinetic experiments confirmed strong substrate affinity for trichloromethane and 1,1,2-trichloroethane (Km  = 30 and 62 µM respectively) and poor substrate affinity for 1,1,1-trichloroethane and 1,1-dichloroethane (Km  = 238 and 837 µM respectively). Comparison of enzyme kinetic and growth data with other trichloromethane respiring organisms (Dehalobacter sp. strain CF and Desulfitobacterium sp. strain PR) suggests an adaptation of strain UNSWDHB to trichloromethane. The trichloromethane RDase (TmrA) expressed by strain UNSWDHB was identified by BN-PAGE and functionally characterized. Amino acid comparison of homologous RDases from all three organisms revealed only six significant amino acid substitutions/deletions, which are likely to be crucial for substrate specificity. Furthermore, strain UNSWDHB was shown to grow without exogenous supply of cobalamin confirming genomic-based predictions of a fully functional cobalamin synthetic pathway. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex

PubMed Central

Weber, Carolyn F.; King, Gary M.

2017-01-01

Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai‘i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia, respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia: Paraburkholderia hiiakae sp. nov. (type strain I2T = DSM 28029T = LMG 27952T); Paraburkholderia paradisi sp. nov. (type strain WAT = DSM 28027T = LMG 27949T); Paraburkholderia peleae sp. nov. (type strain PP52-1T = DSM 28028T = LMG 27950T); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1T = DSM 28030T = LMG 28140T). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38T = DSM 28031T = LMG 28138T). PMID:28270796

Volcanic Soils as Sources of Novel CO-Oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a Member of the Burkholderia cepacia Complex.

PubMed

Weber, Carolyn F; King, Gary M

2017-01-01

Previous studies showed that members of the Burkholderiales were important in the succession of aerobic, molybdenum-dependent CO oxidizing-bacteria on volcanic soils. During these studies, four isolates were obtained from Kilauea Volcano (Hawai'i, USA); one strain was isolated from Pico de Orizaba (Mexico) during a separate study. Based on 16S rRNA gene sequence similarities, the Pico de Orizaba isolate and the isolates from Kilauea Volcano were provisionally assigned to the genera Burkholderia and Paraburkholderia , respectively. Each of the isolates possessed a form I coxL gene that encoded the catalytic subunit of carbon monoxide dehydrogenase (CODH); none of the most closely related type strains possessed coxL or oxidized CO. Genome sequences for Paraburkholderia type strains facilitated an analysis of 16S rRNA gene sequence similarities and average nucleotide identities (ANI). ANI did not exceed 95% (the recommended cutoff for species differentiation) for any of the pairwise comparisons among 27 reference strains related to the new isolates. However, since the highest 16S rRNA gene sequence similarity among this set of reference strains was 98.93%, DNA-DNA hybridizations (DDH) were performed for two isolates whose 16S rRNA gene sequence similarities with their nearest phylogenetic neighbors were 98.96 and 99.11%. In both cases DDH values were <16%. Based on multiple variables, four of the isolates represent novel species within the Paraburkholderia : Paraburkholderia hiiakae sp. nov. (type strain I2 T = DSM 28029 T = LMG 27952 T ); Paraburkholderia paradisi sp. nov. (type strain WA T = DSM 28027 T = LMG 27949 T ); Paraburkholderia peleae sp. nov. (type strain PP52-1 T = DSM 28028 T = LMG 27950 T ); and Paraburkholderia metrosideri sp. nov. (type strain DNBP6-1 T = DSM 28030 T = LMG 28140 T ). The remaining isolate represents the first CO-oxidizing member of the Burkholderia cepacia complex: Burkholderia alpina sp. nov. (type strain PO-04-17-38 T = DSM 28031 T = LMG 28138 T ).

Hydroxylation of the herbicide isoproturon by fungi isolated from agricultural soil.

PubMed

Rønhede, Stig; Jensen, Bo; Rosendahl, Søren; Kragelund, Birthe B; Juhler, René K; Aamand, Jens

2005-12-01

Several asco-, basidio-, and zygomycetes isolated from an agricultural field were shown to be able to hydroxylate the phenylurea herbicide isoproturon [N-(4-isopropylphenyl)-N',N'-dimethylurea] to N-(4-(2-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea and N-(4-(1-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea. Bacterial metabolism of isoproturon has previously been shown to proceed by an initial demethylation to N-(4-isopropylphenyl)-N'-methylurea. In soils, however, hydroxylated metabolites have also been detected. In this study we identified fungi as organisms that potentially play a major role in the formation of these hydroxylated metabolites in soils treated with isoproturon. Isolates of Mortierella sp. strain Gr4, Phoma cf. eupyrena Gr61, and Alternaria sp. strain Gr174 hydroxylated isoproturon at the first position of the isopropyl side chain, yielding N-(4-(2-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea, while Mucor sp. strain Gr22 hydroxylated the molecule at the second position, yielding N-(4-(1-hydroxy-1-methylethyl)phenyl)-N',N'-dimethylurea. Hydroxylation was the dominant mode of isoproturon transformation in these fungi, although some cultures also produced traces of the N-demethylated metabolite N-(4-isopropylphenyl)-N'-methylurea. A basidiomycete isolate produced a mixture of the two hydroxylated and N-demethylated metabolites at low concentrations. Clonostachys sp. strain Gr141 and putative Tetracladium sp. strain Gr57 did not hydroxylate isoproturon but N demethylated the compound to a minor extent. Mortierella sp. strain Gr4 also produced N-(4-(2-hydroxy-1-methylethyl)phenyl)-N'-methylurea, which is the product resulting from combined N demethylation and hydroxylation.

Hydroxylation of the Herbicide Isoproturon by Fungi Isolated from Agricultural Soil

PubMed Central

Rønhede, Stig; Jensen, Bo; Rosendahl, Søren; Kragelund, Birthe B.; Juhler, René K.; Aamand, Jens

2005-01-01

Several asco-, basidio-, and zygomycetes isolated from an agricultural field were shown to be able to hydroxylate the phenylurea herbicide isoproturon [N-(4-isopropylphenyl)-N′,N′-dimethylurea] to N-(4-(2-hydroxy-1-methylethyl)phenyl)-N′,N′-dimethylurea and N-(4-(1-hydroxy-1-methylethyl)phenyl)-N′,N′-dimethylurea. Bacterial metabolism of isoproturon has previously been shown to proceed by an initial demethylation to N-(4-isopropylphenyl)-N′-methylurea. In soils, however, hydroxylated metabolites have also been detected. In this study we identified fungi as organisms that potentially play a major role in the formation of these hydroxylated metabolites in soils treated with isoproturon. Isolates of Mortierella sp. strain Gr4, Phoma cf. eupyrena Gr61, and Alternaria sp. strain Gr174 hydroxylated isoproturon at the first position of the isopropyl side chain, yielding N-(4-(2-hydroxy-1-methylethyl)phenyl)-N′,N′-dimethylurea, while Mucor sp. strain Gr22 hydroxylated the molecule at the second position, yielding N-(4-(1-hydroxy-1-methylethyl)phenyl)-N′,N′-dimethylurea. Hydroxylation was the dominant mode of isoproturon transformation in these fungi, although some cultures also produced traces of the N-demethylated metabolite N-(4-isopropylphenyl)-N′-methylurea. A basidiomycete isolate produced a mixture of the two hydroxylated and N-demethylated metabolites at low concentrations. Clonostachys sp. strain Gr141 and putative Tetracladium sp. strain Gr57 did not hydroxylate isoproturon but N demethylated the compound to a minor extent. Mortierella sp. strain Gr4 also produced N-(4-(2-hydroxy-1-methylethyl)phenyl)-N′-methylurea, which is the product resulting from combined N demethylation and hydroxylation. PMID:16332769

Decolorization of sulfonated azo dye Metanil Yellow by newly isolated bacterial strains: Bacillus sp. strain AK1 and Lysinibacillus sp. strain AK2.

PubMed

Anjaneya, O; Souche, S Yogesh; Santoshkumar, M; Karegoudar, T B

2011-06-15

Two different bacterial strains capable of decolorizing a highly water soluble azo dye Metanil Yellow were isolated from dye contaminated soil sample collected from Atul Dyeing Industry, Bellary, India. The individual bacterial strains Bacillus sp. AK1 and Lysinibacillus sp. AK2 decolorized Metanil Yellow (200 mg L(-1)) completely within 27 and 12h respectively. Various parameters like pH, temperature, NaCl and initial dye concentrations were optimized to develop an economically feasible decolorization process. The maximum concentration of Metanil Yellow (1000 mg L(-1)) was decolorized by strains AK2 and AK1 within 78 and 84 h respectively. These strains could decolorize Metanil Yellow over a broad pH range 5.5-9.0; the optimum pH was 7.2. The decolorization of Metanil Yellow was most efficient at 40°C and confirmed by UV-visible spectroscopy, TLC, HPLC and GC/MS analysis. Further, both the strains showed the involvement of azoreductase in the decolorization process. Phytotoxicity studies of catabolic products of Metanil Yellow on the seeds of chick pea and pigeon pea revealed much reduction in the toxicity of metabolites as compared to the parent dye. These results indicating the effectiveness of strains AK1 and AK2 for the treatment of textile effluents containing azo dyes. Copyright © 2011 Elsevier B.V. All rights reserved.

In-planta Sporulation Capacity Enhances Infectivity and Rhizospheric Competitiveness of Frankia Strains

PubMed Central

Cotin-Galvan, Laetitia; Pozzi, Adrien C.; Schwob, Guillaume; Fournier, Pascale; Fernandez, Maria P.; Herrera-Belaroussi, Aude

2016-01-01

Frankia Sp+ strains maintain their ability to sporulate in symbiosis with actinorhizal plants, producing abundant sporangia inside host plant cells, in contrast to Sp− strains, which are unable to perform in-planta sporulation. We herein examined the role of in-planta sporulation in Frankia infectivity and competitiveness for root infection. Fifteen strains belonging to different Sp+ and Sp− phylogenetic lineages were inoculated on seedlings of Alnus glutinosa (Ag) and A. incana (Ai). Strain competitiveness was investigated by performing Sp−/Sp+ co-inoculations. Plant inoculations were standardized using crushed nodules obtained under laboratory-controlled conditions (same plant species, age, and environmental factors). Specific oligonucleotide primers were developed to identify Frankia Sp+ and/or Sp− strains in the resulting nodules. Single inoculation experiments showed that (i) infectivity by Sp+ strains was significantly greater than that by Sp− strains, (ii) genetically divergent Sp+ strains exhibited different infective abilities, and (iii) Sp+ and Sp− strains showed different host preferences according to the origin (host species) of the inocula. Co-inoculations of Sp+ and Sp− strains revealed the greater competitiveness of Sp+ strains (98.3 to 100% of Sp+ nodules, with up to 15.6% nodules containing both Sp+ and Sp− strains). The results of the present study highlight differences in Sp+/Sp− strain ecological behaviors and provide new insights to strengthen the obligate symbiont hypothesis for Sp+ strains. PMID:26726131

Herbaspirillum canariense sp. nov., Herbaspirillum aurantiacum sp. nov. and Herbaspirillum soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus Herbaspirillum.

PubMed

Carro, Lorena; Rivas, Raúl; León-Barrios, Milagros; González-Tirante, María; Velázquez, Encarna; Valverde, Angel

2012-06-01

Three Gram-negative, motile and slightly curved rod-shaped bacteria, strains SUEMI03(T), SUEMI08(T) and SUEMI10(T), were isolated from an old volcanic mountain soil on Tenerife (Canary Islands). The three strains were related phylogenetically to Herbaspirillum seropedicae. 16S rRNA gene sequence similarity was 99.2-99.6 % among strains SUEMI03(T), SUEMI08(T) and SUEMI10(T), which presented 97.5, 97.8 and 97.7 % identity, respectively, with respect to H. seropedicae DSM 6445(T). The three strains grew optimally in TSB at 28 °C and contained summed features 3 (C(16:1)ω6c and/or C(16:1)ω7c) and 8 (C(18:1)ω6c and/or C(18:1)ω7c) and C(16:0) as major cellular fatty acids. The DNA G+C contents of strains SUEMI03(T), SUEMI08(T) and SUEMI10(T) were 61.6, 60.4 and 61.9 mol%, respectively. Strains SUEMI03(T), SUEMI08(T) and SUEMI10(T) presented less than 60 % interstrain DNA relatedness and less than 30 % relatedness with respect to H. seropedicae DSM 6445(T). In spite of their common geographical origin, the three strains isolated in this study presented several phenotypic differences, presenting phenotypic profiles highly divergent from that of H. seropedicae. Therefore, we propose that the strains isolated in this study represent three novel species of the genus Herbaspirillum, named Herbaspirillum canariense sp. nov. (type strain SUEMI03(T) = LMG 26151(T) = CECT 7838(T)), Herbaspirillum aurantiacum sp. nov. (type strain SUEMI08(T) = LMG 26150(T) = CECT 7839(T)) and Herbaspirillum soli sp. nov. (type strain SUEMI10(T) = LMG 26149(T) = CECT 7840(T)).

Ogataea phyllophila sp. nov., Candida chumphonensis sp. nov. and Candida mattranensis sp. nov., three methylotrophic yeast species from phylloplane in Thailand.

PubMed

Koowadjanakul, Nampueng; Jindamorakot, Sasitorn; Yongmanitchai, Wichien; Limtong, Savitree

2011-08-01

Five strains (LN12, LN14(T), LN15(T), LN16 and LN17(T)) representing three novel methylotrophic yeast species were isolated from the external surface of plant leaves by three-consecutive enrichments. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, the sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene and the phylogenetic analysis, the five strains were assigned to be one novel Ogataea species and two novel Candida species. Three strains (LN12, LN14(T) and LN16) represent a single novel species of the genus Ogataea, for which the name Ogataea phyllophila sp. nov. is proposed. The type strain is LN14(T) (= BCC 42666(T) = NBRC 107780(T) = CBS 12095(T)). Strain LN15(T) was assigned to be Candida chumphonensis sp. nov. (type strain LN15(T) = BCC 42667(T) = NBRC 107781(T) = CBS 12096(T)). Strain LN17(T) represented another novel species of Candida that was named Candida mattranensis sp. nov. (type strain LN17(T) = BCC 42668(T) = NBRC 107782(T) = CBS 12097(T)).

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. Copyright © 2016 da Silva et al.

Periodontopathogen and Epstein-Barr virus-associated periapical periodontitis may be the source of retrograde infectious peri-implantitis.

PubMed

Verdugo, Fernando; Castillo, Ana; Simonian, Krikor; Castillo, Francisca; Farez-Vidal, Esther; D'Addona, Antonio

2015-02-01

Herpesviral-bacterial synergism may play a role in periodontitis and peri-implantitis etiopathogenesis. Periapical periodontitis (PP) lesions can predict future apical peri-implantitis complications. This pilot study aimed to substantiate herpesviral-bacterial coinfection in symptomatic (SP) and asymptomatic (AP) PP and assess associations with periodontopathogen salivary contamination in patients receiving implants. Polymerase chain reaction (PCR)-based identification was performed on PP granulation tissue (GT) from 33 SP and AP patients and compared with unstimulated whole saliva. Quantitative PCR evaluated Epstein-Barr virus (EBV) and cytomegalovirus copy counts. SP GT had higher proportions of periodontopathogens. Symptomatic patients were 3.7 times more likely to be infected with EBV than AP (p = .07; 95% CI: 0.8-16.2). SP were 2.9, 2.1, 3.6, and 1.6 times more likely to be infected with Treponema denticola, Prevotella intermedia, Aggregatibacter actinomycetemcomitans, and Porphyromonas gingivalis, respectively. The odds ratio of EBV infecting PP lesions was two times higher in those positive for the virus in saliva. Saliva Tannerella forsythia-positive patients were 15 times more likely to present this pathogen in PP lesions (p = .038). Saliva EBV-positive individuals were 7 and 3.5 times more likely to yield GT contamination with T. forsythia and T. denticola, respectively. EBV copy counts were significantly higher in SP (p < .01). A causal association between EBV, specific bacterial anaerobic infection, and symptomatic PP is likely. EBV high prevalence underscores the viral etiological importance. Salivary EBV contamination is likely to be associated with viral and bacterial GT infection. Saliva PCR analysis can be a good predictor of GT specific infection and help establish antimicrobial therapy. If confirmed by prospective longitudinal clinical trials, antiviral therapy could possibly benefit SP and nonresponsive to treatment individuals and help prevent potential peri-implant infectious complications. © 2013 Wiley Periodicals, Inc.

Rhodotorula rosulata sp. nov., Rhodotorula silvestris sp. nov. and Rhodotorula straminea sp. nov., novel myo-inositol-assimilating yeast species in the Microbotryomycetes.

PubMed

Golubev, Wladyslav I; Scorzetti, Gloria

2010-10-01

Three novel species are described as Rhodotorula rosulata sp. nov. (type strain VKM Y-2962(T) =CBS 10977(T)), Rhodotorula silvestris sp. nov. (type strain VKM Y-2971(T) =CBS 11420(T)) and Rhodotorula straminea sp. nov. (type strain VKM Y-2964(T) =CBS 10976(T)) based on the study of eight isolates from needle litter. The new species, phylogenetically located within the Microbotryomycetes, are related to glucuronate-assimilating species of the genus Rhodotorula. Sequencing of the D1/D2 domains of the LSU rDNA gene and the internal transcribed spacer (ITS) region, as well as physiological characterization, revealed their distinct taxonomic positions.

Isolation of amylolytic, xylanolytic, and cellulolytic microorganisms extracted from the gut of the termite Reticulitermes santonensis by means of a micro-aerobic atmosphere.

PubMed

Tarayre, Cédric; Brognaux, Alison; Bauwens, Julien; Brasseur, Catherine; Mattéotti, Christel; Millet, Catherine; Destain, Jacqueline; Vandenbol, Micheline; Portetelle, Daniel; De Pauw, Edwin; Eric, Haubruge; Francis, Frédéric; Thonart, Philippe

2014-05-01

The aim of this work was to isolate enzyme-producing microorganisms from the tract of the termite Reticulitermes santonensis. The microorganisms were extracted from the guts and anaerobic (CO₂ or CO₂/H₂) and micro-aerobic atmospheres were used to stimulate growth. Three different strategies were tried out. First, the sample was spread on Petri dishes containing solid media with carboxymethylcellulose, microcrystalline cellulose or cellobiose. This technique allowed us to isolate two bacteria: Streptomyces sp. strain ABGxAviA1 and Pseudomonas sp. strain ABGxCellA. The second strategy consisted in inoculating a specific liquid medium containing carboxymethylcellulose, microcrystalline cellulose, or cellobiose. The samples were then spread on Petri dishes with the same specific medium containing carboxymethylcellulose, microcrystalline cellulose, or cellobiose. This led to the isolation of the mold Aspergillus sp. strain ABGxAviA2. Finally, the third strategy consisted in heating the first culture and spreading samples on agar plates containing rich medium. This led to the isolation of the bacterium Bacillus subtilis strain ABGx. All those steps were achieved in controlled atmospheres. The four enzyme-producing strains which were isolated were obtained by using a micro-aerobic atmosphere. Later, enzymatic assays were performed on the four strains. Streptomyces sp. strain ABGxAviA1 was found to produce only amylase, while Pseudomonas sp. strain ABGxCellA was found to produce β-glucosidase as well. Aspergillus sp. strain ABGxAviA2 showed β-glucosidase, amylase, cellulase, and xylanase activities. Finally, B. subtilis strain ABGx produced xylanase and amylase.

Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., isolated from fermented fish in Thailand.

PubMed

Tanasupawat, S; Shida, O; Okada, S; Komagata, K

2000-07-01

Eleven strains of homofermentative, rod-shaped lactic acid bacteria and five strains of heterofermentative, sphere-shaped lactic acid bacteria were isolated from fermented fish (pla-ra and pla-chom) in Thailand. They were identified as new species and named Lactobacillus acidipiscis sp. nov. and Weissella thailandensis sp. nov., respectively, on the basis of phylogenetic analysis of the 16S rRNA gene sequences, DNA relatedness and phenotypic characteristics. The type strain of L. acidipiscis is FS60-1T (= PCU 207T = NRIC 0300T = HSCC 1411T = JCM 10692T = TISTR 1386T) and the type strain of Weissella thailandensis is FS61-1T (= PCU 210T = NRIC 0298T = HSCC 1412T = JCM 10695T = TISTR 1384T).

Candida olivae sp. nov., a novel yeast species from 'Greek-style' black olive fermentation.

PubMed

Nisiotou, Aspasia A; Panagou, Efstathios Z; Nychas, George-John E

2010-05-01

Two yeast strains (FMCC Y-1(T) and FMCC Y-2) were recovered during a survey of the yeast biota associated with fermenting black olives, collected from an olive tree (Olea europaea L. cv. 'Conservolea') orchard in Central Greece. Phylogenetic analysis based on rRNA gene sequences (18S, 26S, and 5.8S-ITS) indicated that the two strains represent a separate species within the Candida membranifaciens clade, in close relation to Candida blattariae NRRL Y-27703(T). Electrophoretic karyotyping and physiological analysis support the affiliation of the two strains to a novel species as Candida olivae sp. nov. The novel strains are conspecific with two Candida sp. strains previously isolated from the Mid-Atlantic Ridge hydrothermal fields [Gadanho & Sampaio (2005). Microb Ecol 50, 408-417], indicating that Candida olivae sp. nov. may occupy diverse ecological niches. FMCC Y-1(T) (=CBS 11171(T) =ATCC MYA-4568(T)) is the type strain.

Candida andamanensis sp. nov., Candida laemsonensis sp. nov. and Candida ranongensis sp. nov., anamorphic yeast species isolated from estuarine waters in a Thai mangrove forest.

PubMed

Am-In, Somjit; Limtong, Savitree; Yongmanitchai, Wichien; Jindamorakot, Sasitorn

2011-02-01

Five strains (RV5(T), RV140, R31(T), RS17 and RS28(T)) representing three novel anamorphic ascomycetous yeast species were isolated by membrane filtration from estuarine waters collected from a mangrove forest in Laem Son National Park, Ranong Province, Thailand, on different occasions. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 domain of the large-subunit rRNA gene and the internal transcribed spacer region and phylogenetic analysis, three strains were found to represent two novel Candida species. Two strains (RV5(T) and RV140) represented a single novel species, for which the name Candida laemsonensis sp. nov. is proposed. The type strain is RV5(T) (=BCC 35154(T) =NBRC 105873(T) =CBS 11419(T)). Strain R31(T) was assigned to a novel species that was named Candida andamanensis sp. nov. (type strain R31(T) =BCC 25965(T) =NBRC 103862(T) =CBS 10859(T)). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 domain of the large-subunit rRNA gene and phylogenetic analysis, strains RS17 and RS28(T) represented another novel species of Candida, for which the name Candida ranongensis sp. nov. is proposed. The type strain is RS28(T) (=BCC 25964(T) =NBRC 103861(T) =CBS 10861(T)).

Description of chlorophenol-degrading Pseudomonas sp. strains KF1T, KF3, and NKF1 as a new species of the genus Sphingomonas, Sphingomonas subarctica sp. nov.

PubMed

Nohynek, L J; Nurmiaho-Lassila, E L; Suhonen, E L; Busse, H J; Mohammadi, M; Hantula, J; Rainey, F; Salkinoja-Salonen, M S

1996-10-01

Gram-negative polychlorophenol-degrading bacterial strains KF1T (T = type strain), KF3, and NKF1, which were described previously as Pseudomonas saccharophila strains, were studied by chemotaxonomic, genetic, and physiological methods and by electron microscopy and compared with selected xenobiotic compound-degrading bacteria. These strains contained sphingolipids with d-18:0, d-20:1, and d-21:1 as the main dihydrosphingosines, ubiquinone 10 as the main respiratory quinone, and spermidine as the major polyamine, and the DNA G + C content was 66 mol%. The cellular fatty acids included about 60% octadecenoic acid, 9% 2-hydroxymyristic acid, 14% cis-9-hexadecenoic acid, and 10% hexadecanoic acid. These strains exhibited less than 97% 16S ribosomal DNA sequence similarity to all of the other taxa studied. In the DNA-DNA reassociation studies the highest levels of reassociation between these strains and previously described species were less than 40%. Thin sections of cells of strains KF1T, KF3, and NKF1 were examined by electron microscopy, and the results showed that the cells had peculiar concentrically arranged layered membranous blebs that extruded from the outer membrane, especially at the cell division points. On the basis of the results of this study, polychlorophenol-degrading strains KF1T, KF3, and NKF1 are considered members of a new species of the genus Sphingomonas, Sphingomonas subarctica. The polycyclic aromatic hydrocarbon-degrading organism Sphingomonas paucimobilis EPA 505 was closely related to Sphingomonas chlorophenolica as determined by chemotaxonomic, phylogenetic, and physiological criteria. The xenobiotic compound degraders Alcaligenes sp. strain A175 and Pseudomonas sp. strain BN6 were identified as members of species of the genus Sphingomonas.

Methylopila helvetica sp. nov. and Methylobacterium dichloromethanicum sp. nov.--novel aerobic facultatively methylotrophic bacteria utilizing dichloromethane.

PubMed

Doronina, N V; Trotsenko, Y A; Tourova, T P; Kuznetsov, B B; Leisinger, T

2000-06-01

Eight strains of Gram-negative, aerobic, asporogenous, neutrophilic, mesophilic, facultatively methylotrophic bacteria are taxonomically described. These icl- serine pathway methylobacteria utilize dichloromethane, methanol and methylamine as well as a variety of polycarbon compounds as the carbon and energy source. The major cellular fatty acids of the non-pigmented strains DM1, DM3, and DM5 to DM9 are C18:1, C16:0, C18:0, Ccy19:0 and that of the pink-pigmented strain DM4 is C18:1. The main quinone of all the strains is Q-10. The non-pigmented strains have similar phenotypic properties and a high level of DNA-DNA relatedness (81-98%) as determined by hybridization. All strains belong to the alpha-subgroup of the alpha-Proteobacteria. 16S rDNA sequence analysis led to the classification of these dichloromethane-utilizers in the genus Methylopila as a new species - Methylopila helvetica sp.nov. with the type strain DM9 (=VKM B-2189). The pink-pigmented strain DM4 belongs to the genus Methylobacterium but differs from the known members of this genus by some phenotypic properties, DNA-DNA relatedness (14-57%) and 16S rDNA sequence. Strain DM4 is named Methylobacterium dichloromethanicum sp. nov. (VKM B-2191 = DSMZ 6343).

Methylocystis hirsuta sp. nov., a novel methanotroph isolated from a groundwater aquifer.

PubMed

Lindner, Angela S; Pacheco, Adriana; Aldrich, Henry C; Costello Staniec, Andria; Uz, Ilker; Hodson, David J

2007-08-01

Strain CSC1(T), a Gram-negative, aerobic, methane-oxidizing bacterium, was isolated from an uncontaminated aquifer nearly 20 years ago. Based on 16S rRNA gene sequence similarity, this strain was identified as a member of the Alphaproteobacteria, most closely related to an uncultured member of the Methylocystaceae as well as two cultured organisms, Methylocystis sp. L32 and Methylocystis sp. SC2. This strain differed from extant species in cell shape, size, expression of soluble methane monooxygenase and its unique spiny surface layers, composed of polysaccharide. DNA-DNA hybridization results showed only 3.8 % relatedness with Methylocystis echinoides NCIMB 13100 and 41.1 % relatedness with Methylocystis rosea SV97(T). Based on these genotypic and physiological differences, this isolate is proposed as a member of a novel species of the genus Methylocystis, Methylocystis hirsuta sp. nov. (type strain CSC1(T) =ATCC BAA-1344(T) =DSM 18500(T)).

Isolation of a rice endophytic bacterium, Pantoea sp. Sd-1, with ligninolytic activity and characterization of its rice straw degradation ability.

PubMed

Xiong, X Q; Liao, H D; Ma, J S; Liu, X M; Zhang, L Y; Shi, X W; Yang, X L; Lu, X N; Zhu, Y H

2014-02-01

This study focused on an endophytic bacterial strain, Pantoea sp. Sd-1, which can be used to degrade lignin and rice straw. This strain was isolated from rice seeds by an optimized surface sterilization method. Pantoea sp. Sd-1 showed exceptional ability to degrade rice straw and lignin. In rice straw or kraft lignin-containing medium supplemented with 1% glucose and 0.5% peptone, Pantoea sp. Sd-1 effectively reduced the rice straw mass weight by 54.5% after 6 days of treatment. The strain was also capable of reducing the lignin colour (52.4%) and content (69.1%) after 4 days of incubation. The findings suggested that the rice endophytic bacterium Pantoea sp. Sd-1 could be applied for the degradation of lignocellulose biomass, such as rice straw. Rice straw, an abundant agricultural by-product in China, is very difficult to degrade because of its high lignin content. Due to the immense environmental adaptability and biochemical versatility of bacteria, endophytic bacteria are useful resources for biodegradation. In this study, we screened for endophytic bacteria capable of biodegrading rice straw and lignin and obtained one strain, Pantoea sp. Sd-1, with suitable characteristics. Sd-1 could be used for degradation of rice straw and lignin, and may play an important role in biodegradation of this agricultural by-product. © 2013 The Society for Applied Microbiology.

A Survey of Aflatoxin-Producing Aspergillus sp. from Peanut Field Soils in Four Agroecological Zones of China

PubMed Central

Zhang, Chushu; Selvaraj, Jonathan Nimal; Yang, Qingli; Liu, Yang

2017-01-01

Peanut pods are easily infected by aflatoxin-producing Aspergillus sp.ecies from field soil. To assess the aflatoxin-producing Aspergillus sp. in different peanut field soils, 344 aflatoxin-producing Aspergillus strains were isolated from 600 soil samples of four agroecological zones in China (the Southeast coastal zone (SEC), the Yangtze River zone (YZR), the Yellow River zone (YR) and the Northeast zone (NE)). Nearly 94.2% (324/344) of strains were A. flavus and 5.8% (20/344) of strains were A. parasiticus. YZR had the highest population density of Aspergillus sp. and positive rate of aflatoxin production in isolated strains (1039.3 cfu·g−1, 80.7%), the second was SEC (191.5 cfu·g−1, 48.7%), the third was YR (26.5 cfu·g−1, 22.7%), and the last was NE (2.4 cfu·g−1, 6.6%). The highest risk of AFB1 contamination on peanut was in YZR which had the largest number of AFB1 producing isolates in 1g soil, followed by SEC and YR, and the lowest was NE. The potential risk of AFB1 contamination in peanuts can increase with increasing population density and a positive rate of aflatoxin-producing Aspergillus sp. in field soils, suggesting that reducing aflatoxigenic Aspergillus sp. in field soils could prevent AFB1 contamination in peanuts. PMID:28117685

[Genome Rearrangements in Azospirillum brasilense Sp7 with the Involvement of the Plasmid pRhico and the Prophage phiAb-Cd].

PubMed

Katsy, E I; Petrova, L P

2015-12-01

Alphaproteobacteria of the species Azospirillum brasilense have a multicomponent genome that undergoes frequent spontaneous rearrangements, yielding changes in the plasmid profiles of strains. Specifically, variants (Cd, Sp7.K2, Sp7.1, Sp7.4, Sp7.8, etc.) of the type strainA. brasilense Sp7 that had lost a 115-MDa plasmid were previously selected. In many of them, the molecular weight of a 90-MDa plasmid (p90 or pRhico), which is a kind of "depot" for glycopolymer biosynthesis genes, increased. In this study, a collection of primers was designed to the plasmid pRhico and to the DNA of prophage phiAb-Cd integrated in it. The use ofthese primers in polymerase chain reactions allowed the detection of the probable excision of phiAb-Cd phage from the DNA of A. brasilense variants Sp7.4 and Sp7.8 and other alterations of the pRhico structure in A. brasilense strains Cd, Sp7.K2, and Sp7.8. The developed primers and PCR conditions may be recoin mended for primary analysis of spontaneous plasmid rearrangements in A. brasilense Sp7 and related strains.

Candida phyllophila sp. nov. and Candida vitiphila sp. nov., two novel yeast species from grape phylloplane in Thailand.

PubMed

Limtong, Savitree; Kaewwichian, Rungluk

2013-01-01

Three strains (K59(T), K60 and K70 (T)) representing two novel yeast species were isolated from the external surface of leaves of different wine grape (Vitis vinifera) plants, which were collected from the Kanchanaburi Research Station (N14°07'15.1″ E099°19'05.6″), Wang Dong Sub-district, Mueang District, Kanchanaburi Province, Thailand, by an enrichment technique. The sequences of the D1/D2 domain of the large subunit (LSU) rRNA gene of two strains (K59(T) and K60) were identical and differed from that of strain K70(T). In terms of pairwise sequence similarity of the D1/D2 domain, the closest species to the three strains was Candida asparagi but with 2.3% nucleotide substitutions for strains K59(T) and K60, and 2.1% nucleotide substitutions for strain K70(T). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and the sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene, the three strains were assigned to be two novel Candida species. Two strains (K59(T) and K60) were assigned as Candida phyllophila sp. nov. (type strain K59(T)=BCC 42662(T)=NBRC 107776(T)=CBS 12671(T)). Candida vitiphila sp. nov. is proposed for strain K70(T) (=BCC 42663(T)=NBRC 107777(T)=CBS 12672(T)).

Improvement of FK506 Production in the High-Yielding Strain Streptomyces sp. RM7011 by Engineering the Supply of Allylmalonyl-CoA Through a Combination of Genetic and Chemical Approach.

PubMed

Mo, SangJoon; Lee, Sung-Kwon; Jin, Ying-Yu; Suh, Joo-Won

2016-02-01

FK506, a widely used immunosuppressant, is a 23-membered polyketide macrolide that is produced by several Streptomyces species. FK506 high-yielding strain Streptomyces sp. RM7011 was developed from the discovered Streptomyces sp. KCCM 11116P by random mutagenesis in our previous study. The results of transcript expression analysis showed that the transcription levels of tcsA, B, C, and D were increased in Streptomyces sp. RM7011 by 2.1-, 3.1-, 3.3-, and 4.1- fold, respectively, compared with Streptomyces sp. KCCM 11116P. The overexpression of tcsABCD genes in Streptomyces sp. RM7011 gave rise to approximately 2.5-fold (238.1 μg/ml) increase in the level of FK506 production compared with that of Streptomyces sp. RM7011. When vinyl pentanoate was added into the culture broth of Streptomyces sp. RM7011, the level of FK506 production was approximately 2.2-fold (207.7 μg/ml) higher than that of the unsupplemented fermentation. Furthermore, supplementing the culture broth of Streptomyces sp. RM7011 expressing tcsABCD genes with vinyl pentanoate resulted in an additional 1.7-fold improvement in the FK506 titer (498.1 μg/ml) compared with that observed under nonsupplemented condition. Overall, the level of FK506 production was increased approximately 5.2-fold by engineering the supply of allylmalonyl-CoA in the high-yielding strain Streptomyces sp. RM7011, using a combination of overexpressing tcsABCD genes and adding vinyl pentanoate, as compared with Streptomyces sp. RM7011 (95.3 μg/ml). Moreover, among the three precursors analyzed, pentanoate was the most effective precursor, supporting the highest titer of FK506 in the FK506 high-yielding strain Streptomyces sp. RM7011.

A 1,3-1,4-β-glucan utilization regulon in Paenibacillus sp. strain JDR-2

Treesearch

Virginia Chow; Young Sik Kim; Mun Su Rhee; Neha Sawhney; Franz J. St. John; Guang Nong; John D. Rice; James F. Preston

2016-01-01

Paenibacillus sp. strain JDR-2 (Paenibacillus JDR-2) secretes a multimodular cell-associated glycoside hydrolase family 10 (GH10) endoxylanase (XynA10A1) that catalyzes the depolymerization of methylglucuronoxylan (MeGXn) and rapidly assimilates the products of depolymerization....

Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean.

PubMed

Mori, Koji; Maruyama, Akihiko; Urabe, Tetsuro; Suzuki, Ken-Ichiro; Hanada, Satoshi

2008-04-01

A novel thermophilic, strictly anaerobic archaeon, designated strain Arc51T, was isolated from a rock sample collected from a deep-sea hydrothermal field in Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Cells of the isolate were irregular cocci with single flagella and exhibited blue-green fluorescence at 436 nm. The optimum temperature, pH and NaCl concentration for growth were 70 degrees C, pH 6.5 and 3 % (w/v), respectively. Strain Arc51T could grow on thiosulfate or sulfite as an electron acceptor in the presence of hydrogen. This strain required acetate as a carbon source for its growth, suggesting that the reductive acetyl CoA pathway for CO2 fixation was incomplete. In addition, coenzyme M (2-mercaptoethanesulfonic acid), which is a known methyl carrier in methanogenesis, was also a requirement for growth of the strain. Analysis of the 16S rRNA gene sequence revealed that the isolate was similar to members of the genus Archaeoglobus, with sequence similarities of 93.6-97.2 %; the closest relative was Archaeoglobus veneficus. Phylogenetic analyses of the dsrAB and apsA genes, encoding the alpha and beta subunits of dissimilatory sulfite reductase and the alpha subunit of adenosine-5'-phosphosulfate reductase, respectively, produced results similar to those inferred from comparisons based on the 16S rRNA gene sequence. On the basis of phenotypic and phylogenetic data, strain Arc51T represents a novel species of the genus Archaeoglobus, for which the name Archaeoglobus infectus sp. nov. is proposed. The type strain is Arc51T (=NBRC 100649T=DSM 18877T).

Wickerhamomyces tratensis sp. nov. and Candida namnaoensis sp. nov., two novel ascomycetous yeast species in the Wickerhamomyces clade found in Thailand.

PubMed

Nakase, Takashi; Jindamorakot, Sasitorn; Am-In, Somjit; Ninomiya, Shinya; Kawasaki, Hiroko

2012-01-01

Two closely related yeast strains, ST-382 and ST-392, isolated in Thailand showed intermediate relatedness in the DNA-DNA hybridization experiment suggesting that the two strains represent closely related distinct species. In the tree based on the D1/D2 domain sequences of the large subunit rRNA gene, the two strains are located in a subclade in the Wickerhamomyces clade with high bootstrap support. In the D1/D2 domain, the two strains differed by two nucleotides and are assumed to be very closely related. Strain ST-392(T) (=BCC 15102(T) = NBRC 107799(T) = CBS 12176(T) forming hat-shaped ascospores is described as Wickerhamomyces tratensis sp. nov. and strain ST-382(T) (= BCC 15093(T) = NBRC 107800(T) = CBS 12175(T) is described as Candida namnaoensis sp. nov. because ascospores are not found in this strain. In phenotypic characteristics, W. tratensis and C. namnaoensis are discriminated by the ability of alcoholic fermentation and the assimilation of galactose, D-xylose and D-gluconic acid.

Hannaella phyllophila sp. nov., a basidiomycetous yeast species associated with plants in Thailand and Taiwan.

PubMed

Surussawadee, Janjira; Jindamorakot, Sasitorn; Nakase, Takashi; Lee, Ching-Fu; Limtong, Savitree

2015-07-01

Five strains representing one novel anamorphic yeast species were isolated from plant leaves collected in Thailand (strains DMKU-SP186(T), ST-111 and ST-201) and Taiwan (strains FN20L02 and SM13L16). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, they were assigned to a single novel species of the genus Hannaella. The sequences of the D1/D2 regions of the LSU rRNA genes of four of the strains (DMKU-SP186(T), ST-111, FN20L02 and SM13L16) were identical, while differing from strain ST-201 by 2 substitutions and 2 gaps. The nucleotide sequence of the ITS regions of the five strains differed from each other by between 0 and 3 nucleotide substitutions. The novel species was most closely related to Hannaella luteola, but showed 1.0-1.3% nucleotide substitutions (between 6 substitutions out of 568-606 nt and 8 substitutions, and 2 gaps out of 597 nt) in the D1/D2 region of the LSU rRNA gene and 1.4-2.0% nucleotide substitutions (6-9 substitutions out of 435 nt) in the ITS region. Ballistospores were produced by three of the strains on cornmeal agar at 15 and 20 °C after 4 weeks, while H. luteola did not produce ballistospores. The name Hannaella phyllophila sp. nov. is proposed. The type strain is DMKU-SP186(T) ( = BCC 69500(T) = NBRC 110428(T) = CBS 13921(T)).

Draft Genome Sequence of Sphingopyxis sp. Strain MWB1, a Crude-Oil-Degrading Marine Bacterium

PubMed Central

Kim, Jonghyun; Kim, Soo Jung; Kim, Seon Hee; Kim, Seung Il; Moon, Yoon-Jung; Park, Sung-Joon

2014-01-01

Sphingopyxis sp. strain MWB1, which is capable of degrading crude oil, diesel, and kerosene, was isolated from crude oil–contaminated seashore in Tae-an, South Korea. Here, we report the draft genome sequence of this strain, which comprises 3,118,428 bp with a G+C content of 62.85 mol%. PMID:25477411

[Modeling of lactic acid fermentation of leguminous plant juices].

PubMed

Shurkhno, R A; Validov, Sh Z; Boronin, A M; Naumova, R P

2006-01-01

Lactic acid fermentation of leguminous plant juices was modeled to provide a comparative efficiency assessment of the previously selected strains of lactic acid bacteria as potential components of starter cultures. Juices of the legumes fodder galega, red clover, and alfalfa were subjected to lactic acid fermentation in 27 variants of experiment. Local strains (Lactobacillus sp. RS 2, Lactobacillus sp. RS 3, and Lactobacillus sp. RS 4) and the collection strain Lactobacillus plantarum BS 933 appeared the most efficient (with reference to the rate and degree of acidogenesis, ratio of lactic and acetic acids, and dynamics of microflora) in fermenting fodder galega juice; Lactobacillus sp. RS 1, Lactobacillus sp. RS 2, Lactobacillus sp. RS 3, Lactobacillus sp. RS 4, and L. plantarum BS 933 were the most efficient for red clover juice. Correction of alfalfa juice fermentation using the tested lactic acid bacterial strains appeared inefficient, which is explainable by its increased protein content and a low level of the acids produced during fermentation.

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pathak, Ashish; Jaswal, Rajneesh; Stothard, Paul

ABSTRACT The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is reported. The genome comprises 6,706,934 bases, 6,059 coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of biodegradative genes, many located on genomic islands, were identified from strain B1, further enhancing our understanding of the versatile pseudomonads.

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment

DOE PAGES

Pathak, Ashish; Jaswal, Rajneesh; Stothard, Paul; ...

2018-06-21

ABSTRACT The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is reported. The genome comprises 6,706,934 bases, 6,059 coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of biodegradative genes, many located on genomic islands, were identified from strain B1, further enhancing our understanding of the versatile pseudomonads.

Lysophosphatidylcholine up-regulates human endothelial nitric oxide synthase gene transactivity by c-Jun N-terminal kinase signalling pathway

PubMed Central

Xing, Feiyue; Liu, Jing; Mo, Yongyan; Liu, Zhifeng; Qin, Qinghe; Wang, Jingzhen; Fan, Zhenhua; Long, Yutian; Liu, Na; Zhao, Kesen; Jiang, Yong

2009-01-01

Human endothelial nitric oxide synthase (eNOS) plays a pivotal role in maintaining blood pressure homeostasis and vascular integrity. It has recently been reported that mitogen-activated protein kinases (MAPKs) are intimately implicated in expression of eNOS. However detailed mechanism mediated by them remains to be clarified. In this study, eNOS gene transactivity in human umbilical vein endothelial cells was up-regulated by stimulation of lysophosphatidylcholine (LPC). The stimulation of LPC highly activated both extracellular signal-regulated kinase 1/2 (ERK1/2) and c-Jun N-terminal kinase (JNK), with differences in the dynamic processes of activation between them. Unexpectedly, p38 MAPK could not be activated by the stimulation of LPC. The activation of JNK signalling pathway by overexpression of JNK or its upstream kinase active mutant up-regulated the transactivity of eNOS significantly, but the activation of p38 signalling pathway down-regulated it largely. The inhibition of either ERK1/2 or JNK signalling pathway by kinase-selective inhibitors could markedly block the induction of the transactivity by LPC. It was observed by electrophoretic mobility shift assay that LPC stimulated both SP1 and AP1 DNA binding activity to go up. Additionally using decoy oligonucleotides proved that SP1 was necessary for maintaining the basal or stimulated transactivity, whereas AP1 contributed mainly to the increase of the stimulated transactivity. These findings indicate that the up-regulation of the eNOS gene transactivity by LPC involves the enhancement of SP1 transcription factor by the activation of JNK and ERK1/2 signalling pathways and AP1 transcription factor by the activation of JNK signalling pathway. PMID:18624763

Candida baotianmanensis sp. nov. and Candida pseudoviswanathii sp. nov., two ascosporic yeast species isolated from the gut of beetles.

PubMed

Ren, Yong-Cheng; Xu, Long-Long; Zhang, Lin; Hui, Feng-Li

2015-10-01

Four yeast strains were isolated from the gut of beetles collected on Baotianman Mountain and People's Park of Nanyang in Henan Province, China. These strains produced unconjugated asci with one or two ellipsoidal to elongate ascospores in a persistent ascus. Phylogenetic analysis of the D1/D2 domains of the LSU rRNA gene sequences indicated that the isolates represent two novel sexual species in the Candida/Lodderomyces clade. Candida baotianmanensis sp. nov. was located in a statistically well-supported branch together with Candida maltosa. Candida pseudoviswanathii sp. nov. formed a subclade with its closest relative Candida viswanathii supported by a strong bootstrap value. The two novel species were distinguished from their most closely related described species, Candida maltosa and Candida viswanathii, in the D1/D2 LSU rRNA gene and internal transcribed spacer (ITS) sequences and in phenotypic traits. The type strain of Candida baotianmanensis sp. nov. is NYNU 14719T ( = CBS 13915T = CICC 33052T), and the type strain of Candida pseudoviswanathii sp. nov. is NYNU 14772T ( = CBS 13916T = CICC 33053T). The MycoBank numbers for Candida baotianmanensis sp. nov. and Candida pseudoviswanathii sp. nov. are MB 812621 and MB 812622.

Properties of Polyhydroxyalkanoate Granules and Bioemulsifiers from Pseudomonas sp. and Burkholderia sp. Isolates Growing on Glucose.

PubMed

Sacco, Laís Postai; Castellane, Tereza Cristina Luque; Lopes, Erica Mendes; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

2016-03-01

A Burkholderia and Pseudomonas species designated as AB4 and AS1, respectively, were isolated from soil containing decomposing straw or sugar cane bagasse collected from Brazil. This study sought to evaluate the capacities of culture media, cell-free medium, and crude lysate preparations (containing PHB inclusion bodies) from bacterial cell cultures to stabilize emulsions with several hydrophobic compounds. Four conditions showed good production of bioemulsifiers (E24 ≥ 50 %), headed by substantially cell-free media from bacterial cell cultures in which bacterial isolates from Burkholderia sp. strain AB4 and Pseudomonas sp. strain AS1 were grown. Our results revealed that the both isolates (AB4 and AS1 strains) exhibited high emulsification indices (indicating usefulness in bioremediation) and good stabilities.

Bacterial oxidation of the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene.

PubMed Central

Schocken, M J; Gibson, D T

1984-01-01

A Beijerinckia sp. and a mutant strain, Beijerinckia sp. strain B8/36, were shown to cooxidize the polycyclic aromatic hydrocarbons acenaphthene and acenaphthylene. Both organisms oxidized acenaphthene to the same spectrum of metabolites, which included 1-acenaphthenol, 1-acenaphthenone, 1,2-acenaphthenediol, acenaphthenequinone, and a compound that was tentatively identified as 1,2-dihydroxyacenaphthylene. In contrast, acenaphthylene was oxidized to acenaphthenequinone and the compound tentatively identified as 1,2-dihydroxyacenaphthylene by the wild-type strain of Beijerinckia. Both of these products were also formed when the organism was incubated with synthetic cis-1,2-acenaphthenediol. A metabolite identified as cis-1,2-acenaphthenediol was formed from acenaphthylene by the mutant Beijerinckia sp. strain B8/36. Cell extracts prepared from the wild-type Beijerinckia strain contain a constitutive pyridine nucleotide-dependent dehydrogenase which can oxidize 1-acenaphthenol and 9-fluorenol. The results indicate that although acenaphthene and acenaphthylene are both oxidized to acenaphthenequinone, the pathways leading to the formation of this end product are different. PMID:6089663

New anamorphic yeast species: Candida infanticola sp. nov., Candida polysorbophila sp. nov., Candida transvaalensis sp. nov. and Trigonopsis californica sp. nov.

PubMed

Kurtzman, Cletus P

2007-08-01

Three new species of Candida and a new species of Trigonopsis are described based on their recognition from phylogenetic analysis of gene sequences from large subunit ribosomal RNA, ITS1/ITS2 rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II. Candida infanticola sp. nov. (type strain NRRL Y-17858, CBS 7922) was isolated from the ear of an infant in Germany and is closely related to Candida sorbophila. Candida polysorbophila sp. nov. (type strain NRRL Y-27161, CBS 7317) is a member of the Zygoascus clade and was isolated in South Africa as a contaminant from an emulsion of white oil and polysorbate. Candida transvaalensis sp. nov. (type strain NRRL Y-27140, CBS 6663) was obtained from forest litter, the Transvaal, South Africa, and forms an isolated clade with Candida santjacobensis. Trigonopsis californica sp. nov. (type strain NRRL Y-27307, CBS 10351) represents a contaminant from wine in California, and forms a well-supported clade with Trigonopsis cantarellii, Trigonopsis variabilis and Trigonopsis vinaria.

Candida sirachaensis sp. nov. and Candida sakaeoensis sp. nov. two anamorphic yeast species from phylloplane in Thailand.

PubMed

Limtong, Savitree; Koowadjanakul, Nampueng; Jindamorakot, Sasitorn; Yongmanitchai, Wichien; Nakase, Takashi

2012-08-01

Three strains (LM008(T), LM068 and LM078(T)), representing two novel yeast species were isolated from the phylloplane of three plant species by an enrichment technique. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and the sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal spacer region, the three strains were assigned as two novel Candida species. Strain LM008(T) was assigned to be Candida sirachaensis sp. nov. (type strain LM008(T) = BCC 47628(T) = NBRC 108605(T) CBS 12094(T)) in the Starmerella clade. Two strains (LM068 and LM078(T)) represent a single species in the Lodderomyces-Spathaspora clade for which the name Candida sakaeoensis sp. nov. is proposed with the type strain LM078(T) = BCC 47632(T) = NBRC 108895(T) = CBS 12318(T).

Wickerhamomyces xylosica sp. nov. and Candida phayaonensis sp. nov., two xylose-assimilating yeast species from soil.

PubMed

Limtong, Savitree; Nitiyon, Sukanya; Kaewwichian, Rungluk; Jindamorakot, Sasitorn; Am-In, Somjit; Yongmanitchai, Wichien

2012-11-01

Two strains (NT29(T) and NT31(T)) of xylose-assimilating yeasts were obtained from soils collected in northern Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer region, the two strains were found to represent two novel ascomycete yeast species. Strain NT29(T) was assigned to the genus Candida belonging to the Pichia clade as a representative of Candida phayaonensis sp. nov.; the type strain is NT29(T) (=BCC 47634(T)=NBRC 108868(T)=CBS 12319(T)). Strain NT31(T) represented a novel Wickerhamomyces species, which was named Wickerhamomyces xylosica sp. nov.; the type strain is NT31(T) (=BCC 47635(T)=NBRC 108869(T)=CBS 12320(T)).

Characterization of plant growth-promoting traits of free-living diazotrophic bacteria and their inoculation effects on growth and nitrogen uptake of crop plants.

PubMed

Islam, Md Rashedul; Madhaiyan, M; Deka Boruah, Hari P; Yim, Woojong; Lee, Gillseung; Saravanan, V S; Fu, Qingling; Hu, Hongqing; Sa, Tongmin

2009-10-01

The search for diverse plant growth-promoting (PGP) diazotrophic bacteria is gaining momentum as efforts are made to exploit them as biofertilizers for various economically important crops. In the present study, 17 diazotrophic strains belonging to eight different genera isolated from rice paddy fields were screened for multiple PGP traits and evaluated for their inoculation effects on canola and rice plants. All of the strains tested positive for 1- aminocyclopropane-1-carboxylate (ACC) deaminase activity and production of indole 3-acetic acid (IAA) and ammonia (NH3). Additionally, four of the strains were able to solubilize phosphorus (P), five tested positive for zinc (Zn) solubilization and sulfur (S) oxidation, and eight strains produced siderophores. Based on the presence of multiple PGP traits, 10 strains were selected for inoculation studies. Treatment with Herbaspirillum sp. RFNB26 resulted in maximum root length (54.3%), seedling vigor, and dry biomass in canola, whereas Paenibacillus sp. RFNB4 exhibited the lowest activity under gnotobiotic conditions. However, under pot culture conditions, Paenibacillus sp. RFNB4 significantly increased plant height and dry biomass production by 42.3% and 29.5%, respectively. Canola plants and rhizosphere soils inoculated with Bacillus sp. RFNB6 exhibited significantly higher nitrogenase activity. In greenhouse experiments, Serratia sp. RFNB18 increased rice plant height by 35.1%, Xanthomonas sp. RFNB24 enhanced biomass production by 84.6%, and rice rhizosphere soils inoculated with Herbaspirillum sp. RFNB26 exhibited the highest nitrogenase activity. Our findings indicate that most of the selected strains possess multiple PGP properties that significantly improve the growth parameters of the two plants when tested under controlled conditions.

Host innate inflammatory factors and staphylococcal protein A influence the duration of human Staphylococcus aureus nasal carriage.

PubMed

Cole, A L; Muthukrishnan, G; Chong, C; Beavis, A; Eade, C R; Wood, M P; Deichen, M G; Cole, A M

2016-11-01

Human Staphylococcus aureus (SA) nasal carriage provides a reservoir for the dissemination of infectious strains; however, factors regulating the establishment and persistence of nasal colonization are mostly unknown. We measured carriage duration and nasal fluid inflammatory markers after nasally inoculating healthy participants with their previously isolated SA strains. Out of 15 studies, 10 resulted in rapid clearance (9±6 days) that corresponded with upregulated chemokines, growth factors, and predominantly Th1-type cytokines, but not interleukin (IL)-17. Nasal SA persistence corresponded with elevated baseline levels of macrophage inflammatory protein-1β, IL-1β, and IL-6, no induction of inflammatory factors after inoculation, and decreased IL-1 receptor antagonist/IL-1β ratio. SA-expressed staphylococcal protein A (SpA) levels correlated positively with carriage duration. Competitive inoculation studies revealed that isogenic SpA knockout (ΔSpA) strains were cleared faster than wild type only in participants with upregulated inflammatory markers after inoculation. The remaining participants did not mount an inflammatory response and did not clear either strain. ΔSpA strains demonstrated lower growth rates in carrier nasal fluids and lower survival rates when incubated with neutrophils. Collectively, the presented studies identify innate immune effectors that cooperatively modulate nasal carriage duration, and confirm SpA as a bacterial codeterminant of SA nasal carriage.

Host innate inflammatory factors and staphylococcal protein A influence the duration of human Staphylococcus aureus nasal carriage

PubMed Central

Cole, Amy L.; Muthukrishnan, Gowrishankar; Chong, Christine; Beavis, Ashley; Eade, Colleen R.; Wood, Matthew P.; Deichen, Michael G.; Cole, Alexander M.

2016-01-01

Human Staphylococcus aureus (SA) nasal carriage provides a reservoir for the dissemination of infectious strains; however, factors regulating the establishment and persistence of nasal colonization are mostly unknown. We measured carriage duration and nasal fluid inflammatory markers after nasally inoculating healthy participants with their previously isolated SA strains. Ten out of 15 studies resulted in rapid clearance (9±6 days) that corresponded with upregulated chemokines, growth factors, and predominantly Th1-type cytokines, but not IL-17. Nasal SA persistence corresponded with elevated baseline levels of MIP-1β, IL-1β, and IL-6, no induction of inflammatory factors post-inoculation, and decreased IL-1RA:IL-1β ratio. SA-expressed staphylococcal protein A (SpA) levels correlated positively with carriage duration. Competitive inoculation studies revealed that isogenic SpA knockout (ΔSpA) strains were cleared faster than wild-type only in participants with upregulated inflammatory markers post-inoculation. The remaining participants did not mount an inflammatory response and did not clear either strain. ΔSpA strains demonstrated lower growth rates in carrier nasal fluids and lower survival rates when incubated with neutrophils. Collectively, the presented studies identify innate immune effectors that cooperatively modulate nasal carriage duration, and confirm SpA as a bacterial co-determinant of SA nasal carriage. PMID:26838052

Complete Genome Sequence of Sulfuriferula sp. Strain AH1, a Sulfur-Oxidizing Autotroph Isolated from Weathered Mine Tailings from the Duluth Complex in Minnesota

PubMed Central

Roepke, Elizabeth W.; Hua, An An; Flood, Beverly E.; Bailey, Jake V.

2017-01-01

ABSTRACT We report the closed and annotated genome sequence of Sulfuriferula sp. strain AH1. Strain AH1 has a 2,877,007-bp chromosome that includes a partial Sox system for inorganic sulfur oxidation and a complete nitrogen fixation pathway. It also has a single 39,138-bp plasmid with genes for arsenic and mercury resistance. PMID:28798167

Study on the biodegradation of crude oil by free and immobilized bacterial consortium in marine environment.

PubMed

Chen, Qingguo; Li, Jingjing; Liu, Mei; Sun, Huiling; Bao, Mutai

2017-01-01

Five strains of bacteria, namely, Exiguobacterium sp. ASW-1, Pseudomonas aeruginosa strain ASW-2, Alcaligenes sp. ASW-3, Alcaligenes sp. ASS-1, and Bacillus sp. ASS-2, were isolated from the Zhejiang coast in China. The mixed flora of the five strains performed well with degrading 75.1% crude oil (1%, w/v) in 7 days. The calcium alginate-activated carbon embedding carrier was used to immobilize bacterial consortium. Immobilized cells performed better than free ones in variations of environmental factors containing incubated temperature, initial pH, salinity of the medium and crude oil concentration. The degradation process of crude oil by immobilized bacteria was accelerated compared with that of the free ones. Bacterial consortium showed better performance on biodegradation of normal alkanes than that of PAHs. Improvement of immobilization on the biodegradation efficiency of normal alkanes (31.9%) was apparently high than that of PAHs (1.9%).

Study on the biodegradation of crude oil by free and immobilized bacterial consortium in marine environment

PubMed Central

Li, Jingjing; Liu, Mei; Sun, Huiling; Bao, Mutai

2017-01-01

Five strains of bacteria, namely, Exiguobacterium sp. ASW-1, Pseudomonas aeruginosa strain ASW-2, Alcaligenes sp. ASW-3, Alcaligenes sp. ASS-1, and Bacillus sp. ASS-2, were isolated from the Zhejiang coast in China. The mixed flora of the five strains performed well with degrading 75.1% crude oil (1%, w/v) in 7 days. The calcium alginate—activated carbon embedding carrier was used to immobilize bacterial consortium. Immobilized cells performed better than free ones in variations of environmental factors containing incubated temperature, initial pH, salinity of the medium and crude oil concentration. The degradation process of crude oil by immobilized bacteria was accelerated compared with that of the free ones. Bacterial consortium showed better performance on biodegradation of normal alkanes than that of PAHs. Improvement of immobilization on the biodegradation efficiency of normal alkanes (31.9%) was apparently high than that of PAHs (1.9%). PMID:28346510

Bioremediation of kerosene I: A case study in liquid media.

PubMed

Gouda, Mona K; Omar, Sanaa H; Chekroud, Zohra A; Nour Eldin, Hemdan M

2007-11-01

The ability of different local isolates in addition to some isolates from Germany to degrade kerosene in liquid medium was studied. The results showed that the percent of kerosene degradation varied among the different organisms and that 59-94% of kerosene was degraded after 21d. Two local isolates (Pseudomonas sp. AP and Pseudomonas sp. CK) and one German isolate (Gordonia sp. DM) were selected for this study. The addition of wheat bran, as co-substrate, stimulated the kerosene degradation by the two local strains, while glucose inhibited the degradation rate using the three organisms with different rates. Ammonium nitrate and urea was the best nitrogen sources. The use of superphosphate (as phosphorus source) in the presence of urea stimulates the degradation rate. It was also observed that the addition of 1% surfactants, like Triton X-100, Igepal, Tergitol, or Tween 20 and 80 enhanced the kerosene degradation. The degradation percent lied between 94% and 98%. The ability of the tested organisms to degrade kerosene concentration from 2% to 8% was evaluated. It was found that the three organisms degraded about 65-85% from 8% kerosene after 21d. The use of rice straw-immobilized cells reduced the time of degradation and enhanced the degradation ability of the organisms. The sodium dodecyl sulphate-polyacrylamide gel electrophoresis revealed the presence of a common protein band when the tested organisms were grown on kerosene.

Improvement of Fish Sauce Quality by Strain CMC5-3-1: A Novel Species of Staphylococcus sp.

PubMed

Udomsil, Natteewan; Rodtong, Sureelak; Tanasupawat, Somboon; Yongsawatdigul, Jirawat

2015-09-01

Staphylococcus sp. CMC5-3-1 and CMS5-7-5 isolated from fermented fish sauce at 3 to 7 mo, respectively, showed different characteristics on protein hydrolysis and volatile formation. These Gram-positive cocci were able to grow in up to 15% NaCl with the optimum at 0.5% to 5% NaCl in tryptic soy broth. Based on ribosomal 16S rRNA gene sequences, Staphylococcus sp. CMC5-3-1 and CMS5-7-5 showed 99.0% similarity to that of Staphylococcus piscifermentans JCM 6057(T) , but DNA-DNA relatedness was <30%, indicating that they were likely to be new species. DNA relatedness between these 2 strains was only 65%, suggesting that they also belonged to different species. The α-amino group content of 6-month-old fish sauce inoculated with Staphylococcus sp. CMC5-3-1 was 740.5 mM, which was higher than that inoculated by the strain CMS5-7-5 (662.14 mM, P < 0.05). Histamine was not produced during fermentations with both strains. Fish sauce inoculated with Staphylococcus sp. CMC5-3-1 showed the highest content of total glutamic acid (P < 0.05). The major volatile compound detected in fish sauce inoculated with Staphylococcus sp. CMC5-3-1 was 2-methypropanal, contributing to the desirable dark chocolate note. Staphylococcus sp. CMC5-3-1 could be applied as a starter culture to improve the umami and aroma of fish sauce. © 2015 Institute of Food Technologists®

Use of essential gene, encoding prophobilinogen deaminase from extreme psychrophilic Colwellia sp. C1, to generate temperature-sensitive strain of Francisella novicida.

PubMed

Pankowski, J A

2016-08-01

Previously, several essential genes from psychrophilic bacteria have been substituted for their homologues in mesophilic bacterial pathogens to make the latter temperature sensitive. It has been noted that an essential ligA gene from an extreme psychrophile, Colwellia sp. C1, yielded a gene product that is inactivated at 27°C, the lowest that has been observed for any psychrophilic enzyme, and hypothesized that other essential proteins of that strain would also have low inactivation temperatures. This work describes the partial sequencing of the genome of Colwellia sp. C1 strain and the identification of 24 open reading frames encoding homologues of highly conserved bacterial essential genes. The gene encoding porphobilinogen deaminase (hemC), which is involved in the pathway of haem synthesis, has been tested for its ability to convert Francisella novicida into a temperature-sensitive strain. The hybrid strain carrying the C1-derived hemC gene exhibited a temperature-sensitive phenotype with a restrictive temperature of 36°C. These results support the conclusion that Colwellia sp. C1 is a rich source of heat-labile enzymes. The issue of biosafety is often raised when it comes to work with pathogenic organisms. The main concern is caused by the risk of researchers being exposed to infectious doses of dangerous microbes. This paper analyses essential genes identified in partial genomic sequence of the psychrophilic bacterium Collwelia sp. C1. These sequences can be used as a mean of generating temperature-sensitive strains of pathogenic bacteria. Such strains are incapable of surviving at the temperature of human body. This means they could be applied as vaccines or for safer work with dangerous organisms. © 2016 The Society for Applied Microbiology.

Reduction of Selenite to Elemental Red Selenium by Pseudomonas sp. strain CA5

USDA-ARS?s Scientific Manuscript database

A Pseudomonas sp. that may be useful in bioremediation projects was isolated from soil. The strain is of potential value because it reduces selenite to elemental red selenium and is unusual in that it was resistant to high concentrations of both selenate and selenite. Cell of the strain removed 1....

Candida chanthaburiensis sp. nov., Candida kungkrabaensis sp. nov. and Candida suratensis sp. nov., three novel yeast species from decaying plant materials submerged in water of mangrove forests.

PubMed

Limtong, Savitree; Yongmanitchai, Wichien

2010-10-01

In a taxonomic study of yeasts isolated from decaying plant materials submerged in water of mangrove forests in Thailand, three strains isolated from tree bark (EM33(T)), a fallen leaf (EM40(T)) and a detached branch (SM56(T)) were found to represent three novel yeast species. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, the sequence analysis of the D1/D2 domain of the large subunit (LSU) rRNA gene, and the phylogenetic analysis, the three strains were assigned as three novel Candida species. They were named as Candida chanthaburiensis sp. nov. (type strain EM33(T) = BCC 23057(T) = NBRC 102176(T) = CBS 10926(T)), Candida kungkrabaensis sp. nov. (type strain EM40(T) = BCC 23060(T) = NBRC 102179(T) = CBS 10927(T)), and Candida suratensis sp. nov. (type strain SM56(T) = BCC 25961(T) = NBRC 103858(T) = CBS 10928(T)).

A Survey of Aflatoxin-Producing Aspergillus sp. from Peanut Field Soils in Four Agroecological Zones of China.

PubMed

Zhang, Chushu; Selvaraj, Jonathan Nimal; Yang, Qingli; Liu, Yang

2017-01-20

Peanut pods are easily infected by aflatoxin-producing Aspergillus sp.ecies from field soil. To assess the aflatoxin-producing Aspergillus sp. in different peanut field soils, 344 aflatoxin-producing Aspergillus strains were isolated from 600 soil samples of four agroecological zones in China (the Southeast coastal zone (SEC), the Yangtze River zone (YZR), the Yellow River zone (YR) and the Northeast zone (NE)). Nearly 94.2% (324/344) of strains were A. flavus and 5.8% (20/344) of strains were A. parasiticus . YZR had the highest population density of Aspergillus sp. and positive rate of aflatoxin production in isolated strains (1039.3 cfu·g -1 , 80.7%), the second was SEC (191.5 cfu·g -1 , 48.7%), the third was YR (26.5 cfu·g -1 , 22.7%), and the last was NE (2.4 cfu·g -1 , 6.6%). The highest risk of AFB₁ contamination on peanut was in YZR which had the largest number of AFB₁ producing isolates in 1g soil, followed by SEC and YR, and the lowest was NE. The potential risk of AFB₁ contamination in peanuts can increase with increasing population density and a positive rate of aflatoxin-producing Aspergillus sp. in field soils, suggesting that reducing aflatoxigenic Aspergillus sp. in field soils could prevent AFB₁ contamination in peanuts.

Regulation of Anabaena sp. strain PCC 7120 glutamine synthetase activity in a Synechocystis sp. strain PCC 6803 derivative strain bearing the Anabaena glnA gene and a mutated host glnA gene.

