Presence of antioxidative agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro- in newly isolated Streptomyces mangrovisoli sp. nov.

PubMed Central

Ser, Hooi-Leng; Palanisamy, Uma D.; Yin, Wai-Fong; Abd Malek, Sri N.; Chan, Kok-Gan; Goh, Bey-Hing; Lee, Learn-Han

2015-01-01

A novel Streptomyces, strain MUSC 149T was isolated from mangrove soil. A polyphasic approach was used to study the taxonomy of MUSC 149T, which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The diamino acid of the cell wall peptidoglycan was LL-diaminopimelic acid. The predominant menaquinones were identified as MK9(H8) and MK9(H6). Phylogenetic analysis indicated that closely related strains include Streptomyces rhizophilus NBRC 108885T (99.2% sequence similarity), S. gramineus NBRC 107863T (98.7%) and S. graminisoli NBRC 108883T (98.5%). The DNA–DNA relatedness values between MUSC 149T and closely related type strains ranged from 12.4 ± 3.3% to 27.3 ± 1.9%. The DNA G + C content was determined to be 72.7 mol%. The extract of MUSC 149T exhibited strong antioxidant activity and chemical analysis reported identification of an antioxidant agent, Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro-. These data showed that metabolites of MUSC 149T shall be useful as preventive agent against free-radical associated diseases. Based on the polyphasic study of MUSC 149T, the strain merits assignment to a novel species, for which the name S. mangrovisoli sp. nov. is proposed. The type strain is MUSC 149T (=MCCC 1K00699T=DSM 100438T). PMID:26347733

Polyphasic Analyses of Methanogenic Archaeal Communities in Agricultural Biogas Plants▿

PubMed Central

Nettmann, E.; Bergmann, I.; Pramschüfer, S.; Mundt, K.; Plogsties, V.; Herrmann, C.; Klocke, M.

2010-01-01

Knowledge of the microbial consortia participating in the generation of biogas, especially in methane formation, is still limited. To overcome this limitation, the methanogenic archaeal communities in six full-scale biogas plants supplied with different liquid manures and renewable raw materials as substrates were analyzed by a polyphasic approach. Fluorescence in situ hybridization (FISH) was carried out to quantify the methanogenic Archaea in the reactor samples. In addition, quantitative real-time PCR (Q-PCR) was used to support and complete the FISH analysis. Five of the six biogas reactors were dominated by hydrogenotrophic Methanomicrobiales. The average values were between 60 to 63% of archaeal cell counts (FISH) and 61 to 99% of archaeal 16S rRNA gene copies (Q-PCR). Within this order, Methanoculleus was found to be the predominant genus as determined by amplified rRNA gene restriction analysis. The aceticlastic family Methanosaetaceae was determined to be the dominant methanogenic group in only one biogas reactor, with average values for Q-PCR and FISH between 64% and 72%. Additionally, in three biogas reactors hitherto uncharacterized but potentially methanogenic species were detected. They showed closest accordance with nucleotide sequences of the hitherto unclassified CA-11 (85%) and ARC-I (98%) clusters. These results point to hydrogenotrophic methanogenesis as a predominant pathway for methane synthesis in five of the six analyzed biogas plants. In addition, a correlation between the absence of Methanosaetaceae in the biogas reactors and high concentrations of total ammonia (sum of NH3 and NH4+) was observed. PMID:20154117

Cyanobacterial diversity in extreme environments in Baja California, Mexico: a polyphasic study.

PubMed

López-Cortés, A; García-Pichel, F; Nübel, U; Vázquez-Juárez, R

2001-12-01

Cyanobacterial diversity from two geographical areas of Baja California Sur, Mexico, were studied: Bahia Concepcion, and Ensenada de Aripez. The sites included hypersaline ecosystems, sea bottom, hydrothermal springs, and a shrimp farm. In this report we describe four new morphotypes, two are marine epilithic from Bahia Concepcion, Dermocarpa sp. and Hyella sp. The third, Geitlerinema sp., occurs in thermal springs and in shrimp ponds, and the fourth, Tychonema sp., is from a shrimp pond. The partial sequences of the 16S rRNA genes and the phylogenetic relationship of four cyanobacterial strains (Synechococcus cf. elongatus, Leptolyngbya cf. thermalis, Leptolyngbya sp., and Geitlerinema sp.) are also presented. Polyphasic studies that include the combination of light microscopy, cultures and the comparative analysis of 16S rRNA gene sequences provide the most powerful approach currently available to establish the diversity of these oxygenic photosynthetic microorganisms in culture and in nature.

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov

NASA Technical Reports Server (NTRS)

Venkateswaran, K.; Moser, D. P.; Dollhopf, M. E.; Lies, D. P.; Saffarini, D. A.; MacGregor, B. J.; Ringelberg, D. B.; White, D. C.; Nishijima, M.; Sano, H.;

Improved battery charger for electric vehicles

NASA Technical Reports Server (NTRS)

Rippel, W. E.

1981-01-01

Polyphase version of single-phase "boost chopper" significantly reduces ripple and electromagnetic interference (EMI). Drive circuit of n-phase boost chopper incorporates n-phase duty-cycle generator; inductor, transistor, and diode compose chopper which can run on single-phase or three-phase alternating current or on direct current. Device retains compactness and power factors approaching unity, while improving efficiency.

Influence of Geographical Origin and Flour Type on Diversity of Lactic Acid Bacteria in Traditional Belgian Sourdoughs▿ †

PubMed Central

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2007-01-01

A culture-based approach was used to investigate the diversity of lactic acid bacteria (LAB) in Belgian traditional sourdoughs and to assess the influence of flour type, bakery environment, geographical origin, and technological characteristics on the taxonomic composition of these LAB communities. For this purpose, a total of 714 LAB from 21 sourdoughs sampled at 11 artisan bakeries throughout Belgium were subjected to a polyphasic identification approach. The microbial composition of the traditional sourdoughs was characterized by bacteriological culture in combination with genotypic identification methods, including repetitive element sequence-based PCR fingerprinting and phenylalanyl-tRNA synthase (pheS) gene sequence analysis. LAB from Belgian sourdoughs belonged to the genera Lactobacillus, Pediococcus, Leuconostoc, Weissella, and Enterococcus, with the heterofermentative species Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus plantarum, and Lactobacillus pontis as the most frequently isolated taxa. Statistical analysis of the identification data indicated that the microbial composition of the sourdoughs is mainly affected by the bakery environment rather than the flour type (wheat, rye, spelt, or a mixture of these) used. In conclusion, the polyphasic approach, based on rapid genotypic screening and high-resolution, sequence-dependent identification, proved to be a powerful tool for studying the LAB diversity in traditional fermented foods such as sourdough. PMID:17675431

Influence of geographical origin and flour type on diversity of lactic acid bacteria in traditional Belgian sourdoughs.

PubMed

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2007-10-01

A culture-based approach was used to investigate the diversity of lactic acid bacteria (LAB) in Belgian traditional sourdoughs and to assess the influence of flour type, bakery environment, geographical origin, and technological characteristics on the taxonomic composition of these LAB communities. For this purpose, a total of 714 LAB from 21 sourdoughs sampled at 11 artisan bakeries throughout Belgium were subjected to a polyphasic identification approach. The microbial composition of the traditional sourdoughs was characterized by bacteriological culture in combination with genotypic identification methods, including repetitive element sequence-based PCR fingerprinting and phenylalanyl-tRNA synthase (pheS) gene sequence analysis. LAB from Belgian sourdoughs belonged to the genera Lactobacillus, Pediococcus, Leuconostoc, Weissella, and Enterococcus, with the heterofermentative species Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus plantarum, and Lactobacillus pontis as the most frequently isolated taxa. Statistical analysis of the identification data indicated that the microbial composition of the sourdoughs is mainly affected by the bakery environment rather than the flour type (wheat, rye, spelt, or a mixture of these) used. In conclusion, the polyphasic approach, based on rapid genotypic screening and high-resolution, sequence-dependent identification, proved to be a powerful tool for studying the LAB diversity in traditional fermented foods such as sourdough.

Aspergillus korhogoensis, a novel aflatoxin producing species from the Côte d’Ivoire

USDA-ARS?s Scientific Manuscript database

Based on examination of four isolates, this new species is described using a polyphasic approach. A concatenated alignment comprised of nine genes (ITS, benA, cmdA, mcm7, amdS, rpb1, preB, ppgA, preA) was subjected to phylogenetic analysis, and resulted in all four strains being inferred as a distin...

Streptomyces gilvigriseus sp. nov., a novel actinobacterium isolated from mangrove forest soil.

PubMed

Ser, Hooi-Leng; Zainal, Nurullhudda; Palanisamy, Uma Devi; Goh, Bey-Hing; Yin, Wai-Fong; Chan, Kok-Gan; Lee, Learn-Han

2015-06-01

A novel Streptomyces, strain MUSC 26(T), was isolated from mangrove soil at Tanjung Lumpur, Malaysia. The bacterium was observed to be Gram-positive and to form grayish yellow aerial and substrate mycelium on ISP 7 agar. A polyphasic approach was used to study the taxonomy of strain MUSC 26(T), which shows a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. The cell wall peptidoglycan was determined to contain LL-diaminopimelic acid. The predominant menaquinones were identified as MK-9 (H8) and MK-9(H6). The polar lipids detected were identified as diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylmethylethanolamine and hydroxyphosphatidylmethylethanolamine. The predominant cellular fatty acids (>10.0 %) were identified as anteiso-C15:0 (31.4 %), iso-C16:0 (16.3 %), iso-C15:0 (13.9 %) and anteiso-C17:0 (12.6 %). The cell wall sugars were found to be galactose, glucose, mannose, ribose and rhamnose. These results suggest that MUSC 26(T) should be placed within the genus Streptomyces. Phylogenetic analysis indicated that closely related strains include Streptomyces qinglanensis 172205(T) (96.5 % sequence similarity), S. sodiiphilus YIM 80305(T) (96.5 %) and S. rimosus subsp. rimosus ATCC 10970(T) (96.4 %). DNA-DNA relatedness values between MUSC 26(T) and closely related type strains ranged from 17.0 ± 2.2 to 33.2 ± 5.3 %. Comparison of BOX-PCR fingerprints indicated MUSC 26(T) presents a unique DNA profile. The DNA G+C content was determined to be 74.6 mol%. Based on this polyphasic study of MUSC 26(T), it is concluded that this strain represents a novel species, for which the name Streptomyces gilvigriseus sp. nov. is proposed. The type strain is MUSC 26(T) (=DSMZ 42173(T) = MCCC 1K00504(T)).

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

Polyphasic characterization of Gluconacetobacter diazotrophicus isolates obtained from different sugarcane varieties

PubMed Central

Guedes, Helma V.; dos Santos, Samuel T.; Perin, Liamara; Teixeira, Kátia R. dos S.; Reis, Veronica M.; Baldani, José I.

2008-01-01

A polyphasic approach was applied to characterize 35 G. diazotrophicus isolates obtained from sugarcane varieties cultivated in Brazil. The isolates were analyzed by phenotypic (use of different carbon sources) and genotypic tests (ARDRA and RISA–RFLP techniques). Variability among the isolates was observed in relation to the carbon source use preference. Glucose and sucrose were used by all isolates in contrast to myo-inositol, galactose and ribose that were not metabolized. The results of the analysis showed the presence of two groups clustered at 68% of similarity. The genetic distance was higher when RISA-RFLP analysis was used. Analysis of 16S rDNA sequences from isolates showed that all of them belonged to the G. diazotrophicus species. Neither effect of the plant part nor sugarcane variety was observed during the cluster analysis. The observed metabolic and genetic variability will be helpful during the strain selection studies for sugarcane inoculation in association with sugarcane breeding programs. PMID:24031296

Yersinia pekkanenii sp. nov.

PubMed

Murros-Kontiainen, Anna; Johansson, Per; Niskanen, Taina; Fredriksson-Ahomaa, Maria; Korkeala, Hannu; Björkroth, Johanna

2011-10-01

The taxonomic position of three strains from water, soil and lettuce samples was studied by using a polyphasic taxonomic approach. The strains were reported to lack the virulence-encoding genes inv and virF in a previous study. Controversially, API 20 E and some other phenotypic tests suggested that the strains belong to Yersinia pseudotuberculosis, which prompted this polyphasic taxonomic study. In both the phylogenetic analyses of four housekeeping genes (glnA, gyrB, recA and HSP60) and numerical analyses of HindIII and EcoRI ribopatterns, the strains formed a separate group within the genus Yersinia. Analysis of the 16S rRNA gene sequences showed that the strains were related to Yersinia aldovae and Yersinia mollaretii, but DNA-DNA hybridization analysis differentiated them from these species. Based on the results of the phylogenetic and DNA-DNA hybridization analyses, a novel species, Yersinia pekkanenii sp. nov., is proposed. The type strain is ÅYV7.1KOH2(T) ( = DSM 22769(T)  = LMG 25369(T)).

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

A polyphasic approach to gaining insights into causes of acute oak decline in Britain

Treesearch

Sandra Denman

2017-01-01

Acute Oak Decline (AOD) is a complex disease syndrome of native oak, making its first appearance in the 1980s in Britain. Since then increasing reports of its occurrence have raised concerns about cause and effects on these iconic trees. Symptomology studies confirmed that AOD is a distinctive condition with four diagnostic symptoms defining the condition; (a) weeping...

Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella.

PubMed

Chen, Wen-Ming; de Faria, Sergio M; James, Euan K; Elliott, Geoffrey N; Lin, Kuan-Yin; Chou, Jui-Hsing; Sheu, Shih-Yi; Cnockaert, M; Sprent, Janet I; Vandamme, Peter

2007-05-01

Three strains, Br3437(T), Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella (Br3437(T)) and Mimosa bimucronata (Br3461, Br3470), both of which are woody legumes native to Brazil. On the basis of 16S rRNA gene sequence similarities, all the strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA hybridizations, PFGE of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia nodosa sp. nov. is proposed. The type strain, Br3437(T) (=LMG 23741(T)=BCRC 17575(T)), was isolated from nodules of M. scabrella.

A polyphase filter for many-core architectures

NASA Astrophysics Data System (ADS)

Adámek, K.; Novotný, J.; Armour, W.

2016-07-01

In this article we discuss our implementation of a polyphase filter for real-time data processing in radio astronomy. The polyphase filter is a standard tool in digital signal processing and as such a well established algorithm. We describe in detail our implementation of the polyphase filter algorithm and its behaviour on three generations of NVIDIA GPU cards (Fermi, Kepler, Maxwell), on the Intel Xeon CPU and Xeon Phi (Knights Corner) platforms. All of our implementations aim to exploit the potential for data reuse that the algorithm offers. Our GPU implementations explore two different methods for achieving this, the first makes use of L1/Texture cache, the second uses shared memory. We discuss the usability of each of our implementations along with their behaviours. We measure performance in execution time, which is a critical factor for real-time systems, we also present results in terms of bandwidth (GB/s), compute (GFLOP/s/s) and type conversions (GTc/s). We include a presentation of our results in terms of the sample rate which can be processed in real-time by a chosen platform, which more intuitively describes the expected performance in a signal processing setting. Our findings show that, for the GPUs considered, the performance of our polyphase filter when using lower precision input data is limited by type conversions rather than device bandwidth. We compare these results to an implementation on the Xeon Phi. We show that our Xeon Phi implementation has a performance that is 1.5 × to 1.92 × greater than our CPU implementation, however is not insufficient to compete with the performance of GPUs. We conclude with a comparison of our best performing code to two other implementations of the polyphase filter, showing that our implementation is faster in nearly all cases. This work forms part of the Astro-Accelerate project, a many-core accelerated real-time data processing library for digital signal processing of time-domain radio astronomy data.

Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce).

PubMed

Young, Chiu-Chung; Kämpfer, Peter; Shen, Fo-Ting; Lai, Wei-An; Arun, A B

2005-01-01

A yellow-pigmented bacterial strain (CC-H3-2T), isolated from the rhizosphere of Lactuca sativa L. (garden lettuce) in Taiwan, was investigated using a polyphasic taxonomic approach. The cells were Gram-negative, rod-shaped and non-spore-forming. Phylogenetic analyses using the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Chryseobacterium, with the highest sequence similarity to the type strains of Chryseobacterium indoltheticum (97.7 %), Chryseobacterium scophthalmum (97.5 %), Chryseobacterium joostei (97.2 %) and Chryseobacterium defluvii (97.2 %). The major whole-cell fatty acids were iso-C(15 : 0) (52.2 %) and iso-C(17 : 0) 3-OH. DNA-DNA hybridization experiments revealed levels of only 27.4 % to C. scophthalmum, 27.1 % to C. indoltheticum, 14.1 % to C. joostei and 7.8 % to C. defluvii. DNA-DNA relatedness and biochemical and chemotaxonomic properties demonstrate that strain CC-H3-2T represents a novel species, for which the name Chryseobacterium formosense sp. nov. is proposed. The type strain is CC-H3-2T (=CCUG 49271T=CIP 108367T).

A microbial identification framework for risk assessment.

PubMed

Bernatchez, Stéphane; Anoop, Valar; Saikali, Zeina; Breton, Marie

2018-06-01

Micro-organisms are increasingly used in a variety of products for commercial uses, including cleaning products. Such microbial-based cleaning products (MBCP) are represented as a more environmentally-friendly alternative to chemically based cleaning products. The identity of the micro-organisms formulated into these products is often considered confidential business information and is not revealed or it is only partly revealed (i.e., identification to the genus, not to the species). That paucity of information complicates the evaluation of the risk associated with their use. The accurate taxonomic identification of those micro-organisms is important so that a suitable risk assessment of the products can be conducted. To alleviate difficulties associated with adequate identification of micro-organisms in MBCP and other products containing micro-organisms, a microbial identification framework for risk assessment (MIFRA) has been elaborated. It serves to provide guidance on a polyphasic tiered approach, combining the data obtained from the use of various methods (i.e., polyphasic approach) combined with the sequential selection of the methods (i.e., tiered) to achieve a satisfactory identity of the micro-organism to an acceptable taxonomic level. The MIFRA is suitable in various risk assessment contexts for micro-organisms used in any commercial product. Copyright © 2018. Published by Elsevier Ltd.

An OFDM System Using Polyphase Filter and DFT Architecture for Very High Data Rate Applications

NASA Technical Reports Server (NTRS)

Kifle, Muli; Andro, Monty; Vanderaar, Mark J.

2001-01-01

This paper presents a conceptual architectural design of a four-channel Orthogonal Frequency Division Multiplexing (OFDM) system with an aggregate information throughput of 622 megabits per second (Mbps). Primary emphasis is placed on the generation and detection of the composite waveform using polyphase filter and Discrete Fourier Transform (DFT) approaches to digitally stack and bandlimit the individual carriers. The four-channel approach enables the implementation of a system that can be both power and bandwidth efficient, yet enough parallelism exists to meet higher data rate goals. It also enables a DC power efficient transmitter that is suitable for on-board satellite systems, and a moderately complex receiver that is suitable for low-cost ground terminals. The major advantage of the system as compared to a single channel system is lower complexity and DC power consumption. This is because the highest sample rate is half that of the single channel system and synchronization can occur at most, depending on the synchronization technique, a quarter of the rate of a single channel system. The major disadvantage is the increased peak-to-average power ratio over the single channel system. Simulation results in a form of bit-error-rate (BER) curves are presented in this paper.

Development of a biocidal treatment regime to inhibit biological growths on cultural heritage: BIODAM

NASA Astrophysics Data System (ADS)

Young, M. E.; Alakomi, H.-L.; Fortune, I.; Gorbushina, A. A.; Krumbein, W. E.; Maxwell, I.; McCullagh, C.; Robertson, P.; Saarela, M.; Valero, J.; Vendrell, M.

2008-12-01

Existing chemical treatments to prevent biological damage to monuments often involve considerable amounts of potentially dangerous and even poisonous biocides. The scientific approach described in this paper aims at a drastic reduction in the concentration of biocide applications by a polyphasic approach of biocides combined with cell permeabilisers, polysaccharide and pigment inhibitors and a photodynamic treatment. A variety of potential agents were screened to determine the most effective combination. Promising compounds were tested under laboratory conditions with cultures of rock deteriorating bacteria, algae, cyanobacteria and fungi. A subsequent field trial involved two sandstone types with natural biofilms. These were treated with multiple combinations of chemicals and exposed to three different climatic conditions. Although treatments proved successful in the laboratory, field trials were inconclusive and further testing will be required to determine the most effective treatment regime. While the most effective combination of chemicals and their application methodology is still being optimised, results to date indicate that this is a promising and effective treatment for the control of a wide variety of potentially damaging organisms colonising stone substrates.

Sphingomonas kyeonggiense sp. nov., isolated from soil of a ginseng field.

PubMed

Son, Heung-Min; Kook, Moochang; Tran, Hanh T H; Kim, Ki-Young; Park, Sang-Yong; Kim, Ju-Han; Yi, Tae-Hoo

2014-04-01

A Gram-staining negative bacterium, THG-DT81(T), which was isolated from soil of a ginseng field, was investigated using a polyphasic taxonomic approach. Cells were oxidase- and catalase-positive, aerobic, rod-shaped and motile with one polar flagellum. Strain THG-DT81(T) grew optimally at pH 7.0 and in the absence of NaCl on trypticase soy agar. Its optimum growth temperature was 25-28 °C. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain THG-DT81(T) belongs to the family Sphingomonadaceae and was related to Sphingomonas pituitosa EDIV(T) (98.0 % similarity), S. leidyi ATCC 15260(T) (97.8 %), S. trueperi LMG 2142(T) (97.1 %), S. azotifigens NBRC 15497(T) (97.1 %), S. koreensis JSS26 (T) (97.1 %) and S. dokdonensis DS-4(T) (97.0 %). Strain THG-DT81(T) contained Q-10 as the predominant ubiquinone and C18:1 ω7c and C16:0 as the major fatty acids. The G+C content of the genomic DNA was determined to be 66.8 mol %. The major component in the polyamine pattern was identified as sym-homospermidine. The major polar lipids detected in strain THG-DT81(T) were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The DNA-DNA relatedness values of the strain THG-DT81(T) and its closest phylogenetically neighbors were below 21 %. The phenotypic characteristics and genotypic data demonstrated the affiliation of strain THG-DT81(T) to the genus Sphingomonas. On the basis of the polyphasic taxonomic data presented, strain THG-DT81(T) is described as a novel species of genus Sphingomonas, for which the name Sphingomonas kyeonggiense sp. nov. is proposed. The type strain is THG-DT81(T) (= KACC 17173(T) = JCM 18825(T)).

An improved design method based on polyphase components for digital FIR filters

NASA Astrophysics Data System (ADS)

Kumar, A.; Kuldeep, B.; Singh, G. K.; Lee, Heung No

2017-11-01

This paper presents an efficient design of digital finite impulse response (FIR) filter, based on polyphase components and swarm optimisation techniques (SOTs). For this purpose, the design problem is formulated as mean square error between the actual response and ideal response in frequency domain using polyphase components of a prototype filter. To achieve more precise frequency response at some specified frequency, fractional derivative constraints (FDCs) have been applied, and optimal FDCs are computed using SOTs such as cuckoo search and modified cuckoo search algorithms. A comparative study of well-proved swarm optimisation, called particle swarm optimisation and artificial bee colony algorithm is made. The excellence of proposed method is evaluated using several important attributes of a filter. Comparative study evidences the excellence of proposed method for effective design of FIR filter.

Enterococcus Xinjiangensis sp. nov., Isolated from Yogurt of Xinjiang, China.

PubMed

Ren, Xiaopu; Li, Mingyang; Guo, Dongqi

2016-09-01

A Gram-strain-positive bacterial strain 48(T) was isolated from traditional yogurt in Xinjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, polymerase α subunit (rpoA) gene sequence analysis, determination of DNA G+C content, DNA-DNA hybridization with the type strain of Enterococcus ratti and analysis of phenotypic features. Strain 48(T) accounted for 96.1, 95.8, 95.8, and 95.7 % with Enterococcus faecium CGMCC 1.2136(T), Enterococcus hirae ATCC 9790(T), Enterococcus durans CECT 411(T), and E. ratti ATCC 700914(T) in the 16S rRNA gene sequence similarities, respectively. The sequence of rpoA gene showed similarities of 99.0, 96.0, 96.0, and 96 % with that of E. faecium ATCC 19434(T), Enterococcus villorum LMG12287, E. hirae ATCC 9790(T), and E. durans ATCC 19432(T), respectively. Based upon of polyphasic characterization data obtained in the study, a novel species, Enterococcus xinjiangensis sp. nov., was proposed and the type strain was 48(T)(=CCTCC AB 2014041(T) = JCM 30200(T)).

Problem of the thermodynamic status of the mixed-layer minerals

USGS Publications Warehouse

Zen, E.-A.

1962-01-01

Minerals that show mixed layering, particularly with the component layers in random sequence, pose problems because they may behave thermodynamically as single phases or as polyphase aggregates. Two operational criteria are proposed for their distinction. The first scheme requires two samples of mixed-layer material which differ only in the proportions of the layers. If each of these two samples are allowed to equilibrate with the same suitably chosen monitoring solution, then the intensive parameters of the solution will be invariant if the mixed-layer sample is a polyphase aggregate, but not otherwise. The second scheme makes use of the fact that portions of many titration curves of clay minerals show constancy of the chemical activities of the components in the equilibrating solutions, suggesting phase separation. If such phase separation occurs for a mixed-layer material, then, knowing the number of independent components in the system, it should be possible to decide on the number of phases the mixed-layer material represents. Knowledge of the phase status of mixed-layer material is essential to the study of the equilibrium relations of mineral assemblages involving such material, because a given mixed-layer mineral will be plotted and treated differently on a phase diagram, depending on whether it is a single phase or a polyphase aggregate. Extension of the titration technique to minerals other than the mixed-layer type is possible. In particular, this method may be used to determine if cryptoperthites and peristerites are polyphase aggregates. In general, for any high-order phase separation, the method may be used to decide just at what point in this continuous process the system must be regarded operationally as a polyphase aggregate. ?? 1962.

Measuring and Predicting Sleep and Performance During Military Operations

DTIC Science & Technology

2012-08-23

chronobiology , and functions of polyphasic and ultrashort sleep: main issues. In: Stampi C, ed. Why We Nap. Evolution, Chronobiology , and Functions...Alertness: Chronobiological , Behavioural and Medical Aspects of Napping. New York, NY: Raven Press; 1989: 205–220. 82. Dinges DF. Napping patterns and... Chronobiology , and Functions of Polyphasic and Ultrashort Sleep: Main Issues. Boston, Mass: Birkhaüser; 1992: 118–134. 84. Muzet A, Nicolas A, Tassi P

Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels

PubMed Central

Chang, Susane; Porto Carneiro-Leão, Mariele; Ferreira de Oliveira, Benny; Souza-Motta, Cristina; Lima, Nelson; Santos, Cledir; Tinti de Oliveira, Neiva

2016-01-01

Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG)5 and (GACA)4. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol) and B2 (705.83 g/mol). PMID:26927172

Range Sidelobe Response from the Use of Polyphase Signals in Spotlight Synthetic Aperture Radar

DTIC Science & Technology

2015-12-01

come to closure. I also want to thank my mother for raising me and instilling in me the work ethic and values that have propelled me through life. I...to describe the poly-phase signals at baseband. IQ notation is preferred for complex waveforms because it allows for an easy mathematical...variables. 15 Once the Frank-coded phase vector is created, the IQ signal generation discussed in Chapter II was used to generate a Frank-code phase

Deciphering the biodiversity of Listeria monocytogenes lineage III strains by polyphasic approaches.

PubMed

Zhao, Hanxin; Chen, Jianshun; Fang, Chun; Xia, Ye; Cheng, Changyong; Jiang, Lingli; Fang, Weihuan

2011-10-01

Listeria monocytogenes is a foodborne pathogen of humans and animals. The majority of human listeriosis cases are caused by strains of lineages I and II, while lineage III strains are rare and seldom implicated in human listeriosis. We revealed by 16S rRNA sequencing the special evolutionary status of L. monocytogenes lineage III, which falls between lineages I and II strains of L. monocytogenes and the non-pathogenic species L. innocua and L. marthii in the dendrogram. Thirteen lineage III strains were then characterized by polyphasic approaches. Biochemical reactions demonstrated 8 biotypes, internalin profiling identified 10 internal-in types clustered in 4 groups, and multilocus sequence typing differentiated 12 sequence types. These typing schemes show that lineage III strains represent the most diverse population of L. monocytogenes, and comprise at least four subpopulations IIIA-1, IIIA-2, HIB, and IIIC. The in vitro and in vivo virulence assessments showed that two lineage IIIA-2 strains had reduced pathogenicity, while the other lineage III strains had comparable virulence to lineages I and II. The HIB strains are phylogenetically distinct from other sub-populations, providing additional evidence that this sublineage represents a novel lineage. The two biochemical reactions L-rhamnose and L-lactate alkalinization, and 10 internalins were identified as potential markers for lineage III subpopulations. This study provides new insights into the biodiversity and population structure of lineage III strains, which are important for understanding the evolution of the L. mono-cytogenes-L. innocua clade.

Epilithonimonas psychrotolerans sp. nov., isolated from alpine permafrost.

PubMed

Ge, Liang; Zhao, Qi; Sheng, Hongmei; Wu, Jianmin; An, Lizhe

2015-11-01

A bacterial strain, designated TSBY 57T, was isolated during a study on the phylogenetic diversity of culturable bacteria from alpine permafrost in Tianshan Mountains, China, and was classified by means of a polyphasic taxonomic approach. The novel strain was found to belong to the genus Epilithonimonas and was distinguished from recognized species of this genus. Strain TSBY 57T grew aerobically, at 0-30 °C, with 0-1.5% (w/v) NaCl and at pH 6-8.Cells were Gram-stain-negative, non-motile, non-spore-forming rods. Compared with the reference strains, the novel strain was psychrotolerant. The predominant fatty acids were summed feature 3 (consisting of C16:1ω7c and/or C16:1ω6c), anteiso-C15:0 and iso-C15:0.The sole respiratory quinone was MK-6.Phosphatidylethanolamine was predominant in the polar lipid profile of strain TSBY 57T. These chemotaxonomic traits were in good agreement with the characteristics of the genus Epilithonimonas. On the basis of 16S rRNA gene sequence similarity, strain TSBY 57T was a member of the genus Epilithonimonas and was closely related to Epilithonimonas tenax DSM 16811T (99.0%), Epilithonimonas ginsengisoli DCY78T (98.6%) and Epilithonimonas lactis H1T (98.5%). However, DNA-DNA reassociation values between strain TSBY 57T and E. tenax DSM 16811T, E. ginsengisoli DCY78T and E. lactis H1T were 39.5 ± 2.6, 37.7 ± 1.0 and 37.3 ± 1.1%, respectively. The G+C content of the DNA was 34.4 ± 0.2  mol%. Based on data from this polyphasic taxonomic study, strain TSBY 57T represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas psychrotolerans sp. nov. is proposed. The type strain is TSBY 57T ( = NRRL B-51307T=CCTCC AB 207182T).

Polyphasic Temporal Behavior of Finger-Tapping Performance: A Measure of Motor Skills and Fatigue.

PubMed

Aydin, Leyla; Kiziltan, Erhan; Gundogan, Nimet Unay

2016-01-01

Successive voluntary motor movement involves a number of physiological mechanisms and may reflect motor skill development and neuromuscular fatigue. In this study, the temporal behavior of finger tapping was investigated in relation to motor skills and fatigue by using a long-term computer-based test. The finger-tapping performances of 29 healthy male volunteers were analyzed using linear and nonlinear regression models established for inter-tapping interval. The results suggest that finger-tapping performance exhibits a polyphasic nature, and has several characteristic time points, which may be directly related to muscle dynamics and energy consumption. In conclusion, we believe that future studies evaluating the polyphasic nature of the maximal voluntary movement will lead to the definition of objective scales that can be used in the follow up of some neuromuscular diseases, as well as, the determination of motor skills, individual ability, and peripheral fatigue through the use of a low cost, easy-to-use computer-based finger-tapping test.

Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk.

PubMed

Moumene, M; Drissi, F; Croce, O; Djebbari, B; Robert, C; Angelakis, E; Benouareth, D E; Raoult, D; Merhej, V

2016-03-01

We describe using a polyphasic approach that combines proteomic by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, genomic data and phenotypic characterization the features of Lactococcus garvieae strain M14 newly isolated from the fermented milk (known as raib) of an Algerian cow. The 2 188 835 bp containing genome sequence displays a metabolic capacity to form acid fermentation that is very useful for industrial applications and encodes for two bacteriocins responsible for its eventual bioprotective properties.

On-board multicarrier demodulator for mobile applications using DSP implementation

NASA Astrophysics Data System (ADS)

Yim, W. H.; Kwan, C. C. D.; Coakley, F. P.; Evans, B. G.

1990-11-01

This paper describes the design and implementation of an on-board multicarrier demodulator using commercial digital signal processors. This is for use in a mobile satellite communication system employing an up-link SCPC/FDMA scheme. Channels are separated by a flexible multistage digital filter bank followed by a channel multiplexed digital demodulator array. The cross/dot product design approach of error detector leads to a new QPSK frequency control algorithm that allows fast acquisition without special preamble pattern. Timing correction is performed digitally using an extended stack of polyphase sub-filters.

Streptomyces muensis sp. nov.

PubMed

Ningthoujam, Debananda S; Nimaichand, Salam; Ningombam, Dollyca; Tamreihao, K; Li, Li; Zhang, Yong-Guang; Cheng, Juan; Liu, Min-Jiao; Li, Wen-Jun

2013-12-01

A strain of Streptomyces, MBRL 179(T), isolated from a sample from a Limestone quarry located at Hundung, Manipur, India, was characterized by polyphasic taxonomy. The strain formed a monophyletic clade with Streptomyces spinoverrucosus NBRC 14228(T) (16S rRNA gene sequence similarity of 99.3 %) in the Neighbour-joining tree. DNA-DNA hybridization experiment gave a DNA-DNA relatedness value of 34.7 % between MBRL 179(T) and S. spinoverrucosus NBRC 14228(T). Strain MBRL 179(T) contained LL-diaminopimelic acid, xylose, glucose, and mannose in the whole cell-wall hydrolysates along with small amount of ribose. The major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside, with other unknown phospholipids and aminophospholipid. MK-9(H6), MK-9(H8) and MK-9(H4) were the predominant menaquinones detected. The major fatty acids were anteiso-C16:0 (28.1 %), iso-C16:0 (20.3 %), C16:0 (9.4 %) and anteiso-C17:0 (8.3 %). The G+C content of the genomic DNA was 71.1 %. Based on the polyphasic experiment results, the strain MBRL 179(T) merits recognition as a representative of a novel species of the genus Streptomyces for which the name Streptomyces muensis sp. nov. is proposed; the type strain is MBRL 179(T) (=JCM 17576(T) = KCTC 29124(T)).

Method and apparatus for reducing the harmonic currents in alternating-current distribution networks

DOEpatents

Beverly, Leon H.; Hance, Richard D.; Kristalinski, Alexandr L.; Visser, Age T.

1996-01-01

An improved apparatus and method reduce the harmonic content of AC line and neutral line currents in polyphase AC source distribution networks. The apparatus and method employ a polyphase Zig-Zag transformer connected between the AC source distribution network and a load. The apparatus and method also employs a mechanism for increasing the source neutral impedance of the AC source distribution network. This mechanism can consist of a choke installed in the neutral line between the AC source and the Zig-Zag transformer.

Method and apparatus for reducing the harmonic currents in alternating-current distribution networks

DOEpatents

Beverly, L.H.; Hance, R.D.; Kristalinski, A.L.; Visser, A.T.

1996-11-19

An improved apparatus and method reduce the harmonic content of AC line and neutral line currents in polyphase AC source distribution networks. The apparatus and method employ a polyphase Zig-Zag transformer connected between the AC source distribution network and a load. The apparatus and method also employs a mechanism for increasing the source neutral impedance of the AC source distribution network. This mechanism can consist of a choke installed in the neutral line between the AC source and the Zig-Zag transformer. 23 figs.

Apparatus for controlling the firing of rectifiers in polyphase rectifying circuits

DOEpatents

Yarema, R.J.

1979-09-18

A polyphase rectifier is controlled with precision by a circuit that filters and shifts a reference signal associated with each phase and that starts a ramp signal at a zero crossing of the shifted reference signal. The difference between the ramp signal and an external trigger signal is used to generate a pulse that switches power rectifiers into conduction. The circuit reduces effects of variations that introduce subharmonics into a rectified signal and it can be used for constant or time-varying external trigger signals.

Genotypic intraspecies heterogeneity of Enterococcus italicus: data from dairy environments.

PubMed

Borgo, Francesca; Ferrario, Chiara; Ricci, Giovanni; Fortina, Maria Grazia

2013-01-01

The diversity of a collection of 19 Enterococcus italicus strains isolated from different dairy sources was explored using a molecular polyphasic approach, comprising random amplification of polymorphic DNA (RAPD-PCR), repetitive element PCR (REP-PCR), plasmid profiling and ribotyping. The data obtained showed a high-level of biodiversity, not always correlated to the niche of isolation. Particularly, REP-PCR with primer BOXA1R and plasmid profiling allowed the best discrimination at strain level. Exploiting the genome shotgun sequence of the type strain of the species, available in public database, genes related to insertion sequences present on enterococcal Pathogenic Islands (ISEf1, IS905), determinants related to virulence factors (codifying for hemolysin and cell wall surface proteins), exogenously DNA (conjugal transfer protein, replication plasmid protein, pheromone shutdown protein, phage integrase/recombinase) and penicillin binding proteins system were detected. The presence of most of these genes seemed a common genetic trait in the Enterococcus genus, sur gene (cell wall surface protein) was only detected in strains of E. italicus. To our knowledge, this is the first time that specific primers, with the expection of the species-specific probe targeted to 16S rRNA gene, have been designed for this species. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Streptomyces associated with a marine sponge Haliclona sp.; biosynthetic genes for secondary metabolites and products.

PubMed

Khan, Shams Tabrez; Komaki, Hisayuki; Motohashi, Keiichiro; Kozone, Ikuko; Mukai, Akira; Takagi, Motoki; Shin-ya, Kazuo

2011-02-01

Terrestrial actinobacteria have served as a primary source of bioactive compounds; however, a rapid decrease in the discovery of new compounds strongly necessitates new investigational approaches. One approach is the screening of actinobacteria from marine habitats, especially the members of the genus Streptomyces. Presence of this genus in a marine sponge, Haliclona sp., was investigated using culture-dependent and -independent techniques. 16S rRNA gene clone library analysis showed the presence of diverse Streptomyces in the sponge sample. In addition to the dominant genus Streptomyces, members of six different genera were isolated using four different media. Five phylogenetically new strains, each representing a novel species in the genus Streptomyces were also isolated. Polyphasic study suggesting the classification of two of these strains as novel species is presented. Searching the strains for the production of novel compounds and the presence of biosynthetic genes for secondary metabolites revealed seven novel compounds and biosynthetic genes with unique sequences. In these compounds, JBIR-43 exhibited cytotoxic activity against cancer cell lines. JBIR-34 and -35 were particularly interesting because of their unique chemical skeleton. To our knowledge, this is the first comprehensive study detailing the isolation of actinobacteria from a marine sponge and novel secondary metabolites from these strains.

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.

Snow surface microbiome on the High Antarctic Plateau (DOME C).

PubMed

Michaud, Luigi; Lo Giudice, Angelina; Mysara, Mohamed; Monsieurs, Pieter; Raffa, Carmela; Leys, Natalie; Amalfitano, Stefano; Van Houdt, Rob

2014-01-01

The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<10(3) cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.

Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study.

PubMed

Ramos, Vitor M C; Castelo-Branco, Raquel; Leão, Pedro N; Martins, Joana; Carvalhal-Gomes, Sinda; Sobrinho da Silva, Frederico; Mendonça Filho, João G; Vasconcelos, Vitor M

2017-01-01

Microbial mats are complex, micro-scale ecosystems that can be found in a wide range of environments. In the top layer of photosynthetic mats from hypersaline environments, a large diversity of cyanobacteria typically predominates. With the aim of strengthening the knowledge on the cyanobacterial diversity present in the coastal lagoon system of Araruama (state of Rio de Janeiro, Brazil), we have characterized three mat samples by means of a polyphasic approach. We have used morphological and molecular data obtained by culture-dependent and -independent methods. Moreover, we have compared different classification methodologies and discussed the outcomes, challenges, and pitfalls of these methods. Overall, we show that Araruama's lagoons harbor a high cyanobacterial diversity. Thirty-six unique morphospecies could be differentiated, which increases by more than 15% the number of morphospecies and genera already reported for the entire Araruama system. Morphology-based data were compared with the 16S rRNA gene phylogeny derived from isolate sequences and environmental sequences obtained by PCR-DGGE and pyrosequencing. Most of the 48 phylotypes could be associated with the observed morphospecies at the order level. More than one third of the sequences demonstrated to be closely affiliated (best BLAST hit results of ≥99%) with cyanobacteria from ecologically similar habitats. Some sequences had no close relatives in the public databases, including one from an isolate, being placed as "loner" sequences within different orders. This hints at hidden cyanobacterial diversity in the mats of the Araruama system, while reinforcing the relevance of using complementary approaches to study cyanobacterial diversity.

Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study

PubMed Central

Ramos, Vitor M. C.; Castelo-Branco, Raquel; Leão, Pedro N.; Martins, Joana; Carvalhal-Gomes, Sinda; Sobrinho da Silva, Frederico; Mendonça Filho, João G.; Vasconcelos, Vitor M.