PubMed Central

Mérida, A; Flores, E; Florencio, F J

1992-01-01

The glnA gene from Synechocystis sp. strain PCC 6803 was cloned by hybridization with the glnA gene from Anabaena sp. strain PCC 7120, and a deletion-insertion mutation of the Synechocystis gene was generated in vitro. A strain derived from Synechocystis sp. strain PCC 6803 which contained integrated into the chromosome, in addition to its own glnA gene, the Anabaena glnA gene was constructed. From that strain, a Synechocystis sp. glnA mutant could be obtained by transformation with the inactivated Synechocystis glnA gene; this mutant grew by using Anabaena glutamine synthetase and was not a glutamine auxotroph. A Synechocystis sp. glnA mutant could not be obtained, however, from the wild-type Synechocystis sp. The Anabaena glutamine synthetase enzyme was subject to ammonium-promoted inactivation when expressed in the Synechocystis strain but not in the Anabaena strain itself. Images PMID:1345914

Characterization of Paenibacillus sp. MBT213 Isolated from Raw Milk and Its Ability to Convert Ginsenoside Rb1 into Ginsenoside Rd from Panax ginseng

PubMed Central

Cho, Soo Hyun; Park, Young W; Song, Gyu Yong

2017-01-01

This study was conducted to isolate and characterize Paenibacillus sp. MBT213 possessing β-glucosidase activity from raw milk, and examine the enzymatic capacity on the hydrolysis of a major ginsenoside (Rb1). Strain MBT213 was found to have a high hydrolytic ability on ginsenoside Rb1 by Esculin Iron Agar test. 16S rDNA analysis revealed that MBT213 was Paenibacillu sp. Crude enzyme of MBT213 strain exhibited high conversion capacity on ginsenoside Rb1 into ginsenoside Rd proven by TLC and HPLC analyses. The API ZYM kit confirmed that Paenibacillu sp. MBT213 exerted higher β-glucosidase and β-galactosidase activity than other strains. Optimum pH and temperature for crude enzyme were found at 7.0 and 35°C in hydrolysis of ginsenoside Rb1. After 10 d of optimal reaction conditions for the crude enzyme, ginsenoside Rb1 fully converted to ginsenoside Rd. Ginseng roots (20%) were fermented for 14 d, and analyzed by HPLC showed that amount of ginsenoside Rb1 significantly decreased, while that of ginsenoside Rd was significantly increased. The study confirmed that the β-glucosidase produced by Paenibacillus sp. MBT213 can hydrolyze the major ginsenoside Rb1 and convert to Rd during fermentation of the ginseng. The β-glucosidase activity of this novel Paenibacillus sp. MBT213 strain may be utilized in development of variety of health foods, dairy foods and pharmaceutical products. PMID:29147097

Stereospecific oxidation of (R)- and (S)-1-indanol by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4.

PubMed

Lee, K; Resnick, S M; Gibson, D T

1997-05-01

A recombinant Escherichia coli strain which expresses naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 oxidized (S)-1-indanol to trans-(1S,3S)-indan-1,3-diol (95.5%) and (R)-3-hydroxy-1-indanone (4.5%). The same cells oxidized (R)-1-indanol to cis-1,3-indandiol (71%), (R)-3-hydroxy-1-indanone (18.2%), and cis-1,2,3-indantriol (10.8%). Purified NDO oxidized (S)-1-indenol to both syn- and anti-2,3-dihydroxy-1-indanol.

Production of macrolide antibiotics from a cytotoxic soil Streptomyces sp. strain ZDB.

PubMed

Dame, Zerihun T; Ruanpanun, Pornthip

2017-07-01

Crude extract from a culture of a soil Streptomyces sp. strain ZDB showed toxicity towards Artemia salina and antimicrobial activity against Escherichia coli, Bacillus subtilis, Staphylococcus aureus, Chlorella vulgaris, and Chlorella sorokiniana. Large scale fermentation of the strain led to the isolation of the macrolide antibiotics, bafilomycins A1 (1), B1 (2), and D (3) together with nonactic acid (4) and bostrycoidin-9-methyl ether (5). Structures of the antibiotics were determined based on spectral data analysis. We describe the isolation of the compounds and characterization of the producing strain.

Starmerella reginensis f.a., sp. nov. and Starmerella kourouensis f.a., sp. nov., isolated from flowers in French Guiana.

PubMed

Amoikon, Tiemele Laurent Simon; Grondin, Cécile; Djéni, Théodore N'Dédé; Jacques, Noémie; Casaregola, Serge

2018-05-21

Analysis of yeasts isolated from various biotopes in French Guiana led to the identification of two strains isolated from flowers and designated CLIB 1634 T and CLIB 1707 T . Comparison of the D1/D2 domain of the large subunit (LSU D1/D2) rRNA gene sequences of CLIB 1634 T and CLIB 1707 T to those in the GenBank database revealed that these strains belong to the Starmerella clade. Strain CLIB 1634 T was shown to diverge from the closely related Starmerella apicola type strain CBS 2868 T with a sequence divergence of 1.34 and 1.30 %, in the LSU D1/D2 rRNA gene and internal transcribed spacer (ITS) sequences respectively. Strain CLIB 1634 T and Candida apicola CBS 2868 T diverged by 3.81 and 14.96 % at the level of the protein-coding gene partial sequences EF-1α and RPB2, respectively. CLIB 1707 T was found to have sequence divergence of 3.88 and 9.16 % in the LSU D1/D2 rRNA gene and ITS, respectively, from that of the most closely related species Starmerella ratchasimensis type strain CBS 10611 T . The species Starmerella reginensis f.a., sp. nov. and Starmerella kourouensis f.a., sp. nov. are proposed to accommodate strains CLIB 1634 T (=CBS 15247 T ) and CLIB 1707 T (=CBS 15257 T ), respectively.

Draft Genome Sequence of Pseudoalteromonas sp. Strain ND6B, an Oil-Degrading Isolate from Eastern Mediterranean Sea Water Collected at a Depth of 1,210 Meters

DOE PAGES

Harris, Austin P.; Techtmann, Stephen M.; Stelling, Savannah C.; ...

2014-11-26

We report the draft genome of Pseudoalteromonas sp. strain ND6B, which is able to grow with crude oil as a carbon source. Strain ND6B was isolated from eastern Mediterranean Sea deep water at a depth of 1,210 m. The genome of strain ND6B provides insight into the oil-degrading ability of the Pseudoalteromonas species.

Genome sequence of Shigella flexneri strain SP1, a diarrheal isolate that encodes an extended-spectrum β-lactamase (ESBL).

PubMed

Shen, Ping; Fan, Jianzhong; Guo, Lihua; Li, Jiahua; Li, Ang; Zhang, Jing; Ying, Chaoqun; Ji, Jinru; Xu, Hao; Zheng, Beiwen; Xiao, Yonghong

2017-05-12

Shigellosis is the most common cause of gastrointestinal infections in developing countries. In China, the species most frequently responsible for shigellosis is Shigella flexneri. S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on biochemical and serological properties. Moreover, increasing numbers of ESBL-producing Shigella strains have been isolated from clinical samples. Despite this, only a few cases of ESBL-producing Shigella have been described in China. Therefore, a better understanding of ESBL-producing Shigella from a genomic standpoint is required. In this study, a S. flexneri type 1a isolate SP1 harboring bla CTX-M-14 , which was recovered from the patient with diarrhea, was subjected to whole genome sequencing. The draft genome assembly of S. flexneri strain SP1 consisted of 4,592,345 bp with a G+C content of 50.46%. RAST analysis revealed the genome contained 4798 coding sequences (CDSs) and 100 RNA-encoding genes. We detected one incomplete prophage and six candidate CRISPR loci in the genome. In vitro antimicrobial susceptibility testing demonstrated that strain SP1 is resistant to ampicillin, amoxicillin/clavulanic acid, cefazolin, ceftriaxone and trimethoprim. In silico analysis detected genes mediating resistance to aminoglycosides, β-lactams, phenicol, tetracycline, sulphonamides, and trimethoprim. The bla CTX-M-14 gene was located on an IncFII2 plasmid. A series of virulence factors were identified in the genome. In this study, we report the whole genome sequence of a bla CTX-M-14 -encoding S. flexneri strain SP1. Dozens of resistance determinants were detected in the genome and may be responsible for the multidrug-resistance of this strain, although further confirmation studies are warranted. Numerous virulence factors identified in the strain suggest that isolate SP1 is potential pathogenic. The availability of the genome sequence and comparative analysis with other S. flexneri strains provides the basis to further address the evolution of drug resistance mechanisms and pathogenicity in S. flexneri.

Corynebacterium timonense sp. nov. and Corynebacterium massiliense sp. nov., isolated from human blood and human articular hip fluid.

PubMed

Merhej, Vicky; Falsen, Enevold; Raoult, Didier; Roux, Véronique

2009-08-01

Gram-positive, facultatively anaerobic, rod-shaped bacteria were isolated from the blood of a patient with endocarditis (strain 5401744T) and from the hip joint fluid of a patient with an infected orthopaedic prosthesis (strain 5402485T). These strains were characterized by using a polyphasic taxonomic approach. Based on cellular morphology and biochemical criteria the two isolates were tentatively assigned to the genus Corynebacterium, although they did not correspond to any recognized species. The predominant fatty acids were a mix of C18:2omega6,9c and anteiso-C18:0 (32.1% of the total), C16:0 (26.3%) and C18:1omega9c (22.5%) for strain 5402485T and C18:1omega9c (36.4%), C17:1omega9c (27.1%) and C16:0 (10.9%) for strain 5401744T. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain 5401744T was closely related to the type strains of Corynebacterium auris, Corynebacterium capitovis, Corynebacterium lipophiloflavum and Corynebacterium mycetoides (97.0, 96.6, 96.5 and 96.3% similarity, respectively) and strain 5402485T was closely related to the type strains of Corynebacterium macginleyi, Corynebacterium accolens, Corynebacterium tuberculostearicum, Corynebacterium confusum, Corynebacterium mastitidis and Corynebacterium renale (95.6, 95.3, 95.3, 94.5, 94.0 and 93.5%, respectively). On the basis of phenotypic data and phylogenetic inference, these isolates are considered to represent two novel species of the genus Corynebacterium, for which the names Corynebacterium timonense sp. nov. (type strain, 5401744T=CSUR P20T=CIP 109424T=CCUG 53856T) and Corynebacterium massiliense sp. nov. (type strain, 5402485T=CSUR P19T=CIP 109423T=CCUG 53857T) are proposed.

Bacillus thuringiensis subsp. kurstaki HD1 as a factory to synthesize alkali-labile ChiA74∆sp chitinase inclusions, Cry crystals and spores for applied use.

PubMed

Barboza-Corona, José Eleazar; Delgadillo-Ángeles, Jorge Luis; Castañeda-Ramírez, José Cristóbal; Barboza-Pérez, Uriel Eleazar; Casados-Vázquez, Luz Edith; Bideshi, Dennis K; del Rincón-Castro, Ma Cristina

2014-01-24

The endochitinase ChiA74 is a soluble secreted enzyme produced by Bacillus thuringiensis that synergizes the entomotoxigenecity of Cry proteins that accumulate as intracellular crystalline inclusion during sporulation. The purpose of this study was to produce alkaline-soluble ChiA74∆sp inclusions in B. thuringiensis, and to determine its effect on Cry crystal production, sporulation and toxicity to an important agronomical insect, Manduca sexta. To this end we deleted the secretion signal peptide-coding sequence of chiA74 (i.e. chiA74∆sp) and expressed it under its native promoter (pEHchiA74∆sp) or strong chimeric sporulation-dependent cytA-p/STAB-SD promoter (pEBchiA74∆sp) in Escherichia coli, acrystalliferous B. thuringiensis (4Q7) and B. thuringiensis HD1. Based on mRNA analyses, up to ~9-fold increase in expression of chiA74∆sp was observed using the cytA-p/STAB-SD promoter. ChiA74∆sp (~70 kDa) formed intracellular inclusions that frequently accumulated at the poles of cells. ChiA74∆sp inclusions were dissolved in alkali and reducing conditions, similar to Cry crystals, and retained its activity in a wide range of pH (5 to 9), but showed a drastic reduction (~70%) at pH 10. Chitinase activity of E. coli-pEHchiA74∆sp was ~150 mU/mL, and in E. coli-pEBchiA74∆sp, 250 mU/mL. 4Q7-pEBchiA74∆sp and 4Q7-pEHchiA74∆sp had activities of ~127 mU/mL and ~41 mU/mL, respectively. The endochitinase activity in HD1-pEBchiA74∆sp increased 42x when compared to parental HD1 strain. HD1-pEBchiA74∆sp and HD1 harbored typical bipyramidal Cry inclusions, but crystals in the recombinant were ~30% smaller. Additionally, a 3x increase in the number of viable spores was observed in cultures of the recombinant strain when compared to HD1. Bioassays against first instar larvae of M. sexta with spore-crystals of HD1 or spore-crystal-ChiA74∆sp inclusions of HD1-pEBchiA74∆sp showed LC₅₀s of 67.30 ng/cm² and 41.45 ng/cm², respectively. Alkali-labile ChiA74∆sp inclusion bodies can be synthesized in E. coli and B. thuringiensis strains. We demonstrated for the first time the applied utility of synthesis of ChiA74∆sp inclusions, Cry crystals and spores in the same sporangium of HD1, a strain used successfully worldwide to control economically significant lepidopteran pests of agriculture. Our findings will allow to us develop strategies to modify expression of ChiA74∆sp while maximizing Cry crystal synthesis in commercial strains of B. thuringiensis.

Carotenoid production and phenotypic variation in Azospirillum brasilense.

PubMed

Brenholtz, Gal Reem; Tamir-Ariel, Dafna; Okon, Yaacov; Burdman, Saul

2017-06-01

We assessed the occurrence of phenotypic variation in Azospirillum brasilense strains Sp7, Cd, Sp245, Az39 and phv2 during growth in rich media, screening for variants altered in colony pigmentation or extracellular polysaccharide (EPS) production. Previous studies showed that EPS-overproducing variants of Sp7 appear frequently following starvation or growth in minimal medium. In contrast, no such variants were detected during growth in rich media in the tested strains except for few variants of phv2. Regarding alteration in colony pigmentation (from pink to white in strain Cd and from white to pink in the others), strain Sp7 showed a relatively high frequency of variation (0.009-0.026%). Strain Cd showed a lower frequency of alteration in pigmentation (0-0.008%), and this type of variation was not detected in the other strains. In A. brasilense, carotenoid synthesis is controlled by two RpoE sigma factors and their cognate ChrR anti-sigma factors, the latter acting as negative regulators of carotenoid synthesis. Here, all tested (n = 28) pink variants of Sp7 carried mutations in one of the anti-sigma factor genes, chrR1. Our findings indicate that, in A. brasilense, phenotypic variation is strain- and environment-dependent and support the central role of ChrR1 in regulation of carotenoid production. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Algicidal activity against Skeletonema costatum by marine bacteria isolated from a high frequency harmful algal blooms area in southern Chinese coast.

PubMed

Shi, Rongjun; Huang, Honghui; Qi, Zhanhui; Hu, Weian; Tian, Ziyang; Dai, Ming

2013-01-01

Four marine bacterial strains P1, P5, N5 and N21 were isolated from the surface water and sediment of Mirs Bay in southern Chinese coast using the liquid infection method with 48-well plates. These bacteria were all shown to have algicidal activities against Skeletonema costatum. Based on morphological observations, biochemical tests and homology comparisons by 16S rDNA sequences, the isolated strains P1, P5, N5 and N21 were identified as Halobacillus sp., Muricauda sp., Kangiella sp. and Roseivirga sp., respectively. Our results showed that bacterial strain P1 killed S. costatum by release of heat labile algicide, while strains P5, N5 and N21 killed them directly. The algicidal processes of four bacterial strains were different. Strains P1, N5 and N21 disrupted the chain structure and S. costatum appeared as single cells, in which the cellular components were aggregated and the individual cells were inflated and finally lysed, while strain P5 decomposed the algal chains directly. We also showed that the algicidal activities of the bacterial strains were concentration-dependent. More specifically, 10 % (v/v) of bacteria in algae showed the strongest algicidal activities, as all S. costatum cells were killed by strains N5 and N21 within 72 h and by strains P1 and P5 within 96 h. 5 % of bacteria in algae also showed significant algicidal activities, as all S. costatum were killed by strains N5, P5 and N21 within 72, 96 and 120 h, respectively, whereas at this concentration, only 73.4 % of S. costatum cells exposed to strain P1 were killed within 120 h. At the concentration of 1 % bacteria in algae, the number of S. costatum cells continued to increase and the growth rate of algae upon exposure to strain N5 was significantly inhibited.

Enhanced degradation of 1-naphthol in landfill leachate using Arthrobacter sp.

PubMed

Hu, Wenyong; Min, Xiaobo; Li, Xinyu; Liu, Jingyi; Yu, Haibin; Yang, Yuan; Zhang, Jiachao; Luo, Lin; Chai, Liyuan; Zhou, Yaoyu

2017-12-06

Arthrobacter sp. named as JY5-1 isolated from contaminated soil of a coking plant can degrade 1-naphthol as the sole carbon source. Through identification of species, analysis of the optimal degradation condition and kinetic equation, the degradation characteristic of Arthrobacter sp. JY5-1 was obtained. Later, the acclimated strain was added into the bio-reactor to observe treatment performance of landfill leachate. The results showed that the optimal conditions for strain JY5-1 biodegradation in the study were pH 7.0 and 30 o C. The bio-reactor operation experiment declared that Arthrobacter sp. JY5-1 had a strengthened effect on COD removal of landfill leachate. Moreover, the efficiency of COD removal could be high and stable when JY5-1 was accumulated as a biofilm together with active sludge. These results demonstrate that adding 1-naphthol-degrading strain JY5-1 is a feasible technique for the enhanced treatment of sanitary landfill leachate, providing theoretical support for engineering utilization.

Description of Komagataella mondaviorum sp. nov., a new sibling species of Komagataella (Pichia) pastoris.

PubMed

Naumov, Gennadi I; Naumova, Elena S; Boundy-Mills, Kyria L

2018-07-01

Five methylotrophic strains (UCDFST 71-1024 T , UCDFST 54-11.16, UCDFST 54-11.141, UCDFST 68-967.1 and UCDFST 74-1030) from the Phaff Yeast Culture Collection (University of California Davis, USA) that were originally designated as Pichia pastoris were found to represent a novel Komagataella species. Strains of Komagataella mondaviorum sp. nov. UCDFST 71-1024 T (type strain) = CBS 15017, UCDFST 54-11.16, UCDFST 54-11.141, UCDFST 68-967.1, and UCDFST 74-1030 were isolated in USA, respectively, from cottonwood tree Populus deltoides in 1971 (Davis, CA), slime flux of Quercus sp. in 1954 (CA), exudate of black oak Q. kelloggii in 1954 (Central Sierra Nevada. CA), dry frass from Salix sp. in 1968 (Soleduck Road, Olympic National Park, WA) and from flux of hackberry tree Celtis sp. in 1974 (CA). The new species was differentiated from Komagataella kurtzmanii, Komagataella pastoris, Komagataella phaffii, Komagataella populi, Komagataella pseudopastoris and Komagataella ulmi by divergence in gene sequences for D1/D2 LSU rRNA, ITS1-5.8S-ITS2, RNA polymerase subunit I and translation elongation factor-1α. Komagataella mondaviorum sp. nov. is registered in MycoBank under MB 821789.

Endoglucanase and xylanase production by Bacillus sp. AR03 in co-culture.

PubMed

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

2017-07-03

The behavior 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 to evaluate their ability to produce extracellular cellulases and xylanases. Utilizing a peptone-based medium supplemented with carboxymethyl cellulose (CMC), an increase estimation 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 behavior 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 fulfill 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.

Comparative analysis of multiple inducible phages from Mannheimia haemolytica.

PubMed

Niu, Yan D; Cook, Shaun R; Wang, Jiaying; Klima, Cassidy L; Hsu, Yu-hung; Kropinski, Andrew M; Turner, Dann; McAllister, Tim A

2015-08-30

Mannheimia haemolytica is a commensal bacterium that resides in the upper respiratory tract of cattle that can play a role in bovine respiratory disease. Prophages are common in the M. haemolytica genome and contribute significantly to host diversity. The objective of this research was to undertake comparative genomic analysis of phages induced from strains of M. haemolytica serotype A1 (535A and 2256A), A2 (587A and 1127A) and A6 (1152A and 3927A). Overall, four P2-like (535AP1, 587AP1, 1127AP1 and 2256AP1; genomes: 34.9-35.7 kb; G+C content: 41.5-42.1 %; genes: 51-53 coding sequences, CDSs), four λ-like (535AP2, 587AP2, 1152AP2 and 3927AP1; genomes: 48.6-52.1 kb; 41.1-41.4 % mol G+C; genes: 77-83 CDSs and 2 tRNAs) and one Mu-like (3927AP2; genome: 33.8 kb; 43.1 % mol G+C; encoding 50 CDSs) phages were identified. All P2-like phages are collinear with the temperate phage φMhaA1-PHL101 with 535AP1, 2256AP1 and 1152AP1 being most closely related, followed by 587AP1 and 1127AP1. Lambdoid phages are not collinear with any other known λ-type phages, with 587AP2 being distinct from 535AP2, 3927AP1 and 1152AP2. All λ-like phages contain genes encoding a toxin-antitoxin (TA) system and cell-associated haemolysin XhlA. The Mu-like phage induced from 3927A is closely related to the phage remnant φMhaMu2 from M. haemolytica PHL21, with similar Mu-like phages existing in the genomes of M. haemolytica 535A and 587A. This is among the first reports of both λ- and Mu-type phages being induced from M. haemolytica. Compared to phages induced from commensal strains of M. haemolytica serotype A2, those induced from the more virulent A1 and A6 serotypes are more closely related. Moreover, when P2-, λ- and Mu-like phages co-existed in the M. haemolytica genome, only P2- and λ-like phages were detected upon induction, suggesting that Mu-type phages may be more resistant to induction. Toxin-antitoxin gene cassettes in λ-like phages may contribute to their genomic persistence or the establishment of persister subpopulations of M. haemolytica. Further work is required to determine if the cell-associated haemolysin XhlA encoded by λ-like phages contributes to the pathogenicity and ecological fitness of M. haemolytica.

Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China.

PubMed

Itoh, Takashi; Yamaguchi, Takashi; Zhou, Peijin; Takashina, Tomonori

2005-04-01

Three novel isolates of haloalkaliphilic archaea, strains IHC-005T, IHC-010, and N-1311T, from soda lakes in Inner Mongolia, China, were characterized to elucidate their taxonomic positions. The three strains were aerobic, Gram-negative chemoorganotrophs growing optimally at 37-45 degrees C, pH 9.0-9.5, and 15-20% NaCl. Cells of strains IHC-005T/IHC-010 were motile rods, while those of strain N-1311T were non-motile pleomorphic flats or cocci. The three strains contained diphytanyl and phytanyl-sesterterpanyl diether derivatives of phosphatidylglycerol and phosphatidylglycerophosphate methyl ester. No glycolipids were detected. On phylogenetic analysis of 16S rRNA gene sequences, they formed an independent cluster in the Natro group of the family Halobacteriaceae. Comparison of their morphological, physiological, and biochemical properties, DNA G + C content and 16S rRNA gene sequences, and DNA-DNA hybridization study support the view that strains IHC-005T/IHC-010 and strain N-1311T represent separate species. Therefore, we propose Natronolimnobius baerhuensis gen. nov., sp. nov. for strains IHC-005T (=CGMCC 1.3597T =JCM 12253T)/IHC-010 (=CGMCC 1.3598 = JCM 12254) and Natronolimnobius innermongolicus sp. nov. for N-1311T (=CGMCC 1.2124T =JCM 12255T).

The Fatty Acid Profile and Oxidative Stability of Meat from Turkeys Fed Diets Enriched with n-3 Polyunsaturated Fatty Acids and Dried Fruit Pomaces as a Source of Polyphenols.

PubMed

Juskiewicz, Jerzy; Jankowski, Jan; Zielinski, Henryk; Zdunczyk, Zenon; Mikulski, Dariusz; Antoszkiewicz, Zofia; Kosmala, Monika; Zdunczyk, Przemyslaw

2017-01-01

The aim of this study was to determine the efficacy of different dietary fruit pomaces in reducing lipid oxidation in the meat of turkeys fed diets with a high content of n-3 polyunsaturated fatty acids (PUFAs). Over a period of 4 weeks before slaughter, turkeys were fed diets with the addition of 5% dried apple, blackcurrant, strawberry and seedless strawberry pomaces (groups AP, BP, SP and SSP, respectively) and 2.5% linseed oil. Pomaces differed in the content (from 5.5 in AP to 43.1 mg/g in SSP) and composition of polyphenols Proanthocyanidins were the main polyphenolic fraction in all pomaces, AP contained flavone glycosides and dihydrochalcones, BP contained anthocyanins, and SP and SSP-ellagitannins. The n-6/n-3 PUFA ratio in all diets was comparable and lower than 2:1. In comparison with groups C and AP, the percentage of n-3 PUFAs in the total fatty acid pool of white meat from the breast muscles of turkeys in groups BP, SP and SSP was significantly higher, proportionally to the higher content of α-linolenic acid in berry pomaces. The fatty acid profile of dark meat from thigh muscles, including the n-6/n-3 PUFA ratio, was similar and lower than 3:1 in all groups. Vitamin A levels in raw breast muscles were higher in group AP than in groups C and BP (P<0.05). The addition of fruit pomaces to turkey diets lowered vitamin E concentrations (P = 0.001) in raw breast muscles relative to group C. Diets supplemented with fruit pomaces significantly lowered the concentration of thiobarbituric acid reactive substances (TBARS) in raw, frozen and cooked meat. Our results indicate that the dietary application of dried fruit pomaces increases the oxidative stability of meat from turkeys fed linseed oil, and strawberry pomace exerted the most desirable effects due to its highest polyphenol content and antioxidant potential.

The Fatty Acid Profile and Oxidative Stability of Meat from Turkeys Fed Diets Enriched with n-3 Polyunsaturated Fatty Acids and Dried Fruit Pomaces as a Source of Polyphenols

PubMed Central

Juskiewicz, Jerzy; Jankowski, Jan; Zielinski, Henryk; Zdunczyk, Zenon; Mikulski, Dariusz; Antoszkiewicz, Zofia; Kosmala, Monika; Zdunczyk, Przemyslaw

2017-01-01

The aim of this study was to determine the efficacy of different dietary fruit pomaces in reducing lipid oxidation in the meat of turkeys fed diets with a high content of n-3 polyunsaturated fatty acids (PUFAs). Over a period of 4 weeks before slaughter, turkeys were fed diets with the addition of 5% dried apple, blackcurrant, strawberry and seedless strawberry pomaces (groups AP, BP, SP and SSP, respectively) and 2.5% linseed oil. Pomaces differed in the content (from 5.5 in AP to 43.1 mg/g in SSP) and composition of polyphenols Proanthocyanidins were the main polyphenolic fraction in all pomaces, AP contained flavone glycosides and dihydrochalcones, BP contained anthocyanins, and SP and SSP—ellagitannins. The n-6/n-3 PUFA ratio in all diets was comparable and lower than 2:1. In comparison with groups C and AP, the percentage of n-3 PUFAs in the total fatty acid pool of white meat from the breast muscles of turkeys in groups BP, SP and SSP was significantly higher, proportionally to the higher content of α-linolenic acid in berry pomaces. The fatty acid profile of dark meat from thigh muscles, including the n-6/n-3 PUFA ratio, was similar and lower than 3:1 in all groups. Vitamin A levels in raw breast muscles were higher in group AP than in groups C and BP (P<0.05). The addition of fruit pomaces to turkey diets lowered vitamin E concentrations (P = 0.001) in raw breast muscles relative to group C. Diets supplemented with fruit pomaces significantly lowered the concentration of thiobarbituric acid reactive substances (TBARS) in raw, frozen and cooked meat. Our results indicate that the dietary application of dried fruit pomaces increases the oxidative stability of meat from turkeys fed linseed oil, and strawberry pomace exerted the most desirable effects due to its highest polyphenol content and antioxidant potential. PMID:28076425

[Isolation, Identification and Characteristic Analysis of an Oil-producing Chlorella sp. Tolerant to High-strength Anaerobic Digestion Effluent].

PubMed

Yang, Chuang; Wang, Wen-guo; Ma, Dan-wei; Tang, Xiao-yu; Hu, Qi-chun

2015-07-01

A Chlorella strain tolerant to high-strength anaerobic digestion effluent was isolated from the anaerobic digestion effluent with a long-term exposure to air. The strain was identified as a Chlorella by morphological and molecular biological methods, and named Chlorella sp. BWY-1, The anaerobic digestion effluent used in this study was from a biogas plant with the raw materials of swine wastewater after solid-liquid separation. The Chlorella regularis (FACHB-729) was used as the control strain. The comparative study showed that Chlorella sp, BWY-Ihad relatively higher growth rate, biomass accumulation capacity and pollutants removal rate in BG11. and different concentrations of anaerobic digestion effluent. Chlorella sp. BWY-1 had the highest growth rate and biomass productivity (324.40 mg.L-1) in BG11, but its lipid productivity and lipid content increased with the increase of anaerobic digestion effluent concentration, In undiluted anaerobic digestion effluent, the lipid productivity and lipid content of Chlorella sp. BWY-1 were up to 44. 43% and 108. 70 mg.L-1, respectively. Those results showed that the isolated algal strain bad some potential applications in livestock wastewater treatment and bioenergy production, it could be combined with a solid-liquid separation, anaerobic fermentation and other techniques for processing livestock wastewater and producing biodiesel.

Butyric acid from anaerobic fermentation of lignocellulosic biomass hydrolysates by Clostridium sp. strain RPT-4213

USDA-ARS?s Scientific Manuscript database

A novel Clostridium sp. strain RPT-4213 was found producing butyrate under strict anaerobic conditions. This strain produced 9.47 g L-1 butyric acid from MRS media (0.48 g/g glucose). RPT-4213 was also used to ferment dilute acid pretreated hydrolysates including wheat straw (WSH), corn fiber (CFH...

Biohydrogen production by dark fermentation of glycerol using Enterobacter and Citrobacter Sp.

PubMed

Maru, Biniam T; Constanti, Magda; Stchigel, Alberto M; Medina, Francesc; Sueiras, Jesus E

2013-01-01

Glycerol is an attractive substrate for biohydrogen production because, in theory, it can produce 3 mol of hydrogen per mol of glycerol. Moreover, glycerol is produced in substantial amounts as a byproduct of producing biodiesel, the demand for which has increased in recent years. Therefore, hydrogen production from glycerol was studied by dark fermentation using three strains of bacteria: namely, Enterobacter spH1, Enterobacter spH2, and Citrobacter freundii H3 and a mixture thereof (1:1:1). It was found that, when an initial concentration of 20 g/L of glycerol was used, all three strains and their mixture produced substantial amounts of hydrogen ranging from 2400 to 3500 mL/L, being highest for C. freundii H3 (3547 mL/L) and Enterobacter spH1 (3506 mL/L). The main nongaseous fermentation products were ethanol and acetate, albeit in different ratios. For Enterobacter spH1, Enterobacter spH2, C. freundii H3, and the mixture (1:1:1), the ethanol yields (in mol EtOH/mol glycerol consumed) were 0.96, 0.67, 0.31, and 0.66, respectively. Compared to the individual strains, the mixture (1:1:1) did not show a significantly higher hydrogen level, indicating that there was no synergistic effect. Enterobacter spH1 was selected for further investigation because of its higher yield of hydrogen and ethanol. Copyright © 2012 American Institute of Chemical Engineers (AIChE).

Candida dajiaensis sp. nov., Candida yuanshanicus sp. nov., Candida jianshihensis sp. nov., and Candida sanyiensis sp. nov., four anamorphic, ascomycetous yeast species isolated from soil in Taiwan.

PubMed

Liu, Chun-Hao; Young, Shuh-Sen; Chang, Tsung-Chain; Lee, Ching-Fu

2008-08-01

Nine anamorphic, ascomycetous yeast strains belonging to the Pichia anomala clade were recovered from forest soil in 2006 in Taiwan. The nine yeast strains represent four novel yeast species based on the sequences of their D1/D2 domain of the large subunit (LSU) rRNA gene and their physiological characteristics. The scientific names of Candida dajiaensis sp. nov., Candida yuanshanicus sp. nov., Candida jianshihensis sp. nov., and Candida sanyiensis sp. nov. are proposed for these novel yeast species. The type strains are C. dajiaensis SM11S03(T) (=CBS 10590(T)=BCRC 23099(T)), C. yuanshanicus SY3S02(T) (=CBS 10589(T)=BCRC 23100(T)), C. jianshihensis SM8S04(T) (=CBS 10591(T)=BCRC 23096(T)), and C. sanyiensis SA1S06(T) (=CBS 10592(T)=BCRC 23094(T)). Sequence analysis of the D1/D2 of the LSU rRNA gene revealed that the three species, C. dajiaensis, C. yuanshanicus and Pichia onychis, shared a separate branch in the phylogenetic tree, C. jianshihensis is phylogenetically related to Candida ulmi and Pichia alni, and the phylogenetically closest relative of C. sanyiensis is Pichia populi.

Mycophenolic acid attenuates tumor necrosis factor-alpha-induced endothelin-1 production in human aortic endothelial cells.

PubMed

Yang, Won Seok; Lee, Joo Mi; Han, Nam Jeong; Kim, Yoon Ji; Chang, Jai Won; Park, Su-Kil

2010-07-01

Atherosclerotic cardiovascular disease is the major cause of morbidity and mortality in solid organ transplant recipients. Endothelin-1 (ET-1) is implicated in the pathogenesis of atherosclerosis and is one of the potential therapeutic targets. This study was conducted to evaluate the effect of mycophenolic acid (MPA), an immunosuppressant for the transplant recipients, on tumor necrosis factor-alpha (TNF-alpha)-induced ET-1 production in aortic endothelial cells. In cultured human aortic endothelial cells, TNF-alpha increased ET-1 through AP-1 and NF-kappaB, whereas MPA attenuated it by reducing both AP-1 and NF-kappaB DNA-binding activities. TNF-alpha increased ET-1 via c-Jun NH2-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK), but not extracellular signal-regulated kinase. N-acetylcysteine that downregulated TNF-alpha-induced reactive oxygen species (ROS) inhibited JNK activation, but not p38 MAPK. N-acetylcysteine, SP600125 (JNK inhibitor) and SB203580 (p38 MAPK inhibitor) attenuated TNF-alpha-induced DNA-binding activities of both AP-1 and NF-kappaB. MPA inhibited JNK and p38 MAPK activations as well as ROS generation. N-acetylcysteine, SP600125, SB203580 and MPA had no effect on either TNF-alpha-induced IkappaBalpha degradation or p65 nuclear translocation, but attenuated p65 Ser276 phosphorylation. MPA attenuated TNF-alpha-induced ET-1 production through inhibitions of ROS-dependent JNK and ROS-independent p38 MAPK that regulated NF-kappaB as well as AP-1. These findings suggest that MPA could have an effect of amelioration of atherosclerosis. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.

Cloning and Expression of Phytase appA Gene from Shigella sp. CD2 in Pichia pastoris and Comparison of Properties with Recombinant Enzyme Expressed in E. coli

PubMed Central

Pal Roy, Moushree; Mazumdar, Deepika; Dutta, Subhabrata; Saha, Shyama Prasad; Ghosh, Shilpi

2016-01-01

The phytase gene appAS was isolated from Shigella sp. CD2 genomic library. The 3.8 kb DNA fragment contained 1299 bp open reading frame encoding 432 amino acid protein (AppAS) with 22 amino acid signal peptide at N-terminal and three sites of N-glycosylation. AppAS contained the active site RHGXRXP and HDTN sequence motifs, which are conserved among histidine acid phosphatases. It showed maximum identity with phytase AppA of Escherichia coli and Citrobacter braakii. The appAS was expressed in Pichia pastoris and E. coli to produce recombinant phytase rAppAP and rAppAE, respectively. Purified glycosylated rAppAP and nonglycosylated rAppAE had specific activity of 967 and 2982 U mg-1, respectively. Both had pH optima of 5.5 and temperature optima of 60°C. Compared with rAppAE, rAppAP was 13 and 17% less active at pH 3.5 and 7.5 and 11 and 18% less active at temperature 37 and 50°C, respectively; however, it was more active at higher incubation temperatures. Thermotolerance of rAppAP was 33% greater at 60°C and 24% greater at 70°C, when compared with rAppAE. Both the recombinant enzymes showed high specificity to phytate and resistance to trypsin. To our knowledge, this is the first report on cloning and expression of phytase from Shigella sp. PMID:26808559

Cloning and Expression of Phytase appA Gene from Shigella sp. CD2 in Pichia pastoris and Comparison of Properties with Recombinant Enzyme Expressed in E. coli.

PubMed

Pal Roy, Moushree; Mazumdar, Deepika; Dutta, Subhabrata; Saha, Shyama Prasad; Ghosh, Shilpi

2016-01-01

The phytase gene appAS was isolated from Shigella sp. CD2 genomic library. The 3.8 kb DNA fragment contained 1299 bp open reading frame encoding 432 amino acid protein (AppAS) with 22 amino acid signal peptide at N-terminal and three sites of N-glycosylation. AppAS contained the active site RHGXRXP and HDTN sequence motifs, which are conserved among histidine acid phosphatases. It showed maximum identity with phytase AppA of Escherichia coli and Citrobacter braakii. The appAS was expressed in Pichia pastoris and E. coli to produce recombinant phytase rAppAP and rAppAE, respectively. Purified glycosylated rAppAP and nonglycosylated rAppAE had specific activity of 967 and 2982 U mg(-1), respectively. Both had pH optima of 5.5 and temperature optima of 60°C. Compared with rAppAE, rAppAP was 13 and 17% less active at pH 3.5 and 7.5 and 11 and 18% less active at temperature 37 and 50°C, respectively; however, it was more active at higher incubation temperatures. Thermotolerance of rAppAP was 33% greater at 60°C and 24% greater at 70°C, when compared with rAppAE. Both the recombinant enzymes showed high specificity to phytate and resistance to trypsin. To our knowledge, this is the first report on cloning and expression of phytase from Shigella sp.

Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR-ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat analysis, amplified fragment length polymorphism, and surface layer protein A gene sequence typing.

PubMed

Killgore, George; Thompson, Angela; Johnson, Stuart; Brazier, Jon; Kuijper, Ed; Pepin, Jacques; Frost, Eric H; Savelkoul, Paul; Nicholson, Brad; van den Berg, Renate J; Kato, Haru; Sambol, Susan P; Zukowski, Walter; Woods, Christopher; Limbago, Brandi; Gerding, Dale N; McDonald, L Clifford

2008-02-01

Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven Clostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (slpAST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the tcdC gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE, slpAST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of C. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no tcdC gene deletion). REA, slpAST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in tcdC) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks.

Neptunomonas phycophila sp. nov. isolated from a culture of Symbiodinium sp., a dinoflagellate symbiont of the sea anemone Aiptasia tagetes.

PubMed

Frommlet, Jörg; Guimarães, Bárbara; Sousa, Lígia; Serôdio, João; Alves, Artur

2015-03-01

A Gram-stain-negative, facultatively anaerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain SYM1(T), was isolated from a culture of Symbiodinium sp., an algal symbiont of the sea anemone Aiptasia tagetes collected in Puerto Rico. Growth was observed at 4-40 °C (optimum 30 °C), at pH 5.0-11.0 (optimum pH 8.0) and with 0.5-8 % (optimum 2 %) (w/v) NaCl. Phylogenetic analyses of 16S rRNA gene sequences showed that strain SYM1(T) was a member of the genus Neptunomonas with the type strain of Neptunomonas naphthovorans as the closest phylogenetic relative with a pairwise sequence similarity of 98.15 %. However, DNA-DNA relatedness between strain SYM1(T) and N. naphthovorans CIP 106451(T) was 24 %. Moreover, strain SYM1(T) could be distinguished from its closest relative by several phenotypic characteristics such as NaCl, pH and temperature tolerance, nitrate reduction and utilization of carbon substrates. The major cellular fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content of strain SYM1(T) was 45 mol%. Ubiquinone-8 (Q-8) was the only respiratory quinone detected. Based on a polyphasic taxonomic characterization, strain SYM1(T) represents a novel species of the genus Neptunomonas, for which the name Neptunomonas phycophila sp. nov. is proposed. The type strain is SYM1(T) ( = LMG 28329(T) = CECT 8716(T)). © 2015 IUMS.

Chemoheterotrophic Growth of the Cyanobacterium Anabaena sp. Strain PCC 7120 Dependent on a Functional Cytochrome c Oxidase

PubMed Central

Stebegg, Ronald; Wurzinger, Bernhard; Mikulic, Markus

2012-01-01

Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium commonly used as a model organism for studying cyanobacterial cell differentiation and nitrogen fixation. For many decades, this cyanobacterium was considered an obligate photo-lithoautotroph. We now discovered that this strain is also capable of mixotrophic, photo-organoheterotrophic, and chemo-organoheterotrophic growth if high concentrations of fructose (at least 50 mM and up to 200 mM) are supplied. Glucose, a substrate used by some facultatively organoheterotrophic cyanobacteria, is not effective in Anabaena sp. PCC 7120. The gtr gene from Synechocystis sp. PCC 6803 encoding a glucose carrier was introduced into Anabaena sp. PCC 7120. Surprisingly, the new strain containing the gtr gene did not grow on glucose but was very sensitive to glucose, with a 5 mM concentration being lethal, whereas the wild-type strain tolerated 200 mM glucose. The Anabaena sp. PCC 7120 strain containing gtr can grow mixotrophically and photo-organoheterotrophically, but not chemo-organoheterotrophically with fructose. Anabaena sp. PCC 7120 contains five respiratory chains ending in five different respiratory terminal oxidases. One of these enzymes is a mitochondrial-type cytochrome c oxidase. As in almost all cyanobacteria, this enzyme is encoded by three adjacent genes called coxBAC1. When this locus was disrupted, the cells lost the capability for chemo-organoheterotrophic growth. PMID:22730128

Impact of aerosol particle sources on optical properties in urban, regional and remote areas in the north-western Mediterranean

NASA Astrophysics Data System (ADS)

Ealo, Marina; Alastuey, Andrés; Pérez, Noemí; Ripoll, Anna; Querol, Xavier; Pandolfi, Marco

2018-01-01

Further research is needed to reduce the existing uncertainties on the effect that specific aerosol particle sources have on light extinction and consequently on climate. This study presents a new approach that aims to quantify the mass scattering and absorption efficiencies (MSEs and MAEs) of different aerosol sources at urban (Barcelona - BCN), regional (Montseny - MSY) and remote (Montsec - MSA) background sites in the north-western (NW) Mediterranean. An analysis of source apportionment to the measured multi-wavelength light scattering (σsp) and absorption (σap) coefficients was performed by means of a multilinear regression (MLR) model for the periods 2009-2014, 2010-2014 and 2011-2014 at BCN, MSY and MSA respectively. The source contributions to PM10 mass concentration, identified by means of the positive matrix factorization (PMF) model, were used as dependent variables in the MLR model. With this approach we addressed both the effect that aerosol sources have on air quality and their potential effect on light extinction through the determination of their MSEs and MAEs. An advantage of the presented approach is that the calculated MSEs and MAEs take into account the internal mixing of atmospheric particles. Seven aerosol sources were identified at MSA and MSY, and eight sources at BCN. Mineral, aged marine, secondary sulfate, secondary nitrate and V-Ni bearing sources were common at the three sites. Traffic, industrial/metallurgy and road dust resuspension sources were isolated at BCN, whereas mixed industrial/traffic and aged organics sources were identified at MSY and MSA. The highest MSEs were observed for secondary sulfate (4.5 and 10.7 m2 g-1, at MSY and MSA), secondary nitrate (8.8 and 7.8 m2 g-1) and V-Ni bearing source (8 and 3.5 m2 g-1). These sources dominated the scattering throughout the year with marked seasonal trends. The V-Ni bearing source, originating mainly from shipping in the area under study, simultaneously contributed to both σsp and σap, being the second most efficient light-absorbing source in BCN (MAE = 0.9 m2 g-1). The traffic source at BCN and the industrial/traffic at MSY exhibited the highest MAEs (1.7 and 0.9 m2 g-1). These sources were major contributors to σap at BCN and MSY; however at MSA, secondary nitrate exerted the highest influence on σap (MAE = 0.4 m2 g-1). The sources which were predominantly composed of fine and relatively dark particles, such as industrial/traffic, aged organics and V-Ni, were simultaneously characterized by low single scattering albedo (SSA) and a high scattering Ångström exponent (SAE). Conversely, mineral and aged marine showed the lowest SAE and the highest SSA, being scattering the dominant process in the light extinction. The good agreement found between modelled and measured particle optical properties allowed the reconstruction of σsp and σap long-term series over the period 2004-2014 at MSY. Significant decreasing trends were found for the modelled σsp and σap (-4.6 and -4.1 % yr-1).

Crimean-Congo hemorrhagic fever virus lineages Europe 1 and Europe 2 in Bulgarian ticks.

PubMed

Panayotova, Elitsa; Papa, Anna; Trifonova, Iva; Christova, Iva

2016-07-01

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne human viral disease with fatality rate up to 30%. Two genetic lineages of CCHF virus (CCHFV) are present in Europe - lineage Europe 1 which contains pathogenic CCHFV strains, and lineage Europe 2 consisting of AP92 and AP92-like strains. In order to investigate CCHFV distribution and potential risk for humans, ticks were collected from livestock in the five districts where CCHF cases have been reported in the last five years in Bulgaria. CCHFV lineage Europe 1 was detected in 39 of 623 Hyalomma marginatum ticks (6.3%; range per village 2.7-15.2%), while CCHFV lineage Europe 2 was detected for the first time in Bulgaria in 49 of 415 Rhipicephalus sanguineus sensu lato ticks (11.8%; range 0-58.3%). The present study shows that both Europe 1 and Europe 2 CCHFV lineages are present in Bulgaria. The pathogenic role of the AP92-like strains remains to be elucidated. Copyright © 2016 Elsevier GmbH. All rights reserved.

[Susceptibility to antifungal agents of Candida sp. and biofilm formation].

PubMed

Ciok-Pater, Emilia; Białucha, Agata; Gospodarek, Eugenia; Ostafin, Agnieszka

2011-01-01

In recent years the increase in frequency of fungal infections with Candida sp. was noticed. These infections are connected with ability of Candida sp. to form biofilm on surfaces of biomaterials used in medicine. Furthermore fungal infections make serious therapeutic problems because ofbiofilm resistance to antifungal agents actually. The aim of the study was to evaluate the susceptibility to antifungal agents of Candida sp. and their ability to form biofilm on different biomaterials. 50 strains of Candida sp. isolated from patients of University Hospital No. 1 of dr A. Jurasz in Bydgoszcz were examined. API Candida (bioMérieux) tests were used to identify Candida sp. strains. The susceptibility of the yeast strains to antifungal agents was evaluated by ATB FUNGUS 2 INT (bioMérieux) tests. The susceptibility of examined strains to voriconazole, posaconazole, caspofungin and anidulafungin was assessed by means ofEtests (AB BIODISK) method employing drug concentrations from 0,002 to 32 microg/ml. All analysed strains were susceptible to amphotericin B and caspofungin. Biofilm formation on different biomaterials (silicon, latex, polychloride vinyl, polypropylene, nylon) was measured after 72 hour incubation at 37 degrees C. All examined yeasts formed biofilm on all analysed biomaterials. The highest number of strains formed biofilm on surface of polychloride vinyl: 23 (92,0%) by C. albicans strains and 24 (96,0%) Candida non-albicans strains. The lowest number of the strains formed biofilm on the surface of nylon: 12 (48,0%) of C. albicans strains and 9 (36,0%) of Candida non-albicans strains. The studied strains resistant to azoles and anidulafungin display stronger ability to form biofilm on surfaces of all analysed biomaterials.

Genome Sequence of the Alkaline-Tolerant Cellulomonas sp. Strain FA1

DOE PAGES

Cohen, Michael F.; Hu, Ping; Nguyen, My Vu; ...

2015-06-18

We present the genome of the cellulose-degrading Cellulomonas sp. strain FA1 isolated from an actively serpentinizing highly alkaline spring. Knowledge of this genome will enable studies into the molecular basis of plant material degradation in alkaline environments and inform the development of lignocellulose bioprocessing procedures for biofuel production.

Deep Sequencing-Identified Kanamycin-Resistant Paenibacillus sp. Strain KS1 Isolated from Epiphyte Tillandsia usneoides (Spanish Moss) in Central Florida, USA

PubMed Central

Govindarajan, Subramaniam S.; Qi, Feng; Li, Jian-Liang; Sahoo, Malaya K.

2017-01-01

ABSTRACT Paenibacillus sp. strain KS1 was isolated from an epiphyte, Tillandsia usneoides (Spanish moss), in central Florida, USA. Here, we report a draft genome sequence of this strain, which consists of a total of 398 contigs spanning 6,508,195 bp, with a G+C content of 46.5% and comprising 5,401 predicted coding sequences. PMID:28153888

Enhancement of 2,3-butanediol production from Jerusalem artichoke tuber extract by a recombinant Bacillus sp. strain BRC1 with increased inulinase activity.

PubMed

Park, Jang Min; Oh, Baek-Rock; Kang, In Yeong; Heo, Sun-Yeon; Seo, Jeong-Woo; Park, Seung-Moon; Hong, Won-Kyung; Kim, Chul Ho

2017-07-01

A Bacillus sp. strain named BRC1 is capable of producing 2,3-butanediol (2,3-BD) using hydrolysates of the Jerusalem artichoke tuber (JAT), a rich source of the fructose polymer inulin. To enhance 2,3-BD production, we undertook an extensive analysis of the Bacillus sp. BRC1 genome, identifying a putative gene (sacC) encoding a fructan hydrolysis enzyme and characterizing the activity of the resulting recombinant protein expressed in and purified from Escherichia coli. Introduction of the sacC gene into Bacillus sp. BRC1 using an expression vector increased enzymatic activity more than twofold. Consistent with this increased enzyme expression, 2,3-BD production from JAT was also increased from 3.98 to 8.10 g L -1 . Fed-batch fermentation of the recombinant strain produced a maximal level of 2,3-BD production of 28.6 g L -1 , showing a high theoretical yield of 92.3%.

Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation.

PubMed

Tomazetto, Geizecler; Hahnke, Sarah; Maus, Irena; Wibberg, Daniel; Pühler, Alfred; Schlüter, Andreas; Klocke, Michael

2014-12-20

The bacterium Peptoniphilus sp. strain ING2-D1G (DSM 28672), a mesophilic and obligate anaerobic bacterium belonging to the order Clostridiales was isolated from a biogas-producing lab-scale completely stirred tank reactor (CSTR) optimized for anaerobic digestion of maize silage in co-fermentation with pig and cattle manure. In this study, the whole genome sequence of Peptoniphilus sp. strain ING2-D1G, a new isolate potentially involved in protein breakdown and acidogenesis during biomass degradation, is reported. The chromosome of this strain is 1.6Mb in size and encodes genes predicted to be involved in the production of acetate, lactate and butyrate specifying the acidogenic metabolism of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

Dexamethasone inhibits IL-12p40 production in lipopolysaccharide-stimulated human monocytic cells by down-regulating the activity of c-Jun N-terminal kinase, the activation protein-1, and NF-kappa B transcription factors.

PubMed

Ma, Wei; Gee, Katrina; Lim, Wilfred; Chambers, Kelly; Angel, Jonathan B; Kozlowski, Maya; Kumar, Ashok

2004-01-01

IL-12 plays a critical role in the development of cell-mediated immune responses and in the pathogenesis of inflammatory and autoimmune disorders. Dexamethasone (DXM), an anti-inflammatory glucocorticoid, has been shown to inhibit IL-12p40 production in LPS-stimulated monocytic cells. In this study, we investigated the molecular mechanism by which DXM inhibits IL-12p40 production by studying the role of the mitogen-activated protein kinases (MAPKs), and the key transcription factors involved in human IL-12p40 production in LPS-stimulated monocytic cells. A role for c-Jun N-terminal kinase (JNK) MAPK in LPS-induced IL-12p40 regulation in a promonocytic THP-1/CD14 cell line was demonstrated by using specific inhibitors of JNK activation, SP600125 and a dominant-negative stress-activated protein/extracellular signal-regulated kinase kinase-1 mutant. To identify transcription factors regulating IL-12p40 gene transcription, extensive deletion analyses of the IL-12p40 promoter was performed. The results revealed the involvement of a sequence encompassing the AP-1-binding site, in addition to that of NF-kappaB. The role of AP-1 in IL-12p40 transcription was confirmed by using antisense c-fos and c-jun oligonucleotides. Studies conducted to understand the regulation of AP-1 and NF-kappaB activation by JNK MAPK revealed that both DXM and SP600125 inhibited IL-12p40 gene transcription by inhibiting the activation of AP-1 and NF-kappaB transcription factors as revealed by luciferase reporter and gel mobility shift assays. Taken together, our results suggest that DXM may inhibit IL-12p40 production in LPS-stimulated human monocytic cells by down-regulating the activation of JNK MAPK, the AP-1, and NF-kappaB transcription factors.

Stereospecific oxidation of (R)- and (S)-1-indanol by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4.

PubMed Central

Lee, K; Resnick, S M; Gibson, D T

1997-01-01

A recombinant Escherichia coli strain which expresses naphthalene dioxygenase (NDO) from Pseudomonas sp. strain NCIB 9816-4 oxidized (S)-1-indanol to trans-(1S,3S)-indan-1,3-diol (95.5%) and (R)-3-hydroxy-1-indanone (4.5%). The same cells oxidized (R)-1-indanol to cis-1,3-indandiol (71%), (R)-3-hydroxy-1-indanone (18.2%), and cis-1,2,3-indantriol (10.8%). Purified NDO oxidized (S)-1-indenol to both syn- and anti-2,3-dihydroxy-1-indanol. PMID:9143136

Ballistosporomyces changbaiensis sp. nov. and Ballistosporomyces bomiensis sp. nov., two novel species isolated from shrub plant leaves.

PubMed

Han, Pei-Jie; Li, Ai-Hua; Wang, Qi-Ming; Bai, Feng-Yan

2016-07-01

Four strains, CB 266(T), CB 272, XZ 44D1(T) and XZ 49D2, isolated from shrub plant leaves in China were identified as two novel species of the genus Ballistosporomyces by the sequence analysis of the small subunit of ribosomal RNA (SSU rRNA), the D1/D2 domains of the large subunit of rRNA (LSU rRNA) and internal transcribed spacer (ITS) + 5.8S rRNA region, and physiological comparisons. Ballistosporomyces changbaiensis sp. nov. (type strain CB 266(T) = CGMCC 2.02298(T) = CBS 10124(T), Mycobank number MB 815700) and Ballistosporomyces bomiensis sp. nov. (type strain XZ 44D1(T) = CGMCC 2.02661(T) = CBS 12512(T), Mycobank number MB 815701) are proposed to accommodate these two new species.

Detection and Characterization of Conjugative Degradative Plasmids in Xenobiotic-Degrading Sphingomonas Strains

PubMed Central

Basta, Tamara; Keck, Andreas; Klein, Joachim; Stolz, Andreas

2004-01-01

A systematic survey for the presence of plasmids in 17 different xenobiotic-degrading Sphingomonas strains was performed. In almost all analyzed strains, two to five plasmids with sizes of about 50 to 500 kb were detected by using pulsed-field gel electrophoresis. A comparison of plasmid preparations untreated or treated with S1 nuclease suggested that, in general, Sphingomonas plasmids are circular. Hybridization experiments with labeled gene probes suggested that large plasmids are involved in the degradation of dibenzo-p-dioxin, dibenzofuran, and naphthalenesulfonates in S. wittichii RW1, Sphingomonas sp. HH69, and S. xenophaga BN6, respectively. The plasmids which are responsible for the degradation of naphthalene, biphenyl, and toluene by S. aromaticivorans F199 (pNL1) and of naphthalenesulfonates by S. xenophaga BN6 (pBN6) were site-specifically labeled with a kanamycin resistance cassette. The conjugative transfer of these labeled plasmids was attempted with various bacterial strains as putative recipient strains. Thus, a conjugative transfer of plasmid pBN6 from S. xenophaga BN6 to a cured mutant of strain BN6 and to Sphingomonas sp. SS3 was observed. The conjugation experiments with plasmid pNL1 suggested a broader host range of this plasmid, because it was transferred without any obvious structural changes to S. yanoikuyae B1, Sphingomonas sp. SS3, and S. herbicidovorans. In contrast, major plasmid rearrangements were observed in the transconjugants after the transfer of plasmid pNL1 to Sphingomonas sp. HH69 and of pBN6 to Sphingomonas sp. SS3. No indications for the transfer of a Sphingomonas plasmid to bacteria outside of the Sphingomonadaceae were obtained. PMID:15175300

Fimbriiglobus ruber gen. nov., sp. nov., a Gemmata-like planctomycete from Sphagnum peat bog and the proposal of Gemmataceae fam. nov.

PubMed

Kulichevskaya, Irina S; Ivanova, Anastasia A; Baulina, Olga I; Rijpstra, W Irene C; Sinninghe Damsté, Jaap S; Dedysh, Svetlana N

2017-02-01

An aerobic, budding, dark pink to red-pigmented bacterium was isolated from an acidic boreal Sphagnum peat bog and designated strain SP5T. Cells of this strain were non-motile spheres that were uniformly covered with crateriform pits and fimbria, and tended to form aggregates during growth in liquid media. Strain SP5T was capable of growth between pH 4.0 and pH 6.8 (optimum at pH 5.5-6.0) and at temperatures between 10 and 30 °C (optimum at 20-25 °C). The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C20 : 1ω9c, C16 : 1ω9c and C16 : 0, and the major polar lipid was trimethylornithine. Cells contained also significant amounts of bound (ω-1)OH-C30 : 1 fatty acid. The quinone was menaquinone-6, and the G+C content of the DNA was 60.7 mol%. Strain SP5T was a member of the order Planctomycetales and belonged to the phylogenetic lineage defined by the genus Gemmata. It displayed 88 and 89 % 16S rRNA gene sequence similarity to Gemmata obscuriglobusUQM 2246T and 'Gemmata massiliana' IIL30, 89 % to Zavarzinella formosa A10T and 86 % to Telmatocola sphagniphila SP2T. However, strain SP5T differed from members of these genera by cell morphology, substrate utilization pattern and fatty acid composition. Based on these data, the novel isolate should be considered as representing a novel species of a new genus of planctomycetes, for which the name Fimbriiglobus ruber gen. nov., sp. nov, is proposed. The type strain is SP5T (=LMG 29572T=VKM B-3045T). We also suggest the establishment of a novel family, Gemmataceaefam. nov., which includes the phylogenetically related genera Gemmata, Zavarzinella, Telmatocola and Fimbriiglobus.

Mechanical Strain Determines Cilia Length, Motility, and Planar Position in the Left-Right Organizer.

PubMed

Chien, Yuan-Hung; Srinivasan, Shyam; Keller, Ray; Kintner, Chris

2018-05-07

The Xenopus left-right organizer (LRO) breaks symmetry along the left-right axis of the early embryo by producing and sensing directed ciliary flow as a patterning cue. To carry out this process, the LRO contains different ciliated cell types that vary in cilia length, whether they are motile or sensory, and how they position their cilia along the anterior-posterior (A-P) planar axis. Here, we show that these different cilia features are specified in the prospective LRO during gastrulation, based on anisotropic mechanical strain that is oriented along the A-P axis, and graded in levels along the medial-lateral axis. Strain instructs ciliated cell differentiation by acting on a mesodermal prepattern present at blastula stages, involving foxj1. We propose that differential strain is a graded, developmental cue, linking the establishment of an A-P planar axis to cilia length, motility, and planar location during formation of the Xenopus LRO. Copyright © 2018 Elsevier Inc. All rights reserved.

bZIP transcription factor CgAP1 is essential for oxidative stress tolerance and full virulence of the poplar anthracnose fungus Colletotrichum gloeosporioides.

PubMed

Sun, Yingjiao; Wang, Yonglin; Tian, Chengming

2016-10-01

Yeast AP1 transcription factor is a regulator of oxidative stress response. Here, we report the identification and characterization of CgAP1, an ortholog of YAP1 in poplar anthracnose fungus Colletotrichum gloeosporioides. The expression of CgAP1 was highly induced by reactive oxygen species. CgAP1 deletion mutants displayed enhanced sensitivity to oxidative stress compared with the wild-type strain, and their poplar leaf virulence was obviously reduced. However, the mutants exhibited no obvious defects in aerial hyphal growth, conidia production, and appressoria formation. CgAP1::eGFP fusion protein localized to the nucleus after TBH (tert-Butyl hydroperoxide) treatment, suggesting that CgAP1 functions as a redox sensor in C. gloeosporioides. In addition, CgAP1 prevented the accumulation of ROS during early stages of biotrophic growth. CgAP1 also acted as a positive regulator of several ROS-related genes (i.e., Glr1, Hyr1, and Cyt1) involved in the antioxidative response. These results highlight the key regulatory role of CgAP1 transcription factor in oxidative stress response and provide insights into the function of ROS detoxification in virulence of C. gloeosporioides. Copyright © 2016 Elsevier Inc. All rights reserved.

Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces.

PubMed

Wellner, S; Lodders, N; Glaeser, S P; Kämpfer, P

2013-07-01

Three pink-pigmented, aerobic, Gram-stain-negative, rod-shaped and facultatively methylotrophic strains were isolated from the phyllosphere of Trifolium repens and Cerastium holosteoides. 16S rRNA gene sequence analysis support the affiliation of all strains to the genus Methylobacterium. The closest relatives of strains C34(T) and T5 were Methylobacterium gnaphalii 23e(T) (98.0 and 98.5 % sequence similarity, respectively) and Methylobacterium organophilum JCM 2833(T) (97.0 and 97.2 %, respectively). Strain TA73(T) showed the highest sequence similarities to Methylobacterium marchantiae JT1(T) and Methylobacterium bullatum F3.2(T) (both 97.9 %), followed by Methylobacterium phyllosphaerae CBMB27(T) and Methylobacterium brachiatum DSM 19569(T) (both 97.8 %), Methylobacterium cerastii C15(T) and Methylobacterium radiotolerans JCM 2831(T) (both 97.7 %). The major components in the fatty acid profiles were C18 : 1ω7c, C16 : 0 and one unknown fatty acid for strain TA73(T) and C18 : 1ω7c, C16 : 1ω7c/iso-C15 : 0 2-OH, C18 : 0 and C16 : 0 for strains C34(T) and T5. Physiological and biochemical analysis, including DNA-DNA hybridization, revealed clear differences between the investigated strains and their closest phylogenetic neighbours. DNA-DNA hybridization studies also showed high similarities between strains C34(T) and T5 (59.6-100 %). Therefore, the isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium trifolii sp. nov. (type strain TA73(T) = LMG 25778(T) = CCM 7786(T)) and Methylobacterium thuringiense sp. nov. (type strain C34(T) = LMG 25777(T) = CCM 7787(T)) are proposed.

Isolation and characterization of phosphate-solubilizing bacteria from seagrass rhizosphere soil

NASA Astrophysics Data System (ADS)

Ghosh, Upasana; Subhashini, Ponnambalam; Dilipan, Elangovan; Raja, Subramanian; Thangaradjou, Thirunavukarassu; Kannan, Lakshmanan

2012-03-01

Phosphate-solubilizing bacterial strains (6 Nos.) were isolated from the rhizosphere soils of two seagrasses ( Halophila ovalis (R. Br.) Hook and Halodule pinifolia (Miki) Hartog) in the Vellar estuary. Experimental studies found that the strain PSSG6 was effective in phosphate solubilization with Phosphate Solubilization efficiency index E = 375 ± 8.54, followed by the strain PSSG5 with Phosphate Solubilization efficiency index E = 275 ± 27.3. Of the 6 strains isolated, the strains PSSG4 and PSSG5 belonged to the genus Bacillus, and PSSG1, PSSG2 and PSSG3 were identified as Citrobacter sp., Shigella sp., and Klebsiella sp., respectively, by conventional method, and PSSG6 was identified as Bacillus circulans using conventional and molecular methods.

Deep Sequencing-Identified Kanamycin-Resistant Paenibacillus sp. Strain KS1 Isolated from Epiphyte Tillandsia usneoides (Spanish Moss) in Central Florida, USA.

PubMed

Lata, Pushpa; Govindarajan, Subramaniam S; Qi, Feng; Li, Jian-Liang; Sahoo, Malaya K

2017-02-02

Paenibacillus sp. strain KS1 was isolated from an epiphyte, Tillandsia usneoides (Spanish moss), in central Florida, USA. Here, we report a draft genome sequence of this strain, which consists of a total of 398 contigs spanning 6,508,195 bp, with a G+C content of 46.5% and comprising 5,401 predicted coding sequences. Copyright © 2017 Lata et al.

Penilumamide, a novel lumazine peptide isolated from the marine-derived fungus, Penicillium sp. CNL-338.

PubMed

Meyer, Sven W; Mordhorst, Thorsten F; Lee, Choonghwan; Jensen, Paul R; Fenical, William; Köck, Matthias

2010-05-07

A novel lumazine peptide, penilumamide (1), was isolated from the fermentation broth of a marine-derived fungal strain, identified as Penicillium sp. (strain CNL-338) and the structure of the new metabolite was determined by analysis of ESI-TOF MS data combined with 1D and 2D NMR experiments.

Construction of Potent Recombinant Strain Through Intergeneric Protoplast Fusion in Endophytic Fungi for Anticancerous Enzymes Production Using Rice Straw.

PubMed

El-Gendy, Mervat Morsy Abbas Ahmed; Al-Zahrani, Salha Hassan Mastour; El-Bondkly, Ahmed Mohamed Ahmed

2017-09-01

Among all fungal endophytes isolates derived from different ethno-medical plants, the hyper-yield L-asparaginase and L-glutaminase wild strains Trichoderma sp. Gen 9 and Cladosporium sp. Gen 20 using rice straw under solid-state fermentation (SSF) were selected. The selected strains were used as parents for the intergeneric protoplast fusion program to construct recombinant strain for prompt improvement production of these enzymes in one recombinant strain. Among 21 fusants obtained, the recombinant strain AYA 20-1, with 2.11-fold and 2.58-fold increase in L-asparaginase and L-glutaminase activities more than the parental isolates Trichoderma sp. Gen 9 and Cladosporium sp. Gen 20, respectively, was achieved using rice straw under SSF. Both therapeutic enzymes L-asparaginase and L-glutaminase were purified and characterized from the culture supernatant of the recombinant AYA 20-1 strain with molecular weights of 50.6 and 83.2 kDa, respectively. Both enzymes were not metalloenzymes. Whereas thiol group blocking reagents such as p-chloromercurybenzoate and iodoacetamide totally inhibited L-asparaginase activity, which refer to sulfhydryl groups and cysteine residues involved in its catalytic activity, they have no effect toward L-glutaminase activity. Interestingly, potent anticancer, antioxidant, and antimicrobial activities were detected for both enzymes.

Draft genome sequence of Streptomyces sp. strain F1, a potential source for glycoside hydrolases isolated from Brazilian soil.

PubMed

Melo, Ricardo Rodrigues de; Persinoti, Gabriela Felix; Paixão, Douglas Antonio Alvaredo; Squina, Fábio Márcio; Ruller, Roberto; Sato, Helia Harumi

Here, we show the draft genome sequence of Streptomyces sp. F1, a strain isolated from soil with great potential for secretion of hydrolytic enzymes used to deconstruct cellulosic biomass. The draft genome assembly of Streptomyces sp. strain F1 has 69 contigs with a total genome size of 8,142,296bp and G+C 72.65%. Preliminary genome analysis identified 175 proteins as Carbohydrate-Active Enzymes, being 85 glycoside hydrolases organized in 33 distinct families. This draft genome information provides new insights on the key genes encoding hydrolytic enzymes involved in biomass deconstruction employed by soil bacteria. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Rhodotorula bloemfonteinensis sp. nov., Rhodotorula eucalyptica sp. nov., Rhodotorula orientis sp. nov. and Rhodotorula pini sp. nov., yeasts isolated from monoterpene-rich environments.

PubMed

Pohl, Carolina H; Smit, Martha S; Albertyn, Jacobus

2011-09-01

Recent rDNA sequencing of 25 isolates from a previous study, during which limonene-utilizing yeasts were isolated from monoterpene-rich environments by using 1,4-disubstituted cyclohexanes as sole carbon sources, led to the identification of four hitherto unknown Rhodotorula species. Analyses of the 26S rDNA D1/D2 region as well as the internal transcribed spacer (ITS) domain indicated that two isolates (CBS 8499(T) and CBS 10736) were identical and were closely related to Rhodotorula cycloclastica, a previously described limonene-utilizing yeast. These novel isolates differed from known yeast species and could be distinguished from R. cycloclastica by standard physiological tests. The other three isolates represent three novel Rhodotorula species, closely related to Sporobolomyces magnisporus. These three species could also be distinguished from other Rhodotorula species by standard physiological tests. Based on these results, we suggest that the new isolates represent novel species, for which the names Rhodotorula eucalyptica sp. nov. (type strain CBS 8499(T)  = NRRL Y-48408(T)), Rhodotorula pini sp. nov. (type strain CBS 10735(T)  = NRRL Y-48410(T)), Rhodotorula bloemfonteinensis sp. nov. (type strain CBS 8598(T)  = NRRL Y-48407(T)) and Rhodotorula orientis sp. nov. (type strain CBS 8594(T)  = NRRL Y-48719(T)) are proposed. R. eucalyptica and R. pini can also utilize limonene.

Candida saraburiensis sp. nov. and Candida prachuapensis sp. nov., xylose-utilizing yeast species isolated in Thailand.

PubMed

Nitiyon, Sukanya; Boonmak, Chanita; Am-In, Somjit; Jindamorakot, Sasitorn; Kawasaki, Hiroko; Yongmanitchai, Wichien; Limtong, Savitree

2011-02-01

Four strains of two novel xylose-utilizing yeast species were obtained from samples collected in Thailand from decaying corncobs (strains KU-Xs13(T) and KU-Xs18), a decaying grass (KU-Xs20) and estuarine water from a mangrove forest (WB15(T)). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 domain of the large subunit rRNA gene, the four strains were found to represent two novel species of the genus Candida in the Candida albicans/Lodderomyces elongisporus clade. Three strains (KU-Xs13(T), KU-Xs18 and KU-Xs20) were assigned as a single novel species, which was named Candida saraburiensis sp. nov. The type strain is KU-Xs13(T) (=CBS 11696(T)=NBRC 106721(T)=BCC 39601(T)). Strain WB15(T) represented another novel species of the genus Candida that was named Candida prachuapensis sp. nov. The type strain is WB15(T) (=CBS 11024(T)=NBRC 104881(T)=BCC 29904(T)).

[Total serum calcium and corrected calcium as severity predictors in acute pancreatitis].

PubMed

Gutiérrez-Jiménez, A A; Castro-Jiménez, E; Lagunes-Córdoba, R

2014-01-01

To evaluate total serum calcium (TC) and albumin-corrected calcium (ACC) as prognostic severity factors in acute pancreatitis (AP). Ninety-six patients were included in the study. They were diagnosed with AP and admitted to the Hospital Regional de Veracruz within the time frame of January 2010 to December 2012. AP severity was determined through the updated Atlanta Classification (2013). TC and ACC values were measured in the first 24hours of admittance and the percentages of sensitivity (S), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (LR+), and negative likelihood ratio (LR-) were calculated through ROC curves and contingency tables. In accordance with the updated Atlanta Classification, 70 patients presented with mild AP, 17 with moderately severe AP, and 9 with severe AP. Of the patient total, 61.5% were women, and 69.8% presented with biliary etiology. The maximum TC cut-off point was 7.5mg/dL, with values of S, 67%; Sp, 82%; PPV, 27%, and NPV, 96%. The maximum ACC cut-off point was 7.5mg/dL, with values of S, 67%; Sp, 90%; PPV, 40%; NPV, 96%. Both had values similar to those of the Ranson and APACHE II prognostic scales. TC and ACC, measured within the first 24hours, are useful severity predictors in acute pancreatitis, with sensitivity and predictive values comparable or superior to those of the conventional prognostic scales. Copyright © 2013 Asociación Mexicana de Gastroenterología. Published by Masson Doyma México S.A. All rights reserved.

Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments.

PubMed

den Bakker, Henk C; Warchocki, Steven; Wright, Emily M; Allred, Adam F; Ahlstrom, Christina; Manuel, Clyde S; Stasiewicz, Matthew J; Burrell, Angela; Roof, Sherry; Strawn, Laura K; Fortes, Esther; Nightingale, Kendra K; Kephart, Daniel; Wiedmann, Martin

2014-06-01

Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average BLAST nucleotide identity (ANIb) of less than 85% to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria; (i) a clade representing Listeria monocytogenes, L. marthii, L. innocua, L. welshimeri, L. seeligeri and L. ivanovii, which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188(T) = DSM 26686(T) = LMG 28120(T) = BEI NR-42633(T)) and Listeria floridensis sp. nov. (type strain FSL S10-1187(T) = DSM 26687(T) = LMG 28121(T) = BEI NR-42632(T)), (iii) a clade consisting of Listeria rocourtiae, L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210(T) = FSL F6-0969(T) = DSM 26689(T) = LMG 28123(T) = BEI NR-42630(T)), Listeria grandensis sp. nov. (type strain TTU A1-0212(T) = FSL F6-0971(T) = DSM 26688(T) = LMG 28122(T) = BEI NR-42631(T)) and Listeria riparia sp. nov. (type strain FSL S10-1204(T) = DSM 26685(T) = LMG 28119(T) = BEI NR- 42634(T)) and (iv) a clade containing Listeria grayi. Genomic and phenotypic data suggest that the novel species are non-pathogenic. © 2014 IUMS.

Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.

PubMed

Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

1995-05-01

The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases.

Desaturation, dioxygenation, and monooxygenation reactions catalyzed by naphthalene dioxygenase from Pseudomonas sp. strain 9816-4.

PubMed Central

Gibson, D T; Resnick, S M; Lee, K; Brand, J M; Torok, D S; Wackett, L P; Schocken, M J; Haigler, B E

1995-01-01

The stereospecific oxidation of indan and indene was examined with mutant and recombinant strains expressing naphthalene dioxygenase of Pseudomonas sp. strain 9816-4. Pseudomonas sp. strain 9816/11 and Escherichia coli JM109(DE3)[pDTG141] oxidized indan to (+)-(1S)-indanol, (+)-cis-(1R,2S)-indandiol, (+)-(1S)-indenol, and 1-indanone. The same strains oxidized indene to (+)-cis-(1R,2S)-indandiol and (+)-(1S)-indenol. Purified naphthalene dioxygenase oxidized indan to the same four products formed by strains 9816/11 and JM109(DE3)[pDTG141]. In addition, indene was identified as an intermediate in indan oxidation. The major products formed from indene by purified naphthalene dioxygenase were (+)-(1S)-indenol and (+)-(1R,2S)-indandiol. The results show that naphthalene dioxygenase catalyzes the enantiospecific monooxygenation of indan to (+)-(1S)-indanol and the desaturation of indan to indene, which then serves as a substrate for the formation of (+)-(1R,2S)-indandiol and (+)-(1S)-indenol. The relationship of the desaturase, monooxygenase, and dioxygenase activities of naphthalene dioxygenase is discussed with reference to reactions catalyzed by toluene dioxygenase, plant desaturases, cytochrome P-450, methane monooxygenase, and other bacterial monooxygenases. PMID:7751268

Screening and evaluation of antiparasitic and in vitro anticancer activities of Panamanian endophytic fungi.

PubMed

Martínez-Luis, Sergio; Cherigo, Lilia; Higginbotham, Sarah; Arnold, Elizabeth; Spadafora, Carmenza; Ibañez, Alicia; Gerwick, William H; Cubilla-Rios, Luis

2011-06-01

Many compounds produced by fungi have relevant pharmaceutical applications. The purpose of this study was to collect and isolate endophytic fungi from different regions of Panama and then to test their potential therapeutic activities against Leishmania donovani, Plasmodium falciparum, and Trypanosoma cruzi as well as their anticancer activities in MCF-7 cells. Of the 25 fungal isolates obtained, ten of them had good anti-parasitic potential, showing selective activity against L. donovani; four had significant anti-malarial activity; and three inhibited the growth of T. cruzi. Anticancer activity was demonstrated in four isolates. Of the active isolates, Edenia sp. strain F0755, Xylaria sp. strain F1220, Aspergillus sp. strain F1544, Mycoleptodiscus sp. strain F0194, Phomopsis sp. strain F1566, Pycnoporus sp. strain F0305, and Diaporthe sp. strain F1647 showed the most promise based on their selective bioactivity and lack of toxicity in the assays.

Candida ruelliae sp. nov., a novel yeast species isolated from flowers of Ruellia sp. (Acanthaceae).

PubMed

Saluja, Puja; Prasad, Gandham S

2008-06-01

Two novel yeast strains designated as 16Q1 and 16Q3 were isolated from flowers of the Ruellia species of the Acanthaceae family. The D1/D2 domain and ITS sequences of these two strains were identical. Sequence analysis of the D1/D2 domain of large-subunit rRNA gene indicated their relationship to species of the Candida haemulonii cluster. However, they differ from C. haemulonii by 14% nucleotide sequence divergence, from Candida pseudohaemulonii by 16.1% and from C. haemulonii type II by 16.5%. These strains also differ in 18 physiological tests from the type strain of C. haemulonii, and 12 and 16 tests, respectively, from C. pseudohaemulonii and C. haemulonii type II. They also differ from C. haemulonii and other related species by more than 13% sequence divergence in the internal transcribed spacer region. In the SSU rRNA gene sequences, strain 16Q1 differs by 1.7% nucleotide divergence from C. haemulonii. Sporulation was not observed in pure or mixed cultures on several media examined. All these data support the assignment of these strains to a novel species; we have named them as Candida ruelliae sp. nov., and designate strain 16Q1(T)=MTCC 7739(T)=CBS10815(T) as type strain of the novel species.

Differential Response of Potato Toward Inoculation with Taxonomically Diverse Plant Growth Promoting Rhizobacteria.

PubMed

Naqqash, Tahir; Hameed, Sohail; Imran, Asma; Hanif, Muhammad Kashif; Majeed, Afshan; van Elsas, Jan Dirk

2016-01-01

Rhizosphere engineering with beneficial plant growth promoting bacteria offers great promise for sustainable crop yield. Potato is an important food commodity that needs large inputs of nitrogen and phosphorus fertilizers. To overcome high fertilizer demand (especially nitrogen), five bacteria, i.e., Azospirillum sp. TN10, Agrobacterium sp. TN14, Pseudomonas sp. TN36, Enterobacter sp. TN38 and Rhizobium sp. TN42 were isolated from the potato rhizosphere on nitrogen-free malate medium and identified based on their 16S rRNA gene sequences. Three strains, i.e., TN10, TN38, and TN42 showed nitrogen fixation (92.67-134.54 nmol h(-1)mg(-1) protein), while all showed the production of indole-3-acetic acid (IAA), which was significantly increased by the addition of L-tryptophan. Azospirillum sp. TN10 produced the highest amount of IAA, as measured by spectrophotometry (312.14 μg mL(-1)) and HPLC (18.3 μg mL(-1)). Inoculation with these bacteria under axenic conditions resulted in differential growth responses of potato. Azospirillum sp. TN10 incited the highest increase in potato fresh and dry weight over control plants, along with increased N contents of shoot and roots. All strains were able to colonize and maintain their population densities in the potato rhizosphere for up to 60 days, with Azospirillum sp. and Rhizobium sp. showing the highest survival. Plant root colonization potential was analyzed by transmission electron microscopy of root sections inoculated with Azospirillum sp. TN10. Of the five test strains, Azospirillum sp. TN10 has the greatest potential to increase the growth and nitrogen uptake of potato. Hence, it is suggested as a good candidate for the production of potato biofertilizer for integrated nutrient management.

Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

PubMed Central

Peeters, Charlotte; Meier-Kolthoff, Jan P.; Verheyde, Bart; De Brandt, Evie; Cooper, Vaughn S.; Vandamme, Peter

2016-01-01

Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317T = CCUG 68412T), Burkholderia hypogeia sp. nov. (type strain LMG 29322T = CCUG 68407T), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326T = CCUG 68403T), Burkholderia glebae sp. nov. (type strain LMG 29325T = CCUG 68404T), Burkholderia pedi sp. nov. (type strain LMG 29323T = CCUG 68406T), Burkholderia arationis sp. nov. (type strain LMG 29324T = CCUG 68405T), Burkholderia fortuita sp. nov. (type strain LMG 29320T = CCUG 68409T), Burkholderia temeraria sp. nov. (type strain LMG 29319T = CCUG 68410T), Burkholderia calidae sp. nov. (type strain LMG 29321T = CCUG 68408T), Burkholderia concitans sp. nov. (type strain LMG 29315T = CCUG 68414T), Burkholderia turbans sp. nov. (type strain LMG 29316T = CCUG 68413T), Burkholderia catudaia sp. nov. (type strain LMG 29318T = CCUG 68411T) and Burkholderia peredens sp. nov. (type strain LMG 29314T = CCUG 68415T). Furthermore, we present emended descriptions of the species Burkholderia sordidicola, Burkholderia zhejiangensis and Burkholderia grimmiae. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and gyrB gene sequences determined in this study are LT158612-LT158624 and LT158625-LT158641, respectively. PMID:27375597

Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid- Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm

DOE PAGES

O'Dell, Kaela; Woo, Hannah L.; Utturkar, Sagar M.; ...

2015-05-07

Halomonas sp. strain KO116 was isolated from Nile Delta Mediterranean Sea surface water enriched with insoluble organosolv lignin. It was further screened for growth on alkali lignin minimal salts medium agar. The strain tolerates the ionic liquid 1-ethyl-3-methylimidazolium acetate. Its complete genome sequence is presented in this report.

Ability of an alkali-tolerant mutant strain of the microalga Chlorella sp. AT1 to capture carbon dioxide for increasing carbon dioxide utilization efficiency.

PubMed

Kuo, Chiu-Mei; Lin, Tsung-Hsien; Yang, Yi-Chun; Zhang, Wen-Xin; Lai, Jinn-Tsyy; Wu, Hsi-Tien; Chang, Jo-Shu; Lin, Chih-Sheng

2017-11-01

An alkali-tolerant Chlorella sp. AT1 mutant strain was screened by NTG mutagenesis. The strain grew well in pH 6-11 media, and the optimal pH for growth was 10. The CO 2 utilization efficiencies of Chlorella sp. AT1 cultured with intermittent 10% CO 2 aeration for 10, 20 and 30min at 3-h intervals were approximately 80, 42 and 30%, respectively. In alkaline medium (pH=11) with intermittent 10% CO 2 aeration for 30min at 3-, 6- and 12-h intervals, the medium pH gradually changed to 10, and the biomass productivities of Chlorella sp. AT1 were 0.987, 0.848 and 0.710gL -1 d -1 , respectively. When Chlorella sp. AT1 was aerated with 10% CO 2 intermittently for 30min at 3-h intervals in semi-continuous cultivation for 21days, the biomass concentration and biomass productivity were 4.35gL -1 and 0.726gL -1 d -1 , respectively. Our results show that CO 2 utilization efficiency can be markedly increased by intermittent CO 2 aeration and alkaline media as a CO 2 -capturing strategy for alkali-tolerant microalga cultivation. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

Agematu, Hitosi; Suzuki, Kazuya; Tsuya, Hiroaki

2011-01-01

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

Complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from lettuce (Lactuca sativa) originating from a conventional field in Norway.

PubMed

Dees, Merete Wiken; Brurberg, May Bente; Lysøe, Erik

2016-12-01

Here, we present the 3,795,952 bp complete genome sequence of the biofilm-forming Curtobacterium sp. strain BH-2-1-1, isolated from conventionally grown lettuce ( Lactuca sativa ) from a field in Vestfold, Norway. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession CP017580.

Chemically defined medium for cultivation of several epiphytic and phytopathogenic spiroplasmas.

PubMed

Lee, I M; Davis, R E

1983-12-01

A chemically defined medium, LD82, was formulated for in vitro cultivation of spiroplasmas. Medium LD82 supported good growth for four epiphytic and insect-pathogenic spiroplasmas, Spiroplasma floricola 23-6, Spiroplasma sp. strain SR3, Spiroplasma sp. strain brevi, and Spiroplasma sp. strain AS576, and of the phytopathogenic spiroplasmas Spiroplasma citri Maroc R8A2 and PC1. Titers of all six strains grown in defined medium LD82 reached 2.0 x 10 to 6.0 x 10 CFU/ml of culture. All spiroplasma strains tested formed colonies readily on agar medium LD82. None of the spiroplasmas formed typical fried-egg colonies. All formed diffuse colonies, but the forms of colonies differed somewhat among the spiroplasma strains. In preliminary studies of nutritional requirements, phospholipids slightly enhanced the growth of the epiphytic and insect-pathogenic strains in medium LD82 and were found essential for good growth of S. citri.

Aerobic and Anaerobic Transformation of cis-Dichloroethene (cis-DCE) and Vinyl Chloride (VC): Steps for Reliable Remediation

DTIC Science & Technology

2003-12-01

populations. (ii) Characterization of Dehalococeoides sp . strain FL2. The isolate, designate d Dehalococcoides sp . strain FL2, reductively...Pinellas group of the Dehalococcoides cluster, and demonstrated that strain FL2 shared an identical 165 rRNA gene sequence with Dehalococcoides sp ...strain CBDBI, a chlorobenzene-dechlorinating strain. The 165 rRNA gene sequence of Dehalococcoides sp . strain FL2 was submitted to GenBank (AF357918.2

Draft Genome Sequence of Curtobacterium sp. Strain ER1/6, an Endophytic Strain Isolated from Citrus sinensis with Potential To Be Used as a Biocontrol Agent.

PubMed

Garrido, Leandro Maza; Alves, João Marcelo Pereira; Oliveira, Liliane Santana; Gruber, Arthur; Padilla, Gabriel; Araújo, Welington Luiz

2016-11-17

Herein, we report a draft genome sequence of the endophytic Curtobacterium sp. strain ER1/6, isolated from a surface-sterilized Citrus sinensis branch, and it presented the capability to control phytopathogens. Functional annotation of the ~3.4-Mb genome revealed 3,100 protein-coding genes, with many products related to known ecological and biotechnological aspects of this bacterium. Copyright © 2016 Garrido et al.

Metal-backed versus all-polyethylene unicompartmental knee arthroplasty: Proximal tibial strain in an experimentally validated finite element model.

PubMed

Scott, C E H; Eaton, M J; Nutton, R W; Wade, F A; Evans, S L; Pankaj, P

2017-01-01

Up to 40% of unicompartmental knee arthroplasty (UKA) revisions are performed for unexplained pain which may be caused by elevated proximal tibial bone strain. This study investigates the effect of tibial component metal backing and polyethylene thickness on bone strain in a cemented fixed-bearing medial UKA using a finite element model (FEM) validated experimentally by digital image correlation (DIC) and acoustic emission (AE). A total of ten composite tibias implanted with all-polyethylene (AP) and metal-backed (MB) tibial components were loaded to 2500 N. Cortical strain was measured using DIC and cancellous microdamage using AE. FEMs were created and validated and polyethylene thickness varied from 6 mm to 10 mm. The volume of cancellous bone exposed to < -3000 µε (pathological loading) and < -7000 µε (yield point) minimum principal (compressive) microstrain and > 3000 µε and > 7000 µε maximum principal (tensile) microstrain was computed. Experimental AE data and the FEM volume of cancellous bone with compressive strain < -3000 µε correlated strongly: R = 0.947, R 2 = 0.847, percentage error 12.5% (p < 0.001). DIC and FEM data correlated: R = 0.838, R 2 = 0.702, percentage error 4.5% (p < 0.001). FEM strain patterns included MB lateral edge concentrations; AP concentrations at keel, peg and at the region of load application. Cancellous strains were higher in AP implants at all loads: 2.2- (10 mm) to 3.2-times (6 mm) the volume of cancellous bone compressively strained < -7000 µε. AP tibial components display greater volumes of pathologically overstrained cancellous bone than MB implants of the same geometry. Increasing AP thickness does not overcome these pathological forces and comes at the cost of greater bone resection.Cite this article: C. E. H. Scott, M. J. Eaton, R. W. Nutton, F. A. Wade, S. L. Evans, P. Pankaj. Metal-backed versus all-polyethylene unicompartmental knee arthroplasty: Proximal tibial strain in an experimentally validated finite element model. Bone Joint Res 2017;6:22-30. DOI:10.1302/2046-3758.61.BJR-2016-0142.R1. © 2017 Scott et al.

Shewanella canadensis sp. nov. and Shewanella atlantica sp. nov., manganese dioxide- and hexahydro-1,3,5-trinitro-1,3,5-triazine-reducing, psychrophilic marine bacteria.

PubMed

Zhao, Jian-Shen; Manno, Dominic; Thiboutot, Sonia; Ampleman, Guy; Hawari, Jalal

2007-09-01

Two strains belonging to the genus Shewanella, HAW-EB2(T) and HAW-EB5(T), were isolated previously from marine sediment sampled from the Atlantic Ocean, near Halifax harbour in Canada, for their potential to degrade explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, strains HAW-EB2(T) and HAW-EB5(T) were found to display high 16S rRNA gene sequence similarity (90-99.5 %) to species of Shewanella, but their gyrB sequences were significantly different from each other and from species of Shewanella (79-87.6 %). Furthermore, DNA-DNA hybridization showed that the genomic DNA of the two strains was only 22 % related and showed less than 41 % relatedness to closely related species of Shewanella. In comparison to other species of Shewanella, strains HAW-EB2(T) and HAW-EB5(T) were also unique in some phenotypic properties such as activities of beta-galactosidase and tyrosine arylamidase and the ability to metabolize certain organic acids and sugars. Both strains HAW-EB2(T) and HAW-EB5(T) utilize malate, valerate, peptone and yeast extract as sole carbon and energy sources. The major membrane fatty acids of the two strains were C(14 : 0), iso-C(15 : 0), C(16 : 0), C(16 : 1)omega7, C(18 : 1)omega7 and C(20 : 5)omega3 and their major quinones were Q-7, Q-8 and MK-7. On the basis of these results, strain HAW-EB2(T) (=NCIMB 14238(T) =CCUG 54553(T)) is proposed as the type strain of Shewanella canadensis sp. nov. and strain HAW-EB5(T) (=NCIMB 14239(T) =CCUG 54554(T)) is proposed as the type strain of Shewanella atlantica sp. nov.

Chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant Pseudomonas sp. strain BUR11: evidence for possible existence of two pathways for degradation.

PubMed

Pailan, Santanu; Saha, Pradipta

2015-01-01

An organophosphate (OP) degrading chemotactic bacterial strain BUR11 isolated from an agricultural field was identified as a member of Pseudomonas genus on the basis of its 16S rRNA gene sequence. The strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. Optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded within 96 h at 37 °C. Growth studies indicated the strain to be moderately thermo-halo tolerant in nature. Investigation based on identification of intermediates of parathion degradation by thin layer chromatography (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC) and liquid chromatography mass spectrometry (LC-MS/MS) provided evidence for possible existence of two pathways. The first pathway proceeds via 4-nitrophenol (4-NP) while the second proceeds through formation of 4-aminoparathion (4-APar), 4-aminophenol (4-AP) and parabenzoquinone (PBQ). This is the first report of chemotaxis towards organophosphate compound by a thermo-halo tolerant bacterium.

Chemotaxis and degradation of organophosphate compound by a novel moderately thermo-halo tolerant Pseudomonas sp. strain BUR11: evidence for possible existence of two pathways for degradation

PubMed Central

Pailan, Santanu

2015-01-01

An organophosphate (OP) degrading chemotactic bacterial strain BUR11 isolated from an agricultural field was identified as a member of Pseudomonas genus on the basis of its 16S rRNA gene sequence. The strain could utilize parathion, chlorpyrifos and their major hydrolytic intermediates as sole source of carbon for its growth and exhibited positive chemotactic response towards most of them. Optimum concentration of parathion for its growth was recorded to be 200 ppm and 62% of which was degraded within 96 h at 37 °C. Growth studies indicated the strain to be moderately thermo-halo tolerant in nature. Investigation based on identification of intermediates of parathion degradation by thin layer chromatography (TLC), high performance liquid chromatography (HPLC), gas chromatography (GC) and liquid chromatography mass spectrometry (LC-MS/MS) provided evidence for possible existence of two pathways. The first pathway proceeds via 4-nitrophenol (4-NP) while the second proceeds through formation of 4-aminoparathion (4-APar), 4-aminophenol (4-AP) and parabenzoquinone (PBQ). This is the first report of chemotaxis towards organophosphate compound by a thermo-halo tolerant bacterium. PMID:26587344

Deep Desulfurization of Extensively Hydrodesulfurized Middle Distillate Oil by Rhodococcus sp. Strain ECRD-1

PubMed Central

Grossman, M. J.; Lee, M. K.; Prince, R. C.; Minak-Bernero, V.; George, G. N.; Pickering, I. J.

2001-01-01

Dibenzothiophene (DBT), and in particular substituted DBTs, are resistant to hydrodesulfurization (HDS) and can persist in fuels even after aggressive HDS treatment. Treatment by Rhodococcus sp. strain ECRD-1 of a middle distillate oil whose sulfur content was virtually all substituted DBTs produced extensive desulfurization and a sulfur level of 56 ppm. PMID:11282654

Penilumamide, a novel lumazine peptide isolated from the marine-derived fungus, Penicillium sp. CNL-338†

PubMed Central

Meyer, Sven W.; Mordhorst, Thorsten F.; Lee, Choonghwan; Jensen, Paul R.; Fenical, William; Köck, Matthias

2013-01-01

A novel lumazine peptide, penilumamide (1), was isolated from the fermentation broth of a marine-derived fungal strain, identified as Penicillium sp. (strain CNL-338) and the structure of the new metabolite was determined by analysis of ESI-TOF MS data combined with 1D and 2D NMR experiments. PMID:20401392

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.

PubMed Central

Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

2013-01-01

Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes. PMID:24019984

A 22-mer primer enhances discriminatory power of AP-PCR fingerprinting technique in characterization of leptospires.

PubMed

Roy, Subarna; Biswas, Debabrata; Vijayachari, P; Sugunan, A P; Sehgal, Subhash C

2004-11-01

To evaluate the discriminatory power and usefulness of arbitrarily primed-polymerase chain reaction (AP-PCR) characterization of leptospires with M16 primer. AP-PCR fingerprints of 20 reference strains of Leptospira representing 20 different serovars belonging to seven genospecies (Leptospira interrogans, 11; L. noguchii, 2; L. borgpetersenii, 1; L. santarosai, 2; L. biflexa, 2; L. kirschneri, 1; L. weilii, 1) were generated by employing M16 primer. Fingerprints generated with this primer were compared with those generated with two other commonly used primers PB1, and L10. An attempt was also made to type 20 leptospiral isolates with the M16 primer. Fingerprints with M16 primer could not only differentiate between strains of different genospecies, but also between strains of the same genospecies belonging to different serovars. While two commonly used primers (PB1 and L10) failed to discriminate between some of the different serovars belonging to the same genospecies, this primer was able to generate discriminatory fingerprints for all strains tested. All 20 Leptospira isolates, recovered from patients in Andaman Islands, could also be typed by fingerprints generated with the M16 primer. The discriminatory power of M16 primer adds more specificity to the rapidity of this system of characterization and can be used as an excellent tool in epidemiological studies on Leptospira.

Streptomyces chiangmaiensis sp. nov. and Streptomyces lannensis sp. nov., isolated from the South-East Asian stingless bee (Tetragonilla collina).

PubMed

Promnuan, Yaowanoot; Kudo, Takuji; Ohkuma, Moriya; Chantawannakul, Panuwan

2013-05-01

Two novel actinomycetes, strains TA4-1(T) and TA4-8(T,) were isolated from the South-East Asian stingless bee (Tetragonilla collina Smith 1857), collected from Chiang Mai Province, Thailand. The morphological and chemotaxonomic properties of strains TA4-1(T) and TA4-8(T) were consistent with the genus Streptomyces, i.e. the formation of aerial mycelia bearing spiral spore chains, the presence of the ll-isomer of diaminopimelic acid in cell walls, iso- and anteiso-branched fatty acids with carbon chain lengths 14-17 atoms as the major fatty acids and MK-9(H8) as the predominant menaquinone plus minor amounts of MK-9(H6) and MK-9(H10). Analysis of 16S rRNA gene sequences showed that strains TA4-1(T) and TA4-8(T) exhibited 98.8 and 98.1% sequence similarity, respectively, with Streptomyces chromofuscus NRRL B-12175(T) and 98.9% sequence similarity with each other. This study suggested that strains TA4-1(T) and TA4-8(T) were distinct from previously described species of the genus Streptomyces. In addition, the low degrees of DNA-DNA relatedness between the isolates and S. chromofuscus JCM 4354(T) warranted assigning strains TA4-1(T) and TA4-8(T) to two novel species. The names Streptomyces chiangmaiensis sp. nov. (type strain TA4-1(T)  = JCM 16577(T)  = TISTR 1981(T)) and Streptomyces lannensis sp. nov. (type strain TA4-8(T)  = JCM 16578(T)  = TISTR 1982(T)) are proposed. The species names indicate the geographical locations where the stingless bees reside.

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

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

PubMed

Arora, Pankaj Kumar; Sharma, Ashutosh; Mehta, Richa; Shenoy, Belle Damodara; Srivastava, Alok; Singh, Vijay Pal

2012-11-21

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. 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. 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.

Molecular analyses reveal an abundant diversity of ticks and rickettsial agents associated with wild birds in two regions of primary Brazilian Atlantic Rainforest.

PubMed

Luz, Hermes Ribeiro; Faccini, João Luiz Horacio; McIntosh, Douglas

2017-06-01

Brazilian wild birds are recognized as frequent and important hosts for immature stages of more than half of the 32 recognized species of Amblyomma ticks recorded in that country. Several species of Amblyomma harbor rickettsial agents, including members of the spotted fever group (SFG). Most studies on this topic relied primarily on morphological characterization and reported large portions of the collected ticks at the genus rather than species level. Clearly, this factor may have contributed to an underestimation of tick diversity and distribution and makes comparisons between studies difficult. The current investigation combined morphological and molecular analyses to assess the diversity of ticks and rickettsial agents associated with wild birds, captured in two regions of native Atlantic rainforest, in the state of Rio de Janeiro, Brazil. A total of 910 birds were captured, representing two orders, 34 families and 106 species, among which 93 specimens (10.2%), were parasitized by 138 immature ticks (60 larvae and 78 nymphs), representing 10 recognized species of the genus Amblyomma; together with two reasonably well classified haplotypes (Amblyomma sp. haplotype Nazaré and Amblyomma sp. strain USNTC 6792). Amplification by PCR and sequencing of rickettsial genes (htrA, gltA, ompA and ompB), demonstrated the presence of Rickettsia DNA in 48 (34%) of the ticks. Specifically, Rickettsia bellii was detected in a single larva and a single nymph of A. aureolatum; R. amblyomatis was found in 16 of 37 A. longirostre and was recorded for the first time in three nymphs of A. calcaratum; R. rhipicephali was detected in 9 (47%) of 19 Amblyomma sp. haplotype Nazaré ticks. The remaining ticks were infected with genetic variants of R. parkeri, namely strain ApPR in 12 A. parkeri and seven Amblyomma sp. haplotype Nazaré ticks, with the strain NOD found in two specimens of A. nodosum. Interestingly, a single larvae of A. ovale was shown to be infected with the emerging human pathogen Rickettsia sp. strain Atlantic rainforest (ARF), suggesting a possible role for birds in the dispersal of ticks infected with this variant of R. parkeri. The diversity of ticks and Rickettsia recorded in this study is, to our knowledge, the most abundant recorded to date in Brazil and highlighted the value of employing methods capable of providing species level identification of the ixodofauna of wild birds. Copyright © 2017. Published by Elsevier GmbH.

Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius).

PubMed

Ghosh, Pallab; Hsu, Chungyi; Alyamani, Essam J; Shehata, Maher M; Al-Dubaib, Musaad A; Al-Naeem, Abdulmohsen; Hashad, Mahmoud; Mahmoud, Osama M; Alharbi, Khalid B J; Al-Busadah, Khalid; Al-Swailem, Abdulaziz M; Talaat, Adel M

2012-01-01

Mycobacterium avium subspecies paratuberculosis (M. ap) is the causative agent of paratuberculosis or Johne's disease (JD) in herbivores with potential involvement in cases of Crohn's disease in humans. JD is spread worldwide and is economically important for both beef and dairy industries. Generally, pathogenic ovine strains (M. ap-S) are mainly found in sheep while bovine strains (M. ap-C) infect other ruminants (e.g. cattle, goat, deer), as well as sheep. In an effort to characterize this emerging infection in dromedary/Arabian camels, we successfully cultured M. ap from several samples collected from infected camels suffering from chronic, intermittent diarrhea suggestive of JD. Gene-based typing of isolates indicated that all isolates belong to sheep lineage of strains of M. ap (M. ap-S), suggesting a putative transmission from infected sheep herds. Screening sheep and goat herds associated with camels identified the circulation of this type in sheep but not goats. The current genome-wide analysis recognizes these camel isolates as a sub-lineage of the sheep strain with a significant number of single nucleotide polymorphisms (SNPs) between sheep and camel isolates (∼1000 SNPs). Such polymorphism could represent geographical differences among isolates or host adaptation of M. ap during camel infection. To our knowledge, this is the first attempt to examine the genomic basis of this emerging infection in camels with implications on the evolution of this important pathogen. The sequenced genomes of M. ap isolates from camels will further assist our efforts to understand JD pathogenesis and the dynamic of disease transmission across animal species.

Genome-Wide Analysis of the Emerging Infection with Mycobacterium avium Subspecies paratuberculosis in the Arabian Camels (Camelus dromedarius)

PubMed Central

Ghosh, Pallab; Hsu, Chungyi; Alyamani, Essam J.; Shehata, Maher M.; Al-Dubaib, Musaad A.; Al-Naeem, Abdulmohsen; Hashad, Mahmoud; Mahmoud, Osama M.; Alharbi, Khalid B. J.; Al-Busadah, Khalid; Al-Swailem, Abdulaziz M.; Talaat, Adel M.

2012-01-01

Mycobacterium avium subspecies paratuberculosis (M. ap) is the causative agent of paratuberculosis or Johne's disease (JD) in herbivores with potential involvement in cases of Crohn's disease in humans. JD is spread worldwide and is economically important for both beef and dairy industries. Generally, pathogenic ovine strains (M. ap-S) are mainly found in sheep while bovine strains (M. ap-C) infect other ruminants (e.g. cattle, goat, deer), as well as sheep. In an effort to characterize this emerging infection in dromedary/Arabian camels, we successfully cultured M. ap from several samples collected from infected camels suffering from chronic, intermittent diarrhea suggestive of JD. Gene-based typing of isolates indicated that all isolates belong to sheep lineage of strains of M. ap (M. ap-S), suggesting a putative transmission from infected sheep herds. Screening sheep and goat herds associated with camels identified the circulation of this type in sheep but not goats. The current genome-wide analysis recognizes these camel isolates as a sub-lineage of the sheep strain with a significant number of single nucleotide polymorphisms (SNPs) between sheep and camel isolates (∼1000 SNPs). Such polymorphism could represent geographical differences among isolates or host adaptation of M. ap during camel infection. To our knowledge, this is the first attempt to examine the genomic basis of this emerging infection in camels with implications on the evolution of this important pathogen. The sequenced genomes of M. ap isolates from camels will further assist our efforts to understand JD pathogenesis and the dynamic of disease transmission across animal species. PMID:22393374

Iron Corrosion Induced by Nonhydrogenotrophic Nitrate-Reducing Prolixibacter sp. Strain MIC1-1

PubMed Central

Ito, Kimio; Wakai, Satoshi; Tsurumaru, Hirohito; Ohkuma, Moriya; Harayama, Shigeaki

2014-01-01

Microbiologically influenced corrosion (MIC) of metallic materials imposes a heavy economic burden. The mechanism of MIC of metallic iron (Fe0) under anaerobic conditions is usually explained as the consumption of cathodic hydrogen by hydrogenotrophic microorganisms that accelerates anodic Fe0 oxidation. In this study, we describe Fe0 corrosion induced by a nonhydrogenotrophic nitrate-reducing bacterium called MIC1-1, which was isolated from a crude-oil sample collected at an oil well in Akita, Japan. This strain requires specific electron donor-acceptor combinations and an organic carbon source to grow. For example, the strain grew anaerobically on nitrate as a sole electron acceptor with pyruvate as a carbon source and Fe0 as the sole electron donor. In addition, ferrous ion and l-cysteine served as electron donors, whereas molecular hydrogen did not. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MIC1-1 was a member of the genus Prolixibacter in the order Bacteroidales. Thus, Prolixibacter sp. strain MIC1-1 is the first Fe0-corroding representative belonging to the phylum Bacteroidetes. Under anaerobic conditions, Prolixibacter sp. MIC1-1 corroded Fe0 concomitantly with nitrate reduction, and the amount of iron dissolved by the strain was six times higher than that in an aseptic control. Scanning electron microscopy analyses revealed that microscopic crystals of FePO4 developed on the surface of the Fe0 foils, and a layer of FeCO3 covered the FePO4 crystals. We propose that cells of Prolixibacter sp. MIC1-1 accept electrons directly from Fe0 to reduce nitrate. PMID:25548048

Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov.

PubMed

Liu, Chenli; Wu, Yehui; Li, Li; Ma, Yingfei; Shao, Zongze

2007-02-01

Two bacterial strains, M-5T and WP0211T, were isolated from the surface water of a waste-oil pool in a coastal dock and from a deep-sea sediment sample from the West Pacific Ocean, respectively. Analysis of 16S rRNA gene sequences indicated that both strains belonged to the class Alphaproteobacteria and were closely related to Thalassospira lucentensis (96.1 and 96.2 %, gene sequence similarity, respectively). Based on the results of physiological and biochemical tests, as well as DNA-DNA hybridization experiments, it is suggested that these isolates represent two novel species of the genus Thalassospira. Various traits allow both novel strains to be differentiated from Thalassospira lucentensis, including oxygen requirement, nitrate reduction and denitrification abilities and major fatty acid profiles, as well as their ability to utilize six different carbon sources. Furthermore, the novel strains may be readily distinguished from each other by differences in their motility, flagellation, growth at 4 degrees C and 40 degrees C, their ability to hydrolyse Tween 40 and Tween 80, their utilization of 19 different carbon sources and by quantitative differences in their fatty acid contents. It is proposed that the isolates represent two novel species for which the names Thalassospira xiamenensis sp. nov. (type strain, M-5T=DSM 17429T=CGMCC 1.3998T) and Thalassospira profundimaris sp. nov. (type strain, WP0211T=DSM 17430T=CGMCC 1.3997T) are proposed.

Exercise modality modulates body temperature regulation during exercise in uncompensable heat stress.

PubMed

Schlader, Zachary J; Raman, Aaron; Morton, R Hugh; Stannard, Stephen R; Mündel, Toby

2011-05-01

This study evaluated exercise modality [i.e. self-paced (SP) or fixed-intensity (FI) exercise] as a modulator of body temperature regulation under uncompensable heat stress. Eight well-trained male cyclists completed (work-matched) FI and SP cycling exercise bouts in a hot (40.6 ± 0.2°C) and dry (relative humidity 23 ± 3%) environment estimated to elicit 70% of [Formula: see text]O(2)max. Exercise intensity (i.e. power output) decreased over time in SP, which resulted in longer exercise duration (FI 20.3 ± 3.4 min, SP 23.2 ± 4.1 min). According to the heat strain index, the modification of exercise intensity in SP improved the compensability of the thermal environment which, relative to FI, was likely a result of the reductions in metabolic heat production (i.e. [Formula: see text]O(2)). Consequently, the rate of rise in core body temperature was higher in FI (0.108 ± 0.020°C/min) than in SP (0.082 ± 0.016°C/min). Interestingly, cardiac output, stroke volume, and heart rate during exercise were independent of exercise modality. However, core body temperature (FI 39.4 ± 0.3°C, SP 39.1 ± 0.4°C), blood lactate (FI 2.9 ± 0.8 mmol/L, SP 2.3 ± 0.7 mmol/L), perceived exertion (FI 18 ± 2, SP 16 ± 2), and physiological strain (FI 9.1 ± 0.9, SP 8.3 ± 1.1) were all higher in FI compared to SP at exhaustion/completion. These findings indicate that, when exercise is SP, behavioral modification of metabolic heat production improves the compensability of the thermal environment and reduces thermoregulatory strain. Therefore, under uncompensable heat stress, exercise modality modulates body temperature regulation.

Pseudomonas yangmingensis sp. nov., an alkaliphilic denitrifying species isolated from a hot spring.

PubMed

Wong, Biing-Teo; Lee, Duu-Jong

2014-01-01

This study isolated and identified a facultative, alkaliphilic, denitrifying Pseudomonas strain designed as CRS1 from a hot spring, Yang-Ming Mountain, Taiwan. The biochemical characterization, phenotypic characteristics and phylogenetic relationship of strain CRS1 were studied. On the basis of the 16S rRNA sequence similarity, phenotypic and genotypic characteristics and chemotaxonomic data, the strain CRS1 represents a novel species of the genus Pseudomonas, for which the name Pseudomonas yangmingensis sp. nov., is proposed. The strain CRS1 is a facultative autotrophic bacterium that has capability of mixotrophic and heterotrophic denitrification. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Serratia myotis sp. nov. and Serratia vespertilionis sp. nov., isolated from bats hibernating in caves.

PubMed

García-Fraile, P; Chudíčková, M; Benada, O; Pikula, J; Kolařík, M

2015-01-01

During the study of bacteria associated with bats affected by white-nose syndrome hibernating in caves in the Czech Republic, we isolated two facultatively anaerobic, Gram-stain-negative bacteria, designated strains 12(T) and 52(T). Strains 12(T) and 52(T) were motile, rod-like bacteria (0.5-0.6 µm in diameter; 1-1.3 µm long), with optimal growth at 20-35 °C and pH 6-8. On the basis of the almost complete sequence of their 16S rRNA genes they should be classified within the genus Serratia; the closest relatives to strains 12(T) and 52(T) were Serratia quinivorans DSM 4597(T) (99.5 % similarity in 16S rRNA gene sequences) and Serratia ficaria DSM 4569(T) (99.5% similarity in 16S rRNA gene sequences), respectively. DNA-DNA relatedness between strain 12(T) and S. quinivorans DSM 4597(T) was only 37.1% and between strain 52(T) and S. ficaria DSM 4569(T) was only 56.2%. Both values are far below the 70% threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Serratia as representatives of Serratia myotis sp. nov. (type strain 12(T) =CECT 8594(T) =DSM 28726(T)) and Serratia vespertilionis sp. nov. (type strain 52(T) =CECT 8595(T) =DSM 28727(T)). © 2015 IUMS.

Serratia bozhouensis sp. nov., Isolated from Sewage Samples of a Dairy Farm.

PubMed

Shang, Fei; Xue, Ting; Wang, Man; Chen, Xiaolin; Yu, Li; Zhang, Ming

2017-07-01

A Gram-negative, rod-shaped, salt-tolerant, non-pigmented, and non-spore-forming bacterium, designated strain W1 T (type strain CICC 23797 = CGMCC1.14949), was isolated from sewage samples of a dairy farm in Bozhou, Anhui, China. Strain W1 was resistant to lincomycin, troleandomycin, rifamycin, and vancomycin. Sequence analysis of the 16S rDNA gene revealed that the strain showed sequence similarity of 98.2% with the closest related species Serratia quinivorans CP6a T . The genomic DNA G+C content of the isolate was 52.8 mol%. The biochemical characteristics of strain W1 T assessed by the API 20E and Biolog GEN III analysis were different from those of the members of the genus Serratia. On the basis of the phenotypic and genotypic differences, strain W1 was proposed to be a novel Serratia species, Serratia bozhouensis sp. nov W1 T .

Two new species of the genus Candida in the Zygoascus clade, Candida lundiana sp. nov. and Candida suthepensis sp. nov., isolated from raw honey in Thailand.

PubMed

Saksinchai, Sujinan; Suzuki, Motofumi; Lumyong, Saisamorn; Ohkuma, Moriya; Chantawannakul, Panuwan

2012-03-01

During a survey of yeasts associated with raw honey collected in Thailand, two strains of the Zygoascus clade were isolated from the Asian cavity-nesting honeybee Apis cerana and the stingless bee Homotrigona fimbriata. Phylogeny based on 26S rDNA D1/D2 sequences placed these yeasts as members of a clade including Candida bituminiphila, Candida patagonica and Candida polysorbophila. The strains of the two novel species, CBS 12271(T) and CBS 12270(T), respectively, could be unquestionably distinguished from their relatives by rDNA sequences and other taxonomic characteristics. Therefore, the novel anamorphic species, Candida lundiana sp. nov. (type strain CBS 12271(T) = JCM 16823(T)) and Candida suthepensis sp. nov. (type strain CBS 12270(T) = JCM 16822(T)) are described.

Molecular characterization and specific detection of Anaplasma species (AP-sd) in sika deer and its first detection in wild brown bears and rodents in Hokkaido, Japan.

PubMed

Moustafa, Mohamed Abdallah Mohamed; Lee, Kyunglee; Taylor, Kyle; Nakao, Ryo; Sashika, Mariko; Shimozuru, Michito; Tsubota, Toshio

2015-12-01

A previously undescribed Anaplasma species (herein referred to as AP-sd) has been detected in sika deer, cattle and ticks in Japan. Despite being highly similar to some strains of A. phagocytophilum, AP-sd has never been detected in humans. Its ambiguous epidemiology and the lack of tools for its specific detection make it difficult to understand and interpret the prevalence of this Anaplasma species. We developed a method for specific detection, and examined AP-sd prevalence in Hokkaido wildlife. Our study included 250 sika deer (Cervus nippon yesoensis), 13 brown bears (Ursus arctos yesoensis) and 252 rodents including 138 (Apodemus speciosus), 45 (Apodemus argenteus), 42 (Myodes rufocanus) and 27 (Myodes rutilus) were collected from Hokkaido island, northern Japan, collected during 2010 to 2015. A 770 bp and 382 bp segment of the 16S rRNA and gltA genes, respectively, were amplified by nested PCR. Results were confirmed by cloning and sequencing of the positive PCR products. A reverse line blot hybridization (RLB) based on the 16S rRNA gene was then developed for the specific detection of AP-sd. The prevalence of AP-sd by nested PCR in sika deer was 51% (128/250). We detected this Anaplasma sp. for the first time in wild brown bears and rodents with a prevalence of 15% (2/13) and 2.4% (6/252), respectively. The sequencing results of the 16S rRNA and gltA gene amplicons were divergent from the selected A. phagocytophilum sequences in GenBank. Using a newly designed AP-sd specific probe for RLB has enabled us to specifically detect this Anaplasma species. Besides sika deer and cattle, wild brown bears and rodents were identified as potential reservoir hosts for AP-sd. This study provided a high throughput molecular method that specifically detects AP-sd, and which can be used to investigate its ecology and its potential as a threat to humans in Japan. Copyright © 2015 Elsevier B.V. All rights reserved.

Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae.

PubMed

Foesel, Bärbel U; Mayer, Susanne; Luckner, Manja; Wanner, Gerhard; Rohde, Manfred; Overmann, Jörg

2016-01-01

Three Gram-negative, non-spore-forming, encapsulated bacteria were isolated from a Namibian river-bank soil (strains 277T and 307) and a semiarid savannah soil (strain A2-1cT). 16S rRNA gene sequence analyses placed them within subdivision 1 of the Acidobacteria and revealed 100 % similarity between strains 277T and 307 and 98.2 % similarity between A2-1cT and the former two strains. The closest relatives with validly published names were Telmatobacter bradus, Acidicapsa borealis and Acidicapsa ligni (94.7-95.9 % similarity to the type strains). Cells of all three strains were rod-shaped and motile and divided by binary fission. Ultrastructural analyses revealed a thick cell envelope, resulting mainly from a thick periplasmic space. Colonies of strains 277T and 307 were white to cream and light pink, respectively, while strain A2-1cT displayed a bright pink colour. All three strains were aerobic, chemoheterotrophic mesophiles with a broad temperature range for growth and a moderately acidic pH optimum. Sugars and complex proteinaceous substrates were the preferred carbon and energy sources. A few polysaccharides were degraded. The major quinone in all three strains was MK-8; MK-7 occurred in strain A2-1cT as a minor compound. Major fatty acids were iso-C15 : 0 and iso-C17 : 1ω7c. In addition, iso-C17 : 0 occurred in significant amounts. The DNA G+C contents of strains 277T, 307 and A2-1cT were 59.6, 59.9 and 58.5 mol%, respectively. Based on these characteristics, the three isolates are assigned to two novel species of the novel genus Occallatibacter gen. nov., Occallatibacter riparius sp. nov. [type strain 277T ( = DSM 25168T = LMG 26948T) and reference strain 307 ( = DSM 25169 = LMG 26947)] and Occallatibacter savannae sp. nov. [type strain A2-1cT ( = DSM 25170T = LMG 26946T)]. Together with several other recently described taxa, the novel isolates provide the basis for an emended description of the established family Acidobacteriaceae.

Inducamides A–C, Chlorinated Alkaloids from an RNA Polymerase Mutant Strain of Streptomyces sp.

PubMed Central

2015-01-01

Inducamides A–C (1–3), three new chlorinated alkaloids featuring an amide skeleton generated by a tryptophan fragment and a 6-methylsalicylic acid unit, were isolated from a chemically induced mutant strain of Streptomyces sp. with the inducamides only being produced in the mutant strain. Their structures, including stereochemistry, were determined by spectroscopic analysis, Marfey’s method, and CD spectroscopy. PMID:25338006

Detection of Ehrlichia spp., Anaplasma spp., Rickettsia spp., and other eubacteria in ticks from the Thai-Myanmar border and Vietnam.

PubMed

Parola, Philippe; Cornet, Jean-Paul; Sanogo, Yibayiri Osée; Miller, R Scott; Thien, Huynh Van; Gonzalez, Jean-Paul; Raoult, Didier; Telford III, Sam R; Wongsrichanalai, Chansuda

2003-04-01

A total of 650 ticks, including 13 species from five genera, were collected from animals, from people, or by flagging of the vegetation at sites on the Thai-Myanmar border and in Vietnam. They were tested by PCR to detect DNA of bacteria of the order RICKETTSIALES: Three Anaplasma spp. were detected in ticks collected in Thailand, including (i) Anaplasma sp. strain AnDa465, which was considered a genotype of Anaplasma platys (formerly Ehrlichia platys) and which was obtained from Dermacentor auratus ticks collected from dogs; (ii) Anaplasma sp. strain AnAj360, which was obtained from Amblyomma javanense ticks collected on a pangolin; and (iii) Anaplasma sp. strain AnHl446, which was closely related to Anaplasma bovis and which was detected in Haemaphysalis lagrangei ticks collected from a bear. Three Ehrlichia spp. were identified, including (i) Ehrlichia sp. strain EBm52, which was obtained from Boophilus microplus ticks collected from cattle from Thailand; (ii) Ehrlichia sp. strain EHh324, which was closely related to Ehrlichia chaffeensis and which was detected in Haemaphysalis hystricis ticks collected from wild pigs in Vietnam; and (iii) Ehrlichia sp. strain EHh317, which was closely related to Ehrlichia sp. strain EBm52 and which was also detected in H. hystricis ticks collected from wild pigs in Vietnam. Two Rickettsia spp. were detected in Thailand, including (i) Rickettsia sp. strain RDla420, which was detected in Dermacentor auratus ticks collected from a bear, and (ii) Rickettsia sp. strain RDla440, which was identified from two pools of Dermacentor larvae collected from a wild pig nest. Finally, two bacteria named Eubacterium sp. strain Hw124 and Eubacterium sp. strain Hw191 were identified in Haemaphysalis wellingtoni ticks collected from chicken in Thailand; these strains could belong to a new group of bacteria.

Detection of Ehrlichia spp., Anaplasma spp., Rickettsia spp., and Other Eubacteria in Ticks from the Thai-Myanmar Border and Vietnam

PubMed Central

Parola, Philippe; Cornet, Jean-Paul; Sanogo, Yibayiri Osée; Miller, R. Scott; Thien, Huynh Van; Gonzalez, Jean-Paul; Raoult, Didier; Telford III, Sam R.; Wongsrichanalai, Chansuda

2003-01-01

A total of 650 ticks, including 13 species from five genera, were collected from animals, from people, or by flagging of the vegetation at sites on the Thai-Myanmar border and in Vietnam. They were tested by PCR to detect DNA of bacteria of the order Rickettsiales. Three Anaplasma spp. were detected in ticks collected in Thailand, including (i) Anaplasma sp. strain AnDa465, which was considered a genotype of Anaplasma platys (formerly Ehrlichia platys) and which was obtained from Dermacentor auratus ticks collected from dogs; (ii) Anaplasma sp. strain AnAj360, which was obtained from Amblyomma javanense ticks collected on a pangolin; and (iii) Anaplasma sp. strain AnHl446, which was closely related to Anaplasma bovis and which was detected in Haemaphysalis lagrangei ticks collected from a bear. Three Ehrlichia spp. were identified, including (i) Ehrlichia sp. strain EBm52, which was obtained from Boophilus microplus ticks collected from cattle from Thailand; (ii) Ehrlichia sp. strain EHh324, which was closely related to Ehrlichia chaffeensis and which was detected in Haemaphysalis hystricis ticks collected from wild pigs in Vietnam; and (iii) Ehrlichia sp. strain EHh317, which was closely related to Ehrlichia sp. strain EBm52 and which was also detected in H. hystricis ticks collected from wild pigs in Vietnam. Two Rickettsia spp. were detected in Thailand, including (i) Rickettsia sp. strain RDla420, which was detected in Dermacentor auratus ticks collected from a bear, and (ii) Rickettsia sp. strain RDla440, which was identified from two pools of Dermacentor larvae collected from a wild pig nest. Finally, two bacteria named Eubacterium sp. strain Hw124 and Eubacterium sp. strain Hw191 were identified in Haemaphysalis wellingtoni ticks collected from chicken in Thailand; these strains could belong to a new group of bacteria. PMID:12682151

Enhanced polyaromatic hydrocarbon degradation by adapted cultures of actinomycete strains.

PubMed

Bourguignon, Natalia; Isaac, Paula; Alvarez, Héctor; Amoroso, María J; Ferrero, Marcela A

2014-12-01

Fifteen actinomycete strains were evaluated for their potential use in removal of polycyclic aromatic hydrocarbons (PAH). Their capability to degrade of naphthalene, phenanthrene, and pyrene was tested in minimal medium (MM) and MM with glucose as another substrate. Degradation of naphthalene in MM was observed in all isolates at different rates, reaching maximum values near to 76% in some strains of Streptomyces, Rhodococcus sp. 016 and Amycolatopsis tucumanensis DSM 45259. Maximum values of degradation of phenanthrene in MM occurred in cultures of A. tucumanensis DSM 45259 (36.2%) and Streptomyces sp. A12 (20%), while the degradation of pyrene in MM was poor and only significant with Streptomyces sp. A12 (4.3%). Because of the poor performance when growing on phenanthrene and pyrene alone, Rhodococcus sp. 20, Rhodococcus sp. 016, A. tucumanensis DSM 45259, Streptomyces sp. A2, and Streptomyces sp. A12 were challenged to an adaptation schedule of successive cultures on a fresh solid medium supplemented with PAHs, decreasing concentration of glucose in each step. As a result, an enhanced degradation of PAHs by adapted strains was observed in the presence of glucose as co-substrate, without degradation of phenanthrene and pyrene in MM while an increase to up to 50% of degradation was seen with these strains in glucose amended media. An internal fragment of the catA gene, which codes for catechol 1,2-dioxygenase, was amplified from both Rhodococcus strains, showing the potential for degradation of aromatic compounds via salycilate. These results allow us to propose the usefulness of these actinomycete strains for PAH bioremediation in the environment. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Suppression of Damping-Off Disease in Host Plants by the Rhizoplane Bacterium Lysobacter sp. Strain SB-K88 Is Linked to Plant Colonization and Antibiosis against Soilborne Peronosporomycetes

PubMed Central

Islam, Md. Tofazzal; Hashidoko, Yasuyuki; Deora, Abhinandan; Ito, Toshiaki; Tahara, Satoshi

2005-01-01

We previously demonstrated that xanthobaccin A from the rhizoplane bacterium Lysobacter sp. strain SB-K88 suppresses damping-off disease caused by Pythium sp. in sugar beet. In this study we focused on modes of Lysobacter sp. strain SB-K88 root colonization and antibiosis of the bacterium against Aphanomyces cochlioides, a pathogen of damping-off disease. Scanning electron microscopic analysis of 2-week-old sugar beet seedlings from seeds previously inoculated with SB-K88 revealed dense colonization on the root surfaces and a characteristic perpendicular pattern of Lysobacter colonization possibly generated via development of polar, brush-like fimbriae. In colonized regions a semitransparent film apparently enveloping the root and microcolonies were observed on the root surface. This Lysobacter strain also efficiently colonized the roots of several plants, including spinach, tomato, Arabidopsis thaliana, and Amaranthus gangeticus. Plants grown from both sugar beet and spinach seeds that were previously treated with Lysobacter sp. strain SB-K88 displayed significant resistance to the damping-off disease triggered by A. cochlioides. Interestingly, zoospores of A. cochlioides became immotile within 1 min after exposure to a SB-K88 cell suspension, a cell-free supernatant of SB-K88, or pure xanthobaccin A (MIC, 0.01 μg/ml). In all cases, lysis followed within 30 min in the presence of the inhibiting factor(s). Our data indicate that Lysobacter sp. strain SB-K88 has a direct inhibitory effect on A. cochlioides, suppressing damping-off disease. Furthermore, this inhibitory effect of Lysobacter sp. strain SB-K88 is likely due to a combination of antibiosis and characteristic biofilm formation at the rhizoplane of the host plant. PMID:16000790

Microbial iron redox cycling in a circumneutral-pH groundwater seep.

PubMed

Blöthe, Marco; Roden, Eric E

2009-01-01

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Potential Role of Diploscapter sp. Strain LKC25, a Bacterivorous Nematode from Soil, as a Vector of Food-Borne Pathogenic Bacteria to Preharvest Fruits and Vegetables

PubMed Central

Gibbs, Daunte S.; Anderson, Gary L.; Beuchat, Larry R.; Carta, Lynn K.; Williams, Phillip L.

2005-01-01

Diploscapter, a thermotolerant, free-living soil bacterial-feeding nematode commonly found in compost, sewage, and agricultural soil in the United States, was studied to determine its potential role as a vehicle of Salmonella enterica serotype Poona, enterohemorrhagic Escherichia coli O157:H7, and Listeria monocytogenes in contaminating preharvest fruits and vegetables. The ability of Diploscapter sp. strain LKC25 to survive on agar media, in cow manure, and in composted turkey manure and to be attracted to, ingest, and disperse food-borne pathogens inoculated into soil or a mixture of soil and composted turkey manure was investigated. Diploscapter sp. strain LKC25 survived and reproduced in lawns of S. enterica serotype Poona, E. coli O157:H7, and L. monocytogenes on agar media and in cow manure and composted turkey manure. Attraction of Diploscapter sp. strain LKC25 to colonies of pathogenic bacteria on tryptic soy agar within 10, 20, 30, and 60 min and 24 h was determined. At least 85% of the worms initially placed 0.5 to 1 cm away from bacterial colonies migrated to the colonies within 1 h. Within 24 h, ≥90% of the worms were embedded in colonies. The potential of Diploscapter sp. strain LKC25 to shed pathogenic bacteria after exposure to bacteria inoculated into soil or a mixture of soil and composted turkey manure was investigated. Results indicate that Diploscapter sp. strain LKC25 can shed pathogenic bacteria after exposure to pathogens in these milieus. They also demonstrate its potential to serve as a vector of food-borne pathogenic bacteria in soil, with or without amendment with compost, to the surface of preharvest fruits and vegetables in contact with soil. PMID:15870330

[Influence of staphylococcin T on Enterococcus sp. growth].

PubMed

Białucha, Agata; Kozuszko, Sylwia; Gospodarek, Eugenia; Bugalski, Roman Marian; Gierlotka, Krzysztof

2007-01-01

Bacteriocins are ribosomally synthesised, extracellular bacterial products. Generally, spectrum of inhibition is limited to the same or closely related species to bacteriocin producer. Staphylococcin T is produced by Staphylococcus cohnii strain. The present study concerns influence of StT to 267 Enterococcus sp. strains growth isolated between 2003 and 2006 in Department of Microbiology University Hospital of dr. A. Jurasz in Bydgoszcz. S. cohnii T antagonistic ability evaluated towards bacteries on Mueller-Hinton Agar (bio Mérieux) in aerobic conditions. After 24 and 48 hours tested enterococci suspensions were plated perpendiculary. Susceptibility to antibiotics was assessed by disc diffusion method according to the guideless of Clinical and Laboratory Standards Institute and National Reference Centre for Antimicrobial Susceptibility. Among Enterococcus sp. strains tested 7.1% were sensitive to StT. The highest percentage of sensitive enterococci isolated from wound swabs, urine, blood and pus. Enterococcus faecium strains dominated (63.2%) among enterococci sensitive to StT. Moderate inhibition degree on S. cohnii T bacteriocin action was observed in majority sensitive enterococci strains. Enterococcus sp. sensitive to StT strains were frequently multidrug resistant (68.4%). According to the study results and increasing resistance to antibiotics, StT could be an alternative agent used to treat infections caused by Enterococcus sp.

Experimental Investigation of the Short-Period Requirements of MIL-F-8785C. Volume 2.

DTIC Science & Technology

1986-11-01

instrument displays featuring an Attitude Direction Indicator (WDI) and a Horizontal Situation Indicator (HSI) as the primary instruments. The...34 + 2. w s + wi- eg sp sp The primary experiment matrix consisted of three short period fre- quency configurations at three values of (n/a). The points...radians per second. The cost fuction for each match was: NPTS cost= 11 [(AG i) 1 + W (AP)] where AGu X GainHo S - GainLOS [dB] Api = PhaseHOS _ PhaseLOS

Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica.

PubMed

Hirsch, Peter; Gallikowski, Claudia A; Siebert, Jörg; Peissl, Klaus; Kroppenstedt, Reiner; Schumann, Peter; Stackebrandt, Erko; Anderson, Robert

2004-11-01

Six Gram-positive, non-motile, UV- and draught-tolerant bacteria were isolated from antarctic soil and rock samples. The pink to orange cocci grew well on oligotrophic medium PYGV (pH 7.5) at 9-18 degrees C. They tolerated 0-10% NaCl, were aerobic to facultatively anaerobic and contained ornithine in their cell wall (type A3beta, Orn-Gly2). The lipid profiles of four strains were found to be typical for those of D. radiodurans. Major fatty acids were 16:1cis9, 15:1cis9, 17:1cis9 and i17:1cis9, the respiratory quinone of three strains was MK-8. Comparative 16S rDNA gene sequencing revealed phylogenetic relationships to the Deinococcus clade, especially to D. radiopugnans. The levels of 16S rRNA gene sequence similarity and DNA-DNA hybridisation data showed the six isolates represented new taxa. Phenotypic properties supported the description of three new species which were different from the eight known Deinococcus species and particularly from D. radiopugnans. Soil isolate AA-692T (DSM 12807T) is the type strain of Deinococcus frigens sp. nov., with AA-752 (DSM 15993) and AA-829 (DSM 15994) as additional strains from soil. The endolithic isolate AA-1444T, Deinococcus saxicola sp. nov., (DSM 15974T) came from antarctic sandstone, and Deinococcus marmoris sp. nov. (isolate AA-63T [DSM 12784T]) as well as AA-69 (DSM 15951) were isolated from antarctic marble.

Strain identification and quorum sensing inhibition characterization of marine-derived Rhizobium sp. NAO1

NASA Astrophysics Data System (ADS)

Chang, Hong; Zhou, Jin; Zhu, Xiaoshan; Yu, Shenchen; Chen, Lu; Jin, Hui; Cai, Zhonghua

2017-03-01

A novel strategy for combating pathogens is through the ongoing development and use of anti-quorum sensing (QS) treatments such as therapeutic bacteria or their anti-QS substances. Relatively little is known about the bacteria that inhabit the open ocean and of their potential anti-pathogenic attributes; thus, in an initiative to identify these types of therapeutic bacteria, planktonic microbes from the North Atlantic Ocean were collected, isolated, cultured and screened for anti-QS activity. Screening analysis identified one such strain, Rhizobium sp. NAO1. Extracts of Rhizobium sp. NAO1 were identified via ultra-performance liquid chromatography (UPLC) analysis. They were shown to contain N-acyl homoserine lactone (AHL)-based QS analogues (in particular, the N-butyryl homoserine lactone (C4-AHL) analogue) and could disrupt biofilm formation by Pseudomonas aeruginosa PAO1. QS inhibition was confirmed using confocal scanning laser microscopy and growth curves, and it was shown to occur in a dose-dependent manner without affecting bacterial growth. Secondary metabolites of Rhizobium sp. NAO1 inhibited PAO1 pathogenicity by downregulating AHL-mediated virulence factors such as elastase activity and siderophore production. Furthermore, as a result of biofilm structure damage, the secondary metabolite products of Rhizobium sp. NAO1 significantly increased the sensitivity of PAO1 to aminoglycoside antibiotics. Our results demonstrated that Rhizobium sp. strain NAO1 has the ability to disrupt P. aeruginosa PAO1 biofilm architecture, in addition to attenuating P. aeruginosa PAO1 virulence factor production and pathogenicity. Therefore, the newly identified ocean-derived Rhizobium sp. NAO1 has the potential to serve as a QS inhibitor and may be a new microbial resource for drug development.

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

DOE PAGES

Eshraghi, Leila; De Meyer, Sofie E.; Tian, Rui; ...

2015-10-26

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. Finally, the 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167more » contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.« less

High-quality permanent draft genome sequence of Bradyrhizobium sp. strain WSM1743 - an effective microsymbiont of an Indigofera sp. growing in Australia

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eshraghi, Leila; De Meyer, Sofie E.; Tian, Rui

Bradyrhizobium sp. strain WSM1743 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of an Indigofera sp. WSM1743 was isolated from a nodule recovered from the roots of an Indigofera sp. growing 20 km north of Carnarvon in Australia. It is slow growing, tolerates up to 1 % NaCl and is capable of growth at 37 °C. Here we describe the features of Bradyrhizobium sp. strain WSM1743, together with genome sequence information and its annotation. Finally, the 8,341,956 bp high-quality permanent draft genome is arranged into 163 scaffolds and 167more » contigs, contains 7908 protein-coding genes and 75 RNA-only encoding genes and was sequenced as part of the Root Nodule Bacteria chapter of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica.

PubMed

Sedláček, Ivo; Králová, Stanislava; Kýrová, Kamila; Mašlaňová, Ivana; Busse, Hans-Jürgen; Staňková, Eva; Vrbovská, Veronika; Němec, Miroslav; Barták, Miloš; Holochová, Pavla; Švec, Pavel; Pantůček, Roman

2017-06-01

Four rod-shaped and Gram-stain-negative bacterial strains, CCM 8647, CCM 8649T, CCM 8643T and CCM 8648T, were isolated from rock samples collected on James Ross Island, Antarctica. Extensive biotyping, fatty acid profiling, chemotaxonomy, 16S rRNA gene sequencing and whole-genome sequencing was applied to isolates to clarify their taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that all four isolates belonged to the genus Hymenobacter. Strains CCM 8649T and CCM 8647 were most closely related to Hymenobacter arizonensis OR362-8T (94.4 % 16S rRNA gene sequence similarity), strain CCM 8643T to Hymenobacter terrae DG7AT (96.3 %) and strain CCM 8648T to Hymenobacter glaciei VUG-A130T (96.3 %). The predominant fatty acids of CCM 8649T and CCM 8647 were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C16 : 1ω5c and iso-C15 : 0, whereas those of CCM 8643T and CCM 8648T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 1ω5c. The quinone systems contained exclusively menaquinone MK-7. The major polyamine was sym-homospermidine. All four strains contained the major polar lipid phosphatidylethanolamine. The G+C content of genomic DNA ranged from 60-63 mol%. Whole-genome sequencing data supported the finding that isolates represented distinct species of the genus Hymenobacter. On the basis of the results obtained, three novel species are proposed for which the names Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov. are suggested, with the type strains CCM 8649T (=LMG 29441T=P5239T), CCM 8643T (=LMG 29435T=P3150T) and CCM 8648T (=LMG 29440T=P5086T), respectively.