2017-01-01

Microbial mats are complex, micro-scale ecosystems that can be found in a wide range of environments. In the top layer of photosynthetic mats from hypersaline environments, a large diversity of cyanobacteria typically predominates. With the aim of strengthening the knowledge on the cyanobacterial diversity present in the coastal lagoon system of Araruama (state of Rio de Janeiro, Brazil), we have characterized three mat samples by means of a polyphasic approach. We have used morphological and molecular data obtained by culture-dependent and -independent methods. Moreover, we have compared different classification methodologies and discussed the outcomes, challenges, and pitfalls of these methods. Overall, we show that Araruama's lagoons harbor a high cyanobacterial diversity. Thirty-six unique morphospecies could be differentiated, which increases by more than 15% the number of morphospecies and genera already reported for the entire Araruama system. Morphology-based data were compared with the 16S rRNA gene phylogeny derived from isolate sequences and environmental sequences obtained by PCR-DGGE and pyrosequencing. Most of the 48 phylotypes could be associated with the observed morphospecies at the order level. More than one third of the sequences demonstrated to be closely affiliated (best BLAST hit results of ≥99%) with cyanobacteria from ecologically similar habitats. Some sequences had no close relatives in the public databases, including one from an isolate, being placed as “loner” sequences within different orders. This hints at hidden cyanobacterial diversity in the mats of the Araruama system, while reinforcing the relevance of using complementary approaches to study cyanobacterial diversity. PMID:28713360

Thermus anatoliensis sp. nov., a thermophilic bacterium from geothermal waters of Buharkent, Turkey.

PubMed

Kacagan, Murat; Inan, Kadriye; Canakci, Sabriye; Guler, Halil Ibrahim; Belduz, Ali Osman

2015-12-01

A Gram-stain-negative, lack of motility, catalase- and oxidase- positive bacterium (strain MT1(T)) was isolated from Buharkent hot spring in Aydin, Turkey. Its taxonomy was investigated using a polyphasic approach. The strain was able to grow at 45-80 °C, pH 5.5-10.5 and with a NaCI tolerance up to 2.0% (w/v). Strain MT1(T) was able to utilize d-mannitol and l-arabinose, not able to utilize d-cellobiose as sole carbon source. 16S rRNA gene sequence analysis revealed that the strain belonged to the genus Thermus; strain MT1(T) detected low-level similarities of 16S rRNA gene sequences (below 97%) compared with all other species in this genus. The predominant fatty acids of strain MT1(T) were iso-C(15:0) (43.0%) and iso-C(17:0) (27.4%). Polar lipid analysis revealed a major phospholipid, one major glycolipid, one major aminophospholipid, two minor aminolipids, one minor phospholipid, and several minor glycolipids. The major isoprenoid quinone was MK-8. The DNA G+C content of MT1(T) was 69.6 mol%. On the basis of a taxonomic study using a polyphasic approach, strain MT1(T) is considered to represent a novel species of the genus Thermus, for which the name Thermus anatoliensis sp. nov. is proposed. The type strain is MT1(T) (=NCCB 100425(T) =LMG 26880(T)). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.

PubMed

Landwehr, Wiebke; Kämpfer, Peter; Glaeser, Stefanie P; Rückert, Christian; Kalinowski, Jörn; Blom, Jochen; Goesmann, Alexander; Mack, Matthias; Schumann, Peter; Atasayar, Ewelina; Hahnke, Richard L; Rohde, Manfred; Martin, Karin; Stadler, Marc; Wink, Joachim

2018-01-01

Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many micro-organisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named 'Streptomyces davawensis' JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species. As we also worked with another isolate of Streptomyces cinnabarinus JS 360, the producer of the cinnabaramides, we wanted to clarify the taxonomic position of the three isolates by using a polyphasic approach. After analysis of the 16S rRNA gene sequence, we found in total 23 species of the genus Streptomyces that showed a similarity higher than 98.5 % to the three strains. We showed that 'S. davawensis' JCM 4913 and S. cinnabarinus DSM 40467 were very closely related but belong to two different species. Hence, we validate 'S. davawensis' as Streptomyces davaonensis sp. nov. with the type strain JCM 4913 T (=DSM 101723 T ). In addition, the cinnabaramide producer can be clearly differentiated from S. davaonensis and this isolate is described as Streptomyces cinnabarigriseus sp. nov. with strain JS360 T (=NCCB 100590 T =DSM 101724 T ) as the type strain.

Antibacterial, Anticancer and Neuroprotective Activities of Rare Actinobacteria from Mangrove Forest Soils.

PubMed

Azman, Adzzie-Shazleen; Othman, Iekhsan; Fang, Chee-Mun; Chan, Kok-Gan; Goh, Bey-Hing; Lee, Learn-Han

2017-06-01

Mangrove is a complex ecosystem that contains diverse microbial communities, including rare actinobacteria with great potential to produce bioactive compounds. To date, bioactive compounds extracted from mangrove rare actinobacteria have demonstrated diverse biological activities. The discovery of three novel rare actinobacteria by polyphasic approach, namely Microbacterium mangrovi MUSC 115 T , Sinomonas humi MUSC 117 T and Monashia flava MUSC 78 T from mangrove soils at Tanjung Lumpur, Peninsular Malaysia have led to the screening on antibacterial, anticancer and neuroprotective activities. A total of ten different panels of bacteria such as Methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300, ATCC 70069, Pseudomonas aeruginosa NRBC 112582 and others were selected for antibacterial screening. Three different neuroprotective models (hypoxia, oxidative stress, dementia) were done using SHSY5Y neuronal cells while two human cancer cells lines, namely human colon cancer cell lines (HT-29) and human cervical carcinoma cell lines (Ca Ski) were utilized for anticancer activity. The result revealed that all extracts exhibited bacteriostatic effects on the bacteria tested. On the other hand, the neuroprotective studies demonstrated M. mangrovi MUSC 115 T extract exhibited significant neuroprotective properties in oxidative stress and dementia model while the extract of strain M. flava MUSC 78 T was able to protect the SHSY5Y neuronal cells in hypoxia model. Furthermore, the extracts of M. mangrovi MUSC 115 T and M. flava MUSC 78 T exhibited anticancer effect against Ca Ski cell line. The chemical analysis of the extracts through GC-MS revealed that the majority of the compounds present in all extracts are heterocyclic organic compound that could explain for the observed bioactivities. Therefore, the results obtained in this study suggested that rare actinobacteria discovered from mangrove environment could be potential sources of antibacterial, anticancer and neuroprotective agents.

A reconfigurable multicarrier demodulator architecture

NASA Technical Reports Server (NTRS)

Kwatra, S. C.; Jamali, M. M.

1991-01-01

An architecture based on parallel and pipline design approaches has been developed for the Frequency Division Multiple Access/Time Domain Multiplexed (FDMA/TDM) conversion system. The architecture has two main modules namely the transmultiplexer and the demodulator. The transmultiplexer has two pipelined modules. These are the shared multiplexed polyphase filter and the Fast Fourier Transform (FFT). The demodulator consists of carrier, clock, and data recovery modules which are interactive. Progress on the design of the MultiCarrier Demodulator (MCD) using commercially available chips and Application Specific Integrated Circuits (ASIC) and simulation studies using Viewlogic software will be presented at the conference.

Optimized FPGA Implementation of Multi-Rate FIR Filters Through Thread Decomposition

NASA Technical Reports Server (NTRS)

Kobayashi, Kayla N.; He, Yutao; Zheng, Jason X.

2011-01-01

Multi-rate finite impulse response (MRFIR) filters are among the essential signal-processing components in spaceborne instruments where finite impulse response filters are often used to minimize nonlinear group delay and finite precision effects. Cascaded (multistage) designs of MRFIR filters are further used for large rate change ratio in order to lower the required throughput, while simultaneously achieving comparable or better performance than single-stage designs. Traditional representation and implementation of MRFIR employ polyphase decomposition of the original filter structure, whose main purpose is to compute only the needed output at the lowest possible sampling rate. In this innovation, an alternative representation and implementation technique called TD-MRFIR (Thread Decomposition MRFIR) is presented. The basic idea is to decompose MRFIR into output computational threads, in contrast to a structural decomposition of the original filter as done in the polyphase decomposition. A naive implementation of a decimation filter consisting of a full FIR followed by a downsampling stage is very inefficient, as most of the computations performed by the FIR state are discarded through downsampling. In fact, only 1/M of the total computations are useful (M being the decimation factor). Polyphase decomposition provides an alternative view of decimation filters, where the downsampling occurs before the FIR stage, and the outputs are viewed as the sum of M sub-filters with length of N/M taps. Although this approach leads to more efficient filter designs, in general the implementation is not straightforward if the numbers of multipliers need to be minimized. In TD-MRFIR, each thread represents an instance of the finite convolution required to produce a single output of the MRFIR. The filter is thus viewed as a finite collection of concurrent threads. Each of the threads completes when a convolution result (filter output value) is computed, and activated when the first input of the convolution becomes available. Thus, the new threads get spawned at exactly the rate of N/M, where N is the total number of taps, and M is the decimation factor. Existing threads retire at the same rate of N/M. The implementation of an MRFIR is thus transformed into a problem to statically schedule the minimum number of multipliers such that all threads can be completed on time. Solving the static scheduling problem is rather straightforward if one examines the Thread Decomposition Diagram, which is a table-like diagram that has rows representing computation threads and columns representing time. The control logic of the MRFIR can be implemented using simple counters. Instead of decomposing MRFIRs into subfilters as suggested by polyphase decomposition, the thread decomposition diagrams transform the problem into a familiar one of static scheduling, which can be easily solved as the input rate is constant.

Double-sided electromagnetic pump with controllable normal force for rapid solidification of liquid metals

DOEpatents

Kuznetsov, Stephen B.

1987-01-01

A system for casting liquid metals is provided with an electromagnetic pump which includes a pair of primary blocks each having a polyphase winding and being positioned to form a gap through which a movable conductive heat sink passes. A solidifying liquid metal sheet is deposited on the heat sink and the heat sink and sheet are held in compression by forces produced as a result of current flow through the polyphase windings. Shaded-pole interaction between the primary windings, heat sink and solidifying strip produce transverse forces which act to center the strip on the heat sink.

Double-sided electromagnetic pump with controllable normal force for rapid solidification of liquid metals

DOEpatents

Kuznetsov, S.B.

1987-01-13

A system for casting liquid metals is provided with an electromagnetic pump which includes a pair of primary blocks each having a polyphase winding and being positioned to form a gap through which a movable conductive heat sink passes. A solidifying liquid metal sheet is deposited on the heat sink and the heat sink and sheet are held in compression by forces produced as a result of current flow through the polyphase windings. Shaded-pole interaction between the primary windings, heat sink and solidifying strip produce transverse forces which act to center the strip on the heat sink. 5 figs.

Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB▿

PubMed Central

Woo, Patrick C. Y.; Teng, Jade L. L.; Yeung, Juilian M. Y.; Tse, Herman; Lau, Susanna K. P.; Yuen, Kwok-Yung

2011-01-01

Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (http://147.8.74.24/16SpathDB) based on the 16S rRNA gene sequences of all medically important bacteria listed in the Manual of Clinical Microbiology and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the “best match in 16SpathDB.” For the isolate (Gordonibacter pamelaeae) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the Manual of Clinical Microbiology. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories. PMID:21389154

Biodiversity analysis by polyphasic study of marine bacteria associated with biocorrosion phenomena.

PubMed

Boudaud, N; Coton, M; Coton, E; Pineau, S; Travert, J; Amiel, C

2010-07-01

A polyphasic approach was used to study the biodiversity bacteria associated with biocorrosion processes, in particular sulfate-reducing bacteria (SRB) and thiosulfate-reducing bacteria (TRB) which are described to be particularly aggressive towards metallic materials, notably via hydrogen sulfide release. To study this particular flora, an infrared spectra library of 22 SRB and TRB collection strains were created using a Common Minimum Medium (CMM) developed during this study and standardized culture conditions. The CMM proved its ability to allow for growth of both SRB and TRB strains. These sulfurogen collection strains were clearly discriminated and differentiated at the genus level by fourier transform infrared (FT-IR) spectroscopy. In a second step, infrared spectra of isolates, recovered from biofilms formed on carbon steel coupons immersed for 1 year in three different French harbour areas, were compared to the infrared reference spectra library. In parallel, molecular methods (M13-PCR and 16S rRNA gene sequencing) were used to qualitatively evaluate the intra- and inter-species genetic diversity of biofilm isolates. The biodiversity study indicated that strains belonging to the Vibrio genus were the dominant population; strains belonging to the Desulfovibrio genus (SRB) and Peptostreptococcaceae were also identified. Overall, the combination of the FT-IR spectroscopy and molecular approaches allowed for the taxonomic and ecological study of a bacterial flora, cultivated on CMM, associated with microbiology-induced corrosion (MIC) processes. Via the use of the CMM medium, the culture of marine bacteria (including both SRB and TRB bacteria) was allowed, and the implication of nonsulforogen bacteria in MIC was observed. Their involvement in the biocorrosion phenomena will have to be studied and taken into account in the future. © 2009 The Authors. Journal compilation © 2009 The Society for Applied Microbiology.

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products.

PubMed

Marfil-Santana, Miguel David; O'Connor-Sánchez, Aileen; Ramírez-Prado, Jorge Humberto; De Los Santos-Briones, Cesar; López-Aguiar; Lluvia, Korynthia; Rojas-Herrera, Rafael; Lago-Lestón, Asunción; Prieto-Davó, Alejandra

2016-11-01

The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

Polyphasic approach to the identification and characterization of aflatoxigenic strains of Aspergillus section Flavi isolated from peanuts and peanut-based products marketed in Malaysia.

PubMed

Norlia, M; Jinap, S; Nor-Khaizura, M A R; Son, R; Chin, C K; Sardjono

2018-05-31

Peanuts are widely consumed as the main ingredient in many local dishes in Malaysia. However, the tropical climate in Malaysia (high temperature and humidity) favours the growth of fungi from Aspergillus section Flavi, especially during storage. Most of the species from this section, such as A. flavus, A. parasiticus and A. nomius, are natural producers of aflatoxins. Precise identification of local isolates and information regarding their ability to produce aflatoxins are very important to evaluate the safety of food marketed in Malaysia. Therefore, this study aimed to identify and characterize the aflatoxigenic and non-aflatoxigenic strains of Aspergillus section Flavi in peanuts and peanut-based products. A polyphasic approach, consisting of morphological and chemical characterizations was applied to 128 isolates originating from raw peanuts and peanut-based products. On the basis of morphological characters, 127 positively identified as Aspergillus flavus, and the other as A. nomius. Chemical characterization revealed six chemotype profiles which indicates diversity of toxigenic potential. About 58.6%, 68.5%, and 100% of the isolates are positive for aflatoxins, cyclopiazonic acid and aspergillic acid productions respectively. The majority of the isolates originating from raw peanut samples (64.8%) were aflatoxigenic, while those from peanut-based products were less toxigenic (39.1%). The precise identification of these species may help in developing control strategies for aflatoxigenic fungi and aflatoxin contamination in peanuts, especially during storage. These findings also highlight the possibility of the co-occurrence of other toxins, which could increase the potential toxic effects of peanuts. Copyright © 2018. Published by Elsevier B.V.

Polyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica.

PubMed

Jancusova, Miroslava; Kovacik, Lubomir; Pereira, Antonio Batista; Dusinsky, Roman; Wilmotte, Annick

2016-07-01

The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic approach (morphology, 16S rRNA and internal transcribed spacer sequences). The studied taxa are characteristic of coastal Antarctic biotopes, where they form distinct populations and ecologically delimited communities. They were isolated from terrestrial habitats: microbial mats in seepages; crusts on soil, rocks, bones and mosses; mud, sometimes close to bird colonies; and from guano. Based on major phenotypic features, the strains were divided into four distinct morphotypes: Leptolyngbya borchgrevinkii (A), Leptolyngbya frigida (B), Microcoleus sp. (C) and Wilmottia murrayi (D). This morphological identification was in agreement with the phylogenetic relationships. For the first time, the 16S rRNA gene sequence of a strain corresponding to the L. borchgrevinkii morphotype was determined. Morphotype B is most related to sequences assigned to L. frigida isolated from microbial mats of coastal lakes in East Antarctica. Morphotype C belongs to a cluster including strains with morphotypes corresponding to Microcoleus attenuatus, Microcoleus favosus and Microcoleus sp., which are from Antarctica and other continents. Morphotype D is grouped with sequences assigned to W. murrayi mostly isolated from Antarctica. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Gracilibacillus aidingensis sp. nov., a novel moderately halophilic bacterium isolated from Aiding salt lake.

PubMed

Guan, Tong-Wei; Tian, Lei; Li, En-Yuan; Tang, Shu-Kun; Zhang, Xiao-Ping

2017-11-01

A novel Gram-positive, aerobe, moderately halophilic bacterium was isolated from saline soil of Aiding lake in Xinjiang, north-west of China, designated strain YIM 98001 T . Cells were rod-shaped, motile and grew at 5-20% (w/v) NaCl (optimum 10%), pH 6-10 (optimum pH 7.0) and 4-45 °C (optimum 37 °C). The major cellular fatty acids were anteiso C 15:0 , anteiso C 17:0 , iso C 15:0 . The predominant respiratory quinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid were the major polar lipids. Meso-diaminopimelic acid was the diagnostic diamino acid of the cell-wall peptidoglycan. The G+C content was 36.46 mol%. 16S rRNA gene sequence analysis showed that the strain belongs to the family Bacillaceae, with the highest sequence similarity to the type strain Gracilibacillus thailandensis TP2-8 T (96.84%), followed by Gracilibacillus saliphilus YIM 91119 T (96.78%) and Gracilibacillus ureilyticus MF38 T (96.57%), thus confirming the affiliation of strain YIM 98001 T to the genus Gracilibacillus. The polyphasic approach indicates that strain YIM 98001 T represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus aidingensis is proposed. The type strain is YIM 98001 T (=KCTC 42683 T  = DSMZ 104330 T ).

Domibacillus robiginosus gen. nov., sp. nov., isolated from a pharmaceutical clean room.

PubMed

Seiler, Herbert; Wenning, Mareike; Scherer, Siegfried

2013-06-01

A novel red-pigmented bacterial strain, designated WS 4628(T), was isolated from a pharmaceutical clean room of a vaccine-producing company and was investigated in a taxonomic study using a polyphasic approach. The strain was Gram-stain-positive, strictly aerobic, motile, catalase-positive and produced spherical to slightly ellipsoidal endospores in rods. The genomic DNA G+C content was 44.1 mol%. The major fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0 and the predominant quinone was MK-6. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and an unidentified phospholipid. meso-diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan and the major whole-cell sugars were glucose and ribose. The closest phylogenetic neighbours were identified as Bacillus badius ATCC 14574(T) (95.8% 16S rRNA gene sequence similarity), Bacillus indicus Sd/3(T) (94.8%), Jeotgalibacillus alimentarius YKJ-13(T) (94.8%) and Bacillus cibi JG-30(T) (94.8%). Phylogenetic, physiological, biochemical and morphological differences between strain WS 4628(T) and its closest relatives in the families Bacillaceae and Planococcaceae suggest that this strain represents a novel species in a new genus in the family Bacillaceae for which the name Domibacillus robiginosus gen. nov., sp. nov. is proposed; the type strain of the type species is WS 4628(T) (=DSM 25058(T)=LMG 26645(T)).

Negative coupled inductors for polyphase choppers

NASA Technical Reports Server (NTRS)

Jamieson, Robert S. (Inventor)

1984-01-01

A technique for negatively coupling the outputs of polyphase choppers is disclosed, wherein the output inductance of each phase is divided into two windings, and each winding is negatively coupled to a corresponding winding of a neighboring phase. In a preferred embodiment for a three-phase chopper circuit, the output inductance of phase A is divided into windings 100 and 102, the output inductance of phase B is divided into windings 110 and 112, and the output inductance of phase C is divided into windings 120 and 122. Pairs of windings 100 and 110, 112 and 120, and 102 and 122 are respectively disposed in transformers arranged for negatively coupling the windings of each pair.

Nocardiopsis potens sp. nov., isolated from household waste.

PubMed

Yassin, A F; Spröer, C; Hupfer, H; Siering, C; Klenk, H-P

2009-11-01

The taxonomic position of an actinomycete, designated strain IMMIB L-21(T), was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21(T) (=DSM 45234(T)=CCUG 56587(T)).

Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave.

PubMed

Ko, Kwan Su; Kim, Youngju; Seong, Chi Nam; Lee, Soon Dong

2015-11-01

A Gram-reaction-positive, high DNA G+C content, non-motile actinobacterium, strain D7-21T, was isolated from dried bat dung inside a natural cave and its taxonomic status was examined by using a polyphasic approach. The 16S rRNA gene sequence study showed that the isolate belonged to the genus Rhodococcus and formed a cluster with Rhodococcus defluvii (98.98 % gene similarity), Rhodococcus equi (98.62 %) and Rhodococcus kunmingensis (97.66 %). Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H2) was the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phosphoglycolipid and an unknown glycolipid. Mycolic acids were present. The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0. The DNA G+C content was 70.1 mol%. A battery of phenotypic features and DNA-DNA relatedness data support that strain D7-21T ( = KCTC 29469T = DSM 46727T) represents a novel species of the genus Rhodococcus, for which Rhodococcus antrifimi sp. nov. is proposed.

Application of culture-dependent and culture-independent methods for the identification of Lactobacillus kefiranofaciens in microbial consortia present in kefir grains.

PubMed

Hamet, Maria Fernanda; Londero, Alejandra; Medrano, Micaela; Vercammen, Elisabeth; Van Hoorde, Koenraad; Garrote, Graciela L; Huys, Geert; Vandamme, Peter; Abraham, Analía G

2013-12-01

The biological and technological characteristics of kefiran as well as its importance in grain integrity led us to analyze the microbial kefir grain consortium with focus on Lactobacillus kefiranofaciens. The presence of L. kefiranofaciens in the nine kefir grains studied was demonstrated by denaturing gradient gel electrophoresis. By culture dependent methods applying a methodology focused on the search of this species, 22 isolates with typical morphology were obtained and identified applying a combination of SDS-PAGE of whole cell proteins, (GTG)5-PCR and sequence analysis of the housekeeping gene encoding the α-subunit of bacterial phenylalanyl-tRNA synthase (pheS). This polyphasic approach allowed the reliable identification of 11 L. kefiranofaciens, 5 Lactobacillus paracasei, 4 Lactobacillus kefiri and 2 Lactobacillus parakefiri isolates. Isolated L. kefiranofaciens strains produced polysaccharide in strain-dependent concentrations and EPS produced by them also differed in the degree of polymerization. The isolation and accurate identification of L. kefiranofaciens is relevant taking into account the important role of this microorganism in the grain ecosystem as well as its potential application as starter in food fermentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Snow Surface Microbiome on the High Antarctic Plateau (DOME C)

PubMed Central

Michaud, Luigi; Lo Giudice, Angelina; Mysara, Mohamed; Monsieurs, Pieter; Raffa, Carmela; Leys, Natalie; Amalfitano, Stefano; Van Houdt, Rob

2014-01-01

The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<103 cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau. PMID:25101779

Micrococcus yunnanensis sp. nov., a novel actinobacterium isolated from surface-sterilized Polyspora axillaris roots.

PubMed

Zhao, Guo-Zhen; Li, Jie; Qin, Sheng; Zhang, Yu-Qin; Zhu, Wen-Yong; Jiang, Cheng-Lin; Xu, Li-Hua; Li, Wen-Jun

2009-10-01

In this study, strain YIM 65004(T), isolated from roots of Polyspora axillaris, was shown to represent a novel species of the genus Micrococcus by means of a polyphasic approach. Chemotaxonomic data gathered for peptidoglycan type, menaquinones, phospholipids and fatty acids strongly supported the classification of this strain within the genus Micrococcus: the cell-wall peptidoglycan contained lysine, glutamic acid, alanine, glycine and aspartic acid, the predominant menaquinones were MK-8(H(2)) (66.97 %) and MK-7(H(2)) (23.26 %), the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid, and the major cellular fatty acids were anteiso-C(15 : 0) (61.98 %), iso-C(16 : 0) (14.25 %) and iso-C(15 : 0) (13.04 %). The G+C content of the genomic DNA was 71.7 mol%. A number of physiological features were found that clearly distinguished strain YIM 65004(T) from recognized Micrococcus species. DNA-DNA hybridization studies suggested that the novel strain represents a separate genomic species. Based on the above data, a novel species of the genus Micrococcus, Micrococcus yunnanensis sp. nov., is proposed, with the type strain YIM 65004(T) (=CCTCC AA 208060(T)=DSM 21948(T)).

Possible Gems and Ultra-Fine Grained Polyphase Units in Comet Wild 2.

NASA Technical Reports Server (NTRS)

Gainsforth, Z.; Butterworth, A. L.; Jilly-Rehak, C. E.; Westphal, A. J.; Brownlee, D. E.; Joswiak, D.; Ogliore, R. C.; Zolensky, M. E.; Bechtel, H. A.; Ebel, D. S.;

Fundamentals of electric power conversion. Volume 2, Energy-efficient polyphase AC induction motors, final report

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

Umans, S.D.

1992-12-01

Its rugged nature and straightforward design make the induction motor the most commonly used type of electric motor. This motor ranges in size fro the fractional-horsepower, single-phase motors found in household appliances to polyphase motors rated at thousands of horsepower for industrial applications. Volume 1 of this report describes the function of induction motors, their characteristics, and induction motor testing. Volume 2 describes the characteristics of high-efficiency induction motors, with emphasis on the techniques used to obtain high efficiency. This two-volume report is written in nontechnical language and is intended for readers who require background from applications, marketing, motor planning,more » or managerial perspective.« less

Lechevalieria rhizosphaerae sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) and emended description of the genus Lechevalieria.

PubMed

Zhao, Junwei; Li, Wenchao; Shi, Linlin; Wang, Han; Wang, Ying; Zhao, Yue; Xiang, Wensheng; Wang, Xiangjing

2017-11-01

A novel actinomycete, designated strain NEAU-A2 T , was isolated from rhizosphere soil of wheat (Triticum aestivum L.) and characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-A2 T should be assigned to the genus Lechevalieria and forms a distinct branch with its closest neighbour Lechevalieria aerocolonigenes DSM 40034 T (99.0 %). Moreover, key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-A2 T to the genus Lechevalieria. The cell wall contained meso-diaminopimelic acid and the whole-cell hydrolysates were galactose, mannose, rhamnose, glucose and ribose. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositolmannoside and two glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 1ω7c and anteiso-C17 : 0. The DNA G+C content was 68.2 mol%. The combination of the DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-A2 T could be distinguished from its closest relative. Therefore, it is proposed that strain NEAU-A2 T represents a novel species of the genus Lechevalieria, for which the name Lechevalieriarhizosphaerae sp. nov. is proposed. The type strain is NEAU-A2 T (=CGMCC 4.7405 T =DSM 104541 T ).

Bioprospecting highly diverse endophytic Pestalotiopsis spp. with antibacterial properties from Maytenus ilicifolia, a medicinal plant from Brazil.

PubMed

Gomes-Figueiredo, Josiane; Pimentel, Ida C; Vicente, Vânia A; Pie, Marcio R; Kava-Cordeiro, Vanessa; Galli-Terasawa, Lygia; Pereira, José O; de Souza, Antonia Q L; Glienke, Chirlei

2007-10-01

Thirteen endophytic fungal strains of the genus Pestalotiopsis were isolated from the medicinal plant Maytenus ilicifolia Mart. ex. Reiss (commonly known as "espinheira santa") and their antimicrobial properties were investigated. Two isolates were successful in inhibiting the growth of the tested microorganisms (Escherichia coli, Klebsiella pneumoniae, Micrococcus luteus, Staphylococcus aureus, and methicillin-resistant Staphylococcus aureus (MRSA)) using the technique of bioautographic thin-layer chromatography (TLC) agar overlay assay. An analysis based on a polyphasic approach integrating taxonomic information, morphological traits, RAPD markers, and the sequencing of the ITS1-5.8S-ITS2 of the rDNA led to the assignment of the isolates as belonging to the species Pestalotiopsis microspora, Pestalotiopsis vismiae, and Pestalotiopsis leucothoes. Therefore, the present study presents a new approach to the study of endophytic fungi of the genus Pestalotiopsis.

Ceramic Biocomposites as Biodegradable Antibiotic Carriers in the Treatment of Bone Infections

PubMed Central

Ferguson, Jamie; Diefenbeck, Michael; McNally, Martin

2017-01-01

Local release of antibiotic has advantages in the treatment of chronic osteomyelitis and infected fractures. The adequacy of surgical debridement is still key to successful clearance of infection but local antibiotic carriers seem to afford greater success rates by targeting the residual organisms present after debridement and delivering much higher local antibiotic concentrations compared with systemic antibiotics alone. Biodegradable ceramic carriers can be used to fill osseous defects, which reduces the dead space and provides the potential for subsequent repair of the osseous defect as they dissolve away. A dissolving ceramic antibiotic carrier also raises the possibility of single stage surgery with definitive closure and avoids the need for subsequent surgery for spacer removal. In this article we provide an overview of the properties of various biodegradable ceramics, including calcium sulphate, the calcium orthophosphate ceramics, calcium phosphate cement and polyphasic carriers. We summarise the antibiotic elution properties as investigated in previous animal studies as well as the clinical outcomes from clinical research investigating their use in the surgical management of chronic osteomyelitis. Calcium sulphate pellets have been shown to be effective in treating local infection, although newer polyphasic carriers may support greater osseous repair and reduce the risk of further fracture or the need for secondary reconstructive surgery. The use of ceramic biocomposites to deliver antibiotics together with BMPs, bisphosphonates, growth factors or living cells is under investigation and merits further study. We propose a treatment protocol, based on the Cierny-Mader classification, to help guide the appropriate selection of a suitable ceramic antibiotic carrier in the surgical treatment of chronic osteomyelitis. PMID:28529863

Microbial Community Dynamics during Production of the Mexican Fermented Maize Dough Pozol

PubMed Central

ben Omar, Nabil; Ampe, Frédéric

2000-01-01

The dynamics of the microbial community responsible for the traditional fermentation of maize in the production of Mexican pozol was investigated by using a polyphasic approach combining (i) microbial enumerations with culture media, (ii) denaturing gradient gel electrophoresis (DGGE) fingerprinting of total community DNA with bacterial and eukaryotic primers and sequencing of partial 16S ribosomal DNA (rDNA) genes, (iii) quantification of rRNAs from dominant microbial taxa by using phylogenetic oligonucleotide probes, and (iv) analysis of sugars and fermentation products. A Streptococcus species dominated the fermentation and accounted for between 25 and 75% of the total flora throughout the process. Results also showed that the initial epiphytic aerobic microflora was replaced in the first 2 days by heterofermentative lactic acid bacteria (LAB), including a close relative of Lactobacillus fermentum, producing lactic acid and ethanol; this heterolactic flora was then progressively replaced by homofermentative LAB (mainly close relatives of L. plantarum, L. casei, and L. delbrueckii) which continued acidification of the maize dough. At the same time, a very diverse community of yeasts and fungi developed, mainly at the periphery of the dough. The analysis of the DGGE patterns obtained with bacterial and eukaryotic primers targeting the 16S and 18S rDNA genes clearly demonstrated that there was a major shift in the community structure after 24 h and that high biodiversity—according to the Shannon-Weaver index—was maintained throughout the process. These results proved that a relatively high number of species, at least six to eight, are needed to perform this traditional lactic acid fermentation. The presence of Bifidobacterium, Enterococcus, and enterobacteria suggests a fecal origin of some important pozol microorganisms. Overall, the results obtained with different culture-dependent or -independent techniques clearly confirmed the importance of developing a polyphasic approach to study the ecology of fermented foods. PMID:10966374

Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov., isolated from the preen glands of Great Spotted Woodpeckers (Dendrocopos major).

PubMed

Braun, Markus Santhosh; Wang, Erjia; Zimmermann, Stefan; Boutin, Sébastien; Wink, Michael

2018-01-01

Two new species of Gram-positive cocci were isolated from the uropygial glands of wild woodpeckers (Dendrocopos major) originating from different locations in Germany. A polyphasic approach confirmed the affiliation of the isolates to the genus Kocuria. Phylogenetic analysis based on the 16S rRNA gene showed high degree of similarity to Kocuria koreensis DSM 23367 T (99.0% for both isolates). However, low ANIb values of <80% unequivocally separated the new species from K. koreensis. This finding was further corroborated by DNA fingerprinting and analysis of polar lipid profiles. Furthermore, growth characteristics, biochemical tests, MALDI-TOF MS analysis, and G+C contents clearly differentiated the isolates from their known relatives. Besides, the woodpecker isolates significantly differed from each other in their whole-cell protein profiles, DNA fingerprints, and ANIb values. In conclusion, the isolated microorganisms constitute members of two new species, for which the names Kocuria uropygioeca sp. nov. and Kocuria uropygialis sp. nov. are proposed. The type strains are 36 T (DSM 101740 T =LMG 29265 T ) and 257 T (=DSM 101741 T =LMG 29266 T ) for K. uropygialis sp. nov. and K. uropygioeca sp. nov., respectively. Copyright © 2017 Elsevier GmbH. All rights reserved.

Virgibacillus halophilus sp. nov., spore-forming bacteria isolated from soil in Japan.

PubMed

An, Sun-Young; Asahara, Mika; Goto, Keiichi; Kasai, Hiroaki; Yokota, Akira

2007-07-01

Two Gram-positive, round-spore-forming, rod-shaped, halophilic bacterial strains, 5B73C(T) and 5B133E, were isolated from field soil in Kakegawa, Shizuoka, Japan, and were characterized taxonomically using a polyphasic approach. These two strains were found to comprise strictly aerobic, motile rods that formed subterminal endospores. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains 5B73C(T) and 5B133E are phylogenetically affiliated to the genus Virgibacillus, exhibiting sequence similarities of 94.1-96.4 % with respect to the type strains of Virgibacillus species. The DNA G+C contents of strains 5B73C(T) and 5B133E were 42.6 and 42.3 mol%, respectively. The cell-wall peptidoglycan type (meso-diaminopimelic acid), the major cellular fatty acids (anteiso-C(15 : 0), iso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0)) and the quinone type (MK-7) of the isolates support their affiliation to the genus Virgibacillus. On the basis of their genotypic and phenotypic characteristics, the isolates represent a novel species of the genus Virgibacillus, for which the name Virgibacillus halophilus sp. nov. is proposed. The type strain is 5B73C(T) (=IAM 15308(T)=KCTC 13935(T)).

Regional polyphase deformation of the Eastern Sierras Pampeanas (Argentina Andean foreland): strengths and weaknesses of paleostress inversion

NASA Astrophysics Data System (ADS)

Traforti, Anna; Zampieri, Dario; Massironi, Matteo; Viola, Giulio; Alvarado, Patricia; Di Toro, Giulio

2016-04-01

The Eastern Sierras Pampeanas of central Argentina are composed of a series of basement-cored ranges, located in the Andean foreland c. 600 km east of the Andean Cordillera. Although uplift of the ranges is partly attributed to the regional Neogene evolution (Ramos et al. 2002), many questions remain as to the timing and style of deformation. In fact, the Eastern Sierras Pampeanas show compelling evidence of a long lasting brittle history (spanning the Early Carboniferous to Present time), characterised by several deformation events reflecting different tectonic regimes. Each deformation phase resulted in further strain increments accommodated by reactivation of inherited structures and rheological anisotropies (Martino 2003). In the framework of such a polyphase brittle tectonic evolution affecting highly anisotropic basement rocks, the application of paleostress inversion methods, though powerful, suffers from some shortcomings, such as the likely heterogeneous character of fault slip datasets and the possible reactivation of even highly misoriented structures, and thus requires careful analysis. The challenge is to gather sufficient fault-slip data, to develop a proper understanding of the regional evolution. This is done by the identification of internally consistent fault and fracture subsets (associated to distinct stress states on the basis of their geometric and kinematic compatibility) in order to generate a chronologically-constrained evolutionary conceptual model. Based on large fault-slip datasets collected in the Sierras de Cordoba (Eastern Sierras Pampeanas), reduced stress tensors have been generated and interpreted as part of an evolutionary model by considering the obtained results against: (i) existing K-Ar illite ages of fault gouges in the study area (Bense et al. 2013), (ii) the nature and orientation of pre-existing anisotropies and (iii) the present-day stress field due to the convergence of the Nazca and South America plates (main shortening oriented WSW-ENE). Although remarkable differences in reactivation mechanisms have been observed for the various studied lithological domains (schist, gneiss and granitic rocks), the brittle regional polyphase deformation of the Eastern Sierras Pampeanas appears to be dominated by two extensional episodes (σ3 oriented NE/ENE and WNW, respectively), which can be associated with Middle-Late Permian to Early Cretaceous tectonism, followed by a compressional paleostress (σ1 oriented ENE), which is compatible with the present day Andean convergence. Paleostress inversion techniques, despite all uncertainties involved, represent a robust approach to disentangle complex polyphase deformation histories both in term of reactivation mechanisms and strain partitioning. References: Bense, F. A., Wemmer, K., Löbens, S., & Siegesmund, S. (2013). Fault gouge analyses: K-Ar illite dating, clay mineralogy and tectonic significance-a study from the Sierras Pampeanas, Argentina. International Journal of Earth Sciences, 103, 189-218. Martino, R. D. (2003). Las fajas de deformación dúctil de las Sierras Pampeanas de Córdoba : Una reseña general. Revista de La Asociación Geológica Argentina, 58(4), 549-571. Ramos, V. A., Cristallini, E. O., & Perez, D. J. (2002). The Pampean flat-slab of the Central Andes. Journal of South American Earth Sciences, 15, 59-78.

Polyphasic Study of the Spatial Distribution of Microorganisms in Mexican Pozol, a Fermented Maize Dough, Demonstrates the Need for Cultivation-Independent Methods To Investigate Traditional Fermentations

PubMed Central

Ampe, Frédéric; ben Omar, Nabil; Moizan, Claire; Wacher, Carmen; Guyot, Jean-Pierre

1999-01-01

The distribution of microorganisms in pozol balls, a fermented maize dough, was investigated by a polyphasic approach in which we used both culture-dependent and culture-independent methods, including microbial enumeration, fermentation product analysis, quantification of microbial taxa with 16S rRNA-targeted oligonucleotide probes, determination of microbial fingerprints by denaturing gradient gel electrophoresis (DGGE), and 16S ribosomal DNA gene sequencing. Our results demonstrate that DGGE fingerprinting and rRNA quantification should allow workers to precisely and rapidly characterize the microbial assemblage in a spontaneous lactic acid fermented food. Lactic acid bacteria (LAB) accounted for 90 to 97% of the total active microflora; no streptococci were isolated, although members of the genus Streptococcus accounted for 25 to 50% of the microflora. Lactobacillus plantarum and Lactobacillus fermentum, together with members of the genera Leuconostoc and Weissella, were the other dominant organisms. The overall activity was more important at the periphery of a ball, where eucaryotes, enterobacteria, and bacterial exopolysacharide producers developed. Our results also showed that the metabolism of heterofermentative LAB was influenced in situ by the distribution of the LAB in the pozol ball, whereas homolactic fermentation was controlled primarily by sugar limitation. We propose that starch is first degraded by amylases from LAB and that the resulting sugars, together with the lactate produced, allow a secondary flora to develop in the presence of oxygen. Our results strongly suggest that cultivation-independent methods should be used to study traditional fermented foods. PMID:10584005

Enterobacter xiangfangensis sp. nov., isolated from Chinese traditional sourdough, and reclassification of Enterobacter sacchari Zhu et al. 2013 as Kosakonia sacchari comb. nov.

PubMed

Gu, Chun Tao; Li, Chun Yan; Yang, Li Jie; Huo, Gui Cheng

2014-08-01

A Gram-stain-negative bacterial strain, 10-17(T), was isolated from traditional sourdough in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, RNA polymerase β subunit (rpoB) gene sequence analysis, DNA gyrase (gyrB) gene sequence analysis, initiation translation factor 2 (infB) gene sequence analysis, ATP synthase β subunit (atpD) gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain 10-17(T) was phylogenetically related to Enterobacter hormaechei CIP 103441(T), Enterobacter cancerogenus LMG 2693(T), Enterobacter asburiae JCM 6051(T), Enterobacter mori LMG 25706(T), Enterobacter ludwigii EN-119(T) and Leclercia adecarboxylata LMG 2803(T), having 99.5%, 99.3%, 98.7%, 98.5%, 98.4% and 98.4% 16S rRNA gene sequence similarity, respectively. On the basis of polyphasic characterization data obtained in the present study, a novel species, Enterobacter xiangfangensis sp. nov., is proposed and the type strain is 10-17(T) ( = LMG 27195(T) = NCIMB 14836(T) = CCUG 62994(T)). Enterobacter sacchari Zhu et al. 2013 was reclassified as Kosakonia sacchari comb. nov. on the basis of 16S rRNA, rpoB, gyrB, infB and atpD gene sequence analysis and the type strain is strain SP1(T)( = CGMCC 1.12102(T) = LMG 26783(T)). © 2014 IUMS.

Energetic constraints, not predation, influence the evolution of sleep patterning in mammals.