Amphetamine manipulates monoamine oxidase-A level and behavior using theranostic aptamers of transcription factors AP-1/NF-kB.

PubMed

Liu, Christina H; Ren, Jiaqian; Liu, Philip K

2016-02-03

Monoamine oxidase (MAO) enzymes play a critical role in controlling the catabolism of monoamine neurotransmitters and biogenic trace amines and behavior in humans. However, the mechanisms that regulate MAO are unclear. Several transcription factor proteins are proposed to modulate the transcription of MAO gene, but evidence supporting these hypotheses is controversial. We aimed to investigate the mechanism of gene transcription regulator proteins on amphetamine-induced behavior. We applied aptamers containing a DNA binding sequence, as well as a random sequence (without target) to study the modulation of amphetamine-induced MAO levels and hyperactivity in living mice. We pretreated in adult male C57black6 mice (Taconic Farm, Germantown, NY) (n ≥ 3 litters at a time), 2 to 3 months of age (23 ± 2 gm body weight) with double-stranded (ds) DNA aptamers with sequence specific to activator protein-1 (5ECdsAP1), nuclear factor-kappa beta (5ECdsNF-kB), special protein-1 (5ECdsSP-1) or cyclicAMP responsive element binding (5ECdsCreB) protein binding regions, 5ECdsRan [a random sequence without target], single-stranded AP-1 (5ECssAP-1) (8 nmol DNA per kg) or saline (5 μl, intracerebroventricular [icv] injection) control before amphetamine administration (4 mg/kg, i.p.). We then measured and analyzed locomotor activities and the level of MAO-A and MAO-B activity. In the pathological condition of amphetamine exposure, we showed here that pretreatment with 5ECdsAP1 and 5ECdsNF-kB reversed the decrease of MAO-A activity (p < 0.05, t test), but not activity of the B isomer (MAO-B), in the ventral tegmental area (VTA) and substantia nigra (SN) of C57black6 mice. The change in MAO-A level coincided with a reversed amphetamine-induced restless behavior of mice. Pretreatments with saline, 5ECdsCreB, 5ECdsSP-1, 5ECdsRan or 5ECssAP-1 had no effect. Our data lead us to conclude that elevation of AP-1 or NF-kB indirectly decreases MAO-A protein levels which, in turn, diminishes MAO-A ability in the VTA of the mesolimbic dopaminergic pathway that has been implicated in cells under stress especially in the SN and VTA. This study has implications for design for the treatment of drug exposure and perhaps Parkinson's dementia.

Molecular characterization and classification of Trypanosoma spp. Venezuelan isolates based on microsatellite markers and kinetoplast maxicircle genes.

PubMed

Sánchez, E; Perrone, T; Recchimuzzi, G; Cardozo, I; Biteau, N; Aso, P M; Mijares, A; Baltz, T; Berthier, D; Balzano-Nogueira, L; Gonzatti, M I

2015-10-15

Livestock trypanosomoses, caused by three species of the Trypanozoon subgenus, Trypanosoma brucei brucei, T. evansi and T. equiperdum is widely distributed throughout the world and constitutes an important limitation for the production of animal protein. T. evansi and T. equiperdum are morphologically indistinguishable parasites that evolved from a common ancestor but acquired important biological differences, including host range, mode of transmission, distribution, clinical symptoms and pathogenicity. At a molecular level, T. evansi is characterized by the complete loss of the maxicircles of the kinetoplastic DNA, while T. equiperdum has retained maxicircle fragments similar to those present in T. brucei. T. evansi causes the disease known as Surra, Derrengadera or "mal de cadeiras", while T. equiperdum is the etiological agent of dourine or "mal du coit", characterized by venereal transmission and white patches in the genitalia. Nine Venezuelan Trypanosoma spp. isolates, from horse, donkey or capybara were genotyped and classified using microsatellite analyses and maxicircle genes. The variables from the microsatellite data and the Procyclin PE repeats matrices were combined using the Hill-Smith method and compared to a group of T. evansi, T. equiperdum and T. brucei reference strains from South America, Asia and Africa using Coinertia analysis. Four maxicircle genes (cytb, cox1, a6 and nd8) were amplified by PCRfrom TeAp-N/D1 and TeGu-N/D1, the two Venezuelan isolates that grouped with the T. equiperdum STIB841/OVI strain. These maxicircle sequences were analyzed by nucleotide BLAST and aligned toorthologous genes from the Trypanozoon subgenus by MUSCLE tools. Phylogenetic trees were constructed using Maximum Parsimony (MP) and Maximum Likelihood (ML) with the MEGA5.1® software. We characterized microsatellite markers and Procyclin PE repeats of nine Venezuelan Trypanosoma spp. isolates with various degrees of virulence in a mouse model, and compared them to a panel of T. evansi and T. equiperdum reference strains. Coinertia analysis of the combined repeats and previously reported T. brucei brucei microsatellite genotypes revealed three distinct groups. Seven of the Venezuelan isolates grouped with globally distributed T. evansi strains, while TeAp-N/D1 and TeGu-N/D1 strains clustered in a separate group with the T. equiperdum STIB841/OVI strain isolated in South Africa. A third group included T. brucei brucei, two strains previously classified as T. evansi (GX and TC) and one as T. equiperdum (BoTat-1.1). Four maxicircle genes, Cytochrome b, Cythocrome Oxidase subunit 1, ATP synthase subunit 6 and NADH dehydrogenase subunit 8, were identified in the two Venezuelan strains clustering with the T. equiperdum STIB841/OVI strain. Phylogenetic analysis of the cox1 gene sequences further separated these two Venezuelan T. equiperdum strains: TeAp-N/D1 grouped with T. equiperdum strain STIB818 and T. brucei brucei, and TeGu-N/D1 with the T. equiperdum STIB841/OVI strain. Based on the Coinertia analysis and maxicircle gene sequence phylogeny, TeAp-N/D1 and TeGu-N/D1 constitute the first confirmed T. equiperdum strains described from Latin America.

Burkholderia ginsengiterrae sp. nov. and Burkholderia panaciterrae sp. nov., antagonistic bacteria against root rot pathogen Cylindrocarpon destructans, isolated from ginseng soil.

PubMed

Farh, Mohamed El-Agamy; Kim, Yeon-Ju; Van An, Hoang; Sukweenadhi, Johan; Singh, Priyanka; Huq, Md Amdadul; Yang, Deok-Chun

2015-04-01

Strain DCY85(T) and DCY85-1(T), isolated from rhizosphere of ginseng, were rod-shaped, Gram-reaction-negative, strictly aerobic, catalase positive and oxidase negative. 16S rRNA gene sequence analysis revealed that strain DCY85(T) as well as DCY85-1(T) belonged to the genus Burkholderia and were closely related to Burkholderia fungorum KACC 12023(T) (98.1 and 98.0 % similarity, respectively). The major polar lipids of strain DCY85(T) and DCY85-1(T) were phosphatidylethanolamine, one unidentified aminolipid and two unidentified phospholipids. The major fatty acids of both strains are C16:0, C18:1 ω7c and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). The predominant isoprenoid quinone of each strain DCY85(T) and DCY85-1(T) was ubiquinone (Q-8) and the G+C content of their genomic DNA was 66.0 and 59.4 mol%, respectively, which fulfill the characteristic range of the genus Burkholderia. The polyamine content of both DCY85(T) and DCY85-1(T) was putrescine. Although both DCY85(T) and DCY85-1(T) have highly similar 16S rRNA and identical RecA and gyrB sequences, they show differences in phenotypic and chemotaxonomic characteristics. DNA-DNA hybridization results proved the consideration of both strains as two different species. Based on the results from our polyphasic characterization, strain DCY85(T) and DCY85-1(T) are considered novel Burkholderia species for which the name Burkholderia ginsengiterrae sp. nov and Burkholderia panaciterrae sp. nov are, respectively, proposed. An emended description of those strains is also proposed. DCY85(T) and DCY85-1(T) showed antagonistic activity against the common root rot pathogen of ginseng, Cylindrocarpon destructans. The proposed type strains are DCY85(T) (KCTC 42054(T) = JCM 19888(T)) and DCY85-1(T) (KCTC 42055(T) = JCM 19889(T)).

THz+X Seedling Report

DTIC Science & Technology

2005-11-23

lamblia Entamoeba histolytica Toxoplasma Microsporidia Additional viral encephalitides West Nile Virus LaCrosse California encephalitis VEE...Is Catalyzed by Salicylate 1- Monooxygenase from Pseudomonas sp . Strain ATCC 29352; Applied and Environmental Microbiology, July 2004, p. 4040-4047...the Mechanism of RDX Biodegradation by Rhodococcus - 31 - sp . Strain DN22; Applied and Environmental Microbiology, March 2003, p. 1347-1351

Metal-backed versus all-polyethylene unicompartmental knee arthroplasty

PubMed Central

Eaton, M. J.; Nutton, R. W.; Wade, F. A.; Evans, S. L.; Pankaj, P.

2017-01-01

Objectives Up to 40% of unicompartmental knee arthroplasty (UKA) revisions are performed for unexplained pain which may be caused by elevated proximal tibial bone strain. This study investigates the effect of tibial component metal backing and polyethylene thickness on bone strain in a cemented fixed-bearing medial UKA using a finite element model (FEM) validated experimentally by digital image correlation (DIC) and acoustic emission (AE). Materials and Methods A total of ten composite tibias implanted with all-polyethylene (AP) and metal-backed (MB) tibial components were loaded to 2500 N. Cortical strain was measured using DIC and cancellous microdamage using AE. FEMs were created and validated and polyethylene thickness varied from 6 mm to 10 mm. The volume of cancellous bone exposed to < -3000 µε (pathological loading) and < -7000 µε (yield point) minimum principal (compressive) microstrain and > 3000 µε and > 7000 µε maximum principal (tensile) microstrain was computed. Results Experimental AE data and the FEM volume of cancellous bone with compressive strain < -3000 µε correlated strongly: R = 0.947, R2 = 0.847, percentage error 12.5% (p < 0.001). DIC and FEM data correlated: R = 0.838, R2 = 0.702, percentage error 4.5% (p < 0.001). FEM strain patterns included MB lateral edge concentrations; AP concentrations at keel, peg and at the region of load application. Cancellous strains were higher in AP implants at all loads: 2.2- (10 mm) to 3.2-times (6 mm) the volume of cancellous bone compressively strained < -7000 µε. Conclusion AP tibial components display greater volumes of pathologically overstrained cancellous bone than MB implants of the same geometry. Increasing AP thickness does not overcome these pathological forces and comes at the cost of greater bone resection. Cite this article: C. E. H. Scott, M. J. Eaton, R. W. Nutton, F. A. Wade, S. L. Evans, P. Pankaj. Metal-backed versus all-polyethylene unicompartmental knee arthroplasty: Proximal tibial strain in an experimentally validated finite element model. Bone Joint Res 2017;6:22–30. DOI:10.1302/2046-3758.61.BJR-2016-0142.R1 PMID:28077394

Reduction of molybdate to molybdenum blue by Klebsiella sp. strain hkeem.

PubMed

Lim, H K; Syed, M A; Shukor, M Y

2012-06-01

A novel molybdate-reducing bacterium, tentatively identified as Klebsiella sp. strain hkeem and based on partial 16s rDNA gene sequencing and phylogenetic analysis, has been isolated. Strain hkeem produced 3 times more molybdenum blue than Serratia sp. strain Dr.Y8; the most potent Mo-reducing bacterium isolated to date. Molybdate was optimally reduced to molybdenum blue using 4.5 mM phosphate, 80 mM molybdate and using 1% (w/v) fructose as a carbon source. Molybdate reduction was optimum at 30 °C and at pH 7.3. The molybdenum blue produced from cellular reduction exhibited absorption spectrum with a maximum peak at 865 nm and a shoulder at 700 nm. Inhibitors of electron transport system such as antimycin A, rotenone, sodium azide, and potassium cyanide did not inhibit the molybdenum-reducing enzyme. Mercury, silver, and copper at 1 ppm inhibited molybdenum blue formation in whole cells of strain hkeem. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isolation and characterization of Bacillus sp. GFP-2, a novel Bacillus strain with antimicrobial activities, from Whitespotted bamboo shark intestine.

PubMed

Wu, Jia; Xu, Guoqiang; Jin, Yangyang; Sun, Cong; Zhou, Li; Lin, Guodong; Xu, Rong; Wei, Ling; Fei, Hui; Wang, Dan; Chen, Jianqing; Lv, Zhengbing; Liu, Kuancheng

2018-05-22

The abuse of antibiotics and following rapidly increasing of antibiotic-resistant pathogens is the serious threat to our society. Natural products from microorganism are regarded as the important substitution antimicrobial agents of antibiotics. We isolated a new strain, Bacillus sp. GFP-2, from the Chiloscyllium plagiosum (Whitespotted bamboo shark) intestine, which showed great inhibitory effects on the growth of both Gram-positive and Gram-negative bacteria. Additionally, the growth of salmon was effectively promoted when fed with inactivated strain GFP-2 as the inhibition agent of pathogenic bacteria. The genes encoding antimicrobial peptides like LCI, YFGAP and hGAPDH and gene clusters for secondary metabolites and bacteriocins, such as difficidin, bacillibactin, bacilysin, surfactin, butirosin, macrolactin, bacillaene, fengycin, lanthipeptides and LCI, were predicted in the genome of Bacillus sp. GFP-2, which might be expressed and contribute to the antimicrobial activities of this strain. The gene encoding β-1,3-1,4-glucanase was successfully cloned from the genome and this protein was detected in the culture supernatant of Bacillus sp. GFP-2 by the antibody produced in rabbit immunized with the recombinant β-1,3-1,4-glucanase, indicating that this strain could express β-1,3-1,4-glucanase, which might partially contribute to its antimicrobial activities. This study can enhance a better understanding of the mechanism of antimicrobial activities in genus Bacillus and provide a useful material for the biotechnology study in antimicrobial agent development.

Pseudorhodobacter sinensis sp. nov. and Pseudorhodobacter aquaticus sp. nov., isolated from crater lakes.

PubMed

Li, Ai-Hua; Liu, Hong-Can; Hou, Wei-Guo; Zhou, Yu-Guang

2016-08-01

Three Gram-stain negative, aerobic, non-motile, rod-shaped bacterial strains, Y1R2-4T, Y3R2-3 and DC2N1-10T, isolated from two crater lakes of the Daxinganling Mountains, northern China, were studied to determine their taxonomic position. They grew at 4-30 °C (optimally at 20-25 °C), at pH 6.0-7.5 (optimally at pH 7.0) and in the presence of 0-0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, these strains showed 95.3-96.6 % similarity to members of the genus Pseudorhodobacter, including Pseudorhodobacter ferrugineus DSM 5888T, Pseudorhodobacter wandonensis WT-MW11T, Pseudorhodobacter antarcticus ZS3-33T and Pseudorhodobacter aquimaris HDW-19T. All strains contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The main polar lipids for strains Y1R2-4T and Y3R2-3 were phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified aminolipid, three unidentified phospholipids and two unidentified lipids, and those for strain DC2N1-10T were phosphatidylglycerol, phosphatidylcholine, one unidentified aminophospholipid, one unidentified aminolipid, one unidentified phospholipid and several unidentified lipids. The DNA G+C contents of strains Y1R2-4T, Y3R2-3 and DC2N1-10T were 61.9, 61.0 and 60.0 mol%, respectively. In addition, strain Y1R2-4T shared less than 50 % DNA-DNA relatedness to strain DC2N1-10T. Based on these differences in genetic, physiological and chemotaxonomic properties, strains Y1R2-4T, Y3R2-3 and DC2N1-10T were considered to represent two novel species of the genus Pseudorhodobacter, for which the names Pseudorhodobacter sinensis sp. nov. (type strain Y1R2-4T=CGMCC1.14435T=KCTC 52039T) and Pseudorhodobacter aquaticus sp. nov. (type strain DC2N1-10T=CGMCC1.14433T=KCTC 52040T) are proposed.

Sugary Kefir Strain Lactobacillus mali APS1 Ameliorated Hepatic Steatosis by Regulation of SIRT-1/Nrf-2 and Gut Microbiota in Rats.

PubMed

Chen, Yung-Tsung; Lin, Yu-Chun; Lin, Jin-Seng; Yang, Ning-Sun; Chen, Ming-Ju

2018-04-01

Non-alcoholic fatty liver disease (NAFLD) is a common disease that is concomitant with obesity, resulting in increased mortality. To date, the efficiency of NAFLD treatment still needs to be improved. Therefore, we aimed to evaluate the effect of Lactobacillus mali APS1, which was isolated from sugary kefir, on hepatic steatosis in rats fed a high-fat diet (HFD). Sprague Dawley rats were fed a control diet, a HFD with saline, and a HFD with APS1 intervention by gavage daily for 12 weeks. The results showed that APS1 significantly reduced body weight and body weight gain in HFD-fed rats. APS1 reduced hepatic lipid accumulation by regulating SIRT-1/PGC-1α/SREBP-1 expression. Moreover, APS1 increased hepatic antioxidant activity by modulating Nrf-2/HO-1 expression. Notably, APS1 manipulated the gut microbiota, resulting in increasing proportions of the phylum Bacteroidetes/Firmicutes and reducing the abundance of specific NAFLD-associated bacteria. These results suggested that APS1 ameliorated hepatic steatosis by modulating lipid metabolism and antioxidant activity via manipulating specific NAFLD-associated gut microbiota in vivo. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome Sequence of Sphingomonas sp. Strain PAMC 26605, Isolated from Arctic Lichen (Ochrolechia sp.)

PubMed Central

Shin, Seung Chul; Ahn, Do Hwan; Lee, Jong Kyu; Kim, Su Jin; Hong, Soon Gyu; Kim, Eun Hye

2012-01-01

The endosymbiotic bacterium Sphingomonas sp. strain PAMC 26605 was isolated from Arctic lichens (Ochrolechia sp.) on the Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide further insights into the symbiotic mechanism of lichens in extreme environments. PMID:22374946

Streptosporangium jiaoheense sp. nov. and Streptosporangium taraxaci sp. nov., actinobacteria isolated from soil and dandelion root (Taraxacum mongolicum Hand.-Mazz.).

PubMed

Zhao, Junwei; Guo, Lifeng; Li, Zhilei; Piao, Chenyu; Li, Yao; Li, Jiansong; Liu, Chongxi; Wang, Xiangjing; Xiang, Wensheng

2016-06-01

Two novel actinobacteria, designated strains NEAU-Jh1-4T and NEAU-Wp2-0T, were isolated from muddy soil collected from a riverbank in Jiaohe and a dandelion root collected from Harbin, respectively. A polyphasic study was carried out to establish the taxonomic positions of these two strains. The phylogenetic analysis based on the 16S rRNA gene sequences of strains NEAU-Jh1-4T and NEAU-Wp2-0T indicated that strain NEAU-Jh1-4T clustered with Streptosporangium nanhuense NEAU-NH11T (99.32 % 16S rRNA gene sequence similarity), Streptosporangium purpuratum CY-15110T (98.30 %) and Streptosporangium yunnanense CY-11007T (97.95 %) and strain NEAU-Wp2-0T clustered with 'Streptosporangium sonchi  ' NEAU-QS7 (99.39 %), 'Streptosporangium kronopolitis' NEAU-ML10 (99.26 %), 'Streptosporangium shengliense' NEAU-GH7 (98.85 %) and Streptosporangium longisporum DSM 43180T (98.69 %). Moreover, morphological and chemotaxonomic properties of the two isolates also confirmed their affiliation to the genus Streptosporangium. However, the low level of DNA-DNA hybridization and some phenotypic characteristics allowed the isolates to be differentiated from the most closely related species. Therefore, it is proposed that strains NEAU-Jh1-4T and NEAU-Wp2-0T represent two novel species of the genus Streptosporangium, for which the name Streptosporangium jiaoheense sp. nov. and Streptosporangium taraxaci sp. nov. are proposed. The type strains are NEAU-Jh1-4T (=CGMCC 4.7213T=JCM 30348T) and NEAU-Wp2-0T (=CGMCC 4.7217T=JCM 30349T), respectively.

Novel Reaction of Succinyl Coenzyme A (Succinyl-CoA) Synthetase: Activation of 3-Sulfinopropionate to 3-Sulfinopropionyl-CoA in Advenella mimigardefordensis Strain DPN7T during Degradation of 3,3′-Dithiodipropionic Acid ▿ †

PubMed Central

Schürmann, Marc; Wübbeler, Jan Hendrik; Grote, Jessica; Steinbüchel, Alexander

2011-01-01

The sucCD gene of Advenella mimigardefordensis strain DPN7T encodes a succinyl coenzyme A (succinyl-CoA) synthetase homologue (EC 6.2.1.4 or EC 6.2.1.5) that recognizes, in addition to succinate, the structural analogues 3-sulfinopropionate (3SP) and itaconate as substrates. Accumulation of 3SP during 3,3′-dithiodipropionic acid (DTDP) degradation was observed in Tn5::mob-induced mutants of A. mimigardefordensis strain DPN7T disrupted in sucCD and in the defined deletion mutant A. mimigardefordensis ΔsucCD. These mutants were impaired in growth with DTDP and 3SP as the sole carbon source. Hence, it was proposed that the succinyl-CoA synthetase homologue in A. mimigardefordensis strain DPN7T activates 3SP to the corresponding CoA-thioester (3SP-CoA). The putative genes coding for A. mimigardefordensis succinyl-CoA synthetase (SucCDAm) were cloned and heterologously expressed in Escherichia coli BL21(DE3)/pLysS. Purification and characterization of the enzyme confirmed its involvement during degradation of DTDP. 3SP, the cleavage product of DTDP, was converted into 3SP-CoA by the purified enzyme, as demonstrated by in vitro enzyme assays. The structure of 3SP-CoA was verified by using liquid chromatography-electrospray ionization-mass spectrometry. SucCDAm is Mg2+ or Mn2+ dependent and unspecific regarding ATP or GTP. In kinetic studies the enzyme showed highest enzyme activity and substrate affinity with succinate (Vmax = 9.85 ± 0.14 μmol min−1 mg−1, Km = 0.143 ± 0.001 mM). In comparison to succinate, activity with 3SP was only ca. 1.2% (Vmax = 0.12 ± 0.01 μmol min−1 mg−1) and the affinity was 6-fold lower (Km = 0.818 ± 0.046 mM). Based on the present results, we conclude that SucCDAm is physiologically associated with the citric acid cycle but is mandatory for the catabolic pathway of DTDP and its degradation intermediate 3SP. PMID:21515777

[Changes in Cell Surface Properties and Biofilm Formation Efficiency in Azospirillum brasilense Sp245 Mutants in the Putative Genes of Lipid Metabolism mmsB1 and fabG1].

PubMed

Shumilova, E; Shelud'ko, A V; Filip'echeva, Yu A; Evstigneeva, S S; Ponomareva, E G; Petrova, L P; Katsy, E I

2016-01-01

The previously obtained insertion mutants ofAzospirillum brasilense Sp245 in the genes mmsBl and fabG1 (strains SK039 and Sp245.1610, respectively) were characterized by impaired flagellation and motility. The putative products of expression of these genes are 3-hydroxyisobutyrate dehydrogenase and 3-oxoacyl-[acyl-carrier protein] reductase, respectively. In the present work, A. brasilense- Sp245 strains SK039 and Sp245.1610 were found to have differences in the content of 3-hydroxyhexadecanoic, hexadecanoic, 3-hydroxytetradecanoic, hexadecenoic, octadecenoic, and nonadecanoic acids in their lipopolysaccharide prepa- rations, as well as in cell hydrophobicity and hemagglutination activity and dynamics of cell aggregation, in biomass amount, and in the relative content of lipopolysaccharide antigens in mature biofilms formed on hydrophilic or hydrophobic surfaces.

Development of eco-friendly bioplastic like PHB by distillery effluent microorganisms.

PubMed

Gangurde, Nilesh S; Sayyed, Riyaz Z; Kiran, Shashi; Gulati, Arvind

2013-01-01

During screening for poly-β-hydroxybutyrate (PHB) producing bacteria from distillery effluent sample, six out of 30 isolates comprising of three strains of Alcaligenes sp., two strains of Bacillus sp., and one strain of Pseudomonas sp. were found to accumulate varying levels of intracellular PHB. Amongst the various isolates, Alcaligenes sp. RZS4 was found as the potent PHB-producing organism, accumulating higher amounts of PHB. PHB productivity was further enhanced in the presence of oxygen, nitrogen-limiting conditions, and cloning of PHB synthesizing genes of Alcaligenes sp. RZS 4 into Escherichia coli. A twofold increase in PHB yield was obtained from recombinant E. coli vis-à-vis Alcaligenes sp.; the recombinant E. coli accumulated more PHB in NDMM, produced good amount of PHB in a single-stage cultivation process under both nutrient-rich and nutrient-deficient conditions. Extraction of PHB with acetone-alcohol (1:1) was found as suitable method for optimum extraction of PHB as this mixture selectively extracted PHB without affecting the non-PHB cell mass. PHB extract from recombinant E. coli showed the presence of C-H, =O stretching, =C-H deformation, =C-H, =CH, and =C-O functional groups characteristic of PHB.

Two new anamorphic yeasts species, Cyberlindnera samutprakarnensis sp. nov. and Candida thasaenensis sp. nov., isolated from industrial wastes in Thailand.

PubMed

Poomtien, Jamroonsri; Jindamorakot, Sasitorn; Limtong, Savitree; Pinphanichakarn, Pairoh; Thaniyavarn, Jiraporn

2013-01-01

Three yeast strains were isolated from industrial wastes in Thailand. Based on the phylogenetic sequence analysis of the D1/D2 region of the large subunit rRNA gene, the internal transcribed spacer (ITS1-5.8S rRNA gene-ITS2; ITS1-2) region, and their physiological characteristics, the three strains were found to represent two novel species of the ascomycetous anamorphic yeast. Strain JP52(T) represent a novel species which was named Cyberlindnera samutprakarnensis sp. nov. (type strain JP52(T); = BCC 46825(T) = JCM 17816(T) = CBS 12528(T), MycoBank no. MB800879), which was differentiated from the closely related species Cyberlindnera mengyuniae CBS 10845(T) by 2.9 % sequence divergence in the D1/D2 region and 4.4 % sequence divergence in the ITS1-2. Strain JP59(T) and JP60 were identical in their D1/D2 and ITS1-2 regions, which were closely related to those of Scheffersomyces spartinae CBS 6059(T) by 0.9 and 1.0 % sequence divergence, respectively. In addition, supportive evidence of actin gene and translational elongation factor gene by sequence divergence of 6.5 % each confirmed their distinct status. Furthermore, JP59(T) and JP60 differentiated from the closely related species in some biochemical and physiological characteristics. These two strains were assigned as a single novel species which was named Candida thasaenensis sp. nov. (type JP59(T) = BCC 46828(T) = JCM 17817(T) = CBS 12529(T), MycoBank no. MB800880).

Purification, characterization and function of dihydrolipoamide dehydrogenase from the cyanobacterium Anabaena sp. strain P.C.C. 7119.

PubMed Central

Serrano, A

1992-01-01

A dihydrolipoamide dehydrogenase (dihydrolipoamide: NAD+ oxidoreductase, EC 1.8.1.4) (DLD) has been found in the soluble fraction of cells of both unicellular (Synechococcus sp. strain P.C.C. 6301) and filamentous (Calothrix sp. strain P.C.C. 7601 and Anabaena sp. strain P.C.C. 7119) cyanobacteria. DLD from Anabaena sp. was purified 3000-fold to electrophoretic homogeneity. The purified enzyme exhibited a specific activity of 190 units/mg and was characterized as a dimeric FAD-containing protein with a native molecular mass of 104 kDa, a Stokes' radius of 4.28 nm and a very acidic pI value of about 3.7. As is the case with the same enzyme from other sources, cyanobacterial DLD showed specificity for NADH and lipoamide, or lipoic acid, as substrates. Nevertheless, the strong acidic character of the Anabaena DLD is a distinctive feature with respect to the same enzyme from other organisms. The presence of essential thiol groups was suggested by the inactivation produced by thiol-group-reactive reagents and heavy-metal ions, with lipoamide, but not NAD+, behaving as a protective agent. The function and physiological significance of Anabaena DLD are discussed in relation to the fact that 2-oxoacid dehydrogenase complexes have not been detected so far in filamentous cyanobacteria. Glycine decarboxylase activity, which might be involved in photorespiratory metabolism, has been found, however, in cell extracts of Anabaena sp. strain P.C.C. 7119 as the present study demonstrates. Images Fig. 2. PMID:1471997

Non contiguous-finished genome sequence and description of Enorma timonensis sp. nov.

PubMed Central

Ramasamy, Dhamodaran; Dubourg, Gregory; Robert, Catherine; Caputo, Aurelia; Papazian, Laurent; Raoult, Didier; Fournier, Pierre-Edouard

2014-01-01

Enorma timonensis strain GD5T sp. nov., is the type strain of E. timonensis sp. nov., a new member of the genus Enorma within the family Coriobacteriaceae. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old woman hospitalized for 3 months in an intensive care unit. E. timonensis is an obligate anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,365,123 bp long genome (1 chromosome but no plasmid) contains 2,060 protein-coding and 52 RNA genes, including 4 rRNA genes. PMID:25197477

Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp. strain ADP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balotra, Sahil; Newman, Janet; French, Nigel G.

2014-02-19

The amidase domain of the allophanate hydrolase AtzF from Pseudomonas sp. strain ADP has been crystallized and preliminary X-ray diffraction data have been collected. The allophanate hydrolase from Pseudomonas sp. strain ADP was expressed and purified, and a tryptic digest fragment was subsequently identified, expressed and purified. This 50 kDa construct retained amidase activity and was crystallized. The crystals diffracted to 2.5 Å resolution and adopted space group P2{sub 1}, with unit-cell parameters a = 82.4, b = 179.2, c = 112.6 Å, β = 106.6°.

In Vitro Antimicrobial Potential of the Lichen Parmotrema sp. Extracts against Various Pathogens.

PubMed

Chauhan, Ritika; Abraham, Jayanthi

2013-07-01

The ongoing increasing antibiotic resistance is one of the biggest challenges faced by global public health. The perennial need for new antimicrobials against a background of increasing antibiotic resistance in pathogenic and opportunistic microorganisms obliges the scientific community to constantly develop new drugs and antimicrobial agents. Lichens are known prolific sources of natural antimicrobial drugs and biologically active natural products. This study was aimed to explore in vitro antimicrobial activity of lichen Parmotrema sp. The methanol and aqueous extracts of lichen Parmotrema sp. was extracted using Soxhlet extractor. Antibiotic assessment of methanol and aqueous extracts was done against eight bacterial (Escherichia coli, Staphylococcus aureus, Proteus mirabilis, Salmonella sp., Shigella sp., Enterococci faecalis, Pseudomonas aeruginosa, Klebsiella pneumoniae,) clinical pathogens and five plant pathogenic fungal strains (Aspergillus terreus strain JAS1, Scedosporium sp. JAS1, Ganoderma sp. JAS4, Candida tropicalis and Fusarium sp.) by Kirby-Bauer method. The methanol lichen Parmotrema sp. extract inhibited all the test organisms. The highest antibacterial activity was found against Pseudomonas aeruginosa and Staphylococcus aureus. The weakest activity was manifested in Salmonella sp. and Scedosporium sp. JAS1. Strong antifungal effect was found against Ganoderma sp. JAS4 and Fusarium sp. The aqueous lichen Parmotrema sp. extract revealed neither antibacterial nor antifungal activity. The present study shows that tested lichen Parmotrema sp. extracts demonstrated a strong antimicrobial effect. That suggests the active components from methanol extracts of the investigated lichen Parmotrema sp. can be used as natural antimicrobial agent against pathogens.

Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments.

PubMed

Kaye, Jonathan Z; Márquez, M Carmen; Ventosa, Antonio; Baross, John A

2004-03-01

To assess the physiological and phylogenetic diversity of culturable halophilic bacteria in deep-sea hydrothermal-vent environments, six isolates obtained from low-temperature hydrothermal fluids, sulfide rock and hydrothermal plumes in North and South Pacific Ocean vent fields located at 1530-2580 m depth were fully characterized. Three strains were isolated on media that contained oligotrophic concentrations of organic carbon (0.002 % yeast extract). Sequencing of the 16S rRNA gene indicated that all strains belonged to the genus Halomonas in the gamma-subclass of the Proteobacteria. Consistent with previously described species, the novel strains were slightly to moderately halophilic and grew in media containing up to 22-27 % total salts. The isolates grew at temperatures as low as -1 to 2 degrees C and had temperature optima of 30 or 20-35 degrees C. Both the minimum and optimum temperatures for growth were similar to those of Antarctic and sea-ice Halomonas species and lower than typically observed for the genus as a whole. Phenotypic tests revealed that the isolates were physiologically versatile and tended to have more traits in common with each other than with closely related Halomonas species, presumably a reflection of their common deep-sea, hydrothermal-vent habitat of origin. The G+C content of the DNA for all strains was 56.0-57.6 mol%, and DNA-DNA hybridization experiments revealed that four strains (Eplume1(T), Esulfide1(T), Althf1(T) and Slthf2(T)) represented novel species and that two strains (Eplume2 and Slthf1) were related to Halomonas meridiana. The proposed new species names are Halomonas neptunia (type strain Eplume1(T)=ATCC BAA-805(T)=CECT 5815(T)=DSM 15720(T)), Halomonas sulfidaeris (type strain Esulfide1(T)=ATCC BAA-803(T)=CECT 5817(T)=DSM 15722(T)), Halomonas axialensis (type strain Althf1(T)=ATCC BAA-802(T)=CECT 5812(T)=DSM 15723(T)) and Halomonas hydrothermalis (type strain Slthf2(T)=ATCC BAA-800(T)=CECT 5814(T)=DSM 15725(T)).

'Candidatus pasteuria usgae' sp. nov., an obligate endoparasite of the phytoparasitic nematode Belonolaimus longicaudatus.

PubMed

Giblin-Davis, R M; Williams, D S; Bekal, S; Dickson, D W; Brito, J A; Becker, J O; Preston, J F

2003-01-01

Taxonomically relevant characteristics of a fastidiously Gram-positive, obligately endoparasitic prokaryote (strain S-1) that uses the phytoparasitic sting nematode Belonolaimus longicaudatus as its host are reviewed. 16S rDNA sequence similarity (> or = 93%) confirms its congeneric ranking with other Pasteuria species and strains from nematodes and cladocerans and corroborates morphological, morphometric and host range evidence suggesting a novel taxon. The 16S rDNA sequence of strain S-1 has greatest similarity (96%) to the 16S rDNA sequences of both Pasteuria penetrans from root-knot nematodes (Meloidogyne species) and the recently reported strain of Pasteuria isolated from the soybean cyst nematode Heterodera glycines. Because the obligately endoparasitic nature of prokaryotes in the genus Pasteuria prevents isolation of definitive type strains, strain S-1 is proposed as 'Candidatus Pasteuria usgae' sp. nov.

Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs.

PubMed

Miroshnichenko, Margarita L; Kublanov, Ilya V; Kostrikina, Nadezhda A; Tourova, Tatyana P; Kolganova, Tatyana V; Birkeland, Nils-Kåre; Bonch-Osmolovskaya, Elizaveta A

2008-06-01

Five novel strains (2002(T), 2902, 2006, 108(T) and 117) of cellulose-degrading, anaerobic, thermophilic bacteria were isolated from terrestrial hot springs of Kamchatka (Far East, Russia). Strains 2002(T) and 108(T) were non-spore-forming bacteria with a Gram-positive type cell wall and peritrichous flagella. Optimum growth of strains 2002(T) and 108(T) occurred at pH 7.0 and at temperatures of 70 and 65 degrees C, respectively. The G+C contents of the DNA of strains 2002(T) and 108(T) were 35.1 and 36.4 mol%, respectively. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Caldicellulosiruptor. However, DNA-DNA hybridization experiments indicated that the levels of relatedness between strains 2002(T) and 108(T) and those of recognized members of the genus Caldicellulosiruptor ranged between 32 and 54 %. Based on both phenotypic and genomic differences, strains 2002(T) and 108(T) are considered to represent two novel species of the genus Caldicellulosiruptor. The names proposed for these organisms are Caldicellulosiruptor kronotskyensis sp. nov. (type strain 2002(T)=DSM 18902(T)=VKM B-2412(T)) and Caldicellulosiruptor hydrothermalis sp. nov. (type strain 108(T)=DSM 18901(T)=VKM B-2411(T)).

Alkalinity of Lanzarote soils is a factor shaping rhizobial populations with Sinorhizobium meliloti being the predominant microsymbiont of Lotus lancerottensis.

PubMed

León-Barrios, Milagros; Pérez-Yépez, Juan; Dorta, Paola; Garrido, Ana; Jiménez, Concepción

2017-04-01

Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp. and Bradyrhizobium-like. Strains of S. meliloti were distributed along the island and, in most of the localities they were exclusive or major microsymbionts of L. lancerottensis. Phylogeny of the nodulation nodC gene placed the S. meliloti strains within symbiovar lancerottense and the mesorhizobial strains with the symbiovar loti. Although strains from both symbiovars produced effective N 2 -fixing nodules, S. meliloti symbiovar lancerottense was clearly the predominant microsymbiont of L. lancerottensis. This fact correlated with the better adaptation of strains of this species to the alkaline soils of Lanzarote, as in vitro characterization showed that while the mesorhizobial strains were inhibited by alkaline pH, S. meliloti strains grew well at pH 9. Copyright © 2017 Elsevier GmbH. All rights reserved.

Transfer of Natrialba asiatica B1T to Natrialba taiwanensis sp. nov. and description of Natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the Archaea from Egypt that produces extracellular poly(glutamic acid).

PubMed

Hezayen, F F; Rehm, B H; Tindall, B J; Steinbüchel, A

2001-05-01

A novel extremely halophilic member of the Archaea, strain 40T, was isolated from Egypt (Aswan). This isolate requires at least 1.6 M sodium chloride for growth and exhibits optimal growth between 37 and 42 degrees C. Determination of the entire 16S rRNA gene sequence revealed the highest similarity to the type strain of Natrialba asiatica (> 99%). Polar lipid analysis indicated that strain 40T and Natrialba asiatica have essentially identical compositions, indicating that the former is a member of genus Natrialba. However, physiological and biochemical data provided evidence that Natrialba asiatica strains B1T and 172P1T, as well as strain 40T, are sufficiently different to be divided in three different species. The G+C content of strain 40T was 61.5+/-0.6 mol%. In addition, DNA-DNA hybridization data supported the placement of the isolate in a new species in the genus Natrialba, Natrialba aegyptiaca sp. nov., and indicated that Natrialba asiatica strain B1T should also be placed in a separate species, Natrialba taiwanensis sp. nov. Morphological studies of strain 40T indicated clearly that this isolate appears in three completely different cell shapes (cocci, rods, tetrads) under different conditions of growth, including different sodium chloride concentrations and different growth temperatures. Another interesting property of strain 40T is the ability to produce an extracellular polymer, which was found to be composed predominantly of glutamic acid (85% w/w), representing poly(glutamic acid), carbohydrates (12.5% w/w) and unidentified compounds (2.5% w/w). Among the Archaea, production of an extracellular polysaccharide has been described for some members of the genera Haloferax and Haloarcula.

Agrococcus terreus sp. nov. and Micrococcus terreus sp. nov., isolated from forest soil.

PubMed

Zhang, Jia-Yue; Liu, Xing-Yu; Liu, Shuang-Jiang

2010-08-01

Two bacterial strains, DNG5T and V3M1T, isolated from forest soil of the Changbai mountains in China, were characterized using a polyphasic approach. Analysis of their 16S rRNA gene sequences indicated that strains DNG5T and V3M1T were phylogenetically related to members of the genus Agrococcus (96.0-98.4% similarity) and Micrococcus (96.7-98.0% similarity), respectively, within the order Actinomycetales. Strains DNG5T and V3M1T were Gram-stain-positive and strictly aerobic and formed yellow colonies on LB agar. Cells of strain DNG5T were short, non-motile rods, 0.4-0.5x0.8-1.0 microm. Strain DNG5T contained MK-10 and MK-11 as the major respiratory quinones and anteiso-C15:0 (49.2%) and iso-C16:0 (22.4%) as the major fatty acids. The diamino acid in the peptidoglycan of strain DNG5T was 2,4-diaminobutyric acid and the murein was of the acetyl type. Cells of strain V3M1T were cocci, 0.6-0.7 microm in diameter. The cell-wall peptidoglycan of strain V3M1T contained the amino acids lysine, glutamic acid, alanine and glycine. Strain V3M1T contained MK-7, MK-7(H2), MK-8 and MK-8(H2) as respiratory quinones and anteiso-C15:0 (78.2%) and iso-C15:0 (13.1%) as the major cellular fatty acids. The DNA G+C contents of strains DNG5T and V3M1T were 75.9 and 67.2 mol%, respectively. The DNA-DNA relatedness of strain DNG5T to Agrococcus jejuensis DSM 22002T, A. jenensis JCM 9950T, A. baldri JCM 12132T and A. citreus JCM 12398T was 58.3, 43.9, 36.1 and 54.1%, respectively. The DNA-DNA relatedness of strain V3M1T to Micrococcus luteus CGMCC 1.2299T, M. antarcticus CGMCC 1.2373T and M. lylae CGMCC 1.2300T was 57.5, 45.4 and 39.0%, respectively. Combining phenotypic and genotypic traits, strain DNG5T represents a novel species of the genus Agrococcus, for which the name Agrococcus terreus sp. nov. is proposed, with DNG5T (=CGMCC 1.6960T =NBRC 104260T) as the type strain. Strain V3M1T represents a novel species of the genus Micrococcus, for which the name Micrococcus terreus sp. nov. is proposed, with V3M1T (=CGMCC 1.7054T =NBRC 104258T) as the type strain.

Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed.

PubMed

Tanaka, Mami; Endo, Shoko; Kotake, Fumihito; Al-Saari, Nurhidayu; Amin, A K M Rohul; Feng, Gao; Mino, Sayaka; Doi, Hidetaka; Ogura, Yoshitoshi; Hayashi, Tetsuya; Suda, Wataru; Hattori, Masahira; Yumoto, Isao; Sawabe, Toko; Sawabe, Tomoo; Araki, Toshiyoshi

2017-01-01

A novel strain Vibrio aphrogenes sp. nov. strain CA-1004T isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using polyphasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis clade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis clade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004T as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004T was separate from four known Rumoiensis clade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non-motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis clade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis clade, with CA-1004T as the type strain (JCM 31643T = DSM 103759T).

Biodegradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1

PubMed Central

Tallur, Preeti N.; Mulla, Sikandar I.; Megadi, Veena B.; Talwar, Manjunatha P.; Ninnekar, Harichandra Z.

2015-01-01

Pyrethroid pesticide cypermethrin is a environmental pollutant because of its widespread use, toxicity and persistence. Biodegradation of such chemicals by microorganisms may provide an cost-effective method for their detoxification. We have investigated the degradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1 in various matrices such as, polyurethane foam (PUF), polyacrylamide, sodium alginate and agar. The optimum temperature and pH for the degradation of cypermethrin by immobilized cells of Micrococcus sp. were found to be 30 °C and 7.0, respectively. The rate of degradation of 10 and 20 mM of cypermethrin by freely suspended cells were compared with that of immobilized cells in batches and semi-continuous with shaken cultures. PUF-immobilized cells showed higher degradation of cypermethrin (10 mM and 20 mM) than freely suspended cells and cells immobilized in other matrices. The PUF-immobilized cells of Micrococcus sp. strain CPN 1 were retain their degradation capacity. Thus, they can be reused for more than 32 cycles, without losing their degradation capacity. Hence, the PUF-immobilized cells of Micrococcus sp. could potentially be used in the bioremediation of cypermethrin contaminated water. PMID:26413046

Biodegradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1.

PubMed

Tallur, Preeti N; Mulla, Sikandar I; Megadi, Veena B; Talwar, Manjunatha P; Ninnekar, Harichandra Z

2015-01-01

Pyrethroid pesticide cypermethrin is a environmental pollutant because of its widespread use, toxicity and persistence. Biodegradation of such chemicals by microorganisms may provide an cost-effective method for their detoxification. We have investigated the degradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1 in various matrices such as, polyurethane foam (PUF), polyacrylamide, sodium alginate and agar. The optimum temperature and pH for the degradation of cypermethrin by immobilized cells of Micrococcus sp. were found to be 30 °C and 7.0, respectively. The rate of degradation of 10 and 20 mM of cypermethrin by freely suspended cells were compared with that of immobilized cells in batches and semi-continuous with shaken cultures. PUF-immobilized cells showed higher degradation of cypermethrin (10 mM and 20 mM) than freely suspended cells and cells immobilized in other matrices. The PUF-immobilized cells of Micrococcus sp. strain CPN 1 were retain their degradation capacity. Thus, they can be reused for more than 32 cycles, without losing their degradation capacity. Hence, the PUF-immobilized cells of Micrococcus sp. could potentially be used in the bioremediation of cypermethrin contaminated water.

Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1 Acidobacteria from Sphagnum peat and decaying wood.

PubMed

Kulichevskaya, Irina S; Kostina, Lilia A; Valásková, Vendula; Rijpstra, W Irene C; Damsté, Jaap S Sinninghe; de Boer, Wietse; Dedysh, Svetlana N

2012-07-01

Two strains of subdivision 1 Acidobacteria, a pink-pigmented bacterium KA1(T) and a colourless isolate WH120(T), were obtained from acidic Sphagnum peat and wood under decay by the white-rot fungus Hyploma fasciculare, respectively. Cells of these isolates were Gram-negative-staining, non-motile, short rods, which were covered by large polysaccharide capsules and occurred singly, in pairs, or in short chains. Strains KA1(T) and WH120(T) were strictly aerobic mesophiles that grew between 10 and 33 °C, with an optimum at 22-28 °C. Both isolates developed under acidic conditions, but strain WH120(T) was more acidophilic (pH growth range 3.5-6.4; optimum, 4.0-4.5) than strain KA1(T) (pH growth range 3.5-7.3; optimum , 5.0-5.5). The preferred growth substrates were sugars. In addition, the wood-derived isolate WH120(T) grew on oxalate, lactate and xylan, while the peat-inhabiting acidobacterium strain KA1(T) utilized galacturonate, glucuronate and pectin. The major fatty acids were iso-C(15:0) and iso-C(17:1)ω8c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid. The quinone was MK-8. The DNA G+C contents of strains KA1(T) and WH120(T) were 54.1 and 51.7 mol%, respectively. Strains KA1(T) and WH120(T) displayed 97.8% 16S rRNA gene sequence similarity to each other. The closest recognized relatives were Acidobacterium capsulatum and Telmatobacter bradus (93.4-94.3% 16S rRNA gene sequence similarity). These species differed from strains KA1(T) and WH120(T) by their ability to grow under anoxic conditions, the absence of capsules, presence of cell motility and differing fatty acid composition. Based on these differences, the two new isolates are proposed as representing a novel genus, Acidicapsa gen. nov., and two novel species. Acidicapsa borealis gen. nov., sp. nov. is the type species for the new genus with strain KA1(T) (=DSM 23886(T)=LMG 25897(T)=VKM B-2678(T)) as the type strain. The name Acidicapsa ligni sp. nov. is proposed for strain WH120(T) (=LMG 26244(T)=VKM B-2677(T)=NCCB 100371(T)).

Use of molecular techniques to evaluate the survival of a microorganism injected into an aquifer

USGS Publications Warehouse

Thiem, S.M.; Krumme, M.L.; Smith, R.L.; Tiedje, J.M.

1994-01-01

A PCR primer set and an internal probe that are specific for Pseudomonas sp. strain B13, a 3-chlorobenzoate-metabolizing strain, were developed. Using this primer set and probe, we were able to detect Pseudomonas sp. strain B13 DNA sequences in DNA extracted from aquifer samples 14.5 months after Pseudomonas sp. strain B13 had been injected into a sand and gravel aquifer. This primer set and probe were also used to analyze isolates from 3-chlorobenzoate enrichments of the aquifer samples by Southern blot analysis. Hybridization of Southern blots with the Pseudomonas sp. strain B13-specific probe and a catabolic probe in conjunction with restriction fragment length polymorphism (RFLP) analysis of ribosome genes was used to determine that viable Pseudomonas sp. strain B13 persisted in this environment. We isolated a new 3-chlorobenzoate-degrading strain from one of these enrichment cultures. The B13-specific probe does not hybridize to DNA from this isolate. The new strain could be the result of gene exchange between Pseudomonas sp. strain B13 and an indigenous bacterium. This speculation is based on an RFLP pattern of ribosome genes that differs from that of Pseudomonas sp. strain B13, the fact that identically sized restriction fragments hybridized to the catabolic gene probe, and the absence of any enrichable 3-chlorobenzoate-degrading strains in the aquifer prior to inoculation.

Genome Sequence of Sphingomonas sp. Strain PAMC 26621, an Arctic-Lichen-Associated Bacterium Isolated from a Cetraria sp.

PubMed Central

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

2012-01-01

The lichen-associated bacterial strain Sphingomonas sp. PAMC 26621 was isolated from an Arctic lichen Cetraria sp. on Svalbard Islands. Here we report the draft genome sequence of this strain, which could provide novel insights into the molecular principles of lichen-microbe interactions. PMID:22582384

The hyperaccumulator Sedum plumbizincicola harbors metal-resistant endophytic bacteria that improve its phytoextraction capacity in multi-metal contaminated soil.

PubMed

Ma, Ying; Oliveira, Rui S; Nai, Fengjiao; Rajkumar, Mani; Luo, Yongming; Rocha, Inês; Freitas, Helena

2015-06-01

Endophyte-assisted phytoremediation has recently been suggested as a successful approach for ecological restoration of metal contaminated soils, however little information is available on the influence of endophytic bacteria on the phytoextraction capacity of metal hyperaccumulating plants in multi-metal polluted soils. The aims of our study were to isolate and characterize metal-resistant and 1-aminocyclopropane-1-carboxylate (ACC) utilizing endophytic bacteria from tissues of the newly discovered Zn/Cd hyperaccumulator Sedum plumbizincicola and to examine if these endophytic bacterial strains could improve the efficiency of phytoextraction of multi-metal contaminated soils. Among a collection of 42 metal resistant bacterial strains isolated from the tissues of S. plumbizincicola grown on Pb/Zn mine tailings, five plant growth promoting endophytic bacterial strains (PGPE) were selected due to their ability to promote plant growth and to utilize ACC as the sole nitrogen source. The five isolates were identified as Bacillus pumilus E2S2, Bacillus sp. E1S2, Bacillus sp. E4S1, Achromobacter sp. E4L5 and Stenotrophomonas sp. E1L and subsequent testing revealed that they all exhibited traits associated with plant growth promotion, such as production of indole-3-acetic acid and siderophores and solubilization of phosphorus. These five strains showed high resistance to heavy metals (Cd, Zn and Pb) and various antibiotics. Further, inoculation of these ACC utilizing strains significantly increased the concentrations of water extractable Cd and Zn in soil. Moreover, a pot experiment was conducted to elucidate the effects of inoculating metal-resistant ACC utilizing strains on the growth of S. plumbizincicola and its uptake of Cd, Zn and Pb in multi-metal contaminated soils. Out of the five strains, B. pumilus E2S2 significantly increased root (146%) and shoot (17%) length, fresh (37%) and dry biomass (32%) of S. plumbizincicola as well as plant Cd uptake (43%), whereas Bacillus sp. E1S2 significantly enhanced the accumulation of Zn (18%) in plants compared with non-inoculated controls. The inoculated strains also showed high levels of colonization in rhizosphere and plant tissues. Results demonstrate the potential to improve phytoextraction of soils contaminated with multiple heavy metals by inoculating metal hyperaccumulating plants with their own selected functional endophytic bacterial strains. Copyright © 2015 Elsevier Ltd. All rights reserved.

Yamadazyma kitorensis f.a., sp. nov. and Zygoascus biomembranicola f.a., sp. nov., novel yeasts from the stone chamber interior of the Kitora tumulus, and five novel combinations in Yamadazyma and Zygoascus for species of Candida.

PubMed

Nagatsuka, Yuka; Ninomiya, Shinya; Kiyuna, Tomohiko; Kigawa, Rika; Sano, Chie; Sugiyama, Junta

2016-04-01

Analysis of D1/D2 large-subunit (LSU) rRNA gene sequences predicted that 17 yeast isolates, mainly from viscous gels (biofilms) taken from the stone chamber interior of the Kitora tumulus in Nara, Japan, were placed in the Yamadazyma and Zygoascus clades. Polyphasic characterization, including morphological, physiological and chemotaxonomic characteristics, multigene sequence divergence and DNA-DNA hybridization, strongly suggested the assignment of one novel species to each of the clades; these are Yamadazyma kitorensis f.a., sp. nov., with the type strain JCM 31005T (ex-type CBS 14158T=isolate K8617-6-8T), and Zygoascus biomembranicola f.a., sp. nov., with the type strain JCM 31007T (ex-type CBS 14157T=isolate K61208-2-11T). Furthermore, the transfer of five known species of the genus Candida as novel combinations to the genera Yamadazyma and Zygoascus is proposed; these are Yamadazyma olivae f.a., comb. nov. (type strain CBS 11171T=ATCC MYA-4568T), Yamadazyma tumulicola f.a., comb. nov. (type strain JCM 15403T=ex-type CBS 10917T=isolate T6517-9-5T), Yamadazyma takamatsuzukensis f.a., comb. nov. (type strain JCM 15410T=CBS 10916T = isolate T4922-1-1T), Zygoascus polysorbophila f.a., comb. nov. (type strain NRRL Y-27161T=CBS 7317T) and Zygoascus bituminiphila f.a., comb. nov. (type strain CBS 8813T=MUCL 41424T).

Biodegradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1.

PubMed

Mulla, Sikandar I; Hoskeri, Robertcyril S; Shouche, Yogesh S; Ninnekar, Harichandra Z

2011-02-01

A bacterial consortium capable of degrading nitroaromatic compounds was isolated from pesticide-contaminated soil samples by selective enrichment on 2-nitrotoluene as a sole source of carbon and energy. The three different bacterial isolates obtained from bacterial consortium were identified as Bacillus sp. (A and C), Bacillus flexus (B) and Micrococcus sp. (D) on the basis of their morphological and biochemical characteristics and by phylogenetic analysis based on 16S rRNA gene sequences. The pathway for the degradation of 2-nitrotoluene by Micrococcus sp. strain SMN-1 was elucidated by the isolation and identification of metabolites, growth and enzymatic studies. The organism degraded 2-nitrotoluene through 3-methylcatechol by a meta-cleavage pathway, with release of nitrite.

Soil fungi for mycoremediation of arsenic pollution in agriculture soils.

PubMed

Singh, M; Srivastava, P K; Verma, P C; Kharwar, R N; Singh, N; Tripathi, R D

2015-11-01

Soil arsenic (As) contamination of food-chains and public health can be mitigated through fungal bioremediation. To enumerate culturable soil fungi, soils were collected from the As-contaminated paddy fields (3-35 mg kg(-1) ) of the middle Indo-Gangetic Plains. Total 54 fungal strains were obtained and identified at their molecular level. All strains were tested for As tolerance (from 100 to 10,000 mg l(-1) arsenate). Fifteen fungal strains, tolerant to 10,000 mg l(-1) arsenate, were studied for As removal in-vivo for 21 days by cultivating them individually in potato dextrose broth enriched with 10 mg l(-1) As. The bioaccumulation of As in fungal biomass ranged from 0·023 to 0·259 g kg(-1). The biovolatilized As ranged from 0·23 to 6·4 mg kg(-1). Higher As bioaccumulation and biovolatilization observed in the seven fungal strains, Aspergillus oryzae FNBR_L35; Fusarium sp. FNBR_B7, FNBR_LK5 and FNBR_B3; Aspergillus nidulans FNBR_LK1; Rhizomucor variabilis sp. FNBR_B9; and Emericella sp. FNBR_BA5. These fungal strains were also tested and found suitable for significant plant growth promotion in the calendula, withania and oat plants in a greenhouse based pot experiment. These fungal strains can be used for As remediation in As-contaminated agricultural soils. © 2015 The Society for Applied Microbiology.

Proteomic analysis reveals contrasting stress response to uranium in two nitrogen-fixing Anabaena strains, differentially tolerant to uranium.

PubMed

Panda, Bandita; Basu, Bhakti; Acharya, Celin; Rajaram, Hema; Apte, Shree Kumar

2017-01-01

Two strains of the nitrogen-fixing cyanobacterium Anabaena, native to Indian paddy fields, displayed differential sensitivity to exposure to uranyl carbonate at neutral pH. Anabaena sp. strain PCC 7120 and Anabaena sp. strain L-31 displayed 50% reduction in survival (LD 50 dose), following 3h exposure to 75μM and 200μM uranyl carbonate, respectively. Uranium responsive proteome alterations were visualized by 2D gel electrophoresis, followed by protein identification by MALDI-ToF mass spectrometry. The two strains displayed significant differences in levels of proteins associated with photosynthesis, carbon metabolism, and oxidative stress alleviation, commensurate with their uranium tolerance. Higher uranium tolerance of Anabaena sp. strain L-31 could be attributed to sustained photosynthesis and carbon metabolism and superior oxidative stress defense, as compared to the uranium sensitive Anabaena sp. strain PCC 7120. Uranium responsive proteome modulations in two nitrogen-fixing strains of Anabaena, native to Indian paddy fields, revealed that rapid adaptation to better oxidative stress management, and maintenance of metabolic and energy homeostasis underlies superior uranium tolerance of Anabaena sp. strain L-31 compared to Anabaena sp. strain PCC 7120. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic diversity of Vibrio parahaemolyticus strains isolated from farmed Pacific white shrimp and ambient pond water affected by acute hepatopancreatic necrosis disease outbreak in Thailand.

PubMed

Chonsin, Kaknokrat; Matsuda, Shigeaki; Theethakaew, Chonchanok; Kodama, Toshio; Junjhon, Jiraphan; Suzuki, Yasuhiko; Suthienkul, Orasa; Iida, Tetsuya

2016-01-01

Acute hepatopancreatic necrosis disease (AHPND) is an emerging shrimp disease that causes massive die-offs in farmed shrimps. Recent outbreaks of AHPND in Asia have been causing great losses for shrimp culture and have become a serious socioeconomic problem. The causative agent of AHPND is Vibrio parahaemolyticus, which is typically known to cause food-borne gastroenteritis in humans. However, there have been few reports of the epidemiology of V. parahaemolyticus AHPND strains, and the genetic relationship among AHPND strains is unclear. Here, we report the genetic characterization of V. parahaemolyticus strains isolated from AHPND outbreaks in Thailand. We found eight isolates from AHPND-suspected shrimps and pond water that were positive for AHPND markers AP1 and AP2. PCR analysis confirmed that none of these eight AP-positive AHPND strains possesses the genes for the conventional virulence factors affecting to humans, such as thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH) and type III secretion system 2. Phylogenetic analysis by multilocus sequence typing showed that the AHPND strains are genetically diverse, suggesting that AHPND strains were not derived from a single genetic lineage. Our study represents the first report of molecular epidemiology of AHPND-causing V. parahaemolyticus strains using multilocus sequence typing, and provides an insight into their evolutionary mechanisms. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.

PubMed

Kim, Soo-Jin; Lim, Jun-Muk; Ahn, Jae-Hyung; Weon, Hang-Yeon; Hamada, Moriyuki; Suzuki, Ken-ichiro; Ahn, Tae-Young; Kwon, Soon-Wo

2014-02-01

Bacterial strains KIS82-1(T) and GRS42(T) were isolated from soil and from sap of Acer mono, respectively, in the Republic of Korea. Both strains were aerobic, Gram-stain-positive, mesophilic, rod-shaped and motile. Phylogenetically, both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS82-1(T) showed the highest similarity to those of Frondihabitans peucedani RS-15(T) (97.6%), Frigoribacterium mesophilum MSL-08(T) (97.2%) and Labedella gwakjiensis KSW2-17(T) (97.0%), while strain GRS42(T) showed the highest 16S rRNA gene sequence similarity to Frondihabitans peucedani RS-15(T) (98.7%), Frondihabitans cladoniiphilus CafT13(T) (98.4%), Frondihabitans australicus E1HC-02(T) (98.2%) and Frigoribacterium faeni 801(T) (97.3%). The 16S rRNA gene sequence similarity between GRS42(T) and KIS82-1(T) was 97.0%. Phylogenetic trees indicated that strain GRS42(T) was firmly grouped into the genus Frondihabitans, while strain KIS82-1(T) did not show a clear affiliation to any genus within the family Microbacteriaceae. Strain KIS82-1(T) showed type B1β peptidoglycan with 2,4-diamino-L-butyric acid as the diamino acid. It had MK-11, MK-10 and MK-12 as respiratory quinones, anteiso-C(15 : 0), iso-C(16: 0) and iso-C(14 : 0) as major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid as predominant polar lipids. The peptidoglycan of strain GRS42(T) was of type B2β with D-ornithine as the diamino acid. The strain contained MK-8, MK-9 and MK-7 as respiratory quinones, summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c) as major cellular fatty acid and diphosphatidylglycerol, phosphatidylglycerol and three unknown glycolipids as predominant polar lipids. Strain GRS42(T) revealed low DNA-DNA hybridization (<50% relatedness) with closely related strains. Based on the data obtained in the present polyphasic taxonomic study, we propose that strain KIS82-1(T) represents a novel genus and species and that strain GRS42(T) represents a novel species in the family Microbacteriaceae. The genus Galbitalea gen. nov. is proposed, with strain KIS82-1(T) ( = KACC 15520(T) = NBRC 108727(T)) as the type strain of the type species, Galbitalea soli sp. nov. Strain GRS42(T) ( = KACC 15521(T) = NBRC 108728(T)) is proposed as the type strain of Frondihabitans sucicola sp. nov.

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

PubMed Central

Liang, Zhishu; Li, Guiying; Das, Ranjit

2016-01-01

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

Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring Located atop the Himalayan Ranges at Manikaran, India

PubMed Central

Dwivedi, Vatsala; Sangwan, Naseer; Nigam, Aeshna; Garg, Nidhi; Niharika, Neha; Khurana, Paramjit; Khurana, Jitendra P.

2012-01-01

Thermus sp. strain RL was isolated from a hot water spring (90°C to 98°C) at Manikaran, Himachal Pradesh, India. Here we report the draft genome sequence (20,36,600 bp) of this strain. The draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average G+C content of 68.77%. PMID:22689228

Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

PubMed Central

Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.

2013-01-01

Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which might shed light onto the enzymatic machineries that are involved in its production of biogenic amines. PMID:23405290

Avoidance of protein oxidation correlates with the desiccation and radiation resistance of hot and cold desert strains of the cyanobacterium Chroococcidiopsis.

PubMed

Fagliarone, Claudia; Mosca, Claudia; Ubaldi, Ilaria; Verseux, Cyprien; Baqué, Mickael; Wilmotte, Annick; Billi, Daniela

2017-11-01

To investigate the relationship between desiccation and the extent of protein oxidation in desert strains of Chroococcidiopsis a selection of 10 isolates from hot and cold deserts and the terrestrial cyanobacterium Chroococcidiopsis thermalis sp. PCC 7203 were exposed to desiccation (air-drying) and analyzed for survival. Strain CCMEE 029 from the Negev desert and the aquatic cyanobacterium Synechocystis sp. PCC 6803 were further investigated for protein oxidation after desiccation (drying over silica gel), treatment with H 2 O 2 up to 1 M and exposure to γ-rays up to 25 kGy. Then a selection of desert strains of Chroococcidiopsis with different survival rates after prolonged desiccation, as well as Synechocystis sp. PCC 6803 and Chroococcidiopsis thermalis sp. PCC 7203, were analyzed for protein oxidation after treatment with 10 and 100 mM of H 2 O 2 . Results suggest that in the investigated strains a tight correlation occurs between desiccation and radiation tolerance and avoidance of protein oxidation.

Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules.

PubMed

Carro, Lorena; Riesco, Raúl; Spröer, Cathrin; Trujillo, Martha E

2016-09-01

A diversity study on the presence of strains representing the genus Micromonospora in Pisum sativum nodules collected from Cañizal (Spain) has provided evidence of the high number of isolates that might represent novel species. In the present work, we have characterized three of these isolates: GUI23T, GUI43T and GUI63T. Phenotypic and genotypic analyses confirmed that all strains represent novel species of the genus Micromonospora with the following proposed names: Micromonospora ureilytica sp. nov., type strain GUI23T (=CECT 9022T=DSM 101692T), Micromonospora noduli sp. nov., type strain GUI43T (=CECT 9020T=DSM 101694T), and Micromonospora vinacea sp. nov., type strain GUI63T (=CECT 9019T=DSM 101695T).

Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots.

PubMed

Han, Ji-Hye; Kim, Tae-Su; Joung, Yochan; Kim, Mi Na; Shin, Kee-Sun; Bae, Taeok; Kim, Seung Bum

2013-12-01

Two Gram-stain-positive, non-motile, non-spore-forming, rod-shaped actinobacterial strains were isolated from the surface-sterilized roots of mugwort (Artemisia princeps) and horse-weed (Conyza canadensis), and subjected to taxonomic characterization. 16S rRNA gene sequence analysis indicated that the isolates, designated MWE 3-5(T) and HWE 2-02(T), should be placed in the genus Nocardioides of the family Nocardioidaceae. The strains were closely related to Nocardioides hankookensis DS-30(T), which exhibited 16S rRNA gene sequence similarity values of 97.99 and 99.09 % with strains MWE 3-5(T) and HWE 2-02(T), respectively. The genome relatedness of N. hankookensis DS-30(T) with strain MWE 3-5(T) was 35.8 %, and that with strain HWE 2-02(T) was 36.4 %, whereas that between the two isolates was 43.2 %. Strains MWE 3-5(T) and HWE 2-02(T) possessed MK-8(H4) as the major isoprenoid quinone, and ll-diaminopimelic acid in the cell-wall peptidoglycan. The main fatty acids were iso-C16 : 0, iso-C17 : 0 and C18 : 1ω9c for strain MWE 3-5(T) and iso-C16 : 0, 10-methyl C18 : 0 and C18 : 1ω9c for strain HWE 2-02(T). Based on phenotypic, genotypic and phylogenetic studies, the following two novel species are proposed: Nocardioides endophyticus sp. nov. (type strain, MWE 3-5(T) = KCTC 29122(T) = JCM 18532(T)) and Nocardioides conyzicola sp. nov. (type strain, HWE 2-02(T) = KCTC 29121(T) = JCM 18531(T)).

Cryptococcus vaughanmartiniae sp. nov. and Cryptococcus onofrii sp. nov.: two new species isolated from worldwide cold environments.

PubMed

Turchetti, Benedetta; Selbmann, Laura; Blanchette, Robert A; Di Mauro, Simone; Marchegiani, Elisabetta; Zucconi, Laura; Arenz, Brett E; Buzzini, Pietro

2015-01-01

Twenty yeast strains, representing a selection from a wider group of more than 60 isolates were isolated from cold environments worldwide (Antarctica, Iceland, Russia, USA, Italian and French Alps, Apennines). The strains were grouped based on their common morphological and physiological characteristics. A phylogeny based on D1/D2 ribosomal DNA sequences placed them in an intermediate position between Cryptococcus saitoi and Cryptococcus friedmannii; the ITS1 and ITS2 rDNA phylogeny demonstrated that these strains belong to two related but hitherto unknown species within the order Filobasidiales, albidus clade. These two novel species are described with the names Cryptococcus vaughanmartiniae (type strain DBVPG 4736(T)) and Cryptococcus onofrii (type strain DBVPG 5303(T)).

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1.

PubMed Central

Omori, T; Monna, L; Saiki, Y; Kodama, T

1992-01-01

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CS2, FeS2, and even elemental sulfur. Strain SY1 metabolized DBT to dibenzothiophene-5-oxide, DBT sulfone, and 2-hydroxybiphenyl, which was subsequently nitrated to produce at least two different hydroxynitrobiphenyls during cultivation. These metabolites were separated by silica gel column chromatography and identified by nuclear magnetic resonance, UV, and mass spectral techniques. Resting cells of SY1 desulfurized toluenesulfonic acid and released sulfite anion. On the basis of these results, a new DBT degradation pathway is proposed. PMID:1575493

Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei.

PubMed

Young, C-C; Busse, H-J; Langer, S; Chu, Jiunn-Nan; Schumann, P; Arun, A B; Shen, Fo-Ting; Rekha, P D; Kämpfer, P

2010-04-01

Three Gram-positive, rod-shaped bacteria (strains CC-SBCK-209( T), CC-12309(T) and CC-5209(T)) were isolated from the stalk of the edible mushroom Agaricus blazei grown in the laboratory. 16S rRNA gene sequence analysis indicated that all three isolates clearly belonged to the genus Microbacterium. Strains CC-SBCK-209( T) and CC-12309(T) were most related closely to the type strain of Microbacterium halotolerans (95.9 and 96.1 % 16S rRNA gene sequence similarity, respectively). These two novel strains shared 97.9 % 16S rRNA gene sequence similarity. Levels of similarity to the type strains of all other recognized Microbacterium species were lower than 95.5 %. The third strain (CC-5209( T)) showed the highest 16S rRNA gene sequence similarity to the type strain of Microbacterium resistens (97.6 %); levels of similarity to the type strains of all other recognized Microbacterium species were lower than 96 %. The quinone systems of strains CC-SBCK-209(T), CC-12309(T) and CC-5209(T) consisted of MK-11/MK-12, MK-11/MK-10 and MK-13 as major compounds, respectively. All three strains contained ornithine in their peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The polyamine pattern consisted of spermidine and spermine as predominant components. Fatty acid profiles (anteiso-C(15 : 0), iso-C(16 : 0) and anteiso-C(17 : 0 ) as major components) supported the affiliation of all three strains to the genus Microbacterium. The results of physiological and biochemical tests and DNA-DNA hybridization experiments allowed the clear phenotypic and genotypic differentiation of strains CC-SBCK-209(T) and CC-12309( T) from M. halotolerans and other closely related Microbacterium species. Strain CC-5209(T) could be differentiated clearly from M. resistens both genotypically and phenotypically. Based on these data, the novel strains are considered to represent three novel species of the genus Microbacterium. The names proposed for these organisms are Microbacterium agarici sp. nov. [type strain CC-SBCK-209( T) (=DSM 21798(T)=CCM 7686(T))], Microbacterium humi sp. nov. [type strain CC-12309(T) (=DSM 21799(T)=CCM 7687(T))] and Microbacterium pseudoresistens sp. nov. [type strain CC-5209(T) (=DSM 22185(T)=CCM 7688(T))].

Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces.

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj

2014-07-01

Two strains of Gram-negative, methylotrophic bacteria, isolated because of their abilities to promote plant growth, were subjected to a polyphasic taxonomic study. The isolates were strictly aerobic, motile, pink-pigmented, facultatively methylotrophic, non-spore-forming rods. The chemotaxonomic characteristics of the isolates included the presence of C18 : 1ω7c as the major cellular fatty acid. The DNA G+C contents of strains BL36(T) and BL47(T) were 69.4 and 69.8 mol%, respectively. 16S rRNA gene sequence analysis of strains BL36(T) and BL47(T) placed them under the genus Methylobacterium, with the pairwise sequence similarity between them and the type strains of closely related species ranging from 97.2 to 99.0%. On the basis of their phenotypic and phylogenetic distinctiveness and the results of DNA-DNA hybridization analysis, the isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium pseudosasicola sp. nov. (type strain BL36(T) = NBRC 105203(T) = ICMP 17621(T)) and Methylobacterium phyllostachyos sp. nov. (type strain BL47(T) = NBRC 105206(T) = ICMP 17619(T)) are proposed. © 2014 IUMS.

Characterization and Strain Improvement of a Hypercellulytic Variant, Trichoderma reesei SN1, by Genetic Engineering for Optimized Cellulase Production in Biomass Conversion Improvement.

PubMed

Qian, Yuanchao; Zhong, Lixia; Hou, Yunhua; Qu, Yinbo; Zhong, Yaohua

2016-01-01

The filamentous fungus Trichoderma reesei is a widely used strain for cellulolytic enzyme production. A hypercellulolytic T. reesei variant SN1 was identified in this study and found to be different from the well-known cellulase producers QM9414 and RUT-C30. The cellulose-degrading enzymes of T. reesei SN1 show higher endoglucanase (EG) activity but lower β-glucosidase (BGL) activity than those of the others. A uracil auxotroph strain, SP4, was constructed by pyr4 deletion in SN1 to improve transformation efficiency. The BGL1-encoding gene bgl1 under the control of a modified cbh1 promoter was overexpressed in SP4. A transformant, SPB2, with four additional copies of bgl1 exhibited a 17.1-fold increase in BGL activity and a 30.0% increase in filter paper activity. Saccharification of corncob residues with crude enzyme showed that the glucose yield of SPB2 is 65.0% higher than that of SP4. These results reveal the feasibility of strain improvement through the development of an efficient genetic transformation platform to construct a balanced cellulase system for biomass conversion.

Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation.

PubMed

Peng, Bingyin; Huang, Shuangcheng; Liu, Tingting; Geng, Anli

2015-05-17

Xylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. Very few bacterial XIs can function actively in Saccharomyces cerevisiae. Here, we illustrate a group of XIs that would function for xylose fermentation in S. cerevisiae through phylogenetic analysis, recombinant yeast strain construction, and xylose fermentation. Phylogenetic analysis of deposited XI sequences showed that XI evolutionary relationship was highly consistent with the bacterial taxonomic orders and quite a few functional XIs in S. cerevisiae were clustered with XIs from mammal gut Bacteroidetes group. An XI from Bacteroides valgutus in this cluster was actively expressed in S. cerevisiae with an activity comparable to the fungal XI from Piromyces sp. Two XI genes were isolated from the environmental metagenome and they were clustered with XIs from environmental Bacteroidetes group. These two XIs could not be expressed in yeast with activity. With the XI from B. valgutus expressed in S. cerevisiae, background yeast strains were optimized by pentose metabolizing pathway enhancement and adaptive evolution in xylose medium. Afterwards, more XIs from the mammal gut Bacteroidetes group, including those from B. vulgatus, Tannerella sp. 6_1_58FAA_CT1, Paraprevotella xylaniphila and Alistipes sp. HGB5, were individually transformed into S. cerevisiae. The known functional XI from Orpinomyces sp. ukk1, a mammal gut fungus, was used as the control. All the resulting recombinant yeast strains were able to ferment xylose. The respiration-deficient strains harboring B. vulgatus and Alistipes sp. HGB5 XI genes respectively obtained specific xylose consumption rate of 0.662 and 0.704 g xylose gcdw(-1) h(-1), and ethanol specific productivity of 0.277 and 0.283 g ethanol gcdw(-1) h(-1), much comparable to those obtained by the control strain carrying Orpinomyces sp. ukk1 XI gene. This study demonstrated that XIs clustered in the mammal gut Bacteroidetes group were able to be expressed functionally in S. cerevisiae and background strain anaerobic adaptive evolution in xylose medium is essential for the screening of functional XIs. The methods outlined in this paper are instructive for the identification of novel XIs that are functional in S. cerevisiae.

Proposal of Ancylothrix gen. nov., a new genus of Phormidiaceae (Cyanobacteria, Oscillatoriales) based on a polyphasic approach.

PubMed

Martins, Mariellen Dornelles; Rigonato, Janaina; Taboga, Sebastião Roberto; Branco, Luis Henrique Zanini

2016-06-01

During a study about the diversity of Phormidioideae (Phormidiaceae, Oscillatoriales) in Brazil, seven strains from southern and southeastern regions were isolated in monospecifc cultures and submitted to polyphasic evaluation (morphological, ecological, cytological and molecular studies). The populations studied were found to be morphologically similar to Kamptonema (filaments narrowed and bent at the end) and cytologically different (thylakoids' arrangement - radial distribution in Brazilian strains and parietal distribution in Kamptonema). The original habitats were very diverse among the Brazilian strains (freshwater, wet soil and barks of trees). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were placed together in a very distinctive and highly supported clade. Thus, the set of characteristics of the strains resulted in the recognition of the new genus Ancylothrix Martins et Branco gen. nov. with two species [Ancylothrix rivularis gen. nov., sp. nov. (type species) and Ancylothrix terrestris sp. nov.], distinguishable by differences in genetic and ecological characteristics and described under the provisions of the International Code of Nomenclature for algae, fungi and plants. Secondary structures of D1-D1', box-B and V3 regions were conserved in A. rivularis gen. nov. sp. nov. and more variable in A. terrestris sp. nov.

Candida potacharoeniae sp. nov. and Candida spenceri sp. nov., two novel galactose-containing ascomycetous anamorphic yeast species isolated in Thailand.

PubMed

Nakase, Takashi; Jindamorakot, Sasitorn; Imanishi, Yumi; Am-In, Somjit; Ninomiya, Shinya; Kawasaki, Hiroko; Limtong, Savitree

2010-08-01

Fifteen strains of anamorphic yeasts isolated from various natural substrates collected in various places in Thailand were found to represent two novel species of anamorphic yeast genus Candida based on the sequence analysis of the D1/D2 domain of the large subunit rRNA genes, chemotaxonomic and conventional properties used for the classification of yeasts. These strains are located in the clade including Candida etchellsii and Candida magnoliae. Fourteen strains represented by ST-490(T) (BCC 15176(T)=NBRC 106439(T)= CBS 11674(T)) are closely related to Candida sorbosivorans in the D1/D2 sequences but 11 nucleotides (2.4%) were substituted. The remaining strain, ST-594(T) (=BCC 15278(T)=NBRC 106446(T)=CBS 11673(T)) showed a close relationship to Candida geochares but 21 nucleotides (4.7%) were substituted. Apparently, these strains represent two novel Candida species of the Starmerella clade. The two species are described as Candida potacharoeniae sp. nov. and Candida spenceri sp. nov. in the present paper. Like the most species of this clade, the two species contain galactose in the cells in addition to glucose and mannose and have high mol% G + C of 54.4-55.9 and 54.9, respectively.

Microbial Degradation of Chlorogenic Acid by a Sphingomonas sp. Strain.

PubMed

Ma, Yuping; Wang, Xiaoyu; Nie, Xueling; Zhang, Zhan; Yang, Zongcan; Nie, Cong; Tang, Hongzhi

2016-08-01

In order to elucidate the metabolism of chlorogenic acid by environmental microbes, a strain of Sphingomonas sp. isolated from tobacco leaves was cultured under various conditions, and chlorogenic acid degradation and its metabolites were investigated. The strain converting chlorogenic acid was newly isolated and identified as a Sphingomonas sp. strain by 16S rRNA sequencing. The optimal conditions for growth and chlorogenic acid degradation were 37 °C and pH 7.0 with supplementation of 1.5 g/l (NH4)2SO4 as the nitrogen source and 2 g/l chlorogenic acid as the sole carbon source. The maximum chlorogenic acid tolerating capability for the strain was 5 g/l. The main metabolites were identified as caffeic acid, shikimic acid, and 3,4-dihydroxybenzoic acid based on gas chromatography-mass spectrometry analysis. The analysis reveals the biotransformation mechanism of chlorogenic acid in microbial cells isolated from the environment.

Biodegradation analyses of trichloroethylene (TCE) by bacteria and its use for biosensing of TCE.

PubMed

Chee, Gab-Joo

2011-09-30

Trichloroethylene (TCE) is a toxic, recalcitrant groundwater pollutant. TCE-degrading microorganisms were isolated from various environments. The aerobic bacteria isolated from toluene- and tryptophan-containing media were Pseudomonas sp. strain ASA86 and Burkholderia sp. strain TAM17, respectively; these are necessary for inducing TCE biodegradation in a selective medium. The half-degradation time of TCE to a concentration of 1mg/L was 18 h for strain ASA86 and 7 days for strain TAM17. While identifying toluene/TCE degradation genes, we found that in strain ASA86, the gene was the same as the todC1 gene product encoding toluene dioxygenase identified in Pseudomonas putida F1, and that in strain TAM17, the gene was similar to the tecA1 gene product encoding chlorobenzene dioxygenase identified in Burkholderia sp. PS12. A novel TCE biosensor was developed using strain ASA86 as the inducer of toluene under aerobic conditions. The TCE biosensor exhibited a linear relationship below 3 ppm TCE. Detection limit of the biosensor was 0.05 ppm TCE. The response time of the biosensor was less than 10 min. The biosensor response displayed a constant level during a 2 day period. The TCE biosensor displayed sufficient sensitivity for monitoring TCE in environmental systems. Copyright © 2011 Elsevier B.V. All rights reserved.

Metabolic engineering of Synechocystis sp. PCC 6803 for enhanced ethanol production based on flux balance analysis.

PubMed

Yoshikawa, Katsunori; Toya, Yoshihiro; Shimizu, Hiroshi

2017-05-01

Synechocystis sp. PCC 6803 is an attractive host for bio-ethanol production due to its ability to directly convert atmospheric carbon dioxide into ethanol using photosystems. To enhance ethanol production in Synechocystis sp. PCC 6803, metabolic engineering was performed based on in silico simulations, using the genome-scale metabolic model. Comprehensive reaction knockout simulations by flux balance analysis predicted that the knockout of NAD(P)H dehydrogenase enhanced ethanol production under photoautotrophic conditions, where ammonium is the nitrogen source. This deletion inhibits the re-oxidation of NAD(P)H, which is generated by ferredoxin-NADP + reductase and imposes re-oxidation in the ethanol synthesis pathway. The effect of deleting the ndhF1 gene, which encodes NADH dehydrogenase subunit 5, on ethanol production was experimentally evaluated using ethanol-producing strains of Synechocystis sp. PCC 6803. The ethanol titer of the ethanol-producing ∆ndhF1 strain increased by 145%, compared with that of the control strain.

Identities of Microbacterium spp. Encountered in Human Clinical Specimens▿

PubMed Central

Gneiding, Kathrina; Frodl, Reinhard; Funke, Guido

2008-01-01

In the present study, 50 strains of yellow-pigmented gram-positive rods that had been isolated from human clinical specimens and collected over a 5-year period were further characterized by phenotypic and molecular genetic methods. All 50 strains belonged to the genus Microbacterium, and together they represented 18 different species. Microbacterium oxydans (n = 11), M. paraoxydans (n = 9), and M. foliorum (n = 7) represented more than half of the strains included in the present study. The isolation of strains belonging to M. hydrocarbonoxydans (n = 2), M. esteraromaticum (n = 1), M. oleivorans (n = 1), M. phyllosphaerae (n = 1), and M. thalassium (n = 1) from humans is reported for the first time. Microbacterium sp. strain VKM Ac-1389 (n = 1) and the previously uncultured Microbacterium sp. clone YJQ-29 (n = 1) probably represent new species. Comprehensive antimicrobial susceptibility data are given for the 50 Microbacterium isolates. This study is, so far, the largest on Microbacterium spp. encountered in human clinical specimens and outlines the heterogeneity of clinical Microbacterium strains. PMID:18799696

Simultaneous microalgal biomass production and CO2 fixation by cultivating Chlorella sp. GD with aquaculture wastewater and boiler flue gas.

PubMed

Kuo, Chiu-Mei; Jian, Jhong-Fu; Lin, Tsung-Hsien; Chang, Yu-Bin; Wan, Xin-Hua; Lai, Jinn-Tsyy; Chang, Jo-Shu; Lin, Chih-Sheng

2016-12-01

A microalgal strain, Chlorella sp. GD, cultivated in aquaculture wastewater (AW) aerated with boiler flue gas, was investigated. When AW from a grouper fish farm was supplemented with additional nutrients, the microalgal biomass productivity after 7days of culture was 0.794gL -1 d -1 . CO 2 fixation efficiencies of the microalgal strains aerated with 0.05, 0.1, 0.2, and 0.3vvm of boiler flue gas (containing approximately 8% CO 2 ) were 53, 51, 38, and 30%, respectively. When the microalgal strain was cultured with boiler flue gas in nutrient-added AW, biomass productivity increased to 0.892gL -1 d -1 . In semi-continuous cultures, average biomass productivities of the microalgal strain in 2-day, 3-day, and 4-day replacement cultures were 1.296, 0.985, and 0.944gL -1 d -1 , respectively. These results demonstrate the potential of using Chlorella sp. GD cultivations in AW aerated with boiler flue gas for reusing water resources, reducing CO 2 emission, and producing microalgal biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

Immunogenicity of adenovirus vaccines expressing the PCV2 capsid protein in pigs.

PubMed

Li, Delong; Du, Qian; Wu, Bin; Li, Juejun; Chang, Lingling; Zhao, Xiaomin; Huang, Yong; Tong, Dewen

2017-08-24

Porcine circovirus type 2 (PCV2) is the main pathogen of porcine circovirus associated disease (PCVAD), causing great economic losses in pig industry. In previous study, we constructed adenovirus vector vaccines expressing PCV2 Cap either modified with Intron A and WPRE, or CD40L and GMCSF, and evaluated all of these vaccines in mice and in pigs. Although Ad-A-C-W and Ad-CD40L-Cap-GMCSF could induce stronger immune responses than Ad-Cap, neither of them was better than commercial inactivated vaccine PCV2 SH-strain. In this study, secretory recombinant adenoviruses (Ad-A-spCap-W and Ad-A-spCD40L-spCap-spGMCSF-W) and non-secretory recombinant adenovirus Ad-A-CD40L-Cap-GMCSF-W were constructed, and identified by western blot and confocal laser microscope observation. The results of ELISA and VN showed that humoral immune responses induced by Ad-A-spCap-W and Ad-A-CD40L-Cap-GMCSF-W were not significantly different from SH-strain, but Ad-A-spCD40L-spCap-spGMCSF-W could induce significantly higher humoral immune response than SH-strain. Lymphocytes proliferative and cytokines releasing levels of Ad-A-spCap-W and Ad-A-CD40L-Cap-GMCSF-W were not significantly different from SH-strain, but Ad-A-spCD40L-spCap-spGMCSF-W was significantly higher than SH-strain. PCV2-challenge experiment showed that virus loads were significantly reduced in Ad-A-spCD40L-spCap-spGMCSF-W vaccinated group, and no obviously clinical and microscopic lesions were observed in Ad-A-spCD40L-spCap-spGMCSF-W vaccinated group. Altogether, these results demonstrate that recombinant adenovirus vaccine Ad-A-spCD40L-spCap-spGMCSF-W induces stronger immune responses and provides better protection than commercial inactivated vaccine PCV2 SH-strain, and suggest that Ad-A-spCD40L-spCap-spGMCSF-W could be a potential vaccine candidate against PCVAD. Copyright © 2017 Elsevier Ltd. All rights reserved.

Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex.

PubMed

Maggini, Valentina; Presta, Luana; Miceli, Elisangela; Fondi, Marco; Bosi, Emanuele; Chiellini, Carolina; Fagorzi, Camilla; Bogani, Patrizia; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Firenzuoli, Fabio; Perrin, Elena; Fani, Renato

2017-05-18

In this announcement, we detail the draft genome sequence of the Pseudomonas sp. strain Ep R1, isolated from the roots of the medicinal plant Echinacea purpurea The elucidation of this genome sequence may allow the identification of genes associated with the production of antimicrobial compounds. Copyright © 2017 Maggini et al.

Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex

PubMed Central

Maggini, Valentina; Presta, Luana; Miceli, Elisangela; Fondi, Marco; Bosi, Emanuele; Chiellini, Carolina; Fagorzi, Camilla; Bogani, Patrizia; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Firenzuoli, Fabio; Perrin, Elena

2017-01-01

ABSTRACT In this announcement, we detail the draft genome sequence of the Pseudomonas sp. strain Ep R1, isolated from the roots of the medicinal plant Echinacea purpurea. The elucidation of this genome sequence may allow the identification of genes associated with the production of antimicrobial compounds. PMID:28522712

A Trichodorus (Triplonchida: Trichodoridae) nematode from thrips (Thysanoptera: Panchaetothripinae)

USDA-ARS?s Scientific Manuscript database

A thrips insect Caliothrips sp. (Thysanoptera: Panchaetothripinae) from persimmon fruit (Ebenaceae: Diospyros sp.) from an unknown origin, possibly Asia, was intercepted in a passenger bag in November 2012 at the Peace Arch Border Crossing from Surrey, British Columbia to Blaine, Washington by an AP...

Biosynthesis of Polyhydroxyalkanoate from Steamed Soybean Wastewater by a Recombinant Strain of Pseudomonas sp. 61-3.

PubMed

Hokamura, Ayaka; Yunoue, Yuko; Goto, Saki; Matsusaki, Hiromi

2017-08-08

Pseudomonas sp. 61-3 accumulates a blend of poly(3-hydroxybutyrate) [P(3HB)] homopolymer and a random copolymer, poly(3-hydroxybutyrate- co -3-hydroxyalkanoate) [P(3HB- co -3HA)], consisting of 3HA units of 4-12 carbon atoms. Pseudomonas sp. 61-3 possesses two types of PHA synthases, PHB synthase (PhbC) and PHA synthases (PhaC1 and PhaC2), encoded by the phb and pha loci, respectively. The P(94 mol% 3HB- co -6 mol% 3HA) copolymer synthesized by the recombinant strain of Pseudomonas sp. 61-3 ( phbC :: tet ) harboring additional copies of phaC1 gene is known to have desirable physical properties and to be a flexible material with moderate toughness, similar to low-density polyethylene. In this study, we focused on the production of the P(3HB- co -3HA) copolymer using steamed soybean wastewater, a by-product in brewing miso , which is a traditional Japanese seasoning. The steamed soybean wastewater was spray-dried to produce a powder (SWP) and used as the sole nitrogen source for the synthesis of P(3HB- co -3HA) by the Pseudomonas sp. 61-3 recombinant strain. Hydrolyzed SWP (HSWP) was also used as a carbon and nitrogen source. P(3HB- co -3HA)s with relatively high 3HB fractions could be synthesized by a recombinant strain of Pseudomonas sp. 61-3 ( phbC :: tet ) harboring additional copies of the phaC1 gene in the presence of 2% glucose and 10-20 g/L SWP as the sole nitrogen source, producing a PHA concentration of 1.0-1.4 g/L. When HSWP was added to a nitrogen- and carbon-free medium, the recombinant strain could synthesize PHA without glucose as a carbon source. The recombinant strain accumulated 32 wt% P(3HB- co -3HA) containing 80 mol% 3HB and 20 mol% medium-chain-length 3HA with a PHA concentration of 1.0 g/L when 50 g/L of HSWP was used. The PHA production yield was estimated as 20 mg-PHA/g-HSWP, which equates to approximately 1.0 g-PHA per liter of soybean wastewater.

Biosynthesis of Polyhydroxyalkanoate from Steamed Soybean Wastewater by a Recombinant Strain of Pseudomonas sp. 61-3

PubMed Central

Hokamura, Ayaka; Yunoue, Yuko; Goto, Saki; Matsusaki, Hiromi

2017-01-01

Pseudomonas sp. 61-3 accumulates a blend of poly(3-hydroxybutyrate) [P(3HB)] homopolymer and a random copolymer, poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [P(3HB-co-3HA)], consisting of 3HA units of 4–12 carbon atoms. Pseudomonas sp. 61-3 possesses two types of PHA synthases, PHB synthase (PhbC) and PHA synthases (PhaC1 and PhaC2), encoded by the phb and pha loci, respectively. The P(94 mol% 3HB-co-6 mol% 3HA) copolymer synthesized by the recombinant strain of Pseudomonas sp. 61-3 (phbC::tet) harboring additional copies of phaC1 gene is known to have desirable physical properties and to be a flexible material with moderate toughness, similar to low-density polyethylene. In this study, we focused on the production of the P(3HB-co-3HA) copolymer using steamed soybean wastewater, a by-product in brewing miso, which is a traditional Japanese seasoning. The steamed soybean wastewater was spray-dried to produce a powder (SWP) and used as the sole nitrogen source for the synthesis of P(3HB-co-3HA) by the Pseudomonas sp. 61-3 recombinant strain. Hydrolyzed SWP (HSWP) was also used as a carbon and nitrogen source. P(3HB-co-3HA)s with relatively high 3HB fractions could be synthesized by a recombinant strain of Pseudomonas sp. 61-3 (phbC::tet) harboring additional copies of the phaC1 gene in the presence of 2% glucose and 10–20 g/L SWP as the sole nitrogen source, producing a PHA concentration of 1.0–1.4 g/L. When HSWP was added to a nitrogen- and carbon-free medium, the recombinant strain could synthesize PHA without glucose as a carbon source. The recombinant strain accumulated 32 wt% P(3HB-co-3HA) containing 80 mol% 3HB and 20 mol% medium-chain-length 3HA with a PHA concentration of 1.0 g/L when 50 g/L of HSWP was used. The PHA production yield was estimated as 20 mg-PHA/g-HSWP, which equates to approximately 1.0 g-PHA per liter of soybean wastewater. PMID:28952548

The heterocyclic ring fission and dehydroxylation of catechins and related compounds by Eubacterium sp. strain SDG-2, a human intestinal bacterium.

PubMed

Wang, L Q; Meselhy, M R; Li, Y; Nakamura, N; Min, B S; Qin, G W; Hattori, M

2001-12-01

A human intestinal bacterium, Eubacterium (E.) sp. strain SDG-2, was tested for its ability to metabolize various (3R)- and (3S)-flavan-3-ols and their 3-O-gallates. This bacterium cleaved the C-ring of (3R)- and (3S)-flavan-3-ols to give 1,3-diphenylpropan-2-ol derivatives, but not their 3-O-gallates. Furthermore, E. sp. strain SDG-2 had the ability of p-dehydroxylation in the B-ring of (3R)-flavan-3-ols, such as (-)-catechin, (-)-epicatechin, (-)-gallocatechin and (-)-epigallocatechin, but not of (3S)-flavan-3-ols, such as (+)-catechin and (+)-epicatechin.

Screening of Microorganisms Producing Cold-Active Oxidoreductases to Be Applied in Enantioselective Alcohol Oxidation. An Antarctic Survey

PubMed Central

Araújo, Lidiane S.; Kagohara, Edna; Garcia, Thaís P.; Pellizari, Vivian H.; Andrade, Leandro H.

2011-01-01

Several microorganisms were isolated from soil/sediment samples of Antarctic Peninsula. The enrichment technique using (RS)-1-(phenyl)ethanol as a carbon source allowed us to isolate 232 psychrophile/psychrotroph microorganisms. We also evaluated the enzyme activity (oxidoreductases) for enantioselective oxidation reactions, by using derivatives of (RS)-1-(phenyl)ethanol as substrates. Among the studied microorganisms, 15 psychrophile/psychrotroph strains contain oxidoreductases that catalyze the (S)-enantiomer oxidation from racemic alcohols to their corresponding ketones. Among the identified microorganisms, Flavobacterium sp. and Arthrobacter sp. showed excellent enzymatic activity. These new bacteria strains were selected for optimization study, in which the (RS)-1-(4-methyl-phenyl)ethanol oxidation was evaluated in several reaction conditions. From these studies, it was observed that Flavobacterium sp. has an excellent enzymatic activity at 10 °C and Arthrobacter sp. at 15 and 25 °C. We have also determined the growth curves of these bacteria, and both strains showed optimum growth at 25 °C, indicating that these bacteria are psychrotroph. PMID:21673897

Wickerhamiella pagnoccae sp. nov. and Candida tocantinsensis sp. nov., two ascomycetous yeasts from flower bracts of Heliconia psittacorum (Heliconiaceae).

PubMed

Barbosa, Anne C; Morais, Camila G; Morais, Paula B; Rosa, Luiz H; Pimenta, Raphael S; Lachance, Marc-André; Rosa, Carlos A

2012-02-01

Two novel yeast species were isolated from nectar of flower bracts of Heliconia psittacorum (Heliconiaceae) collected in a Cerrado ecosystem in the state of Tocantins, northern Brazil. Wickerhamiella pagnoccae sp. nov., which is closely related to Candida jalapaonensis, is heterothallic and produces one spheroid ascospore per ascus. Candida tocantinsensis sp. nov. belongs to the Metschnikowiaceae clade and its nearest relative is Candida ubatubensis, but the sequence identity (%) in the D1/D2 domains of the rRNA gene is low. The type strain of W. pagnoccae is UFMG-F18C1(T) ( = CBS 12178(T) = NRRL Y-48735(T)) and the type strain of C. tocantinsensis is UFMG-F16D1(T) ( = CBS 12177(T) = NRRL Y-48734(T)).

Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan.

PubMed

Yuliana, Tri; Nakajima, Nobuyoshi; Yamamura, Shigeki; Tomita, Masaru; Suzuki, Haruo; Amachi, Seigo

2017-01-01

Roseovarius sp. A-2 is a heterotrophic iodide (I - )-oxidizing bacterium isolated from iodide-rich natural gas brine water in Chiba, Japan. This strain oxidizes iodide to molecular iodine (I 2 ) by means of an extracellular multicopper oxidase. Here we report the draft genome sequence of strain A-2. The draft genome contained 46 tRNA genes, 1 copy of a 16S-23S-5S rRNA operon, and 4,514 protein coding DNA sequences, of which 1,207 (27%) were hypothetical proteins. The genome contained a gene encoding IoxA, a multicopper oxidase previously found to catalyze the oxidation of iodide in Iodidimonas sp. Q-1. This draft genome provides detailed insights into the metabolism and potential application of Roseovarius sp. A-2.

Improvement of the Uranium Sequestration Ability of a Chlamydomonas sp. (ChlSP Strain) Isolated From Extreme Uranium Mine Tailings Through Selection for Potential Bioremediation Application.

PubMed

Baselga-Cervera, Beatriz; Romero-López, Julia; García-Balboa, Camino; Costas, Eduardo; López-Rodas, Victoria

2018-01-01

The extraction and processing of uranium (U) have polluted large areas worldwide, rendering anthropogenic extreme environments inhospitable to most species. Noticeably, these sites are of great interest for taxonomical and applied bioprospection of extremotolerant species successfully adapted to U tailings contamination. As an example, in this work we have studied a microalgae species that inhabits extreme U tailings ponds at the Saelices mining site (Salamanca, Spain), characterized as acidic (pH between 3 and 4), radioactive (around 4 μSv h -1 ) and contaminated with metals, mainly U (from 25 to 48 mg L -1 ) and zinc (from 17 to 87 mg L -1 ). After isolation of the extremotolerant ChlSP strain, morphological characterization and internal transcribed spacer (ITS)-5.8S gene sequences placed it in the Chlamydomonadaceae , but BLAST analyses identity values, against the nucleotide datasets at the NCBI database, were very low (<92%). We subjected the ChlSP strain to an artificial selection protocol to increase the U uptake and investigated its response to selection. The ancestral strain ChlSP showed a U-uptake capacity of ≈4.30 mg U g -1 of dry biomass (DB). However, the artificially selected strain ChlSG was able to take up a total of ≈6.34 mg U g -1 DB, close to the theoretical maximum response (≈7.9 mg U g -1 DB). The selected ChlSG strain showed two possible U-uptake mechanisms: the greatest proportion by biosorption onto cell walls (ca. 90%), and only a very small quantity, ~0.46 mg g -1 DB, irreversibly bound by bioaccumulation. Additionally, the kinetics of the U-uptake process were characterized during a microalgae growth curve; ChlSG cells removed close to 4 mg L -1 of U in 24 days. These findings open up promising prospects for sustainable management of U tailings waters based on newly evolved extremotolerants and outline the potential of artificial selection in the improvement of desired features in microalgae by experimental adaptation and selection.

Improvement of the Uranium Sequestration Ability of a Chlamydomonas sp. (ChlSP Strain) Isolated From Extreme Uranium Mine Tailings Through Selection for Potential Bioremediation Application

PubMed Central

Baselga-Cervera, Beatriz; Romero-López, Julia; García-Balboa, Camino; Costas, Eduardo; López-Rodas, Victoria

2018-01-01

The extraction and processing of uranium (U) have polluted large areas worldwide, rendering anthropogenic extreme environments inhospitable to most species. Noticeably, these sites are of great interest for taxonomical and applied bioprospection of extremotolerant species successfully adapted to U tailings contamination. As an example, in this work we have studied a microalgae species that inhabits extreme U tailings ponds at the Saelices mining site (Salamanca, Spain), characterized as acidic (pH between 3 and 4), radioactive (around 4 μSv h−1) and contaminated with metals, mainly U (from 25 to 48 mg L−1) and zinc (from 17 to 87 mg L−1). After isolation of the extremotolerant ChlSP strain, morphological characterization and internal transcribed spacer (ITS)-5.8S gene sequences placed it in the Chlamydomonadaceae, but BLAST analyses identity values, against the nucleotide datasets at the NCBI database, were very low (<92%). We subjected the ChlSP strain to an artificial selection protocol to increase the U uptake and investigated its response to selection. The ancestral strain ChlSP showed a U-uptake capacity of ≈4.30 mg U g−1 of dry biomass (DB). However, the artificially selected strain ChlSG was able to take up a total of ≈6.34 mg U g−1 DB, close to the theoretical maximum response (≈7.9 mg U g−1 DB). The selected ChlSG strain showed two possible U-uptake mechanisms: the greatest proportion by biosorption onto cell walls (ca. 90%), and only a very small quantity, ~0.46 mg g−1 DB, irreversibly bound by bioaccumulation. Additionally, the kinetics of the U-uptake process were characterized during a microalgae growth curve; ChlSG cells removed close to 4 mg L−1 of U in 24 days. These findings open up promising prospects for sustainable management of U tailings waters based on newly evolved extremotolerants and outline the potential of artificial selection in the improvement of desired features in microalgae by experimental adaptation and selection. PMID:29662476

Biotransformation of ginsenoside Rb1 to ginsenoside Rg3 by endophytic bacterium Burkholderia sp. GE 17-7 isolated from Panax ginseng.

PubMed

Fu, Y; Yin, Z-H; Yin, C-Y

2017-06-01

To isolate a novel endophytic bacterium from Panax ginseng that could have excellent properties in converting ginsenoside Rb1 to ginsenoside Rg3. Based on a 16S rDNA gene sequence, the strain named GE 17-7 was identified as Burkholderia sp. This strain has shown the highest activity in converting ginsenoside Rb1 to 20(S)-ginsenoside Rg3. During the biotransformation of ginsenoside Rb1, the final metabolite was identified by nuclear magnetic resonance analysis and the transformation pathway of ginsenoside Rb1 was also identified by thin-layer chromatography and high performance liquid chromatography analysis in this study. We have successfully isolated a β-glucosidase-producing endophytic bacterium GE 17-7 from P. ginseng. Ginsenoside Rg3 was produced by strain GE 17-7 from ginsenoside Rb1 via ginsenoside Rd. This is the first report of the conversion of major ginsenoside Rb1 into minor ginsenoside Rg3 by fermentation with Burkholderia sp. endophytic bacteria in P. ginseng. These results suggest a new preparation method for ginsenoside Rg3 using strain GE 17-7 in the pharmaceutical industry. © 2017 The Society for Applied Microbiology.

Spiribacter roseus sp. nov., a moderately halophilic species of the genus Spiribacter from salterns.

PubMed

León, María José; Vera-Gargallo, Blanca; Sánchez-Porro, Cristina; Ventosa, Antonio

2016-10-01

Four pink-pigmented, non-motile, Gram-staining-negative and moderately halophilic curved rods, designated strains SSL50T, SSL25, SSL97 and SSL4, were isolated from a saltern located in Isla Cristina, Huelva, south-west Spain. Phylogenetic analyses based on 16S rRNA gene sequences showed that they were members of the genus Spiribacter, most closely related to Spiribacter curvatus UAH-SP71T (99.3-99.5 % sequence similarity) and Spiribacter salinus M19-40T (96.5-96.7 %). Other related strains were Alkalilimnicola ehrlichii MLHE-1T (95.1-95.3 %), Arhodomonas recens RS91T (95.1-95.2 %) and Arhodomonas aquaeolei ATCC 49307T (95.0-95.1 %), all members of the family Ectothiorhodospiraceae. The major fatty acids were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0 and C12 : 0. The DNA G+C range was 64.0-66.3 mol%. The DNA-DNA hybridization values between strains SSL50T, SSL25, SSL97, SSL4 and S. piribacter. curvatus UAH-SP71T were 37-49 %. The average nucleotide identity (ANIb) values between the genome of strain SSL50T and those of the two other representatives of the genus Spiribacter, S. curvatus UAH-SP71T and S. salinus M19-40T, were 82.4 % and 79.1 %, respectively, supporting the proposal of a novel species of the genus Spiribacter. On the basis of the polyphasic analysis, the four new isolates are considered to represent a novel species of the genus Spiribacter, for which the name Spiribacter roseus sp. nov. is proposed. The type strain is SSL50T (=CECT 9117T=IBRC-M 11076T).

Immunolocalization of Substance P and NK-1 Receptor in ADIPOSE Stem Cells.

PubMed

Muñoz, Miguel; Muñoz, Mario F; Ayala, Antonio

2017-12-01

Substance P (SP) is a neuropeptide belonging to the thachykinin peptide family. SP, after binding to its receptor, the neurokinin 1 receptor (NK1R), controls several transcription factors such as NF-κB, hypoxia inducible factor (HIF-1α), c-myc, c-fos, c-jun, and AP-1. SP and NK1R have a widespread distribution in both the central and peripheral nervous systems. They are also present in cells not belonging to the nervous system (immune cells, placenta, etc.). SP is located in all body fluids, that is, blood, cerebrospinal fluid, etc., making it ubiquitous throughout the human body. SP and NK1R genes are expressed in the stem cell line TF-1 and in primary stem cells derived from human placental cord blood. However, to our knowledge, the presence of SP and the NK1R receptor in adipose stem cells (ADSC) is unknown. We demonstrated by immunofluorescence the localization of SP and NK1R in human and rat ADSC. SP and NK1R are located in both the cytoplasm and the nucleus of these cells. The NK1R is higher in the nucleus than in the cytoplasm of ADSCs. By Western blot we demonstrated the presence of different isoforms of NK1R that have different subcellular locations in the ADSC. SP induces proliferation and mitogenesis through NK1R in ADSCs. These findings reported here for the first time suggest an important role for a SP/NK1R system, either as genetic and/or epigenetic factor, in both the cytoplasm and nucleus functions of the ADSCs. J. Cell. Biochem. 118: 4686-4696, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity.

PubMed

Yang, Shanjun; Yu, Mingjia; Chen, Jianming

Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Enantioselective biodegradation of the pyrethroid (±)-lambda-cyhalothrin by marine-derived fungi.

PubMed

Birolli, Willian G; Vacondio, Bruna; Alvarenga, Natália; Seleghim, Mirna H R; Porto, André L M

2018-04-01

The contamination of agricultural lands by pesticides is a serious environmental issue. Consequently, the development of bioremediation methods for different active ingredients, such as pyrethroids, is essential. In this study, the enantioselective biodegradation of (±)-lambda-cyhalothrin ((±)-LC) by marine-derived fungi was studied. Experiments were performed with different fungi strains (Aspergillus sp. CBMAI 1829, Acremonium sp. CBMAI 1676, Microsphaeropsis sp. CBMAI 1675 and Westerdykella sp. CBMAI 1679) in 3% malt liquid medium with 100 mg L -1 of (±)-LC. All strains biodegraded this insecticide and the residual concentrations of (±)-LC (79.2-55.2 mg L -1 , i.e., 20.8-44.8% biodegradation), their enantiomeric excesses (2-42% ee) and the 3-phenoxybenzoic acid (PBAc) concentrations (0.0-4.1 mg L -1 ) were determined. In experiments for 28 days of biodegradation in the absence and presence of artificial seawater (ASW) with the most efficient strain Aspergillus sp. CBMAI 1829, increasing concentrations of PBAc with (0.0-4.8 mg L -1 ) and without ASW (0.0-15.3 mg L -1 ) were observed. In addition, a partial biodegradation pathway was proposed. All the evaluated strains biodegraded preferentially the (1R,3R,αS)-gamma-cyhalothrin enantiomer. Therefore, marine-derived fungi enantioselectively biodegraded (±)-LC and can be applied in future studies for bioremediation of contaminated areas. This enantioselective biodegradation indicates that the employment of the most active enantiomer GC as insecticide not only enable the use of a lower amount of pesticide, but also a more easily biodegradable product, reducing the possibility of environmental contamination. Copyright © 2018 Elsevier Ltd. All rights reserved.

Transformation of Dibenzo-p-Dioxin by Pseudomonas sp. Strain HH69

PubMed Central

Harms, Hauke; Wittich, Rolf-Michael; Sinnwell, Volker; Meyer, Holger; Fortnagel, Peter; Francke, Wittko

1990-01-01

Dibenzo-p-dioxin was oxidatively cleaved by the dibenzofuran-degrading bacterium Pseudomonas sp. strain HH69 to produce minor amounts of 1-hydroxydibenzo-p-dioxin and catechol, while a 2-phenoxy derivative of muconic acid was formed as the major product. Upon acidic methylation, the latter yielded the dimethylester of cis, trans-2-(2-hydroxyphenoxy)-muconic acid. PMID:16348160

Thermostable hemicellulases of a bacterium, Geobacillus sp. DC3, isolated from the former Homestake Gold Mine in Lead, South Dakota

USDA-ARS?s Scientific Manuscript database

A thermophilic strain, Geobacillus sp. DC3, capable of producing hemicellulolytic enzymes was isolated from the 1.5-km depth of the former Homestake gold mine in Lead, South Dakota. The DC3 strain expressed a high level of extracellular endoxylanase at 39.5 U/mg protein with additional hemicellulase...

Antibacterial synergic effect of honey from two stingless bees: Scaptotrigona bipunctata Lepeletier, 1836, and S. postica Latreille, 1807

NASA Astrophysics Data System (ADS)

Nishio, E. K.; Ribeiro, J. M.; Oliveira, A. G.; Andrade, C. G. T. J.; Proni, E. A.; Kobayashi, R. K. T.; Nakazato, G.

2016-02-01

Several studies have tested antimicrobial activity of combinations of honey and various substances. In this study, we tested a combination of two stingless bee honeys against various bacterial strains. In particular: the antibacterial activity of honeys produced by Scaptotrigona bipunctata (SB) and Scaptotrigona postica (SP) was evaluated against Gram-positive and Gram-negative bacterial strains by agar well diffusion assays, minimum inhibitory concentration (MIC) assessment, construction of growth and viability curves and scanning electron microscopy (SEM). The interaction of the two honeys was also evaluated by the checkerboard assay. Inhibition zones ranged from 8 to 22 mm. The MIC values of the individual honeys ranged from 0.62 to 10% (v v-1) and decreased to 1/4 to 1/32 when the honeys were combined. SEM images showed division inhibition and cell wall disruption for the SB and SP honeys, respectively, and these alterations were observed in same field when the SB and SP honeys were combined. This study demonstrated that the natural honeys possess in vitro antimicrobial activity against Gram-positive and Gram-negative bacteria, including multidrug-resistant strains. Combination of the SB and SP honeys could lead to the development of new broad-spectrum antimicrobials that have the potential to prevent the emergence of resistant bacterial strains.

Antibacterial synergic effect of honey from two stingless bees: Scaptotrigona bipunctata Lepeletier, 1836, and S. postica Latreille, 1807

PubMed Central

Nishio, E. K.; Ribeiro, J. M.; Oliveira, A. G.; Andrade, C. G. T. J.; Proni, E. A.; Kobayashi, R. K. T.; Nakazato, G.

2016-01-01

Several studies have tested antimicrobial activity of combinations of honey and various substances. In this study, we tested a combination of two stingless bee honeys against various bacterial strains. In particular: the antibacterial activity of honeys produced by Scaptotrigona bipunctata (SB) and Scaptotrigona postica (SP) was evaluated against Gram-positive and Gram-negative bacterial strains by agar well diffusion assays, minimum inhibitory concentration (MIC) assessment, construction of growth and viability curves and scanning electron microscopy (SEM). The interaction of the two honeys was also evaluated by the checkerboard assay. Inhibition zones ranged from 8 to 22 mm. The MIC values of the individual honeys ranged from 0.62 to 10% (v v−1) and decreased to 1/4 to 1/32 when the honeys were combined. SEM images showed division inhibition and cell wall disruption for the SB and SP honeys, respectively, and these alterations were observed in same field when the SB and SP honeys were combined. This study demonstrated that the natural honeys possess in vitro antimicrobial activity against Gram-positive and Gram-negative bacteria, including multidrug-resistant strains. Combination of the SB and SP honeys could lead to the development of new broad-spectrum antimicrobials that have the potential to prevent the emergence of resistant bacterial strains. PMID:26869239

The Marine Fungi Rhodotorula sp. (Strain CNYC4007) as a Potential Feed Source for Fish Larvae Nutrition

PubMed Central

Barra, M.; Llanos-Rivera, A.; Cruzat, F.; Pino-Maureira, N.; González-Saldía, R. R.

2017-01-01

Fish oil is used in the production of feed for cultured fish owing to its high polyunsaturated fatty acid content (PUFA). The over-exploitation of fisheries and events like “El Niño” are reducing the fish oil supply. Some marine microorganisms are considered potentially as alternative fatty acid sources. This study assesses a strain of Rhodotorula sp. (strain CNYC4007; 27% docosahexaenoic acid (DHA) of total fatty acids), as feed for fish larvae. The total length and ribonucleic acid (RNA)/deoxyribonucleic acid (DNA) ratio of Danio rerio larvae was determined at first feeding at six and 12 days old (post-yolk absorption larvae). Larvae fed with microencapsulated Rhodotorula sp. CNYC4007 had a significantly higher RNA/DNA ratio than control group (C1). At six days post-yolk absorption group, the RNA/DNA ratio of larvae fed with Rhodotorula sp. bioencapsulated in Brachionus sp. was significantly higher than control group fed with a commercial diet high in DHA (C2-DHA). Finally, at 12 days post-yolk absorption, the RNA/DNA ratio was significantly higher in larvae fed with Rhodotorula sp. CNYC4007 and C2-DHA (both bioencapsulated in Artemia sp. nauplii) than in control group (C1). These results suggest that Rhodotorula sp. CNYC4007 can be an alternative source of DHA for feeding fish at larval stage, providing a sustainable source of fatty acids. PMID:29194350

Proposal of Henriciella barbarensis sp. nov. and Henriciella algicola sp. nov., stalked species of the genus and emendation of the genus Henriciella.

PubMed

Abraham, Wolf-Rainer; de Carvalho, Maira Peres; da Costa Neves, Thais Souto Paula; Memoria, Marina Torquato; Tartuci, Iago Toledo; Vancanneyt, Marc; Smit, John; Rohde, Manfred

2017-08-01

Two Gram-negative, heterotrophic, aerobic, prosthecated, marine bacteria, designated strains MCS23T and MCS27T, were isolated from seawater samples. NaCl was required for growth. The major polar lipid detected in strain MCS27T was phosphatidylglycerol, whereas those detected in MCS23T were phosphatidylglycerol, sulfoquinovosyl diacylglycerol and 1,2-diacyl-3-α-d-glucuronopyranosyl-sn-glycerol taurineamide. The most abundant cellular fatty acids were C18 : 1ω7 and C16 : 0, hydroxyl-fatty acids were 3-OH C12 : 0 in both strains and 3-OH C11 : 0 in MCS23T. Strains MCS23T and MCS27T had DNA G+C contents of 57.0 and 55.0 mol%, respectively. The two strains shared 99.3 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Henriciella were 99.4-97.8 % but DNA-DNA hybridizations were 53 % or lower. Besides their 16S rRNA gene sequences, the novel strains can be differentiated from other species of the genus Henriciella by cell morphology, lipid and fatty acid patterns and enzyme activities. The data obtained led to the identification of two novel species, for which the names Henriciella barbarensis sp. nov. (type strain MCS23T=LMG 28705T=CCUG 66934T) and Henriciella algicola sp. nov. (type strain MCS27T=LMG 29152T=CCUG 67844T) are proposed. As these two novel species are the first prosthecate species in the genus Henriciella, an emended genus description is also provided.

Streptosporangium sonchi sp. nov. and Streptosporangium kronopolitis sp. nov., two novel actinobacteria isolated from a root of common sowthistle (Sonchus oleraceus L.) and a millipede (Kronopolites svenhedind Verhoeff).

PubMed

Ma, Zhaoxu; Liu, Hui; Liu, Chongxi; He, Hairong; Zhao, Junwei; Wang, Xin; Li, Jiansong; Wang, Xiangjing; Xiang, Wensheng

2015-06-01

Two novel actinobacteria, designated strains NEAU-QS7(T) and NEAU-ML10(T), were isolated from a root of Sonchus oleraceus L. and a Kronopolites svenhedind Verhoeff specimen, respectively, collected from Wuchang, Heilongjiang Province, China. A polyphasic study was carried out to establish the taxonomic positions of these strains. The two strains were observed to form abundant aerial hyphae that differentiated into spherical spore vesicles. The phylogenetic analysis based on the 16S rRNA gene sequences of strains NEAU-QS7(T) and NEAU-ML10(T) showed that the two novel isolates exhibited 99.7 % 16S rRNA gene sequence similarity with each other and that they are most closely related to Streptosporangium shengliense NEAU-GH7(T) (99.1, 99.0 %) and Streptosporangium longisporum DSM 43180(T) (99.1, 99.0 %). However, the DNA-DNA hybridization value between strains NEAU-QS7(T) and NEAU-ML10(T) was 46.5 %, and the values between the two strains and their closest phylogenetic relatives were also below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, the two strains can be distinguished from each other and their closest phylogenetic relatives. Thus, strains NEAU-QS7(T) and NEAU-ML10(T) represent two novel species of the genus Streptosporangium, for which the names Streptosporangium sonchi sp. nov. and Streptosporangium kronopolitis sp. nov. are proposed. The type strains are NEAU-QS7(T) (=CGMCC 4.7142(T) =DSM 46717(T)) and NEAU-ML10(T) (=CGMCC 4.7153(T) =DSM 46720(T)), respectively.

Comparative evaluation of Amblyomma ovale ticks infected and noninfected by Rickettsia sp. strain Atlantic rainforest, the agent of an emerging rickettsiosis in Brazil.

PubMed

Krawczak, Felipe S; Agostinho, Washington C; Polo, Gina; Moraes-Filho, Jonas; Labruna, Marcelo B

2016-04-01

In 2010, a novel spotted fever group rickettsiosis was reported in the Atlantic rainforest coast of Brazil. The etiological agent was identified as Rickettsia sp. strain Atlantic rainforest, and the tick Amblyomma ovale was incriminated as the presumed vector. The present study evaluated under laboratory conditions four colonies of A. ovale: two started from engorged females that were naturally infected by Rickettsia sp. strain Atlantic rainforest (designated as infected groups); the two others started from noninfected females (designated as control groups). All colonies were reared in parallel from F0 engorged female to F2 unfed nymphs. Tick-naïve vesper mice (Calomys callosus) or domestic rabbits were used for feeding of each tick stage. Rickettsia sp. strain Atlantic rainforest was preserved by transstadial maintenance and transovarial transmission in A. ovale ticks for at least 2 generations (from F0 females to F2 nymphs), because nearly 100% of the tested larvae, nymphs, and adults from the infected groups were shown by PCR to contain rickettsial DNA. All vesper mice and rabbits infested by larvae and nymphs, and 50% of the rabbits infested by adults from the infected groups seroconverted, indicating that these tick stages were vector competent for Rickettsia sp. strain Atlantic rainforest. Expressive differences in mortality rates and reproductive performance were observed between engorged females from the infected and control groups, as indicated by 75.0% and 97.1% oviposition success, respectively, and significantly lower egg mass weight, conversion efficiency index, and percentage of egg hatching for the infected groups. Our results indicate that A. ovale can act as a natural reservoir for Rickettsia sp. strain Atlantic rainforest. However, due to deleterious effect caused by this rickettsial agent on engorged females, amplifier vertebrate hosts might be necessary for persistent perpetuation of Rickettsia sp. strain Atlantic rainforest in A. ovale under natural conditions. Copyright © 2016 Elsevier GmbH. All rights reserved.

A Bacillus sp. strain with antagonistic activity against Fusarium graminearum kills Microcystis aeruginosa selectively.

PubMed

Xuan, Huanling; Dai, Xianzhu; Li, Jing; Zhang, Xiaohui; Yang, Caiyun; Luo, Feng

2017-04-01

Cyanobacterial harmful algal blooms (CyanoHABs) cause severe environmental problems, economic losses and threaten human health seriously. In the present study, a Bacillus sp. strain, designated as AF-1, with strong antagonistic activity against plant pathogenic fungus Fusarium graminearum was isolated from purple soil. Bacillus sp. AF-1 selectively killed Microcystis aeruginosa at low cell density (1.6×10 3 cfu/mL), and showed the strongest bactericidal activity against M. aeruginosa NIES-843 (A e =93%, t=6d). The algicidal substances originated from strain AF-1 were stable in the temperature range of 35-100°C, and pH range of 3-11. Cell-free filtrate of AF-1 culture caused excessive accumulation of intracellular reactive oxygen species (ROS), cell death and the efflux of intracellular components of M. aeruginosa NIES-843 cells. The expression of genes recA, psbA1, psbD1, rbcL and mcyB, involved in DNA repair, photosynthesis and microcystin synthesis of NIES 843, were significantly influenced by the cell-free filtrate of AF-1 culture. Bacillus sp. AF-1 has the potential to be developed as a bifunctional biocontrol agent to control CyanoHABs and F. graminearum caused plant disease. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacillus beijingensis sp. nov. and Bacillus ginsengi sp. nov., isolated from ginseng root.

PubMed

Qiu, Fubin; Zhang, Xiaoxia; Liu, Lin; Sun, Lei; Schumann, Peter; Song, Wei

2009-04-01

Four alkaligenous, moderately halotolerant strains, designated ge09, ge10(T), ge14(T) and ge15, were isolated from the internal tissue of ginseng root and their taxonomic positions were investigated by using a polyphasic approach. Cells of the four strains were Gram-positive-staining, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains ge09 and ge10(T) formed one cluster and strains ge14(T) and ge15 formed another separate cluster within the genus Bacillus. 16S rRNA gene sequence similarities with type strains of other Bacillus species were less than 97 %. Levels of DNA-DNA relatedness among the four strains showed that strains ge09 and ge10(T) and strains ge14(T) and ge15 belonged to two separate species; the mean level of DNA-DNA relatedness between ge10(T) and ge14(T) was only 28.7 %. Their phenotypic and physiological properties supported the view that the two strains represent two different novel species of the genus Bacillus. The DNA G+C contents of strains ge10(T) and ge14(T) were 49.9 and 49.6 mol%, respectively. Strains ge10(T) and ge14(T) showed the peptidoglycan type A4alpha l-Lys-d-Glu. The lipids present in strains ge10(T) and ge14(T) were diphosphatidylglycerol, phosphatidylglycerol, a minor amount of phosphatidylcholine and two unknown phospholipids. Their predominant respiratory quinone was MK-7. The fatty acid profiles of the four novel strains contained large quantities of branched and saturated fatty acids. The predominant cellular fatty acids were iso-C(15 : 0) (42.5 %), anteiso-C(15 : 0) (22.2 %), anteiso-C(17 : 0) (7.3 %) and C(16 : 1)omega7c alcohol (5.7 %) in ge10(T) and iso-C(15 : 0) (50.7 %) and anteiso-C(15 : 0) (20.1 %) in ge14(T). On the basis of their phenotypic properties and phylogenetic distinctiveness, two novel species of the genus Bacillus are proposed, Bacillus beijingensis sp. nov. (type strain ge10(T) =DSM 19037(T) =CGMCC 1.6762(T)) and Bacillus ginsengi sp. nov. (type strain ge14(T) =DSM 19038(T) =CGMCC 1.6763(T)).

Poly-3-hydroxybutyrate (PHB) production from alkylphenols, mono and poly-aromatic hydrocarbons using Bacillus sp. CYR1: A new strategy for wealth from waste.

PubMed

Venkateswar Reddy, M; Mawatari, Yasuteru; Yajima, Yuka; Seki, Chigusa; Hoshino, Tamotsu; Chang, Young-Cheol

2015-09-01

In the present study five different types of alkylphenols, each of the two different types of mono and poly-aromatic hydrocarbons were selected for degradation, and conversion into poly-3-hydroxybutyrate (PHB) using the Bacillus sp. CYR1. Strain CYR1 showed growth with various toxic organic compounds. Degradation pattern of all the organic compounds at 100 mg/l concentration with or without addition of tween-80 were analyzed using high pressure liquid chromatography (HPLC). Strain CYR1 showed good removal of compounds in the presence of tween-80 within 3 days, but it took 6 days without addition of tween-80. Strain CYR1 showed highest PHB production with phenol (51 ± 5%), naphthalene (42 ± 4%), 4-chlorophenol (32 ± 3%) and 4-nonylphenol (29 ± 3%). The functional groups, structure, and thermal properties of the produced PHB were analyzed. These results denoted that the strain Bacillus sp. CYR1 can be used for conversion of different toxic compounds persistent in wastewaters into useable biological polyesters. Copyright © 2015 Elsevier Ltd. All rights reserved.

Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr.

PubMed

Piao, Chenyu; Zheng, Weiwei; Li, Yao; Liu, Chongxi; Jin, Liying; Song, Wei; Yan, Kai; Wang, Xiangjing; Xiang, Wensheng

2017-09-01

Two novel actinomycetes, designated strains 2C-SSA16(2) T and 1C-GS8 T , were isolated from the cuticle of Camponotus japonicus Mayr, collected from Northeast Agricultural University, Heilongjiang Province, north China. Both of them contained genes (involved in antibiotics biosynthesis) of the ketosynthase (KS) and methyl malonyl transferase domains (PKS-I) and the adenylation domain (NRPS). A polyphasic study was carried out to establish the taxonomic positions of these strains. The 16S rRNA gene sequence analysis showed that the two novel isolates 2C-SSA16(2) T and 1C-GS8 T exhibited 98.8% similarity with each other and that they are most closely related to Streptomyces umbrinus JCM 4521 T (99.0, 98.6%), Streptomyces ederensis JCM 4958 T (98.9, 98.7%), Streptomyces aurantiacus JCM 4453 T (98.6, 98.2%), Streptomyces glomeroaurantiacus JCM 4677 T (98.6, 98.1%), Streptomyces tauricus JCM4837 T (98.2, 98.0%) and Streptomyces phaeochromogenes JCM 4070 T (98.2, 99.2%). The corresponding phylogenetic analysis based on partial gyrB gene sequences showed that strains 2C-SSA16(2) T and 1C-GS8 T formed a cluster with the above-mentioned strains. The DNA-DNA hybridization data and phenotypic characteristics indicated that strains 2C-SSA16(2) T and 1C-GS8 T could be readily distinguished from each other and their closest phylogenetic relatives. Therefore, these two strains are suggested to represent two novel species of the genus Streptomyces, for which the names Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. are proposed. The type strains are 2C-SSA16(2) T (=CGMCC 4.7276 T  = DSM 100522 T ) and 1C-GS8 T (=CGMCC 4.7348 = DSM 103127 T ), respectively.

Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov.

PubMed

Christensen, H; Nicklas, W; Bisgaard, M

2014-11-01

Eleven strains from hamster of Bisgaard taxa 23 and 24, also referred to as Krause's groups 2 and 1, respectively, were investigated by a polyphasic approach including data published previously. Strains showed small, regular and circular colonies with smooth and shiny appearance, typical of members of the family Pasteurellaceae. The strains formed two monophyletic groups based on 16S rRNA gene sequence comparison to other members of the family Pasteurellaceae. Partial rpoB sequencing as well as published data on DNA-DNA hybridization showed high genotypic relationships within both groups. Menaquinone 7 (MK7) was found in strains of both groups as well as an unknown ubiquinone with shorter chain length than previously reported for any other member of the family Pasteurellaceae. A new genus with one species, Mesocricetibacter intestinalis gen. nov., sp. nov., is proposed to accommodate members of taxon 24 of Bisgaard whereas members of taxon 23 of Bisgaard are proposed to represent Cricetibacter osteomyelitidis gen. nov., sp. nov. Major fatty acids of type strains of type species of both genera are C(14:0), C(14:0) 3-OH/iso-C(16:1) I, C(16:1)ω7c and C(16:0). The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae. The type strain of Mesocricetibacter intestinalis is HIM 933/7(T) ( =Kunstyr 246/85(T) =CCUG 28030(T) =DSM 28403(T)) while the type strain of Cricetibacter osteomyelitidis is HIM943/7(T) ( =Kunstyr 507/85(T) =CCUG 36451(T) =DSM 28404(T)). © 2014 IUMS.

Cryptococcus lacticolor sp. nov. and Rhodotorula oligophaga sp. nov., novel yeasts isolated from the nasal smear microbiota of Queensland koalas kept in Japanese zoological parks.

PubMed

Satoh, Kazuo; Maeda, Mari; Umeda, Yoshiko; Sugamata, Miho; Makimura, Koichi

2013-07-01

A total of 515 yeast strains were isolated from the nasal smears of Queensland koalas and their breeding environments in Japanese zoological parks between 2005 and 2012. The most frequent species in the basidiomycetous yeast biota isolated from koala nasal passages was Cryptococcus neoformans, followed by Rhodotorula minuta. R. minuta was the most frequent species in the breeding environments, while C. neoformans was rare. Seven strains representing two novel yeast species were identified. Analyses of the 26S rDNA (LSU) D1/D2 domain and nuclear ribosomal DNA internal transcribed spacer region sequences indicated that these strains represent new species with close phylogenetic relationships to Cryptococcus and Rhodotorula. A sexual state was not found for either of these two novel yeasts. Key phenotypic characters confirmed that these strains could be placed in Cryptococcus and Rhodotorula. The names Cryptococcus lacticolor sp. nov. (type strain TIMM 10013(T) = JCM 15449(T) = CBS 10915(T) = DSM 21093(T), DDBJ/EMBL/Genbank Accession No.; AB375774 (ITS) and AB375775 (26S rDNA D1/D2 region), MycoBank ID; MB 802688, Fungal Barcoding Database ID; 3174), and Rhodotorula oligophaga sp. nov. (type strain TIMM 10017(T) = JCM 18398(T) = CBS 12623(T) = DSM 25814(T), DDBJ/EMBL/Genbank Accession No.; AB702967 (ITS) and AB702967 (26S rDNA D1/D2 region), MycoBank ID; MB 802689, Fungal Barcoding Database ID; 3175) are proposed for these new species.

Desulfurization of dibenzothiophene by Corynebacterium sp. strain SY1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Omori, Toshio; Monna, L.; Saiki, Yuko

1992-03-01

Strain SY1, identified as a Corynebacterium sp., was isolated on the basis of the ability to utilize dibenzothiophene (DBT) as a sole source of sulfur. Strain SY1 could utilize a wide range of organic and inorganic sulfur compounds, such as DBT sulfone, dimethyl sulfide, dimethyl sulfoxide, dimethyl sulfone, CS{sub 2}, FeS{sub 2}, and even elemental sulfur. Strain SY1 metabolized DBT to dibenzothiophene-5-oxide, DBT sulfone, and 2-hydroxybiphenyl, which was subsequently nitrated to produce at least two different hydroxynitrobiphenyls during cultivation. These metabolites were separated by silica gel column chromatography and identified by nuclear magnetic resonance, UV, and mass spectral techniques. Restingmore » cells of SY1 desulfurized toluenesulfonic acid and released sulfite anion. On the basis of these results, a new DBT degradation pathway is proposed.« less

Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.

PubMed

Francis, Isolde M; Jochimsen, Kenneth N; De Vos, Paul; van Bruggen, Ariena H C

2014-04-01

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas-like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA-DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium, Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1(T) = LMG 17323(T) = ATCC 49355(T)), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9(T) ( = LMG 12560(T) = ATCC 51296(T)), WI4(T) ( = LMG 11032(T) = ATCC 51292(T)) and SP1(T) ( = LMG 12581(T) = ATCC 51289(T)), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic.

[Isolation, identification and characterization of ACC deaminase-containing endophytic bacteria from halophyte Suaeda salsa].

PubMed

Teng, Songshan; Liu, Yanping; Zhao, Lei

2010-11-01

We Isolated and characterized 1-aminocyclopropane-1-carboxylate (ACC) deaminase-containing endophytic bacteria from halophyte Suaeda salsa to understand the interactions between endophytes and halophyte. ACC deaminase-containing endophytic bacteria were isolated from root, stalk and leaf of Suaeda salsa and were identified based on morphological, physiological-biochemical properties, API and 16S rRNA sequence analysis. Isolates were evaluated for their ACC deaminase, antifungal, protease activity, siderophores and phytohormones, such as indole-3-acetic acid, gibberellic acid and abscisic acid production, as well as atmospheric nitrogen fixation and phosphate solubilization. Four ACC deaminase-containing endophytic bacteria strains named as LP11, SS12, TW1 and TW2 were isolated and identified as Pseudomonas oryzihabitans, Pseudomonas sp., Pantoea agglomerans and Pseudomonas putida respectively. All the strains possessed the phosphate-solubilizing ability and could produce siderophores and phytohormones more or less. None of them could fix atmospheric nitrogen or produce protease. Only strain SS12 showed antagonism against two phytopathogenic fungi viz Fusarium oxysporum f. sp. conglutinans and F. oxysporum f. sp. cucumerinum. ACC deaminase-containing endophytic bacteria of Pseudomonas sp. and Pantoea sp. isolated from halophyte Suaeda salsa have abundant biological characteristics related to plant growth promotion, stress homeostasis regulation and biocontrol activity.

Cellulosilyticum ruminicola gen. nov., sp. nov., isolated from the rumen of yak, and reclassification of Clostridium lentocellum as Cellulosilyticum lentocellum comb. nov.

PubMed

Cai, Shichun; Dong, Xiuzhu

2010-04-01

An obligate anaerobic, Gram-staining-negative, mesophilic, cellulolytic bacterium, strain H1(T), was isolated from the rumen content of yak. Cells were straight to slightly curved rods, 0.8-1.0 x 3.0-4.0 microm in size, non-motile and encapsulated with mucous materials. Elliptical and terminal spores that swelled the cells were produced occasionally. The strain grew at 25-45 degrees C (optimum, 38 degrees C) and pH 6.0-7.8 (optimum, pH 6.7). Cellulose, cellobiose, xylan, xylose and maltose were used as carbon and energy sources, but not glucose. Products from cellulose and cellobiose fermentation were formic acid, acetic acid, carbon dioxide and trace amounts of ethanol, lactic acid and succinic acid. The genomic DNA G+C content was 33.7+/-1.2 mol%. The predominant fatty acids were C(16 : 0) (27.1 %), C(14 : 0) (9.2 %) and iso-C( 16 : 0) (6.4%). Based on the 16S rRNA gene sequence analysis, strain H1(T) was affiliated to the clostridial rRNA cluster XIVb and showed the highest 16S rRNA gene sequence similarity to Clostridium lentocellum DSM 5427(T) (96.0 %). These two strains formed a distinct lineage of the family 'Lachnospiraceae '. Based on data from this polyphasic taxonomic study, a new genus, Cellulosilyticum gen. nov., is proposed. Cellulosilyticum ruminicola sp. nov. is proposed for strain H1(T). The type strain of Cellulosilyticum ruminicola sp. nov. is strain H1(T) (=CGMCC 1.5065(T)=JCM 14822(T)). Clostridium lentocellum was reclassified in the new genus as Cellulosilyticum lentocellum comb. nov. (type strain RHM5(T)=ATCC 49066( T)=DSM 5427(T)=NCIMB 11756(T)).