PubMed

Capellini, I; Nunn, C L; McNamara, P; Preston, B T; Barton, R A

2008-10-01

Mammalian sleep is composed of two distinct states - rapid-eye-movement (REM) and non-REM (NREM) sleep - that alternate in cycles over a sleep bout. The duration of these cycles varies extensively across mammalian species. Because the end of a sleep cycle is often followed by brief arousals to waking, a shorter sleep cycle has been proposed to function as an anti-predator strategy. Similarly, higher predation risk could explain why many species exhibit a polyphasic sleep pattern (division of sleep into several bouts per day), as having multiple sleep bouts avoids long periods of unconsciousness, potentially reducing vulnerability.Using phylogenetic comparative methods, we tested these predictions in mammals, and also investigated the relationships among sleep phasing, sleep-cycle length, sleep durations and body mass.Neither sleep-cycle length nor phasing of sleep was significantly associated with three different measures of predation risk, undermining the idea that they represent anti-predator adaptations.Polyphasic sleep was associated with small body size, shorter sleep cycles and longer sleep durations. The correlation with size may reflect energetic constraints: small animals need to feed more frequently, preventing them from consolidating sleep into a single bout. The reduced daily sleep quotas in monophasic species suggests that the consolidation of sleep into one bout per day may deliver the benefits of sleep more efficiently and, since early mammals were small-bodied and polyphasic, a more efficient monophasic sleep pattern could be a hitherto unrecognized advantage of larger size.

All-digital multicarrier demodulators for on-board processing satellites in mobile communication systems

NASA Astrophysics Data System (ADS)

Yim, Wan Hung

Economical operation of future satellite systems for mobile communications can only be fulfilled by using dedicated on-board processing satellites, which would allow both cheap earth terminals and lower space segment costs. With on-board modems and codecs, the up-link and down-link can be optimized separately. An attractive scheme is to use frequency-division multiple access/single chanel per carrier (FDMA/SCPC) on the up-link and time division multiplexing (TDM) on the down-link. This scheme allows mobile terminals to transmit a narrow band, low power signal, resulting in smaller dishes and high power amplifiers (HPA's) with lower output power. On the up-link, there are hundreds to thousands of FDM channels to be demodulated on-board. The most promising approach is the use of all-digital multicarrier demodulators (MCD's), where analog and digital hardware are efficiently shared among channels, and digital signal processing (DSP) is used at an early stage to take advantage of very large scale integration (VLSI) implementation. A MCD consists of a channellizer for separation of frequency division multiplexing (FDM) channels, followed by individual modulators for each channel. Major research areas in MCD's are in multirate DSP, and the optimal estimation for synchronization, which form the basis of the thesis. Complex signal theories are central to the development of structured approaches for the sampling and processing of bandpass signals, which are the foundations in both channellizer and demodulator design. In multirate DSP, polyphase theories replace many ad-hoc, tedious and error-prone design procedures. For example, a polyphase-matrix deep space network frequency and timing system (DFT) channellizer includes all efficient filter bank techniques as special cases. Also, a polyphase-lattice filter is derived, not only for sampling rate conversion, but also capable of sampling phase variation, which is required for symbol timing adjustment in all-digital demodulators. In modulation schemes, a systematic survey is reported, based on two expressions that includes all formats in linear and constant envelope modulation. In synchronization techniques, classifications according to the criterion of statistical optimization, the data dependecy, and the method of parameter extraction, reflect the inherent complexity and performance of numerous existing algorithms. The designs of two new algorithms are presented: a differential decision frequency error detector that is simple and fast; a dual-comb-filter frequency/timing error detector that is targeted at VLSI implementation. The real-time implementation of a complete 4 x 16 kb/s MCD for the T-SAT project is described in detail, which proved many of the structured design concepts developed in this thesis. The requirements of software tools for various levels of simulation in multirate DSP and communications are analyzed. This led to the implementation of a data-flow oriented simulation system, which was used in all research work in the thesis.

Actinomadura algeriensis sp. nov., an actinobacterium isolated from Saharan soil.

PubMed

Lahoum, Abdelhadi; Bouras, Noureddine; Mathieu, Florence; Schumann, Peter; Spröer, Cathrin; Klenk, Hans-Peter; Sabaou, Nasserdine

2016-01-01

During the course of a screening programme for new taxa of actinobacteria, a strain designated ACD1(T), was isolated from a Saharan soil in the Hoggar region (Algeria). The taxonomic position of this strain was determined using a polyphasic taxonomic approach. The strain was observed to form extensively branched, non-fragmenting substrate mycelium, and aerial mycelium with straight to flexuous, hooked and irregular spirals (1-2 turns) forming short chains of spores. The diamino acid present in the cell wall is meso-diaminopimelic acid. Galactose, glucose, madurose, mannose and ribose occur in whole-cell hydrolysates. The diagnostic phospholipids detected were diphosphatidylglycerol and phosphatidylinositol. The major menaquinones were identified as MK-9 (H4) and MK-9 (H2). The major fatty acids were found to be C16:0, C18:1 cis9, iso-C16:0 and 10-methyl C18:0. Phylogenetic analysis based on the 16S rRNA gene showed that the strain belongs to the genus Actinomadura, and is closely related to Actinomadura sediminis DSM 45500(T) (98.5 % similarity) and Actinomadura cremea subsp. cremea DSM 43676(T) (98.3 % similarity). However, DNA-DNA hybridization revealed only 48.0 % relatedness with A. sediminis DSM 45500(T) and 33.2 % relatedness with A. cremea subsp. cremea DSM 43676(T). The combined phenotypic and genotypic data showed that the strain represents a novel species of the genus Actinomadura, for which the name Actinomadura algeriensis sp. nov. is proposed, with the type strain ACD1(T) (= DSM 46744(T) = CECT 8841(T)).

Naumannella halotolerans gen. nov., sp. nov., a Gram-positive coccus of the family Propionibacteriaceae isolated from a pharmaceutical clean room and from food.

PubMed

Rieser, Gernot; Scherer, Siegfried; Wenning, Mareike

2012-12-01

Four Gram-stain-positive, aerobic bacterial strains isolated from a pharmaceutical clean room (strain WS4616(T)), a dessert milk product (strain WS4617) and from raw milk (strains WS4623 and WS4624) were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences showed that they formed a distinct lineage within the family Propionibacteriaceae. Similarity values between 16S rRNA gene sequences of the four novel strains and the type species of all genera belonging to the family Propionibacteriaceae were 89.2-94.1%. The major cellular fatty acid was anteiso-C(15:0) and the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were MK-8(H(4)) and MK-9(H(4)). The cell-wall peptidoglycan of type A3γ contained ll-diaminopimelic acid, alanine, glycine and glutamic acid. The G+C content of the genomic DNA of strain WS4616(T) was 67.7 mol%. The whole-cell sugar pattern contained ribose, mannose, arabinose, glucose and galactose. On the basis of phenotypic and genetic data, strains WS4616(T), WS4617, WS4623 and WS4624 are classified as members of a novel species in a new genus of the family Propionibacteriaceae, for which the name Naumannella halotolerans gen. nov., sp. nov. is proposed. The type strain is WS4616(T) ( = DSM 24323(T) = LMG 26184(T)) and three additional strains are WS4617, WS4623 and WS4624.

Principal components - Petrology and chemistry of polyphase units in chondritic porous interplanetary dust particles

NASA Astrophysics Data System (ADS)

Rietmeijer, Frans J. M.

1997-03-01

Chondritic porous (CP) interplanetary dust particles (IDPs) can be described as 'cosmic sediments'. It should be possible to recognize in these IDPs the 4500 Myrs old solar nebula dusts. The studies of unaltered chondritic IDPs show that their matrices are a mixture of three different principal components (PCs) that also describe variable C/Si ratios of chondritic IDPs. Among others, PCs include polyphase units (PUs) that are amorphous to holocrystalline, both ultrafine- and coarse-grained, ferromagnesiosilica(te) materials with minor Al and Ca. The properties of PCs and their alteration products define the physical and chemical processes that produced and altered these components. PCs are also cornerstones of IDP classification. For example, the bulk composition of ultrafine-grained PCs can be reconstructed using the 'butterfly method' and also allows an evaluation of the metamorphic signatures, (e.g., dynamic pyrometamorphism), in chondritic IDPs.

Polyphase tectonics at the southern tip of the Manila trench, Mindoro-Tablas Islands, Philippines

NASA Astrophysics Data System (ADS)

Marchadier, Yves; Rangin, Claude

1990-11-01

The southern termination of the Manila trench within the South China Sea continental margin in Mindoro is marked by a complex polyphase tectonic fabric in the arc-trench gap area. Onshore Southern Mindoro the active deformation front of the Manila trench is marked by parallel folds and thrusts, grading southward to N50° W-trending left-lateral strike-slip faults. This transpressive tectonic regime, active at least since the Late Pliocene, has overprinted the collision of an Early Miocene volcanic arc with the South China Sea continental margin (San Jose platform). The collision is postdated by deposition of the Late Miocene-Early Pliocene elastics of the East Mindoro basin. The tectonic and geological framework of this arc, which overlies a metamorphic basement and Eocene elastics, suggests that it was built on a drifted block of the South China Sea continental margin.

Using a PFET To Commutate an SCR

NASA Technical Reports Server (NTRS)

Edwards, D. B.; Ripple, W. E.

1984-01-01

Accidental turn-on prevented. PFET diverts load current around SCR to prevent false SCR triggering from current and voltage switching transients. New circuit used in all types of single phase and polyphase inverters and in buck-boost-, and flyback regulators.

Aspergillus bertholletius sp. nov. from Brazil Nuts

PubMed Central

Taniwaki, Marta H.; Pitt, John I.; Iamanaka, Beatriz T.; Sartori, Daniele; Copetti, Marina V.; Balajee, Arun; Fungaro, Maria Helena P.; Frisvad, Jens C.

2012-01-01

During a study on the mycobiota of brazil nuts (Bertholletia excelsa) in Brazil, a new Aspergillus species, A. bertholletius, was found, and is described here. A polyphasic approach was applied using morphological characters, extrolite data as well as partial β-tubulin, calmodulin and ITS sequences to characterize this taxon. A. bertholletius is represented by nineteen isolates from samples of brazil nuts at various stages of production and soil close to Bertholletia excelsa trees. The following extrolites were produced by this species: aflavinin, cyclopiazonic acid, kojic acid, tenuazonic acid and ustilaginoidin C. Phylogenetic analysis using partial β-tubulin and camodulin gene sequences showed that A. bertholletius represents a new phylogenetic clade in Aspergillus section Flavi. The type strain of A. bertholletius is CCT 7615 ( = ITAL 270/06 = IBT 29228). PMID:22952594

Sol-Gel Synthesis and Crystallization of Magnesium and Calcium Rich Silicate Dust Analogs

NASA Astrophysics Data System (ADS)

Gillot, J.; Roskosz, M.; Depecker, C.; Roussel, P.; Leroux, H.

2009-03-01

A new sol-gel method optimized to synthesize amorphous and porous silicate dust analogs is proposed. The crystallization of such analogs is metastable and polyphasic. Their high reactivity is probably due to high surface/volume ratio.

Geological evolution of the Pietersburg greenstonebelt, South Africa and associated gold mineralization

NASA Technical Reports Server (NTRS)

Jones, M. G.; Dewit, M. J.

1986-01-01

The polyphase history of gold mineralization seen in the Pietersburg greenstone belt is integrated with the geochemical and tectonic evolution of greenstone belts as a whole. The four distinct regional geological settings of gold mineralization are described.

Analysis of bacterial community during the fermentation of pulque, a traditional Mexican alcoholic beverage, using a polyphasic approach.

PubMed

Escalante, Adelfo; Giles-Gómez, Martha; Hernández, Georgina; Córdova-Aguilar, María Soledad; López-Munguía, Agustín; Gosset, Guillermo; Bolívar, Francisco

2008-05-31

In this study, the characterization of the bacterial community present during the fermentation of pulque, a traditional Mexican alcoholic beverage from maguey (Agave), was determined for the first time by a polyphasic approach in which both culture and non-culture dependent methods were utilized. The work included the isolation of lactic acid bacteria (LAB), aerobic mesophiles, and 16S rDNA clone libraries from total DNA extracted from the maguey sap (aguamiel) used as substrate, after inoculation with a sample of previously produced pulque and followed by 6-h fermentation. Microbiological diversity results were correlated with fermentation process parameters such as sucrose, glucose, fructose and fermentation product concentrations. In addition, medium rheological behavior analysis and scanning electron microscopy in aguamiel and during pulque fermentation were also performed. Our results showed that both culture and non-culture dependent approaches allowed the detection of several new and previously reported species within the alpha-, gamma-Proteobacteria and Firmicutes. Bacteria diversity in aguamiel was composed by the heterofermentative Leuconostoc citreum, L. mesenteroides, L. kimchi, the gamma-Proteobacteria Erwinia rhapontici, Enterobacter spp. and Acinetobacter radioresistens. Inoculation with previously fermented pulque incorporated to the system microbiota, homofermentative lactobacilli related to Lactobacillus acidophilus, several alpha-Proteobacteria such as Zymomonas mobilis and Acetobacter malorum, other gamma-Proteobacteria and an important amount of yeasts, creating a starting metabolic diversity composed by homofermentative and heterofermentative LAB, acetic and ethanol producing microorganisms. At the end of the fermentation process, the bacterial diversity was mainly composed by the homofermentative Lactobacillus acidophilus, the heterofermentative L. mesenteroides, Lactococcus lactis subsp. lactis and the alpha-Proteobacteria A. malorum. After a 6-h fermentation, 83.27% of total sugars detected after inoculation were consumed (228.4 mM hexose equivalents) and a carbon (C) recovery of 66.18% in fermentation products was estimated. They were produced 284.4 mM C as ethanol, 71.5 mM C as acetic acid and 19 mM C as lactic acid, demonstrating the presence of homo- and heterofermentative, acetic and alcoholic metabolisms in the final product. It was also found, after hydrolysis, that the exopolysaccharide produced during the fermentation was mainly composed by fructose residues, probably inulin or levan.

Belliella buryatensis sp. nov., isolated from alkaline lake water.

PubMed

Kozyreva, Lyudmila; Egorova, Darya; Anan'ina, Lyudmila; Plotnikova, Elena; Ariskina, Elena; Prisyazhnaya, Natalya; Radnaeva, Larisa; Namsaraev, Bair

2016-01-01

Two bacterial isolates from water of the alkaline brackish Lake Solenoe (Buryatia, Russia), 2C and 5CT, were characterized by using a polyphasic taxonomic approach. The strains were small, non-motile, Gram-stain-negative rods that formed small orange-red colonies on the surface of marine agar. Studies based on 16S rRNA gene sequences showed that the strains were related closely to Belliella pelovolcani CC-SAL-25T (98.7 % sequence similarity). The G+C content of the DNA was 38-40 mol%. DNA-DNA hybridization values between strains 2C and 5CT and B. pelovolcani CC-SAL-25T were 56-58 mol%. A menaquinone with seven isoprene units (MK-7) was the major respiratory quinone. The fatty acid profiles were slightly different from that of B. pelovolcani CC-SAL-25T. The novel strains could be distinguished from the phylogenetically closest species B. pelovolcani CC-SAL-25T based on matrix-assisted laser desorption ionization time-of-flight mass spectra of whole cells and a range of physiological and biochemical characteristics. The data obtained suggest that strains 2C and 5CT represent a novel species of the genus Belliella, for which the name Belliella buryatensis sp. nov. is proposed. The type strain is 5CT ( = VKM B-2724T = KCTC 32194T).

Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae".

PubMed

Suresh, K; Mayilraj, S; Chakrabarti, T

2006-07-01

A Gram-negative bacterial isolate (designated SRC-1(T)) was isolated from an occasional drainage system and characterized by a polyphasic approach to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain SRC-1(T) with the family "Flexibacteraceae" of the phylum Bacteroidetes. It showed greatest sequence similarity to Pontibacter actiniarum KMM 6156(T) (95.5 %) followed by Adhaeribacter aquaticus MBRG1.5(T) (89.0 %) and Hymenobacter roseosalivarius DSM 11622(T) (88.9 %), but it differed from these micro-organisms in many phenotypic characteristics. Strain SRC-1(T) was an obligate aerobe and its cells were non-motile, irregular rods. The major fatty acids included mainly unsaturated and hydroxy fatty acids, including 17 : 1 iso I/anteiso B (36.7 %), 15 : 0 iso (15.8 %) and 17 : 0 iso 3-OH (10.3 %), and the DNA G+C content was 59.5 mol%. From the phenotypic and genotypic analyses it was clear that strain SRC-1(T) was quite different from members other genera in the family '"Flexibacteraceae". Therefore we conclude that strain SRC-1(T) represents a novel genus, for which the name Effluviibacter gen. nov., containing a single species Effluviibacter roseus sp. nov., is proposed. The type species of the genus is Effluviibacter roseus, the type strain of which is strain SRC-1(T) (=MTCC 7260(T)=DSM 17521(T)).

Streptomyces krungchingensis sp. nov., isolated from soil.

PubMed

Sripreechasak, Paranee; Phongsopitanun, Wongsakorn; Tamura, Tomohiko; Tanasupawat, Somboon

2017-01-01

A novel actinomycete, designated strain KC-035T, was isolated from soil collected from Krung Ching Waterfall National Park, Nakhon Si Thammarat Province, Thailand. Its taxonomic position was determined using a polyphasic approach. The strain had morphological and chemotaxonomic properties typical of members of the genus Streptomyces: flexuous spore chain; ll-diaminopimelic acid in the cell-wall peptidoglycan; MK-9(H8), MK-9(H6) and MK-9(H4) as menaquinones; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as phospholipids; anteiso-C15 : 0, C16 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 as major cellular fatty acids; and DNA G+C content of 72 mol%. 16S rRNA gene sequence analysis revealed that strain KC-035T showed high similarity to Streptomyces albiflavescens n20T (99.16 %) and Streptomyces siamensis KC-038T (98.43 %) as well as formed a monophyletic clade with them in the phylogenetic tree. On the basis of comparison of phenotypic properties and the low level of DNA-DNA relatedness, strain KC-035T could be distinguished from its closely related Streptomyces species and is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces krungchingensis sp. nov. is proposed. The type strain is KC-035T (=NBRC 110087T=KCTC 29503T=TISTR 2402T).

Micrococcus endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots.

PubMed

Chen, Hua-Hong; Zhao, Guo-Zhen; Park, Dong-Jin; Zhang, Yu-Qin; Xu, Li-Hua; Lee, Jae-Chan; Kim, Chang-Jin; Li, Wen-Jun

2009-05-01

A Gram-positive bacterial strain, designated YIM 56238(T), was isolated from plant roots (Aquilaria sinensis), and characterized by using a polyphasic approach. Strain YIM 56238(T) grew optimally at pH 7.0-8.0 and at 28 degrees C. Analysis of the 16S rRNA gene sequence of strain YIM 56238(T) indicated that it belongs to the genus Micrococcus. Chemotaxonomic data strongly supported the classification of this strain within the genus Micrococcus: the cell-wall peptidoglycan contained lysine, glutamic acid, alanine and glycine; the predominant menaquinones were MK-8(H(2)) (63.6 %) and MK-7(H(2)) (21.1 %); the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid; and the major cellular fatty acids were iso-C(15 : 0) (30.95 %) and anteiso-C(15 : 0) (53.75 %). The G+C content of the genomic DNA was 72.9 mol%. A number of physiological features were found that clearly distinguished strain YIM 56238(T) from recognized species of the genus Micrococcus. DNA-DNA hybridization studies suggested that the novel strain represents a separate genomic species. On the basis of the data, therefore, strain YIM 56238(T) represents a novel species of the genus Micrococcus, for which the name Micrococcus endophyticus sp. nov. is proposed. The type strain is YIM 56238(T) (=DSM 17945(T)=KCTC 19156(T)).

Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort.

PubMed

Schauer, S; Kämpfer, P; Wellner, S; Spröer, C; Kutschera, U

2011-04-01

A pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1(T), was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27(T), Methylobacterium fujisawaense DSM 5686(T), Methylobacterium radiotolerans JCM 2831(T) and Methylobacterium jeotgali S2R03-9(T), with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA-DNA relatedness between strain JT1(T) and these and the type strains of other closely related species were lower than 70 %. Cells of JT1(T) stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm(-2)). Major fatty acids were C(18 : 1)ω7c and C(16 : 0). Based on the morphological, physiological and biochemical data presented, strain JT1(T) is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1(T) ( = DSM 21328(T)  = CCUG 56108(T)).

A high reliability battery management system

NASA Technical Reports Server (NTRS)

Moody, M. H.

1986-01-01

Over a period of some 5 years Canadian Astronautics Limited (CAL) has developed a system to autonomously manage, and thus prolong the life of, secondary storage batteries. During the development, the system was aimed at the space vehicle application using nickel cadmium batteries, but is expected to be able to enhance the life and performance of any rechargeable electrochemical couple. The system handles the cells of a battery individually and thus avoids the problems of over, and under, drive that inevitably occur in a battery of cells managed by an averaging system. This individual handling also allow cells to be totally bypassed in the event of failure, thus avoiding the losses associated with low capacity, partial short circuit, and the catastrophe of open circuit. The system has an optional capability of managing redundant batteries simultaneously, adding the advantage of on line reconditioning of one battery, while the other maintains the energy storage capability of the overall system. As developed, the system contains a dedicated, redundant, microprocessor, but the capability exists to have this computing capability time shared, or remote, and operating through a data link. As adjuncts to the basic management system CAL has developed high efficiency, polyphase, power regulators for charge and discharge power conditioning.

Polyphasic taxonomic characterisation of a novel strain as Pararhizobium haloflavum sp. nov., isolated from soil samples near a sewage treatment tank.

PubMed

Shen, Xia; Li, Yu; Zhao, Zhe; Han, Yi-Fan; Zhang, Wen-Wu; Yu, Xiao-Yun; Zhang, Chong-Ya; Sun, Cong; Wu, Min

2018-04-01

A Gram-stain negative, aerobic, motile and ovoid- to rod-shaped bacteria strain, designated XC0140 T , was isolated from soil samples near the sewage treatment tank of a chemical factory in Zhejiang Province, China, and subjected to polyphasic taxonomic investigation. Strain XC0140 T grew at 10-37 °C and pH 6.0-9.0 (optimum, 35 °C and pH 7.5) and with 0-17% (w/v) NaCl (optimum, 1%). According to phylogenetic analysis based on 16S rRNA gene sequences, strain XC0140 T was assigned to the genus Pararhizobium with high 16S rRNA gene sequence similarity of 95.97% to "Pararhizobium helanshanense CCNWQTX14 T" , followed by Pararhizobium sphaerophysae CCNWGS0238 T (95.95%). Chemotaxonomic analysis showed that strain XC0140 T contains ubiquinone-10 as the predominant respiratory quinone and possessed summed feature 8 (comprising C 18: 1 ω7c and/or ω6c), 11-methyl C 18:1 ω7c, C 18: 0 and C 16: 0 as predominant forms of fatty acids. The polar lipids of strain XC0140 T consisted of seven phospholipids (PL), two aminolipids (AL), one glycolipid (GL) and three unidentified lipids (L1, L2 and L3). The DNA G+C content was 62.7 mol%. Based on the polyphasic taxonomic characterization, strain XC0140 T is considered to represent a novel species of the genus Pararhizobium, for which the name Pararhizobium haloflavum sp. nov. is proposed. (type strain XC0140 T  = MCCC 1K03228 T  = KCTC 52582 T ).

Point-contact tunneling in monophasic and polyphasic Y-Ba-Cu-O samples: Experiment and model

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

Gonnelli, R.S.; Andreone, D.; Lacquaniti, V.

1989-02-01

Tunneling experiments using large-area point-contact structures have been performed on several monophasic polycrystalline Ba/sub 2/Cu/sub 3/O/sub 7-//sub delta/ samples and on polyphasic samples containing, mixed with the previous superconducting phase, also about 11% of the so-called green phase (BaY/sub 2/CuO/sub 5/). Both niobium and Y-Ba-Cu-O tips were used as counterelectrodes and measurements were made at 4.2 and 77 K. Results obtained at different experimental conditions show great reproducibility indicating the presence of the gap voltage at about 20 mV in the dynamic resistance curves. A phenomenological model was then developed to interpret in a quantitative way our data by meansmore » of a decomposition of the experimental conductance into a background component and a superconducting-tunneling component. The former results essentially in a parabolic contribution versus the bias voltage typical of a tunneling between normallike junction electrodes while the latter component is smeared out in voltage by a large amount of broadening. Using the model in a least-squares fit of the experimental data of Nb/Y-Ba-Cu-O junctions, values V/sub G/ = 21.3 +- 0.8 mV and V/sub G/ = 22.0 +- 0.6 mV for the voltage gaps at 4.2 K of monophasic and polyphasic materials, respectively, have been determined. These results have been well confirmed by measurements on Y-Ba-Cu-O/Y-Ba-Cu-O junctions while, at 77 K, there are no indications of a superconducting tunneling. We obtained also the parameters of the background conductance, which indicates the presence of a nonsuperconducting layer at the surface of the material.« less

Phanerozoic polyphase orogenies recorded in the northeastern Okcheon Belt, Korea from SHRIMP U-Pb detrital zircon and K-Ar illite geochronologies

NASA Astrophysics Data System (ADS)

Jang, Yirang; Kwon, Sanghoon; Song, Yungoo; Kim, Sung Won; Kwon, Yi Kyun; Yi, Keewook

2018-05-01

We present the SHRIMP U-Pb detrital zircon and K-Ar illite 1Md/1M and 2M1 ages, suggesting new insight into the Phanerozoic polyphase orogenies preserved in the northeastern Okcheon Belt, Korea since the initial basin formation during Neoproterozoic rifting through several successive contractional orogens. The U-Pb detrital zircon ages from the Early Paleozoic strata of the Taebaeksan Zone suggest a Cambrian maximum deposition age, and are supported by trilobite and conodont biostratigraphy. Although the age spectra from two sedimentary groups, the Yeongwol and Taebaek Groups, show similar continuous distributions from the Late Paleoproterozoic to Early Paleozoic ages, a Grenville-age hiatus (1.3-0.9 Ga) in the continuous stratigraphic sequence from the Taebaek Group suggests the existence of different peripheral clastic sources along rifted continental margin(s). In addition, we present the K-Ar illite 1Md/1M ages of the fault gouges, which confirm fault formation/reactivation during the Late Cretaceous to Early Paleogene (ca. 82-62 Ma) and the Early Miocene (ca. 20-18 Ma). The 2M1 illite ages, at least those younger than the host rock ages, provide episodes of deformation, metamorphism and hydrothermal effects related to the tectonic events during the Devonian (ca.410 Ma) and Permo-Triassic (ca. 285-240 Ma). These results indicate that the northeastern Okcheon Belt experienced polyphase orogenic events, namely the Okcheon (Middle Paleozoic), Songrim (Late Paleozoic to Early Mesozoic), Daebo (Middle Mesozoic) and Bulguksa (Late Mesozoic to Early Cenozoic) Orogenies, reflecting the Phanerozoic tectonic evolution of the Korean Peninsula along the East Asian continental margin.

Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn.

PubMed

Rachniyom, Hathairat; Matsumoto, Atsuko; Inahashi, Yuki; Take, Akira; Takahashi, Yoko; Thamchaipenet, Arinthip

2018-05-01

A novel actinomycete strain, designated GKU 128 T , isolated from the roots of an Indian oak tree [Barringtonia acutangula (L.) Gaertn.] at Khao Khitchakut district, Chantaburi province, Thailand, was characterized by using a polyphasic approach. The strain formed a branched substrate and aerial mycelia which differentiated into straight to flexuous chains of smooth-ornamented spores. Analysis of the cell wall revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, mannose, rhamnose and ribose. Mycolic acids were absent. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside. The predominant menaquinones were MK-9(H6), MK-9(H8), MK-9(H0) and MK-9(H4). The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The genomic DNA G+C content was 70.5 mol%. Based on 16S rRNA gene sequence analysis, strain GKU 128 T was closely related to the type strains of Actinomadura nitritigenes NBRC 15918 T (99.2 % sequence similarity) and Actinomadura fibrosa JCM 9371 T (98.7 %). The levels of DNA-DNA relatedness between strain GKU 128 T and the closely related type species were less than 19 %. On the basis of phenotypic and genotypic characteristics, strain GKU 128 T could be distinguished from its closely related type strains and represents a novel species of the genus Actinomadura, for which the name Actinomadura barringtoniae sp. nov. (=TBRC 7225 T =NBRC 113074 T ) is proposed.

Streptomyces tremellae sp. nov., isolated from a culture of the mushroom Tremella fuciformis.

PubMed

Wen, Zhi-Qiang; Chen, Bingzhi; Li, Xiao; Li, Bing-Bing; Li, Cheng-Huan; Huang, Qing-Hua; Zhang, Qi-Hui; Dai, Wei-Hao; Jiang, Yu-Ji

2016-12-01

A novel actinomycete strain, designated Js-1T, was isolated from Tremella fuciformis collected from Gutian, Fujian Province, in southeastern China. The taxonomic status of this strain was determined by a polyphasic approach, which demonstrated that the novel strain was a member of the genus Streptomyces. The cell walls of this strain were found to contain ll-diaminopimelic acid, muramic acid and glycine. An analysis of whole-cell hydrolysates revealed that no characteristic sugar was present. The key identified menaquinones were MK-9 (H6) and MK-9 (H8), while the diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmethylethanolamine and phosphatidylglycerol. The main cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. An analysis of an almost complete 16S rRNA gene sequence showed that the strain shared the highest levels of sequence similarity with Streptomyces sannanensisKC-7038T (97.87 %), Streptomyces hebeiensis YIM 001T (97.84 %), Streptomyces pathocidini NBRC 13812T (97.80 %), Streptomyces cocklensis BK168T (97.25 %), Streptomyces coerulescens NBRC 12758T (97.12 %), Streptomyces aurantiogriseus NBRC 12842T (97.06 %) and Streptomyces rimosussubsp. rimosus ATCC 10970T (97.04 %). The DNA G+C content of the genomic DNA of strain Js-1T was 70.1 mol%. Furthermore, DNA-DNA hybridization tests revealed that the relatedness values between strain Js-1T and the most closely related species ranged from 15.10 to 47.20 %. Based on its phenotypic and genotypic characteristics, strain Js-1T (=CCTCC M 2011365T=JCM 30846T) is considered to represent a novel species within the genus Streptomyces, which we classified as Streptomycestremellae sp. nov.

Fodinicola feengrottensis gen. nov., sp. nov., an actinomycete isolated from a medieval mine.

PubMed

Carlsohn, Marc René; Groth, Ingrid; Saluz, Hans-Peter; Schumann, Peter; Stackebrandt, Erko

2008-07-01

A filamentous, Gram-positive actinobacterium was isolated from acidic rocks in a medieval alum slate mine and was investigated by means of a polyphasic taxonomic approach. A 16S rRNA gene sequence similarity study indicated that strain HKI 0501(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genus Cryptosporangium (family 'Kineosporiaceae') and the other by members of the genera Frankia and Acidothermus (family Frankiaceae and family Acidothermaceae, respectively). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and xylose as the characteristic cell-wall sugar. The muramic acid in the peptidoglycan was found to be N-acetylated. The major menaquinones were MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) and the fatty acid profile was characterized by the predominance of iso-C(16 : 0), 10-methyl C(17 : 0), C(17 : 1) cis9 and 10-methyl iso-C(18 : 0). The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol and several unknown phospholipids and glycolipids. Mycolic acids were absent. The DNA G+C content was 65 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain HKI 0501(T) represents a novel genus and species, for which the name Fodinicola feengrottensis gen. nov., sp. nov. is proposed. The type strain of Fodinicola feengrottensis is HKI 0501(T) (=DSM 19247(T) =JCM 14718(T)).

Nonomuraea zeae sp. nov., isolated from the rhizosphere of corn (Zea mays L.).

PubMed

Shen, Yue; Jia, Feiyu; Liu, Chongxi; Li, Jiansong; Guo, Siyu; Zhou, Shuyu; Wang, Xiangjing; Xiang, Wensheng

2016-06-01

A novel actinobacterium, designated strain NEAU-ND5T, was isolated from the rhizosphere of corn (Zea mays L.) collected in Heilongjiang Province, north-east China, and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain NEAU-ND5T was a member of the genus Nonomuraea, with highest sequence similarities to Nonomuraea jabiensis A4036T (98.29 %), Nonomuraea rosea GW12687T (98.25 %), Nonomuraea candida HMC10T (98.22 %), Nonomuraea rhizophila YIM 67092T (98.04 %) and Nonomuraea kuesteri NRRL B-24325T (98.04 %). Similarities to other type strains of the genus Nonomuraea were lower than 98 %. Morphological and chemotaxonomic properties of strain NEAU-ND5T were also consistent with the description of the genus Nonomuraea. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, ribose and madurose. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major menaquinones were MK-9(H4), MK-9(H2) and MK-9(H0). The predominant cellular fatty acids were iso-C16:0 and 10-methyl C17:0. A combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-ND5T was clearly distinguished from its closely related Nonomuraea species. Consequently, it is concluded that strain NEAU-ND5T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea zeae sp. nov. is proposed. The type strain is NEAU-ND5T (=CGMCC 4.7280T=DSM 100528T).

Streptomyces xiangtanensis sp. nov., isolated from a manganese-contaminated soil.

PubMed

Mo, Ping; Yu, Yi-Zun; Zhao, Jia-Rong; Gao, Jian

2017-03-01

An actinomycete strain, designated strain LUSFXJ T , was isolated from a soil sample obtained near the Xiangtan Manganese Mine, Central-South China and characterised using a polyphasic taxonomic approach. The 16S rRNA gene sequence-based phylogenetic analysis indicated that this strain belongs to the genus Streptomyces. The DNA-DNA relatedness between this strain and two closely related type strains, Streptomyces echinatus CGMCC 4.1642 T and Streptomyces lanatus CGMCC 4.137 T , were 28.7 ± 0.4 and 19.9 ± 2.0%, respectively, values which are far lower than the 70% threshold for the delineation of a novel prokaryotic species. The DNA G+C content of strain LUSFXJ T is 75.0 mol%. Chemotaxonomic analysis revealed that the menaquinones of strain LUSFXJ T are MK-9(H 6 ), MK-9(H 8 ), MK-9(H 2 ) and MK-8(H 8 ). The polar lipid profile of strain LUSFXJ T was found to contain diphosphatidylglycerol and an unidentified polar lipid. The major cellular fatty acids were identified as iso-C 15:0 , anteiso-C 15:0 , iso-C 16:0 , C 16:0 and Summed feature 3. Strain LUSFXJ T was found to contain meso-diaminopimelic acid as the diagnostic cell wall diamino acid and the whole cell hydrolysates were found to be rich in ribose, mannose and glucose. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, it is concluded that strain LUSFXJ T represents a novel species of the genus Streptomyces, for which the name S. xiangtanensis sp. nov. is proposed. The type strain is LUSFXJ T (=GDMCC 4.133 T  = KCTC 39829 T ).

Streptomyces ovatisporus sp. nov., isolated from deep marine sediment.

PubMed

Veyisoglu, Aysel; Cetin, Demet; Inan Bektas, Kadriye; Guven, Kiymet; Sahin, Nevzat

2016-11-01

The taxonomic position of a Gram-staining-positive strain, designated strain S4702T was isolated from a marine sediment collected from the southern Black Sea coast, Turkey, determined using a polyphasic approach. The isolate was found to have chemotaxonomic, morphological and phylogenetic properties consistent with its classification as representing a member of the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree. S4702T was found to be most closely related to the type strains of Streptomyces marinus(DSM 41968T; 97.8 % sequence similarity) and Streptomyces abyssalis (YIM M 10400T; 97.6 %). 16S rRNA gene sequence similarities with other members of the genus Streptomyces were lower than 97.5 %. DNA-DNA relatedness of S4702T and the most closely related strain S. marinus DSM 41968T was 21.0 %. The G+C content of the genomic DNA was 72.5 mol%. The cell wall of the strain contained l,l-diaminopimelic acid and the cell-wall sugars were glucose and ribose. The major cellular fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H8). The polar lipid profile of S4702T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. S4702T could be distinguished from its closest phylogenetic neighbours using a combination of chemotaxonomic, morphological and physiological properties. Consequently, it is proposed that S4702T represents a novel species of the genus Streptomyces, for which the name Streptomyces ovatisporus sp. nov. is proposed. The type strain is S4702T (DSM 42103T=KCTC 29206T=CGMCC 4.7357T).

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.

New insights on pressure, temperature, and chemical stability of CsAlSi5O12, a potential host for nuclear waste

NASA Astrophysics Data System (ADS)

Gatta, G. D.; Brundu, A.; Cappelletti, P.; Cerri, G.; de'Gennaro, B.; Farina, M.; Fumagalli, P.; Guaschino, L.; Lotti, P.; Mercurio, M.

2016-10-01

A Cs-bearing polyphase aggregate with composition (in wt%): 76(1)CsAlSi5O12 + 7(1)CsAlSi2O6 + 17(1)amorphous, was obtained from a clinoptilolite-rich epiclastic rock after a beneficiation process of the starting material (aimed to increase the fraction of zeolite to 90 wt%), cation exchange and then thermal treatment. CsAlSi5O12 is an open-framework compound with CAS topology; CsAlSi2O6 is a pollucite-like material with ANA topology. The thermal stability of this polyphase material was investigated by in situ high- T X-ray powder diffraction, the combined P- T effects by a series of runs with a single-stage piston cylinder apparatus, and its chemical stability following the "availability test" ("AVA test") protocol. A series of additional investigations were performed by WDS-electron microprobe analysis in order to describe the P- T-induced modification of the material texture, and to chemically characterize the starting material and the run products. The "AVA tests" of the polyphase aggregate show an extremely modest release of Cs+: 0.05 mg/g. In response to applied temperature and at room P, CsAlSi5O12 experiences an unquenchable and displacive Ama2-to- Amam phase transition at about 770 K, and the Amam polymorph is stable in its crystalline form up to 1600 K; a crystalline-to-amorphous phase transition occurs between 1600 and 1650 K. In response to the applied P = 0.5 GPa, the crystalline-to-amorphous transition of CsAlSi5O12 occurs between 1670 and 1770 K. This leads to a positive Clapeyron slope (i.e., d P/d T > 0) of the crystalline-to-amorphous transition. When the polyphase aggregate is subjected at P = 0.5 GPa and T > 1770 K, CsAlSi5O12 melts and only CsAlSi2O6 (pollucite-like; dominant) and Cs-rich glass (subordinate) are observed in the quenched sample. Based on its thermo-elastic behavior, P- T phase stability fields, and Cs+ retention capacity, CsAlSi5O12 is a possible candidate for use in the immobilization of radioactive isotopes of Cs, or as potential solid hosts for 137Cs γ-radiation source in sterilization applications. More in general, even the CsAlSi5O12-rich aggregate obtained by a clinoptilolite-rich epiclastic rock appears to be suitable for this type of utilizations.

Streptomyces jeddahensis sp. nov., an oleaginous bacterium isolated from desert soil.

PubMed

Röttig, Annika; Atasayar, Ewelina; Meier-Kolthoff, Jan Philipp; Spröer, Cathrin; Schumann, Peter; Schauer, Jennifer; Steinbüchel, Alexander

2017-06-01

A novel strain, G25T, was isolated from desert soil collected near Jeddah in Saudi Arabia. The strain could accumulate nearly 65 % of its cell dry weight as fatty acids, grow on a broad range of carbon sources and tolerate temperatures of up to 50 °C. With respect to to its 16S rRNA gene sequence, G25T is most closely related to Streptomyces massasporeus DSM 40035T, Streptomyces hawaiiensis DSM 40042T, Streptomyces indiaensis DSM 43803T, Streptomyces luteogriseus DSM 40483T and Streptomyces purpurascens DSM 40310T. Conventional DNA-DNA hybridization (DDH) values ranged from 18.7 to 46.9 % when G25T was compared with these reference strains. Furthermore, digital DDH values between the draft genome sequence of G25T and the genome sequences of other species of the genus Streptomyces were also significantly below the threshold of 70 %. The DNA G+C content of the draft genome sequence, consisting of 8.46 Mbp, was 70.3 %. The prevalent cellular fatty acids of G25T comprised anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The polar lipids profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides as well as unidentified phospholipids and phosphoaminolipids. The cell wall contained ll-diaminopimelic acid. Whole-cell sugars were predominantly glucose with small traces of ribose and mannose. The results of the polyphasic approach confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces jeddahensis sp. nov. is proposed. The type strain of this species is G25T (=DSM 101878T =LMG 29545T =NCCB 100603T).

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

NASA Astrophysics Data System (ADS)

Sangal, Vartul; Goodfellow, Michael; Jones, Amanda L.; Schwalbe, Edward C.; Blom, Jochen; Hoskisson, Paul A.; Sutcliffe, Iain C.

2016-12-01

Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

10 CFR 431.12 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Standard 112-1996, Test Procedure for Polyphase Induction Motors and Generators, and Test Method (1) of CSA... a system, that has its own rules of procedure and management, for giving written assurance that a... operated by an entity independent of both the party seeking the written assurance and the party providing...

10 CFR 431.12 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Standard 112-1996, Test Procedure for Polyphase Induction Motors and Generators, and Test Method (1) of CSA... a system, that has its own rules of procedure and management, for giving written assurance that a... operated by an entity independent of both the party seeking the written assurance and the party providing...

Alternating-Current Motor Drive for Electric Vehicles

NASA Technical Reports Server (NTRS)

Krauthamer, S.; Rippel, W. E.

1982-01-01

New electric drive controls speed of a polyphase as motor by varying frequency of inverter output. Closed-loop current-sensing circuit automatically adjusts frequency of voltage-controlled oscillator that controls inverter frequency, to limit starting and accelerating surges. Efficient inverter and ac motor would give electric vehicles extra miles per battery charge.

Description of Campylobacter fetus subsp. testudinum subsp. nov., isolated from humans and reptiles

USDA-ARS?s Scientific Manuscript database

A polyphasic study was undertaken to determine the taxonomic position of 13 Campylobacter fetus-like isolates from humans (n=8) and reptiles (n=5). Phenotypic characterization, Genusgenus-specific and sap insertion-PCR initially identified all human isolates as type A Campylobacter fetus. Phylogenet...

Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces.

PubMed

Osawa, Ro; Fujisawa, Tomohiko; Pukall, Rüdiger

2006-07-01

A Gram-positive, rod-shaped, non-endospore-forming bacterium, strain ASB1(T), able to degrade tannin, was isolated from faeces of the Japanese large wood mouse, Apodemus speciosus. Comparative analysis of the 16S rRNA gene sequence revealed that the strain could be assigned as a member of the genus Lactobacillus. The nearest phylogenetic neighbours were determined as Lactobacillus animalis DSM 20602(T) (98.9 % 16S rRNA gene sequence similarity) and Lactobacillus murinus ASF 361 (98.9 %). Subsequent polyphasic analysis, including automated ribotyping and DNA-DNA hybridization experiments, confirmed that the isolate represents a novel species, for which the name Lactobacillus apodemi sp. nov. is proposed. The DNA G+C content of the novel strain is 38.5 mol%. The cell-wall peptidoglycan is of type A4alpha L-lys-D-asp. The type strain is ASB1(T) (=DSM 16634(T)=CIP 108913(T)).

Lactobacillus nantensis sp. nov., isolated from French wheat sourdough.

PubMed

Valcheva, Rosica; Ferchichi, Mounir F; Korakli, Maher; Ivanova, Iskra; Gänzle, Michael G; Vogel, Rudi F; Prévost, Hervé; Onno, Bernard; Dousset, Xavier

2006-03-01

A polyphasic taxonomic study of the bacterial flora isolated from traditional French wheat sourdough, using phenotypic characterization and phylogenetic as well as genetic methods, revealed a consistent group of isolates that could not be assigned to any recognized species. These results were confirmed by randomly amplified polymorphic DNA and amplified fragment length polymorphism fingerprinting analyses. Cells were Gram-positive, homofermentative rods. Comparative 16S rRNA gene sequence analysis of the representative strain LP33T indicated that these strains belong to the genus Lactobacillus and that they formed a branch distinct from their closest relatives Lactobacillus farciminis, Lactobacillus alimentarius, Lactobacillus paralimentarius and Lactobacillus mindensis. DNA-DNA reassociation experiments with the three phylogenetically closest Lactobacillus species confirmed that LP33T (= DSM 16982T = CIP 108546T = TMW 1.1265T) represents the type strain of a novel species, for which the name Lactobacillus nantensis sp. nov. is proposed.

Yeast microbiota associated with spontaneous sourdough fermentations in the production of traditional wheat sourdough breads of the Abruzzo region (Italy).

PubMed

Valmorri, Sara; Tofalo, Rosanna; Settanni, Luca; Corsetti, Aldo; Suzzi, Giovanna

2010-02-01

The aims of this study were to describe the yeast community of 20 sourdoughs collected from central Italy and to characterize the sourdoughs based on chemical properties. A polyphasic approach consisting of traditional culture-based tests (spore-forming and physiological tests) and molecular techniques (PCR-RFLP, RAPD-PCR, PCR-DGGE) and chemical analysis (total acidity, acids, and sugar contents), was utilized to describe the yeast population and to investigate the chemical composition of the doughs. PCR-RFLP analysis identified 85% of the isolates as Saccharomyces cerevisiae, with the other dominant species being Candida milleri (11%), Candida krusei (2.5%), and Torulaspora delbrueckii (1%). RAPD-PCR analysis, performed with primers M13 and LA1, highlighted intraspecific polymorphism among the S. cerevisiae strains. The diversity of the sourdoughs from the Abruzzo region is reflected in the chemical composition, yeast species, and strain polymorphism. Our approach using a combination of phenotypic and genotypic methods identified the yeast species in the 20 sourdough samples and provided a complete overview of the yeast populations found in sourdoughs from the Abruzzo region.

Solibacillus kalamii sp. nov., isolated from a high-efficiency particulate arrestance filter system used in the International Space Station.

PubMed

Checinska Sielaff, Aleksandra; Kumar, Rajendran Mathan; Pal, Deepika; Mayilraj, Shanmugam; Venkateswaran, Kasthuri

2017-04-01

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterial strain, designated ISSFR-015T, was isolated from a high-efficiency particulate arrestance filter in the International Space Station and was characterized by polyphasic taxonomy. A comparative analysis of the 16S rRNA gene sequence (1494 bp) of strain ISSFR-015T showed highest similarity to Solibacillus isronensis B3W22T (98.9 %), followed by Solibacillus silvestris HR3-23T (98.6 %) and Bacillus cecembensis PN5T (96.7 %). DNA-DNA hybridization analysis revealed that the DNA relatedness values of strain ISSFR-015T with other closely related species were in the range of 41-47 % [S. silvestrisMTCC 10789T (47 %), S. isronensis MTCC 7902T (41 %) and B. cecembensis MTCC 9127T (43 %)]. The DNA G+C content of strain ISSFR-015T was 45.4 mol%. The major fatty acids were iso-C15 : 0 (45.2 %) and C17 : 1ω10c (12.1 %). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and one unknown phospholipid. The isoprenoid quinones present in strain ISSFR-015T were MK-7 (86.8 %), MK-6 (11.6 %) and MK-8 (1.0 %). The peptidoglycan type of the cell wall was A4α l-Lys-d-Glu. Based on the phylogenetic analysis, strain ISSFR-015T belongs to the genus Solibacillus. The polyphasic taxonomic data, including low DNA-DNA hybridization values, and the chemotaxonomic analysis confirmed that strain ISSFR-015T represents a novel species, for which the name Solibacillus kalamii sp. nov. is proposed. The type strain for this proposed species is ISSFR-015T (=NRRL B-65388T=DSM 101595T).

Blastococcus colisei sp. nov, isolated from an archaeological amphitheatre.

PubMed

Hezbri, Karima; Nouioui, Imen; Rohde, Manfred; Schumann, Peter; Gtari, Maher; Klenk, Hans-Peter; Montero-Calasanz, Maria Del Carmen; Ghodhbane-Gtari, Faten

2017-03-01

The taxonomic position of an actinobacterial isolate, designated strain BMG 822 T , isolated from limestone from the Amphitheater of El Jem (Coliseum Thysdrus), Tunisia, was established using a polyphasic approach. Strain BMG 822 T was found to grow well at 30 °C and pH 6.5-8.0, and to be coral-coloured, Gram-positive, catalase and oxidase negative. Whole cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, glucose, galactose and ribose. The phospholipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, an unidentified glycophospholipid and six unidentified phospholipids. MK-9(H 4 ) was found to be the predominant menaquinone, followed by MK-9(H 2 ) and MK-9. The major cellular fatty acids were identified as iso-C 16:0 , C 18:1 ω9c, C 17:1 ω8c and iso-H-C 16:1 . The G+C content of the DNA (73.2%) is typical of the genus. High degrees of 16S rRNA gene sequence similarity were found with the type strains of the genus Blastococcus (97.1-98.3%) followed by the type strains of Modestobacter (96.8-97.8%). Based on the above data and the phenotypic differences from the type strains of Blastococcus species, it is proposed that the isolate BMG 822 T (=DSM 46837 T =CECT 8823 T ) should be classified as the type strain of a novel species, Blastococcus colisei sp. nov.

Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch.

PubMed

Liu, Yang; Yao, Su; Lee, Yong-Jae; Cao, Yanhua; Zhai, Lei; Zhang, Xin; Su, Jiaojiao; Ge, Yuanyuan; Kim, Song-Gun; Cheng, Chi

2015-09-01

Two yellow bacterial strains, designated NBD5(T) and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6(T) (96.9% similarity), Sphingomonas polyaromaticivorans B2-7(T) (95.8%), Sphingomonas yantingensis 1007(T) (94.9%), Sphingomonas sanguinis IFO 13937(T) (94.7%), Sphingomonas ginsenosidimutans Gsoil 1429(T) (94.6%), Sphingomonas wittichii RW1(T) (94.6%) and Sphingomonas formosensis CC-Nfb-2(T) (94.5%). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5(T) and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5(T) and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5(T) ( = DSM 29151(T) = KCTC 42183(T) = CICC 10879(T)).

Pseudomonas gallaeciensis sp. nov., isolated from crude-oil-contaminated intertidal sand samples after the Prestige oil spill.

PubMed

Mulet, Magdalena; Sánchez, David; Rodríguez, Ana C; Nogales, Balbina; Bosch, Rafael; Busquets, Antonio; Gomila, Margarita; Lalucat, Jorge; García-Valdés, Elena

2018-04-11

Strains V113 T , V92 and V120 have been isolated from sand samples taken at the Atlantic intertidal shore in Galicia, Spain, after the Prestige oil spill. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus, but they were distinct from any known Pseudomonas species. They were extensively characterized by a polyphasic taxonomic approach and phylogenetic data that confirmed that these strains belonged to the Pseudomonas pertucinogena group. Phylogenetic analysis of 16S rRNA, gyrB and rpoD gene sequences showed that the three strains were 99% similar and were closely related to members of the P. pertucinogena group, with less than 94% similarity to strains of established species; Pseudomonas pachastrellae was the closest relative. The Average Nucleotide Index based on blast values was 89.0% between V113 T and the P. pachastrellae type strain, below the accepted species level (95%). The predominant cellular fatty acid contents and whole cell protein profiles determined by MALDI-TOF mass spectrometry also differentiated the studied strains from known Pseudomonas species. We therefore conclude that strains V113 T , V92 and V120 represent a novel species of Pseudomonas, for which the name Pseudomonas gallaeciensis is proposed; the type strain is V113 T (=CCUG 67583 T =LMG 29038 T ). Copyright © 2018 Elsevier GmbH. All rights reserved.

Streptomyces verrucosisporus sp. nov., isolated from marine sediments.

PubMed

Phongsopitanun, Wongsakorn; Kudo, Takuji; Ohkuma, Moriya; Pittayakhajonwut, Pattama; Suwanborirux, Khanit; Tanasupawat, Somboon

2016-09-01

Five actinomycete isolates, CPB1-1T, CPB2-10, BM1-4, CPB3-1 and CPB1-18, belonging to the genus Streptomyces were isolated from marine sediments collected from Chumphon Province, Thailand. They produced open loops of warty spore chains on aerial mycelia. ll-Diaminopimelic acid, glucose and ribose were found in their whole-cell hydrolysates. Polar lipids found were diphosphatidylglycerol, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. Menaquinones were MK-9(H6), MK-9(H8), MK-10(H6) and MK-10(H8). Major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The taxonomic position of the strains was described using a polyphasic approach. blastn analysis of the 16S rRNA gene sequence revealed that these five strains exhibited the highest similarities with 'Streptomyces mangrovicola' GY1 (99.0 %), Streptomyces fenghuangensisGIMN4.003T (98.6 %), Streptomyces barkulensisRC 1831T (98.5 %) and Streptomyces radiopugnans R97T (98.3 %). However, their phenotypic characteristics and 16S rRNA gene sequences as well as DNA-DNA relatedness differentiated these five strains from the other species of the genus Streptomyces. Here, we propose the novel actinomycetes all being representatives of the same novel species, Streptomyces verrucosisporus, with type strain CPB1-1T (=JCM 18519T=PCU 343T=TISTR 2344T).

Chryseobacterium chaponense sp. nov., isolated from farmed Atlantic salmon (Salmo salar).

PubMed

Kämpfer, Peter; Fallschissel, Kerstin; Avendaño-Herrera, Ruben

2011-03-01

Two bacterial strains, designated Sa 1147-06(T) and Sa 1143-06, were isolated from Atlantic salmon (Salmo salar) farmed in Lake Chapo, Chile, and were studied using a polyphasic approach. Both isolates were very similar; cells were rod-shaped, formed yellow-pigmented colonies and were Gram-reaction-negative. Based on 16S rRNA gene sequence analysis, strains Sa 1147-06(T) and Sa 1143-06 shared 100  % sequence similarity and showed 98.9 and 97.5 % sequence similarity to Chryseobacterium jeonii AT1047(T) and Chryseobacterium antarcticum AT1013(T), respectively. Sequence similarities to all other members of the genus Chryseobacterium were below 97.3  %. The major fatty acids of strain Sa 1147-06(T) were iso-C₁₃:₀, iso-C₁₅:₀, anteiso-C₁₅:₀ and iso-C₁₇:₁ω9c, with iso-C₁₅:₀ 3-OH, iso-C₁₆:₀ 3-OH and iso-C₁₇:₀ 3-OH constituting the major hydroxylated fatty acids. DNA-DNA hybridizations with C. jeonii JMSNU 14049(T) and C. antarcticum JMNSU 14040(T) gave relatedness values of 20.7  % (reciprocal 15.1  %) and 15.7 % (reciprocal 25.7  %), respectively. Together, the DNA-DNA hybridization results and differentiating biochemical properties showed that strains Sa 1147-06(T) and Sa 1143-06 represent a novel species, for which the name Chryseobacterium chaponense sp. nov. is proposed. The type strain is Sa 1147-06(T) (=DSM 23145(T) =CCM 7737(T)).

Micrococcus cohnii sp. nov., isolated from the air in a medical practice.

PubMed

Rieser, Gernot; Scherer, Siegfried; Wenning, Mareike

2013-01-01

Three Gram-reaction-positive bacteria, isolated from the air in a medical practice (strains WS4601(T), WS4602) or a pharmaceutical clean room (strain WS4599), were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA and recA gene sequences of the three novel strains showed that they formed a distinct lineage within the genus Micrococcus, sharing 16S rRNA gene sequence similarities of 96.1-98.0 % with other species of this genus. Chemotaxonomic features also supported the classification of the three novel strains within the genus Micrococcus. The major cellular fatty acids of strain WS4601(T) were anteiso-C(15 : 0) and iso-C(15 : 0), the cell-wall peptidoglycan was of type A3α (L-Lys-L-Ala), and the predominant respiratory quinones were MK-7(H(2)) and MK-8(H(2)). The polar lipid profile contained diphosphatidylglycerol and phosphatidylglycerol, but no phosphatidylinositol. The G+C content of the genomic DNA was 70.4 mol%. Numerous physiological properties were found that clearly distinguished strains WS4599, WS4601(T) and WS4602 from established members of the genus Micrococcus. Based on the phenotypic and phylogenetic data, strains WS4599, WS4601(T) and WS4602 are considered to represent three different strains of a novel species of the genus Micrococcus, for which the name Micrococcus cohnii sp. nov. is proposed. The type strain is WS4601(T) (=DSM 23974(T)=LMG 26183(T)).

Characteristics of Rare or Recently Described Corynebacterium Species Recovered from Human Clinical Material in Canada

PubMed Central

Bernard, K. A.; Munro, C.; Wiebe, D.; Ongsansoy, E.

2002-01-01

Nineteen new Corynebacterium species or taxa described since 1995 have been associated with human disease. We report the characteristics of 72 strains identified as or most closely resembling 14 of these newer, medically relevant Corynebacterium species or taxa, as well as describe in brief an isolate of Corynebacterium bovis, a rare pathogen for humans. The bacteria studied in this report were nearly all derived from human clinical specimens and were identified by a polyphasic approach. Most were characterized by nearly full 16S rRNA gene sequence analysis. Some isolates were recovered from previously unreported sources and exhibited unusual phenotypes or represented the first isolates found outside Europe. Products of fermentation, with emphasis on the presence or absence of propionic acid, were also studied in order to provide an additional characteristic with which to differentiate among phenotypically similar species. PMID:12409436

Penicillium gravinicasei, a new species isolated from cave cheese in Apulia, Italy.

PubMed

Anelli, Pamela; Peterson, Steve W; Haidukowski, Miriam; Logrieco, Antonio F; Moretti, Antonio; Epifani, Filomena; Susca, Antonia

2018-06-08

Several species of the genus Penicillium were isolated during a survey of the mycobiota of Apulian cave cheeses ripened in a cave in Gravina di Puglia, Italy. A novel species, Penicillium gravinicasei, is described in Penicillium section Cinnamopurpurea. Its taxonomic novelty was determined using a polyphasic approach, combining phenotypic, molecular (β-tubulin, calmodulin, ITS and DNA dependent RNA polymerase) DNA sequences and mycotoxin production data. Phylogenetic analyses of the RPB2 data showed that isolates of the novel species form a clade most closely related to Penicillium cinnamopurpureum and P. parvulum with high bootstrap support. The fungus did not produce ochratoxin A, citrinin, patulin, sterigmatocystin or aflatoxin B 1 on standard agar media. The novel species had a high growth rate on agar media supplemented with 5% NaCl, and could be distinguished from other Penicillium section Cinnamopurpurea species by phenotypic and molecular characteristics. Copyright © 2018 Elsevier B.V. All rights reserved.

Stenotrophomonas sp. RZS 7, a novel PHB degrader isolated from plastic contaminated soil in Shahada, Maharashtra, Western India.

PubMed

Wani, S J; Shaikh, S S; Tabassum, B; Thakur, R; Gulati, A; Sayyed, R Z

2016-12-01

This paper reports an isolation and identification of novel poly-β-hydroxybutyrate (PHB) degrading bacterium Stenotrophomonas sp. RZS 7 and studies on its extracellular PHB degrading depolymerase enzyme. The bacterium isolated from soil samples of plastic contaminated sites of municipal area in Shahada, Maharashtra, Western India. It was identified as Stenotrophomonas sp. RZS 7 based on polyphasic approach. The bacterium grew well in minimal salt medium (MSM) and produced a zone (4.2 mm) of PHB hydrolysis on MSM containing PHB as the only source of nutrient. An optimum yield of enzyme was obtained on the fifth day of incubation at 37 °C and at pH 6.0. Further increase in enzyme production was recorded with Ca 2+ ions, while other metal ions like Fe 2+ (1 mM) and chemical viz. mercaptoethanol severally affected the production of enzyme.

Autonomous Non-Linear Classification of LPI Radar Signal Modulations

DTIC Science & Technology

2007-09-01

Wigner - Ville distribution ( WVD ), the Choi-Williams distribution (CWD) and a Quadrature...accomplished using the images from the Wigner - Ville distribution and the Choi-Williams distribution for polyphase modulations. For the WVD images, radon...this work. Four detection techniques including the Wigner - Ville distribution ( WVD ), the Choi-Williams distribution (CWD), Quadrature Mirror

Campylobacter pinnipediorum sp. nov., isolated from pinnipeds, comprising Campylobacter pinnipediorum subsp. pinnipediorum subsp. nov. and Campylobacter pinnipediorum subsp. caledonicus subsp. nov.

USDA-ARS?s Scientific Manuscript database

During independent diagnostic screenings of otariid seals in California (US) and phocid seals in Scotland (UK), Campylobacter-like isolates, which differed from the established Campylobacter taxa, were cultured from abscesses and internal organs of different seal species. A polyphasic study was unde...

Current responsive devices for synchronous generators

DOEpatents

Karlicek, Robert F.

1983-01-01

A device for detecting current imbalance between phases of a polyphase alternating current generator. A detector responds to the maximum peak current in the generator, and detecting means generates an output for each phase proportional to the peak current of each phase. Comparing means generates an output when the maximum peak current exceeds the phase peak current.

Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees

USDA-ARS?s Scientific Manuscript database

A polyphasic study was carried out to establish the taxonomic status of an Atacama Desert isolate, Streptomyces strain C34T, which synthesises novel antibiotics, the chaxalactins and chaxamycins. The organism was shown to have chemotaxonomic, cultural, and morphological properties consistent with it...

Simplified High-Power Inverter

NASA Technical Reports Server (NTRS)

Edwards, D. B.; Rippel, W. E.

1984-01-01

Solid-state inverter simplified by use of single gate-turnoff device (GTO) to commutate multiple silicon controlled rectifiers (SCR's). By eliminating conventional commutation circuitry, GTO reduces cost, size and weight. GTO commutation applicable to inverters of greater than 1-kilowatt capacity. Applications include emergency power, load leveling, drives for traction and stationary polyphase motors, and photovoltaic-power conditioning.

Polyphasic taxonomy of the genus Talaromyces

PubMed Central

Yilmaz, N.; Visagie, C.M.; Houbraken, J.; Frisvad, J.C.; Samson, R.A.

2014-01-01

The genus Talaromyces was described by Benjamin in 1955 as a sexual state of Penicillium that produces soft walled ascomata covered with interwoven hyphae. Phylogenetic information revealed that Penicillium subgenus Biverticillium and Talaromyces form a monophyletic clade distinct from the other Penicillium subgenera. Subsequently, in combination with the recent adoption of the one fungus one name concept, Penicillium subgenus Biverticillium was transferred to Talaromyces. At the time, the new combinations were made based only on phylogenetic information. As such, the aim of this study was to provide a monograph on Talaromyces applying a polyphasic species concept, including morphological, molecular and physiological characters. Based on an ITS, BenA and RPB2 multigene phylogeny, we propose a new sectional classification for the genus, placing the 88 accepted species into seven sections, named sections Bacillispori, Helici, Islandici, Purpurei, Subinflati, Talaromyces and Trachyspermi. We provide morphological descriptions for each of these species, as well as notes on their identification using morphology and DNA sequences. For molecular identification, BenA is proposed as a secondary molecular marker to the accepted ITS barcode for fungi. PMID:25492983

Myodegeneration with fibrosis and regeneration in the pectoralis major muscle of broilers.

PubMed

Sihvo, H-K; Immonen, K; Puolanne, E

2014-05-01

A myopathy affecting the pectoralis major muscle of the commercial broiler has emerged creating remarkable economic losses as well as a potential welfare problem of the birds. We here describe the macroscopic and histologic lesions of this myopathy within 10 pectoralis major muscles of 5- to 6-week-old broilers in Finland. Following macroscopic evaluation and palpation of the muscles, a tissue sample of each was fixed in formalin, processed for histology, and histologically evaluated. The muscles that were macroscopically hard, outbulging, pale, and often accompanied with white striping histologically exhibited moderate to severe polyphasic myodegeneration with regeneration as well as a variable amount of interstitial connective tissue accumulation or fibrosis. All affected cases also exhibited perivenular lymphocyte accumulation. The etiology of this myodegenerative lesion remains yet open. Polyphasic myodegeneration is associated with several previously known etiologies, but palpatory hardness focusing on the pectoralis major, together with perivenular lymphocytes, has not been described in relation to them. The results of this study provide the pathological basis for further studies concerning the etiology of the currently described myopathy.

Porphyry copper deposits distribution along the western Tethyan and Andean subductions: insights from a paleogeographic approach

NASA Astrophysics Data System (ADS)

Bertrand, G.

2012-12-01

The genesis of many types of mineral deposits is closely linked to tectonic and petrographic conditions resulting from specific geodynamic contexts. Porphyry deposits, for instance, are associated to calc-alkaline magmatism of subduction zones. In order to better understand the relationships between ore deposit distribution and their tectonic context, and help identifying geodynamic-related criteria of favorability that would, in turn, help mineral exploration, we propose a paleogeographic approach. Paleogeographic reconstructions, based on global or regional plate tectonic models, are crucial tools to assess tectonic and kinematic contexts of the past. We use this approach to study the distribution of porphyry copper deposits along the western Tethyan and Andean subductions since Lower Cretaceous and Paleocene, respectively. For both convergent contexts, databases of porphyry copper deposits, including, among other data, their age and location, were compiled. Spatial and temporal distribution of the deposits is not random and show that they were emplaced in distinct clusters. Five clusters are identified along the western Tethyan suture, from Lower Cretaceous to Pleistocene, and at least three along the Andes, from Paleocene to Miocene. Two clusters in the Aegean-Balkan-Carpathian area, that were emplaced in Upper Cretaceous and Oligo-Miocene, and two others in the Andes, that were emplaced in late Eocene and Miocene, are studied in details and correlated with the past kinematics of the Africa-Eurasia and Nazca-South America plate convergences, respectively. All these clusters are associated with a similar polyphased kinematic context that is closely related to the dynamics of the subductions. This context is characterized by 1) a relatively fast convergence rate, shortly followed by 2) a drastic decrease of this rate. To explain these results, we propose a polyphased genetic model for porphyry copper deposits with 1) a first stage of rapid subduction rate, favoring high melt production in the mantle wedge, by dehydration of the subducted oceanic crust, and increased influx of mafic magmas in the MASH (Melting, Assimilation, Storage, Homogenization) zone, and 2) a subsequent significant decrease in subduction rate, favoring extensional regime within the upper plate and easing upward migration of fertile magmas to the upper crust. This second effect seems to be confirmed in the Aegean-Balkan-Carpathian area where the two clusters are spatially and temporally correlated with known extensional regimes. Although preliminary, these results highlight the control of the geodynamic context, and especially the subduction kinematics, on the spatial and temporal distribution of porphyry copper deposits. This study also confirms that the paleogeographic approach is a promising tool that could help identifying geodynamic and tectonic criteria favoring the genesis of various ore deposit types. Correlatively, ore deposits may be considered, in future studies, as possible markers of past geodynamic contexts.

Evolution of the Oxidation State of the Earth's Mantle: Challenges of High Pressure Quenching

NASA Technical Reports Server (NTRS)

Danielson, L. R.; Righter, K.; Keller, L.; Christoffersen, R.; Rahman, Z.

2015-01-01

The oxidation state of the Earth's mantle during formation remains an unresolved question, whether it was constant throughout planetary accretion, transitioned from reduced to oxidized, or from oxidized to reduced. We investigate the stability of Fe3+ at depth, in order to constrain processes (water, late accretion, dissociation of FeO) which may reduce or oxidize the Earth's mantle. Experiments of more mafic compositions and at higher pressures commonly form a polyphase quench intergrowth composed primarily of pyroxenes, with interstitial glass which hosts nearly all of the more volatile minor elements. In our previous experiments on shergottite compositions, variable fO2, T, and P is less than 4 GPa, Fe3+/TotFe decreased slightly with increasing P, similar to terrestrial basalt. For oxidizing experiments less than 7GPa, Fe3+/TotFe decreased as well, but it's unclear from previous modelling whether the deeper mantle could retain significant Fe3+. Our current experiments expand our pressure range deeper into the Earth's mantle and focus on compositions and conditions relevant to the early Earth. Experiments with Knippa basalt as the starting composition were conducted at 1-8 GPa and 1800 C, using a molybdenum capsule to set the fO2 near IW, by buffering with Mo-MoO3. TEM and EELS analyses revealed the run products from 7-8 GPa quenched to polycrystalline phases, with the major phase pyroxene containing approximately equal Fe3+/2+. A number of different approaches have been employed to produce glassy samples that can be measured by EELS and XANES. A more intermediate andesite was used in one experiment, and decompression during quenching was attempted after, but both resulted in a finer grained polyphase texture. Experiments are currently underway to test different capsule materials may affect quench texture. A preliminary experiment using liquid nitrogen to greatly enhance the rate of cooling of the assembly has also been attempted and this technique will be refined in further experiments.

Burkholderia novacaledonica sp. nov. and B. ultramafica sp. nov. isolated from roots of Costularia spp. pioneer plants of ultramafic soils in New Caledonia.

PubMed

Guentas, Linda; Gensous, Simon; Cavaloc, Yvon; Ducousso, Marc; Amir, Hamid; De Georges de Ledenon, Benjamin; Moulin, Lionel; Jourand, Philippe

2016-05-01

The taxonomic status of eleven rhizospheric bacterial strains belonging to the genus Burkholderia and isolated from roots of Costularia (Cyperaceae), tropical herbaceous pioneer plants growing on ultramafic soils in New Caledonia, was investigated using a polyphasic taxonomic approach. The genetic analyses (16S rRNA genes, gyrB, recA, nreB and cnr) confirmed that all strains are Burkholderia and cluster into two separated groups. The DNA hybridization results showed low relatedness values to the closest relatives Burkholderia species. The phenotypic analyses confirmed that the two groups of strains could be differentiated from each other and from other known Burkholderia species. This polyphasic study revealed that these two groups of strains represent each a novel species of Burkholderia, for which the names Burkholderia novacaledonica sp. nov. (type strain STM10272(T)=LMG28615(T)=CIP110887(T)) and B. ultramafica sp. nov. (type strain STM10279(T)=LMG28614(T)=CIP110886(T)) are proposed, respectively. These strains of Burkholderia presented specific ecological traits such as the tolerance to the extreme edaphic constraints of ultramafic soils: they grew at pH between 4 and 8 and tolerate the strong unbalanced Ca/Mg ratio (1/19) and the high concentrations of heavy metals i.e. Co, Cr, Mn and Ni. Noteworthy B. ultramafica tolerated nickel until 10mM and B. novacaledonica up to 5mM. The presence of the nickel (nreB) and cobalt/nickel (cnr) resistance determinants encoding for protein involved in metal tolerance was found in all strains of both groups. Moreover, most of the strains were able to produce plant growth promoting molecules (ACC, IAA, NH3 and siderophores). Such ecological traits suggest that these new species of Burkholderia might be environmentally adaptable plant-associated bacteria and beneficial to plants. Copyright © 2016 Elsevier GmbH. All rights reserved.

Chemically anomalous, pre-accretionally irradiated grains in interplanetary dust -- interstellar grains?. [Abstract only

NASA Technical Reports Server (NTRS)

Bradley, J. P.

1994-01-01

Ultrafine-grained matrix is a unique and fundamental building block of chondritic porous (CP) interplanetary dust particles. Most IDPs so far determined to be of cometary origin belong to the CP class. The matrix in CP IDPs is not homogeneous but rather a loose mixture of discrete single crystals (e.g., olivine, pyroxene, Fe sulfides) and polyphase grains. The petrographic diversity observed among the polyphase grains suggest that they were formed under variable physiochemical conditions. One particular class of polyphase grains are a dominant component in cometary IDPs. Although their occurrence is well documented, the terminology used to describe them is confused. They have been called many names. Here they are simply called GEMS (Glass with Embedded Metal and Sulfides). The bulk compositions of GEMS are within a factor of 3 chondritic (solar) for all major elements except C. Quantitative thin-film X-ray (EDS) analyses have shown that GEMS are systematically depleted in Mg and Si, enriched in S, Fe, and Ni, and stoichiometrically enriched in O. Electron energy-loss spectroscopy (EELS) suggests that the excess O is present as hydroxyl (-OH) groups. These same chemical 'anomalies' were observed in solar-wind-irradiated amorphous rims on the surfaces of IDPs, suggesting that the compositions of GEMS reflect prior exposure to ionizing radiation. In order to test this hypothesis, a sample of Allende (CV3) matrix was exposed to proton flux. Radiation-damaged amorphous rims on olivine and pyroxene crystals in the Allende sample were found to be depleted in Mg and Ca, enriched in S, Fe, and Ni, and stoichiometrically enriched in O. Thus, the compositions of GEMS are indeed consistent with exposure to ionizing radiation. This study suggests that chemical as well as isotopic anomalies may be used to identify presolar interstellar grains in primitive meteoritic materials.

Reclassification of "Dactylosporangium variesporum" as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev.

USDA-ARS?s Scientific Manuscript database

In the course of a polyphasic study it was observed that “Dactylosporangium variesporum” NRRL B-16296 is misclassified as a member of the genus Dactylosporangium becasuse it exhibits properties consistent with its assignment to the genus Saccharothrix. Phylogenetic analyses based on 16S rRNA gene se...

10 CFR 431.444 - Test procedures for the measurement of energy efficiency.

Code of Federal Regulations, 2012 CFR

2012-01-01

... the following test methods: (1) Single-phase small electric motors: either IEEE Std 114, (incorporated...) Polyphase small electric motors less than or equal to 1 horsepower (0.746 kW): IEEE Std 112 (incorporated by... (0.746 kW): IEEE Std 112 (incorporated by reference, see § 431.443), Test Method B. ...

Current responsive devices for synchronous generators

DOEpatents

Karlicek, R.F.

1983-09-27

A device for detecting current imbalance between phases of a polyphase alternating current generator. A detector responds to the maximum peak current in the generator, and detecting means generates an output for each phase proportional to the peak current of each phase. Comparing means generates an output when the maximum peak current exceeds the phase peak current. 11 figs.

Polyphasic characterization of Trichocoleus desertorum sp. nov. (Pseudanabaenales, Cyanobacteria) from desert soils and phylogenetic placement of the genus Trichocoleus

Treesearch

Radka Muhlsteinova; Jeffrey R. Johansen; Nicole Pietrasiak; Michael P. Martin; Karina Osorio-Santos; Steven D. Warren

2014-01-01

Little is known about the taxonomic diversity of cyanobacteria in deserts, despite their important ecological roles in these ecosystems. In this study, cyanobacterial strains from the Atacama, Colorado, and Mojave Deserts were isolated and characterized using molecular, morphological, and ecological information. Phylogenetic placement of these strains was revealed...

A Study of Interior Wiring, Color Coding, and Switching Principles by Simulation and Practice.

ERIC Educational Resources Information Center

McCormick, B. G.; McCormick, Robert S.

After a preliminary introduction and a chapter on wiring and electricity safety procedures, this study text proceeds to offer a general coverage of single and polyphase alternating current electrical systems used to power factories, farms, small businesses, and homes. Electrical power, from its generation to its application, is discussed, with the…

Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957

USDA-ARS?s Scientific Manuscript database

A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9T, was found to have chemotaxonomic, cultural, and morphological properties that...

Streptomyces asenjonii sp. nov., isolated from arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958

USDA-ARS?s Scientific Manuscript database

A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from arid Atacama Desert soils. Analysis of the 16S rRNA gene sequences of the isolates showed that they formed a well-defined lineage that was loosely associated with the type strains of several Str...

Detection and Jamming Low Probability of Intercept (LPI) Radars

DTIC Science & Technology

2006-09-01

69 The resulting WVD is, therefore ( ) 2 1 ’ 0 , 2 ( ) . j knN N l n W l k f n e π− − = = ∑ (3.11) Equation (3.11) is the final...of FMCW and P-4 polyphase LPI waveforms. 2002 IEEE International Conference on Acoustics, Speech , and Signal Processing.Proceedings (Cat.no.02CH37334

Polyphase alloys as rechargeable electrodes in advanced battery systems

NASA Technical Reports Server (NTRS)

Huggins, Robert A.

1987-01-01

The rechargeability of electrochemical cells is often limited by negative electrode problems. These may include loss of capacity, increased impedance, macroscopic shape change, dendrite growth, or a tendency for filamentary or whisker growth. In principle, these problems can be reduced or eliminated by the use of alloys that undergo either displacement or insertion reactions at reactant species activities less than unity, rather than pure elements. The fundamental reasons for some of these problems with elemental electrodes, as well as the basic principles involved in the different behavior of alloys, are briefly discussed. More information is now available concerning the thermodynamic and kinetic properties of a number of alloys of potential interest for use as electrodes in elevated temperature lithium battery systems. Recent results have extended these results down to ambient temperatures, indicating that some such materials may be of interest for use with new low temperature molten salt electrolytes, or with organic solvent electrolytes. The all solid mixed conductor matrix concept is also reviewed.

Isolation of the Paenibacillus phoenicis, a Spore-Forming Bacterium

NASA Technical Reports Server (NTRS)

Benardini, James N.; Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Osman, Shariff; Satomi, Masataka

2010-01-01

A microorganism was isolated from the surfaces of the cleanroom facility in which the Phoenix lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Paenibacillus and represents a novel species. Bacillus spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Spores of Bacillus species are of particular concern to planetary protection due to the extreme resistance of some members of the genus to space environmental conditions such as UV and gamma radiation, vacuum, oxidation, and temperature fluctuation. These resistive spore phenotypes have enhanced potential for transfer, and subsequent proliferation, of terrestrial microbes on another solar body. Due to decreased nutrient conditions within spacecraft assembly facility clean rooms, the vegetative cells of Bacillus species and other spore-forming Paenibacillus species are induced to sporulate, thereby enhancing their survivability of bioreduction

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp.

PubMed Central

On, Stephen L. W.; Miller, William G.; Houf, Kurt; Fox, James G.; Vandamme, Peter

2017-01-01

Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended. PMID:29034857

Reclassification of Flexibacter tractuosus NBRC 15981T as Marivirga harenae sp. nov. in the family Flammeovirgaceae.

PubMed

Muramatsu, Yuki; Kamakura, Yuki; Takahashi, Mai; Nakagawa, Yasuyoshi

2017-06-01

Flexibacter tractuosa [Lewin, 1969] was reclassified as Marivirga tractuosa. Flexibacter tractuosus NBRC 15981T was reclassified herein by using a polyphasic taxonomic approach. Cells of the strain were strictly aerobic, Gram-stain-negative, slender rods, which were motile by gliding. The major respiratory quinone was menaquinone-7 and the predominant (>5 %) cellular fatty acids were iso-C15 : 0, iso-G-C15 : 1, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipid pattern indicated the presence of a phosphatidylethanolamine, several unidentified aminolipids, glycolipids and five unidentified polar lipids. The G+C content of the genomic DNA was 35.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NBRC 15981T clustered with members of the genus Marivirga in the family Flammeovirgaceae of the phylum Bacteroidetes. Levels of DNA-DNA relatedness were less than 16 % between strain NBRC 15981T and the two closely related species, Marivirga sericea NBRC 15983T and Marivirga tractuosa NBRC 15989T. Strain NBRC 15981T could be differentiated from these type strains in the genus Marivirga based on the polar lipid pattern and the activity of α-chymotrypsin, as well as by α-glucosidase and β-glucosidase activity. On the basis of these results, NBRC 15981T is proposed as representing a novel species of the genus Marivirga, named Marivirga harenae sp. nov. The type strain is JK11T (=NBRC 15981T=NCIMB 1429T).

Cellulosimicrobium marinum sp. nov., an actinobacterium isolated from sea sediment.

PubMed

Hamada, Moriyuki; Shibata, Chiyo; Tamura, Tomohiko; Nurkanto, Arif; Ratnakomala, Shanti; Lisdiyanti, Puspita; Suzuki, Ken-Ichiro

2016-07-01

A novel Gram stain positive actinobacterium, designated RS-7-4(T), was isolated from a sea sediment sample collected in Indonesia, and its taxonomic position was investigated using a polyphasic approach. Strain RS-7-4(T) was observed to form vegetative hyphae in the early phase of growth, but the hyphae eventually fragmented into short rods to coccoid cells. Growth occurred at 15-37 °C, pH 6.0-11.0 and in the presence of 0-7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain RS-7-4(T) was closely related to the members of the genus Cellulosimicrobium, with a similarity range of 98.08-99.10 %. The peptidoglycan type of strain RS-7-4(T) was found to be A4α L-Lys-L-Thr-D-Asp. The predominant menaquinone was MK-9(H4), and the major fatty acids were anteiso-C15:0, iso-C15:0 and anteiso-C17:0. The DNA G+C content was 75.6 mol%. These chemotaxonomic features corresponded to those of the genus Cellulosimicrobium. Meanwhile, the results of DNA-DNA hybridization, and physiological and biochemical tests revealed that strain RS-7-4(T) was different from the recognized species of the genus Cellulosimicrobium. Therefore, strain RS-7-4(T) represents a novel species of the genus Cellulosimicrobium, for which the name Cellulosimicrobium marinum sp. nov. is proposed. The type strain is RS-7-4(T) (=NBRC 110994(T) =InaCC A726(T)).

Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area.

PubMed

Ming, Hong; Yin, Yi-Rui; Li, Shuai; Nie, Guo-Xing; Yu, Tian-Tian; Zhou, En-Min; Liu, Lan; Dong, Lei; Li, Wen-Jun

2014-02-01

Two thermophilic bacterial strains, designated YIM 77925(T) and YIM 77777, were isolated from two hot springs, one in the Hydrothermal Explosion (Shuirebaozhaqu) area and Frog Mouth Spring in Tengchong county, Yunnan province, south-western China. The taxonomic positions of the two isolates were investigated by a polyphasic approach. Cells of the two strains were Gram-stain-negative, aerobic and rod-shaped. They were able to grow at 50-70 °C, pH 6.0-8.0 and with a NaCl tolerance up to 0.5% (w/v). Colonies are circular, convex, non-transparent and produce yellow pigment. Phylogenetic analyses based on 16S rRNA gene sequences comparison clearly demonstrated that strains YIM 77925(T) and YIM 77777 represent members of the genus Thermus, and they also detected low-level similarities of 16S rRNA gene sequences (below 97%) compared with all other species in this genus. Their predominant menaquinone was MK-8. The genomic DNA G+C contents of strains YIM 77925(T) and YIM 77777 were 65.6 mol% and 67.2 mol%, respectively. Based on the results of physiological and biochemical tests and phylogenetic analyses, strains YIM 77925(T) and YIM 77777 could not be classified as representing any species of the genus Thermus with a validly published name. Thus the two strains are considered to represent a novel species of the genus Thermus, for which the name Thermus caliditerrae sp. nov. is proposed. The type strain is YIM 77925(T) ( = DSM 25901(T) = CCTCC 2012061(T)).

Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch.