Colonization and Maize Growth Promotion Induced by Phosphate Solubilizing Bacterial Isolates.

PubMed

Li, Yongbin; Liu, Xiaomeng; Hao, Tianyi; Chen, Sanfeng

2017-06-29

Phosphorus (P) limits the production of maize, one of the major food crops in China. Phosphate-solubilizing bacteria (PSB) have the capacity to solubilize phosphate complexes into plant absorbable and utilizable forms by the process of acidification, chelation, and exchange reactions. In this study, six bacteria, including one Paenibacillus sp. B1 strain, four Pseudomonas sp. strains (B10, B14, SX1, and SX2) and one Sphingobium sp. SX14 strain, were those isolated from the maize rhizosphere and identified based on their 16S rRNA sequences. All strains could solubilize inorganic P (Ca₃(PO₄)₂, FePO₄ and AlPO₄), and only B1 and B10 organic P (lecithin). All strains, except of SX1, produced IAA, and SX14 and B1 showed the highest level. B1 incited the highest increase in root length and the second increase in shoot and total dry weight, shoot length, and total P and nitrogen (N), along with increased root length. In addition, by confocal laser scanning microscopy (CLSM), we found that green fluorescent protein (GFP)-labeled B1 mainly colonized root surfaces and in epidermal and cortical tissue. Importantly, B1 can survive through forming spores under adverse conditions and prolong quality guarantee period of bio-fertilizer. Therefore, it can act as a good substitute for bio-fertilizer to promote agricultural sustainability.

Thermococcus guaymasensis sp. nov. and Thermococcus aggregans sp. nov., two novel thermophilic archaea isolated from the Guaymas Basin hydrothermal vent site.

PubMed

Canganella, F; Jones, W J; Gambacorta, A; Antranikian, G

1998-10-01

Thermococcus strains TYST and TYT isolated from the Guaymas Basin hydrothermal vent site and previously described were compared by DNA-DNA hybridization analysis with the closest Thermococcus species in terms of physiology and nutritional aspects. On the basis of the new data and taking into consideration the molecular, physiological and morphological traits published previously, it is proposed that strains TYT and TYST should be classified as new species named Thermococcus aggregans sp. nov. and Thermococcus guaymasensis sp. nov., respectively. The type strain of T. aggregans is strain TYT (= DSM 10597T) and the type strain of T. guaymasensis is strain TYST (= DSM 11113T).

Draft Genome Sequence of Haloferax sp. Strain ATB1, Isolated from a Semi-Arid Region in the Brazilian Caatinga.

PubMed

Castro, Wendel de Oliveira; Torres-Ballesteros, Adriana Maria; Nakayama, Cristina Rossi; Melo, Itamar Soares; Pellizari, Vivian Helena; Silva, Artur; Ramos, Rommel Thiago Jucá

2014-08-14

Organisms in the Haloferax genus are extreme halophiles that grow in environments with pH values between 4 and 12, and temperatures between 0°C and 60°C. In the present study, a draft of the first Haloferax sp. strain ATB1 genome isolated from the region of Cariri (in Paraíba State, Brazil) is presented. Copyright © 2014 Castro et al.

Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus

PubMed Central

Servín-Garcidueñas, Luis E.; Rogel, Marco A.; Ormeño-Orrillo, Ernesto; Zayas-del Moral, Alejandra; Sánchez, Federico

2016-01-01

We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, a nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus. Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island. PMID:26988045

Bst1 is required for Candida albicans infecting host via facilitating cell wall anchorage of Glycosylphosphatidyl inositol anchored proteins

PubMed Central

Liu, Wei; Zou, Zui; Huang, Xin; Shen, Hui; He, Li Juan; Chen, Si Min; Li, Li Ping; Yan, Lan; Zhang, Shi Qun; Zhang, Jun Dong; Xu, Zheng; Xu, Guo Tong; An, Mao Mao; Jiang, Yuan Ying

2016-01-01

Glycosylphosphatidyl inositol anchored proteins (GPI-APs) on fungal cell wall are essential for invasive infections. While the function of inositol deacylation of GPI-APs in mammalian cells has been previously characterized the impact of inositol deacylation in fungi and implications to host infection remains largely unexplored. Herein we describe our identification of BST1, an inositol deacylase of GPI-Aps in Candida albicans, was critical for GPI-APs cell wall attachment and host infection. BST1-deficient C. albicans (bst1Δ/Δ) was associated with severely impaired cell wall anchorage of GPI-APs and subsequen unmasked β-(1,3)-glucan. Consistent with the aberrant cell wall structures, bst1Δ/Δ strain did not display an invasive ability and could be recognized more efficiently by host immune systems. Moreover, BST1 null mutants or those expressing Bst1 variants did not display inositol deacylation activity and exhibited severely attenuated virulence and reduced organic colonization in a murine systemic candidiasis model. Thus, Bst1 can facilitate cell wall anchorage of GPI-APs in C. albicans by inositol deacylation, and is critical for host invasion and immune escape. PMID:27708385

A promising strain of Streptomyces sp. with agricultural traits for growth promotion and disease management.

PubMed

Alam, Mansoor; Dharni, Seema; Abdul-Khaliq; Srivastava, Santosh Kumar; Samad, Abdul; Gupta, Mahesh Kumar

2012-08-01

A bacterial strain, Streptomyces sp. CIMAP- A1 was isolated from Geranium rhizosphere and identified by morphological, physiological, biochemical and molecular characters (16S rDNA gene sequence). Phylogenetically, it was found most closely related to S. vinacendrappus, strain NRRL-2363 with 99% sequence similarity. The strain had potential antagonistic activity (in vitro) against wide range of phytopathogenic fungi like Stemphylium sp., Botrytis cinerea, Sclerotinia sclerotiorum, Colletotrichum spp., Curvularia spp., Corynespora cassicola and Thielavia basicola. The extracellular secondary metabolites produced by the strain in the culture filtrates significantly inhibited the spore germination, growth of germ tube of the germinated spores and radial growth of Alternaria alternata, Colletotrichum acutatum, Curvularia andropogonis and Fusarium moniliforme. The extraction of culture filtrate with solvents and purification by following VLC and PTLC methods always yielded a 10th fraction antifungal compound showing activity against wide range of phytopathogenic fungi. The strain was able to produce siderophores and indole-3-acetic acid. The strain was found to enhance the growth and biomass production of Geranium. It increased 11.3% fresh shoot biomass of Geranium and 21.7% essential oil yield.

Rhizosphere colonization and arsenic translocation in sunflower (Helianthus annuus L.) by arsenate reducing Alcaligenes sp. strain Dhal-L.

PubMed

Cavalca, Lucia; Corsini, Anna; Bachate, Sachin Prabhakar; Andreoni, Vincenza

2013-10-01

In the present study, six arsenic-resistant strains previously isolated were tested for their plant growth promoting characteristics and heavy metal resistance, in order to choose one model strain as an inoculum for sunflower plants in pot experiments. The aim was to investigate the effect of arsenic-resistant strain on sunflower growth and on arsenic uptake from arsenic contaminated soil. Based on plant growth promoting characteristics and heavy metal resistance, Alcaligenes sp. strain Dhal-L was chosen as an inoculum. Beside the ability to reduce arsenate to arsenite via an Ars operon, the strain exhibited 1-amino-cyclopropane-1-carboxylic acid deaminase activity and it was also able to produce siderophore and indole acetic acid. Pot experiments were conducted with an agricultural soil contaminated with arsenic (214 mg kg⁻¹). A real time PCR method was set up based on the quantification of ACR3(2) type of arsenite efflux pump carried by Alcaligenes sp. strain Dhal-L, in order to monitor presence and colonisation of the strain in the bulk and rhizospheric soil. As a result of strain inoculation, arsenic uptake by plants was increased by 53 %, whereas ACR3(2) gene copy number in rhizospheric soil was 100 times higher in inoculated than in control pots, indicating the colonisation of strain. The results indicated that the presence of arsenate reducing strains in the rhizosphere of sunflower influences arsenic mobilization and promotes arsenic uptake by plant.

Isolation and characterization of an isoproturon mineralizing Sphingomonas sp. strain SH from a French agricultural soil.

PubMed

Hussain, Sabir; Devers-Lamrani, Marion; El Azhari, Najoi; Martin-Laurent, Fabrice

2011-06-01

The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized in an agricultural soil in France that had been periodically exposed to IPU. Enrichment cultures from samples of this soil isolated a bacterial strain able to mineralize IPU. 16S rRNA sequence analysis showed that this strain belonged to the phylogeny of the genus Sphingomonas (96% similarity with Sphingomonas sp. JEM-14, AB219361) and was designated Sphingomonas sp. strain SH. From this strain, a partial sequence of a 1,2-dioxygenase (catA) gene coding for an enzyme degrading catechol putatively formed during IPU mineralization was amplified. Phylogenetic analysis revealed that the catA sequence was related to Sphingomonas spp. and showed a lack of congruence between the catA and 16S rRNA based phylogenies, implying horizontal gene transfer of the catA gene cluster between soil microbiota. The IPU degrading ability of strain SH was strongly influenced by pH with maximum degradation taking place at pH 7.5. SH was only able to mineralize IPU and its known metabolites including 4-isopropylaniline and it could not degrade other structurally related phenylurea herbicides such as diuron, linuron, monolinuron and chlorotoluron or their aniline derivatives. These observations suggest that the catabolic abilities of the strain SH are highly specific to the metabolism of IPU.

Evaluation of insecticidal activity of a bacterial strain, Serratia sp. EML-SE1 against diamondback moth.

PubMed

Jeong, Hyung Uk; Mun, Hye Yeon; Oh, Hyung Keun; Kim, Seung Bum; Yang, Kwang Yeol; Kim, Iksoo; Lee, Hyang Burm

2010-08-01

To identify novel bioinsecticidal agents, a bacterial strain, Serratia sp. EML-SE1, was isolated from a dead larva of the lepidopteran diamondback moth (Plutella xylostella) collected from a cabbage field in Korea. In this study, the insecticidal activity of liquid cultures in Luria-Bertani broth (LBB) and nutrient broth (NB) of a bacterial strain, Serratia sp. EML-SE1 against thirty 3rd and 4th instar larvae of the diamondback moth was investigated on a Chinese cabbage leaf housed in a round plastic cage (Ø 10 x 6 cm). 72 h after spraying the cabbage leaf with LBB and NB cultures containing the bacterial strain, the mortalities of the larvae were determined to be 91.7% and 88.3%, respectively. In addition, the insecticidal activity on potted cabbage containing 14 leaves in a growth cage (165 x 83 x 124 cm) was found to be similar to that of the plastic cage experiment. The results of this study provided valuable information on the insecticidal activity of the liquid culture of a Serratia species against the diamondback moth.

Transcriptional analysis of the multicopy hao gene coding for hydroxylamine oxidoreductase in Nitrosomonas sp. strain ENI-11.

PubMed

Hirota, Ryuichi; Kuroda, Akio; Ikeda, Tsukasa; Takiguchi, Noboru; Ohtake, Hisao; Kato, Junichi

2006-08-01

The nitrifying bacterium Nitrosomonas sp. strain ENI-11 has three copies of the gene encoding hydroxylamine oxidoreductase (hao(1), hao(2), and hao(3)) on its genome. Broad-host-range reporter plasmids containing transcriptional fusion genes between hao copies and lacZ were constructed to analyze the expression of each hydroxylamine oxidoreductase gene (hao) copy individually and quantitatively. beta-Galactosidase assays of ENI-11 harboring reporter plasmids revealed that all hao copies were transcribed in the wild-type strain. Promoter analysis of hao copies revealed that transcription of hao(3) was highest among the hao copies. Expression levels of hao(1) and hao(2) were 40% and 62% of that of hao(3) respectively. Transcription of hao(1) was negatively regulated, whereas a portion of hao(3) transcription was read through transcription from the rpsT promoter. When energy-depleted cells were incubated in the growth medium, only hao(3) expression increased. This result suggests that it is hao(3) that is responsible for recovery from energy-depleted conditions in Nitrosomonas sp. strain ENI-11.

Enzymes Involved in Naproxen Degradation by Planococcus sp. S5.

PubMed

Wojcieszyńska, Danuta; Domaradzka, Dorota; Hupert-Kocurek, Katarzyna; Guzik, Urszula

2016-01-01

Naproxen is a one of the most popular non-steroidal anti-inflammatory drugs (NSAIDs) entering the environment as a result of high consumption. For this reason, there is an emerging need to recognize mechanisms of its degradation and enzymes engaged in this process. Planococcus sp. S5 is a gram positive strain able to degrade naproxen in monosubstrate culture (27%). However, naproxen is not a sufficient growth substrate for this strain. In the presence of benzoate, 4-hydroxybenzoic acid, 3,4-dihydroxybenzoic acid or vanillic acid as growth substrates, the degradation of 21.5%, 71.71%, 14.75% and 8.16% of naproxen was observed respectively. It was shown that the activity of monooxygenase, hydroxyquinol 1,2-dioxygenase, protocatechuate 3,4-dioxygenase and protocatechuate 4,5-dioxyegnase in strain S5 was induced after growth of the strain with naproxen and 4-hydroxybenzoate. Moreover, in the presence of naproxen activity of gentisate 1,2-dioxygenase, enzyme engaged in 4-hydroxybenzoate metabolism, was completely inhibited. The obtained results suggest that monooxygenase and hydroxyquinol 1,2-dioxygenase are the main enzymes in naproxen degradation by Planococcus sp. S5.

Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma.

PubMed

Finster, Kai Waldemar; Herbert, Rodney Andrew; Lomstein, Bente Aagaard

2009-04-01

Two pigmented, Gram-negative, non-motile, pleomorphic rod-shaped bacteria (strains SPM-9(T) and SPM-10(T)) were isolated from a permafrost soil collected from the Adventdalen valley, Spitsbergen, northern Norway. A third isolate (strain M5-H2) was recovered from the same soil sample after the sample had been exposed to simulated Martian environmental conditions. The three strains were characterized taxonomically by using a polyphasic approach. Phylogenetic, chemotaxonomic, physiological and morphological analyses demonstrated that the three isolates were most closely related to members of the genus Spirosoma. 16S rRNA gene sequence data indicated that the three isolates could be divided into two clusters: (i) strain SPM-9(T) and (ii) strains SPM-10(T) and M5-H2. This grouping was confirmed by DNA-DNA hybridization experiments. Strains SPM-9(T) and SPM-10(T) exhibited 92 % 16S rRNA gene sequence similarity to both Spirosoma linguale LMG 10896(T) and Spirosoma rigui WPCB 118(T). The major fatty acids present in all three isolates were summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16 : 1)omega7c; 43.0-48.2 % of the total), C(16 : 1)omega5c (19.1-21.3 %), C(16 : 0) (6.7-7.3 %), iso-C(17 : 0) 3-OH (4.7-6.0 %) and iso-C(15 : 0) (2.6-5.7 %). On the basis of their phenotypic and genotypic characteristics, the new strains are assigned to two novel species of the genus Spirosoma, for which the names Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov. are proposed. The type strain of Spirosoma spitsbergense is SPM-9(T) (=NCIMB 14407(T)=DSM 19989(T)) and the type strain of Spirosoma luteum is SPM-10(T) (=NCIMB 14406(T)=DSM 19990(T)). An emended description of the genus Spirosoma is also proposed.

Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms.

PubMed

King, C E; King, G M

2014-08-01

Two thermophilic, Gram-stain-positive, rod-shaped, non-spore-forming bacteria (strains KI3(T) and KI4(T)) were isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai'i, USA). Strain KI3(T) grew over an examined temperature range of 50-70 °C (no growth at 80 °C) and a pH range of 6.0-9.0, with optimum growth at 70 °C and pH 7.0. Strain KI4(T) grew at temperatures of 55-70 °C and a pH range of 5.8-8.0, with optimum growth at 65 °C and pH 6.7-7.1. The DNA G+C contents of strains KI3(T) and KI4(T) were 66.0 and 60.7 mol%, respectively. The major fatty acid for both strains was 12-methyl C(18 : 0). Polar lipids in strain KI3(T) were dominated by glycolipids and phosphatidylinositol, while phosphatidylinositol and phosphoglycolipids dominated in strain KI4(T). Strain KI3(T) oxidized carbon monoxide [6.7±0.8 nmol CO h(-1) (mg protein)(-1)], but strain KI4(T) did not. 16S rRNA gene sequence analyses determined that the strains belong to the class Thermomicrobia, and that strains KI3(T) and KI4(T) are related most closely to Thermomicrobium roseum DSM 5159(T) (96.5 and 91.1% similarity, respectively). 16S rRNA gene sequence similarity between strain KI3(T) and strain KI4(T) was 91.4%. Phenotypic features and phylogenetic analyses supported the affiliation of strain KI3(T) to the genus Thermomicrobium, while results of chemotaxonomic, physiological and biochemical assays differentiated strains KI3(T) and KI4(T) from Thermomicrobium roseum. Strain KI3(T) ( = DSM 27067(T) = ATCC BAA-2535(T)) is thus considered to be the type strain of a novel species, for which the name Thermomicrobium carboxidum sp. nov. is proposed. Additionally, the characterization and phylogenetic position of strain KI4(T) showed that it represents a novel species of a new genus, for which the name Thermorudis peleae gen. nov., sp. nov. is proposed. The type strain of Thermorudis peleae is KI4(T) ( = DSM 27169(T) = ATCC BAA-2536(T)). © 2014 IUMS.

Whole Genome Sequence Analysis of an Alachlor and Endosulfan Degrading Micrococcus sp. strain 2385 Isolated from Ochlockonee River, Florida

PubMed Central

Pathak, Ashish; Chauhan, Ashvini; Ewida, Ayman Y.I.; Stothard, Paul

2016-01-01

We recently isolated Micrococcus sp. strain 2385 from Ochlockonee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides- alachlor [(2-chloro-2`,6`-diethylphenyl-N (methoxymethyl)acetanilide)] and endosulfan [(6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,3,4-benzo(e)di-oxathiepin-3-oxide], respectively. To further identify the repertoire of metabolic functions possessed by strain 2385, a draft genome sequence was obtained, assembled, annotated and analyzed. The genome sequence of Micrococcus sp. strain 2385 consisted of 1,460,461,440 bases which assembled into 175 contigs with an N50 contig length of 50,109 bases and a coverage of 600x. The genome size of this strain was estimated at 2,431,226 base pairs with a G+C content of 72.8 and a total number of 2,268 putative genes. RAST annotated a total of 340 subsystems in the genome of strain 2385 along with the presence of 2,177 coding sequences. A genome wide survey indicated that that strain 2385 harbors a plethora of genes to degrade other pollutants including caprolactam, PAHs (such as naphthalene), styrene, toluene and several chloroaromatic compounds. PMID:27672405

Whole Genome Sequence Analysis of an Alachlor and Endosulfan Degrading Micrococcus sp. strain 2385 Isolated from Ochlockonee River, Florida.

PubMed

Pathak, Ashish; Chauhan, Ashvini; Ewida, Ayman Y I; Stothard, Paul

2016-01-01

We recently isolated Micrococcus sp. strain 2385 from Ochlockonee River, Florida and demonstrated potent biodegradative activity against two commonly used pesticides- alachlor [(2-chloro-2`,6`-diethylphenyl-N (methoxymethyl)acetanilide)] and endosulfan [(6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,3,4-benzo(e)di-oxathiepin-3-oxide], respectively. To further identify the repertoire of metabolic functions possessed by strain 2385, a draft genome sequence was obtained, assembled, annotated and analyzed. The genome sequence of Micrococcus sp. strain 2385 consisted of 1,460,461,440 bases which assembled into 175 contigs with an N50 contig length of 50,109 bases and a coverage of 600x. The genome size of this strain was estimated at 2,431,226 base pairs with a G+C content of 72.8 and a total number of 2,268 putative genes. RAST annotated a total of 340 subsystems in the genome of strain 2385 along with the presence of 2,177 coding sequences. A genome wide survey indicated that that strain 2385 harbors a plethora of genes to degrade other pollutants including caprolactam, PAHs (such as naphthalene), styrene, toluene and several chloroaromatic compounds.

U.S. EPA, Pesticide Product Label, , 11/05/1985

EPA Pesticide Factsheets

2011-04-21

... Ap,l, ., p,.-~I... •• 1 ~I ••• "ra". Us. 0.75 I. I p •••• , r 100 ,.II •• s •• ,.ndiA, 00 dis •• s. ,.v.rily. ",y •• IS.. it lOountnh sp,.ys .t •• uiulnl nhs. fll' it,"1 .ppli,.tion II. ...

Fluctuation of Bacteria on Bleb Surface After Trabeculectomy With Adjunctive Mitomycin C.

PubMed

Takahashi, Nobumichi; Sawada, Akira; Mochizuki, Kiyofumi; Katada, Toshihiko; Yamamoto, Tetsuya

2016-05-01

To determine whether the bacterial and floral patterns on the bleb surface are affected by the season in eyes that had undergone trabeculectomy with adjunctive mitomycin C. Forty-four glaucoma patients who had an avascular or a hypovascular cystic filtering bleb were studied. Swabs of the bleb surface were taken 4 times in 1 year. The samples were cultured, and all organisms isolated were identified and tested for antibiotic sensitivity and resistance. Of the 176 specimens, 48 tested positive in cultures. Out of the 44 glaucoma eyes that had undergone trabeculectomy, 30 (68.2%) eyes were culture positive. A total of 58 strains were isolated. The organisms isolated were 22 strains of Staphylococcus epidermidis, 21 strains of Propionibacterium acnes, 8 strains of Corynebacterium sp., 5 strains of Staphylococcus sp., and 1 strain of both Neisseria sp., and Candida parapsilosis. Fifteen eyes had a positive culture ≥2 times, and in 10 of these eyes, the same strain was isolated. There was no resistance to vancomycin by S. epidermidis, P. acnes, and Corynebacterium sp. All of the isolates of S.epidermidis were sensitive to minocycline and amikacin. The rate of bacterial detection in the spring was 13.6%, summer was 20.5%, autumn was 45.5%, and winter was 29.5%. The increase in the incidence of bacterial presence during autumn was significant (P=0.006; the Fisher exact probability test). It is not rare to detect the bacterial organisms on the bleb surface in glaucomatous eyes that had undergone trabeculectomy. The prevalence varied with the season and was highest in the autumn.

Methylobacterium oryzae sp. nov., an aerobic, pink-pigmented, facultatively methylotrophic, 1-aminocyclopropane-1-carboxylate deaminase-producing bacterium isolated from rice.

PubMed

Madhaiyan, Munusamy; Kim, Byung-Yong; Poonguzhali, Selvaraj; Kwon, Soon-Wo; Song, Myung-Hee; Ryu, Jeoung-Hyun; Go, Seung-Joo; Koo, Bon-Sung; Sa, Tong-Min

2007-02-01

A pink-pigmented, facultatively methylotrophic bacterium, strain CBMB20T, isolated from stem tissues of rice, was analysed by a polyphasic approach. Strain CBMB20T utilized 1-aminocyclopropane 1-carboxylate (ACC) as a nitrogen source and produced ACC deaminase. It was related phylogenetically to members of the genus Methylobacterium. 16S rRNA gene sequence analysis indicated that strain CBMB20T was most closely related to Methylobacterium fujisawaense, Methylobacterium radiotolerans and Methylobacterium mesophilicum; however, DNA-DNA hybridization values were less than 70 % with the type strains of these species. The DNA G+C content of strain CBMB20T was 70.6 mol%. The study presents a detailed phenotypic characterization of strain CBMB20T that allows its differentiation from other Methylobacterium species. In addition, strain CBMB20T is the only known member of the genus Methylobacterium to be described from the phyllosphere of rice. Based on the data presented, strain CBMB20T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium oryzae sp. nov. is proposed, with strain CBMB20T (=DSM 18207T=LMG 23582T=KACC 11585T) as the type strain.

A paradoxical increase of a metabolite upon increased expression of its catabolic enzyme: the case of diadenosine tetraphosphate (Ap4A) and Ap4A phosphorylase I in Saccharomyces cerevisiae.

PubMed Central

Avila, D M; Robinson, A K; Kaushal, V; Barnes, L D

1991-01-01

The APA1 gene in Saccharomyces cerevisiae encodes Ap4A phosphorylase I, the catabolic enzyme for diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A). APA1 has been inserted into a multicopy plasmid and into a centromeric plasmid with a GAL1 promoter. Enhanced expression of APA1 via the plasmids resulted in 10- and 90-fold increases in Ap4A phosphorylase activity, respectively, as assayed in vitro. However, the intracellular concentration of Ap4A exhibited increases of 2- and 15-fold, respectively, from the two different plasmids. Intracellular Ap4A increased 3- to 20-fold during growth on galactose of a transformant with APA1 under the control of the GAL1 promoter. Intracellular adenosine 5'-P1-tetraphospho-P4-5"'-guanosine (Ap4G) and diguanosine 5',5"'-P1,P4-tetraphosphate (Gp4G) also increased in the transformant under these conditions. The chromosomal locus of APA1 has been disrupted in a haploid strain. The Ap4A phosphorylase activity decreased by 80% and the intracellular Ap4A concentration increased by a factor of five in the null mutant. These results with the null mutant agree with previous results reported by Plateau et al. (P. Plateau, M. Fromant, J.-M. Schmitter, J.-M. Buhler, and S. Blancquet, J. Bacteriol. 171:6437-6445, 1989). The paradoxical increase in Ap4A upon enhanced expression of APA1 indicates that the metabolic consequences of altered gene expression may be more complex than indicated solely by assay of enzymatic activity of the gene product. PMID:1660456

A paradoxical increase of a metabolite upon increased expression of its catabolic enzyme: the case of diadenosine tetraphosphate (Ap4A) and Ap4A phosphorylase I in Saccharomyces cerevisiae.

PubMed

Avila, D M; Robinson, A K; Kaushal, V; Barnes, L D

1991-12-01

The APA1 gene in Saccharomyces cerevisiae encodes Ap4A phosphorylase I, the catabolic enzyme for diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A). APA1 has been inserted into a multicopy plasmid and into a centromeric plasmid with a GAL1 promoter. Enhanced expression of APA1 via the plasmids resulted in 10- and 90-fold increases in Ap4A phosphorylase activity, respectively, as assayed in vitro. However, the intracellular concentration of Ap4A exhibited increases of 2- and 15-fold, respectively, from the two different plasmids. Intracellular Ap4A increased 3- to 20-fold during growth on galactose of a transformant with APA1 under the control of the GAL1 promoter. Intracellular adenosine 5'-P1-tetraphospho-P4-5"'-guanosine (Ap4G) and diguanosine 5',5"'-P1,P4-tetraphosphate (Gp4G) also increased in the transformant under these conditions. The chromosomal locus of APA1 has been disrupted in a haploid strain. The Ap4A phosphorylase activity decreased by 80% and the intracellular Ap4A concentration increased by a factor of five in the null mutant. These results with the null mutant agree with previous results reported by Plateau et al. (P. Plateau, M. Fromant, J.-M. Schmitter, J.-M. Buhler, and S. Blancquet, J. Bacteriol. 171:6437-6445, 1989). The paradoxical increase in Ap4A upon enhanced expression of APA1 indicates that the metabolic consequences of altered gene expression may be more complex than indicated solely by assay of enzymatic activity of the gene product.

Candida aechmeae sp. nov. and Candida vrieseae sp. nov., novel yeast species isolated from the phylloplane of bromeliads in Southern Brazil.

PubMed

Landell, Melissa Fontes; Billodre, Raisa; Ramos, Jesus P; Leoncini, Orílio; Vainstein, Marilene H; Valente, Patrícia

2010-01-01

Two novel yeast species, Candida aechmeae sp. nov. and Candida vrieseae sp. nov., were isolated from bromeliads in Itapuã Park, Rio Grande do Sul, Brazil. These species are genetically isolated from all other currently recognized ascomycetous yeasts based on their sequence divergence in the D1/D2 domain of the LSU rRNA gene. C. aechmeae sp. nov. is phylogenetically close to Candida ubatubensis, a species also isolated from bromeliads in Brazil, but the novel species can be differentiated on the basis of differences in the D1/D2 domain and positive results for the assimilation of l-arabinose, raffinose, inulin and citrate. Candida vrieseae sp. nov. is phylogenetically placed in a clade near Candida membranifaciens that is composed of several species associated with insects, but the novel species can be differentiated from them by the D1/D2 and ITS gene sequences, positive results for the assimilation of nitrite and a negative result for the assimilation of ethylamine. The type strain for Candida aechmeae sp. nov. is BI153(T) (=CBS 10831(T)=NRRL Y-48456(T)) and the type strain for C. vrieseae sp. nov. is BI146(T) (=CBS 10829(T)=NRRL Y-48461(T)).

Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov.

PubMed Central

Linson, Sarah E.; Ojeda Saavedra, Matthew; Cantu, Concepcion; Davis, James J.; Brettin, Thomas; Olsen, Randall J.

2017-01-01

ABSTRACT In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all recognized Klebsiella spp. We closed the genome of strain KPN1705 using a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For this novel species, we propose the name Klebsiella quasivariicola sp. nov. PMID:29051239

3,6-Anhydro-L-galactonate cycloisomerase from Vibrio sp. strain EJY3: crystallization and X-ray crystallographic analysis.

PubMed

Lee, Saeyoung; Yun, Eun Ju; Kim, Kyoung Heon; Kim, Hye Yeon; Choi, In Geol

2017-09-01

3,6-Anhydro-L-galactonate cycloisomerase (ACI), which is found in the marine bacterium Vibrio sp. strain EJY3, converts 3,6-anhydro-L-galactonate into 2-keto-3-deoxygalactonate. ACI is a key enzyme in the metabolic pathway of 3,6-anhydro-L-galactose (AHG). Study of AHG metabolism is important for the efficient fermentation of agar and biofuel production, because AHG is a sugar that is non-fermentable by commercial microorganisms. The aci gene from Vibrio sp. strain EJY3 was cloned, and the recombinant protein was overexpressed and crystallized in order to determine the structure and understand the function of the protein. The crystals diffracted to 2.2 Å resolution and belonged to space group P4 1 2 1 2 or P4 3 2 1 2, with unit-cell parameters a = b = 87.9, c = 143.5 Å. The Matthews coefficient was 2.3 Å 3  Da -1 , with a solvent content of 47%.

Genetic evidence for the involvement of the S-layer protein gene sap and the sporulation genes spo0A, spo0B, and spo0F in Phage AP50c infection of Bacillus anthracis.

PubMed

Plaut, Roger D; Beaber, John W; Zemansky, Jason; Kaur, Ajinder P; George, Matroner; Biswas, Biswajit; Henry, Matthew; Bishop-Lilly, Kimberly A; Mokashi, Vishwesh; Hannah, Ryan M; Pope, Robert K; Read, Timothy D; Stibitz, Scott; Calendar, Richard; Sozhamannan, Shanmuga

2014-03-01

In order to better characterize the Bacillus anthracis typing phage AP50c, we designed a genetic screen to identify its bacterial receptor. Insertions of the transposon mariner or targeted deletions of the structural gene for the S-layer protein Sap and the sporulation genes spo0A, spo0B, and spo0F in B. anthracis Sterne resulted in phage resistance with concomitant defects in phage adsorption and infectivity. Electron microscopy of bacteria incubated with AP50c revealed phage particles associated with the surface of bacilli of the Sterne strain but not with the surfaces of Δsap, Δspo0A, Δspo0B, or Δspo0F mutants. The amount of Sap in the S layer of each of the spo0 mutant strains was substantially reduced compared to that of the parent strain, and incubation of AP50c with purified recombinant Sap led to a substantial reduction in phage activity. Phylogenetic analysis based on whole-genome sequences of B. cereus sensu lato strains revealed several closely related B. cereus and B. thuringiensis strains that carry sap genes with very high similarities to the sap gene of B. anthracis. Complementation of the Δsap mutant in trans with the wild-type B. anthracis sap or the sap gene from either of two different B. cereus strains that are sensitive to AP50c infection restored phage sensitivity, and electron microscopy confirmed attachment of phage particles to the surface of each of the complemented strains. Based on these data, we postulate that Sap is involved in AP50c infectivity, most likely acting as the phage receptor, and that the spo0 genes may regulate synthesis of Sap and/or formation of the S layer.

Genetic Evidence for the Involvement of the S-Layer Protein Gene sap and the Sporulation Genes spo0A, spo0B, and spo0F in Phage AP50c Infection of Bacillus anthracis

PubMed Central

Beaber, John W.; Zemansky, Jason; Kaur, Ajinder P.; George, Matroner; Biswas, Biswajit; Henry, Matthew; Bishop-Lilly, Kimberly A.; Mokashi, Vishwesh; Hannah, Ryan M.; Pope, Robert K.; Read, Timothy D.; Stibitz, Scott; Calendar, Richard; Sozhamannan, Shanmuga

2014-01-01

In order to better characterize the Bacillus anthracis typing phage AP50c, we designed a genetic screen to identify its bacterial receptor. Insertions of the transposon mariner or targeted deletions of the structural gene for the S-layer protein Sap and the sporulation genes spo0A, spo0B, and spo0F in B. anthracis Sterne resulted in phage resistance with concomitant defects in phage adsorption and infectivity. Electron microscopy of bacteria incubated with AP50c revealed phage particles associated with the surface of bacilli of the Sterne strain but not with the surfaces of Δsap, Δspo0A, Δspo0B, or Δspo0F mutants. The amount of Sap in the S layer of each of the spo0 mutant strains was substantially reduced compared to that of the parent strain, and incubation of AP50c with purified recombinant Sap led to a substantial reduction in phage activity. Phylogenetic analysis based on whole-genome sequences of B. cereus sensu lato strains revealed several closely related B. cereus and B. thuringiensis strains that carry sap genes with very high similarities to the sap gene of B. anthracis. Complementation of the Δsap mutant in trans with the wild-type B. anthracis sap or the sap gene from either of two different B. cereus strains that are sensitive to AP50c infection restored phage sensitivity, and electron microscopy confirmed attachment of phage particles to the surface of each of the complemented strains. Based on these data, we postulate that Sap is involved in AP50c infectivity, most likely acting as the phage receptor, and that the spo0 genes may regulate synthesis of Sap and/or formation of the S layer. PMID:24363347

Isolation of a buprofezin co-metabolizing strain of Pseudomonas sp. DFS35-4 and identification of the buprofezin transformation pathway.

PubMed

Chen, Kai; Liu, Xiao-Mei; Li, Rong; Liu, Yuan; Hu, Hai; Li, Shun-Peng; Jiang, Jian-Dong

2011-11-01

Buprofezin is a widely used insecticide that has caused environmental pollution in many areas. However, biodegradation of buprofezin by pure cultures has not been extensively studied, and the transformation pathway of buprofezin remains unclear. In this paper, a buprofezin co-metabolizing strain of DFS35-4 was isolated from a buprofezin-polluted soil in China. Strain DFS35-4 was preliminarily identified as Pseudomonas sp. based on its morphological, physiological, and biochemical properties, as well as 16S rRNA gene analysis. In the presence of 2.0 g l(-1) sodium citrate, strain DFS35-4 degraded over 70% of 50 mg l(-1) buprofezin in 3 days. Strain DFS35-4 efficiently degraded buprofezin in the pH range of 5.0-10.0 and at temperatures between 20 and 30°C. Three metabolites, 2-imino-5-phenyl-3-(propan-2-yl)-1,3,5-thiadiazinan-4-one, 2-imino-5-phenyl-1,3,5-thiadiazinan-4-one, and methyl(phenyl) carbamic acid, were identified during the degradation of buprofezin using gas chromatography-mass spectrometry (GC-MS) and tandem mass spectrometry (MS/MS). A partial transformation pathway of buprofezin in Pseudomonas sp. DFS35-4 was proposed based on these metabolites.

Isolation, Characterization, and Polyaromatic Hydrocarbon Degradation Potential of Aerobic Bacteria from Marine Macrofaunal Burrow Sediments and Description of Lutibacterium anuloederans gen. nov., sp. nov., and Cycloclasticus spirillensus sp. nov.†

PubMed Central

Chung, W. K.; King, G. M.

2001-01-01

Two new polyaromatic hydrocarbon-degrading marine bacteria have been isolated from burrow wall sediments of benthic macrofauna by using enrichments on phenanthrene. Strain LC8 (from a polychaete) and strain M4-6 (from a mollusc) are aerobic and gram negative and require sodium chloride (>1%) for growth. Both strains can use 2- and 3-ring polycyclic aromatic hydrocarbons as their sole carbon and energy sources, but they are nutritionally versatile. Physiological and phylogenetic analyses based on 16S ribosomal DNA sequences suggest that strain M4-6 belongs to the genus Cycloclasticus and represents a new species, Cycloclasticus spirillensus sp. nov. Strain LC8 appears to represent a new genus and species, Lutibacterium anuloederans gen. nov., sp. nov., within the Sphingomonadaceae. However, when inoculated into sediment slurries with or without exogenous phenanthrene, only L. anuloederans appeared to sustain a significant phenanthrene uptake potential throughout a 35-day incubation. In addition, only L. anuloederans appeared to enhance phenanthrene degradation in heavily contaminated sediment from Little Mystic Cove, Boston Harbor, Boston, Mass. PMID:11722910

Identification and cloning of a regulatory gene for nitrogen assimilation in the cyanobacterium Synechococcus sp. strain PCC 7942.

PubMed Central

Vega-Palas, M A; Madueño, F; Herrero, A; Flores, E

1990-01-01

Twenty-seven mutants that were unable to assimilate nitrate were isolated from Synechococcus sp. strain PCC 7942. In addition to mutants that lacked nitrate reductase or nitrite reductase, seven pleiotropic mutants impaired in both reductases, glutamine synthetase, and methylammonium transport were also isolated. One of the pleiotropic mutants was complemented by transformation with a cosmid gene bank from wild-type strain PCC 7942. Three complementing cosmids were isolated, and a 3.1-kilobase-pair DNA fragment that was still able to complement the mutant was identified. The regulatory gene that was cloned (ntcA) appeared to be required for full expression of proteins subject to ammonium repression in Synechococcus sp. PMID:1967601

Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

PubMed Central

Barrett, Nolan H.; McCarthy, Peter J.

2017-01-01

ABSTRACT The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. PMID:28153886

DNA–DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov

PubMed Central

Holmes, B.; Steigerwalt, A. G.; Nicholson, A. C.

2015-01-01

The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA–DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indoleproducing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530T=CCUG 60564T=CDC G229T), Chryseobacterium carnis sp. nov. (type strain NCTC 13525T=CCUG 60559T=CDC G81T), Chryseobacterium lactis sp. nov. (type strain NCTC 11390T=CCUG 60566T=CDC KC1864T) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529T=CCUG 60563T=CDC G41T). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490T=X-65T=CCTCC AB 208154T=NRRL B-51322T) is also proposed to accommodate the reclassified Planobacterium taklimakanense. PMID:23934253

Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.

PubMed

Kim, Soo-Jin; Moon, Ji-Young; Lim, Jun-Muk; Ahn, Jae-Hyung; Weon, Hang-Yeon; Ahn, Tae-Young; Kwon, Soon-Wo

2014-03-01

Two strains, designated 5413J-26(T) and KIS18-15(T), were isolated from the air and forest soil, respectively, in South Korea. Cells of the two strains were Gram-stain-negative, aerobic, polar-flagellated and rod-shaped. According to the phylogenetic tree, strains 5413J-26(T) and KIS18-15(T) fell into the cluster of Sphingomonas sensu stricto. Strain 5413J-26(T) showed the highest sequence similarities with Sphingomonas trueperi LMG 2142(T) (96.6%), Sphingomonas molluscorum KMM 3882(T) (96.5%), Sphingomonas azotifigens NBRC 15497(T) (96.3 %) and Sphingomonas pituitosa EDIV(T) (96.1 %), while strain KIS18-15(T) had the highest sequence similarity with Sphingomonas soli T5-04(T) (96.8%), Sphingomonas pituitosa EDIV(T) (96.6%), Sphingomonas leidyi ATCC 15260(T) (96.6 %), Sphingomonas asaccharolytica NBRC 15499(T) (96.6 %) and Sphingomonas koreensis JSS26(T) (96.6 %). The 16S rRNA gene sequence similarity between strains 5413J-26(T) and KIS18-15(T) was 95.4 %. Ubiquinone 10 was the predominant respiratory quinone and homospermidine was the major polyamine. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids. The main cellular fatty acids (>10% of the total fatty acids) of strain 5413J-26(T) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C14 : 0 2-OH, and those of strain KIS18-15(T) were summed feature 8 and C16 : 0. Based on the results of 16S rRNA gene sequence analysis, and physiological and biochemical characterization, two novel species with the suggested names Sphingomonas aerophila sp. nov. (type strain 5413J-26(T) = KACC 16533(T) = NBRC 108942(T)) and Sphingomonas naasensis sp. nov. (type strain KIS18-15(T) = KACC 16534(T) = NBRC 108943(T)) are proposed.

Heterotrophic nitrogen removal by Acinetobacter sp. Y1 isolated from coke plant wastewater.

PubMed

Liu, YuXiang; Hu, Tingting; Song, Yujie; Chen, Hongping; Lv, YongKang

2015-11-01

A strain of Acinetobacter sp. Y1, which exhibited an amazing ability to remove ammonium, nitrite and nitrate, was isolated from the activated sludge of a coking wastewater treatment plant. The aim of this work was to study the ability, influence factors and possible pathway of nitrogen removal by Acinetobacter sp. Y1. Results showed that maximum removal rate of NH4(+)-N by the strain was 10.28 mg-N/L/h. Carbon source had significant influence on the growth and ammonium removal efficiencies of strain Y1. Pyruvate, citrate and acetate were favourable carbon sources for the strain. Temperature, pH value and shaking speed could affect the growth and nitrogen removal ability. Nitrate or nitrite could be used as a sole nitrogen source for the growth and removed efficiently by the strain. N2 levels increased to 53.74%, 50.21% and 55.13% within 36 h when 100 mg/L NH4(+)-N, NO2(-)-N or NO3(-) -N was used as sole nitrogen source in the gas detection experiment. The activities of hydroxylamine oxidoreductase (HAO), nitrate reductase (NR) and nitrite reductase (NiR), which are key enzymes in heterotrophic nitrification and aerobic denitrification, were all detectable in the strain. Consequently, a possible pathway for ammonium removal by the strain was also suggested. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Biotransformation of 4-chloro-2-nitrophenol into 5-chloro-2-methylbenzoxazole by a marine Bacillus sp. strain MW-1.

PubMed

Arora, Pankaj Kumar; Jain, Rakesh Kumar

2012-04-01

Decolourization, detoxification and biotransformation of 4-chloro-2-nitrophenol (4C2NP) by Bacillus sp. strain MW-1 were studied. This strain decolorized 4C2NP only in the presence of an additional carbon source. On the basis of thin layer chromatography (TLC), high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS), 4-chloro-2-aminophenol, 4-chloro-2-acetaminophenol and 5-chloro-2-methylbenzoxazole were identified as metabolites. Resting cells depleted 4C2NP with stoichiometric formation of 5-chloro-2-methyl benzoxazole. This is the first report of the formation of 5-chloro-2-methylbenzoxazole from 4C2NP by any bacterial strain.

Capsule Polysaccharide Mediates Bacterial Resistance to Antimicrobial Peptides

PubMed Central

Campos, Miguel A.; Vargas, Miguel A.; Regueiro, Verónica; Llompart, Catalina M.; Albertí, Sebastián; Bengoechea, José A.

2004-01-01

The innate immune system plays a critical role in the defense of areas exposed to microorganisms. There is an increasing body of evidence indicating that antimicrobial peptides and proteins (APs) are one of the most important weapons of this system and that they make up the protective front for the respiratory tract. On the other hand, it is known that pathogenic organisms have developed countermeasures to resist these agents such as reducing the net negative charge of the bacterial membranes. Here we report the characterization of a novel mechanism of resistance to APs that is dependent on the bacterial capsule polysaccharide (CPS). Klebsiella pneumoniae CPS mutant was more sensitive than the wild type to human neutrophil defensin 1, β-defensin 1, lactoferrin, protamine sulfate, and polymyxin B. K. pneumoniae lipopolysaccharide O antigen did not play an important role in AP resistance, and CPS was the only factor conferring protection against polymyxin B in strains lacking O antigen. In addition, we found a significant correlation between the amount of CPS expressed by a given strain and the resistance to polymyxin B. We also showed that K. pneumoniae CPS mutant bound more polymyxin B than the wild-type strain with a concomitant increased in the self-promoted pathway. Taken together, our results suggest that CPS protects bacteria by limiting the interaction of APs with the surface. Finally, we report that K. pneumoniae increased the amount of CPS and upregulated cps transcription when grown in the presence of polymyxin B and lactoferrin. PMID:15557634

Candida spencermartinsiae sp. nov., Candida taylorii sp. nov. and Pseudozyma abaconensis sp. nov., novel yeasts from mangrove and coral reef ecosystems.

PubMed

Statzell-Tallman, Adele; Scorzetti, Gloria; Fell, Jack W

2010-08-01

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.

Endosulfan Degradation by Selected Strains of Plant Growth Promoting Rhizobacteria.

PubMed

Rani, Rupa; Kumar, Vipin

2017-07-01

Sixty endosulfan tolerant bacterial strains were isolated from pesticide stressed agricultural soils. Five most tolerant strains were tested for plant growth promoting (PGP) activities and endosulfan degradation under different optimizing conditions in broth and soil. The strains PRB101 and PRB77 were the most efficient in terms of endosulfan degradation and PGP activities and showed solubilization indexes of 3.3 and 3.1 mm, indole acetic acid production of 71 and 68 μg mL -1 , siderophore zones of 13 mm each at the recommended dosage, respectively. Hydrogen cyanide and ammonia production remained unaffected in the presence of endosulfan. PRB101 and PRB77 strains were able to degrade 74% and 70% of endosulfan in broth and 67% and 63% in soil, respectively. Based on 16S rDNA analysis, the strains PRB101 and PRB77 exhibited 99% homology with Bacillus sp. KF984414 and Bacillus sp. LN849696, respectively.

Functional consortium for denitrifying sulfide removal process.

PubMed

Chen, Chuan; Ren, Nanqi; Wang, Aijie; Liu, Lihong; Lee, Duu-Jong

2010-03-01

Denitrifying sulfide removal (DSR) process simultaneously converts sulfide, nitrate, and chemical oxygen demand from industrial wastewaters to elemental sulfur, nitrogen gas, and carbon dioxide, respectively. This investigation utilizes a dilution-to-extinction approach at 10(-2) to 10(-6) dilutions to elucidate the correlation between the composition of the microbial community and the DSR performance. In the original suspension and in 10(-2) dilution, the strains Stenotrophomonas sp., Thauera sp., and Azoarcus sp. are the heterotrophic denitrifiers and the strains Paracoccus sp. and Pseudomonas sp. are the sulfide-oxidizing denitrifers. The 10(-4) dilution is identified as the functional consortium for the present DSR system, which comprises two functional strains, Stenotrophomonas sp. strain Paracoccus sp. At 10(-6) dilution, all DSR performance was lost. The functions of the constituent cells in the DSR granules were discussed based on data obtained using the dilution-to-extinction approach.

Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus.

PubMed

Ramírez-Bahena, Martha Helena; Peix, Alvaro; Rivas, Raúl; Camacho, María; Rodríguez-Navarro, Dulce N; Mateos, Pedro F; Martínez-Molina, Eustoquio; Willems, Anne; Velázquez, Encarna

2009-08-01

Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1% similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S-23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA-DNA hybridization analysis which revealed 21% genetic relatedness between strains PAC48T and PAC68T and 46% and 25%, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed.

Methyl Red Decolorization Efficiency of a Korea Strain of Aspergillus sp. Immobilized into Different Polymeric Matrices.

PubMed

Kim, Beom-Su; Blaghen, Mohamed; Lee, Kang-Min

2017-07-01

  Intensive research studies have revealed that fungal decolorization of dye wastewater is a promising replacement for the current process of dye wastewater decolorization. The authors isolated an Aspergillus sp. from the effluent of a textile industry area in Korea and assessed the effects of a variety of operational parameters on the decolorization of methyl red (MR) by this strain of Aspergillus sp. This Aspergillus sp. was then immobilized by entrapment in several polymeric matrices and the effects of operational conditions on MR decolorization were investigated again. The optimal decolorization activity of this Aspergillus sp. was observed in 1% glucose at a temperature of 37 °C and pH of 6.0. Furthermore, stable decolorization efficiency was observed when fungal biomass was immobilized into alginate gel during repeated batch experiment. These results suggest that the Aspergillus sp. isolated in Korea could be used to treat industrial wastewaters containing MR dye.

Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.

PubMed

Liu, Qing; Liu, Hongcan; Zhang, Jianli; Zhou, Yuguang; Xin, Yuhua

2013-08-01

In this study, two psychrophilic bacterial strains were isolated from the China No. 1 glacier in Xinjiang, north-west China. Cells were Gram-positive rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains belonged to the genus Cryobacterium. Phylogenetic analysis showed that they clustered together and are most closely related to Cryobacterium luteum CGMCC 1.11210(T), Cryobacterium flavum CGMCC 1.11215(T), Cryobacterium psychrophilum CGMCC 1.4292(T), Cryobacterium psychrotolerans CGMCC 1.5382(T) and Cryobacterium roopkundense CGMCC 1.10672(T). The major cellular fatty acids of the novel strains were anteiso-C15 : 0, anteiso-C15 : 1 A, iso-C16 : 0 and iso-C15 : 0. Both strains contained diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid in the cell membrane. The results of DNA-DNA hybridization and physiological tests allowed the genotypic and phenotypic differentiation of strains Hh34(T) and Hh28 from related species. However, their high DNA-DNA relatedness showed that they belong to the same novel species. Strain Hh34(T) (= NBRC 107883(T) = CGMCC 1.11211(T)) was selected as the type strain to represent this novel species, for which the name Cryobacterium levicorallinum sp. nov. is proposed.

Isolation and characterization of fatty acid methyl ester (FAME)-producing Streptomyces sp. S161 from sheep (Ovis aries) faeces.

PubMed

Lu, Y; Wang, J; Deng, Z; Wu, H; Deng, Q; Tan, H; Cao, L

2013-09-01

An actinomycete producing oil-like mixtures was isolated and characterized. The strain was isolated from sheep faeces and identified as Streptomyces sp. S161 based on 16S rRNA gene sequence analysis. The strain showed cellulase and xylanase activities. The (1) H nuclear magnetic resonance (NMR) spectra of the mixtures showed that the mixtures were composed of fatty acid methyl esters (52·5), triglycerides (13·7) and monoglycerides (9·1) (mol.%). Based on the gas chromatography-mass spectrometry (GC-MS) analysis, the fatty acid methyl esters were mainly composed of C14-C16 long-chain fatty acids. The results indicated that Streptomyces sp. S161 could produce fatty acid methyl esters (FAME) directly from starch. To our knowledge, this is the first isolated strain that can produce biodiesel (FAME) directly from starch. © 2013 The Society for Applied Microbiology.

Influence of a bacteriophage on the population dynamics of toxic dinoflagellates by lysis of algicidal bacteria.

PubMed

Cai, Wenwei; Wang, Hui; Tian, Yun; Chen, Feng; Zheng, Tianling

2011-11-01

A lytic phage (øZCW1) was isolated from an algicidal bacterium Pseudoalteromonas sp. strain SP48 that specifically kills the toxic dinoflagellate Alexandrium tamarense. We demonstrated that øZCW1 could trigger the growth of A. tamarense by inhibiting the growth of algicidal bacterium SP48. In contrast, the growth of A. tamarense was suppressed when cocultured with either SP48 or the øZCW1-resistant mutant of SP48. This study provides the first evidence of the indirect impact of bacteriophage on bloom-forming microalgae via phage lysis of alga-killing bacteria.

Enzymic Dehalogenation of 4-Chlorobenzoyl Coenzyme A in Acinetobacter sp. Strain 4-CB1

PubMed Central

Copley, Shelley D.; Crooks, Gwen P.

1992-01-01

4-Chlorobenzoate degradation in cell extracts of Acinetobacter sp. strain 4-CB1 occurs by initial synthesis of 4-chlorobenzoyl coenzyme A (4-chlorobenzoyl CoA) from 4-chlorobenzoate, CoA, and ATP. 4-Chlorobenzoyl CoA is dehalogenated to 4-hydroxybenzoyl CoA. Following the dehalogenation reaction, 4-hydroxybenzoyl CoA is hydrolyzed to 4-hydroxybenzoate and CoA. Possible roles for the CoA moiety in the dehalogenation reaction are discussed. PMID:16348702

Molecular phylogeny, pathogenicity and toxigenicity of Fusarium oxysporum f. sp. lycopersici

PubMed Central

Nirmaladevi, D.; Venkataramana, M.; Srivastava, Rakesh K.; Uppalapati, S. R.; Gupta, Vijai Kumar; Yli-Mattila, T.; Clement Tsui, K. M.; Srinivas, C.; Niranjana, S. R.; Chandra, Nayaka S.

2016-01-01

The present study aimed at the molecular characterization of pathogenic and non pathogenic F. oxysporum f. sp. lycopersici strains isolated from tomato. The causal agent isolated from symptomatic plants and soil samples was identified based on morphological and molecular analyses. Pathogenicity testing of 69 strains on five susceptible tomato varieties showed 45% of the strains were highly virulent and 30% were moderately virulent. Molecular analysis based on the fingerprints obtained through ISSR indicated the presence of wide genetic diversity among the strains. Phylogenetic analysis based on ITS sequences showed the presence of at least four evolutionary lineages of the pathogen. The clustering of F. oxysporum with non pathogenic isolates and with the members of other formae speciales indicated polyphyletic origin of F. oxysporum f. sp. lycopersici. Further analysis revealed intraspecies variability and nucleotide insertions or deletions in the ITS region among the strains in the study and the observed variations were found to be clade specific. The high genetic diversity in the pathogen population demands for development of effective resistance breeding programs in tomato. Among the pathogenic strains tested, toxigenic strains harbored the Fum1 gene clearly indicating that the strains infecting tomato crops have the potential to produce Fumonisin. PMID:26883288

Wickerhamomyces queroliae sp. nov. and Candida jalapaonensis sp. nov., two yeast species isolated from Cerrado ecosystem in North Brazil.

PubMed

Rosa, Carlos A; Morais, Paula B; Lachance, Marc-André; Santos, Renata O; Melo, Weilan G P; Viana, Rodney H O; Bragança, Marcos A L; Pimenta, Raphael S

2009-05-01

Two novel yeast species, Wickerhamomyces queroliae sp. nov. and Candida jalapaonensis sp. nov., were isolated, respectively, from larvae of Anastrepha mucronata (Diptera: Tephritidae) collected from ripe fruit of Peritassa campestris ('Bacupari', Hippocrateaceae) and from flowers of Centropogon cornutus (Campanulaceae) in the Cerrado ecosystem of the state of Tocantins, Brazil. Analysis of the D1/D2 large-subunit rRNA gene sequences placed W. queroliae in the Wickerhamomyces clade near Wickerhamomyces ciferri and Candida silvicultrix. Candida jalapaonensis belongs to the Wickerhamiella clade and is related to Candida drosophilae. The type strain of Wickerhamomyces queroliae is UFMG-05-T200.1(T) (=CBS 10936(T)=NRRL Y-48478(T)) and the type strain of Candida jalapaonensis is UFMG-03-T210(T) (=CBS 10935(T)=NRRL Y-48477(T)).

Arcticibacter pallidicorallinus sp. nov. isolated from glacier ice.

PubMed

Liu, Qing; Kim, Song-gun; Liu, Hong-can; Xin, Yu-hua; Zhou, Yu-guang

2014-07-01

A Gram-stain-negative, rod-shaped bacterium (strain Hh36(T)) was isolated from the No. 1 glacier in Xinjiang, north-west China. Colonies of strain Hh36(T) were pink, convex and round on PYG medium plates. Strain Hh36(T) was able to grow at 4-30 °C and pH 6.0-8.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh36(T) was related to members of the genus Arcticibacter. The major cellular fatty acids of the novel strain were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The G+C content of the genomic DNA was 44.0 mol%. On the basis of phenotypic characteristics and phylogenetic analysis, strain Hh36(T) is considered to represent a novel species of the genus Arcticibacter, for which the name Arcticibacter pallidicorallinus sp. nov. is proposed. The type strain is Hh36(T) ( = CGMCC 1.9313(T)  = KCTC 32542(T)). © 2014 Institute of Microbiology, Chinese Academy of Sciences.

Biochemical characterization of sunscreening mycosporine-like amino acids from two Nostoc species inhabiting diverse habitats.

PubMed

Richa; Sinha, Rajeshwar P

2015-01-01

We have screened two Nostoc species inhabiting diverse habitats for the presence of sunscreening mycosporine-like amino acid (MAA) compounds. The identification and characterization of one MAA (RT 3.1-3.8 min, λmax -334 nm) from both Nostoc species were performed using absorption spectroscopy, high-performance liquid chromatography (HPLC), electrospray ionization-mass spectrometry (ESI-MS), Fourier transform infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy. Shinorine and porphyra-334 were commonly present in both Nostoc sp. strain HKAR-2 and Nostoc sp. strain HKAR-6. Nostoc sp. strain HKAR-2 also showed the presence of an unknown MAAs with retention time of 6.9 min and a corresponding λmax of 334 nm. Present investigation clearly demonstrated the presence of diverse profile of MAAs in the hot spring cyanobacterium in comparison to the rice field isolate. Thus, Nostoc sp. strain HKAR-2 would be a better source for the production of MAAs that can be used as a potent natural sunscreen against UV-B irradiation.

Metalaxyl Degradation by Mucorales Strains Gongronella sp. and Rhizopus oryzae.

PubMed

Martins, Maria Rosário; Santos, Cledir; Pereira, Pablo; Cruz-Morais, Júlio; Lima, Nelson

2017-12-14

In this study, the degradation of metalaxyl was investigated in the presence of two Mucorales strains, previously isolated from soil subjected to repeated treatments with this fungicide and selected after enrichment technique. Fungal strains were characterised by a polyphasic approach using phylogenetic analysis of the Internal Transcribed Spacer (ITS) gene region, phenotypic characterisation by Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) spectral analysis, and growth kinetics experiments. The strains were identified as Gongronella sp. and Rhizopus oryzae . The fungal growth kinetics in liquid cultures containing metalaxyl fits with Haldane model. Under laboratory conditions, the ability of Gongronella sp. and R. oryzae cultures to degrade metalaxyl was evaluated in liquid cultures and soil experiments. Both species were able to: (a) use metalaxyl as the main carbon and energy source; and (b) degrade metalaxyl in polluted soils, with rates around 1.0 mg kg - ¹ d - ¹. This suggests these strains could degrade metalaxyl in soils contaminated with this fungicide.

Application of two bacterial strains for wastewater bioremediation and assessment of phenolics biodegradation.

PubMed

Paisio, Cintia E; Quevedo, María R; Talano, Melina A; González, Paola S; Agostini, Elizabeth

2014-08-01

The use of native bacteria is a useful strategy to decontaminate industrial effluents. In this work, two bacterial strains isolated from polluted environments constitutes a promising alternative since they were able to remove several phenolic compounds not only from synthetic solutions but also from effluents derived from a chemical industry and a tannery which are complex matrices. Acinetobacter sp. RTE 1.4 showed ability to completely remove 2-methoxyphenol (1000 mg/L) while Rhodococcus sp. CS 1 not only degrade the same concentration of this compound but also removed 4- chlorophenol, 2,4-dichlorophenol and pentachlorophenol with high efficiency. Moreover, both bacteria degraded phenols naturally present or even exogenously added at high concentrations in effluents from the chemical industry and a tannery in short time (up to 5 d). In addition, a significant reduction of biological oxygen demand and chemical oxygen demand values was achieved after 7 d of treatment for both effluents using Acinetobacter sp. RTE 1.4 and Rhodococcus sp. CS1, respectively. These results showed that Acinetobacter sp. RTE1.4 and Rhodococcus sp. CS 1 might be considered as useful biotechnological tools for an efficient treatment of different effluents, since they showed wide versatility to detoxify these complex matrices, even supplemented with high phenol concentrations.

Wet-plate culture studies of Penicillium sp. PT95 and Q1 for mass production of sclerotia.

PubMed

Zhao, Wen-Jing; An, Cui-Hong; Han, Jian-Rong

2014-04-01

Penicillium sp. PT95 and Q1 strains were able to form abundant orange, sand-shaped sclerotia in which carotenoids were accumulated. To determine the potential availability of the wet-plate method for mass production of sclerotia, nine kinds of liquid media were used culture the PT95 and Q1 strains. The results of the wet-plate culture showed that on 25% glycerol nitrate broth medium, the growth of both strains was relatively slow, and no sclerotia were found. Q1 strain cultured on Czapek's yeast extract broth medium could not form sclerotia. On other media, both strains could form sclerotia. For PT95 strain, the highest sclerotial biomass (380 mg plate(-1) ) and carotenoids yield (20.88 µg plate(-1) ) could be obtained on Czapek's yeast extract broth and Georgiou's liquid medium, respectively. For Q1 strain, malt extract broth medium gave the highest sclerotial biomass (340 mg plate(-1) ) and omitting iron Joham's liquid medium gave the highest carotenoids yield (18.29 µg plate(-1) ). The results from this study suggest the potential usage of wet-plate method in the mass production of sclerotia of the PT95 and Q1 strains. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient biodegradation of phenanthrene by a novel strain Massilia sp. WF1 isolated from a PAH-contaminated soil.

PubMed

Wang, Haizhen; Lou, Jun; Gu, Haiping; Luo, Xiaoyan; Yang, Li; Wu, Laosheng; Liu, Yong; Wu, Jianjun; Xu, Jianming

2016-07-01

A novel phenanthrene (PHE)-degrading strain Massilia sp. WF1, isolated from PAH-contaminated soil, was capable of degrading PHE by using it as the sole carbon source and energy in a range of pH (5.0-8.0), temperatures (20-35 °C), and PHE concentrations (25-400 mg L(-1)). Massilia sp. WF1 exhibited highly effective PHE-degrading ability that completely degraded 100 mg L(-1) of PHE over 2 days at optimal conditions (pH 6.0, 28 °C). The kinetics of PHE biodegradation by Massilia sp. WF1 was well represented by the Gompertz model. Results indicated that PHE biodegradation was inhibited by the supplied lactic acid but was promoted by the supplied carbon sources of glucose, citric acid, and succinic acid. Salicylic acid (SALA) and phthalic acid (PHTA) were not utilized by Massilia sp. WF1 and had no obvious effect on PHE biodegradation. Only two metabolites, 1-hydroxy-2-naphthoic acid (1H2N) and PHTA, were identified in PHE biodegradation process. Quantitatively, nearly 27.7 % of PHE was converted to 1H2N and 30.3 % of 1H2N was further metabolized to PHTA. However, the PHTA pathway was broken and the SALA pathway was ruled out in PHE biodegradation process by Massilia sp. WF1.

Purification and Characterization of a Protease Produced by a Planomicrobium sp. L-2 from Gut of Octopus vulgaris

PubMed Central

Liu, Qing; Sun, Shujing; Piao, Meizi; Yang, Ji Young

2013-01-01

Protease widely exists in the digestive tract of animals and humans, playing a very important role in protein digestion and absorption. In this study, a high protease-producing strain Planomicrobium sp. L-2 was isolated and identified from the digestive tract of Octopus variabilis. The strain was identified by physiological and biochemical experiments and 16S rDNA sequences analysis. A protease was obtained from the strain Planomicrobium sp. L-2 through ammonium sulfate precipitation, dialysis and enrichment, DEAE-Sephadex A50 anion-exchange chromatography, and Sephadex G-100 gel chromatography. The molecular weight and properties of the protease were characterized, including optimum temperature and pH, thermal stability, protease inhibitions and metal ions. According to our results, the protease from Planomicrobium sp. L-2 strain designated as F1-1 was obtained by three-step separation and purification from crude enzyme. The molecular weight of the protease was 61.4 kDa and its optimum temperature was 40°C. The protease F1-1 showed a broad pH profile for casein hydrolysis between 5.0~11.0. No residual activity was observed after incubation for 40 min at 60°C and 60 min at 50°C. F1-1 protease was inhibited by Mn2+, Hg2+, Pb2+, Zn2+, and Cu2+ ions, as well as PMSF, indicating that the protease F1-1 was a serine protease. Additionally, research basis provided by this study could be considered for industrial application of octopus intestinal proteases. PMID:24551830

A freshwater bacterial strain, Shewanella sp. Lzh-2, isolated from Lake Taihu and its two algicidal active substances, hexahydropyrrolo[1,2-a]pyrazine-1,4-dione and 2, 3-indolinedione.

PubMed

Li, Zhenghua; Lin, Shengqin; Liu, Xianglong; Tan, Jing; Pan, Jianliang; Yang, Hong

2014-05-01

Cyanobacterial blooms have become a serious problem in Lake Taihu during the last 20 years, and Microcystis aeruginosa and Synechococcus sp. are the two dominant species in cyanobacterial blooms of Lake Taihu. A freshwater bacterial strain, Shewanella sp. Lzh-2, with strong algicidal properties against harmful cyanobacteria was isolated from Lake Taihu. Two substances with algicidal activity secreted extracellularly by Shewanella sp. Lzh-2, S-2A and S-2B, were purified from the bacterial culture of strain Lzh-2 using ethyl acetate extraction, column chromatography, and high performance liquid chromatography (HPLC) in turn. The substances S-2A and S-2B were identified as hexahydropyrrolo[1,2-a]pyrazine-1,4-dione and 2, 3-indolinedione (isatin), respectively, based on liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), and hydrogen-nuclear magnetic resonance (H-NMR) analyses, making this the first report of their algicidal activity toward cyanobacteria. S-2A (hexahydropyrrolo[1,2-a]pyrazine-1,4-dione) had no algicidal effects against Synechococcus sp. BN60, but had a high level of algicidal activity against M. aeruginosa 9110. The LD50 value of S-2A against M. aeruginosa 9110 was 5.7 μg/ml. S-2B (2, 3-indolinedione) showed a potent algicidal effect against both M. aeruginosa 9110 and Synechococcus sp. BN60, and the LD50 value of S-2B against M. aeruginosa 9110 and Synechococcus sp. BN60 was 12.5 and 34.2 μg/ml, respectively. Obvious morphological changes in M. aeruginosa 9110 and Synechococcus sp. BN60 were observed after they were exposed to S-2A (or S-2B) for 24 h. Approximately, the algicidal activity, the concentration of S-2A and S-2B, and the cell density of Lzh-2 were positively related to each other during the cocultivation process. Overall, these findings increase our knowledge about algicidal substances secreted by algicidal bacteria and indicate that strain Lzh-2 and its two algicidal substances have the potential for use as a bio-agent in controlling cyanobacterial blooms in Lake Taihu.

Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

PubMed

Wang, Guojun; Barrett, Nolan H; McCarthy, Peter J

2017-02-02

The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. Copyright © 2017 Wang et al.

Methylobacterium suomiense sp. nov. and Methylobacterium lusitanum sp. nov., aerobic, pink-pigmented, facultatively methylotrophic bacteria.

PubMed

Doronina, Nina V; Trotsenko, Yuri A; Kuznetsov, Boris B; Tourova, Tatjana P; Salkinoja-Salonen, Mirja S

2002-05-01

Two aerobic, pink-pigmented, facultatively methylotrophic bacteria, strains F20T and RXM(T), are described taxonomically. On the basis of their phenotypic and genotypic properties, the isolates are proposed as novel species of the genus Methylobacterium, Methylobacterium suomiense sp. nov. (type strain F20T = VKM B-2238T = NCIMB 13778T) and Methylobacterium lusitanum sp. nov. (type strain RXMT = VKM B-2239T = NCIMB 13779T).