PubMed

Liu, Yang; Zhai, Lei; Yao, Su; Cao, Yanhua; Cao, Yu; Zhang, Xin; Su, Jiaojiao; Ge, Yuanyuan; Zhao, Ran; Cheng, Chi

2015-11-01

A Gram-stain-positive bacterial strain, designated as NR2T, isolated from noni (Morinda citrifolia L.) branch was investigated using a polyphasic taxonomic approach. The cells were small coccoid to ovoid, non-spore-forming and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a representative of a member of the genus Brachybacterium, to which the most closely related neighbours were Brachybacterium squillarum M-6-3T (97.90 % similarity), Brachybacterium faecium DSM 4810T (97.50 %), Brachybacterium sacelli LMG 20345T (97.41 %), Brachybacterium phenoliresistens phenol-AT (97.36 %), Brachybacterium nesterenkovii DSM 9573T (97.36 %) and Brachybacterium rhamnosum LMG 19848T (97.32 %). The polar lipid profile of strain NR2T consisted of diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and unknown glycolipids. The predominant respiratory quinone was MK-8, with MK-9 and MK-7 as minor components. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Strain NR2T was clearly distinguishable from the type strains of related species on the basis of phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis and a range of physiological and comparison of biochemical characteristics. It is evident from the genotypic and phenotypic data that strain NR2T represents a novel species of the genus Brachybacterium, for which the name Brachybacterium hainanense sp. nov. is proposed. The type strain is NR2T ( = DSM 29535T = CICC 10874T).

Emticicia oligotrophica gen. nov., sp. nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes.

PubMed

Saha, P; Chakrabarti, T

2006-05-01

An aquatic bacterium, strain GPTSA100-15T, was isolated on nutritionally poor medium TSBA100 (tryptic soy broth diluted 100 times and solidified with 1.5 % agarose) and characterized using a polyphasic approach. The isolate was unable to grow on commonly used nutritionally rich media such as tryptic soy agar, nutrient agar and Luria-Bertani agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was affiliated with the family 'Flexibacteraceae' in the phylum Bacteroidetes. Phylogenetically, it showed closest similarity (94.0 %) with an uncultured bacterial clone, HP1A92, detected in a sludge microbial community. Among the culturable bacteria, the isolate had highest 16S rRNA gene sequence similarity with Leadbetterella byssophila 4M15T (87.8 %). Sequence similarities with other members of the phylum Bacteroidetes were less than 85 %. The fatty acid profile of the isolate grown on TSBA100 indicated that the major fatty acid was iso-C15:0, which is also present in many members of the family 'Flexibacteraceae'. Cells of strain GPTSA100-15T are Gram-negative, strictly aerobic rods. The DNA G+C content of the isolate is 36.9 mol%. Results of phenotypic, chemotaxonomic and phylogenetic analyses clearly indicate that strain GPTSA100-15T represents a new genus within the family 'Flexibacteraceae'; the name Emticicia gen. nov. is proposed for the genus, with Emticicia oligotrophica sp. nov. as the type species. The type strain of Emticicia oligotrophica is GPTSA100-15T (=MTCC 6937T=DSM 17448T).

Aquimonas voraii gen. nov., sp. nov., a novel gammaproteobacterium isolated from a warm spring of Assam, India.

PubMed

Saha, P; Krishnamurthi, S; Mayilraj, S; Prasad, G S; Bora, T C; Chakrabarti, T

2005-07-01

A bacterial strain designated GPTSA 20(T), which was isolated from a warm spring in Assam, India, was characterized by using a polyphasic approach. The cells were Gram-negative, aerobic rods, which could not utilize or produce acid from most of the carbohydrates tested. The predominant fatty acids were C(15:0) iso (25.04%), C(17:1) iso omega9c (19.28%), C(16:0) iso (17.73%) and C(11:0) iso 3-OH (9.34%). The G+C content was 75 mol%. From 16S rRNA gene sequence analysis (1433 nucleotides, continuous stretch), it was confirmed that strain GPTSA 20(T) belonged to the class 'Gammaproteobacteria'. The closest 16S rRNA gene sequence similarity found (98.2%) was with an uncultured bacterium clone, NB-03 (accession no. AB117707), from an autotrophic nitrifying biofilm. Among culturable bacteria, the closest sequence similarities were with Fulvimonas soli (93.0%), Silanimonas lenta (92.8%), Thermomonas hydrothermalis (92.4%), Frateuria aurantia (91.9%), Rhodanobacter lindaniclasticus (91.9%), Thermomonas haemolytica (91.9%) and Pseudoxanthomonas taiwanensis (91.8%); similarities of less than 91.8% were obtained with other members of the class 'Gammaproteobacteria'. From the biochemical, physiological, chemotaxonomic and phylogenetic analysis, it was clear that strain GPTSA 20(T) was quite different from members of known genera of the class 'Gammaproteobacteria'. Therefore, it is proposed that strain GPTSA 20(T) represents a novel species within a new genus, with the name Aquimonas voraii gen. nov., sp. nov. The type strain is GPTSA 20(T) (=MTCC 6713(T)=JCM 12896(T)).

Spirosoma flavum sp. nov., isolated from Arctic tundra soil.

PubMed

Zou, Rui; Zhang, Yumin; Zhou, Xueyin; Wang, Yang; Peng, Fang

2017-12-01

A yellow-pigmented strain, designated Y4AR-5 T , was characterized by using a polyphasic approach. The strain was isolated from a tundra soil from near Longyearbyen, Svalbard Islands, Norway. The cells were Gram-stain-negative, aerobic, rod-shaped and non-motile. Growth occurred at 4-28 °C (optimum 20 °C) and pH 6.0-9.0 (optimum pH 8.0) and with 0-0.5 % (w/v) NaCl (optimum 0 %). The major respiratory quinone was MK-7. The polar lipids were phosphatidylethanolamine (PE), an aminophospholipid (APL), a phospholipid (PL), an unidentified aminolipid (AL) and two unidentified lipids. The results of analysis of the 16S rRNA gene indicated that the novel strain was most closely related to members of the genus Spirosoma (96.2 % sequence similarity with Spirosoma endophyticum). The genomic DNA G+C content was 45.9 mol%. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. On the basis of its phenotypic and genotypic properties, strain Y4AR-5 T should be classified as representing a novel species of the genus Spirosoma, for which the name Spirosomaflavum sp. nov. is proposed. The type strain is Y4AR-5 T (=CCTCC AB 2015352 T =KCTC 52490 T ).

A combined morphological, ultrastructural, molecular, and biochemical study of the peculiar family Gomontiellaceae (Oscillatoriales) reveals a new cylindrospermopsin-producing clade of cyanobacteria.

PubMed

Bohunická, Markéta; Mareš, Jan; Hrouzek, Pavel; Urajová, Petra; Lukeš, Martin; Šmarda, Jan; Komárek, Jiří; Gaysina, Lira A; Strunecký, Otakar

2015-12-01

Members of the morphologically unusual cyanobacterial family Gomontiellaceae were studied using a polyphasic approach. Cultured strains of Hormoscilla pringsheimii, Starria zimbabweënsis, Crinalium magnum, and Crinalium epipsammum were thoroughly examined, and the type specimen of the family, Gomontiella subtubulosa, was investigated. The results of morphological observations using both light microscopy and transmission electron microscopy were consistent with previous reports and provided evidence for the unique morphological and ultrastructural traits of this family. Analysis of the 16S rRNA gene confirmed the monophyletic origin of non-marine repre-sentatives of genera traditionally classified into this family. The family was phylogenetically placed among other groups of filamentous cyanobacterial taxa. The presence of cellulose in the cell wall was analyzed and confirmed in all cultured Gomontiellaceae members using Fourier transform infrared spectroscopy and fluorescence microscopy. Evaluation of toxins produced by the studied strains revealed the hepatotoxin cylindrospermopsin (CYN) in available strains of the genus Hormoscilla. Production of this compound in both Hormoscilla strains was detected using high-performance liquid chromatography in tandem with high resolution mass spectrometry and confirmed by positive PCR amplification of the cyrJ gene from the CYN biosynthetic cluster. To our knowledge, this is the first report of CYN production by soil cyanobacteria, establishing a previously unreported CYN-producing lineage. This study indicates that cyanobacteria of the family Gomontiellaceae form a separate but coherent cluster defined by numerous intriguing morphological, ultrastructural, and biochemical features, and exhibiting a toxic potential worthy of further investigation. © 2015 Phycological Society of America.

Lelliottia aquatilis sp. nov., isolated from drinking water.

PubMed

Kämpfer, Peter; Glaeser, Stefanie P; Packroff, Gabriele; Behringer, Katja; Exner, Martin; Chakraborty, Trinad; Schmithausen, Ricarda M; Doijad, Swapnil

2018-06-22

Five beige-pigmented, oxidase-negative bacterial isolates, 6331-17 T , 6332-17, 6333-17, 6334-17 and 9827-07, isolated either from a drinking water storage reservoir or drinking water in 2006 and 2017 in Germany, were examined in detail applying by a polyphasic taxonomic approach. Cells of the isolates were rod-shaped and Gram-stain-negative. Comparison of the 16S rRNA gene sequences of these five isolates showed highest sequence similarities to Lelliottia amnigena (99.98 %) and Lelliottia nimipressuralis (99.99 %). Multilocus sequence analyses based on concatenated partial rpoB, gyrB, infB and atpD sequences confirmed the clustering of these isolates with Lelliottia species, but also revealed a clear distinction to the closest related type strains. Analysis of the genome sequences of these isolates indicated >70 % in silico DNA-DNA hybridization and high average nucleotide identities between strains. Nevertheless, they showed only <70 and <95 % similarity to the type strains of these two Lelliottia species. The fatty acid profiles of these isolates were very similar and consisted of the major fatty acids C16:0, C17 : 0cyclo, C15 : 0iso 2-OH/C16 : 1ω7c and C18 : 1ω7c. In addition, physiological/biochemical tests revealed high phenotypic similarity to each other. These cumulative data indicate that these isolates represent a novel Lelliottia species, for which the name Lelliottia aquatilis sp. nov. is proposed, with strain 6331-17 T (=CCM 8846 T =CIP 111609 T =LMG 30560 T ) as the type strain.

Streptomyces songpinggouensis sp. nov., a Novel Actinomycete Isolated from Soil in Sichuan, China.

PubMed

Guan, Xuejiao; Li, Wenchao; Liu, Chongxi; Jin, Pinjiao; Guo, Siyu; Wang, Xiangjing; Xiang, Wensheng

2016-12-01

During a screening for novel and biotechnologically useful actinobacteria, a novel actinobacteria with weak antifungal activity, designated strain NEAU-Spg19 T , was isolated from a soil sample collected from pine forest in Songpinggou, Sichuan, southwest China. The strain was characterized using a polyphasic taxonomic approach which confirmed that it belongs to the genus Streptomyces. Growth occurred at a temperature range of 10-30 °C, pH 5.0-11.0 and NaCl concentrations of 0-5 %. The cell wall peptidoglycan consisted of LL-diaminopimelic acid and glycine. The major menaquinones were MK-9(H 6 ), MK-9(H 8 ) and MK-9(H 4 ). The phospholipid profile contained diphosphatidylglycerol (DPG), phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were iso-C 15:0 , iso-C 16:0 , and C 16:0 . 16S rRNA gene sequence similarity studies showed that strain NEAU-Spg19 T belongs to the genus Streptomyces with the highest sequence similarities to Streptomyces tauricus JCM 4837 T (98.6 %) and Streptomyces rectiviolaceus JCM 9092 T (98.3 %). Some physiological and biochemical properties and low DNA-DNA relatedness values enabled the strain to be differentiated from S. tauricus JCM 4837 T and S. rectiviolaceus JCM 9092 T . Hence, on the basis of phenotypic and genetic analyses, it is proposed that strain NEAU-Spg19 T represents a novel species of the genus Streptomyces, for which the name Streptomyces songpinggouensis sp. nov. is proposed. The type strain is NEAU-Spg19 T (=CGMCC 4.7140 T =DSM 42141 T ).

Streptomyces camponoticapitis sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicus Mayr).

PubMed

Li, Yao; Ye, Lan; Wang, Xiangjing; Zhao, Junwei; Ma, Zhaoxu; Yan, Kai; Xiang, Wensheng; Liu, Chongxi

2016-10-01

A novel single-spore-producing actinomycete, designated strain 2H-TWYE14T, was isolated from the head of an ant (Camponotus japonicus Mayr) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 2H-TWYE14T belongs to the genus Streptomyces, with highest sequence similarity to Streptomyces niveus NRRL 2466T (98.84 %). Analysis based on the gyrB gene also indicated that strain 2H-TWYE14T should be assigned to the genus Streptomyces. The chemotaxonomic properties of strain 2H-TWYE14T were consistent with those of members of the genus Streptomyces. The cell wall contained ll-diaminopimelic acid. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0 and iso-C15 : 0. DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 2H-TWYE14T and its phylogenetically closely related strain S. niveus JCM 4251T, which further clarified their relatedness and demonstrated that 2H-TWYE14T could be distinguished from S. niveus. Therefore, it is concluded that strain 2H-TWYE14T can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces camponoticapitis sp. nov. is proposed. The type strain is 2H-TWYE14T (=DSM 100523T=CGMCC 4.7275T).

Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of Iris and emended description of the genus Nitrospirillum.

PubMed

Chung, Eu Jin; Park, Tae Soon; Kim, Kyung Hyun; Jeon, Che Ok; Lee, Hae-In; Chang, Woo-Suk; Aslam, Zubair; Chung, Young Ryun

2015-09-01

A polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated YC6995(T), isolated from the rhizosphere soil of Iris ensata var. spontanea (Makino) Nakai inhabiting a wetland located at an altitude of 960 m on Jiri Mountain, Korea. Strain YC6995(T) cells were Gram-negative, and rod-shaped, with motility provided by a single polar flagellum. Optimal growth conditions were 30 °C and pH 7.0. The major fatty acids of strain YC6995(T) were C18:1 ω7c, C18:1 2-OH and C16:0 3-OH. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipids were phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified glycolipids. The genomic DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed strain YC6995(T) to form a phyletic lineage with Nitrospirillum amazonense DSM 2787(T) with a high sequence similarity (97.2 %), but it displayed low sequence similarity with other remotely related genera, including Azospirillum (<93 %), Rhodocista (93.1-93.4 %), and Skermanella (91.2-93.3 %) in the family Alphaproteobacteria. Based on the phenotypic, chemotaxonomic, and phylogenetic evidences, strain YC6995(T) represents a novel species within the genus Nitrospirillum, for which the name Nitrospirillum irinus sp. nov. is proposed. The type strain is YC6995(T) (= KACC 13777(T) = DSM 22198(T)). An emended description of the genus Nitrospirillum is also proposed.

A favorable impact of preoperative FPLC chemotherapy on patients with gastric cardia cancer.

PubMed

Wang, X L; Wu, G X; Zhang, M D; Guo, M; Zhang, H; Sun, X F

2000-01-01

The aim of this study is to evaluate the effects of preoperative chemotherapy with fluorouracili polyphase liposome composita pro orale (FPLC) on the tumour cells and the survival rate of the patients with gastric cardia cancer. Sixty patients with gastric cardia cancer were randomly divided into two groups. Thirty patients were treated with FPLC prior to surgical resection, the other 30, as controls, did not receive the preoperative chemotherapy. Pathological responses of the tumours to the FPLC chemotherapy were determined by gross and microscopic assessments of tumour size, tumour emboli, cell degeneration and necrosis. Expressions of nm23 and CD44 were detected by flow cytometry. All patients were followed up to 5 years. In the FPLC-treated patients, the tumour size (p<0. 01), the number of tumour emboli (p=0.04) and the intensity of CD44 expression (p<0.001), were significantly reduced, while cell degeneration (p<0.001), necrosis (p<0.01) and the expression of nm23 (p<0.001) were increased, when compared with those observations seen in the controls. The postoperative 5-year survival rate was 40% in the FPLC-treated group and 23% in the controls (p=0.17). Preoperative FPLC chemotherapy might improve the survival rate of patients with gastric cardia cancer by inhibiting tumour proliferative, invasive and metastatic activities, and stimulating the patient's immune system.

Microbacterium lemovicicum sp. nov., a bacterium isolated from a natural uranium-rich soil.

PubMed

Mondani, Laure; Piette, Laurie; Christen, Richard; Bachar, Dipankar; Berthomieu, Catherine; Chapon, Virginie

2013-07-01

An actinobacterial strain, designated ViU22(T), was isolated from a natural uranium-rich soil and was studied using a polyphasic approach. Cells formed orange-pigmented colonies, were rod-shaped, Gram-positive (non-staining method), non-motile and non-spore-forming. This organism grew in 0-4.5 % (w/v) NaCl and at 15-37 °C, with optimal growth occurring in 0.5 % (w/v) NaCl and at 30 °C. Comparative 16S rRNA gene sequence analysis revealed that the strain ViU22(T) belonged to the genus Microbacterium. It exhibited highest 16S rRNA gene sequence similarity with the type strains of Microbacterium testaceum (98.14 %) and Microbacterium binotii (98.02 %). The DNA-DNA relatedness of strains ViU22(T) with the most closely related type strains Microbacterium testaceum and Microbacterium binotii DSM 19164(T) was 20.10 % (± 0.70) and 28.05 % (± 0.35), respectively. Strain ViU22(T) possessed a type B2β peptidoglycan with partial substitution of glutamic acid by 3-hydroxy glutamic acid. The major menaquinones were MK-11 and MK-12. Major polar lipids detected in the strain ViU22(T) were diphosphatidylglycerol, phosphatidylglycerol, an unknown phospholipid and unknown glycolipids. The predominant fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, a pattern reported for other Microbacterium species. The major cell-wall sugars were galactose, xylose and mannose and the DNA G+C content was 71 mol%. Together, the DNA-DNA hybridization results and the differentiating phenotypic characteristics, showed that strain ViU22(T) should be classified as the type strain of a novel species within the genus Microbacterium, for which the name Microbacterium lemovicicum sp. nov. is proposed. The type strain is ViU22(T) ( = ATCC BAA-2396(T) = CCUG 62198(T) = DSM 25044(T)).

Microbispora camponoti sp. nov., a novel actinomycete isolated from the cuticle of Camponotus japonicus Mayr.

PubMed

Han, Chuanyu; Liu, Chongxi; Zhao, Junwei; Guo, Lifeng; Lu, Chang; Li, Jiansong; Jia, Feiyu; Wang, Xiangjing; Xiang, Wensheng

2016-02-01

A novel actinomycete, designated strain 2C-HV3(T), was isolated from the cuticle of Camponotus japonicus Mayr collected from Harbin, Heilongjiang province, north China and characterised using a polyphasic approach. The 16S rRNA gene sequence of strain 2C-HV3(T) showed that it has high sequence similarities with Microbispora bryophytorum NEAU-TX2-2(T) (99.9 %), Microbispora amethystogenes JCM 3021(T) (98.9 %) and Microbispora rosea subsp. rosea JCM 3006(T) (98.6 %). Phylogenetic analysis based on 16S rRNA and gyrB gene sequences demonstrated that strain 2C-HV3(T) clusters with M. bryophytorum NEAU-TX2-2(T) using two tree-making algorithms. Moreover, key morphological and chemotaxonomic properties also confirmed the affiliation of strain 2C-HV3(T) to the genus Microbispora. Longitudinal paired spores were observed to be born on short sporophores branching from the aerial hyphae. The cell wall was found to contain meso-diaminopimelic acid as the diagnostic diamino acid; madurose was found in the whole cell hydrolysate. The polar lipid profile was found to consist of diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, ninhydrin-positive glycophospholipids, an unidentified phospholipid and an unidentified glycolipid. The predominant menaquinones were identified as MK-9(H2) and MK-9(H4). The major fatty acids were identified as 10-methyl C17:0 and iso-C16:0. However, a combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain 2C-HV3(T) can be distinguished from its closely related relatives. Consequently, it is proposed that strain 2C-HV3(T) represents a new species of the genus Microbispora, for which the name Microbispora camponoti sp. nov. is proposed. The type strain is 2C-HV3(T) (=CGMCC 4.7281(T) = DSM 100527(T)).

Bacillus ciccensis sp. nov., isolated from maize (Zea mays L.) seeds.

PubMed

Liu, Yang; Li, Nannan; Eom, Mi Kyung; Schumann, Peter; Zhang, Xin; Cao, Yanhua; Ge, Yuanyuan; Xiao, Ming; Zhao, Jiuran; Cheng, Chi; Kim, Song-Gun

2017-11-01

Two Gram-stain-positive bacterial strains, designated as 5L6 T and 6L6, isolated from seeds of hybrid maize (Zea mays L., Jingke 968) were investigated using a polyphasic taxonomic approach. The cells were aerobic, motile, endospore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were recognized as a species of the genus Bacillus, to which the five closest neighbours are Bacillus solani FJAT-18043 T (99.8 % similarity), Bacillus horneckiae DSM 23495 T (97.7 %), Bacillus eiseniae A1-2 T (97.4 %), Bacillus kochii WCC 4582 T (97.1 %) and Bacillus purgationiresistens DS22 T (97.0 %). The DNA G+C content of strain 5L6 T was 37.4 mol%. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was MK-7 and the major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0, anteiso-C17 : 0 and C16 : 1 ω7c alcohol. The cell-wall peptidoglycan contained ornithine, serine, aspartic acid, glutamic acid and alanine while diaminopimelic acid could not be detected. Strains 5L6 T and 6L6 were clearly distinguished from the type strains of related validly named species using phylogenetic analysis, DNA-DNA hybridization, fatty acid analysis, peptidoglycan analysis and comparison of a range of physiological and biochemical characteristics. The genotypic and phenotypic data show that strains 5L6 T and 6L6 represent a novel species of the genus Bacillus, for which the name Bacillusciccensis sp. nov. is proposed. The type strain is 5L6 T (=KCTC 33663 T =CICC 23855 T =DSM 104513 T ).

Streptomyces luozhongensis sp. nov., a novel actinomycete with antifungal activity and antibacterial activity.

PubMed

Zhang, Renwen; Han, Xiaoxue; Xia, Zhanfeng; Luo, Xiaoxia; Wan, Chuanxing; Zhang, Lili

2017-02-01

A novel actinomycete strain, designated TRM 49605 T , was isolated from a desert soil sample from Lop Nur, Xinjiang, north-west China, and characterised using a polyphasic taxonomic approach. The strain exhibited antifungal activity against the following strains: Saccharomyces cerevisiae, Curvularia lunata, Aspergillus flavus, Aspergillus niger, Fusarium oxysporum, Penicillium citrinum, Candida albicans and Candida tropicalis; Antibacterial activity against Bacillus subtilis, Staphylococcus epidermidis and Micrococcus luteus; and no antibacterial activity against Escherichia coli. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 49605 T to the genus Streptomyces. Strain TRM 49605 T shows high sequence similarities to Streptomyces roseolilacinus NBRC 12815 T (98.62 %), Streptomyces flavovariabilis NRRL B-16367 T (98.45 %) and Streptomyces variegatus NRRL B-16380 T (98.45 %). Whole cell hydrolysates of strain TRM 49605 T were found to contain LL-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, xylose and mannose as the major whole cell sugars. The major fatty acids in strain TRM 49605 T were identified as iso C 16:0 , anteiso C 15:0 , C 16:0 and Summed Feature 5 as defined by MIDI. The main menaquinones were identified as MK-9(H 4 ), MK-9(H 6 ), MK-9(H 8 ) and MK-10(H 6 ). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The G+C content of the genomic DNA was determined to be 71.2 %. The DNA-DNA relatedness between strain TRM 49605 T and the phylogenetically related strain S. roseolilacinus NBRC 12815 T was 60.12 ± 0.06 %, which is lower than the 70 % threshold value for delineation of genomic prokaryotic species. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain TRM 49605 T (=CCTCC AA2015026 T  = KCTC 39666 T ) should be designated as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces luozhongensis sp. nov. is proposed.

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-03-01

The Earth's Critical Zone (CZ) is the critical, outer shell of the Earth that provides an arena for the interplay of diverse physical, chemical, and biological processes that are fundamental for sustaining life. As microbes are the principle drivers of biogeochemical cycles, it is necessary to understand the biodiversity of the CZ unseen majority and their impact on life-sustaining processes. This review aims to summarize the factors controlling where microbes (prokaryotes and micro-eukaryotes) live within the CZ and what is known to date about their diversity and function. Microbes live in all regions of the CZ down to 5 km depth, but due to changing habitat complexity, e.g., variability in pore spaces, water, oxygen, and nutrients, their functional role changes with depth. The abundance of prokaryotes and micro-eukaryotes decreases from a maximum of 1010 or 107 cells g soil-1 up to eight orders of magnitude with depth. Symbiotic mycorrhizal fungi and free-living decomposers are best understood in soil habitats, where they are up to 103 cells g soil-1. However, little is known about their identity and impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that these organisms are either limited in space or nutrients or unable to cope with oxygen limitations. Since deep regions of the CZ are limited in the recent input of photosynthesis-derived carbon, microbes are dependent on deposited organic material or on chemolithoautotrophic metabolism that allows for the establishment of a complete food chain independent from the surface. However, the energy flux available might only allow cell growth over tens to thousands of years. The recent development of "omics" technologies has provided microbial ecologists with methods to link the composition and function of in situ microbial communities. We should expect new metabolic discoveries as we have a closer look utilizing a polyphasic approach into the microbial communities of the CZ. Thus, future work is still needed to link microbial biodiversity to the exact role of microbes in weathering and geochemical cycling in the CZ, especially in subsurface habitats.

Phylogenetic analysis of family Neisseriaceae based on genome sequences and description of Populibacter corticis gen. nov., sp. nov., a member of the family Neisseriaceae, isolated from symptomatic bark of Populus × euramericana canker.

PubMed

Li, Yong; Xue, Han; Sang, Sheng-Qi; Lin, Cai-Li; Wang, Xi-Zhuo

2017-01-01

Two Gram-stain negative aerobic bacterial strains were isolated from the bark tissue of Populus × euramericana. The novel isolates were investigated using a polyphasic approach including 16S rRNA gene sequencing, genome sequencing, average nucleotide identity (ANI) and both phenotypic and chemotaxonomic assays. The genome core gene sequence and 16S rRNA gene phylogenies suggest that the novel isolates are different from the genera Snodgrassella and Stenoxybacter. Additionally, the ANI, G+C content, main fatty acids and phospholipid profile data supported the distinctiveness of the novel strain from genus Snodgrassella. Therefore, based on the data presented, the strains constitute a novel species of a novel genus within the family Neisseriaceae, for which the name Populibacter corticis gen. nov., sp. nov. is proposed. The type strain is 15-3-5T (= CFCC 13594T = KCTC 42251T).

Micromonospora phytophila sp. nov. and Micromonospora luteiviridis sp. nov., isolated as natural inhabitants of plant nodules.

PubMed

Carro, Lorena; Veyisoglu, Aysel; Riesco, Raúl; Spröer, Cathrin; Klenk, Hans-Peter; Sahin, Nevzat; Trujillo, Martha E

2018-01-01

Two actinobacterial isolates, strains SG15 T and SGB14 T , were recovered through a microbial diversity study of nitrogen fixing nodules from Pisum sativum plants collected in Salamanca (Spain). The taxonomic status of these isolates was determined using a polyphasic approach and both presented chemotaxonomic and morphological properties consistent with their classification in the genus Micromonospora. For strains SG15 T and SGB14 T , the highest 16S rRNA gene sequence similarities were observed with Micromonospora coxensis JCM 13248 T (99.2 %) and Micromonospora purpureochromogenes DSM 43821 T (99.4 %), respectively. However, strains SG15 T and SGB14 T were readily distinguished from their phylogenetic neighbours both genetically and phenotypically indicating that they represent two new Micromonospora species. The following names are proposed for these species: Micromonosporaphytophila sp. nov. type strain SG15 T (=CECT 9369 T ; =DSM 105363 T ), and Micromonosporaluteiviridis sp. nov. type strain SGB14 T (=CECT 9370 T ; =DSM 105362 T ).

Reclassification of Flexibacter tractuosus (Lewin 1969) Leadbetter 1974 and 'Microscilla sericea' Lewin 1969 in the genus Marivirga gen. nov. as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov.

PubMed

Nedashkovskaya, Olga I; Vancanneyt, Marc; Kim, Seung Bum; Bae, Kyung Sook

2010-08-01

The taxonomic position of the misclassified strains [Flexibacter] tractuosus KCTC 2958T and '[Microscilla] sericea' LMG 13021 was studied using a polyphasic approach. The two strains shared 99.1% 16S rRNA gene sequence similarity and 28% DNA-DNA relatedness. On the basis of the phylogenetic evidence supported by genotypic and phenotypic data [Flexibacter] tractuosus KCTC 2958T and '[Microscilla] sericea' LMG 13021 are classified as two distinct species in a novel genus, Marivirga, in the family 'Flammeovirgaceae', as Marivirga tractuosa comb. nov. and Marivirga sericea nom. rev., comb. nov., with strains KCTC 2958T (=ATCC 23168T =CIP 106410T =DSM 4126T =NBRC 15989T =NCIMB 1408T =VKM B-1430T) and LMG 13021T (=ATCC 23182T =NBRC 15983T =NCIMB 1403T), respectively, as the type strains. The type species is Marivirga tractuosa.

Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobacteriaceae fam. nov.

PubMed

Steyn, P L; Segers, P; Vancanneyt, M; Sandra, P; Kersters, K; Joubert, J J

1998-01-01

Sixteen heparinase-producing isolates, related to Sphingobacterium heparinum, were grouped into three major clusters by SDS-PAGE and DNA-rRNA hybridizations. Based on a polyphasic approach, it was shown that isolates of two of these clusters and S. heparinum species belong to a new genus for which the name Pedobacter is proposed. The genus consists of Pedobacter heparinus comb. nov. (formerly Sphingobacterium heparinum), which is the type species, Pedobacter piscium comb. nov. (formerly Sphingobacterium piscium), Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. and four as-yet-unnamed DNA hybridization groups. All the previously named taxa can be discriminated by phenotypic features, but have strong overall similarities with representatives of the genus Sphingobacterium and the misclassified species [Flexibacter] canadensis. All these organisms constitute a separate rRNA branch in rRNA superfamily V for which the family Sphingobacteriaceae fam. nov. is proposed.

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.

Fusarium Species and Their Associated Mycotoxins.

PubMed

Munkvold, Gary P

2017-01-01

The genus Fusarium includes numerous toxigenic species that are pathogenic to plants or humans, and are able to colonize a wide range of environments on earth. The genus comprises around 70 well-known species, identified by using a polyphasic approach, and as many as 300 putative species, according to phylogenetic species concepts; many putative species do not yet have formal names. Fusarium is one of the most economically important fungal genera because of yield loss due to plant pathogenic activity; mycotoxin contamination of food and feed products which often render them unaccep for marketing; and health impacts to humans and livestock, due to consumption of mycotoxins. Among the most important mycotoxins produced by species of Fusarium are the trichothecenes and the fumonisins. Fumonisins cause fatal livestock diseases and are considered potentially carcinogenic mycotoxins for humans, while trichothecenes are potent inhibitors of protein synthesis. This chapter summarizes the main aspects of morphology, pathology, and toxigenicity of the main Fusarium species that colonize different agricultural crops and environments worldwide, and cause mycotoxin contamination of food and feed.

Nocardiopsis arabia sp. nov., a halotolerant actinomycete isolated from a sand-dune soil.

PubMed

Hozzein, Wael N; Goodfellow, Michael

2008-11-01

The taxonomic status of an unknown actinomycete isolated from a sand-dune soil was established using a polyphasic approach. Isolate S186(T) had chemotaxonomic and morphological properties consistent with its classification in the genus Nocardiopsis, grew on agar plates at NaCl concentrations of up to 15 % (w/v) and formed a distinct phyletic line in the Nocardiopsis 16S rRNA gene sequence tree. Its closest phylogenetic neighbours were Nocardiopsis chromatogenes, Nocardiopsis composta, Nocardiopsis gilva and Nocardiopsis trehalosi, with sequence similarity to the various type strains of 96.9 %, but it was readily distinguished from the type strains of these and related species using a range of phenotypic properties. It is apparent from the genotypic and phenotypic data that strain S186(T) belongs to a novel species of the genus Nocardiopsis, for which the name Nocardiopsis arabia sp. nov. is proposed. The type strain is S186(T) (=CGMCC 4.2057(T) =DSM 45083(T)).

3D Rheological Modeling of NW Intraplate Europe, Deciphering Spatial Integrated strength patterns, Mechanical Strong Layering and EET

NASA Astrophysics Data System (ADS)

Beekman, F.; Hardebol, N.; Cloetingh, S.; Tesauro, M.

2006-12-01

Better understanding of 3D rheological heterogeneity of the European Lithosphere provide the key to tie the recorded intraplate deformation pattern to stress fields transmitted into plate interior from plate boundary forces. The first order strain patterns result from stresses transmitted through the European lithosphere that is marked by a patchwork of high strength variability from inherited structural and compositional heterogeneities and upper mantle thermal perturbations. As the lithospheric rheology depends primarily on its spatial structure, composition and thermal estate, the 3D strength model for the European lithosphere relies on a 3D compositional model that yields the compositional heterogeneities and an iteratively calculated thermal cube using Fouriers law for heat conduction. The accurate appraisal of spatial strength variability results from proper mapping and integration of the geophysical compositional and thermal input parameters. Therefore, much attention has been paid to a proper description of first order structural and tectonic features that facilitate compilation of the compositional and thermal input models. As such, the 3D strength model reflects the thermo-mechanical structure inherited from the Europeans polyphase deformation history. Major 3D spatial mechanical strength variability has been revealed. The East-European and Fennoscandian Craton to the NE exhibit high strength (30-50 1012 N/m) from low mantle temperatures and surface heatflow of 35-60 mW/m2 while central and western Europe reflect a polyphase Phanerozoic thermo- tectonic history. Here, regions with high rigidity are formed primarily by patches of thermally stabilized Variscan Massifs (e.g. Rhenish, Armorican, Bohemian, and Iberian Massif) with low heatflow and lithospheric thickness values (50-65 mW/m2; 110-150 km) yielding strengths of ~15-25 1012 N/m. In contrast, major axis of weakened lithosphere coincides with Cenozoic Rift System (e.g. Upper and Lower Rhine Grabens, Pannonian Basin and Massif Central) attributed to the presence of tomographically imaged plumes. This study has elucidated the memory of the present-days Europeans lithosphere induced by compositional and thermal heterogeneities. The resulting lateral strength variations has a clear signature of the pst lithospheres polyphase deformation and also entails active tectonics, tectonically induced topography and surface processes.

A micro-kinematic framework for vorticity analysis in polyphase shear zones using integrated field, microstructural and crystallographic orientation-dispersion methods

NASA Astrophysics Data System (ADS)

Kruckenberg, S. C.; Michels, Z. D.; Parsons, M. M.

2017-12-01

We present results from integrated field, microstructural and textural analysis in the Burlington mylonite zone (BMZ) of eastern Massachusetts to establish a unified micro-kinematic framework for vorticity analysis in polyphase shear zones. Specifically, we define the vorticity-normal surface based on lattice-scale rotation axes calculated from electron backscatter diffraction data using orientation statistics. In doing so, we objectively identify a suitable reference frame for rigid grain methods of vorticity analysis that can be used in concert with textural studies to constrain field- to plate-scale deformation geometries without assumptions that may bias tectonic interpretations, such as relationships between kinematic axes and fabric forming elements or the nature of the deforming zone (e.g., monoclinic vs. triclinic shear zones). Rocks within the BMZ comprise a heterogeneous mix of quartzofeldspathic ± hornblende-bearing mylonitic gneisses and quartzites. Vorticity axes inferred from lattice rotations lie within the plane of mylonitic foliation perpendicular to lineation - a pattern consistent with monoclinic deformation geometries involving simple shear and/or wrench-dominated transpression. The kinematic vorticity number (Wk) is calculated using Rigid Grain Net analysis and ranges from 0.25-0.55, indicating dominant general shear. Using the calculated Wk values and the dominant geographic fabric orientation, we constrain the angle of paleotectonic convergence between the Nashoba and Avalon terranes to 56-75º with the convergence vector trending 142-160° and plunging 3-10°. Application of the quartz recrystallized grain size piezometer suggests differential stresses in the BMZ mylonites ranging from 44 to 92 MPa; quartz CPO patterns are consistent with deformation at greenschist- to amphibolite-facies conditions. We conclude that crustal strain localization in the BMZ involved a combination of pure and simple shear in a sinistral reverse transpressional shear zone formed at or near the brittle-ductile transition under relatively high stress conditions. Moreover, we demonstrate the utility of combined crystallographic and rigid grain methods of vorticity analysis for deducing deformation geometries, kinematics, and tectonic histories in polyphase shear zones.

Interaction of Extreme Halophilic Archaea With the Evaporites of the Solar Salterns Guerrero Negro Baja California, Mexico

NASA Astrophysics Data System (ADS)

Tamez, P.; Lopez-Cortés, A.

2008-12-01

Hypersaline environments have been significant reservoirs for the long-term evolution of specifically adapted microorganisms. Characterized to have higher salt concentrations (up to 35 g/L), they are worldwide distributed and have a commercial significance. Exportadora de Sal, Guerrero Negro, Mexico has a multipond salterns system designed to harvest common salt (NaCl) from sea water. To achieve this purpose, sea water is pumped through a set of shallow ponds where water evaporates and salts concentrate. Sequential precipitation of CaCO3, CaSO4 2H2O and NaCl occurs in a mineral formations call it evaporites. In the interior of those gypsum-encrusted and halite-encrusted minerals, communities of extremely salt-loving archaea prosper. Previous studies have showed the influence of Haloarchaeal cells in the formation of larger fluid inclusions than crystals formed in sterile salt solutions. S-layer envelopes and cells of Haloarcula strain SP8807 contributed to the nucleation of new crystals of NaCl. Given the significance of the scope in phylogenetic archaeal diversity research, this study had a polyphasic approach. SEM micrographs from a 21- 31% (w/v) gradient salt multipond system evaporites, gave an insight profile of the extreme halophilic archaeal communities thriving in the surface of the gypsum and halite evaporites. Halite crystals were form after 21 days of incubation in solid medium with archaeal cells. Both culture and non-culture dependent methods, Nested-PCR-DGGE analysis and sequencing of 16S rDNA amplified fragment genes from environmental samples and isolated strains were used for this purpose. We isolate three strains from Pond 9 (21.07% total salt concentration) and one strain from Cristallizer 20 (25.15% total salt concentration). 16S rDNA signaling gave 99% of similarity with Halogeometricum borinquense, sequence AF002984, two other strains were 99% of similarity with Halobacterium salinarum, sequence AJ496185 these strains shown different colony morphology. Other strain match, with 99% of similarity, with three sequences Haloarcula: Haloarcula japonica (EF645686), Haloarcula hispanica (DQ089681) and Haloarcula marismortui (X61689), differences among them were only 3 base pairs. We suggest that strain, C205030908, could correspond to Haloarcula californiae previously reported by Javor et al, (1982), from which there is not sequence known. Nested-PCR-DGGE analysis showed a pattern of 11 bands, meaning the archaeal community is more complex than we could detect by culture approach.

Burkholderia paludis sp. nov., an Antibiotic-Siderophore Producing Novel Burkholderia cepacia Complex Species, Isolated from Malaysian Tropical Peat Swamp Soil.

PubMed

Ong, Kuan Shion; Aw, Yoong Kit; Lee, Learn Han; Yule, Catherine M; Cheow, Yuen Lin; Lee, Sui Mae

2016-01-01

A novel Gram negative rod-shaped bacterium, designated strain MSh1 T , was isolated from Southeast Pahang tropical peat swamp forest soil in Malaysia and characterized using a polyphasic taxonomy approach. The predominant cellular fatty acids (>10.0%) were C 16:0 (31.7%), C 17:0 cyclo (26.6%), and C 19:0 cyclo ω8c (16.1%). The polar lipids detected were phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol. The predominant ubiquinone was Q-8. This revealed that strain MSh1 T belongs to the genus Burkholderia . The type strain MSh1 T can be differentiated from other Burkholderia cepacia complex (Bcc) species by phylogenetic analysis of 16S rRNA gene sequence, multilocus sequence analysis (MLSA), average nucleotide identity (ANI) and biochemical tests. DNA-DNA relatedness values between strain MSh1 T and closely related type strains were below the 70% threshold value. Based on this polyphasic study of MSh1 T , it can be concluded that this strain represents a novel species within the Bcc, for which the name Burkholderia paludis sp. nov. is proposed. The type strain is MSh1 T (= DSM 100703 T = MCCC 1K01245 T ). The dichloromethane extract of MSh1 T exhibited antimicrobial activity against four Gram positive bacteria ( Enterococcus faecalis ATCC 29212, E. faecalis ATCC 700802, Staphylococcus aureus ATCC 29213, S. aureus ATCC 700699) and a Gram negative bacteria ( Escherichia coli ATCC 25922). Further purification work has led to the isolation of Compound 1, pyochelin. Pyochelin demonstrated antimicrobial activity against four S. aureus strains and three E . faecalis strains with MIC-values of 3.13 μg/ml and 6.26 μg/ml, respectively. SEM analysis showed that the cellular morphology of E. faecalis ATCC 700802 was not affected by pyochelin; suggesting that it might target the intracellular components. Pyochelin, a siderophore with antimicrobial activity might be useful in treating bacterial infections caused by S. aureus and E. faecalis , however further work has to be done.

Decision feedback loop for tracking a polyphase modulated carrier

NASA Technical Reports Server (NTRS)

Simon, M. K. (Inventor)

1974-01-01

A multiple phase modulated carrier tracking loop for use in a frequency shift keying system is described in which carrier tracking efficiency is improved by making use of the decision signals made on the data phase transmitted in each T-second interval. The decision signal is used to produce a pair of decision-feedback quadrature signals for enhancing the loop's performance in developing a loop phase error signal.

Induction machine

DOEpatents

Owen, Whitney H.

1980-01-01

A polyphase rotary induction machine for use as a motor or generator utilizing a single rotor assembly having two series connected sets of rotor windings, a first stator winding disposed around the first rotor winding and means for controlling the current induced in one set of the rotor windings compared to the current induced in the other set of the rotor windings. The rotor windings may be wound rotor windings or squirrel cage windings.

Silicon controlled rectifier polyphase bridge inverter commutated with gate-turn-off thyristor

NASA Technical Reports Server (NTRS)

Edwards, Dean B. (Inventor); Rippel, Wally E. (Inventor)

1986-01-01

A polyphase SCR inverter (10) having N switching poles, each comprised of two SCR switches (1A, 1B; 2A, 2B . . . NA, NB) and two diodes (D1B; D1B; D2A, D2B . . . DNA, DNB) in series opposition with saturable reactors (L1A, L1B; L2A, L2B . . . LNA, LNB) connecting the junctions between the SCR switches and diodes to an output terminal (1, 2 . . . 3) is commutated with only one GTO thyristor (16) connected between the common negative terminal of a dc source and a tap of a series inductor (14) connected to the positive terminal of the dc source. A clamp winding (22) and diode (24) are provided, as is a snubber (18) which may have its capacitance (c) sized for maximum load current divided into a plurality of capacitors (C.sub.1, C.sub.2 . . . C.sub.N), each in series with an SCR switch S.sub.1, S.sub.2 . . . S.sub.N). The total capacitance may be selected by activating selected switches as a function of load current. A resistor 28 and SCR switch 26 shunt reverse current when the load acts as a generator, such as a motor while braking.

Streptomyces lacrimifluminis sp. nov., a novel actinobacterium that produces antibacterial compounds, isolated from soil.

PubMed

Zhang, Binglin; Tang, Shukun; Chen, Ximing; Zhang, Ling; Zhang, Gaoseng; Zhang, Wei; Liu, Guangxiu; Chen, Tuo; Li, Shiweng; Dyson, Paul

2016-12-01

A novel actinobacterial strain, designated Z1027T, was isolated from a soil sample collected near the Tuotuo River, Qinghai-Tibet Plateau (China). The strain exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus. The taxonomic position of strain Z1027T was determined using a polyphasic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree, together with Streptomyces turgidiscabies ATCC 700248T (99.19 % similarity), Streptomyces graminilatus JL-6T (98.84 %) and Streptomyces reticuliscabiei CFBP 4531T (98.36 %). The genomic DNA G+C content of strain Z1027T was 74±1 mol%. The DNA-DNA relatedness values between strain Z1027T and Streptomyces turgidiscabies ATCC 700248T and Streptomyces reticuliscabiei CFBP 4531T were 38.5±0.4 and 26.2±1.2 %, respectively, both of them significantly lower than 70 %. Chemotaxonomic data revealed that strain Z1027T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, ll-diaminopimelic acid as the diagnostic diamino acid and galactose as a whole-cell sugar. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatydilinositol and seven other unknown polar lipids were detected; iso-C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1027T (=CGMCC 4.7272T=JCM 31054T) should be classified as the type strain of a novel species of the genus Streptomyces,Streptomyces lacrimifluminis sp. nov.

Paenibacillus qinlingensis sp. nov., an indole-3-acetic acid-producing bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying.

PubMed

Xin, Kaiyun; Li, Muhang; Chen, Chaoqiong; Yang, Xu; Li, Qiqi; Cheng, Juanli; Zhang, Lei; Shen, Xihui

2017-04-01

A novel indole-3-acetic acid-producing bacterium, designated TEGT-2T, was isolated from the roots of Sinopodophyllum hexandrum collected from the Qinling Mountains in shaanxi province, northwestern China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain TEGT-2T were Gram-stain-positive, strictly aerobic, endospore-forming rods and motile by means of peritrichous flagella. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TEGT-2T was a member of the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus pectinilyticus KCTC 13222T (97.9 %), Paenibacillus frigoriresistens CCTCC AB 2011150T (97.3 %), Paenibacillus ferrarius CCTCC AB 2013369T (96.9 %) and Paenibacillus alginolyticus NBRC 15375T (96.5 %). The only menaquinone detected was MK-7, and the major fatty acid was anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids, an unidentified aminolipid and two unidentified lipids. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 46.6 mol%. DNA-DNA relatedness values for strain TEGT-2T with respect to its closest phylogenetic relatives Paenibacilluspectinilyticus KCTC 13222T and Paenibacillus. frigoriresistens CCTCC AB 2011150T were lower than 40 %. Based on the phenotypic, phylogenetic and genotypic data, strain TEGT-2T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus qinlingensis sp. nov. is proposed. The type strain is TEGT-2T (=CCTCC AB 2015258T=KCTC 33806T).

Thalassospira indica sp. nov., isolated from deep seawater.

PubMed

Liu, Yang; Lai, Qiliang; Du, Juan; Sun, Fengqin; Shao, Zongze

2016-12-01

A taxonomic study using a polyphasic approach was carried out on strain PB8BT, which was isolated from the deep water of the Indian Ocean. Cells of the bacterium were Gram-stain-negative, oxidase- and catalase-positive, curved rods and motile. Growth was observed at salinities of 0-15 % and at temperatures of 10-41°C. The isolate could reduce nitrate to nitrite and degrade Tween 80, but not degrade gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PB8BT belonged to the genus Thalassospira, with the highest sequence similarity to the closely related type strain Thalassospira tepidiphila 1-1BT (99.7 %), followed by Thalassospira profundimaris WP0211T (99.6 %). Multilocus sequence analysis demonstrated low similarities of 94.1 and 93.7 % between strain PB8BT and the two reference type strains. Digital DNA-DNA hybridization values between strain PB8BT and the two above-mentioned type strains were, respectively, 56.3 and 55.3 %. The principal fatty acids of strain PB8BT were C18 : 1ω6c/C18 : 1ω7c, C19 : 0 cyclo ω8c and C16 : 0. The G+C content of the chromosomal DNA was 54.9 mol%. The quinone was determined to be Q-10 (100 %). Phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids were present. Based on phenotypic and genotypic characteristics, strain PB8BT represents a novel species within the genus Thalassospira, for which the name Thalassospira indica sp. nov. is proposed. The type strain of the novel species is PB8BT (=MCCC 1A01103T=LMG 29620T).

Listeria fleischmannii sp. nov., isolated from cheese.

PubMed

Bertsch, David; Rau, Jörg; Eugster, Marcel R; Haug, Martina C; Lawson, Paul A; Lacroix, Christophe; Meile, Leo

2013-02-01

A study was performed on three isolates (LU2006-1(T), LU2006-2 and LU2006-3), which were sampled independently from cheese in western Switzerland in 2006, as well as a fourth isolate (A11-3426), which was detected in 2011, using a polyphasic approach. The isolates could all be assigned to the genus Listeria but not to any known species. Phenotypic and chemotaxonomic data were compatible with the genus Listeria and phylogenetic analysis based on 16S rRNA gene sequences confirmed that the closest relationships were with members of this genus. However, DNA-DNA hybridization demonstrated that the isolates did not belong to any currently described species. Cell-wall-binding domains of Listeria monocytogenes bacteriophage endolysins were able to attach to the isolates, confirming their tight relatedness to the genus Listeria. Although PCR targeting the central portion of the flagellin gene flaA was positive, motility was not observed. The four isolates could not be discriminated by Fourier transform infrared spectroscopy or pulsed-field gel electrophoresis. This suggests that they represent a single species, which seems to be adapted to the environment in a cheese-ripening cellar as it was re-isolated from the same type of Swiss cheese after more than 5 years. Conjugation experiments demonstrated that the isolates harbour a transferable resistance to clindamycin. The isolates did not exhibit haemolysis or show any indication of human pathogenicity or virulence. The four isolates are affiliated with the genus Listeria but can be differentiated from all described members of the genus Listeria and therefore they merit being classified as representatives of a novel species, for which we propose the name Listeria fleischmannii sp. nov.; the type strain is LU2006-1(T) ( = DSM 24998(T)  = LMG 26584(T)).

Enterobacter muelleri sp. nov., isolated from the rhizosphere of Zea mays.

PubMed

Kämpfer, Peter; McInroy, John A; Glaeser, Stefanie P

2015-11-01

A beige-pigmented, oxidase-negative bacterial strain (JM-458T), isolated from a rhizosphere sample, was studied using a polyphasic taxonomic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain JM-458T with sequences of the type strains of closely related species of the genus Enterobacter showed that it shared highest sequence similarity with Enterobacter mori (98.7 %), Enterobacter hormaechei (98.3 %), Enterobacter cloacae subsp. dissolvens, Enterobacter ludwigii and Enterobacter asburiae (all 98.2 %). 16S rRNA gene sequence similarities to all other Enterobacter species were below 98 %. Multilocus sequence analysis based on concatenated partial rpoB, gyrB, infB and atpD gene sequences showed a clear distinction of strain JM-458T from its closest related type strains. The fatty acid profile of the strain consisted of C16 : 0, C17 : 0 cyclo, iso-C15 : 0 2-OH/C16 : 1ω7c and C18 : 1ω7c as major components. DNA-DNA hybridizations between strain JM-458T and the type strains of E. mori, E. hormaechei and E. ludwigii resulted in relatedness values of 29 % (reciprocal 25 %), 24 % (reciprocal 43 %) and 16 % (reciprocal 17 %), respectively. DNA-DNA hybridization results together with multilocus sequence analysis results and differential biochemical and chemotaxonomic properties showed that strain JM-458T represents a novel species of the genus Enterobacter, for which the name Enterobacter muelleri sp. nov. is proposed. The type strain is JM-458T ( = DSM 29346T = CIP 110826T = LMG 28480T = CCM 8546T).

Jatrophihabitans endophyticus gen. nov., sp. nov., an endophytic actinobacterium isolated from a surface-sterilized stem of Jatropha curcas L.

PubMed

Madhaiyan, Munusamy; Hu, Chuan Jiong; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo; Ji, Lianghui

2013-04-01

A short rod-shaped Gram-stain-positive actinobacterium was isolated as an endophyte from the tissues of Jatropha curcas cv. KB27 and was investigated by means of a polyphasic taxonomic approach. An analysis of its 16S rRNA gene sequence indicated that strain S9-650(T) forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genera Frankia (family Frankiaceae) and Acidothermus (family Acidothermaceae) and the other by members of the genera Geodermatophilus, Blastococcus and Modestobacter (family Geodermatophilaceae). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. The acyl type was found to be N-glycolylated. The major menaquinone was MK-9(H4) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, C18 : 1ω9c, anteiso-C17 : 0 and C17 : 1ω8c. The polar lipids comprised diphosphatidylglycerol, an unidentified glycolipid, phospholipids and aminolipids. The G+C content of the genomic DNA was 71.2 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain S9-650(T) represents a novel species in a new genus, for which the name Jatrophihabitans endophyticus gen. nov., sp. nov. is proposed. The type strain of the type species is S9-650(T) ( = DSM 45627(T) = KACC 16232(T)).

Actinophytocola glycyrrhizae sp. nov. isolated from the rhizosphere of Glycyrrhiza inflata.

PubMed

Cao, Chengliang; Sun, Yong; Wu, Bo; Zhao, Shuai; Yuan, Bo; Qin, Sheng; Jiang, Jihong; Huang, Ying

2018-06-25

A Gram-stain-positive, aerobic actinomycete, designated strain BMP B8152 T , was isolated from the rhizosphere of Glycyrrhiza inflata collected ashore, in Kashi, Xinjiang province, northwest PR China. A polyphasic approach was used to establish the taxonomic position of this strain. BMP B8152 T was observed to form non-fragmented substrate mycelium, and relatively scanty aerial mycelium with rod-shaped spores. Cell-wall hydrolysates contained meso-diaminopimelic acid, galactose, arabinose, glucose and rhamnose (trace). Mycolic acids were not detected. The diagnostic phospholipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, ninhydrin-positive phosphoglycolipid and phosphatidylinositol. The predominant menaquinone and fatty acid were MK-9(H4) and iso-branched hexadecanoate (iso-C16 : 0), respectively. The phylogenetic analyses based on the 16S rRNA gene sequences indicated that BMP B8152 T formed a distinct monophyletic clade clustered with Actinophytocola timorensisID05-A0653 T (98.8 % 16S rRNA gene sequence similarity), Actinophytocola oryzaeGMKU 367 T (98.6 %), Actinophytocola corallinaID06-A0464 T (98.2 %) and Actinophytocola burenkhanensisMN08-A0203 T (97.5 %). In addition, DNA-DNA hybridization values between BMP B8152 T and A. timorensisID05-A0653 T (44.2±3.6 %) and A. oryzaeGMKU 367 T (36.7±2.3 %) were well below the 70 % limit for species identification. The combined phenotypic and genotypic data indicate that the isolate represents a novel species of the genus Actinophytocola, for which the name Actinophytocola glycyrrhizae sp. nov., is proposed, with the type strain BMP B8152 T (=KCTC 49002 T =CGMCC 4.7433 T ).

Lactobacillus ixorae sp. nov., isolated from a flower (West-Indian jasmine).

PubMed

Techo, Sujitra; Miyashita, Mika; Shibata, Chiyo; Tanaka, Naoto; Wisetkhan, Preeyarach; Visessanguan, Wonnop; Tanasupawat, Somboon

2016-12-01

A Gram-stain-positive, lactic acid bacterium, strain Ru20-1T, was isolated from a flower (West-Indian jasmine) collected from Kalasin province, Thailand. A polyphasic approach was used to determine the taxonomic position of this strain. Studies of morphological and biochemical characteristics revealed that strain Ru20-1T belonged to the genus Lactobacillus. The strain was heterofermentative, non-spore-forming and rod-shaped. It produced dl-lactic acid. Based on 16S rRNA gene sequence similarity, this strain was closely related to Lactobacillus lindneri LMG 14528T (96.8 %), Lactobacillus sanfranciscensis NRIC 1548T (95.4 %) and Lactobacillus florum NRIC 0771T (95.2 %), respectively. In addition, the pheS gene sequence of strain Ru20-1T was closely related to those of L. sanfranciscensis NRIC 1548T (92.0 %), L. lindneri LMG 14528T (89.0 %) and L. florum NRIC 0771T(85.0 %). Phylogenetic analysis indicated that strain Ru20-1T was clearly separated from closely related species of the genus Lactobacillus. The DNA G+C content of strain Ru20-1T was 47.8 mol %. The cell-wall peptidoglycan type was l-Lys-d-Asp. The major cellular fatty acids were C18 : 1ω9c, C20 : 0, C20 : 1ω9c and summed feature 7 (unknown 18.846 and/or C19 : 1ω6c and/or C19 : 0 cyclo). On the basis of the data provided, strain Ru20-1T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus ixorae sp. nov. is proposed. The type strain is Ru20-1T (=LMG 29008T=NBRC 111239T=PCU 346T=TISTR 2381T).

Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden.

PubMed

Huq, Md Amdadul

2018-03-01

A novel bacterial strain MAH-8 T was isolated from a soil sample of a Korean pine garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, pinkish yellow colored, motile and vibrio-shaped. The strain was aerobic and catalase, oxidase positive, optimum growth temperature and pH were 28-30 °C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain MAH-8 T belongs to the genus Caenispirillum and is most closely related to Caenispirillum bisanense KCTC 12839 T (98.14%), Caenispirillum deserti KCTC 42064 T (96.35%), and Caenispirillum salinarum JCM 17360 T (95.76%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-8 T and its closest phylogenetic neighbor was below 45.0%. The DNA G + C content was 70.5 mol% and the predominant respiratory quinone was ubiquinone-10. Flexirubin-type pigments were present and the major cellular fatty acids were C 18:1 ω7c/C 18:1 ω6c, C 16:1 ω7c/C 16:1 ω6c and C 16:0 . The results of DNA-DNA hybridization and genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-8 T represented a novel species within the genus Caenispirillum, for which the name Caenispirillum humi, is proposed. The type strain is MAH-8 T (= KACC 19294 T  = CGMCC 1.16224 T ). The NCBI GenBank Accession Number for the 16S rRNA gene sequence of strain MAH-8 T is KY964275.

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

PubMed

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

2016-09-01

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

Saccharomonospora piscinae sp. nov., a novel actinobacterium from fishpond sediment in Taiwan.

PubMed

Tseng, Min; Chiang, Wan-Ping; Liao, Hsuen-Chun; Hsieh, Sung-Yuan; Yuan, Gao-Fung

2018-05-01

Strain 06168H-1 T was isolated from a fishpond sediment sample collected from the southern area of Taiwan, and a polyphasic approach was used to determine its taxonomic position. The isolate grew between 20-40 °C and 0-8 % (w/v) NaCl. It produced branched and unfragmented substrate mycelia. Short spore chains (3-10 spores per chain) formed on branched aerial mycelia. The spore chains contained non-motile, smooth-surfaced, oval spores. Galactose, arabinose and ribose were the whole-cell sugars and meso-diaminopimelic acid was present in its peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, hydroxyphosphati dylethanolamine and a ninhydrin-positive phosphoglycolipid. The predominant menaquinone was MK-9(H4) and minor components were MK-8(H4) and MK-9(H6). Mycolic acids were not detected. The major cellular fatty acids were iso-C16 : 0 and C17 : 1ω6c and C17 : 0ω8c. The DNA G+C content of the strain was 70.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed this strain clustered with the members of the genus Saccharomonospora and was closely related to Saccharomonospora xinjiangensis, Saccharomonospora azurea and Saccharomonosporacyanea. The levels of similarity between this strain and the closely related species were: Sxinjiangensis BCRC16887 T , 98.34 %; S. azurea BCRC 16220 T , 98.27 %; and S. cyanea BCRC 16886 T , 97.99 %. Based on phylogenetic characteristics, strain 06168H-1 T represents a novel species of the genus Saccharomonospora. We thus propose the name Saccharomonospora piscinae sp. nov. for this novel strain, with strain 06168H-1 T (=BCRC 16893 T =KCTC 19743 T ) as the type strain.

Streptomyces salilacus sp. nov., an actinomycete isolated from a salt lake.

PubMed

Luo, Xiao-Xia; Gao, Guang-Bin; Xia, Zhan-Feng; Chen, Zheng-Jun; Wan, Chuan-Xing; Zhang, Li-Li

2018-05-01

The taxonomic position of a novel actinomycete, strain TRM 41337 T , isolated from sediment of a salt lake, Xiaoerkule Lake, Xinjiang, China, was determined by a polyphasic approach. Strain TRM 41337 T grew optimally at 28 °C and in the presence of 1 % (w/v) NaCl. It grew at up to pH 12. The whole-cell sugars of strain TRM 41337 T were ribose and xylose. The diagnostic diamino acid contained ll-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside and two other unidentified phospholipids. The predominant menaquinones were MK-9(H8), MK-9, MK-9(H4) and MK-9(H6). The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 1 H. Based on morphological and chemotaxonomic characteristics, the isolate was determined to belong to the genus Streptomyces. The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1498 nt) with representative strains showed that the strain consistently falls into a distinct phyletic lineage together with Streptomyces barkulensis DSM 42082 T (97.48 % similarity) and a subclade consisting of Streptomyces fenghuangensis GIMN 4.003 T (97.20 %), Streptomyces macrosporus NBRC 14748 T (97.14 %) and Streptomyces radiopugnans R97 T (97.01 %). On the basis of these data, strain TRM 41337 T should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces salilacus sp. nov. is proposed. The type strain is TRM 41337 T (=CCTCC AA 2015030 T =KCTC 39726 T ).

Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae.

PubMed

Cole, Jessica K; Morton, Beau R; Cardamone, Hayley C; Lake, Hannah R R; Dohnalkova, Alice C; Kim, Young-Mo; Kyle, Jennifer E; Maezato, Yukari; Dana, Karl L; Metz, Thomas O; Romine, Margaret F; Nelson, William C; Lindemann, Stephen R

2018-05-01

A halophilic bacterial strain, HL-109 T , was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109 T is representative of a new lineage, for which the name Salinivirga fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109 T (=JCM 31876 T =DSM 102886 T ). In addition, examination of the phylogenetics of strain HL-109 T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Salinivirga and Salinarimonas (the type genus of the family).

Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.

PubMed

Liu, Sha; Jin, Dong; Lan, Ruiting; Wang, Yiting; Meng, Qiong; Dai, Hang; Lu, Shan; Hu, Shoukui; Xu, Jianguo

2015-07-01

The taxonomic position of a group of seven closely related lactose-negative enterobacterial strains, which were isolated from fresh faecal samples of Marmota himalayana collected from the Qinghai-Tibetan plateau, China, was determined by using a polyphasic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods (0.5-1 × 1-2.5 μm). By 16S rRNA gene sequences, the representative strain, HT073016(T), showed highest similarity values with Escherichia fergusonii ATCC 35469(T) at 99.3%, Escherichia coli ATCC 11775(T) at 99.2%, Escherichia albertii LMG 20976(T) at 98.9%, Escherichia hermannii CIP 103176(T) at 98.4%, and Escherichia vulneris ATCC 33821(T) at 97.7%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the seven strains formed a monophyletic group with five other species of the genus Escherichia. Digital DNA-DNA hybridization studies between strain HT073016(T) and five other species of the genus Escherichia showed that it shared less than 70% DNA-DNA relatedness with all known species of the genus Escherichia, supporting the novel species status of the strain. The DNA G+C content of strain HT073016(T) was 53.8 mol%. On the basis of phenotypic and phylogenetic characteristics, strain HT073016(T) and the six other HT073016(T)-like strains were clearly distinct from the type strains of other recognized species of the genus Escherichia and represent a novel species of the genus Escherichia, for which the name Escherichia marmotae sp. nov. is proposed, with HT073016(T) ( = CGMCC 1.12862(T) = DSM 28771(T)) as the type strain.

Streptomyces lonarensis sp. nov., isolated from Lonar Lake, a meteorite salt water lake in India.

PubMed

Sharma, Trupti K; Mawlankar, Rahul; Sonalkar, Vidya V; Shinde, Vidhya K; Zhan, Jing; Li, Wen-Jun; Rele, Meenakshi V; Dastager, Syed G; Kumar, Lalitha Sunil

2016-02-01

A novel alkaliphilic actinomycete, strain NCL716(T), was isolated from a soil sample collected from the vicinity of Lonar Lake, an alkaline salt water meteorite lake in Buldhana district of Maharashtra State in India. The strain was characterised using a polyphasic taxonomic approach which confirmed that it belongs to the genus Streptomyces. Growth was observed over a pH range of 7-11 at 28 °C. The cell wall was found to contain LL-diaminopimelic acid and traces of meso-diaminopimelic acid. The major fatty acid components were identified as iso-C16:0 (46.8 %), C17:1 (12.4 %), anteiso-C15:0 (5.1 %) and anteiso-C17:1 (4.8 %). The major polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The major menaquinones were determined to be MK-9 (H6) (70.3 %), MK-9 (H4) (15.5 %) and MK-9 (H8) (7.2 %). The G+C content of the DNA of the type strain was determined to be 71.4 mol %. The 16S rRNA gene sequence has been deposited in GenBank with accession number FJ919811. Although the 16S rRNA gene sequence analysis revealed that strain NCL716(T) shares >99 % similarity with that of Streptomyces bohaiensis strain 11A07(T), DNA-DNA hybridization revealed only 33.2 ± 3.0 % relatedness between them. Moreover, these two strains can be readily distinguished by some distinct phenotypic characteristics. Hence, on the basis of phenotypic and genetic analyses, it is proposed that strain NCL716(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces lonarensis sp. nov., is proposed. The type strain is NCL 716(T) (=DSM 42084(T) = MTCC 11708(T) = KCTC 39684(T)).

Streptomyces xinjiangensis sp. nov., an actinomycete isolated from Lop Nur region.

PubMed

Cheng, Cong; Li, Yu-Qian; Asem, Mipeshwaree Devi; Lu, Chun-Yan; Shi, Xiao-Han; Chu, Xiao; Zhang, Wan-Qin; Di An, Deng-; Li, Wen-Jun

2016-10-01

A novel actinobacterial strain, designated LPA192(T), was isolated from a soil sample collected from Lop Nur, Xinjiang Uygur Autonomous Region, Northwest China. A polyphasic approach was used to investigate the taxonomic position of strain LPA192(T). The isolate showed morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. Peptidoglycan was found to contain LL-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H6) and MK-10(H4). Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol. Major cellular fatty acids consist of C16:0, anteiso-C15:0 and C18:1 ω9c. The sugar in whole-cell hydrolysates was mannose. Phylogenetic analysis indicated that strain LPA192(T) is closely related to Streptomyces tanashiensis LMG 20274(T) (99.3 %), Streptomyces gulbargensis DAS131(T) (99.3 %), Streptomyces nashvillensis NBRC 13064(T) (99.3 %), Streptomyces roseolus NBRC 12816(T) (99.2 %) and Streptomyces filamentosus NBRC 12767(T) (99.1 %) while showing below 98.5 % sequencing similarities with other validly published Streptomyces species. However, DNA-DNA relatedness values between LPA192(T) and the closely related type strains were below 40 %, which are much lower than 70 % threshold value for species delineation. The genomic DNA G + C content of strain LPA192(T) was 69.3 mol %. Based on the differences in genotypic and phenotypic characteristics from the closely related strains, strain LPA192(T) is considered to represent a novel species of the genus Streptomyces for which the name Streptomyces xinjiangensis sp. nov. is proposed. The type strain is LPA192(T) (=KCTC 39601(T) = CGMCC 4.7288(T)).

Streptomyces cerasinus sp. nov., isolated from soil in Thailand.

PubMed

Kanchanasin, Pawina; Moonmangmee, Duangtip; Phongsopitanun, Wongsakorn; Tanasupawat, Somboon; Moonmangmee, Somporn

2017-10-01

A novel actinomycete, strain SR3-134 T , belonging to the genus Streptomyces, was isolated from soil collected from the Sakaerat Environmental Research Station, Thailand Institute of Scientific and Technological Research, Nakhon Ratchasima Province, Thailand. The taxonomic position of the strain was characterized by using a polyphasic approach. ll-Diaminopimelic acid, glucose, mannose and ribose were detected in its whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. The menaquinones were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2). The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. blast analysis of the almost-complete 16S rRNA gene showed 98.7 % sequence similarities to Streptomyces lanatus JCM 4588 T and Streptomyces psammoticus JCM 4434 T . The DNA G+C content was 71.4 mol%. Strain SR3-134 T showed low DNA-DNA relatedness (12.9±4.0-44.1±1.0 %) to S. lanatus JCM 4588 T and S. psammoticus JCM 4434 T . The new strain could also be distinguished from its closely related strains by differences in their phenotypic characteristics. The results of taxonomic analysis suggested that strain SR3-134 T represented a novel species of the genus Streptomyces for which the name Streptomyces cerasinus sp. nov. is proposed. The type strain is SR3-134 T (=TISTR 2494 T =KCTC 39910 T ).

Streptomyces bryophytorum sp. nov., an endophytic actinomycete isolated from moss (Bryophyta).

PubMed

Li, Chuang; Jin, Pinjiao; Liu, Chongxi; Ma, Zhaoxu; Zhao, Junwei; Li, Jiansong; Wang, Xiangjing; Xiang, Wensheng

2016-09-01

A novel endophytic actinomycete, designated strain NEAU-HZ10(T) was isolated from moss and characterised using a polyphasic approach. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Streptomyces. Strain NEAU-HZ10(T) formed grayish aerial mycelia, which differentiated into straight to flexuous chains of cylindrical spores. The cell wall peptidoglycan was found to contain LL-diaminopimelic acid. Predominant menaquinones were identified as MK-9(H6) and MK-9(H8). The polar lipid profile was found to consist of phosphatidylethanolamine, phosphatidylinositol and two unidentified phospholipids. The major fatty acids were identified as iso-C16:0, anteiso-C15:0 and C16:0. 16S rRNA gene sequence similarity studies showed that strain NEAU-HZ10(T) belongs to the genus Streptomyces and exhibits high sequence similarity to Streptomyces cocklensis DSM 42063(T) (98.9 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain NEAU-HZ10(T) clustered with S. cocklensis DSM 42063(T), Streptomyces yeochonensis CGMCC 4.1882(T) (98.7 %), Streptomyces paucisporeus CGMCC 4.2025(T) (98.4 %) and Streptomyces yanglinensis CGMCC 4.2023(T) (98.1 %). However, a combination of DNA-DNA hybridisation results and some phenotypic characteristics indicated that strain NEAU-HZ10(T) can be distinguished from its phylogenetically closely related strains. Therefore, it is proposed that strain NEAU-HZ10(T) represents a novel species of the genus Streptomyces for which the name Streptomyces bryophytorum sp. nov. is proposed. The type strain is NEAU-HZ10(T) (= CGMCC 4.7151(T) = DSM 42138(T)).

(GTG)5-PCR reference framework for acetic acid bacteria.

PubMed

Papalexandratou, Zoi; Cleenwerck, Ilse; De Vos, Paul; De Vuyst, Luc

2009-11-01

One hundred and fifty-eight strains of acetic acid bacteria (AAB) were subjected to (GTG)(5)-PCR fingerprinting to construct a reference framework for their rapid classification and identification. Most of them clustered according to their respective taxonomic designation; others had to be reclassified based on polyphasic data. This study shows the usefulness of the method to determine the taxonomic and phylogenetic relationships among AAB and to study the AAB diversity of complex ecosystems.

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

PubMed

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

2015-09-01

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

Roseomonas wooponensis sp. nov., isolated from wetland freshwater.

PubMed

Lee, Ji Hee; Kim, Mi Sun; Baik, Keun Sik; Kim, Hyang Mi; Lee, Kang Hyun; Seong, Chi Nam

2015-11-01

A non-motile, cocobacilli-shaped and pink-pigmented bacterium, designated strain WW53T, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram-stain-negative, catalase- and oxidase-positive. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0.The predominant quinone and polyamine were ubiquinone 10 (Q-10) and spermidine, respectively. The DNA G+C content was 71 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WW53T belongs to the family Acetobacteraceae, and is related to the genus Roseomonas. Strain WW53T was most closely related to Roseomonas stagni HS-69T (95.3 % 16S rRNA gene sequence similarity). Results of a polyphasic taxonomy study suggested that the isolate represents a novel species in the genus Roseomonas, for which the name Roseomonas wooponensis sp. nov. is proposed. The type strain is WW53T ( = KCTC 32534T = JCM 19527T).

Deformation of polyphase aggregates, forsterite+MgO, at pressures and temperatures of the Earth's upper mantle

NASA Astrophysics Data System (ADS)

Bejina, F.; Bystricky, M.; Ingrin, J.

2012-12-01

Modelling the solid-state flow of the upper mantle requires a thorough understanding of its rheology and therefore necessitates to perform deformation experiments on mantle rocks (or analogues) at very high pressures and temperatures. Minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. Nevertheless, most experimental studies to date have focused on the deformation properties of olivine single crystals or monomineralic olivine aggregates. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO, at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases were sintered by spark plasma sintering (SPS) at temperatures of 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Microstructural analysis by SEM reveals equilibrated microstructures with forsterite and MgO grain sizes of a few microns. Deformation experiments on samples 1.2 mm in diameter and 1.2 mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens, respectively a monomineralic and a polyphase aggregate, were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. As expected, the harder phase, forsterite, sustains much higher stress levels than MgO, in agreement with numerical models for two-phase flow. Results on stress and strain partitioning in polyphase aggregates and on the effect of the presence of a weak phase on the rheology of forsterite-rich aggregates will be discussed.

ION SOURCE FOR CALUTRONS

DOEpatents

Tolmie, J.R.

1958-09-16

An improvement is presented in ion sources of the type employed in calutron devices. The described ion source has for its inventive contribution the incorporation of a plate-like cathode having the general configuration of a polygon including a given number of apices. When a polyphase source of current has a phase connected to each of the apices, the cathode is heated and rendered electron emissive. This particular cathode configuration is of sturdy construction and provides unuform emission over a considerable area.

Investigation of Doppler Effects on the Detection of Polyphase Coded Radar Waveforms

DTIC Science & Technology

2003-02-01

wave2 = amp * sin(2*pi*two+(2*pi/7)); %the second modulated waveform %wave = [wavec wave1 wave2 wavec]; %the wave form put togther wave = amp...waveform wave1 = sin(2*pi*two+(pi/2)); %the first modulated waveform wave2 = sin(2*pi*two+(2*pi/7)); %the second modulated waveform...wave = [wavec wave1 wave2 wavec]; %the wave form put togther normval = max(abs(xcorr(wave,wave))); N=length

Mycobacterium hippocampi sp. nov., a rapidly growing scotochromogenic species isolated from a seahorse with tail rot.

PubMed

Balcázar, José Luis; Planas, Miquel; Pintado, José

2014-09-01

A Gram-positive, aerobic, non-motile, non-sporulating, acid-fast, and rod-shaped bacterium (BFLP-6(T)), previously isolated from a seahorse (Hippocampus guttulatus) with tail rot, was studied using a polyphasic taxonomic approach. Growth occurred at 15-35 °C (optimum 25 °C), at pH 5.0-10.0 (optimum pH 7.0) and at NaCl concentrations between 0 and 6 % (w/v). The G+C content of DNA was 66.7 mol%. The predominant fatty acids were C(18:1) ω9c, C(16:0) and C(16:1) ω6c. A mycolic acid pattern of alpha-mycolates and keto-mycolates was detected. Analysis of concatenated sequences (16S rRNA, rpoB, ssrA and tuf genes), and chemotaxonomic and phenotypic features indicated that strain BFLP-6(T) represents a novel species within the genus Mycobacterium, for which the name Mycobacterium hippocampi sp. nov. is proposed. The type strain is BFLP-6(T) (=DSM 45391(T) =LMG 25372(T)).

Identification of Antipathogenic Bacterial Coral Symbionts Against Porites Ulcerative White Spots Disease

NASA Astrophysics Data System (ADS)

Sa'adah, Nor; Sabdono, Agus; Diah Permata Wijayanti, dan

2018-02-01

Coral reef ecosystems are ecosystems that are vulnerable and susceptible to damage due to the exploitation of ocean resources. One of the factors that cause coral damage is the disease that attacks the coral. Porites Ulcerative White Spots (PUWS) is a coral disease found in Indonesia and attacks the coral genera Porites allegedly caused by pathogenic microbial attacks. The purpose of this study was to identify the symbiotic bacteria on healthy coral that have antipatogenic potency against PUWS. The method used in this research was descriptive explorative. Sampling was done in Kemujan Island, Karimunjawa. Bacteria were isolated from healthy coral and coral affected by PUWS disease. Streak method was used to purify coral bacteria, while overlay and agar diffusion were used to test antipathogenic activity. Bacterial identification was carried out based on polyphasic approach. The results of this study showed that coral bacterial symbionts have antipathogenic activity against PUWS disease. The selected bacteria NM 1.2, NM 1.3 and KPSH 5. NM1.2 were closely related to Pseudoalteromonas piscicida, Pseudoalteromonas flavipulchra and Bacillus flexus, respectively.

Streptomyces castaneus sp. nov., a novel actinomycete isolated from the rhizosphere of Peucedanum praeruptorum Dunn.

PubMed

Zhou, Shuyu; Li, Zhilei; Bai, Lu; Yan, Kai; Zhao, Junwei; Lu, Chang; Liu, Chongxi; Wang, Xiangjing; Xiang, Wensheng

2017-01-01

During an investigation of microbial diversity in medicinal herbs, a novel actinomycete, strain NEAU-QHHV11 T was isolated from the rhizosphere of Peucedanum praeruptorum Dunn collected from Xianglu Mountain in Heilongjiang Province, northeast China and characterized using a polyphasic approach. The organism was found to have typical characteristics of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequence also indicated that strain NEAU-QHHV11 T belongs to the genus Streptomyces and was most closely related to Streptomyces graminilatus NBRC 108882 T (98.7 % sequence similarity) and Streptomyces turgidiscabies NBRC 16080 T (98.7 % sequence similarity). The results of DNA-DNA hybridization and some phenotypic characteristics indicated that strain NEAU-QHHV11 T could be distinguished from its close phylogenetic relatives. Thus, strain NEAU-QHHV11 T represents a novel species of the genus Streptomyces, for which the name Streptomyces castaneus sp. nov. is proposed. The type strain is NEAU-QHHV11 T (=CGMCC 4.7235 T  = DSM 100520 T ).

Actinomadura gamaensis sp. nov., a novel actinomycete isolated from soil in Gama, Chad.

PubMed

Abagana, Adam Yacoub; Sun, Pengyu; Liu, Chongxi; Cao, Tingting; Zheng, Weiwei; Zhao, Shanshan; Xiang, Wensheng; Wang, Xiangjing

2016-06-01

A novel single spore-producing actinomycete, designated strain NEAU-Gz5(T), was isolated from a soil sample from Gama, Chad. A polyphasic taxonomic study was carried out to establish the status of this strain. The diamino acid present in the cell wall is meso-diaminopimelic acid. Glucose, mannose and madurose occur in whole cell hydrolysates. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and an unidentified glycolipid. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The predominant cellular fatty acids were found to be C16:0, iso-C15:0, iso-C16:0 and C18:0 10-methyl. Phylogenetic analysis based on the 16S rRNA gene showed that strain NEAU-Gz5(T) belongs to the genus Actinomadura and is closely related to Actinomadura oligospora JCM 10648(T) (ATCC 43269(T); 98.3 % similarity). However, the low level of DNA-DNA relatedness and some different phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain NEAU-Gz5(T) represents a novel species of the genus of Actinomadura, for which the name Actinomadura gamaensis sp. nov. is proposed. The type strain is NEAU-Gz5(T) (= CGMCC 4.7301(T) = DSM 100815(T)).

Dynamic exophthalmos and lateral strabismus in a dog caused by masticatory muscle myositis.

PubMed

Czerwinski, Sarah L; Plummer, Caryn E; Greenberg, Shari M; Craft, William F; Conway, Julia A; Perez, Mayrim L; Cooke, Kirsten L; Winter, Matthew D

2015-11-01

A 5.5-year-old neutered male mixed-breed dog was presented for evaluation of a 5-month history of deviation of the right globe upon opening the mouth and a 1-month history of conjunctivitis in the same eye. Clinical findings, diagnostic imaging results, treatment and follow-up are described. When the mouth was opened, the right globe deviated rostrally and laterally. There was no pain or resistance to opening the mouth, or resistance to retropulsion of the globe. No other abnormalities were observed. Computed tomography was performed, revealing a contrast-enhancing region associated with the right masseter muscle impinging into the right orbit; this was more pronounced with the mouth open. Cytology revealed a small number of mildly to moderately atypical mesenchymal cells. Histopathology was consistent with polyphasic myositis, with a predominance of lymphocytes and plasma cells. No infectious agents were identified. Serum antibody titers for Toxoplasma gondii and Neospora caninum were negative. Serum titers for 2 M antibody were positive at 1:500, consistent with a diagnosis of masticatory muscle myositis. Therapy with prednisone was initiated. During a follow-up period of 5 months, there was no recurrence of clinical signs, and the dose of prednisone was reduced by 25%. To the authors' knowledge, this is the first reported case of masticatory muscle myositis causing dynamic exophthalmos and strabismus in a dog. © 2015 American College of Veterinary Ophthalmologists.

Actinomadura amylolytica sp. nov. and Actinomadura cellulosilytica sp. nov., isolated from geothermally heated soil.

PubMed

Jiao, Jian-Yu; Liu, Lan; Zhou, En-Min; Wei, Da-Qiao; Ming, Hong; Xian, Wen-Dong; Yuan, Chang-Guo; Zhong, Jing-Mei; Li, Wen-Jun

2015-07-01

Two aerobic, Gram-positive actinomycetes, designated YIM 77502(T) and YIM 77510(T), were isolated from geothermally heated soil of Tengchong county, Yunnan province, south-west China. The taxonomic position of strains YIM 77502(T) and YIM 77510(T) were investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains YIM 77502(T) and YIM 77510(T) belong to the genus Actinomadura. Both strains form extensively-branched substrate and aerial mycelia which differentiated into short spore chains. The cell wall of the two strains contained meso-diaminopimelic acid, while the whole-cell sugars detected were glucose, madurose, mannose and rhamnose. The polar lipid profile of strain YIM 77502(T) was found to consist of diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, two unidentified phospholipids and an unidentified polar lipid, while strain YIM 77510(T) consisted of diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The respiratory quinones of strains YIM 77502(T) and YIM 77510(T) were MK-9(H6) and MK-9(H8). The major fatty acids (>10 %) of strain YIM 77502(T) were C17:0, iso-C16:0, C17:010-methyl and iso-C18:0, and those of strain YIM 77510(T) were iso-C16:0, C17:010-methyl and iso-C18:0. The G+C contents of strains YIM 77502(T) and YIM 77510(T) were determined to be 71.3 and 70.2 mol%, respectively. The DNA-DNA hybridization values of strains YIM 77502(T), YIM 77510(T) and their closest phylogenetic neighbours Actinomadura echinospora BCRC 12547(T) and Actinomadura umbrina KCTC 9343(T) were less than 70 %. Based on the morphological and physiological properties, and phylogenetic analyses, strains YIM 77502(T) and YIM 77510(T) are considered to represent two novel species of the genus Actinomadura, for which the names Actinomadura amylolytica sp. nov. (type strain YIM 77502(T) = DSM 45822(T) = CCTCC AA 2012024(T)) and Actinomadura cellulosilytica sp. nov. (type strain YIM 77510(T) = DSM 45823(T) = CCTCC AA 2012023(T)) are proposed.

Streptomyces pini sp. nov., an actinomycete isolated from phylloplane of pine (Pinus sylvestris L.) needle-like leaves.