Identification of the main mechanisms involved in the tolerance and bioremediation of Cr(VI) by Bacillus sp. SFC 500-1E.

PubMed

Ontañon, Ornella M; Fernandez, Marilina; Agostini, Elizabeth; González, Paola S

2018-06-01

Chromium pollution is a problem that affects different areas worldwide and, therefore, must be solved. Bioremediation is a promising alternative to treat environmental contamination, but finding bacterial strains able to tolerate and remove different contaminants is a major challenge, since most co-polluted sites contain mixtures of organic and inorganic substances. In the present work, Bacillus sp. SFC 500-1E, isolated from the bacterial consortium SFC 500-1 native to tannery sediments, showed tolerance to various concentrations of different phenolic compounds and heavy metals, such as Cr(VI). This strain was able to efficiently remove Cr(VI), even in the presence of phenol. The detection of the chrA gene suggested that Cr(VI) extrusion could be a mechanism that allowed this strain to tolerate the heavy metal. However, reduction through cytosolic NADH-dependent chromate reductases may be the main mechanism involved in the remediation. The information provided in this study about the mechanisms through which Bacillus sp. SFC 500-1E removes Cr(VI) should be taken into account for the future application of this strain as a possible candidate to remediate contaminated environments.

Internal desynchronization in a model of night-work by forced activity in rats.

PubMed

Salgado-Delgado, R; Angeles-Castellanos, M; Buijs, M R; Escobar, C

2008-06-26

Individuals engaged in shift- or night-work show disturbed diurnal rhythms, out of phase with temporal signals associated to the light/dark (LD) cycle, resulting in internal desynchronization. The mechanisms underlying internal desynchrony have been mainly investigated in experimental animals with protocols that induce phase shifts of the LD cycle and thus modify the activity of the suprachiasmatic nucleus (SCN). In this study we developed an animal model of night-work in which the light-day cycle remained stable and rats were required to be active in a rotating wheel for 8 h daily during their sleeping phase (W-SP). This group was compared with rats that were working in the wheel during their activity phase (W-AP) and with undisturbed rats (C). We provide evidence that forced activity during the sleeping phase (W-SP group) alters not only activity, but also the temporal pattern of food intake. In consequence W-SP rats showed a loss of glucose rhythmicity and a reversed rhythm of triacylglycerols. In contrast W-AP rats did not show such changes and exhibited metabolic rhythms similar to those of the controls. The three groups exhibited the nocturnal corticosterone increase, in addition the W-SP and W-AP groups showed increase of plasma corticosterone associated with the start of the working session. Forced activity during the sleep phase did not modify SCN activity characterized by the temporal patterns of PER1 and PER2 proteins, which remained in phase with the LD cycle. These observations indicate that a working regimen during the sleeping period elicits internal desynchronization in which activity combined with feeding uncouples metabolic functions from the biological clock which remains fixed to the LD cycle. The present data suggest that in the night worker the combination of work and eating during working hours may be the cause of internal desynchronization.

Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata

PubMed Central

Sutherland, Kathryn Patterson; Shaban, Sameera; Joyner, Jessica L.; Porter, James W.; Lipp, Erin K.

2011-01-01

Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments were conducted with A. palmata maintained in closed aquaria to determine infectivity of strain PDR60 from reef and wastewater sources. Strain PDR60 from wastewater and diseased A. palmata caused disease signs in elkhorn coral in as little as four and five days, respectively, demonstrating that wastewater is a definitive source of APS and identifying human strain PDR60 as a coral pathogen through fulfillment of Koch's postulates. A. palmata inoculated with strain PDR60 from C. abbreviata showed limited virulence, with one of three inoculated fragments developing APS signs within 13 days. Strain PDR60 from non-host coral S. siderea showed a delayed pathogenic effect, with disease signs developing within an average of 20 days. These results suggest that C. abbreviata and non-host corals may function as reservoirs or vectors of the APS pathogen. Our results provide the first example of a marine “reverse zoonosis” involving the transmission of a human pathogen (S. marcescens) to a marine invertebrate (A. palmata). These findings underscore the interaction between public health practices and environmental health indices such as coral reef survival. PMID:21858132

Kribbella deserti sp. nov., isolated from rhizosphere soil of Ammopiptanthus mongolicus.

PubMed

Sun, Ji-Quan; Xu, Lian; Guo, Yan; Li, Wei-Le; Shao, Zhong-Qiu; Yang, Yuan-Liang; Wu, Xiao-Lei

2017-03-01

A Gram-stain-positive, aerobic bacterial strain, designated SL15-1 T , was isolated from desert soil which was sampled from the rhizosphere of Ammopiptanthus mongolicus, Hangjin Banner, Ordos, Inner Mongolia, northern China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SL15-1 T was clustered with Kribbella strains, sharing the highest similarity of 16S rRNA gene sequence (96.97 %) with Kribbella sandramycini DSM 15626 T . Strain SL15-1 T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an unknown phospholipid, an unknown lipid and two unknown aminophospholipids as the major polar lipids. MK-9(H4) was the predominant menaquinone, while anteiso-C15 : 0, iso-C16 : 0, C17 : 1ω8c and iso-C14 : 0 were the major cellular fatty acids. Its genomic DNA G+C content was 65.3 mol%. The results of physiological and biochemical tests allowed the discrimination of strain SL15-1 T from its phylogenetic relatives. Kribbella deserti sp. nov. is therefore proposed with strain SL15-1 T (=CGMCC 1.15906 T =KCTC 39825 T ) as the type strain.

Growth of Chlamydomonas reinhardtii in acetate-free medium when co-cultured with alginate-encapsulated, acetate-producing strains of Synechococcus sp. PCC 7002.

PubMed

Therien, Jesse B; Zadvornyy, Oleg A; Posewitz, Matthew C; Bryant, Donald A; Peters, John W

2014-01-01

The model alga Chlamydomonas reinhardtii requires acetate as a co-substrate for optimal production of lipids, and the addition of acetate to culture media has practical and economic implications for algal biofuel production. Here we demonstrate the growth of C. reinhardtii on acetate provided by mutant strains of the cyanobacterium Synechococcus sp. PCC 7002. Optimal growth conditions for co-cultivation of C. reinhardtii with wild-type and mutant strains of Synechococcus sp. 7002 were established. In co-culture, acetate produced by a glycogen synthase knockout mutant of Synechococcus sp. PCC 7002 was able to support the growth of a lipid-accumulating mutant strain of C. reinhardtii defective in starch production. Encapsulation of Synechococcus sp. PCC 7002 using an alginate matrix was successfully employed in co-cultures to limit growth and maintain the stability. The ability of immobilized strains of the cyanobacterium Synechococcus sp. PCC 7002 to produce acetate at a level adequate to support the growth of lipid-accumulating strains of C. reinhartdii offers a potentially practical, photosynthetic alternative to providing exogenous acetate into growth media.

Strain selection of microalgae isolated from Tunisian coast: characterization of the lipid profile for potential biodiesel production.

PubMed

Gnouma, Asma; Sehli, Emna; Medhioub, Walid; Ben Dhieb, Rym; Masri, Mahmoud; Mehlmer, Norbert; Slimani, Wissem; Sebai, Khaled; Zouari, Amel; Brück, Thomas; Medhioub, Amel

2018-06-26

Microalgae could be of importance for future biodiesel production as an alternative for a third generation of biofuels. To select the most appropriate strain for biodiesel production, three microalgae species, namely Isochrysis sp., Nannochloropsis maritima and Tetraselmis sp., isolated from Tunisian coast, were biochemically characterized. Initially, gas chromatography analysis showed that Isochrysis sp. and N. maritima contained 5- and 10-fold total fatty acids, respectively, more than Tetraselmis sp. Then, the two microalgae Isochrysis sp. and N. maritima were subject to random mutagenesis using ultraviolet-C radiation. Subsequently, a total of 18 mutants were obtained from both species. The neutral lipid evaluation on said 18 mutants allowed the retention of only 7 to further fatty acid characterization. Finally, gas chromatography revealed that the mutant 5c Isochrysis sp. was characterized by a high level of saturated fatty acids (52.3%), higher amount of monounsaturated fatty acids (29.3%), lower level of polyunsaturated fatty acids (18.4%) and a significant 1.3-fold increase in its C16-C18 content compared to the wild-type strain, which would make it an interesting candidate for biofuel production.

Flavobacterium xueshanense sp. nov. and Flavobacterium urumqiense sp. nov., two psychrophilic bacteria isolated from glacier ice.

PubMed

Dong, Kun; Liu, Hongcan; Zhang, Jianli; Zhou, Yuguang; Xin, Yuhua

2012-05-01

Two Gram-stain-negative, rod-shaped bacteria, designated strains Sr22(T) and Sr25(T), were isolated from water of melted ice from the China No.1 glacier, Xinjiang Uygur Autonomous Region, China. Cells formed yellow, circular, convex colonies. 16S rRNA gene sequence analysis indicated that strains Sr22(T) and Sr25(T) belong to the genus Flavobacterium, sharing ≤99.1  and ≤99.6 % similarity, respectively, with the type strains of recognized species of the genus. Strain Sr22(T) shared highest 16S rRNA gene sequence similarity with Flavobacterium tiangeerense CGMCC 1.6847(T) (98.6 %), Flavobacterium fryxellicola LMG 22022(T) (98.1 %) and Flavobacterium omnivorum CGMCC 1.2747(T) (99.1 %). Strain Sr25(T) shared highest similarity with Flavobacterium sinopsychrotolerans CGMCC 1.8704(T) (98.5 %), Flavobacterium degerlachei NBRC 102677(T) (98.4 %) and Flavobacterium xinjiangense CGMCC 1.2749(T) (99.5 %). The predominant fatty acids of strain Sr22(T) were iso-C(15 : 1) G (6.01 %), iso-C(15 : 0) (8.93 %), iso-C(16 : 1) H (12.68 %), iso-C(16 : 0) (10.4 %), C(15 : 1)ω6c (8.97 %), C(17 : 1)ω6c (5.96 %), iso-C(16 : 0) 3-OH (11.14 %) and summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c, 12.33 %). The major fatty acids of strain Sr25(T) were iso-C(15 : 0) (10.8 %), anteiso-C(15 : 0) (5.23 %), C(15 : 1)ω6c (11.79 %), C(17 : 1)ω6c (5.43 %), iso-C(16 : 0) 3-OH (7.04 %) and summed feature 3 (20.42 %). The genomic DNA G+C contents of strains Sr22(T) and Sr25(T) were 37.2 and 35.1 mol%. On the basis of differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus Flavobacterium, for which the names Flavobacterium xueshanense sp. nov. (type strain Sr22(T)  = CGMCC 1.9227(T)  = NBRC 106479(T)) and Flavobacterium urumqiense sp. nov. (type strain Sr25(T)  = CGMCC 1.9230(T)  = NBRC 106480(T)) are proposed.

Transcription of mouse Sp2 yields alternatively spliced and sub-genomic mRNAs in a tissue- and cell-type-specific fashion.

PubMed

Yin, Haifeng; Nichols, Teresa D; Horowitz, Jonathan M

2010-07-01

The Sp-family of transcription factors is comprised by nine members, Sp1-9, that share a highly conserved DNA-binding domain. Sp2 is a poorly characterized member of this transcription factor family that is widely expressed in murine and human cell lines yet exhibits little DNA-binding or trans-activation activity in these settings. As a prelude to the generation of a "knock-out" mouse strain, we isolated a mouse Sp2 cDNA and performed a detailed analysis of Sp2 transcription in embryonic and adult mouse tissues. We report that (1) the 5' untranslated region of Sp2 is subject to alternative splicing, (2) Sp2 transcription is regulated by at least two promoters that differ in their cell-type specificity, (3) one Sp2 promoter is highly active in nine mammalian cell lines and strains and is regulated by at least five discrete stimulatory and inhibitory elements, (4) a variety of sub-genomic messages are synthesized from the Sp2 locus in a tissue- and cell-type-specific fashion and these transcripts have the capacity to encode a novel partial-Sp2 protein, and (5) RNA in situ hybridization assays indicate that Sp2 is widely expressed during mouse embryogenesis, particularly in the embryonic brain, and robust Sp2 expression occurs in neurogenic regions of the post-natal and adult brain. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut.

PubMed

Praet, Jessy; Cnockaert, Margo; Meeus, Ivan; Smagghe, Guy; Vandamme, Peter

2017-06-01

Spectra of five isolates (LMG 28358 T , LMG 29879 T , LMG 29880 T , LMG 28359 T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359 T and R-53705 which also grouped in the same MALDI-TOF MS cluster, while different DNA fingerprints were obtained for the other isolates. Comparative 16S rRNA gene sequence analysis of the four different strains identified Gilliamella apicola NCIMB 14804 T as nearest neighbour species. Average nucleotide identity values of draft genome sequences of the four isolates and of G. apicola NCIMB 14804 T were below the 96% threshold value for species delineation and all four strains and G. apicola NCIMB 14804 T were phenotypically distinct. Together, the draft genome sequences and phylogenetic and phenotypic data indicate that the four strains represent four novel Gilliamella species for which we propose the names Gilliamella intestini sp. nov., with LMG 28358 T as the type strain, Gilliamella bombicola sp. nov., with LMG 28359 T as the type strain, Gilliamella bombi sp. nov., with LMG 29879 T as the type strain and Gilliamella mensalis sp. nov., with LMG 29880 T as the type strain. Copyright © 2017 Elsevier GmbH. All rights reserved.

Candida wancherniae sp. nov. and Candida morakotiae sp. nov., two novel ascomycetous anamorphic yeast species found in Thailand.

PubMed

Nakase, Takashi; Jindamorakot, Sasitorn; Ninomiya, Shinya; Imanishi, Yumi; Kawasaki, Hiroko

2009-04-01

Seven yeast strains isolated from natural substrates of Thailand were found to represent two novel species of Candida, an ascomycetous anamorphic genus. Three strains, ST-233, ST-259 and ST-260, isolated from insect frass and plant leaves were found to represent a single novel species related to Metschnikowia agaves in a tree based on the D1/D2 domain sequences of the 26S rRNA genes. This species is clearly discriminated from M. agaves by the carbon assimilation patterns and required vitamins. The remaining four strains, ST-18, ST-261, ST-606 and ST-658, isolated from the fruit body of a mushroom, insect frass, decayed jack fruit and an unidentified flower, were found to represent a single species which is related to Candida corydali, a recently described insect-associated species, in a neighbor-joining tree based on the D1/D2 sequences. This species is clearly discriminated from C. corydali by the ability to assimilate propane-1,2-diol and the inability to assimilate glucono-delta-lactone. They are described as Candida wancherniae sp. nov. and Candida morakotiae sp. nov., respectively.

Yeasts associated with the curculionid beetle Xyloterinus politus: Candida xyloterini sp. nov., Candida palmyrensis sp. nov. and three common ambrosia yeasts.

PubMed

Suh, Sung-Oui; Zhou, Jianlong

2010-07-01

Seven yeast strains were isolated from the body surface and galleries of Xyloterinus politus, the ambrosia beetle that attacks black oak trees. Based on rDNA sequence comparisons and other taxonomic characteristics, five of the strains were identified as members of the species Saccharomycopsis microspora, Wickerhamomyces hampshirensis and Candida mycetangii, which have been reported previously as being associated with insects. The remaining two yeast strains were proposed as representatives of two novel species, Candida xyloterini sp. nov. (type strain ATCC 62898(T)=CBS 11547(T)) and Candida palmyrensis sp. nov. (type strain ATCC 62899(T)=CBS 11546(T)). C. xyloterini sp. nov. is a close sister taxon to Ogataea dorogensis and assimilates methanol as a sole carbon source but lacks ascospores. On the other hand, C. palmyrensis sp. nov. is phylogenetically distinct from any other ambrosia yeast reported so far. The species was placed near Candida sophiae-reginae and Candida beechii based on DNA sequence analyses, but neither of these were close sister taxa to C. palmyrensis sp. nov.

Kinetics of sulfate and hydrogen uptake by the thermophilic sulfate-reducing bacteria thermodesulfobacterium sp. Strain JSP and thermodesulfovibrio sp. Strain R1Ha3

PubMed

Sonne-Hansen; Westermann; Ahring

1999-03-01

Half-saturation constants (Km), maximum uptake rates (Vmax), and threshold concentrations for sulfate and hydrogen were determined for two thermophilic sulfate-reducing bacteria (SRB) in an incubation system without headspace. Km values determined for the thermophilic SRB were similar to the constants described for mesophilic SRB isolated from environments with low sulfate concentrations.

Kinetics of Sulfate and Hydrogen Uptake by the Thermophilic Sulfate-Reducing Bacteria Thermodesulfobacterium sp. Strain JSP and Thermodesulfovibrio sp. Strain R1Ha3

PubMed Central

Sonne-Hansen, Jacob; Westermann, Peter; Ahring, Birgitte K.

1999-01-01

Half-saturation constants (Km), maximum uptake rates (Vmax), and threshold concentrations for sulfate and hydrogen were determined for two thermophilic sulfate-reducing bacteria (SRB) in an incubation system without headspace. Km values determined for the thermophilic SRB were similar to the constants described for mesophilic SRB isolated from environments with low sulfate concentrations. PMID:10049897

Draft Genome Sequence of Cellulolytic and Xylanolytic Cellulomonas sp. Strain B6 Isolated from Subtropical Forest Soil

PubMed Central

Piccinni, Florencia; Murua, Yanina; Ghio, Silvina; Talia, Paola; Rivarola, Máximo

2016-01-01

Cellulomonas sp. strain B6 was isolated from a subtropical forest soil sample and presented (hemi)cellulose-degrading activity. We report here its draft genome sequence, with an estimated genome size of 4 Mb, a G+C content of 75.1%, and 3,443 predicted protein-coding sequences, 92 of which are glycosyl hydrolases involved in polysaccharide degradation. PMID:27563050

Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola.

PubMed

Borsodi, Andrea K; Korponai, Kristóf; Schumann, Peter; Spröer, Cathrin; Felföldi, Tamás; Márialigeti, Károly; Szili-Kovács, Tibor; Tóth, Erika

2017-12-01

Three alkaliphilic and halotolerant bacterial strains, designated ZV-19 T , R4-8 T and S4-12, were isolated from the water of soda pans located in the Kiskunság National Park, Hungary. Cells of all three strains were Gram-staining-negative, rod-shaped, motile and non-endospore-forming. They were facultatively anaerobic, and oxidase- and catalase-positive. Their major isoprenoid quinone was Q-8, and their predominant fatty acids were C18 : 1ω7c, C16 : 1ω7c and C16 : 0. The DNA G+C content was 54.5 mol% in strain ZV-19 T and 45.8 mol% in strain R4-8 T . The 16S rRNA gene based phylogenetic analysis showed that all three strains were members of the genus Nitrincola (family Oceanospirillaceae, class Gammaproteobacteria). Strain ZV-19 T showed 96.6 and 95.5 % sequence similarities and 19±3 and 18±3 % DNA-DNA relatedness to Nitrincolalacisaponensis DSM 16316 T and Nitrincolaalkalisediminis JCM 19317 T , respectively. Strains R4-8 T and S4-12 exhibited 97.9 and 98.6 % sequence matches and 34±4 and 13±8 % DNA-DNA hybridization values with N. lacisaponensis DSM 16316 T and N. alkalisediminis JCM 19317 T , respectively. According to the phenotypic, chemotaxonomic and phylogenetic data, the strains studied represent two novel species, Nitrincola alkalilacustris sp. nov. with the type strain ZV-19 T (=DSM 29817 T =NCAIM B 02612 T ) and Nitrincola schmidtii sp. nov. with the type strain R4-8 T (=DSM 100788 T =NCAIM B.02626 T ). An emended description of the genus Nitrincola is also presented.

Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.

PubMed

Lee, Hyo-Jin; Whang, Kyung-Sook

2016-09-01

Three novel isolates belonging to the genus Streptomyces, designated JR-35T, JR-46 and WH-9T, were isolated from bamboo forest soil in Damyang, Korea. The 16S rRNA gene sequences of strains JR-35T and JR-46 showed highest similarities with Streptomyces olivochromogenes NBRC 3178T (99.1 %), Streptomyces siamensis KC-038T (98.9 %), Streptomyces chartreusis NBRC 12753T (98.9 %), Streptomyces resistomycificus NRRL ISP-5133T (98.9 %) and Streptomyces bobili JCM 4627T (98.8 %), and strain WH-9Tshowed highest sequence similarities with Streptomyces. bobili JCM 4627T (99.2 %), Streptomyces phaeoluteigriseus NRRL ISP-5182T (99.2 %), Streptomyces alboniger NBRC 12738T (99.2 %), Streptomyces galilaeus JCM 4757T (99.1 %) and Streptomyces pseudovenezuelae NBRC 12904T (99.1 %). The predominant menaquinones were MK-9 (H6) and MK-9 (H8). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and iso-C15 : 0 for strains JR-35T and JR-46 and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 for strain WH-9T. The G+C content of the genomic DNA of strains JR-35T, JR-46 and WH-9T were 69.4, 74.4 and 74.1 mol%, respectively. Based on the phenotypic and genotypic data, the three strains are assigned to two novel species of the genus Streptomyces, for which the names Streptomyces rhizosphaerihabitans sp. nov. (type stain JR-35T=KACC 17181T=NBRC 109807T) and Streptomyces adustus sp. nov. (type strain WH-9T=KACC 17197T=NBRC 109810T) are proposed.

Experimental infection in Cavia porcellus by infected Amblyomma ovale nymphs with Rickettsia sp. (Atlantic rainforest strain).

PubMed

Brustolin, Joice Magali; da Silva Krawczak, Felipe; Alves, Marta Elena Machado; Weiller, Maria Amélia; de Souza, Camila Lopes; Rosa, Fábio Brum; Cadore, Gustavo Cauduro; Dos Anjos Lopes, Sônia Terezinha; Labruna, Marcelo Bahia; Vogel, Fernanda Silveira Flores; de Avila Botton, Sônia; Sangioni, Luís Antônio

2018-03-01

This study describes experimental infection of guinea pigs (Cavia porcellus) infested with naturally infected Amblyomma ovale nymphs with Rickettsia sp. (Atlantic rainforest strain), and the capacity of A. ovale nymphs to transmit this bacterium. Twenty-six guinea pigs were divided into the following groups: G1, 10 animals infested with uninfected A. ovale nymphs; G2, 10 animals infested with nymphs infected with Rickettsia sp. (Atlantic rainforest strain); and G3, 6 animals without tick infestation. Blood samples were taken 7, 14, 21, and 28 days post-infestation for serological and hematological tests. For histopathological analysis and rickettsial DNA detection, fragments of the spleen, lung, brain, and liver were harvested after euthanasia. The average feeding period for nymphs was 6.6 days for G1 and 6 days for G2. Hemolymph and PCR assays, performed to detect the causative agent in ticks, indicated that in G1, all ticks were negative, and in G2, all nymphs were positive by PCR and 80% (8/10) was positive by hemolymph tests. The only clinical change was skin scarring at the tick attachment site. Hematological parameters indicated leukopenia and total plasma protein (TPP) increased with decreased platelets in G1. In G2, leukocytosis, neutrophilia, monocytosis, an increase in platelets, and reduced TPP were observed. Only G2 guinea pigs were seroconverted (80%; 8/10). Histopathology tests indicated mild, diffuse hemosiderosis and mild, multifocal, follicular hyperplasia in the spleen. Molecular analysis did not detect Rickettsia sp. DNA in C. porcellus tissues. We demonstrated the capacity of A. ovale nymphs to transmit Rickettsia sp. (Atlantic rainforest strain) to guinea pigs.

Lactobacillus paralimentarius sp. nov., isolated from sourdough.

PubMed

Cai, Y; Okada, H; Mori, H; Benno, Y; Nakase, T

1999-10-01

Six strains of lactic acid bacteria isolated from sourdough were characterized taxonomically. They were Gram-positive, catalase-negative, facultatively anaerobic rods that did not produce gas from glucose. Morphological and physiological data indicated that the strains belong to the genus Lactobacillus and they were similar to Lactobacillus alimentarius in phenotypic characteristics. These strains shared the same phenotypic characteristics and exhibited intragroup DNA homology values of over 89.8%, indicating that they comprised a single species. The G + C content of the DNA for the strains was 37.2-38.0 mol%. The 16S rRNA sequence of representative strain TB 1T was determined and aligned with that of other Lactobacillus species. This strain was placed in the genus Lactobacillus on the basis of phylogenetic analysis. L. alimentarius was the most closely related species in the phylogenetic tree and this species also showed the highest sequence homology value (96%) with strain TB 1T. DNA-DNA hybridization indicated that strain TB 1T did not belong to L. alimentarius. It is proposed that these strains are placed in the genus Lactobacillus as a new species, Lactobacillus paralimentarius sp. nov. The type strain of L. paralimentarius is TB 1T, which has been deposited in the Japan Collection of Microorganisms (JCM) as strain JCM 10415T.

Co2 + interaction with Azospirillum brasilense Sp7 cells: a 57Co emission Mössbauer spectroscopic study

NASA Astrophysics Data System (ADS)

Kamnev, Alexander A.; Tugarova, Anna V.; Biró, Borbála; Kovács, Krisztina; Homonnay, Zoltán; Kuzmann, Ernő; Vértes, Attila

2012-03-01

Preliminary 57Co emission Mössbauer spectroscopic data were obtained for the soil bacterium Azospirillum brasilense Sp7 ( T = 80 K) in frozen 57Co2 + -containing suspensions and in their dried residues. The Mössbauer parameters were compared with those for A. brasilense strain Sp245 differing from strain Sp7 by ecological behaviour. Live cells of both strains showed metabolic transformations of 57Co2 + within an hour. Differences in the parameters observed for the two strains under similar conditions suggest dissimilarities in their metabolic response to Co2 + .

Growth kinetics and biodeterioration of polypropylene microplastics by Bacillus sp. and Rhodococcus sp. isolated from mangrove sediment.

PubMed

Auta, H S; Emenike, C U; Jayanthi, B; Fauziah, S H

2018-02-01

Interest in the biodegradation of microplastics is due to their ubiquitous distribution, availability, high persistence in the environment and deleterious impact on marine biota. The present study evaluates the growth response and mechanism of polypropylene (PP) degradation by Bacillus sp. strain 27 and Rhodococcus sp. strain 36 isolated from mangrove sediments upon exposure to PP microplastics. Both bacteria strains were able to utilise PP microplastic for growth as confirmed by the reduction of the polymer mass. The weight loss was 6.4% by Rhodococcus sp. strain 36 and 4.0% by Bacillus sp. strain 27 after 40days of incubation. PP biodegradation was further confirmed using Fourier-transform infrared spectroscopy and scanning electron microscopy analyses, which revealed structural and morphological changes in the PP microplastics with microbial treatment. These analyses showed that the isolates can colonise, modify and utilise PP microplastics as carbon source. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cloning and Characterization of Benzoate Catabolic Genes in the Gram-Positive Polychlorinated Biphenyl Degrader Rhodococcus sp. Strain RHA1

PubMed Central

Kitagawa, Wataru; Miyauchi, Keisuke; Masai, Eiji; Fukuda, Masao

2001-01-01

Benzoate catabolism is thought to play a key role in aerobic bacterial degradation of biphenyl and polychlorinated biphenyls (PCBs). Benzoate catabolic genes were cloned from a PCB degrader, Rhodococcus sp. strain RHA1, by using PCR amplification and temporal temperature gradient electrophoresis separation. A nucleotide sequence determination revealed that the deduced amino acid sequences encoded by the RHA1 benzoate catabolic genes, benABCDK, exhibit 33 to 65% identity with those of Acinetobacter sp. strain ADP1. The gene organization of the RHA1 benABCDK genes differs from that of ADP1. The RHA1 benABCDK region was localized on the chromosome, in contrast to the biphenyl catabolic genes, which are located on linear plasmids. Escherichia coli cells containing RHA1 benABCD transformed benzoate to catechol via 2-hydro-1,2-dihydroxybenzoate. They transformed neither 2- nor 4-chlorobenzoates but did transform 3-chlorobenzoate. The RHA1 benA gene was inactivated by insertion of a thiostrepton resistance gene. The resultant mutant strain, RBD169, neither grew on benzoate nor transformed benzoate, and it did not transform 3-chlorobenzoate. It did, however, exhibit diminished growth on biphenyl and growth repression in the presence of a high concentration of biphenyl (13 mM). These results indicate that the cloned benABCD genes could play an essential role not only in benzoate catabolism but also in biphenyl catabolism in RHA1. Six rhodococcal benzoate degraders were found to have homologs of RHA1 benABC. In contrast, two rhodococcal strains that cannot transform benzoate were found not to have RHA1 benABC homologs, suggesting that many Rhodococcus strains contain benzoate catabolic genes similar to RHA1 benABC. PMID:11673430

Enterococcus camelliae sp. nov., isolated from fermented tea leaves in Thailand.

PubMed

Sukontasing, Sirapan; Tanasupawat, Somboon; Moonmangmee, Somporn; Lee, Jung-Sook; Suzuki, Ken-Ichiro

2007-09-01

A Gram-positive and catalase-negative coccus that formed chains, strain FP15-1(T), isolated from fermented tea leaves ('miang'), was studied systematically. The strain was facultatively anaerobic and produced l-lactic acid from glucose. Demethylmenaquinone (DMK-7) was the major menaquinone. Straight-chain unsaturated fatty acids C(16 : 1) and C(18 : 1) were the dominant components. The DNA G+C content was 37.8 mol%. On the basis of 16S rRNA and RNA polymerase alpha subunit (rpoA) gene sequence analysis, strain FP15-1(T) was closely related to Enterococcus italicus KCTC 5373(T), with 99.2 and 93.8 % similarity, respectively. The strain could be clearly distinguished from E. italicus ATCC 5373(T) by low DNA-DNA relatedness (< or =33.8 %) and phenotypic characteristics. Therefore, this strain represent a novel species of the genus Enterococcus, for which the name Enterococcus camelliae sp. nov. is proposed. The type strain is FP15-1(T) (=KCTC 13133(T) =NBRC 101868(T) =NRIC 0105(T) =TISTR 932(T) =PCU 277(T)).

Isolation and characterization of a novel violacein-like pigment producing psychrotrophic bacterial species Janthinobacterium svalbardensis sp. nov.

PubMed

Ambrožič Avguštin, Jerneja; Žgur Bertok, Darja; Kostanjšek, Rok; Avguštin, Gorazd

2013-04-01

A bacterial strain designated JA-1, related to Janthinobacterium lividum, was isolated from glacier ice samples from the island Spitsbergen in the Arctic. The strain was tested for phenotypic traits and the most prominent appeared to be the dark red brown to black pigmentation different from the violet pigment of Janthinobacterium, Chromobacterium and Iodobacter. Phylogenetic analysis based on 16S rRNA gene sequences and DNA-DNA hybridization tests showed that strain JA-1 belongs to the genus Janthinobacterium but represents a novel lineage distinct from the two known species of this genus, J. lividum and Janthinobacterium agaricidamnosum. The DNA G + C content of strain JA-1 was determined to be 62.3 mol %. The isolate is a psychrotrophic Gram negative bacterium, rod-shaped with rounded ends, containing intracellular inclusions and one polar flagellum. On the basis of the presented results strain JA-1 is proposed as the type strain of a novel species of the genus Janthinobacterium, for which the name Janthinobacterium svalbardensis sp. nov. is proposed (JA-1(T) = DSM 25734, ZIM B637).

Biodegradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid by a New Isolated Strain of Achromobacter sp. LZ35.

PubMed

Xia, Zhen-Yuan; Zhang, Long; Zhao, Yan; Yan, Xin; Li, Shun-Peng; Gu, Tao; Jiang, Jian-Dong

2017-02-01

In this study, a bacterial strain of Achromobacter sp. LZ35, which was capable of utilizing 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxy acetic acid (MCPA) as the sole sources of carbon and energy for growth, was isolated from the soil in a disused pesticide factory in Suzhou, China. The optimal 2,4-D degradation by strain LZ35 occurred at 30 °C and pH 8.0 when the initial 2,4-D concentration was 200 mg L -1 . Strain LZ35 harbored the conserved 2,4-D/alpha-ketoglutarate dioxygenase (96%) and 2,4-dichlorophenol hydroxylase (99%), and catabolized 2,4-D via the intermediate 2,4-dichlorophenol. The inoculation of 7.8 × 10 6  CFU g -1 soil of strain LZ35 cells to 2,4-D-contaminated soil could efficiently remove over 75 and 90% of 100 and 50 mg L -1 2,4-D in 12 days and significantly released the phytotoxicity of maize caused by the 2,4-D residue. This is the first report of an Achromobacter sp. strain that was capable of mineralizing both 2,4-D and MCPA. This study provides us a promising candidate for its application in the bioremediation of 2,4-D- or MCPA-contaminated sites.

Biodegradation of 5-chloro-2-picolinic acid by novel identified co-metabolizing degrader Achromobacter sp. f1.

PubMed

Wu, Zhi-Guo; Wang, Fang; Ning, Li-Qun; Stedtfeld, Robert D; Yang, Zong-Zheng; Cao, Jing-Guo; Sheng, Hong-Jie; Jiang, Xin

2017-06-01

Several bacteria have been isolated to degrade 4-chloronitrobenzene. Degradation of 4-chloronitrobenzene by Cupriavidus sp. D4 produces 5-chloro-2-picolinic acid as a dead-end by-product, a potential pollutant. To date, no bacterium that degrades 5-chloro-2-picolinic acid has been reported. Strain f1, isolated from a soil polluted by 4-chloronitrobenzene, was able to co-metabolize 5-chloro-2-picolinic acid in the presence of ethanol or other appropriate carbon sources. The strain was identified as Achromobacter sp. based on its physiological, biochemical characteristics, and 16S rRNA gene sequence analysis. The organism completely degraded 50, 100 and 200 mg L -1 of 5-chloro-2-picolinic acid within 48, 60, and 72 h, respectively. During the degradation of 5-chloro-2-picolinic acid, Cl - was released. The initial metabolic product of 5-chloro-2-picolinic acid was identified as 6-hydroxy-5-chloro-2-picolinic acid by LC-MS and NMR. Using a mixed culture of Achromobacter sp. f1 and Cupriavidus sp. D4 for degradation of 4-chloronitrobenzen, 5-chloro-2-picolinic acid did not accumulate. Results infer that Achromobacter sp. f1 can be used for complete biodegradation of 4-chloronitrobenzene in remedial applications.

FTIR spectroscopic study of biofilms formed by the rhizobacterium Azospirillum brasilense Sp245 and its mutant Azospirillum brasilense Sp245.1610

NASA Astrophysics Data System (ADS)

Tugarova, Anna V.; Scheludko, Andrei V.; Dyatlova, Yulia A.; Filip'echeva, Yulia A.; Kamnev, Alexander A.

2017-07-01

Biofilms are spatially and metabolically structured communities of microorganisms, representing a mode of their existence which is ubiquitous in nature, with cells localised within an extracellular biopolymeric matrix, attached to each other, at an interface. For plant-growth-promoting rhizobacteria (PGPR), the formation of biofilms is of special importance due to their primary localisation at the surface of plant root systems. In this work, FTIR spectroscopy was used, for the first time for bacteria of the genus Azospirillum, to comparatively study 6-day-mature biofilms formed on the surface of ZnSe discs by the rhizobacterium Azospirillum brasilense Sp245 and its mutant A. brasilense Sp245.1610. The mutant strain, having an Omegon Km insertion in the gene of lipid metabolism fabG1 on the plasmid AZOBR_p1, as compared to the wild-type strain Sp245 (see http://dx.doi.org/10.1134/S1022795413110112)

DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov.

PubMed

Holmes, B; Steigerwalt, A G; Nicholson, A C

2013-12-01

The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T) = CCUG 60564(T) = CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T) = CCUG 60559(T) = CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T) = CCUG 60566(T) = CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T) = CCUG 60563(T) = CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T) = X-65(T) = CCTCC AB 208154(T) = NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.

Organophosphonates utilization by soil strains of Ochrobactrum anthropi and Achromobacter sp.

PubMed

Ermakova, Inna T; Shushkova, Tatyana V; Sviridov, Alexey V; Zelenkova, Nina F; Vinokurova, Natalya G; Baskunov, Boris P; Leontievsky, Alexey A

2017-07-01

Four bacterial strains from glyphosate- or alkylphosphonates-contaminated soils were tested for ability to utilize different organophosphonates. All studied strains readily utilized methylphosphonic acid and a number of other phosphonates, but differed in their ability to degrade glyphosate. Only strains Ochrobactrum anthropi GPK 3 and Achromobacter sp. Kg 16 utilized this compound after isolation from enrichment cultures with glyphosate. Achromobacter sp. MPK 7 from the same enrichment culture, similar to Achromobacter sp. MPS 12 from methylphosphonate-polluted source, required adaptation to growth on GP. Studied strains varied significantly in their growth parameters, efficiency of phosphonates degradation and characteristic products of this process, as well as in their energy metabolism. These differences give grounds to propose a possible model of interaction between these strains in microbial consortium in phosphonate-contaminated soils.

Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsenophilum sp. nov., new members of the Sulfurospirillum clade of the ε-Proteobacteria

USGS Publications Warehouse

Stolz, J.F.; Ellis, D.J.; Blum, J.S.; Ahmann, D.; Lovley, D.R.; Oremland, R.S.

1999-01-01

Two strains of dissimilatory arsenate-reducing vibrio-shaped bacteria are assigned to the genus Sulfurospirillum. These two new species, Sulfurospirillum barnesii strain SES-3(T) and Sulfurospirillum arsenophilum strain MIT-13(T), in addition to Sulfurospirillum sp. SM-5, two strains of Sulfurospirillum deleyianum, and Sulfurospirillum arcachonense, form a distinct clade within the ?? subclass of the Proteobacteria based on 16S rRNA analysis.

Chemical composition of essential oil from ripe fruit of Schinus terebinthifolius Raddi and evaluation of its activity against wild strains of hospital origin

PubMed Central

Cole, E.R.; dos Santos, R.B.; Júnior, V. Lacerda; Martins, J.D.L.; Greco, S.J.; Neto, A. Cunha

2014-01-01

The essential oil (EO) composition of ripe fruit of S. terebinthifolius Raddi was analyzed by GC-MS. The oil extraction yielded 6.54 ± 1.06% (w/w). Seventeen compounds were identified, accounting for 91.15% of the total oil, where monoterpenes constituted the main chemical class (85.81%), followed by sesquiterpenes (5.34%). The major monoterpene identified was δ-3-carene (30.37%), followed by limonene (17.44%), α-phellandrene (12.60%) and α-pinene (12.59%). Trans-caryophyllene (1.77%) was the major sesquiterpene identified. The antibacterial activity of the essential oil was evaluated against wild strains of hospital origin (Escherichia coli, Pseudomonas sp., Klebsiella oxytoca, Corynebacterium sp., Staphylococcus aureus, Enterobacter sp., Enterobacter agglomerans, Bacillus sp., Nocardia sp. and Streptococcus group D). The essential oil of the ripe fruit of S. terebinthifolius Raddi has shown to be active against all tested wild strains, with minimum inhibitory concentration ranging from 3.55 μg/mL to 56.86 μg/mL. However, it has revealed some differences in susceptibility: the general, Gram-positive species showed greater sensitivity to the action of EO, which is probably due to the lower structural complexity of their cell walls. PMID:25477913

Chemical composition of essential oil from ripe fruit of Schinus terebinthifolius Raddi and evaluation of its activity against wild strains of hospital origin.

PubMed

Cole, E R; dos Santos, R B; Lacerda Júnior, V; Martins, J D L; Greco, S J; Cunha Neto, A

2014-01-01

The essential oil (EO) composition of ripe fruit of S. terebinthifolius Raddi was analyzed by GC-MS. The oil extraction yielded 6.54 ± 1.06% (w/w). Seventeen compounds were identified, accounting for 91.15% of the total oil, where monoterpenes constituted the main chemical class (85.81%), followed by sesquiterpenes (5.34%). The major monoterpene identified was δ-3-carene (30.37%), followed by limonene (17.44%), α-phellandrene (12.60%) and α-pinene (12.59%). Trans-caryophyllene (1.77%) was the major sesquiterpene identified. The antibacterial activity of the essential oil was evaluated against wild strains of hospital origin (Escherichia coli, Pseudomonas sp., Klebsiella oxytoca, Corynebacterium sp., Staphylococcus aureus, Enterobacter sp., Enterobacter agglomerans, Bacillus sp., Nocardia sp. and Streptococcus group D). The essential oil of the ripe fruit of S. terebinthifolius Raddi has shown to be active against all tested wild strains, with minimum inhibitory concentration ranging from 3.55 μg/mL to 56.86 μg/mL. However, it has revealed some differences in susceptibility: the general, Gram-positive species showed greater sensitivity to the action of EO, which is probably due to the lower structural complexity of their cell walls.

Cesiribacter roseus sp. nov., a pink-pigmented bacterium isolated from desert sand.

PubMed

Liu, Ming; Qi, Huan; Luo, Xuesong; Dai, Jun; Peng, Fang; Fang, Chengxiang

2012-01-01

A pink-pigmented, Gram-negative, rod-shaped, motile, strictly aerobic bacterium, designated strain 311(T), was isolated from desert sand in Xinjiang, China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 311(T) was related closely to Cesiribacter andamanensis AMV16(T) (94.6% similarity). The DNA G+C content of strain 311(T) was 47.1 mol% and the major respiratory quinone was menaquinone 7 (MK-7). The main cellular fatty acids were C(16:1)ω5c (29.9%), iso-C(15:0) (21.9%), iso-C(17:0) 3-OH (13.3%) and summed feature 4 (iso-C(17:1) I and/or anteiso-C(17:1) B; 13.0%). Based on phenotypic and chemotaxonomic data and phylogenetic analysis, strain 311(T) is considered to represent a novel species of the genus Cesiribacter, for which the name Cesiribacter roseus sp. nov. is proposed. The type strain is 311(T) (=CCTCC AB 207142(T) =KACC 15456(T)).

Extraction of extracellular lipids from chemoautotrophic bacteria Serratia sp. ISTD04 for production of biodiesel.

PubMed

Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

2014-08-01

A CO2 sequestering bacterial strain, Serratia sp. ISTD04, that produces a significant amount of extracellular lipids was isolated from marble mine rocks. (14)C labeling analysis revealed that the rate of assimilation of CO2 by the strain is 0.756×10(-9)μmolCO2fixedcell(-1)h(-1). It was found to produce 466mg/l of extracellular lipid which was characterized using (1)H NMR. After transesterification of lipids, the total saturated and unsaturated FAME was found to be 51% and 49% respectively. The major FAME contained in the biodiesel were palmitic acid methyl ester (C16:0), oleic acid methyl ester (C18:1) and 10-nonadecenoic acid methyl ester (C19:1). Biodiesel produced by Serratia sp. ISTD04 is balanced in terms of FAME composition of good quality. It also contained higher proportion of oleic acid (35%) which makes it suitable for utilization in existing engines. Thus, the strain can be harnessed commercially to sequester CO2 into biodiesel. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thalassospira alkalitolerans sp. nov. and Thalassospira mesophila sp. nov., isolated from a decaying bamboo sunken in the marine environment, and emended description of the genus Thalassospira.

PubMed

Tsubouchi, Taishi; Ohta, Yukari; Haga, Takuma; Usui, Keiko; Shimane, Yasuhiro; Mori, Kozue; Tanizaki, Akiko; Adachi, Akiko; Kobayashi, Kiwa; Yukawa, Kiyotaka; Takagi, Emiko; Tame, Akihiro; Uematsu, Katsuyuki; Maruyama, Tadashi; Hatada, Yuji

2014-01-01

Two marine bacteria, designated strains MBE#61(T) and MBE#74(T), were isolated from a piece of sunken bamboo in the marine environment in Japan. Both of these strains were Gram-stain-negative, but had different cell shapes: MBE#61(T) was spiral, whereas MBE#74(T) was rod-shaped. The temperature, pH and salt concentration ranges for growth of strain MBE#61(T) were 4-38 °C (optimal at 32 °C), pH 4.5-11.0 (optimal at pH 7.0-8.0) and 1-11 % (optimal at 2 %) NaCl, whereas those of strain MBE#74(T) were 4-36 °C (optimal at 30 °C), pH 4.0-10.5 (optimal at pH 7.0-8.0) and 1-12 % (optimal at 4 %) NaCl. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that both strains belong to the genus Thalassospira within the class Alphaproteobacteria. Similarity between the 16S rRNA gene sequence of strain MBE#61(T) and those of the type strains of species of the genus Thalassospira was 97.5-99.0 %, and that of strain MBE#74(T) was 96.9-98.6 %; these two isolates were most closely related to Thalassospira lucentensis QMT2(T). However, the DNA-DNA hybridization values between T. lucentensis QMT2(T) and strain MBE#61(T) or MBE#74(T) were only 16.0 % and 7.1 %, respectively. The DNA G+C content of strain MBE#61(T) was 54.4 mol%, and that of strain MBE#74(T) was 55.9 mol%. The predominant isoprenoid quinone of the two strains was Q-10 (MBE#61(T), 97.3 %; MBE#74(T), 93.5 %). The major cellular fatty acids of strain MBE#61(T) were C18 : 1ω7c (31.1 %), summed feature 3 comprising C16 : 0ω7c/iso-C15 : 0 2-OH (26.1 %) and C16 : 0 (20.9 %); those of strain MBE#74(T) were C16 : 0 (26.2 %), C17 : 0 cyclo (19.9 %) and C18 : 1ω7c (12.1 %). On the basis of these results, strain MBE#61(T) and strain MBE#74(T) are considered to represent novel species of the genus Thalassospira, for which names Thalassospira alkalitolerans sp. nov. and Thalassospira mesophila sp. nov. are proposed. The type strains are MBE#61(T) ( = JCM 18968(T) = CECT 8273(T)) and MBE#74(T) ( = JCM 18969(T) = CECT 8274(T)), respectively. An emended description of the genus Thalassospira is also proposed.

Synthesis of Cryptophycin Affinity Labels and Tubulin Labeling

DTIC Science & Technology

2006-05-01

Nostoc sp.), are a new and potent tumor-selective class of tubulin-binding antimitotic agents1 that show excellent activity against MDR cancer cell...lines and were exceptionally active against mammary derived tumors.2,3 Cryptophycin-1 (1, Fig. 1) is the major cytotoxin in Nostoc sp.4,5 and...arenastatin A), isolated from the Okinawan marine sponge Dysidea arenaria6 and later from Nostoc sp. strain GSV 224,7 is also a potent inhibitor of tubulin

Molecular detection of the human pathogenic Rickettsia sp. strain Atlantic rainforest in Amblyomma dubitatum ticks from Argentina.

PubMed

Monje, Lucas D; Nava, Santiago; Eberhardt, Ayelen T; Correa, Ana I; Guglielmone, Alberto A; Beldomenico, Pablo M

2015-02-01

To date, three tick-borne pathogenic Rickettsia species have been reported in different regions of Argentina, namely, R. rickettsii, R. parkeri, and R. massiliae. However, there are no reports available for the presence of tick-borne pathogens from the northeastern region of Argentina. This study evaluated the infection with Rickettsia species of Amblyomma dubitatum ticks collected from vegetation and feeding from capybaras (Hydrochoerus hydrochaeris) in northeastern Argentina. From a total of 374 A. dubitatum ticks collected and evaluated by PCR for the presence of rickettsial DNA, 19 were positive for the presence of Rickettsia bellii DNA, two were positive for Rickettsia sp. strain COOPERI, and one was positive for the pathogenic Rickettsia sp. strain Atlantic rainforest. To our knowledge, this study is the first report of the presence of the human pathogen Rickettsia sp. strain Atlantic rainforest and Rickettsia sp. strain COOPERI in Argentina. Moreover, our findings posit A. dubitatum as a potential vector for this pathogenic strain of Rickettsia.

[Fundamental studies on legionellosis--the growth with in Acanthamoeba sp. and antibiotics susceptibility of Legionella spp. isolated from soil samples in Japan].

PubMed

Furuhata, Katsunori; Miyamoto, Hiroshi; Hara, Motonobu; Fukuyama, Masafumi

2003-02-01

As part of an epidemiological study of legionellosis, we investigated the growth within Acanthamoeba sp. and antibiotic susceptibility of 62 strains of Legionella spp. isolated from surface soils nationwide in 2001. 1) All strains tested grew in Acanthamoeba sp., suggesting that the strains were pathogenic. The minimum bacterial number required for the growth in the amoeba was 10(3)-10(8) CFU/ml and there were differences between the strains. 2) Susceptibility to 10 drugs was investigated using the Etest. The MIC90 values of imipenem, as a beta-lactam, and rifampicin, as an antitubercular agent, were 0.047 microgram/ml and 0.064 microgram/ml, respectively, showing high sensitivity. In contrast, sensitivity to minocycline, as a tetracycline, and piperacillin, as a beta-lactam, was low and the MIC90 values were 12 micrograms/ml and 16 micrograms/ml, respectively. Sensitivity to minocycline was particularly low, with a MIC value of 32 micrograms/ml, in two strains. The above findings suggested that all soil-derived strains were pathogenic, and susceptibility of the strains tended to be slightly lower than that of clinical isolates.

Biobegradation and metabolic mechanism of cyprodinil by strain Acinetobacter sp. from a contaminated-agricultural soil in China.

PubMed

Chen, Xiaoxin; He, Sheng; Liu, Xiaolu; Hu, Jiye

2018-09-15

Using sequential soil and liquid culture enrichments with cyprodinil as the sole carbon source, a Gram-negative cyprodinil-degrader from cyprodinil-polluted agricultural soil was isolated. The sequencing analysis of 16 S rRNA indicated that the strain showed 99% homology to Acinetobacter sp. The strain could effectively degrade cyprodinil at the neutral condition. At the initial concentrations of 10, 20, 50, 100, 150 and 200 mg L -1 in minimal medium, cyprodinil was degraded by 10, 20, 49.3, 64.2, 57 and 24 mg L -1 within 14 days, respectively. Two metabolites (4-cyclopropyl-6-methyl-2-pyrimidpyridine amine and monohydroxylated para-substitution) were identified using high performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS/MS). A biodegradation pathway involving imines hydrolysis and monohydroxyl substitution on benzene ring was proposed on basis of the identified metabolites. Acinetobacter sp. would have a potential application in bioremediation of cyprodinil-contaminated soil, and the strain might have important implications in detoxification and bioremediation of pyrimidine analogues. Copyright © 2018 Elsevier Inc. All rights reserved.

In vitro digestibility and prebiotic potential of curdlan (1 → 3)-β-d-glucan oligosaccharides in Lactobacillus species.

PubMed

Shi, Yuqin; Liu, Jun; Yan, Qiaojuan; You, Xin; Yang, Shaoqing; Jiang, Zhengqiang

2018-05-15

Prebiotic effects of curdlan (1 → 3)-β-d-glucan oligosaccharides (GOS) were examined. GOS was tolerant against simulated gastrointestinal digestion, as well as low pH, thermal, and Maillard reaction conditions likely occurred during food processing. Growth of tested Lactobacillus (L.) strains was improved by GOS except L. brevis NRRL B-4527. E. coli did not grow on GOS as the only carbon source. In vitro batch fermentation using human faecal microbiota showed that GOS significantly increased the population of Lactobacillus sp. followed by Bifidobacterium sp. and Bacteroides sp. Growth of L. strains on GOS produced lactic acid, acetic, and propionic acid with decreased culture medium pH. Utilization pattern of GOS by representative L. strains was strain dependent. GOS with degree of polymerization (DP) of 2 and 3 were readily consumed. Findings here indicated that curdlan GOS (DP = 2 and 3) are promising physiologically active prebiotics for improvement of human intestinal health. Copyright © 2018 Elsevier Ltd. All rights reserved.

Characterization of Two Novel Propachlor Degradation Pathways in Two Species of Soil Bacteria

PubMed Central

Martin, Margarita; Mengs, Gerardo; Allende, Jose Luis; Fernandez, Javier; Alonso, Ramon; Ferrer, Estrella

1999-01-01

Propachlor (2-chloro-N-isopropylacetanilide) is an acetamide herbicide used in preemergence. In this study, we isolated and characterized a soil bacterium, Acinetobacter strain BEM2, that was able to utilize this herbicide as the sole and limiting carbon source. Identification of the intermediates of propachlor degradation by this strain and characterization of new metabolites in the degradation of propachlor by a previously reported strain of Pseudomonas (PEM1) support two different propachlor degradation pathways. Washed-cell suspensions of strain PEM1 with propachlor accumulated N-isopropylacetanilide, acetanilide, acetamide, and catechol. Pseudomonas strain PEM1 grew on propachlor with a generation time of 3.4 h and a Ks of 0.17 ± 0.04 mM. Acinetobacter strain BEM2 grew on propachlor with a generation time of 3.1 h and a Ks of 0.3 ± 0.07 mM. Incubations with strain BEM2 resulted in accumulation of N-isopropylacetanilide, N-isopropylaniline, isopropylamine, and catechol. Both degradative pathways were inducible, and the principal product of the carbon atoms in the propachlor ring was carbon dioxide. These results and biodegradation experiments with the identified metabolites indicate that metabolism of propachlor by Pseudomonas sp. strain PEM1 proceeds through a different pathway from metabolism by Acinetobacter sp. strain BEM2. PMID:9925619

Silencing Inhibits Cre-Mediated Recombination of the Z/AP and Z/EG Reporters in Adult Cells

PubMed Central

Long, Michael A.; Rossi, Fabio M. V.

2009-01-01

Background The Cre-loxP system has been used to enable tissue specific activation, inactivation and mutation of many genes in vivo and has thereby greatly facilitated the genetic dissection of several cellular and developmental processes. In such studies, Cre-reporter strains, which carry a Cre-activated marker gene, are frequently utilized to validate the expression profile of Cre transgenes, to act as a surrogate marker for excision of a second allele, and to irreversibly label cells for lineage tracing experiments. Principal Findings We have studied three commonly used Cre-reporter strains, Z/AP, Z/EG and R26R-EYFP and have demonstrated that although each reporter can be reliably activated by Cre during early development, exposure to Cre in adult hematopoietic cells results in a much lower frequency of marker-positive cells in the Z/AP or Z/EG strains than in the R26R-EYFP strain. In marker negative cells derived from the Z/AP and Z/EG strains, the transgenic promoter is methylated and Cre-mediated recombination of the locus is inhibited. Conclusions These results show that the efficiency of Cre-mediated recombination is not only dependent on the genomic context of a given loxP-flanked sequence, but also on stochastic epigenetic mechanisms underlying transgene variegation. Furthermore, our data highlights the potential shortcomings of utilizing the Z/AP and Z/EG reporters as surrogate markers of excision or in lineage tracing experiments. PMID:19415111

Silencing inhibits Cre-mediated recombination of the Z/AP and Z/EG reporters in adult cells.

PubMed

Long, Michael A; Rossi, Fabio M V

2009-01-01

The Cre-loxP system has been used to enable tissue specific activation, inactivation and mutation of many genes in vivo and has thereby greatly facilitated the genetic dissection of several cellular and developmental processes. In such studies, Cre-reporter strains, which carry a Cre-activated marker gene, are frequently utilized to validate the expression profile of Cre transgenes, to act as a surrogate marker for excision of a second allele, and to irreversibly label cells for lineage tracing experiments. We have studied three commonly used Cre-reporter strains, Z/AP, Z/EG and R26R-EYFP and have demonstrated that although each reporter can be reliably activated by Cre during early development, exposure to Cre in adult hematopoietic cells results in a much lower frequency of marker-positive cells in the Z/AP or Z/EG strains than in the R26R-EYFP strain. In marker negative cells derived from the Z/AP and Z/EG strains, the transgenic promoter is methylated and Cre-mediated recombination of the locus is inhibited. These results show that the efficiency of Cre-mediated recombination is not only dependent on the genomic context of a given loxP-flanked sequence, but also on stochastic epigenetic mechanisms underlying transgene variegation. Furthermore, our data highlights the potential shortcomings of utilizing the Z/AP and Z/EG reporters as surrogate markers of excision or in lineage tracing experiments.

Characterisation of a detergent-stable alkaline protease from a novel thermophilic strain Paenibacillus tezpurensis sp. nov. AS-S24-II.

PubMed

Rai, Sudhir K; Roy, Jetendra K; Mukherjee, Ashis K

2010-02-01

An alkaline-protease-producing bacterial strain (AS-S24-II) isolated from a soil sample in Assam is a Gram-stain-positive, catalase-positive, endospore-forming rod and grows at temperatures ranging from 30 degrees C to 60 degrees C and salinity ranging from 0% to 7% (w/v) NaCl. Phenotypic characterisation, chemotaxonomic properties, presence of Paenibacillus-specific signature sequences, and ribotyping data suggested that the strain AS-S24-II represents a novel species of the genus Paenibacillus, for which the name Paenibacillus tezpurensis sp. nov. (MTCC 8959) is proposed. Phylogenetic analysis revealed that P. lentimorbus strain DNG-14 and P. lentimorbus strain DNG-16 represent the closest phylogenetic neighbour of this novel strain. Alkaline protease production (598 x 10(3) U l(-1)) by P. tezpurensis sp. nov. in SmF was optimised by response surface method. A laundry-detergent-stable, Ca(2+)-independent, 43-kDa molecular weight alkaline serine protease from this strain was purified with a 1.7-fold increase in specific activity. The purified protease displayed optimum activity at pH 9.5 and 45-50 degrees C temperature range and exhibited a significant stability and compatibility with surfactants and most of the tested commercial laundry detergents at room temperature. Further, the protease improved the wash performance of detergents, thus demonstrating its feasibility for inclusion in laundry detergent formulations.

Isolation and characterization of a novel simazine-degrading bacterium from agricultural soil of central Chile, Pseudomonas sp. MHP41.

PubMed

Hernández, Marcela; Villalobos, Patricio; Morgante, Verónica; González, Myriam; Reiff, Caroline; Moore, Edward; Seeger, Michael

2008-09-01

s-Triazine herbicides are used extensively in South America in agriculture and forestry. In this study, a bacterium designated as strain MHP41, capable of degrading simazine and atrazine, was isolated from agricultural soil in the Quillota valley, central Chile. Strain MHP41 is able to grow in minimal medium, using simazine as the sole nitrogen source. In this medium, the bacterium exhibited a growth rate of mu=0.10 h(-1), yielding a high biomass of 4.2 x 10(8) CFU mL(-1). Resting cells of strain MHP41 degrade more than 80% of simazine within 60 min. The atzA, atzB, atzC, atzD, atzE and atzF genes encoding the enzymes of the simazine upper and lower pathways were detected in strain MHP41. The motile Gram-negative bacterium was identified as a Pseudomonas sp., based on the Biolog microplate system and comparative sequence analyses of the 16S rRNA gene. Amplified ribosomal DNA restriction analysis allowed the differentiation of strain MHP41 from Pseudomonas sp. ADP. The comparative 16S rRNA gene sequence analyses suggested that strain MHP41 is closely related to Pseudomonas nitroreducens and Pseudomonas multiresinovorans. This is the first s-triazine-degrading bacterium isolated in South America. Strain MHP41 is a potential biocatalyst for the remediation of s-triazine-contaminated environments.

Inhibition of integrin-linked kinase expression by emodin through crosstalk of AMPKα and ERK1/2 signaling and reciprocal interplay of Sp1 and c-Jun.

PubMed

Tang, Qing; Zhao, Shunyu; Wu, Jingjing; Zheng, Fang; Yang, LiJun; Hu, JingHeng; Hann, Swei Sunny

2015-07-01

Despite the anti-cancer effect of emodin observed in several cancers, the underlying molecular mechanism remains to be elucidated. In this study, we showed that emodin-inhibited NSCLC cell growth and increased phosphorylation of AMPKα and ERK1/2. In addition, emodin-inhibited ILK protein expression. The overexpression of ILK reversed the effect of emodin on cell growth inhibition. Furthermore, the blockade of AMPK by compound C abrogated, while metformin, an activator of AMPK, strengthened the effect of emodin on the inhibition of ILK expression. Interestingly, the inhibitor of MAPK extracellular signaling-regulated kinase (ERK) kinase (MEK)/ERK1/2 (PD98059) attenuated emodin-induced phosphorylation of AMPKα. Moreover, emodin reduced the protein expression of Sp1 and AP-1 subunit c-Jun. Exogenous expression of Sp1 and c-Jun diminished emodin-reduced ILK protein expression. Emodin suppressed ILK promoter activity, which was not observed in cells overexpression of Sp1 and treated with compound C. Intriguingly, exogenous expression of c-Jun overcame the emodin-inhibited Sp1 protein expression. Collectively, our results demonstrate that emodin inhibits ILK expression through AMPKα-mediated reduction of Sp1 and c-Jun. Metformin enhances the effects of emodin. Exogenous expression of Sp1 and c-Jun resists emodin-inhibited ILK promoter activity and protein expression. In addition, the overexpression of c-Jun diminishes emodin-induced AMPKα signaling. Thus, the crosstalk of AMPKα and MEK/ERK1/2 signaling and the reciprocal interaction between Sp1 and c-Jun proteins contribute to the overall responses of emodin. This novel signaling axis may be a therapeutic potential for prevention and treatment of NSCLC. Copyright © 2015 Elsevier Inc. All rights reserved.

Taonella mepensis gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from activated sludge.

PubMed

Xi, Xue-dong; Dong, Wei-liang; Zhang, Jun; Huang, Yan; Cui, Zhong-li

2013-07-01

A novel Gram-negative, non-spore-forming, rod-shaped strain, H1(T), was isolated from activated sludge by micromanipulation. No close relatives among cultured bacterial isolates were found; phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H1(T) forms a deep single branch in the family Rhodospirillaceae. Cells of strain H1(T) were slightly curved to straight rods (1.2-1.4 × 1.5-1.7 µm) and motile by a single polar flagellum. Strain H1(T) was able to grow in the presence of 0-4 % NaCl and grew optimally at 37 °C and pH 6.0-7.0. Chemotaxonomic analysis revealed that strain H1(T) possessed Q-10 as the predominant ubiquinone and C18 : 1ω7c, C16 : 0 and C19 : 0 cyclo ω8c as the major fatty acids. The DNA G+C content of strain H1(T) was 65.1 mol%. Comparative analysis of 16S rRNA gene sequences, and phenotypic and chemotaxonomic data, indicate that strain H1(T) should represent a novel genus and species of the family Rhodospirillaceae. The name Taonella mepensis gen. nov., sp. nov. is proposed. The type strain of Taonella mepensis is H1(T) ( = CICC 10529(T) = CCTCC AB 2012861(T) = KACC 16940(T)).

Candida kantuleensis sp. nov., a d-xylose-fermenting yeast species isolated from peat in a tropical peat swamp forest.

PubMed

Nitiyon, Sukanya; Khunnamwong, Pannida; Lertwattanasakul, Noppon; Limtong, Savitree

2018-05-24

Three strains (DMKU-XE11 T , DMKU-XE15 and DMKU-XE20) representing a single novel anamorphic and d-xylose-fermenting yeast species were obtained from three peat samples collected from Khan Thulee peat swamp forest in Surat Thani province, Thailand. The strains differed from each other by one to two nucleotide substitutions in the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and zero to one nucleotide substitution in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the combined sequences of the ITS and the D1/D2 regions showed that the three strains represented a single Candida species that was distinct from the other related species in the Lodderomyces/Candida albicans clade. The three strains form a subclade with the other Candida species including Candida sanyaensis, Candida tropicalis and Candida sojae. C. sanyaensis was the most closely related species, with 2.1-2.4 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 3.8-4.0 % nucleotide substitutions in the ITS region. The three strains (DMKU-XE11 T , DMKU-XE15 and DMKU-XE20) were assigned as a single novel species, which was named Candida kantuleensis sp. nov. The type strain is DMKU-XE11 T (=CBS 15219 T =TBRC 7764 T ). The MycoBank number for C. kantuleensis sp. nov. is MB 824179.

Designed Reduction of Streptococcus pneumoniae Pathogenicity via Synthetic Changes in Virulence Factor Codon-pair Bias

PubMed Central

Coleman, J. Robert; Papamichail, Dimitris; Yano, Masahide; García-Suárez, María del Mar

2011-01-01

In this study, we used a previously described method of controlling gene expression with computer-based gene design and de novo DNA synthesis to attenuate the virulence of Streptococcus pneumoniae. We produced 2 S. pneumoniae serotype 3 (SP3) strains in which the pneumolysin gene (ply) was recoded with underrepresented codon pairs while retaining its amino acid sequence and determined their ply expression and pneumolysin production in vitro and their virulence in a mouse pulmonary infection model. Expression of ply and production of pneumolysin of the recoded SP3 strains were decreased, and the recoded SP3 strains were less virulent in mice than the wild-type SP3 strain or a Δply SP3 strain. Further studies showed that the least virulent recoded strain induced a markedly reduced inflammatory response in the lungs compared with the wild-type or Δply strain. These findings suggest that reducing pneumococcal virulence gene expression by altering codon-pair bias could hold promise for rational design of live-attenuated pneumococcal vaccines. PMID:21343143

Antioxidant and antimicrobial potential of the Bifurcaria bifurcata epiphytic bacteria.

PubMed

Horta, André; Pinteus, Susete; Alves, Celso; Fino, Nádia; Silva, Joana; Fernandez, Sara; Rodrigues, Américo; Pedrosa, Rui

2014-03-24

Surface-associated marine bacteria are an interesting source of new secondary metabolites. The aim of this study was the isolation and identification of epiphytic bacteria from the marine brown alga, Bifurcaria bifurcata, and the evaluation of the antioxidant and antimicrobial activity of bacteria extracts. The identification of epiphytic bacteria was determined by 16S rRNA gene sequencing. Bacteria extracts were obtained with methanol and dichloromethane (1:1) extraction. The antioxidant activity of extracts was performed by quantification of total phenolic content (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and oxygen radical absorbance capacity (ORAC). Antimicrobial activities were evaluated against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Salmonella enteritidis, Staphylococcus aureus, Saccharomyces cerevisiae and Candida albicans. A total of 39 Bifurcaria bifurcata-associated bacteria were isolated and 33 were identified as Vibrio sp. (48.72%), Alteromonas sp. (12.82%), Shewanella sp. (12.26%), Serratia sp. (2.56%), Citricoccus sp. (2.56%), Cellulophaga sp. (2.56%), Ruegeria sp. (2.56%) and Staphylococcus sp. (2.56%). Six (15.38%) of the 39 bacteria Bifurcaria bifurcata-associated bacteria presented less than a 90% Basic Local Alignment Search Tool (BLAST) match, and some of those could be new. The highest antioxidant activity and antimicrobial activity (against B. subtilis) was exhibited by strain 16 (Shewanella sp.). Several strains also presented high antimicrobial activity against S. aureus, mainly belonging to Alteromonas sp. and Vibrio sp. There were no positive results against fungi and Gram-negative bacteria. Bifurcaria bifurcata epiphytic bacteria were revealed to be excellent sources of natural antioxidant and antimicrobial compounds.