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Saravanan, Venkatakrishnan Sivaraj; Duraipandiyan, Veeramuthu; Al-Dhabi, Naif Abdullah; Pragatheswari, Dhandapani; Santhanakrishnan, Palani; Kim, Soo-Jin; Weon, Hang-Yeon; Kwon, Soon-Wo

2016-10-01

A novel siderophore-producing actinomycete, designated PL19T, was isolated from the Scots-pine needle-like leaves collected from TNAU campus, Coimbatore, India. The isolate was chemoorganotrophic in nutrition and able to grow at 30 °C, and the optimum pH and NaCl facilitated the growth pH 6-11 and 0-8 % (w/v), respectively. The cells are filamentous and the mycelia formed are basically of wide and intricately branched substrate mycelium from which aerial mycelia arises, later gets differentiated into spores that are warty and arranged spirally. The 16S rRNA gene of strain PL19T was sequenced and was highly similar to the type strains of species of the genus Streptomyces, including Streptomyces barkulensis RC1831T (98.8 % pairwise similarity), Streptomyces fenghuangensis GIMN4.003T (98.2 %), Streptomyces nanhaiensis SCSIO 01248T (98.0 %), Streptomyces radiopugnans R97T (97.9 %), Streptomyces atacamensis C60T (97.8 %) and Streptomyces macrosporus NBRC 14749T (97.2 %), all of which were subjected to taxonomical characterization using a polyphasic approach. The strains showed unique carbon utilization patterns, and it possesses iso-C16 : 0 anteiso-C15 : 0 and anteiso-C17 : 0 as a major cellular fatty acids. The cell-wall was dominated with ll-type diaminopimelic acid, and the menaquinone type was MK-9(H6, H8). These chemotaxonomic evidences placed strain PL19T within the genus Streptomyces. The determination of G+C ratio (69.5 mol%) and DNA-DNA hybridization values (13.4-31.8 % with the phylogenetically related species) helped in further hierarchical classification of strain PL19T. Based on morphological, physiological and chemotaxonomic data as well as DNA-DNA hybridization values, strain PL19T could be distinguished from the evolutionarily closest species currently available. All these collective data show that strain PL19T represents a novel species of the genus Streptomyces, for which the name Streptomyces pini sp. nov. is proposed. The type strain is PL19T (=NRRL B-24728T=ICMP 17783T).

A novel genus of the class Actinobacteria, Longivirga aurantiaca gen. nov., sp. nov., isolated from lake sediment.

PubMed

Qu, Jian-Hang; Zhang, Lu-Jie; Fu, Yun-Hui; Li, Xiao-Dan; Li, Hai-Feng; Tian, Hai-Long

2018-03-01

A novel actinobacterial strain, designated X5 T , was isolated from the sediment of Taihu Lake in China and was subjected to a polyphasic taxonomic characterization. The strain formed orange-red colonies comprising aerobic, Gram-stain-negative, rod-shaped cells on R2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the organism was closely related to the genus Sporichthya and consistently formed a distinct clade along with the members of this genus. The closest phylogenetic neighbour was Sporichthya polymorpha NBRC 12702 T with 93.7 % 16S rRNA gene sequence similarity. The major fatty acids (>10 %) were iso-C16 : 0 (18.7 %), C18 : 1ω9c (18.6 %) and C17 : 1ω8c (14.0 %). The genomic DNA G+C content was 74.4 mol%. The organism contained menaquinone MK-8(H2), MK-9(H4) and an unidentified menaquinone. Polar lipids were composed of phosphatidylglycerol, an unidentified lipid, two unidentified phospholipids and two unidentified aminolipids. The whole-cell sugars contained ribose, xylose, mannose, glucose and galactose. The cell-wall peptidoglycan contained ll-diaminopimelic acid. Based on the physiological, biochemical and chemotaxonomic data, the organism is proposed to represent a novel genus and species, for which the name Longivirga aurantiaca gen. nov., sp. nov. is proposed. The type strain is X5 T (=CGMCC 4.7317 T =NBRC 112237 T ).

MARSnet: Mission-aware Autonomous Radar Sensor Network for Future Combat Systems

DTIC Science & Technology

2009-03-23

15 , , L x(s)x*(s) ds WdB = lOlog Jo Y ; ; (19) In addition, the sidelobe structure is changed because of the Dop])ler shift...Synchro- nous CDMA Systems.’’ IEICE Trans.Fundamentals. E832A(11): 1 16, 2000. 24 [10] P. Z. Fan. "New Direction in Spreading Sequence Design and the...Suehiro , N Kuroyanagi and P Z Fan. "Two types of polyphase sequence set. for approximately synchronized CDMA systems." IEICE Trans. Fundamentals. E862A

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

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

Thompson, Cristiane C.; Amaral, Gilda R.; Campeão, Mariana

2014-12-23

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.

PubMed

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

2014-11-01

A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6B(T), was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6B(T) were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6B(T) was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-20.0% (w/v), with optimum growth occurring at 10.0% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6B(T) was shown to belong to the phylum Firmicutes and its closest phylogenetic similarities were with the species Virgibacillus koreensis BH30097(T) (97.5%), Virgibacillus albus YIM 93624(T) (97.4%), Sediminibacillus halophilus EN8d(T) (96.8%), Sediminibacillus albus NHBX5(T) (96.6%), Virgibacillus carmonensis LMG 20964(T) (96.3%) and Paraliobacillus quinghaiensis YIM-C158(T) (96.0%), respectively. Phylogenetic analysis revealed that strain B6B(T), along with V. koreensis BH30097(T) and V. albus YIM 93624(T), clustered in a separate clade in the family Bacillaceae. The DNA G+C content of the novel isolate was 35.8 mol%. DNA-DNA hybridization experiments revealed low levels of relatedness between strain B6B(T)and V. koreensis BH30097(T) (13%) and V. albus YIM 93624(T) (33%). The major cellular fatty acid of strain B6B(T) was anteiso-C15 : 0 (75.1%) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90%) and MK-6 (3%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6B(T) within the phylum Firmicutes. It is closely related to V. koreensis and V. albus, but with features that clearly distinguish it from species of the genus Virgibacillus or of other related genera. On the basis of the polyphasic evidence derived in this study, we propose that strain B6B(T) be placed within a new genus, as Aquibacillus halophilus gen. nov., sp. nov., with B6B(T) as the type strain ( =IBRC-M 10775(T) =KCTC 13828(T)). We also propose that V. koreensis and V. albus should be transferred to this new genus and be named Aquibacillus koreensis comb. nov. and Aquibacillus albus comb. nov., respectively. The type strain of Aquibacillus koreensis comb. nov. is BH30097(T) ( =KCTC 3823(T) =IBRC-M 10657(T) =JCM 12387(T)) and the type strain of Aquibacillus albus comb. nov. is YIM 93624(T) ( =DSM 23711(T) =IBRC-M 10798(T) =JCM 17364(T)). © 2014 IUMS.

Polyphasic analysis of an Azoarcus-Leptothrix-dominated bacterial biofilm developed on stainless steel surface in a gasoline-contaminated hypoxic groundwater.

PubMed

Benedek, Tibor; Táncsics, András; Szabó, István; Farkas, Milán; Szoboszlay, Sándor; Fábián, Krisztina; Maróti, Gergely; Kriszt, Balázs

2016-05-01

Pump and treat systems are widely used for hydrocarbon-contaminated groundwater remediation. Although biofouling (formation of clogging biofilms on pump surfaces) is a common problem in these systems, scarce information is available regarding the phylogenetic and functional complexity of such biofilms. Extensive information about the taxa and species as well as metabolic potential of a bacterial biofilm developed on the stainless steel surface of a pump submerged in a gasoline-contaminated hypoxic groundwater is presented. Results shed light on a complex network of interconnected hydrocarbon-degrading chemoorganotrophic and chemolitotrophic bacteria. It was found that besides the well-known hydrocarbon-degrading aerobic/facultative anaerobic biofilm-forming organisms (e.g., Azoarcus, Leptothrix, Acidovorax, Thauera, Pseudomonas, etc.), representatives of Fe(2+)-and Mn(2+)-oxidizing (Thiobacillus, Sideroxydans, Gallionella, Rhodopseudomonas, etc.) as well as of Fe(3+)- and Mn(4+)-respiring (Rhodoferax, Geobacter, Magnetospirillum, Sulfurimonas, etc.) bacteria were present in the biofilm. The predominance of β-Proteobacteria within the biofilm bacterial community in phylogenetic and functional point of view was revealed. Investigation of meta-cleavage dioxygenase and benzylsuccinate synthase (bssA) genes indicated that within the biofilm, Azoarcus, Leptothrix, Zoogloea, and Thauera species are most probably involved in intrinsic biodegradation of aromatic hydrocarbons. Polyphasic analysis of the biofilm shed light on the fact that subsurface microbial accretions might be reservoirs of novel putatively hydrocarbon-degrading bacterial species. Moreover, clogging biofilms besides their detrimental effects might supplement the efficiency of pump and treat systems.

Streptomyces roietensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of jasmine rice, Oryza sativa KDML 105.

PubMed

Kaewkla, Onuma; Franco, Christopher Milton Mathew

2017-11-01

An endophytic actinobacterium, strain WES2 T , was isolated from the stem of a jasmine rice plant collected from a paddy field in Thung Gura Rong Hai, Roi Et province, Thailand. As a result of a polyphasic study, this strain was identified as representing a novel member of the genus Streptomyces. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia and forming chains of looped spores. The closest phylogenetic relations, which shared the highest 16S rRNA gene sequence similarity, were Streptomyces nogalater JCM 4799 T and Streptomyces lavenduligriseus NRRL-ISP 5487 T at 99.1 and 99.0 %, respectively. Chemotaxonomic data, including major fatty acids, cell wall components and major menaquinones, confirmed the affiliation of WES2 T to the genus Streptomyces. The data from the phylogenetic analysis, including physiological and biochemical studies and DNA-DNA hybridization, revealed the genotypic and phenotypic differentiation of WES2 T from the most closely related species with validly published names. The name proposed for the novel species is Streptomycesroietensis sp. nov. The type strain is WES2 T (=DSM 101729=NRRL B-65344).

Lactobacillus crustorum sp. nov., isolated from two traditional Belgian wheat sourdoughs.

PubMed

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Huys, Geert; Vandamme, Peter; De Vuyst, Luc; Vancanneyt, Marc

2007-07-01

A polyphasic taxonomic study of the lactic acid bacteria (LAB) population in three traditional Belgian sourdoughs, sampled between 2002 and 2004, revealed a group of isolates that could not be assigned to any recognized LAB species. Initially, sourdough isolates were screened by means of (GTG)(5)-PCR fingerprinting. Four isolates displaying unique (GTG)(5)-PCR patterns were further investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and represented a bifurcated branch that could not be allocated to any LAB species present in the in-house pheS database. Their phylogenetic affiliation was determined using 16S rRNA gene sequence analysis and showed that the four sourdough isolates belong to the Lactobacillus plantarum group with Lactobacillus mindensis, Lactobacillus farciminis and Lactobacillus nantensis as closest relatives. Further genotypic and phenotypic studies, including whole-cell protein analysis (SDS-PAGE), amplified fragment length polymorphism (AFLP) fingerprinting, DNA-DNA hybridization, DNA G+C content analysis, growth characteristics and biochemical features, demonstrated that the new sourdough isolates represent a novel Lactobacillus species for which the name Lactobacillus crustorum sp. nov. is proposed. The type strain of the new species is LMG 23699(T) (=CCUG 53174(T)).

Acaricomes phytoseiuli gen. nov., sp. nov., isolated from the predatory mite Phytoseiulus persimilis.

PubMed

Pukall, Rüdiger; Schumann, Peter; Schütte, Conny; Gols, Rieta; Dicke, Marcel

2006-02-01

A Gram-positive, rod-shaped, non-spore-forming bacterium, strain CSCT, was isolated from diseased, surface-sterilized specimens of the predatory mite Phytoseiulus persimilis Athias-Henriot and subjected to polyphasic taxonomic analysis. Comparative analysis of the 16S rRNA gene sequence revealed that the strain was a new member of the family Micrococcaceae. Nearest phylogenetic neighbours were determined as Renibacterium salmoninarum (94.0%), Arthrobacter globiformis (94.8%) and Arthrobacter russicus (94.6%). Although the predominant fatty acids (anteiso C15:0), cell-wall sugars (galactose, glucose) and polar lipids (diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol) are in accordance with those of members of the genus Arthrobacter, strain CSCT can be distinguished from members of the genus Arthrobacter by biochemical tests, the absence of a rod-coccus life cycle and the occurrence of the partially saturated menaquinone MK-10(H2) as the predominant menaquinone. The DNA G+C content is 57.7 mol%. On the basis of morphological, chemotaxonomic and phylogenetic differences from other species of the Micrococcaceae, a novel genus and species are proposed, Acaricomes phytoseiuli gen. nov., sp. nov. The type strain is CSCT (=DSM 14247T=CCUG 49701T).

[Identification of Hydrocarbon-Oxidizing Dietzia Bacteria from Petroleum Reservoirs Based on Phenotypic Properties and Analysis of the 16S rRNA and gyrB Genes].

PubMed

Nazina, T N; Shumkova, E S; Sokolova, D Sh; Babich, T L; Zhurina, M V; Xue, Yan-Fen; Osipov, G A; Poltaraus, A B; Tourova, T P

2015-01-01

The taxonomic position of hydrocarbon-oxidizing bacterial strains 263 and 32d isolated from formation water of the Daqing petroleum reservoir (PRC) was determined by polyphasic taxonomy techniques, including analysis of the 16S rRNA and the gyrB genes. The major chemotaxonomic characteristics of both strains, including the IV type cell wall, composition of cell wall fatty acids, mycolic acids, and menaquinones, agreed with those typical of Dietzia strains. The DNA G+C content of strains 263 and 32d were 67.8 and 67.6 mol%, respectively. Phylogenetic analysis of the 16S rRNA gene of strain 32d revealed 99.7% similarity to the gene of D. maris, making it possible to identify strain 32d as belonging to this species. The 16S rRNA gene sequence of strain 263 exhibited 99.7 and 99.9% similarity to those of D. natronolimnaea and D. cercidiphylli YIM65002(T), respectively. Analysis of the gyrB genes of the subterranean isolates and of a number of Dietzia type strains confirmed classiffication of strain 32d as a D. maris strain and of strain 263, as a D. natronolimnaea strain. A conclusion was made concerning higher resolving power of phylogenetic analysis of the gyrB gene compared to the 16S rRNA gene analysis in the case of determination of the species position of Dietzia isolates.

Actinopolyspora biskrensis sp. nov., a novel halophilic actinomycete isolated from Northern Sahara.

PubMed

Saker, Rafika; Bouras, Noureddine; Meklat, Atika; Zitouni, Abdelghani; Schumann, Peter; Spröer, Cathrin; Klenk, Hans-Peter; Sabaou, Nasserdine

2015-03-01

A novel halophilic, filamentous actinomycete, designated H254(T), was isolated from a Saharan soil sample collected from Biskra (Northern Sahara), and subjected to a polyphasic taxonomic characterization. The strain is Gram-positive, aerobic, and halophilic, and the optimum NaCl concentration for growth is 15-20 % (w/v). The cell-wall hydrolysate contained meso-diaminopimelic acid, and the diagnostic whole-cell sugars were arabinose and galactose. The diagnostic phospholipid detected was phosphatidylcholine, and MK-9(H4) was the predominant menaquinone. The major fatty acid profiles were anteiso-C17:0 (32.8 %), C15:0 (28 %), and iso-C17:0 (12.3 %). Comparative analysis of the 16S rRNA gene sequences revealed that the strain H254(T) formed a well-separated sub-branch within the radiation of the genus Actinopolyspora, and the microorganism was most closely related to Actinopolyspora saharensis DSM 45459(T) (99.2 %), Actinopolyspora halophila DSM 43834(T) (99.1 %), and Actinopolyspora algeriensis DSM 45476(T) (99.0 %). Nevertheless, the strain had relatively lower mean values for DNA-DNA relatedness with the above strains (57.2, 68.4, and 45.6 %, respectively). Based on phenotypic features and phylogenetic position, we propose that strain H254(T) represents a novel species of the genus Actinopolyspora, for which the name Actinopolyspora biskrensis sp. nov. is proposed. The type strain of A. biskrensis is strain H254(T) (=DSM 46684(T) =CECT 8576(T)).

Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5).

PubMed

Yu, Jiang; Guan, Xuejiao; Liu, Chongxi; Xiang, Wensheng; Yu, Zhenhua; Liu, Xiaobing; Wang, Guanghua

2016-10-01

A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).

Functionalized poly(arylene ethers) as toughness modifiers for bismaleimides

NASA Technical Reports Server (NTRS)

Stenzenberger, H. D.; Roemer, W.; Hergenrother, P. M.; Jensen, B.; Breitigam, W.

1990-01-01

A family of novel, low molecular weight functionalized poly(arylene ether) resins has been investigated to ascertain its members' toughness-imparting contribution to neat bismaleimide (BMI) resin and BMI-matrix laminate composite properties. Attention is given to the contribution of the reactive poly(arylene ether)'s backbone chemistry to fracture toughness, as well as to the comparative influence of high and low molecular weight reactive poly(arylene ether) types on the modified BMI resin systems. The modified BMIs possess a polyphase morphology, with good adhesion between the thermoplastic nodules and the host thermoset systems.

Energy-efficient electric motors study

NASA Astrophysics Data System (ADS)

1981-03-01

A survey conducted of purchasers of integral horsepower polyphase motors measured current knowledge of and awareness of energy efficient motors, decision making criteria, information sources, purchase and usage patterns, and related factors. The data obtained were used for the electric motor market penetration analysis. Additionally, a telephone survey was made. The study also provides analyses of distribution channels, commercialization constraints, and the impacts of government programs and rising energy prices. Study findings, conclusions, and recommendations are presented. Sample questionnaires and copies of letters to respondents are presented in appendices as well as descriptions of the methods used.

Polyphase Pulse Compression Waveforms

DTIC Science & Technology

1982-01-05

nreuction wzsahrvr mfnolhnr mehid for ic-dmurin the "ur4s at nr-tgtec y Snnian1 : and .%ckrfnYd j91 T-henu ap;xroa4ch was fri r-Tlxrh) thei phase’ý of a...errors were due only to the A/D converters and that the matched-filter phases and amplitude were perfect . The results are shown in Fig. 16 where each...Electronic System," May 1981, AES-17, pp. 364-372. 6. C. Cook and M. Bernfield, "Radar Signals, An Introduction to Thery and Applications," New York

Limnobacter thiooxidans gen. nov., sp. nov., a novel thiosulfate-oxidizing bacterium isolated from freshwater lake sediment.

PubMed

Spring, S; Kämpfer, P; Schleifer, K H

2001-07-01

Two novel thiosulfate-oxidizing strains were isolated from sediment of the littoral zone of a freshwater lake (Lake Chiemsee, Bavaria, Germany). The new isolates, designated CS-K1 and CS-K2T, were gram-negative, slightly curved rods with pointed ends that were motile by means of single polar flagella. Both strains were obligately aerobic and grew on a variety of organic substrates, but not autotrophically. The utilization of thiosulfate led to an increase in the growth yield, indicating that these strains were able to grow chemolithoheterotrophically by oxidation of thiosulfate to sulfate. The optimum thiosulfate concentrations for growth were determined to be 10 mM for strain CS-K1 and 20 mM for strain CS-K2T. Phylogenetically, both strains were affiliated to the beta-Proteobacteria. Their characterization by a polyphasic approach resulted in the placement of both strains into a single species that is related only distantly to any known type species. Thus, the creation of a novel taxon is proposed, with the name Limnobacter thiooxidans gen. nov., sp. nov., to include the novel strains. In addition, the phylogenetic position of the chemolithoheterotrophic strain 'Thiobacillus' Q was determined.

New Penicillium and Talaromyces species from honey, pollen and nests of stingless bees.

PubMed

Barbosa, Renan N; Bezerra, Jadson D P; Souza-Motta, Cristina M; Frisvad, Jens C; Samson, Robert A; Oliveira, Neiva T; Houbraken, Jos

2018-04-13

Penicillium and Talaromyces species have a worldwide distribution and are isolated from various materials and hosts, including insects and their substrates. The aim of this study was to characterize the Penicillium and Talaromyces species obtained during a survey of honey, pollen and the inside of nests of Melipona scutellaris. A total of 100 isolates were obtained during the survey and 82% of those strains belonged to Penicillium and 18% to Talaromyces. Identification of these isolates was performed based on phenotypic characters and β-tubulin and ITS sequencing. Twenty-one species were identified in Penicillium and six in Talaromyces, including seven new species. These new species were studied in detail using a polyphasic approach combining phenotypic, molecular and extrolite data. The four new Penicillium species belong to sections Sclerotiora (Penicillium fernandesiae sp. nov., Penicillium mellis sp. nov., Penicillium meliponae sp. nov.) and Gracilenta (Penicillium apimei sp. nov.) and the three new Talaromyces species to sections Helici (Talaromyces pigmentosus sp. nov.), Talaromyces (Talaromyces mycothecae sp. nov.) and Trachyspermi (Talaromyces brasiliensis sp. nov.). The invalidly described species Penicillium echinulonalgiovense sp. nov. was also isolated during the survey and this species is validated here.

Neisseria arctica sp. nov. isolated from nonviable eggs of greater white-fronted geese (Anser albifrons) in Arctic Alaska

USGS Publications Warehouse

Hansen, Cristina M.; Himschoot, Elizabeth; Hare, Rebekah F.; Meixell, Brandt W.; Van Hemert, Caroline R.; Hueffer, Karsten

2017-01-01

During the summers of 2013 and 2014, isolates of a novel Gram-negative coccus in the Neisseria genus were obtained from the contents of nonviable greater white-fronted goose (Anser albifrons) eggs on the Arctic Coastal Plain of Alaska. We used a polyphasic approach to determine whether these isolates represent a novel species. 16S rRNA gene sequences, 23S rRNA gene sequences, and chaperonin 60 gene sequences suggested that these Alaskan isolates are members of a distinct species that is most closely related to Neisseria canis, N. animaloris, and N. shayeganii. Analysis of the rplF gene additionally showed that our isolates are unique and most closely related to N. weaveri. Average nucleotide identity of the whole genome sequence of our type strain was between 71.5% and 74.6% compared to close relatives, further supporting designation as a novel species. Fatty acid methyl ester analysis showed a predominance of C14:0, C16:0, and C16:1ω7c fatty acids. Finally, biochemical characteristics distinguished our isolates from other Neisseria species. The name Neisseria arctica (type strain KH1503T = ATCC TSD-57T = DSM 103136T) is proposed.

Resident lactic acid bacteria in raw milk Canestrato Pugliese cheese.

PubMed

Aquilanti, L; Dell'Aquila, L; Zannini, E; Zocchetti, A; Clementi, F

2006-08-01

Investigation of the autochthonous lactic acid bacteria (LAB) population of the raw milk protected designation of origin Canestrato Pugliese cheese using phenotypic and genotypic methodologies. Thirty phenotypic assays and three molecular techniques (restriction fragment length polymorphism, partial sequencing of the 16S rRNA gene and recA multiplex PCR assay) were applied to the identification of 304 isolates from raw milk Canestrato Pugliese cheese. As a result, 168 of 207 isolates identified were ascribed to genus Enterococcus, 25 to Lactobacillus, 13 to Lactococcus and one to Leuconostoc. More in details among the lactobacilli, the species Lactobacillus brevis and Lactobacillus plantarum were predominant, including 13 and 10 isolates respectively, whereas among the lactococci, Lactococcus lactis subsp.cremoris [corrected] was the species more frequently detected (seven isolates). Except for the enterococci, phenotypic tests were not reliable enough for the identification of the isolates, if not combined to the genotype-based molecular techniques. The polyphasic approach utilized allowed 10 different LAB species to be detected; thus suggesting the appreciable LAB diversity of the autochthonous microbial population of the Canestrato Pugliese cheese. A comprehensive study of the resident raw milk Canestrato Pugliese cheese microbial population has been undertaken.

Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa.

PubMed

Xie, Cheng-Hui; Yokota, Akira

2006-04-01

Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99.9 % 16S rRNA gene sequence similarity and greater than 70 % DNA-DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99.5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68.0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA-DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39T (=NBRC 15497T = IAM 15283T = CCTCC AB205007T).

Saccharothrix ghardaiensis sp. nov., an actinobacterium isolated from Saharan soil.

PubMed

Bouznada, Khaoula; Bouras, Noureddine; Mokrane, Salim; Chaabane Chaouch, Fawzia; Zitouni, Abdelghani; Pötter, Gabriele; Spröer, Cathrin; Klenk, Hans-Peter; Sabaou, Nasserdine

2017-03-01

The taxonomic position of a new Saccharothrix strain, designated MB46 T , isolated from a Saharan soil sample collected in Mzab region (Ghardaïa province, South Algeria) was established following a polyphasic approach. The novel microorganism has morphological and chemical characteristics typical of the members of the genus Saccharothrix and formed a phyletic line at the periphery of the Saccharothrix espanaensis subcluster in the 16S rRNA gene dendrograms. Results of the 16S rRNA gene sequence comparisons revealed that strain MB46 T shares high degrees of similarity with S. espanaensis DSM 44229 T (99.2%), Saccharothrix variisporea DSM 43911 T (98.7%) and Saccharothrix texasensis NRRL B-16134 T (98.6%). However, the new strain exhibited only 12.5-17.5% DNA relatedness to the neighbouring Saccharothrix spp. On the basis of phenotypic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridizations, strain MB46 T is concluded to represent a novel species of the genus Saccharothrix, for which the name Saccharothrix ghardaiensis sp. nov. (type strain MB46 T  = DSM 46886 T  = CECT 9046 T ) is proposed.

Genetic diversity reflects geographical origin of Ralstonia solanacearum strains isolated from plant and water sources in Spain.

PubMed

Caruso, Paola; Biosca, Elena G; Bertolini, Edson; Marco-Noales, Ester; Gorris, María Teresa; Licciardello, Concetta; López, María M

2017-12-01

The characterization and intraspecific diversity of a collection of 45 Ralstonia solanacearum strains isolated in Spain from different sources and geographical origins is reported. To test the influence of the site and the host on strain diversity, phenotypic and genotypic analysis were performed by a polyphasic approach. Biochemical and metabolic profiles were compared. Serological relationship was evaluated by Indirect-ELISA using polyclonal and monoclonal antibodies. For genotypic analysis, hrpB and egl DNA sequence analysis, repetitive sequences (rep-PCR), amplified fragment length polymorphism (AFLP) profiles and macrorestriction with XbaI followed by pulsed field gel electrophoresis (PFGE) were performed. The biochemical and metabolic characterization, serological tests, rep-PCR typing and phylogenetic analysis showed that all analysed strains belonged to phylotype II sequevar 1 and shared homogeneous profiles. However, interesting differences among strains were found by AFLP and macrorestriction with XbaI followed by PFGE techniques, some profiles being related to the geographical origin of the strains. Diversity results obtained offer new insights into the biogeography of this quarantine organism and its possible sources and reservoirs in Spain and Mediterranean countries. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Hypersaline sapropels act as hotspots for microbial dark matter

DOE PAGES

Andrei, Adrian -Stefan; Baricz, Andreea; Robeson, Michael Scott; ...

2017-07-21

Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions.more » Furthermore, the polyphasic approach combined deep coverage SSU rRNA gene amplicon sequencing and bioinformatics with RT-qPCR and physicochemical investigations. We found that sapropels developed an analogous elemental milieu and harbored prokaryotes affiliated with fifty-nine phyla, among which the most abundant were Proteobacteria, Bacteroidetes and Chloroflexi. Containing thirty-two candidate divisions and possibly undocumented prokaryotic lineages, the hypersaline sapropels were found to accommodate one of the most diverse and novel ecosystems reported to date and may contribute to completing the phylogenetic branching of the tree of life.« less

Identification, characterization and description of Arcobacter faecis sp. nov., isolated from a human waste septic tank.

PubMed

Whiteduck-Léveillée, Kerri; Whiteduck-Léveillée, Jenni; Cloutier, Michel; Tambong, James T; Xu, Renlin; Topp, Edward; Arts, Michael T; Chao, Jerry; Adam, Zaky; Lévesque, C André; Lapen, David R; Villemur, Richard; Khan, Izhar U H

2016-03-01

A study on the taxonomic classification of Arcobacter species was performed on the cultures isolated from various fecal sources where an Arcobacter strain AF1078(T) from human waste septic tank near Ottawa, Ontario, Canada was characterized using a polyphasic approach. Genetic investigations including 16S rRNA, atpA, cpn60, gyrA, gyrB and rpoB gene sequences of strain AF1078(T) are unique in comparison with other arcobacters. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain is most closely related to Arcobacter lanthieri and Arcobacter cibarius. Analyses of atpA, cpn60, gyrA, gyrB and rpoB gene sequences suggested that strain AF1078(T) formed a phylogenetic lineage independent of other species in the genus. Whole-genome sequence, DNA-DNA hybridization, fatty acid profile and phenotypic analysis further supported the conclusion that strain AF1078(T) represents a novel Arcobacter species, for which the name Arcobacter faecis sp. nov. is proposed, with type strain AF1078(T) (=LMG 28519(T); CCUG 66484(T)). Crown Copyright © 2015. Published by Elsevier GmbH. All rights reserved.

Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov.

PubMed

Bach, Evelise; Sant'Anna, Fernando Hayashi; Magrich Dos Passos, João Frederico; Balsanelli, Eduardo; de Baura, Valter Antonio; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Passaglia, Luciane Maria Pereira

2017-08-31

The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biodiversity of species of Aspergillus section Fumigati in semi-desert soils in Argentina.

PubMed

Giusiano, Gustavo E; Piontelli, Eduardo; Fernández, Mariana S; Mangiaterra, Magdalena L; Cattana, María E; Kocsubé, Sándor; Varga, János

The distribution of Aspergillus species in soil has been widely studied all over the world. The aim of this study was the phenotypic and genotypic characterization of species Aspergillus belonging to section Fumigati present in soils from two Argentinian semi-desert areas having different geological conditions. Altogether, 23 isolates belonging to Aspergillus section Fumigati were recovered and identified using a polyphasic approach including phenotypic and molecular identifications. Aspergillus fumigatus sensu stricto and Aspergillus fumigatiaffinis had the highest frequency, of occurrence while isolates closely related to Aspergillus udagawae and Aspergillus felis were rarely observed. A. fumigatiaffinis and isolates closer to A. udagawae were isolated for the first time from Argentinian soils and this is the first report on the occurrence of species belonging to the A. felis clade in South America. Recent scientific interests in biodiversity, as well as the increasing importance of aspergilli as causative agents of human and animal diseases increase the need to understand the diversity and occurrence of these fungi in nature. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Polyphasic Microbial Analysis of Traditional Korean Jeung-Pyun Sourdough Fermented with Makgeolli.

PubMed

Lim, Sae Bom; Tingirikari, Jagan Mohan Rao; Kwon, Ye Won; Li, Ling; Kim, Grace E; Han, Nam Soo

2017-02-28

Jeung-pyun, a fermented rice cake, is prepared by fermenting rice sourdough using makgeolli, a traditional Korean rice wine, in the presence of yeast and lactic acid bacteria (LAB). The goal of this study was to conduct biochemical and microbial analyses of five different rice sourdoughs, each fermented with a different commercial makgeolli, using culture-dependent and culture-independent approaches. All sourdough samples fermented with different makgeolli for 6.5 h showed different profiles in pH, total titratable acidity, organic acid concentration, and microbial growth. LAB belonging to different genera were identified based on colony morphology on modified MRS and sourdough bacteria agar medium. PCR-denaturinggradient gel electrophoresis analyses of the five sourdoughs showed different bands corresponding to LAB and yeast. 16S/26S rRNA gene sequence analyses of the samples confirmed that the predominant LAB in the five fermented rice doughs was Lactobacillus plantarum , Lb. pentosus , and Lb. brevis . Various other Lactobacillus spp. and Saccharomyces cerevisiae were common in all five fermented samples. This study provides comprehensive and comparative information on the microflora involved in fermentation of rice sourdough and signifies the need to develop effective starters to enrich the quality of jeung-pyun.

Nocardioides albertanoniae sp. nov., isolated from Roman catacombs.

PubMed

Alias-Villegas, Cynthia; Jurado, Valme; Laiz, Leonila; Miller, Ana Z; Saiz-Jimenez, Cesareo

2013-04-01

A Gram-reaction-positive, aerobic, non-spore-forming, rod- or coccoid-shaped, strain, CD40127(T), was isolated from a green biofilm covering the wall of the Domitilla Catacombs in Rome, Italy. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CD40127(T) belongs to the genus Nocardioides, closely related to Nocardioides luteus DSM 43366(T) and Nocardioides albus DSM 43109(T) with 98.86 % and 98.01 % similarity values, respectively. Strain CD40127(T) exhibited 16S rRNA gene sequence similarity values below 96.29 % with the rest of the species of the genus Nocardioides. The G+C content of the genomic DNA was 69.7 mol%. The predominant fatty acid was iso-C16 : 0 and the major menaquinone was MK-8(H4) in accordance with the phenotypes of other species of the genus Nocardioides. A polyphasic approach using physiological tests, fatty acid profiles, DNA base ratios and DNA-DNA hybridization showed that isolate CD40127(T) represents a novel species within the genus Nocardioides, for which the name Nocardioides albertanoniae is proposed. The type strain is CD40127(T) ( = DSM 25218(T) = CECT 8014(T)).

Streptomyces atlanticus sp. nov., a novel actinomycete isolated from marine sponge Aplysina fulva (Pallas, 1766).

PubMed

Silva, Fábio Sérgio Paulino; Souza, Danilo Tosta; Zucchi, Tiago Domingues; Pansa, Camila Cristiane; de Figueiredo Vasconcellos, Rafael Leandro; Crevelin, Eduardo José; de Moraes, Luiz Alberto Beraldo; Melo, Itamar Soares

2016-11-01

The taxonomic position of a novel marine actinomycete isolated from a marine sponge, Aplysina fulva, which had been collected in the Archipelago of Saint Peter and Saint Paul (Equatorial Atlantic Ocean), was determined by using a polyphasic approach. The organism showed a combination of morphological and chemotaxonomic characteristics consistent with its classification in the genus Streptomyces and forms a distinct branch within the Streptomyces somaliensis 16S rRNA gene tree subclade. It is closely related to Streptomyces violascens ISP 5183 T (97.27 % 16S rRNA gene sequence similarity) and Streptomyces hydrogenans NBRC 13475 T (97.15 % 16S rRNA gene sequence similarity). The 16S rRNA gene similarities between the isolate and the remaining members of the subclade are lower than 96.77 %. The organism can be distinguished readily from other members of the S. violacens subclade using a combination of phenotypic properties. On the basis of these results, it is proposed that isolate 103 T (=NRRL B-65309 T  = CMAA 1378 T ) merits recognition as the type strain of a new Streptomyces species, namely Streptomyces atlanticus sp. nov.

Streptomyces tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.).

PubMed

Zhao, Junwei; Shi, Linlin; Li, Wenchao; Wang, Jiabin; Wang, Han; Tian, Yuanyuan; Xiang, Wensheng; Wang, Xiangjing

2018-02-01

Two novel actinomycete isolates, designated strains NEAU-A4 T and NEAU-A3, were isolated from rhizosphere soil of wheat (Triticumaestivum L.) and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics of the two strains coincided with those of the genus Streptomyces. The 16S rRNA gene sequence analysis showed that the two isolates exhibited 99.6 % 16S rRNA gene sequence similarity with each other and that they were most closely related to Streptomyces violaceorectus DSM 40279 T (98.8, 99.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains clustered together and formed a separate subclade. Furthermore, a combination of DNA-DNA hybridization results and some physiological and biochemical properties demonstrated that the two strains could be distinguished from its closest relative. Therefore, it is proposed that strains NEAU-A4 T and NEAU-A3 should be classified as representatives of a novel species of the genus Streptomyces, for which the name Streptomycestritici sp. nov. is proposed. The type strain is NEAU-A4 T (=CGMCC 4.7393 T =DSM 104540 T ).

Hypersaline sapropels act as hotspots for microbial dark matter

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

Andrei, Adrian -Stefan; Baricz, Andreea; Robeson, Michael Scott

Present-day terrestrial analogue sites are crucial ground truth proxies for studying life in geochemical conditions close to those assumed to be present on early Earth or inferred to exist on other celestial bodies (e.g. Mars, Europa). Although hypersaline sapropels are border-of-life habitats with moderate occurrence, their microbiological and physicochemical characterization lags behind. Here, we study the diversity of life under low water activity by describing the prokaryotic communities from two disparate hypersaline sapropels (Transylvanian Basin, Romania) in relation to geochemical milieu and pore water chemistry, while inferring their role in carbon cycling by matching taxa to known taxon-specific biogeochemical functions.more » Furthermore, the polyphasic approach combined deep coverage SSU rRNA gene amplicon sequencing and bioinformatics with RT-qPCR and physicochemical investigations. We found that sapropels developed an analogous elemental milieu and harbored prokaryotes affiliated with fifty-nine phyla, among which the most abundant were Proteobacteria, Bacteroidetes and Chloroflexi. Containing thirty-two candidate divisions and possibly undocumented prokaryotic lineages, the hypersaline sapropels were found to accommodate one of the most diverse and novel ecosystems reported to date and may contribute to completing the phylogenetic branching of the tree of life.« less

Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India.

PubMed

Shinde, Varsha Laxman; Meena, Ram Murti; Shenoy, Belle Damodara

2018-03-01

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons. Copyright © 2018 Elsevier Ltd. All rights reserved.

Streptococcus penaeicida sp. nov., isolated from a diseased farmed Pacific white shrimp (Penaeus vannamei).

PubMed

Morales-Covarrubias, Maria Soledad; Del Carmen Bolan-Mejía, María; Vela Alonso, Ana Isabel; Fernandez-Garayzabal, Jose F; Gomez-Gil, Bruno

2018-05-01

Strain CAIM 1838 T , isolated from the hepatopancreas of a cultured diseased Pacific white shrimp (Penaeus vannamei), was subjected to characterization by a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analysis, strain CAIM 1838 T was most closely related to Streptococcus bovimastitidis 99.3 % and to other species of the Pyogenes clade of Streptococcus with lower similarity values. Average nucleotide identity values and the genome-to-genome distance of strain CAIM 1838 T , as compared with the type strains, confirmed the separate species status with closely related species of the genus Streptococcus and were all below the thresholds to delimit a species, 93.1 and 49.4 %, respectively. The DNA G+C content was 38.1 mol%. Differential phylogenetic distinctiveness together with phenotypic properties obtained in this study revealed that strain CAIM 1838 T could be differentiated from the closely related species. Based on these results it is proposed that strain CAIM 1838 T represents a novel species in the genus Streptococcus, for which the name Streptococcus penaeicida sp. nov is proposed (type strain, CAIM 1838 T =CECT 8596 T ,=DSM26545 T ), is proposed.

Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water.

PubMed

Wong, Shu-Kuan; Park, Sanghwa; Lee, Jung-Sook; Lee, Keun Chul; Chiura, Hiroshi Xavier; Kogure, Kazuhiro; Hamasaki, Koji

2015-10-01

A slightly curved-rod-shaped, pink-pigmented, Gram-stain-negative, aerobic bacterial strain with gliding motility, designated SK-8T, was isolated from coastal surface water of Misaki, Japan. Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain SK-8T belonged to the genus Fabibacter and showed 96.0 % sequence similarity to the type strain of the most closely related species, Fabibacter pacificus DY53T. The novel isolate was phenotypically and physiologically different from previously described strains. The major cellular fatty acids were iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. Major polar lipids were phosphatidylethanolamine, two aminophospholipids and an unidentified phospholipid. The DNA G+C content was 39.1 mol% and MK-7 was the only predominant isoprenoid quinone. On the basis of this taxonomic study employing a polyphasic approach, it was suggested that strain SK-8T represents a novel species of the genus Fabibacter, with the newly proposed name Fabibacter misakiensis sp. nov. The type strain is SK-8T ( = NBRC 110216T = KCTC 32969T).

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.

Transfer of Pseudomonas flectens Johnson 1956 to Phaseolibacter gen. nov., in the family Enterobacteriaceae, as Phaseolibacter flectens gen. nov., comb. nov.

PubMed

Halpern, Malka; Fridman, Svetlana; Aizenberg-Gershtein, Yana; Izhaki, Ido

2013-01-01

Pseudomonas flectens Johnson 1956, a plant-pathogenic bacterium on the pods of the French bean, is no longer considered to be a member of the genus Pseudomonas sensu stricto. A polyphasic approach that included examination of phenotypic properties and phylogenetic analyses based on 16S rRNA, rpoB and atpD gene sequences supported the transfer of Pseudomonas flectens Johnson 1956 to a new genus in the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Two strains of Phaseolibacter flectens were studied (ATCC 12775(T) and LMG 2186); the strains shared 99.8 % sequence similarity in their 16S rRNA genes and the housekeeping gene sequences were identical. Strains of Phaseolibacter flectens shared 96.6 % or less 16S rRNA gene sequence similarity with members of different genera in the family Enterobacteriaceae and only 84.7 % sequence similarity with Pseudomonas aeruginosa LMG 1242(T), demonstrating that they are not related to the genus Pseudomonas. As Phaseolibacter flectens formed an independent phyletic lineage in all of the phylogenetic analyses, it could not be affiliated to any of the recognized genera within the family Enterobacteriaceae and therefore was assigned to a new genus. Cells were Gram-negative, straight rods, motile by means of one or two polar flagella, fermentative, facultative anaerobes, oxidase-negative and catalase-positive. Growth occurred in the presence of 0-60 % sucrose. The DNA G+C content of the type strain was 44.3 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, Pseudomonas flectens Johnson 1956 is transferred to the novel genus Phaseolibacter gen. nov. as Phaseolibacter flectens gen. nov., comb. nov. The type strain of Phaseolibacter flectens is ATCC 12775(T) = CFBP 3281(T) = ICMP 745(T) = LMG 2187(T) = NCPPB 539(T).