Antioxidant and Antimicrobial Potential of the Bifurcaria bifurcata Epiphytic Bacteria

PubMed Central

Horta, André; Pinteus, Susete; Alves, Celso; Fino, Nádia; Silva, Joana; Fernandez, Sara; Rodrigues, Américo; Pedrosa, Rui

2014-01-01

Surface-associated marine bacteria are an interesting source of new secondary metabolites. The aim of this study was the isolation and identification of epiphytic bacteria from the marine brown alga, Bifurcaria bifurcata, and the evaluation of the antioxidant and antimicrobial activity of bacteria extracts. The identification of epiphytic bacteria was determined by 16S rRNA gene sequencing. Bacteria extracts were obtained with methanol and dichloromethane (1:1) extraction. The antioxidant activity of extracts was performed by quantification of total phenolic content (TPC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity and oxygen radical absorbance capacity (ORAC). Antimicrobial activities were evaluated against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Salmonella enteritidis, Staphylococcus aureus, Saccharomyces cerevisiae and Candida albicans. A total of 39 Bifurcaria bifurcata-associated bacteria were isolated and 33 were identified as Vibrio sp. (48.72%), Alteromonas sp. (12.82%), Shewanella sp. (12.26%), Serratia sp. (2.56%), Citricoccus sp. (2.56%), Cellulophaga sp. (2.56%), Ruegeria sp. (2.56%) and Staphylococcus sp. (2.56%). Six (15.38%) of the 39 bacteria Bifurcaria bifurcata-associated bacteria presented less than a 90% Basic Local Alignment Search Tool (BLAST) match, and some of those could be new. The highest antioxidant activity and antimicrobial activity (against B. subtilis) was exhibited by strain 16 (Shewanella sp.). Several strains also presented high antimicrobial activity against S. aureus, mainly belonging to Alteromonas sp. and Vibrio sp. There were no positive results against fungi and Gram-negative bacteria. Bifurcaria bifurcata epiphytic bacteria were revealed to be excellent sources of natural antioxidant and antimicrobial compounds. PMID:24663118

Enhanced biodegradation of alkane hydrocarbons and crude oil by mixed strains and bacterial community analysis.

PubMed

Chen, Yu; Li, Chen; Zhou, Zhengxi; Wen, Jianping; You, Xueyi; Mao, Youzhi; Lu, Chunzhe; Huo, Guangxin; Jia, Xiaoqiang

2014-04-01

In this study, two strains, Acinetobacter sp. XM-02 and Pseudomonas sp. XM-01, were isolated from soil samples polluted by crude oil at Bohai offshore. The former one could degrade alkane hydrocarbons (crude oil and diesel, 1:4 (v/v)) and crude oil efficiently; the latter one failed to grow on alkane hydrocarbons but could produce rhamnolipid (a biosurfactant) with glycerol as sole carbon source. Compared with pure culture, mixed culture of the two strains showed higher capability in degrading alkane hydrocarbons and crude oil of which degradation rate were increased from 89.35 and 74.32 ± 4.09 to 97.41 and 87.29 ± 2.41 %, respectively. In the mixed culture, Acinetobacter sp. XM-02 grew fast with sufficient carbon source and produced intermediates which were subsequently utilized for the growth of Pseudomonas sp. XM-01 and then, rhamnolipid was produced by Pseudomonas sp. XM-01. Till the end of the process, Acinetobacter sp. XM-02 was inhibited by the rapid growth of Pseudomonas sp. XM-01. In addition, alkane hydrocarbon degradation rate of the mixed culture increased by 8.06 to 97.41 % compared with 87.29 % of the pure culture. The surface tension of medium dropping from 73.2 × 10(-3) to 28.6 × 10(-3) N/m. Based on newly found cooperation between the degrader and the coworking strain, rational investigations and optimal strategies to alkane hydrocarbons biodegradation were utilized for enhancing crude oil biodegradation.

Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter

PubMed Central

Flanagan, Jennifer C.; Stump, Andrew; Alexiev, Alexandra; Lang, Jenna M.

2015-01-01

A novel, Gram-negative, non-spore-forming, pleomorphic yellow-orange bacterial strain was isolated from a stadium seat. Strain CoronadoT falls within the Erythrobacteraceae family and the genus Porphyrobacter based on 16S rRNA phylogenetic analysis. This strain has Q-10 as the predominant respiratory lipoquinone, as do other members of the family. The fatty acid profile of this strain is similar to other Porphyrobacter, however CoronadoT contains predominately C18:1ω7cis and C16:0, a high percentage of the latter not being observed in any other Erythrobacteraceae. This strain is catalase-positive and oxidase-negative, can grow from 4 to 28 °C, at NaCl concentrations 0.1–1.5%, and at pH 6.0–8.0. On the basis of phenotypic and phylogenetic data presented in this study, strain CoronadoT represents a novel species in the Porphyrobacter genus for which the name Porphyrobacter mercurialis sp. nov. is proposed; the type strain is CoronadoT (=DSMZ 29971, =LMG 28700). PMID:26587357

Potential down-regulation of salivary gland AQP5 by LPS via cross-coupling of NF-kappaB and p-c-Jun/c-Fos.

PubMed

Yao, Chenjuan; Purwanti, Nunuk; Karabasil, Mileva Ratko; Azlina, Ahmad; Javkhlan, Purevjav; Hasegawa, Takahiro; Akamatsu, Tetsuya; Hosoi, Toru; Ozawa, Koichiro; Hosoi, Kazuo

2010-08-01

The mRNA and protein levels of aquaporin (AQP)5 in the parotid gland were found to be potentially decreased by lipopolysaccharide (LPS) in vivo in C3H/HeN mice, but only weakly in C3H/HeJ, a TLR4 mutant mouse strain. In the LPS-injected mice, pilocarpine-stimulated saliva production was reduced by more than 50%. In a tissue culture system, the LPS-induced decrease in the AQP5 mRNA level was blocked completely by pyrrolidine dithiocarbamate, MG132, tyrphostin AG126, SP600125, and partially by SB203580, which are inhibitors for IkappaB kinase, 26S proteasome, ERK1/2, JNK, and p38 MAPK, respectively. In contrast, the expression of AQP1 mRNA was down-regulated by LPS and such down-regulation was blocked only by SP600125. The transcription factors NF-kappaB (p65 subunit), p-c-Jun, and c-Fos were increased by LPS given in vivo, whereas the protein-binding activities of the parotid gland extract toward the sequences for NF-kappaB but not AP-1-responsive elements present at the promoter region of the AQP5 gene were increased by LPS injection. Co-immunoprecipitation by using antibody columns suggested the physical association of the three transcription factors. These results suggest that LPS-induced potential down-regulation of expression of AQP5 mRNA in the parotid gland is mediated via a complex(es) of these two classes of transcription factors, NF-kappaB and p-c-Jun/c-Fos.

Propensity for HBZ-SP1 isoform of HTLV-I to inhibit c-Jun activity correlates with sequestration of c-Jun into nuclear bodies rather than inhibition of its DNA-binding activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clerc, Isabelle, E-mail: isabelle.clerc@univ-montp1.f; CNRS, UM5236, CPBS, F-34965 Montpellier; Universite Montpellier 2, CPBS, F-34095 Montpellier

2009-09-01

HTLV-I bZIP factor (HBZ) contains a C-terminal zipper domain involved in its interaction with c-Jun. This interaction leads to a reduction of c-Jun DNA-binding activity and prevents the protein from activating transcription of AP-1-dependent promoters. However, it remained unclear whether the negative effect of HBZ-SP1 was due to its weak DNA-binding activity or to its capacity to target cellular factors to transcriptionally-inactive nuclear bodies. To answer this question, we produced a mutant in which specific residues present in the modulatory and DNA-binding domain of HBZ-SP1 were substituted for the corresponding c-Fos amino acids to improve the DNA-binding activity of themore » c-Jun/HBZ-SP1 heterodimer. The stability of the mutant, its interaction with c-Jun, DNA-binding activity of the resulting heterodimer, and its effect on the c-Jun activity were tested. In conclusion, we demonstrate that the repression of c-Jun activity in vivo is mainly due to the HBZ-SP1-mediated sequestration of c-Jun to the HBZ-NBs.« less

Ogataea pignaliae sp. nov., the teleomorph of Candida pignaliae.

PubMed

Péter, Gábor; Tornai-Lehoczki, Judit; Dlauchy, Dénes

2010-10-01

Six ascosporulating Candida pignaliae strains were isolated from epigeal plant parts in Hungary. They share identical D1/D2 LSU rRNA gene sequences with the type strain of C. pignaliae, and the physiological characteristics investigated are also very similar to that of the type strain. The only substantial difference compared to the type strain of C. pignaliae is their ability to assimilate β-glucosides (cellobiose, salicin and arbutin). The majority of the isolation sources of the strains reported in this study have the common feature of containing tannic acid, while the type strain of C. pignaliae was recovered from tanning fluid. We were able to induce ascosporulation also in the type strain of C. pignaliae. Therefore, Ogataea pignaliae Péter, Tornai-Lehoczki & Dlauchy sp. nov. is proposed as the teleomorph of C. pignaliae (F. H. Jacob) S. A. Meyer & Yarrow. The type strain is CBS 6071(T).

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.

Description of Kuraishia piskuri f.a., sp. nov., a new methanol assimilating yeast and transfer of phylogenetically related Candida species to the genera Kuraishia and Nakazawaea as new combinations

USDA-ARS?s Scientific Manuscript database

The new anamorphic yeast Kuraishia piskuri, f.a., sp. nov. is described for three strains that were isolated from insect frass from trees growing in Florida, USA (type strain, NRRL YB-2544, CBS 13714). Species placement was based on phylogenetic analysis of nuclear gene sequences for the D1/D2 domai...

Draft Genome Sequence of Cellulolytic and Xylanolytic Cellulomonas sp. Strain B6 Isolated from Subtropical Forest Soil.

PubMed

Piccinni, Florencia; Murua, Yanina; Ghio, Silvina; Talia, Paola; Rivarola, Máximo; Campos, Eleonora

2016-08-25

Cellulomonas sp. strain B6 was isolated from a subtropical forest soil sample and presented (hemi)cellulose-degrading activity. We report here its draft genome sequence, with an estimated genome size of 4 Mb, a G+C content of 75.1%, and 3,443 predicted protein-coding sequences, 92 of which are glycosyl hydrolases involved in polysaccharide degradation. Copyright © 2016 Piccinni et al.

Genome sequence of the photoarsenotrophic bacterium Ectothiorhodospira sp. strain BSL-9, isolated from a hypersaline alkaline arsenic-rich extreme environment

USGS Publications Warehouse

Hernandez-Maldonado, Jaime; Stoneburner, Brendon; Boren, Alison; Miller, Laurence; Rosen, Michael R.; Oremland, Ronald S.; Saltikov, Chad W

2016-01-01

The full genome sequence of Ectothiorhodospira sp. strain BSL-9 is reported here. This purple sulfur bacterium encodes an arxA-type arsenite oxidase within the arxB2AB1CD gene island and is capable of carrying out “photoarsenotrophy” anoxygenic photosynthetic arsenite oxidation. Its genome is composed of 3.5 Mb and has approximately 63% G+C content.

Influence of a Bacteriophage on the Population Dynamics of Toxic Dinoflagellates by Lysis of Algicidal Bacteria▿†

PubMed Central

Cai, Wenwei; Wang, Hui; Tian, Yun; Chen, Feng; Zheng, Tianling

2011-01-01

A lytic phage (øZCW1) was isolated from an algicidal bacterium Pseudoalteromonas sp. strain SP48 that specifically kills the toxic dinoflagellate Alexandrium tamarense. We demonstrated that øZCW1 could trigger the growth of A. tamarense by inhibiting the growth of algicidal bacterium SP48. In contrast, the growth of A. tamarense was suppressed when cocultured with either SP48 or the øZCW1-resistant mutant of SP48. This study provides the first evidence of the indirect impact of bacteriophage on bloom-forming microalgae via phage lysis of alga-killing bacteria. PMID:21890676

Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes.

PubMed

Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Ormeño-Orrillo, Ernesto; Parma, Marcia Maria; Melo, Itamar Soares; Martínez-Romero, Esperanza; Hungria, Mariangela

2015-12-01

Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).

Microbial Community Dynamics during the Bioremediation Process of Chlorimuron-Ethyl-Contaminated Soil by Hansschlegelia sp. Strain CHL1

PubMed Central

Yang, Liqiang; Li, Xinyu; Li, Xu; Su, Zhencheng; Zhang, Chenggang; Zhang, Huiwen

2015-01-01

Long-term and excessive application of chlorimuron-ethyl has led to a series of environmental problems. Strain Hansschlegelia sp. CHL1, a highly efficient chlorimuron-ethyl degrading bacterium isolated in our previous study, was employed in the current soil bioremediation study. The residues of chlorimuron-ethyl in soils were detected, and the changes of soil microbial communities were investigated by phospholipid fatty acid (PLFA) analysis. The results showed that strain CHL1 exhibited significant chlorimuron-ethyl degradation ability at wide range of concentrations between 10μg kg-1 and 1000μg kg-1. High concentrations of chlorimuron-ethyl significantly decreased the total concentration of PLFAs and the Shannon-Wiener indices and increased the stress level of microbes in soils. The inoculation with strain CHL1, however, reduced the inhibition on soil microbes caused by chlorimuron-ethyl. The results demonstrated that strain CHL1 is effective in the remediation of chlorimuron-ethyl-contaminated soil, and has the potential to remediate chlorimuron-ethyl contaminated soils in situ. PMID:25689050

Biological Activities and Chemical Composition of Methanolic Extracts of Selected Autochthonous Microalgae Strains from the Red Sea.

PubMed

Pereira, Hugo; Custódio, Luísa; Rodrigues, Maria João; de Sousa, Carolina Bruno; Oliveira, Marta; Barreira, Luísa; Neng, Nuno da Rosa; Nogueira, José Manuel Florêncio; Alrokayan, Salman A; Mouffouk, Fouzi; Abu-Salah, Khalid M; Ben-Hamadou, Radhouan; Varela, João

2015-06-03

Four lipid-rich microalgal species from the Red Sea belonging to three different genera (Nannochloris, Picochlorum and Desmochloris), previously isolated as novel biodiesel feedstocks, were bioprospected for high-value, bioactive molecules. Methanol extracts were thus prepared from freeze-dried biomass and screened for different biological activities. Nannochloris sp. SBL1 and Desmochloris sp. SBL3 had the highest radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl, and the best copper and iron chelating activities. All species had potent butyrylcholinesterase inhibitory activity (>50%) and mildly inhibited tyrosinase. Picochlorum sp. SBL2 and Nannochloris sp. SBL4 extracts significantly reduced the viability of tumoral (HepG2 and HeLa) cells with lower toxicity against the non-tumoral murine stromal (S17) cells. Nannochloris sp. SBL1 significantly reduced the viability of Leishmania infantum down to 62% (250 µg/mL). Picochlorum sp. SBL2 had the highest total phenolic content, the major phenolic compounds identified being salicylic, coumaric and gallic acids. Neoxanthin, violaxanthin, zeaxanthin, lutein and β-carotene were identified in the extracts of all strains, while canthaxanthin was only identified in Picochlorum sp. SBL2. Taken together, these results strongly suggest that the microalgae included in this work could be used as sources of added-value products that could be used to upgrade the final biomass value.

Biological Activities and Chemical Composition of Methanolic Extracts of Selected Autochthonous Microalgae Strains from the Red Sea

PubMed Central

Pereira, Hugo; Custódio, Luísa; Rodrigues, Maria João; Bruno de Sousa, Carolina; Oliveira, Marta; Barreira, Luísa; Neng, Nuno da Rosa; Nogueira, José Manuel Florêncio; Alrokayan, Salman A.; Mouffouk, Fouzi; Abu-Salah, Khalid M.; Ben-Hamadou, Radhouan; Varela, João

2015-01-01

Four lipid-rich microalgal species from the Red Sea belonging to three different genera (Nannochloris, Picochlorum and Desmochloris), previously isolated as novel biodiesel feedstocks, were bioprospected for high-value, bioactive molecules. Methanol extracts were thus prepared from freeze-dried biomass and screened for different biological activities. Nannochloris sp. SBL1 and Desmochloris sp. SBL3 had the highest radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl, and the best copper and iron chelating activities. All species had potent butyrylcholinesterase inhibitory activity (>50%) and mildly inhibited tyrosinase. Picochlorum sp. SBL2 and Nannochloris sp. SBL4 extracts significantly reduced the viability of tumoral (HepG2 and HeLa) cells with lower toxicity against the non-tumoral murine stromal (S17) cells. Nannochloris sp. SBL1 significantly reduced the viability of Leishmania infantum down to 62% (250 µg/mL). Picochlorum sp. SBL2 had the highest total phenolic content, the major phenolic compounds identified being salicylic, coumaric and gallic acids. Neoxanthin, violaxanthin, zeaxanthin, lutein and β-carotene were identified in the extracts of all strains, while canthaxanthin was only identified in Picochlorum sp. SBL2. Taken together, these results strongly suggest that the microalgae included in this work could be used as sources of added-value products that could be used to upgrade the final biomass value. PMID:26047482

Improvement of strain Penicillium sp. EZ-ZH190 for tannase production by induced mutation.

PubMed

Zakipour-Molkabadi, E; Hamidi-Esfahani, Z; Sahari, M A; Azizi, M H

2013-11-01

In the search for an efficient producer of tannase, Penicillium sp. EZ-ZH190 was subjected to mutagenesis using heat treatment and strain EZ-ZH290 was isolated. The maximum tannase in this mutant strain was 4.32 U/mL with an incubation period of 84 h as compared to wild strain EZ-ZH190 where the incubation period was 96 h with a maximum enzyme activity of 4.33 U/mL. Also, the Penicillium sp. EZ-ZH290 tannase had a maximum activity at 40 °C and pH 5.5. Then, the spores of strain EZ-ZH290 were subjected to γ irradiation mutagenesis and strain EZ-ZH390 was isolated. Strain EZ-ZH390 exhibited higher tannase activity (7.66 U/mL) than the parent strain EZ-ZH290. It was also found that Penicillium sp. EZ-ZH390 tannase had an optimum activity at 35 °C and a broad pH profile with an optimum at pH 5.5. The tannase pH stability of Penicillium sp. EZ-ZH390 and its maximum production of tannase followed the same trend for five generations confirming the occurrence of stable mutant. This paper is shown that γ irradiation can mutate the Penicillium sp. leading to increase the tannase production.

Antibacterial activities of multi drug resistant Myroides odoratimimus bacteria isolated from adult flesh flies (Diptera: sarcophagidae) are independent of metallo beta-lactamase gene

PubMed Central

Dharne, M.S.; Gupta, A.K.; Rangrez, A.Y.; Ghate, H.V.; Patole, M.S.; Shouche, Y.S.

2008-01-01

Flesh flies (Diptera: Sarcophagidae) are well known cause of myiasis and their gut bacteria have never been studied for antimicrobial activity against bacteria. Antimicrobial studies of Myroides spp. are restricted to nosocomial strains. A Gram-negative bacterium, Myroides sp., was isolated from the gut of adult flesh flies (Sarcophaga sp.) and submitted to evaluation of nutritional parameters using Biolog GN, 16S rRNA gene sequencing, susceptibility to various antimicrobials by disc diffusion method and detection of metallo β-lactamase genes (TUS/MUS). The antagonistic effects were tested on Gram-negative and Gram-positive bacteria isolated from human clinical specimens, environmental samples and insect mid gut. Bacterial species included were Aeromonas hydrophila, A. culicicola, Morganella morganii subsp. sibonii, Ochrobactrum anthropi, Weissella confusa, Escherichia coli, Ochrobactrum sp., Serratia sp., Kestersia sp., Ignatzschineria sp., Bacillus sp. The Myroides sp. strain was resistant to penicillin-G, erythromycin, streptomycin, amikacin, kanamycin, gentamycin, ampicillin, trimethoprim and tobramycin. These strain showed antibacterial action against all bacterial strains except W. confusa, Ignatzschineria sp., A. hydrophila and M. morganii subsp. sibonii. The multidrug resistance of the strain was similar to the resistance of clinical isolates, inhibiting growth of bacteria from clinical, environmental and insect gut samples. The metallo β-lactamase (TUS/MUS) genes were absent, and resistance due to these genes was ruled out, indicating involvement of other secretion machinery. PMID:24031236

Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes.

PubMed

Choi, Eun Ju; Beatty, Deanna S; Paul, Lauren A; Fenical, William; Jensen, Paul R

2013-04-01

Bacterial strains CNX-216(T) and CNU-914(T) were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were gram-negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216(T) were short, non-motile rods, whereas cells of strain CNU-914(T) were short, curved rods with gliding motility. The DNA G+C contents of CNX-216(T) and CNU-914(T) were respectively 57.7 and 44.4 mol%. Strains CNX-216(T) and CNU-914(T) contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes. Strain CNX-216(T) exhibited low 16S rRNA gene sequence identity (87.1 %) to the nearest type strain, Cesiribacter roseus 311(T), and formed a well-supported lineage that is outside all currently described families in the order Cytophagales. Strain CNU-914(T) shared 97.6 % 16S rRNA gene sequence identity with 'Porifericola rhodea' N5EA6-3A2B and, together with 'Tunicatimonas pelagia' N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales. Based on our polyphasic taxonomic characterization, we propose that strains CNX-216(T) and CNU-914(T) represent novel genera and species, for which we propose the names Mooreia alkaloidigena gen. nov., sp. nov. (type strain CNX-216(T)  = DSM 25187(T)  = KCCM 90102(T)) and Catalinimonas alkaloidigena gen. nov., sp. nov. (type strain CNU-914(T)  = DSM 25186(T)  = KCCM 90101(T)) within the new families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov.

Penicillium araracuarense sp. nov., Penicillium elleniae sp. nov., Penicillium penarojense sp. nov., Penicillium vanderhammenii sp. nov. and Penicillium wotroi sp. nov., isolated from leaf litter.

PubMed

Houbraken, Jos; López-Quintero, Carlos A; Frisvad, Jens C; Boekhout, Teun; Theelen, Bart; Franco-Molano, Ana Esperanza; Samson, Robert A

2011-06-01

Several species of the genus Penicillium were isolated during a survey of the mycobiota of leaf litter and soil in Colombian Amazon forest. Five species, Penicillium penarojense sp. nov. (type strain CBS 113178(T) = IBT 23262(T)), Penicillium wotroi sp. nov. (type strain CBS 118171(T) = IBT 23253(T)), Penicillium araracuarense sp. nov. (type strain CBS 113149(T) = IBT 23247(T)), Penicillium elleniae sp. nov. (type strain CBS 118135(T) = IBT 23229(T)) and Penicillium vanderhammenii sp. nov. (type strain CBS 126216(T) = IBT 23203(T)) are described here as novel species. Their taxonomic novelty was determined using a polyphasic approach, combining phenotypic, molecular (ITS and partial β-tubulin sequences) and extrolite data. Phylogenetic analyses showed that each novel species formed a unique clade for both loci analysed and that they were most closely related to Penicillium simplicissimum, Penicillium janthinellum, Penicillium daleae and Penicillium brasilianum. An overview of the phylogeny of this taxonomically difficult group is presented, and 33 species are accepted. Each of the five novel species had a unique extrolite profile of known and uncharacterized metabolites and various compounds, such as penicillic acid, andrastin A, pulvilloric acid, paxillin, paspaline and janthitrem, were commonly produced by these phylogenetically related species. The novel species had a high growth rate on agar media, but could be distinguished from each other by several macro- and microscopical characteristics.

Coralloluteibacterium stylophorae gen. nov., sp. nov., a new member of the family Lysobacteraceae isolated from the reef-building coral Stylophora sp.

PubMed

Chen, Wen-Ming; Xie, Pei-Bei; Tang, Sen-Lin; Sheu, Shih-Yi

2018-04-01

A bacterial strain, designated Sty a-1 T , was isolated from a reef-building coral Stylophora sp., collected off coast of Southern Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain Sty a-1 T were Gram-staining-negative, aerobic, poly-β-hydroxybutyrate accumulating, motile by means of flagella, non-spore forming, straight rod-shaped and colonies were yellow and circular. Growth occurred at 15-40 °C (optimum, 30-35 °C), at pH 6-10 (optimum, pH 6.5-8) and with 0-7% NaCl (optimum, 2-3%). The predominant fatty acids were iso-C 15:0 , iso-C 17:1 ω9c, summed feature 3 (comprising C 16:1 ω7c and/or C 16:1 ω6c) and iso-C 17:0 . The major isoprenoid quinone was Q-8 and the DNA G+C content was 68.5 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminophospholipid and three uncharacterized lipids. The major polyamines were spermidine, putrescine and homospermidine. Phylogenetic analyses based on 16S rRNA and four housekeeping gene sequences (recA, atpD, rpoA and rpoB) showed that strain Sty a-1 T forms a distinct lineage with respect to closely related genera in the family Lysobacteraceae, most closely related to Lysobacter, Silanimonas, Arenimonas and Luteimonas and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 95%. On the basis of the genotypic and phenotypic data, strain Sty a-1 T represents a novel genus and species of the family Lysobacteraceae, for which the name Coralloluteibacterium stylophorae gen. nov., sp. nov. is proposed. The type strain is Sty a-1 T (= BCRC 80968 T  = LMG 29479 T  = KCTC 52167 T ).

Characterization of hydrocarbon-degrading and biosurfactant-producing Pseudomonas sp. P-1 strain as a potential tool for bioremediation of petroleum-contaminated soil.

PubMed

Pacwa-Płociniczak, Magdalena; Płaza, Grażyna Anna; Poliwoda, Anna; Piotrowska-Seget, Zofia

2014-01-01

The Pseudomonas sp. P-1 strain, isolated from heavily petroleum hydrocarbon-contaminated soil, was investigated for its capability to degrade hydrocarbons and produce a biosurfactant. The strain degraded crude oil, fractions A5 and P3 of crude oil, and hexadecane (27, 39, 27 and 13% of hydrocarbons added to culture medium were degraded, respectively) but had no ability to degrade phenanthrene. Additionally, the presence of gene-encoding enzymes responsible for the degradation of alkanes and naphthalene in the genome of the P-1 strain was reported. Positive results of blood agar and methylene blue agar tests, as well as the presence of gene rhl, involved in the biosynthesis of rhamnolipid, confirmed the ability of P-1 for synthesis of glycolipid biosurfactant. 1H and 13C nuclear magnetic resonance, Fourier transform infrared spectrum and mass spectrum analyses indicated that the extracted biosurfactant was affiliated with rhamnolipid. The results of this study indicate that the P-1 and/or biosurfactant produced by this strain have the potential to be used in bioremediation of hydrocarbon-contaminated soils.

Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin from soils inoculated with Sphingomonas sp. strain RW1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halden, R.U.; Halden, B.G.; Dwyer, D.F.

Removal of dibenzofuran, dibenzo-p-dioxin, and 2-chlorodibenzo-p-dioxin (2-CDD) (10 ppm each) from soil microcosms to final concentrations in the parts-per-billion range was affected by the addition of Sphingomonas sp. strain RW1. Rates and extents of removal were influenced by the density of RW1 organisms. For 2-CDD, the rate of removal was dependent on the content of soil organic matter (SOM), with half-life values ranging from 5.8 h (0% SOM) to 26.3 h (5.5% SOM).

Quinolactacins A, B and C: novel quinolone compounds from Penicillium sp. EPF-6. I. Taxonomy, production, isolation and biological properties.

PubMed

Kakinuma, N; Iwai, H; Takahashi, S; Hamano, K; Yanagisawa, T; Nagai, K; Tanaka, K; Suzuki, K; Kirikae, F; Kirikae, T; Nakagawa, A

2000-11-01

Quinolactacins A (1), B (2) and C (3), novel quinolone antibiotics have been found from the cultured broth of a fungal strain isolated from the larvae of the mulberry pyralid Margaronia pyloalis Welker). The fungal strain, EPF-6 was identified as Penicillium sp. from its morphological characteristics. Quinolactacins were obtained from the culture medium by solvent extraction and chromatographic purification. Compound 1 showed inhibitory activity against tumor necrosis factor (TNF) production induced by murine peritoneal macrophages and macrophage-like J774.1 cells stimulated with lipopolysaccharide (LPS).

Mutational analysis of the multicopy hao gene coding for hydroxylamine oxidoreductase in Nitrosomonas sp. strain ENI-11.

PubMed

Yamagata, A; Hirota, R; Kato, J; Kuroda, A; Ikeda, T; Takiguchi, N; Ohtake, H

2000-08-01

The ammonia-oxidizing bacterium Nitrosomonas sp. strain ENI-11 contains three copies of the hao gene (hao1, hao2, and hao3) coding for hydroxylamine oxidoreductase (HAO). Three single mutants (hao1::kan, hao2::kan, or hao3::kan) had 68 to 75% of the wild-type growth rate and 58 to 89% of the wild-type HAO activity when grown under the same conditions. A double mutant (hao1::kan and hao3::amp) also had 68% of the wild-type growth and 37% of the wild-type HAO activity.

Speckle-tracking strain assessment of left ventricular dysfunction in synthetic cannabinoid and heroin users.

PubMed

Demirkıran, Aykut; Albayrak, Neslihan; Albayrak, Yakup; Zorkun, Cafer Sadık

2018-06-01

There is growing evidence regarding the numerous adverse effects of synthetic cannabinoids (SCBs) on the cardiovascular system; however, no studies have shown the cardiovascular effects of opioids using strain echocardiography. This study examines the cardiac structure and function using echocardiographic strain imaging in heroin and synthetic cannabinoid users. This double-blind study included patients who were admitted or referred to a rehabilitation center for heroin (n=31) and synthetic cannabinoid users (n=30). Heroin users and synthetic cannabinoid users were compared with healthy volunteers (n=32) using two-dimensional (2D) speckle-tracking (ST) echocardiography. No differences were found in the baseline characteristics and 2D echocardiography values. The mean global longitudinal strain value was -20.5%±2.4% for SCB users, -22.3%±2.4% for opioid users, and -22.5%±2.2% for healthy volunteers (p=0.024). The mean apical 2-chamber (AP2C) L-strain values were -20.1%±3.1%, -22.4%±3.0%, and -22.3%±2.8% for SCB users, opioid users, and healthy volunteers, respectively (p=0.032). The mean apical 4-chamber (AP4C) L-strain values were -20.7%±2.5% for SCB users, -23.2%±3.2% for opioid users, and -23.8%±3.1% for healthy volunteers (p<0.001). SCBs are potential causes of subclinical left ventricular dysfunction.

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

PubMed Central

Chénard, Caroline; Wirth, Jennifer F.

2016-01-01

ABSTRACT   Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages. PMID:27302758

Candida amazonensis sp. nov., an ascomycetous yeast isolated from rotting wood in the Amazonian forest.

PubMed

Cadete, Raquel M; Melo, Monaliza A; Lopes, Mariana R; Pereira, Gilmara M D; Zilli, Jerri E; Vital, Marcos J S; Gomes, Fátima C O; Lachance, Marc-André; Rosa, Carlos A

2012-06-01

Five strains of a novel yeast species were isolated from rotting wood samples collected in an Amazonian forest site in the state of Roraima, northern Brazil. The sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that this species belongs to the Scheffersomyces clade and is related to Candida coipomoensis, Candida lignicola and Candida queiroziae. The novel species Candida amazonensis sp. nov. is proposed to accommodate these isolates. The type strain of C. amazonensis sp. nov. is UFMG-HMD-26.3(T) ( = CBS 12363(T) = NRRL Y-48762(T)).

Antagonistic effect of chosen lactic acid bacteria strains on Yersinia enterocolitica species in model set-ups, meat and fermented sausages.

PubMed

Gomółka-Pawlicka, M; Uradziński, J

2003-01-01

The present study was aimed at determining the influence of 15 strains of lactic acid bacteria on the growth of 8 Yersinia enterocolitica strains in model set-ups, and in meat and ageing fermented sausages. The investigations were performed within the framework of three alternate stages which differed in respect to the products studied, the number of Lactobacillus sp. strains and, partly, methodological approach. The ratio between lactic acid bacteria and Yersinia enterocolitica strains studied was, depending on the variant of experiment, 1:1, 1:2 and 2:1, respectively. The study also considered water activity (aw) and pH of the products investigated. The results suggest that all the lactic acid bacteria strains used within the framework of the model set-ups had antagonistic effect on all the Salmonella sp. strains. However, this ability was not observed with respect to of tested lactic acid bacteria strains in meat and fermented sausage. This ability was possessed by one of the strains investigated--Lactobacillus helveticus T 78. The temperature and time of the incubation of sausages, but not aw and pH, were found to have a distinct influence on the antagonistic interaction between the bacteria tested.

Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.

PubMed

Madhaiyan, Munusamy; Alex, Tan Hian Hwee; Cho, Hayoung; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Whitman, William B; Ji, Lianghui

2017-12-01

Two yellow-pigmented isolates, S5-249 T and L9-754 T , originating from surface-sterilized plant tissues of Jatropha curcas L. (Jatropha) cultivars were characterized using a polyphasic taxonomic approach. Strains S5-249 T and L9-754 T had 16S rRNA genes sharing 94.2 % sequence similarity with each other and 91.6-97.2 % sequence similarity with those of other species in the genus Sphingomonas, suggesting that they represent two potentially novel species. The 16S rRNA gene sequences of strains S5-249 T and L9-754 T shared the highest similarity to that of Sphingomonas sanguinis NBRC 13937 T (96.1 and 97.2 %, respectively). The genomic DNA G+C contents of strains S5-249 T and L9-754 T were 66.9 and 68.5 mol%, respectively. The respiratory quinone was determined to be Q-10, and the major polyamine was homospermidine. Strains S5-249 T and L9-754 T contained summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), C16 : 1, C14 : 0 2-OH and summed feature 4 (C16 : 1ω7t, iso-C15 : 0 2-OH and C16 : 1ω7c) as the major cellular fatty acids. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and sphingoglycolipid. The average nucleotide identity (ANI) values between S. sanguinis NBRC 13937 T and the two type strains (S5-249 T and L9-754 T ) were 72.31 and 77.73 %, respectively. Digital DNA-DNA hybridization (dDDH) studies between the novel strains (S5-249 T and L9-754 T ) and other species of the genus Sphingomonas were well below the thresholds used to discriminate between bacterial species. The results of dDDH and physiological tests allowed genotypic and phenotypic differentiation of the strains from each other as well as from the species of the genus Sphingomonas with validly published names. These data strongly support the classification of the strains as representatives of novel species, for which we propose the names Sphingomonas jatrophae sp. nov. (type strain S5-249 T =DSM 27345 T =KACC 17593 T ) and Sphingomonas carotinifaciens sp. nov. (type strain L9-754 T =DSM 27347 T =KACC 17595 T ).

Biodegradation of sulfamethoxazole in bacteria from three different origins.

PubMed

Mulla, Sikandar I; Hu, Anyi; Sun, Qian; Li, Jiagwei; Suanon, Fidèle; Ashfaq, Muhammad; Yu, Chang-Ping

2018-01-15

Sulfamethoxazole (SMX) is a common medicine prescribed to treat infections. Due to vast use, SMX has been detected in different parts of the world. Hence, it has become a high risk because of its long term persistence with high biological activity in the ecosystem. Therefore, it is necessary to understand the mechanism of SMX degradation in different genus of bacteria, which is presently unclear. In the present study, degradation of 5 mg L -1 SMX was studied in three isolated pure bacterial cultures, Ochrobactrum sp. SMX-PM1-SA1, Labrys sp. SMX-W1-SC11 and Gordonia sp. SMX-W2-SCD14 and results showed up to 45.2%, 62.2% and 51.4% degradation, respectively within 288 h. Additionally, strain SA1 and strain SCD14 showed up to 66.2% and 69.2% of 4-aminophenol degradation at an initial concentration of 5 mg L -1 within 216 h whereas Labrys sp. SMX-W1-SC11 completely degraded 4-aminophenol at the same concentration within 120 h. Moreover, all three pure bacteria also completely degraded 3-amino-5-methylisoxazole at initial concentration of 4 mg L -1 within 120 h. Furthermore, gas chromatography-mass spectrometry and quadrupole time-of-flight mass spectrometry analysis results revealed that 3-amino-5-methylisoxazole, 4-aminophenol and hydroquinone were the three main by-products of SMX catabolism. In addition, cell free extracts of both Labrys sp. SMX-W1-SC11 and Gordonia sp. SMX-W2-SCD14 showed hydroquinone dioxygenase activity. Besides, all three bacterial strains showed resistance to different heavy metals. Moreover, all three pure bacterial cultures also showed positive chemotactic response toward 3-amino-5-methylisoxazole and hydroquinone based on the drop plate assay. The results of this study recommend these microorganisms for bioremediation of SMX contaminated sites. Copyright © 2017. Published by Elsevier Ltd.

National Epidemiologic Surveys of Enterobacter aerogenes in Belgian Hospitals from 1996 to 1998

PubMed Central

De Gheldre, Y.; Struelens, M. J.; Glupczynski, Y.; De Mol, P.; Maes, N.; Nonhoff, C.; Chetoui, H.; Sion, C.; Ronveaux, O.; Vaneechoutte, M.

2001-01-01

Two national surveys were conducted to describe the incidence and prevalence of Enterobacter aerogenes in 21 Belgian hospitals in 1996 and 1997 and to characterize the genotypic diversity and the antimicrobial resistance profiles of clinical strains of E. aerogenes isolated from hospitalized patients in Belgium in 1997 and 1998. Twenty-nine hospitals collected 10 isolates of E. aerogenes, which were typed by arbitrarily primed PCR (AP-PCR) using two primers and pulsed-field gel electrophoresis. MICs of 10 antimicrobial agents were determined by the agar dilution method. Beta-lactamases were detected by the double-disk diffusion test and characterized by isoelectric point. The median incidence of E. aerogenes colonization or infection increased from 3.3 per 1,000 admissions in 1996 to 4.2 per 1000 admissions in the first half of 1997 (P < 0.01). E. aerogenes strains (n = 260) clustered in 25 AP-PCR types. Two major types, BE1 and BE2, included 36 and 38% of strains and were found in 21 and 25 hospitals, respectively. The BE1 type was indistinguishable from a previously described epidemic strain in France. Half of the strains produced an extended-spectrum beta-lactamase, either TEM-24 (in 86% of the strains) or TEM-3 (in 14% of the strains). Over 75% of the isolates were resistant to ceftazidime, piperacillin-tazobactam, and ciprofloxacin. Over 90% of the strains were susceptible to cefepime, carbapenems, and aminoglycosides. In conclusion, these data suggest a nationwide dissemination of two epidemic multiresistant E. aerogenes strains in Belgian hospitals. TEM-24 beta-lactamase was frequently harbored by one of these epidemic strains, which appeared to be genotypically related to a TEM-24-producing epidemic strain from France, suggesting international dissemination. PMID:11230400

Reductive dehalogenation of 3,5-dibromo-4-hydroxybenzoate by an aerobic strain of Delftia sp. EOB-17.

PubMed

Chen, Kai; Jian, Shanshan; Huang, Linglong; Ruan, Zhepu; Li, Shunpeng; Jiang, Jiandong

2015-12-01

To confirm the reductive dehalogenation ability of the aerobic strain of Delftia sp. EOB-17, finding more evidences to support the hypothesis that reductive dehalogenation may occur extensively in aerobic bacteria. Delftia sp. EOB-17, isolated from terrestrial soil contaminated with halogenated aromatic compounds, completely degraded 0.2 mM DBHB in 28 h and released two equivalents of bromides under aerobic conditions in the presence of sodium succinate. LC-MS analysis revealed that DBHB was transformed to 4-hydroxybenzoate via 3-bromo-4-hydroxybenzoate by successive reductive dehalogenation. Highly conserved DBHB-degrading genes, including reductive dehalogenase gene (bhbA3) and the extra-cytoplasmic binding receptor gene (bhbB3), were also found in strain EOB-17 by genome sequencing. The optimal temperature and pH for DBHB reductive dehalogenation activity are 30 °C and 8, respectively, and 0.1 mM Cd(2+), Cu(2+), Hg(2+) and Zn(2+) strongly inhibited dehalogenation activity. The aerobic strain of Delftia sp. EOB-17 was confirmed to reductively dehalogenate DBHB under aerobic conditions, providing another evidence to support the hypothesis that reductive dehalogenation occurs extensively in aerobic bacteria.

α-Tocopherol Is Essential for Acquired Chill-Light Tolerance in the Cyanobacterium Synechocystis sp. Strain PCC 6803▿ †

PubMed Central

Yang, Yang; Yin, Chuntao; Li, Weizhi; Xu, Xudong

2008-01-01

Unlike Escherichia coli, the cyanobacterium Synechocystis sp. strain PCC 6803 is insensitive to chill (5°C) in the dark but rapidly losses viability when exposed to chill in the light (100 μmol photons m−2 s−1). Preconditioning at a low temperature (15°C) greatly enhances the chill-light tolerance of Synechocystis sp. strain PCC 6803. This phenomenon is called acquired chill-light tolerance (ACLT). Preconditioned wild-type cells maintained a substantially higher level of α-tocopherol after exposure to chill-light stress. Mutants unable to synthesize α-tocopherol, such as slr1736, slr1737, slr0089, and slr0090 mutants, almost completely lost ACLT. When exposed to chill without light, these mutants showed no or a slight difference from the wild type. When complemented, the slr0089 mutant regained its ACLT. Copper-regulated expression of slr0090 from PpetE controlled the level of α-tocopherol and ACLT. We conclude that α-tocopherol is essential for ACLT of Synechocystis sp. strain PCC 6803. The role of α-tocopherol in ACLT may be based largely on a nonantioxidant activity that is not possessed by other tocopherols or pathway intermediates. PMID:18165303

Diversity and physiological characterization of D-xylose-fermenting yeasts isolated from the Brazilian Amazonian Forest.

PubMed

Cadete, Raquel M; Melo, Monaliza A; Dussán, Kelly J; Rodrigues, Rita C L B; Silva, Silvio S; Zilli, Jerri E; Vital, Marcos J S; Gomes, Fátima C O; Lachance, Marc-André; Rosa, Carlos A

2012-01-01

This study is the first to investigate the Brazilian Amazonian Forest to identify new D-xylose-fermenting yeasts that might potentially be used in the production of ethanol from sugarcane bagasse hemicellulosic hydrolysates. A total of 224 yeast strains were isolated from rotting wood samples collected in two Amazonian forest reserve sites. These samples were cultured in yeast nitrogen base (YNB)-D-xylose or YNB-xylan media. Candida tropicalis, Asterotremella humicola, Candida boidinii and Debaryomyces hansenii were the most frequently isolated yeasts. Among D-xylose-fermenting yeasts, six strains of Spathaspora passalidarum, two of Scheffersomyces stipitis, and representatives of five new species were identified. The new species included Candida amazonensis of the Scheffersomyces clade and Spathaspora sp. 1, Spathaspora sp. 2, Spathaspora sp. 3, and Candida sp. 1 of the Spathaspora clade. In fermentation assays using D-xylose (50 g/L) culture medium, S. passalidarum strains showed the highest ethanol yields (0.31 g/g to 0.37 g/g) and productivities (0.62 g/L · h to 0.75 g/L · h). Candida amazonensis exhibited a virtually complete D-xylose consumption and the highest xylitol yields (0.55 g/g to 0.59 g/g), with concentrations up to 25.2 g/L. The new Spathaspora species produced ethanol and/or xylitol in different concentrations as the main fermentation products. In sugarcane bagasse hemicellulosic fermentation assays, S. stipitis UFMG-XMD-15.2 generated the highest ethanol yield (0.34 g/g) and productivity (0.2 g/L · h), while the new species Spathaspora sp. 1 UFMG-XMD-16.2 and Spathaspora sp. 2 UFMG-XMD-23.2 were very good xylitol producers. This study demonstrates the promise of using new D-xylose-fermenting yeast strains from the Brazilian Amazonian Forest for ethanol or xylitol production from sugarcane bagasse hemicellulosic hydrolysates.

Legionella saoudiensis sp. nov., isolated from a sewage water sample.

PubMed

Bajrai, Leena Hussein; Azhar, Esam Ibraheem; Yasir, Muhammad; Jardot, Priscilla; Barrassi, Lina; Raoult, Didier; La Scola, Bernard; Pagnier, Isabelle

2016-11-01

A Gram-stain-negative, bacilli-shaped bacterial strain, LS-1T, was isolated from a sewage water sample collected in Jeddah, Saudi Arabia. The taxonomic position of strain LS-1T was investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences and those of four other genes indicated that strain LS-1T belongs to the genus Legionella in the family Legionellaceae. Regarding the 16S rRNA gene, the most closely related species are Legionella rowbothamii LLAP-6T (98.6 %) and Legionella lytica L2T (98.5 %). The mip gene sequence of strain LS-1T showed 94 % sequence similarity with that of L. lytica L2T and 93 % similarity with that of L. rowbothamii LLAP-6T. Strain LS-1T grew optimally at a temperature of 32 °C on a buffered charcoal yeast extract (BCYE) agar plate in a 5 % CO2 atmosphere and had a flagellum. The combined phylogenetic, phenotypic and genomic sequence data suggest that strain LS-1T represents a novel species of the genus Legionella, for which the name Legionella saoudiensis sp. nov. is proposed. The type strain is LS-1T (=DSM 101682T=CSUR P2101T).

Draft Genome Sequence of a Sphingomonas sp., an Endosymbiotic Bacterium Isolated from an Arctic Lichen Umbilicaria sp.

PubMed Central

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

2012-01-01

Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on the Svalbard Islands. Here we present the draft genome sequence of this strain, which represents a valuable resource for understanding the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in extreme environments. PMID:22582371

Production of hydrogen and volatile fatty acid by Enterobacter sp. T4384 using organic waste materials.

PubMed

Kim, Byung-Chun; Deshpande, Tushar R; Chun, Jongsik; Yi, Sung Chul; Kim, Hyunook; Um, Youngsoon; Sang, Byoung-In

2013-02-01

In a study of hydrogen-producing bacteria, strain T4384 was isolated from rice field samples in the Republic of Korea. The isolate was identified as Enterobacter sp. T4384 by phylogenetic analysis of 16S rRNA and rpoB gene sequences. Enterobacter sp. T4384 grew at a temperature range of 10-45 degrees C and at an initial pH range of 4.5-9.5. Strain T4384 produced hydrogen at 0-6% NaCl by using glucose, fructose, and mannose. In serum bottle cultures using a complete medium, Enterobacter sp. T4384 produced 1,098 ml/l H2, 4.0 g/l ethanol, and 1.0 g/l acetic acid. In a pH-regulated jar fermenter culture with the biogas removed, 2,202 ml/l H2, 6.2 g/l ethanol, and 1.0 g/l acetic acid were produced, and the lag-phase time was 4.8 h. Strain T4384 metabolized the hydrolysate of organic waste for the production of hydrogen and volatile fatty acid. The strain T4384 produced 947 ml/l H2, 3.2 g/l ethanol, and 0.2 g/l acetic acid from 6% (w/v) food waste hydrolysate; 738 ml/l H2, 4.2 g/l ethanol, and 0.8 g/l acetic acid from Miscanthus sinensis hydrolysate; and 805 ml/l H2, 5.0 g/l ethanol, and 0.7 g/l acetic acid from Sorghum bicolor hydrolysate.

[Reconstructed ambient light extinction coefficient and its contribution factors in Beijing in January, 2010].

PubMed

Zhu, Li-Hua; Tao, Jun; Chen, Zhong-Ming; Zhao, Yue; Zhang, Ren-Jian; Cao, Jun-Ji

2012-01-01

Aerosol samples for PM2.5 were collected from 1st January to 31st January 2010, in Beijing. The concentrations of organic carbon, elemental carbon, water-solubile ions and soil elements of all particle samples were determined by thermal/optical carbon analyzer, ion chromatography and X-ray fluorescence spectrometer, respectively. The scattering coefficients (b(sp)), absorbing coefficients (b(ap)) and meteorological parameters for this period were also measured. Ambient light extinction coefficients were reconstructed by IMPROVE formula and were compared with measured light extinction coefficients. The results showed that the average mass concentration of PM2.5 was (144.3 +/- 89.1) microg x m(-3) during campaigning period. The average values of measured b(ap), b(sp) and extinction coefficient (b(ext)) were (67.4 +/- 54.3), (328.5 +/- 353.8) and (395.9 +/- 405.2) Mm(-1), respectively. IMPROVE formula is suitable for source apportionment of light extinction coefficient in campaign period. The average value of calculated b'(ext) was (611 +/- 503) Mm(-1) in January, 2010. The major contributors to ambient light extinction coefficients included (NH4) 2SO4 (24.6%), NH4NO3 (11.6%), OM (45.5%), EC (11.9%) and FS (6.4%), respectively.

Lentzea soli sp. nov., an actinomycete isolated from soil.

PubMed

Li, Dongmei; Zheng, Weiwei; Zhao, Junwei; Han, Liyuan; Zhao, Xueli; Jiang, Hao; Wang, Xiangjing; Xiang, Wensheng

2018-05-01

A novel actinobacterium, designated strain NEAU-LZC 7 T , was isolated from soil collected from Mount Song and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LZC 7 T belonged to the genus Lentzea, with highest sequence similarity to Lentzea violacea JCM 10975 T (98.1 %). Morphological and chemotaxonomic characteristics of the strain also supported its assignment to the genus Lentzea. However, DNA-DNA relatedness, physiological and biochemical data showed that strain NEAU-LZC 7 T could be distinguished from its closest relative. Therefore, strain NEAU-LZC 7 T represents a novel species of the genus Lentzea, for which the name Lentzea soli sp. nov. is proposed, with NEAU-LZC 7 T (=CCTCC AA 2017027 T =JCM 32384 T ) as the type strain.

Diverse Responses to UV-B Radiation and Repair Mechanisms of Bacteria Isolated from High-Altitude Aquatic Environments▿

PubMed Central

Fernández Zenoff, V.; Siñeriz, F.; Farías, M. E.

2006-01-01

Acinetobacter johnsonii A2 isolated from the natural community of Laguna Azul (Andean Mountains at 4,560 m above sea level), Serratia marcescens MF42, Pseudomonas sp. strain MF8 isolated from the planktonic community, and Cytophaga sp. strain MF7 isolated from the benthic community from Laguna Pozuelos (Andean Puna at 3,600 m above sea level) were subjected to UV-B (3,931 J m−2) irradiation. In addition, a marine Pseudomonas putida strain, 2IDINH, and a second Acinetobacter johnsonii strain, ATCC 17909, were used as external controls. Resistance to UV-B and kinetic rates of light-dependent (UV-A [315 to 400 nm] and cool white light [400 to 700 nm]) and -independent reactivation following exposure were determined by measuring the survival (expressed as CFU) and accumulation of cyclobutane pyrimidine dimers (CPD). Significant differences in survival after UV-B irradiation were observed: Acinetobacter johnsonii A2, 48%; Acinetobacter johnsonii ATCC 17909, 20%; Pseudomonas sp. strain MF8, 40%; marine Pseudomonas putida strain 2IDINH, 12%; Cytophaga sp. strain MF7, 20%; and Serratia marcescens, 21%. Most bacteria exhibited little DNA damage (between 40 and 80 CPD/Mb), except for the benthic isolate Cytophaga sp. strain MF7 (400 CPD/Mb) and Acinetobacter johnsonii ATCC 17909 (160 CPD/Mb). The recovery strategies through dark and light repair were different in all strains. The most efficient in recovering were both Acinetobacter johnsonii A2 and Cytophaga sp. strain MF7; Serratia marcescens MF42 showed intermediate recovery, and in both Pseudomonas strains, recovery was essentially zero. The UV-B responses and recovery abilities of the different bacteria were consistent with the irradiation levels in their native environment. PMID:17056692

Antagonistic activities of some Bifidobacterium sp. strains isolated from resident infant gastrointestinal microbiota on Gram-negative enteric pathogens.

PubMed

Delcaru, Cristina; Alexandru, Ionela; Podgoreanu, Paulina; Cristea, Violeta Corina; Bleotu, Coralia; Chifiriuc, Mariana Carmen; Bezirtzoglou, Eugenia; Lazar, Veronica

2016-06-01

The gastrointestinal microbiota contributes to the consolidation of the anti-infectious barrier against enteric pathogens. The purpose of this study was to investigate the influence of Bifidobacterium sp. strains, recently isolated from infant gastrointestinal microbiota on the in vitro growth and virulence features expression of enteropathogenic bacterial strains. The antibacterial activity of twelve Bifidobacterium sp. strains isolated from human feces was examined in vitro against a wide range of Gram negative pathogenic strains isolated from 30 infant patients (3 days to 5 years old) with diarrhea. Both potential probiotic strains (Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium catenulatum, Bifidobacterium breve, Bifidobacterium ruminantium) and enteropathogenic strains (EPEC, EIEC, Klebsiella pneumoniae, Salmonella sp., Yersinia enterocolitica, Pseudomonas aeruginosa) were identified by MALDI-TOF and confirmed serologically when needed. The bactericidal activity, growth curve, adherence to the cellular HEp-2 substratum and production of soluble virulence factors have been assessed in the presence of different Bifidobacterium sp. cultures and fractions (whole culture and free-cell supernatants). Among the twelve Bifidobacterium sp. strains, the largest spectrum of antimicrobial activity against 9 of the 18 enteropathogenic strains was revealed for a B. breve strain recently isolated from infant intestinal feces. The whole culture and free-cell supernatant of B. breve culture decreased the multiplication rate, shortened the log phase and the total duration of the growth curve, with an earlier entrance in the decline phase and inhibited the adherence capacity to a cellular substratum and the swimming/swarming motility too. These results indicate the significant probiotic potential of the B. breve strain. Copyright © 2016 Elsevier Ltd. All rights reserved.

Candida ficus sp. nov., a novel yeast species from the gut of Apriona germari larvae.

PubMed

Hui, Feng-Li; Niu, Qiu-Hong; Ke, Tao; Liu, Zheng

2012-11-01

A novel yeast species is described based on three strains from the gut of wood-boring larvae collected in a tree trunk of Ficus carica cultivated in parks near Nanyang, central China. Phylogenetic analysis based on sequences of the D1/D2 domains of the large subunit rRNA gene showed that these strains occurred in a separate clade that was genetically distinct from all known ascomycetous yeasts. In terms of pairwise sequence divergence, the novel strains differed by 15.3% divergence from the type strain of Pichia terricola, and by 15.8% divergence from the type strains of Pichia exigua and Candida rugopelliculosa in the D1/D2 domains. All three are ascomycetous yeasts in the Pichia clade. Unlike P. terricola, P. exigua and C. rugopelliculosa, the novel isolates did not ferment glucose. The name Candida ficus sp. nov. is proposed to accommodate these highly divergent organisms, with STN-8(T) (=CICC 1980(T)=CBS 12638(T)) as the type strain.

Enhanced biological fixation of methane for microbial lipid production by recombinant Methylomicrobium buryatense

DOE PAGES

Fei, Qiang; Puri, Aaron W.; Smith, Holly; ...

2018-05-04

Due to the success of shale gas development in the US, the production cost of natural gas has been reduced significantly, which in turn has made methane (CH 4), the major component of natural gas, a potential alternative substrate for bioconversion processes compared with other high-price raw material sources or edible feedstocks. Therefore, exploring effective ways to use CH 4 for the production of biofuels is attractive. Biological fixation of CH 4 by methanotrophic bacteria capable of using CH 4 as their sole carbon and energy source has obtained great attention for biofuel production from this resource. Here, a fast-growingmore » and lipid-rich methanotroph, Methylomicrobium buryatense 5GB1 and its glycogen-knock-out mutant (AP18) were investigated for the production of lipids derived from intracellular membranes, which are key precursors for the production of green diesel. The effects of culture conditions on cell growth and lipid production were investigated in high cell density cultivation with continuous feeding of CH 4 and O2. The highest dry cell weight observed was 21.4 g/L and the maximum lipid productivity observed was 45.4 mg/L/h obtained in batch cultures, which corresponds to a 2-fold enhancement in cell density and 3-fold improvement in lipid production, compared with previous reported data from cultures of 5GB1. A 90% enhancement of lipid content was achieved by limiting the biosynthesis of glycogen in strain AP18. Increased CH 4/O 2 uptake and CO 2 evaluation rates were observed in AP18 cultures suggesting that more carbon substrate and energy are needed for AP18 growth while producing lipids. The lipid produced by M. buryatense was estimated to have a cetane number of 75, which is 50% higher than biofuel standards requested by US and EU. Cell growth and lipid production were significantly influenced by culture conditions for both 5GB1 and AP18. Enhanced lipid production in terms of titer, productivity, and content was achieved under high cell density culture conditions by blocking glycogen accumulation as a carbon sink in the strain AP18. Differences observed in CH 4/O 2 gas uptake and CO 2 evolution rates as well as cell growth and glycogen accumulation between 5GB1 and AP18 suggest changes in the metabolic network between these strains. This bioconversion process provides a promising opportunity to transform CH 4 into biofuel molecules and encourages further investigation to elucidate the remarkable CH 4 biofixation mechanism used by these bacteria.« less

Enhanced biological fixation of methane for microbial lipid production by recombinant Methylomicrobium buryatense

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fei, Qiang; Puri, Aaron W.; Smith, Holly

Due to the success of shale gas development in the US, the production cost of natural gas has been reduced significantly, which in turn has made methane (CH 4), the major component of natural gas, a potential alternative substrate for bioconversion processes compared with other high-price raw material sources or edible feedstocks. Therefore, exploring effective ways to use CH 4 for the production of biofuels is attractive. Biological fixation of CH 4 by methanotrophic bacteria capable of using CH 4 as their sole carbon and energy source has obtained great attention for biofuel production from this resource. Here, a fast-growingmore » and lipid-rich methanotroph, Methylomicrobium buryatense 5GB1 and its glycogen-knock-out mutant (AP18) were investigated for the production of lipids derived from intracellular membranes, which are key precursors for the production of green diesel. The effects of culture conditions on cell growth and lipid production were investigated in high cell density cultivation with continuous feeding of CH 4 and O2. The highest dry cell weight observed was 21.4 g/L and the maximum lipid productivity observed was 45.4 mg/L/h obtained in batch cultures, which corresponds to a 2-fold enhancement in cell density and 3-fold improvement in lipid production, compared with previous reported data from cultures of 5GB1. A 90% enhancement of lipid content was achieved by limiting the biosynthesis of glycogen in strain AP18. Increased CH 4/O 2 uptake and CO 2 evaluation rates were observed in AP18 cultures suggesting that more carbon substrate and energy are needed for AP18 growth while producing lipids. The lipid produced by M. buryatense was estimated to have a cetane number of 75, which is 50% higher than biofuel standards requested by US and EU. Cell growth and lipid production were significantly influenced by culture conditions for both 5GB1 and AP18. Enhanced lipid production in terms of titer, productivity, and content was achieved under high cell density culture conditions by blocking glycogen accumulation as a carbon sink in the strain AP18. Differences observed in CH 4/O 2 gas uptake and CO 2 evolution rates as well as cell growth and glycogen accumulation between 5GB1 and AP18 suggest changes in the metabolic network between these strains. This bioconversion process provides a promising opportunity to transform CH 4 into biofuel molecules and encourages further investigation to elucidate the remarkable CH 4 biofixation mechanism used by these bacteria.« less

Enhanced biological fixation of methane for microbial lipid production by recombinant Methylomicrobium buryatense.

PubMed

Fei, Qiang; Puri, Aaron W; Smith, Holly; Dowe, Nancy; Pienkos, Philip T

2018-01-01

Due to the success of shale gas development in the US, the production cost of natural gas has been reduced significantly, which in turn has made methane (CH 4 ), the major component of natural gas, a potential alternative substrate for bioconversion processes compared with other high-price raw material sources or edible feedstocks. Therefore, exploring effective ways to use CH 4 for the production of biofuels is attractive. Biological fixation of CH 4 by methanotrophic bacteria capable of using CH 4 as their sole carbon and energy source has obtained great attention for biofuel production from this resource. In this study, a fast-growing and lipid-rich methanotroph , Methylomicrobium buryatense 5GB1 and its glycogen-knock-out mutant (AP18) were investigated for the production of lipids derived from intracellular membranes, which are key precursors for the production of green diesel. The effects of culture conditions on cell growth and lipid production were investigated in high cell density cultivation with continuous feeding of CH 4 and O 2 . The highest dry cell weight observed was 21.4 g/L and the maximum lipid productivity observed was 45.4 mg/L/h obtained in batch cultures, which corresponds to a 2-fold enhancement in cell density and 3-fold improvement in lipid production, compared with previous reported data from cultures of 5GB1. A 90% enhancement of lipid content was achieved by limiting the biosynthesis of glycogen in strain AP18. Increased CH 4 /O 2 uptake and CO 2 evaluation rates were observed in AP18 cultures suggesting that more carbon substrate and energy are needed for AP18 growth while producing lipids. The lipid produced by M. buryatense was estimated to have a cetane number of 75, which is 50% higher than biofuel standards requested by US and EU. Cell growth and lipid production were significantly influenced by culture conditions for both 5GB1 and AP18. Enhanced lipid production in terms of titer, productivity, and content was achieved under high cell density culture conditions by blocking glycogen accumulation as a carbon sink in the strain AP18. Differences observed in CH 4 /O 2 gas uptake and CO 2 evolution rates as well as cell growth and glycogen accumulation between 5GB1 and AP18 suggest changes in the metabolic network between these strains. This bioconversion process provides a promising opportunity to transform CH 4 into biofuel molecules and encourages further investigation to elucidate the remarkable CH 4 biofixation mechanism used by these bacteria.

Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in South Korea.

PubMed

Nguyen, Tuan Manh; Kim, Jaisoo

2017-05-01

White and pale yellow coloured bacteria were isolated from the riverside soil, Daejeon, South Korea, and were designated UCM-11 T , UCM-F25, and UCM-80 T . We found that all strains were able to reduce nitrate, and the cells were aerobic and motile. The DNA G+C contents of UCM-11 T , UCM-F25, and UCM-80 T were between 68.9 to 71.2 mol% and the main ubiquinone was observed as Q-8. Based on16S rRNA gene sequences, strains UCM-11 T and UCM-F25 were found to closely match with Azohydromonas australica IAM 12664 T (98.48-98.55%), and the strain UCM-80 T was the closest match with Azohydromonas lata IAM 12599 T (98.34%). The presence of summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c), C 16:0 , summed feature 8 (C 18:1 ω7c and/or C 18:1 ω6c) as well as twokinds of hydroxyfatty acids consisting of C 10:0 3-OH and C 12:0 2-OH, and branched fatty acids containing C 16:0 iso and C 17:0 cyclo were detected in all the strains. Phosphatidylethanolamine was a major polar lipid. DNA-DNA relatedness confirmed UCM-11 T , UCM-F25 and UCM-80 T as novel members of the genus Azohydromonas. Based on the morphological, physiological, biochemical and genotypic characteristics, we suggest that strains UCM-11 T , UCM-F25, and UCM-80 T represent novel species within the genus Azohydromonas. The names Azohydromonas riparia sp. nov., and Azohydromonas ureilytica sp. nov. are proposed for the type strains UCM-11 T (=KACC 18570 T =NBRC 111646 T ) and UCM-80 T (=KACC 18576 T =NBRC 111658 T ), respectively.

New strains of oil-degrading microorganisms for treating contaminated soils and wastes

NASA Astrophysics Data System (ADS)

Muratova, A. Yu; Panchenko, L. V.; Semina, D. V.; Golubev, S. N.; Turkovskaya, O. V.

2018-01-01

Two new strains Achromobacter marplatensis101n and Acinetobacter sp. S-33, capable of degrading 49 and 46% of oil within 7 days were isolated, identified, and characterized. The application of A. marplatensis 101n in combination with ammonium nitrate (100 mg·kg-1) for 30 days of cultivation resulted in the degradation of 49% of the initial total petroleum hydrocarbon content (274 g·kg-1) in the original highly acid (pH 4.9) oil-contaminated waste. Up to 30% of oil sludge added to a liquid mineral medium at a concentration of 15% was degraded after 10 days of cultivation of A. marplatensis 101n. Application of yellow alfalfa (Medicago falcata L.) plants with Acinetobacter sp. S-33 for bioremediation of oil-sludge-contaminated soil improved the quality of cleanup in comparison with the bacterium- or plant-only treatment. Inoculation of Acinetobacter sp. S-33 increased the growth of both roots and shoots by more than 40%, and positively influenced the soil microflora. We conclude that the new oil-degrading strains, Acinetobacter sp. S-33 and A. marplatensis 101n, can serve as the basis for new bioremediation agents for the treatment of oil contaminated soils and waste.

Floricoccus tropicus gen. nov., sp. nov. and Floricoccus penangensis sp. nov. isolated from fresh flowers of durian tree and hibiscus.

PubMed

Chuah, Li-Oon; Yap, Kien-Pong; Shamila-Syuhada, Ahamed Kamal; Thong, Kwai Lin; Ahmad, Rosma; Liong, Min Tze; Rusul, Gulam

2017-12-01

Three strains of Gram-staining-positive, coccus-shaped, lactic acid bacteria, designated as HibF3 T , HibF2 and HibF5 were isolated from fresh flowers of hibiscus, and a fourth, DF1 T , was isolated from fresh flowers of durian tree, in Penang, Malaysia. Taxonomic characterisation was performed by polyphasic analysis. Sequence similarities of the 16S rRNA gene and the housekeeping rpoA and pheS genes of these strains with their closely-related lactococcal and streptococcal relatives were 92-94, 78 and 81 %, respectively. The results of phylogenetic analysis indicated that strains DF1 T , HibF2, HibF5 and HibF3 T were clustered together but were clearly separated from species of the genera Streptococcus and Lactococcus, indicating that they represent members of a novel genus of the family Streptococcaceae. Calculation of average nucleotide identity (ANI) values between the genomes of DF1 T and HibF3 T yielded values of 92.50-92.93 %. ANI values below the cut-off value and distinctive chemotaxonomic characteristics supported the hypothesis that these strains represented two novel species. Major cellular fatty acids in DF1 T , HibF2 and HibF5 were C18 : 1ω7c and C16 : 0, while C12 : 0 and C14 : 0 were also dominant, in addition to C18 : 1ω7c and C16 : 0, in HibF3 T . A novel genus is proposed with the name Floricoccus gen. nov. which consists of two species, Floricoccus tropicus sp. nov as the type species, and Floricoccus penangensis sp. nov. The respective type strains are DF1 T (=LMG 29833 T =JCM 31733 T ) and HibF3 T (=LMG 29831 T =DSM 31735 T ).

The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage.

PubMed

Roszniowski, Bartosz; Latka, Agnieszka; Maciejewska, Barbara; Vandenheuvel, Dieter; Olszak, Tomasz; Briers, Yves; Holt, Giles S; Valvano, Miguel A; Lavigne, Rob; Smith, Darren L; Drulis-Kawa, Zuzanna

2017-02-01

Burkholderia phage AP3 (vB_BceM_AP3) is a temperate virus of the Myoviridae and the Peduovirinae subfamily (P2likevirus genus). This phage specifically infects multidrug-resistant clinical Burkholderia cenocepacia lineage IIIA strains commonly isolated from cystic fibrosis patients. AP3 exhibits high pairwise nucleotide identity (61.7 %) to Burkholderia phage KS5, specific to the same B. cenocepacia host, and has 46.7-49.5 % identity to phages infecting other species of Burkholderia. The lysis cassette of these related phages has a similar organization (putative antiholin, putative holin, endolysin, and spanins) and shows 29-98 % homology between specific lysis genes, in contrast to Enterobacteria phage P2, the hallmark phage of this genus. The AP3 and KS5 lysis genes have conserved locations and high amino acid sequence similarity. The AP3 bacteriophage particles remain infective up to 5 h at pH 4-10 and are stable at 60 °C for 30 min, but are sensitive to chloroform, with no remaining infective particles after 24 h of treatment. AP3 lysogeny can occur by stable genomic integration and by pseudo-lysogeny. The lysogenic bacterial mutants did not exhibit any significant changes in virulence compared to wild-type host strain when tested in the Galleria mellonella moth wax model. Moreover, AP3 treatment of larvae infected with B. cenocepacia revealed a significant increase (P < 0.0001) in larvae survival in comparison to AP3-untreated infected larvae. AP3 showed robust lytic activity, as evidenced by its broad host range, the absence of increased virulence in lysogenic isolates, the lack of bacterial gene disruption conditioned by bacterial tRNA downstream integration site, and the absence of detected toxin sequences. These data suggest that the AP3 phage is a promising potent agent against bacteria belonging to the most common B. cenocepacia IIIA lineage strains.