Nocardiopsis akesuensis sp. nov., an actinomycete isolated from a salt water beach.

PubMed

Gao, Guang-Bin; Luo, Xiao-Xia; Xia, Zhan-Feng; Zhang, Yao; Wan, Chuan-Xing; Zhang, Li-Li

2016-12-01

The taxonomic position of a novel actinomycete, strain TRM 46250T, isolated from the sediment of a salt water beach at Baicheng, Xinjiang, China, was determined by a polyphasic approach. Strain TRM 46250T grew optimally in the presence of 2 % (w/v) NaCl and an optimum temperature range for growth of 28-37 °C. The whole-cell sugars of strain TRM 46250T were ribose, xylose, mannose and galactose. The diagnostic diamino acid was meso-diaminopimelic acid. The polar lipids were phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethyl ethanolamine and six unidentified phospholipids. The predominant menaquinones were MK-10, MK-10(H6) and MK-10(H8). The major fatty acids were 10-methyl C18 : 0, iso-C16 : 0, C16 : 0, iso-G C16 : 1 and C18 : 1ω9c. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Nocardiopsis. The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1493 nt) with those of representative strains showed that the strain consistently falls into a distinct phyletic line together with Nocardiopsis gilva YIM 90087T (97.68 % similarity) and a subclade consisting of Nocardiopsis composta KS9T (97.52 %), Nocardiopsis rosea YIM 90094T (97.44 %) and Nocardiopsis rhodophaea YIM 90096T (97.16 %). However, DNA-DNA hybridization studies between strain TRM 46250T and N. gilva YIM 90087T showed only 36.94 % relatedness. On the basis of these data, strain TRM 46250T should be designated as a representative of a novel species of the genus Nocardiopsis, for which the name Nocardiopsis akesuensis sp. nov. is proposed. The type strain is TRM 46250T (=CCTCC AA 2015027T=KCTC 39725T).

Rudaeicoccus suwonensis gen. nov., sp. nov., an actinobacterium isolated from the epidermal tissue of a root of a Phalaenopsis orchid.

PubMed

Kim, Soo-Jin; Jang, Yun-Hee; Ahn, Jae-Hyung; Weon, Hang-Yeon; Schumann, Peter; Chun, Se-Chul; Kwon, Soon-Wo; Kim, Wan-Gyu

2013-04-01

A bacterial strain, designated HOR6-4(T), was isolated from the epidermal tissue of a root of a Phalaenopsis orchid. Strain HOR6-4(T) was characterized using a polyphasic approach. The cells were aerobic, Gram-stain-positive, non-motile coccoids. Phylogenetic analysis of its 16S rRNA gene sequence revealed a clear affiliation with the family Dermacoccaceae. Strain HOR6-4(T) showed relatively low 16S rRNA gene sequence similarity (below 95.9 %) to type strains of species with validly published names, showing the highest sequence similarities to the type strains of Flexivirga alba (95.8 %) and Yimella lutea (95.5 %). The DNA G+C content of strain HOR6-4(T) was 64.7 mol%. Strain HOR6-4(T) had anteiso-C17 : 0 (19.3 %), 10-methyl C18 : 0 (tuberculostearic acid; 13.5 %) and 10-methyl C17 : 0 (11.7 %) as the major fatty acids and contained MK-8(H4) and MK-8(H6) as the predominant quinones. Polar lipids were diphosphatidylglycerol, phosphatidylinositol, three aminophospholipids, two phospholipids and an aminolipid. The peptidoglycan type was A4α, with an L-Lys-L-Thr-D-Glu interpeptide bridge with a glycine residue bound to the alpha-carboxyl group of D-Glu in position 2 of the peptide subunit. Mycolic acids were not present. On the basis of comparative analysis of phenotypic and phylogenetic traits, strain HOR6-4(T) is considered to represent a novel species in a new genus in the family Dermacoccaceae, for which the name Rudaeicoccus suwonensis gen. nov., sp. nov. is proposed. The type strain of Rudaeicoccus suwonensis is HOR6-4(T) ( = KACC 12637(T)  = DSM 19560(T)).

Aquipuribacter nitratireducens sp. nov., isolated from a soil sample of a mud volcano.

PubMed

Srinivas, T N R; Anil Kumar, P; Tank, M; Sunil, B; Poorna, Manasa; Zareena, Begum; Shivaji, S

2015-08-01

A novel Gram-stain-positive, coccoid, non-motile bacterium, designated strain AMV4T, was isolated from a soil sample collected from a mud volcano located in the Andaman Islands, India. The colony was pale orange. Strain AMV4T was positive for oxidase, aesculinase, lysine decarboxylase and ornithine decarboxylase activities and negative for amylase, catalase, cellulase, protease, urease and lipase activities. 16S rRNA gene sequence analysis indicated that strain AMV4T was a member of the order Actinomycetales and was closely related to Aquipuribacter hungaricus with a sequence similarity of 97.13% (pairwise alignment). Phylogenetic analyses showed that strain AMV4T clustered with Aquipuribacter hungaricus and was distantly related to the other genera of the family Intrasporangiaceae. DNA-DNA hybridization between strains AMV4T and Aquipuribacter hungaricus IV-75T showed a relatedness of 28%. The predominant cellular fatty acids were iso-C15 : 0 (6.9%), anteiso-C15 : 0 (25.3%), C16 : 0 (12.9%), anteiso-C16 : 0 (5.6%), C18 : 1ω9c (19.8%) and C18 : 3ω6,9,12c (9.1%). The diagnostic diamino acid in the cell-wall peptidoglycan of strain AMV4T was meso-diaminopimelic acid. Strain AMV4T contained MK-10(H4) as the predominant respiratory quinone. The polar lipids consisted of phosphatidylglycerol, one unidentified glycolipid, two unidentified phospholipids and five unidentified lipids. The DNA G+C content of strain AMV4T was 74.3 mol%. Based on data from this taxonomic study using a polyphasic approach, it is proposed that strain AMV4T represents a novel species of the genus Aquipuribacter, with the suggested name Aquipuribacter nitratireducens sp. nov. The type strain is AMV4T ( = CCUG 58430T = DSM 22863T = NBRC 107137T).

Actinoplanes rhizophilus sp. nov., an actinomycete isolated from the rhizosphere of Sansevieria trifasciata Prain.

PubMed

He, Hairong; Xing, Jia; Liu, Chongxi; Li, Chuang; Ma, Zhaoxu; Li, Jiansong; Xiang, Wensheng; Wang, Xiangjing

2015-12-01

A novel actinomycete, designated strain NEAU-A-2T, was isolated from the rhizosphere soil of Sansevieria trifasciata Prain collected from Heilongjiang province, north-east China. The taxonomic status of this organism was established using a polyphasic approach. The isolate formed irregular sporangia containing motile spores on the substrate mycelium. The whole-cell sugars were xylose and galactose. The predominant menaquinones were MK-9(H10), MK-9(H2), MK-10(H2) and MK-10(H4). The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylinositol, three unidentified phospholipids and an unidentified glycolipid. 16S rRNA gene sequence similarity studies showed that strain NEAU-A-2T belongs to the genus Actinoplanes with the highest sequence similarities to Actinoplanes globisporus NBRC 13912T (97.7 % 16S rRNA gene sequence similarity), Actinoplanes ferrugineus IMSNU 22125T (97.5 %), Actinoplanes toevensis MN07-A0368T (97.2 %) and Actinoplanes rishiriensis NBRC 108556T (97.2 %); similarities to type strains of other species of this genus were < 97 %. Two tree-making algorithms showed that strain NEAU-A-2T formed a distinct clade with A. globisporus NBRC 13912T and A. rishiriensis NBRC 108556T. However, low DNA-DNA relatedness values allowed the isolate to be differentiated from the above-mentioned two species of the genus Actinoplanes. Moreover, strain NEAU-A-2T could also be distinguished from the most closely related species by morphological and physiological characteristics. Therefore, in conclusion, isolate NEAU-A-2T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes rhizophilus sp. nov. is proposed. The type strain is NEAU-A-2T ( = CGMCC 4.7133T = DSM 46672T).

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 ).

Streptomyces zhihengii sp. nov., isolated from rhizospheric soil of Psammosilene tunicoides.

PubMed

Huang, Mei-Juan; Fei, Jing-Jing; Salam, Nimaichand; Kim, Chang-Jin; Hozzein, Wael N; Xiao, Min; Huang, Hai-Quan; Li, Wen-Jun

2016-10-01

An actinomycete strain, designated YIM T102(T), was isolated from the rhizospheric soil of Psammosilene tunicoides W. C. Wu et C. Y. Wu collected from Lijiang, Yunnan Province, China. The taxonomic position of the new isolate was investigated by a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YIM T102(T) belongs to the genus Streptomyces. Strain YIM T102(T) was most closely related to Streptomyces eurocidicus NRRL B-1676(T) with a pairwise 16S rRNA gene sequence similarity of 98.9 %. However, DNA-DNA relatedness value between strain YIM T102(T) and S. eurocidicus NBRC 13491(T) was found to be 37.8 ± 1.8 %. The menaquinone composition detected for strain YIM T102(T) was MK-9 (H6) and MK-9 (H8), while the major fatty acids were summed feature 4 (38.0 %), anteiso-C15:0 (13.1 %), iso-C16:0 (10.1 %), summed feature 3 (9.8 %) and C16:0 (9.0 %) and iso-C15:0 (5.2 %). The whole-cell hydrolysates contained galactose, glucose, ribose and mannose, along with LL-diaminopimelic acid as the diagnostic diamino acid in the peptidoglycan. The DNA G+C content was 70.7 mol%. Strain YIM T102(T) also exhibited antagonistic activity against Alternaria alternata, Alternaria brassicae and Colletotrichum nicotianae Averna, based on the findings from the comparative analyses of phenotypic and genotypic characteristics; it is proposed that strain YIM T102 represents a novel species of the genus Streptomyces, for which the name Streptomyces zhihengii sp. nov. is proposed. The type strain is YIM T102(T) (=KCTC 39115(T) = DSM 42176(T) = CGMCC 4.7248(T)).

Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant.

PubMed

Srinivasan, Sathiyaraj; Kim, Myung Kyum; Lim, Sangyong; Joe, Minho; Lee, Myungjin

2012-06-01

A Gram-stain-positive, strictly aerobic, spherical, non-motile red-pigmented bacterial strain, designated MJ27(T), was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was used to study the taxonomic position of strain MJ27(T). Strain MJ27(T) shared highest 16S rRNA gene sequence similarity with Deinococcus grandis DSM 3963(T) (98.8 %), Deinococcus caeni Ho-08(T) (97.5 %) and Deinococcus aquaticus PB314(T) (96.6 %.); levels of sequence similarity with the type strains of other Deinococcus species were less than 96.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ27(T) belonged to the clade formed by members of the genus Deinococcus in the family Deinococcaceae. The G+C content of the genomic DNA of strain MJ27(T) was 67.6 mol%. The chemotaxonomic characteristics of strain MJ27(T) were typical of members of the genus Deinococcus, with MK-8 as the predominant respiratory quinone, C(16:1)ω7c, C(15:1)ω6c, C(16:0) and C(15:0) as major fatty acids (>12 %), ornithine as the diamino acid in the cell-wall peptidoglycan and resistance to gamma radiation [D(10) (dose required to reduce the bacterial population by tenfold) >9 kGy]. The low levels of DNA-DNA relatedness reported here (5.3±1.5-29.2±2.3 %) indicate that strain MJ27(T) represents a species that is separate from its closest relatives in the genus Deinococcus. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ27(T) is considered to represent a novel species of the genus Deinococcus, for which the name Deinococcus daejeonensis sp. nov. is proposed. The type strain is MJ27(T) ( = KCTC 13751(T) = JCM 16918(T)).

A review of the arcuate structures in the Iberian Variscides; constraints and genetic models

NASA Astrophysics Data System (ADS)

Dias, R.; Ribeiro, A.; Romão, J.; Coke, C.; Moreira, N.

2016-06-01

The main Ibero-Armorican Arc (IAA) is essentially defined by a predominant NW-SE trend in the Iberian branch and an E-W trend in the Brittany one. However, in northern Spain it presents a 180° rotation, sometimes known as the Cantabrian Arc (CA). The relation between both arcs is controversial, being considered either as a single arc due to one tectonic event, or as the result of a polyphasic process. According to the last assumption, there is a later arcuate structure (CA), overlapping a previous major one (IAA). Whatever the models, they must be able to explain the presence of a Variscan sinistral transpression in Iberia and a dextral one in Armorica, and a deformation spanning from the Devonian to the Upper Carboniferous. Another arcuate structure, in continuity with the CA, the Central-Iberian Arc (CIA) was recently proposed mainly based upon on magnetic anomalies, geometry of major folds and Ordovician paleocurrents. The critical review of the structural, stratigraphic and geophysical data supports both the IAA and the CA, but as independent structures. However, the presence of a CIA is highly questionable and could not be supported. The complex strain pattern of the IAA and the CA could be explained by a Devonian - Carboniferous polyphasic indentation of a Gondwana promontory. In this model the CA is essentially a thin-skinned arc, while the IAA has a more complex and longer evolution that has led to a thick-skinned first order structure. Nevertheless, both arcs are essentially the result of a lithospheric bending process during the Iberian Variscides.

Optimized FPGA Implementation of Multi-Rate FIR Filters Through Thread Decomposition

NASA Technical Reports Server (NTRS)

Zheng, Jason Xin; Nguyen, Kayla; He, Yutao

2010-01-01

Multirate (decimation/interpolation) filters are among the essential signal processing components in spaceborne instruments where Finite Impulse Response (FIR) filters are often used to minimize nonlinear group delay and finite-precision effects. Cascaded (multi-stage) designs of Multi-Rate FIR (MRFIR) filters are further used for large rate change ratio, in order to lower the required throughput while simultaneously achieving comparable or better performance than single-stage designs. Traditional representation and implementation of MRFIR employ polyphase decomposition of the original filter structure, whose main purpose is to compute only the needed output at the lowest possible sampling rate. In this paper, an alternative representation and implementation technique, called TD-MRFIR (Thread Decomposition MRFIR), is presented. The basic idea is to decompose MRFIR into output computational threads, in contrast to a structural decomposition of the original filter as done in the polyphase decomposition. Each thread represents an instance of the finite convolution required to produce a single output of the MRFIR. The filter is thus viewed as a finite collection of concurrent threads. The technical details of TD-MRFIR will be explained, first showing its applicability to the implementation of downsampling, upsampling, and resampling FIR filters, and then describing a general strategy to optimally allocate the number of filter taps. A particular FPGA design of multi-stage TD-MRFIR for the L-band radar of NASA's SMAP (Soil Moisture Active Passive) instrument is demonstrated; and its implementation results in several targeted FPGA devices are summarized in terms of the functional (bit width, fixed-point error) and performance (time closure, resource usage, and power estimation) parameters.

Behaviour of lactic acid bacteria populations in Pecorino di Carmasciano cheese samples submitted to environmental conditions prevailing in the gastrointestinal tract: evaluation by means of a polyphasic approach.

PubMed

Ricciardi, Annamaria; Blaiotta, Giuseppe; Di Cerbo, Alessandro; Succi, Mariantonietta; Aponte, Maria

2014-06-02

The survival of the autochthonous microflora, of samples collected during Pecorino di Carmasciano cheese manufacturing, was evaluated along the passage through a model mimicking the gastro-intestinal tract. The aim was the selection of lactic acid bacteria potentially able to arrive alive and metabolically active to the colon. The dynamics of lactic microbiota, throughout simulated digestion of cheese samples, were evaluated by means of an approach PCR-DGGE-based. Dominant species after cheese digestion could be related to the Lactobacillus plantarum and Lactobacillus casei groups. Sixty-three strains, which survived to simulated gastro-intestinal transit, were further evaluated for technological features and tolerance to human digestion in several experimental conditions, according to routinely used protocols. Bacterial survival appeared to be, more than strain-specific, strongly affected by experimental conditions, i.e. some strains showed an acceptable survival when resuspended in skim milk but not in ewe milk and vice versa. Nevertheless according to data, one gram of fresh Pecorino di Carmasciano cheese may convey to human colon about the same amount of viable LAB of a probiotic drink. Although it cannot be assumed that lactobacilli introduced with Pecorino have beneficial effects on the host, the healthy impact of autochthonous lactic acid bacteria of naturally fermented food has a broad consensus in the current literature. Copyright © 2014 Elsevier B.V. All rights reserved.

POWTEX Neutron Diffractometer at FRM II - New Perspectives for In-Situ Rock Deformation Analysis

NASA Astrophysics Data System (ADS)

Walter, J. M.; Stipp, M.; Ullemeyer, K.; Klein, H.; Leiss, B.; Hansen, B. T.; Kuhs, W. F.

2012-04-01

In Geoscience quantitative texture analysis here defined as the quantitative analysis of the crystallographic preferred orientation (CPO), is a common tool for the investigation of fabric development in mono- and polyphase rocks, their deformation histories and kinematics. Bulk texture measurements also allow the quantitative characterisation of the anisotropic physical properties of rock materials. A routine tool to measure bulk sample volumes is neutron texture diffraction, as neutrons have large penetration capabilities of several cm in geological sample materials. The new POWTEX (POWder and TEXture) Diffractometer at the neutron research reactor FRM II in Garching, Germany is designed as a high-intensity diffractometer by groups from the RWTH Aachen, Forschungszentrum Jülich and the University of Göttingen. Complementary to existing neutron diffractometers (SKAT at Dubna, Russia; GEM at ISIS, UK; HIPPO at Los Alamos, USA; D20 at ILL, France; and the local STRESS-SPEC and SPODI at FRM II) the layout of POWTEX is focused on fast time-resolved experiments and the measurement of larger sample series as necessary for the study of large scale geological structures. POWTEX is a dedicated beam line for geoscientific research. Effective texture measurements without sample tilting and rotation are possible firstly by utilizing a range of neutron wavelengths simultaneously (Time-of-Flight technique) and secondly by the high detector coverage (9.8 sr) and a high flux (~1 - 107 n/cm2s) at the sample. Furthermore the instrument and the angular detector resolution is designed also for strong recrystallisation textures as well as for weak textures of polyphase rocks. These instrument characteristics allow in-situ time-resolved texture measurements during deformation experiments on rocksalt, ice and other materials as large sample environments will be implemented at POWTEX. The in-situ deformation apparatus is operated by a uniaxial spindle drive with a maximum axial load of 250 kN, which will be redesigned to minimize shadowing effects inside the cylindrical detector. The HT deformatione experiments will be carried out in uniaxial compression or extension and an upgrade to triaxial deformation conditions is envisaged. The load frame can alternatively be used for ice deformation by inserting a cryostat cell for temperatures down to 77 K with a triaxial apparatus allowing also simple shear experiments on ice. Strain rates range between 10-8 and 10-3 s-1 reaching to at least 50 % axial strain. The deformation apparatus is designed for continuous long-term deformation experiments and can be exchanged between in-situ and ex-situ placements during continuous operation inside and outside the neutron detector.

Graded pitch electromagnetic pump for thin strip metal casting systems

DOEpatents

Kuznetsov, Stephen B.

1986-01-01

A metal strip casing system is provided with an electromagnetic pump which includes a pair of primary blocks having a graded pole pitch, polyphase ac winding and being arranged on opposite sides of a movable heat sink. A nozzle is provided for depositing liquid metal on the heat sink such that the resulting metal strip and heat sink combination is subjected to a longitudinal electromagnetic field which increases in wavelength in the direction of travel of the heat sink, thereby subjecting the metal and heat sink to a longitudinal force having a magnitude which increases in the direction of travel.

Colwellia aestuarii sp. nov., isolated from a tidal flat sediment in Korea.

PubMed

Jung, Seo-Youn; Oh, Tae-Kwang; Yoon, Jung-Hoon

2006-01-01

A novel Colwellia-like bacterial strain, SMK-10T, was isolated from a tidal flat sediment in Korea and subjected to a polyphasic taxonomic analysis. Cells of strain SMK-10T were Gram-negative, motile, greyish yellow-pigmented, curved rods. Optimal growth occurred at 25-30 degrees C and in the presence of 2-3 % (w/v) NaCl. Strain SMK-10T contained Q-8 as the predominant ubiquinone and C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, C(17 : 1), C(15 : 1) and iso-C(16 : 0) as major fatty acids. The DNA G+C content was 39.3 mol%. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain SMK-10T belonged to the genus Colwellia. 16S rRNA gene sequence similarity values (94.7-96.7 %) to the type strains of all other Colwellia species and various differential phenotypic properties were sufficient to distinguish strain SMK-10T from recognized Colwellia species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain SMK-10T (= KCTC 12480T = DSM 17314T) is classified as the type strain of a novel Colwellia species, for which the name Colwellia aestuarii sp. nov. is proposed.

Nocardioides rubroscoriae sp. nov., isolated from volcanic ash.

PubMed

Lee, Soon Dong; Lee, Dong Wan

2014-06-01

A rod-shaped actinobacterium, designated Sco-A25(T), was isolated from a red-coloured layer of scoria (volcanic ash) in the Republic of Korea and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Sco-A25(T) is a member of the genus Nocardioides and formed a tight monophyletic unit with the type strain of Nocardioides plantarum (98.7 % gene similarity). LL-Diaminopimelic acid was detected in the cell wall. The predominant menaquinone is MK-8(H4). The polar lipids found were phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, and an unknown phospholipid. The fatty acid profile was represented by large amounts of saturated, unsaturated and iso-branched fatty acids. The DNA G+C content was 71.6 mol %. Genomic DNA similarity between strain Sco-A25(T) and N. plantarum KCTC 9577(T) was 47.8 %. On the basis of the results of phenotypic, genetic and phylogenetic analyses presented here, strain Sco-A25(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides rubroscoriae sp. nov. is proposed. The type strain is Sco-A25(T) (=KCTC 19805(T) = DSM 23986(T) = NBRC 107916(T)).

Dokdonia flava sp. nov., isolated from the seaweed Zostera marina.

PubMed

Choi, Seon; Kang, Joo Won; Yoon, Jung-Hoon; Seong, Chi Nam

2018-03-01

A non-motile, proteorhodopsin-containing, yellow and rod-shaped bacterial strain, designated ZODW10 T , was isolated from the seaweed Zostera marina collected from the West Sea, Republic of Korea. Cells were Gram-stain-negative, aerobic and non-motile. The isolate required sea salts for growth. A carotenoid pigment was produced. A phylogenetic tree based on 16S rRNA gene sequences showed that strain ZODW10 T forms an evolutionary lineage within the radiation enclosing members of the genus Dokdonia with Dokdoniadiaphoros CIP 108745 T (96.7 % sequence similarity) as its nearest neighbour. The major fatty acids were iso-C15:0, iso-C17 : 0 3-OH and iso-C15 : 1 G. Strain ZODW10 T contained menaquinone 6 (MK-6) and phosphatidylethanolamine, an unidentified aminolipid and an unidentified polar lipid as the only isoprenoid quinone and the major polar lipids, respectively. The DNA G+C content of strain ZODW10 T was 36 mol%. On the basis of the present polyphasic characterization, it is suggested that the isolate represents a novel species of the genus Dokdonia, for which the name Dokdonia flava sp. nov. (type strain, ZODW10 T =KCTC 52953 T =JCM 32293 T ) is proposed.

Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm.

PubMed

Jurado, Valme; Kroppenstedt, Reiner M; Saiz-Jimenez, Cesáreo; Klenk, Hans-Peter; Mouniée, Delphine; Laiz, Leonila; Couble, Andrée; Pötter, Gabriele; Boiron, Patrick; Rodríguez-Nava, Verónica

2009-12-01

A novel actinomycete, strain OFN S31(T), was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31(T) formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31(T) (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31(T) is characterized by the absence of mycelium and mycolic acids. Strain OFN S31(T) had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31(T) is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31(T) (=CIP 109864(T) =DSM 45258(T)).

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

PubMed

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

2010-05-01

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

Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level.

PubMed

Jarocki, Piotr; Podleśny, Marcin; Komoń-Janczara, Elwira; Kucharska, Jagoda; Glibowska, Agnieszka; Targoński, Zdzisław

2016-07-22

Members of the genus Bifidobacterium are anaerobic Gram-positive Actinobacteria, which are natural inhabitants of human and animal gastrointestinal tract. Certain bifidobacteria are frequently used as food additives and probiotic pharmaceuticals, because of their various health-promoting properties. Due to the enormous demand on probiotic bacteria, manufacture of high-quality products containing living microorganisms requires rapid and accurate identification of specific bacteria. Additionally, isolation of new industrial bacteria from various environments may lead to multiple isolations of the same strain, therefore, it is important to apply rapid, low-cost and effective procedures differentiating bifidobacteria at the intra-species level. The identification of new isolates using microbiological and biochemical methods is difficult, but the accurate characterization of isolated strains may be achieved using a polyphasic approach that includes classical phenotypic methods and molecular procedures. However, some of these procedures are time-consuming and cumbersome, particularly when a large group of new isolates is typed, while some other approaches may have too low discriminatory power to distinguish closely related isolates obtained from similar sources. This work presents the evaluation of the discriminatory power of four molecular methods (ARDRA, RAPD-PCR, rep-PCR and SDS-PAGE fingerprinting) that are extensively used for fast differentiation of bifidobacteria up to the strain level. Our experiments included 17 reference strains and showed that in comparison to ARDRA, genotypic fingerprinting procedures (RAPD and rep-PCR) seemed to be less reproducible, however, they allowed to differentiate the tested microorganisms even at the intra-species level. In general, RAPD and rep-PCR have similar discriminatory power, though, in some instances more than one oligonucleotide needs to be used in random amplified polymorphic DNA analysis. Moreover, the results also demonstrated a high discriminatory power of SDS-PAGE fingerprinting of whole-cell proteins. On the other hand, the protein profiles obtained were rather complex, and therefore, difficult to analyze. Among the tested procedures, rep-PCR proved to be the most effective and reliable method allowing rapid differentiation of Bifidobacterium strains. Additionally, the use of the BOXA1R primer in the differentiation of 21 Bifidobacterium strains, newly isolated from infant feces, demonstrated slightly better discriminatory power in comparison to PCR reactions with the (GTG)5 oligonucleotide. Thus, BOX-PCR turned out to be the most appropriate and convenient molecular technique in differentiating Bifidobacterium strains at all taxonomic levels.

Inversion of calcite twin data for paleostress orientations and magnitudes: A new technique tested and calibrated on numerically-generated and natural data

NASA Astrophysics Data System (ADS)

Parlangeau, Camille; Lacombe, Olivier; Schueller, Sylvie; Daniel, Jean-Marc

2018-01-01

The inversion of calcite twin data is a powerful tool to reconstruct paleostresses sustained by carbonate rocks during their geological history. Following Etchecopar's (1984) pioneering work, this study presents a new technique for the inversion of calcite twin data that reconstructs the 5 parameters of the deviatoric stress tensors from both monophase and polyphase twin datasets. The uncertainties in the parameters of the stress tensors reconstructed by this new technique are evaluated on numerically-generated datasets. The technique not only reliably defines the 5 parameters of the deviatoric stress tensor, but also reliably separates very close superimposed stress tensors (30° of difference in maximum principal stress orientation or switch between σ3 and σ2 axes). The technique is further shown to be robust to sampling bias and to slight variability in the critical resolved shear stress. Due to our still incomplete knowledge of the evolution of the critical resolved shear stress with grain size, our results show that it is recommended to analyze twin data subsets of homogeneous grain size to minimize possible errors, mainly those concerning differential stress values. The methodological uncertainty in principal stress orientations is about ± 10°; it is about ± 0.1 for the stress ratio. For differential stresses, the uncertainty is lower than ± 30%. Applying the technique to vein samples within Mesozoic limestones from the Monte Nero anticline (northern Apennines, Italy) demonstrates its ability to reliably detect and separate tectonically significant paleostress orientations and magnitudes from naturally deformed polyphase samples, hence to fingerprint the regional paleostresses of interest in tectonic studies.

The polyphased tectonic evolution of the Anegada Passage in the northern Lesser Antilles subduction zone

NASA Astrophysics Data System (ADS)

Laurencin, M.; Marcaillou, B.; Graindorge, D.; Klingelhoefer, F.; Lallemand, S.; Laigle, M.; Lebrun, J.-F.

2017-05-01

The influence of the highly oblique plate convergence at the northern Lesser Antilles onto the margin strain partitioning and deformation pattern, although frequently invoked, has never been clearly imaged. The Anegada Passage is a set of basins and deep valleys, regularly related to the southern boundary of the Puerto Rico-Virgin Islands (PRVI) microplate. Despite the publications of various tectonic models mostly based on bathymetric data, the tectonic origin and deformation of this Passage remains unconstrained in the absence of deep structure imaging. During cruises Antithesis 1 and 3 (2013-2016), we recorded the first deep multichannel seismic images and new multibeam data in the northern Lesser Antilles margin segment in order to shed a new light on the structure and tectonic pattern of the Anegada Passage. We image the northeastern extent of the Anegada Passage, from the Sombrero Basin to the Lesser Antilles margin front. Our results reveal that this northeastern segment is an EW trending left-stepping en échelon strike-slip system that consists of the Sombrero and Malliwana pull-apart basins, the Malliwana and Anguilla left-lateral faults, and the NE-SW compressional restraining bend at the Malliwana Hill. Reviewing the structure of the Anegada Passage, from the south of Puerto Rico to the Lesser Antilles margin front, reveals a polyphased tectonic history. The Anegada Passage is formed by a NW-SE extension, possibly related to the rotation or escape of PRVI block due to collision of the Bahamas Bank. Currently, it is deformed by an active WNW-ESE strike-slip deformation associated to the shear component of the strain partitioning resulting from the subduction obliquity.

Sleep characteristics in the quail Coturnix coturnix.

PubMed

Mexicano, Graciela; Montoya-Loaiza, Bibiana; Ayala-Guerrero, Fructuoso

2014-04-22

As mammals, birds exhibit two sleep phases, slow wave sleep (SWS) and REM (Rapid Eye Movement) sleep characterized by presenting different electrophysiological patterns of brain activity. During SWS a high amplitude slow wave pattern in brain activity is observed. This activity is substituted by a low amplitude fast frequency pattern during REM sleep. Common quail (Coturnix coturnix) is an animal model that has provided information related to different physiological mechanisms present in man. There are reports related to its electrophysiological brain activity, however the sleep characteristics that have been described are not. The objectives of this study is describing the sleep characteristics throughout the nychthemeral cycle of the common quail and consider this bird species as an avian model to analyze the regulatory mechanisms of sleep. Experiments were carried out in implanted exemplars of C. coturnix. Under general anesthesia induced by ether inhalation, stainless steel electrodes were placed to register brain activity from the anterior and posterior areas during 24 continuous hours throughout the sleep-wake cycle. Ocular and motor activities were visually monitored. Quail showed four electrophysiologically and behaviorally different states of vigilance: wakefulness (53.28%), drowsiness (14.27%), slow wave sleep (30.47%) and REM sleep (1.98%). The animals presented 202 REM sleep episodes throughout the nychthemeral cycle. Sleep distribution was polyphasic; however sleep amount was significantly greater during the period corresponding to the night. The number of nocturnal REM sleep episodes was significantly greater than that of diurnal one. The quail C. coturnix shows a polyphasic distribution of sleep; however the amount of this state of vigilance is significantly greater during the nocturnal period. Copyright © 2014 Elsevier Inc. All rights reserved.

Three-dimensional eddy current solution of a polyphase machine test model (abstract)

NASA Astrophysics Data System (ADS)

Pahner, Uwe; Belmans, Ronnie; Ostovic, Vlado

1994-05-01

This abstract describes a three-dimensional (3D) finite element solution of a test model that has been reported in the literature. The model is a basis for calculating the current redistribution effects in the end windings of turbogenerators. The aim of the study is to see whether the analytical results of the test model can be found using a general purpose finite element package, thus indicating that the finite element model is accurate enough to treat real end winding problems. The real end winding problems cannot be solved analytically, as the geometry is far too complicated. The model consists of a polyphase coil set, containing 44 individual coils. This set generates a two pole mmf distribution on a cylindrical surface. The rotating field causes eddy currents to flow in the inner massive and conducting rotor. In the analytical solution a perfect sinusoidal mmf distribution is put forward. The finite element model contains 85824 tetrahedra and 16451 nodes. A complex single scalar potential representation is used in the nonconducting parts. The computation time required was 3 h and 42 min. The flux plots show that the field distribution is acceptable. Furthermore, the induced currents are calculated and compared with the values found from the analytical solution. The distribution of the eddy currents is very close to the distribution of the analytical solution. The most important results are the losses, both local and global. The value of the overall losses is less than 2% away from those of the analytical solution. Also the local distribution of the losses is at any given point less than 7% away from the analytical solution. The deviations of the results are acceptable and are partially due to the fact that the sinusoidal mmf distribution was not modeled perfectly in the finite element method.

Partial melting of UHP calc-gneiss from the Dabie Mountains

NASA Astrophysics Data System (ADS)

Liu, Penglei; Wu, Yao; Liu, Qiang; Zhang, Junfeng; Zhang, Li; Jin, Zhenmin

2014-04-01

Exhumation melting has been proposed for the ultra-high pressure (UHP) metamorphic rocks in the Dabie Mountains based on melting experiments. We document here the first petrological and mineralogical evidence demonstrating that the UHP calc-gneisses from the Ganjialing area in the Dabie Mountains experienced partial melting during early exhumation. The assemblage of garnet, phengite (Si = 3.65 pfu), coesite, rutile and carbonate preserved in the calc-gneisses indicates a peak metamorphic condition of 692-757 °C and 4.0-4.8 GPa. Partial melting is indicated by several lines of evidence: the melting textures of phengite, the feldspar-dominated films, bands, branches, blebs and veins, the euhedral K-feldspars, the intergrowth film of plagioclase and K-feldspar, the plagioclase + biotite intergrowth after garnet and the epidote poikiloblasts. Polyphase inclusions in garnet are characterized with wedge-like offshoots and serrate outlines whereas those in epidote display negative crystal shapes, which can be best interpreted by entrapment of former melts. We propose a wet melting reaction of Phn + Q ± Na-Cpx + H2O = Bt + Pl + Grt + felsic melts, which likely took place at ca.650-800 °C and ca.1.0-2.0 GPa, to interpret the melting event in the calc-gneisses. Chemical exchanges between garnet and melts produced new garnet domains with higher almandine, spessartine, MREE, HREE and Y but lower grossular, pyrope, P, Sc, Ti, V and Zr contents. Zr-in-rutile thermometer reveals a low temperature of 620-643 °C at 5 GPa, indicating a later reset for Zr in rutile. Healed fractures are suggested to be responsible for the formation of some polyphase inclusions in garnet.

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).

Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean

PubMed Central

Konstantinou, Despoina; Gerovasileiou, Vasilis; Voultsiadou, Eleni

2018-01-01

Sponge-cyanobacteria associations have attracted research interest from an ecological, evolutionary and biotechnological perspective. Current knowledge is, in its majority, “hidden” in metagenomics research studying the entire microbial communities of sponges, while knowledge on these associations is totally missing for certain geographic areas. In this study, we (a) investigated the occurrence of cyanobacteria in 18 sponge species, several of which are studied for the first time for their cyanobionts, from a previously unexplored eastern Mediterranean ecoregion, the Aegean Sea, (b) isolated sponge-associated cyanobacteria, and characterized them based on a polyphasic (morphological-morphometric and molecular phylogenetic analysis) approach, and (c) conducted a meta-analysis on the global diversity of sponge species hosting cyanobacteria, as well as the diversity of cyanobacterial symbionts. Our research provided new records for nine sponge species, previously unknown for this association, while the isolated cyanobacteria were found to form novel clades within Synechococcus, Leptolyngbyaceae, Pseudanabaenaceae, and Schizotrichaceae, whose taxonomic status requires further investigation; this is the first report of a Schizotrichaceae cyanobacterium associated with sponges. The extensive evaluation of the literature along with the new data from the Aegean Sea raised the number of sponge species known for hosting cyanobacteria to 320 and showed that the cyanobacterial diversity reported from sponges is yet underestimated. PMID:29596453

Biodiversity of Environmental Leptospira: Improving Identification and Revisiting the Diagnosis.

PubMed

Thibeaux, Roman; Girault, Dominique; Bierque, Emilie; Soupé-Gilbert, Marie-Estelle; Rettinger, Anna; Douyère, Anthony; Meyer, Michael; Iraola, Gregorio; Picardeau, Mathieu; Goarant, Cyrille

2018-01-01

Leptospirosis is an important environmental disease and a major threat to human health causing at least 1 million clinical infections annually. There has recently been a growing interest in understanding the environmental lifestyle of Leptospira . However, Leptospira isolation from complex environmental samples is difficult and time-consuming and few tools are available to identify Leptospira isolates at the species level. Here, we propose a polyphasic isolation and identification scheme, which might prove useful to recover and identify environmental isolates and select those to be submitted to whole-genome sequencing. Using this approach, we recently described 12 novel Leptospira species for which we propose names. We also show that MALDI-ToF MS allows rapid and reliable identification and provide an extensive database of Leptospira MALDI-ToF mass spectra, which will be valuable to researchers in the leptospirosis community for species identification. Lastly, we also re-evaluate some of the current techniques for the molecular diagnosis of leptospirosis taking into account the extensive and recently revealed biodiversity of Leptospira in the environment. In conclusion, we describe our method for isolating Leptospira from the environment, confirm the usefulness of mass spectrometry for species identification and propose names for 12 novel species. This also offers the opportunity to refine current molecular diagnostic tools.

Branchiibius cervicis sp. nov., a novel species isolated from patients with atopic dermatitis.

PubMed

Tomida, Junko; Sakamoto, Dai; Sugita, Takashi; Fujiwara, Nagatoshi; Naka, Takashi; Hamada, Moriyuki; Morita, Yuji; Kawamura, Yoshiaki

2011-11-01

Novel actinobacterial strains, PAGU 1247(T), PAGU 1251 and PAGU 1252, were isolated from the skin of atopic dermatitis patients and were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were located within the family Dermacoccaceae. The most closely related species of PAGU 1247(T) in phylogenetic terms was Branchiibius hedensis Mer 29717(T), with 16S rRNA gene sequence similarity of 99.6%, although the DNA-DNA relatedness value was less than 43.9%. Some biochemical traits, such as lipase (C14) and α-galactosidase activity, could distinguish these isolates from B. hedensis. Strain PAGU 1247(T) contained iso-C(16:0) and brC(18:0) as the major fatty acids. The quinone system consisted of menaquinone MK-8(H(6) and H(4)). The G+C content of the genomic DNA was 67.6mol%. On the basis of its phenotypic properties and genetic distinctiveness, strains PAGU 1247(T), PAGU 1251 and PAGU 1252 represents a novel species of the genus Branchiibius, for which the name Branchiibius cervicis sp. nov. is proposed. The type strain is PAGU 1247(T) (=NBRC 106593(T)=DSM 24166(T)). Copyright © 2011 Elsevier GmbH. All rights reserved.

Microbial minorities modulate methane consumption through niche partitioning

PubMed Central

Bodelier, Paul LE; Meima-Franke, Marion; Hordijk, Cornelis A; Steenbergh, Anne K; Hefting, Mariet M; Bodrossy, Levente; von Bergen, Martin; Seifert, Jana

2013-01-01

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity–ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy. PMID:23788331

Requalification of a Brazilian Trichoderma Collection and Screening of Its Capability to Decolourise Real Textile Effluent.

PubMed

Silva Lisboa, Dianny; Santos, Cledir; Barbosa, Renan N; Magalhães, Oliane; Paiva, Laura M; Moreira, Keila A; Lima, Nelson; Souza-Motta, Cristina M

2017-04-01

Water contamination with large amounts of industrial textile coloured effluents is an environmental concern. For the treatment of textile effluents, white-rot fungi have received extensive attention due to their powerful capability to produce oxidative (e.g., ligninolytic) enzymes. In addition, other groups of fungi, such as species of Aspergillus and Trichoderma , have also been used for textile effluents treatment. The main aim of the present study was to requalify a Brazilian Trichoderma culture collection of 51 Trichoderma strains, isolated from different sources in Brazil and preserved in the oldest Latin-American Fungal Service Culture Collection, The Micoteca URM WDCM 804 (Recife, Brazil). Fungal isolates were re-identified through a polyphasic approach including macro- and micro-morphology and molecular biology, and screened for their capability to decolourise real effluents collected directly from storage tanks of a textile manufacture. Trichoderma atroviride URM 4950 presented the best performance on the dye decolourisation in real textile effluent and can be considered in a scale-up process at industrial level. Overall, the potential of Trichoderma strains in decolourising real textile dye present in textile effluent and the production of the oxidative enzymes Lac, LiP and MnP was demonstrated. Fungal strains are available in the collection e-catalogue to be further explored from the biotechnological point of view.

Chocolate tablet aspects of cytherean Meshkenet Tessera

NASA Technical Reports Server (NTRS)

Raitala, J.

1993-01-01

Meshkenet Tessera structures were mapped from Magellan data and several resemblances to chocolate tablet boudinage were found. The complex fault sets display polyphase tectonic sequences of a few main deformation phases. Shear and tension have contributed to the areal deformation. Main faults cut the 1600-km long Meshkenet Tessera highland into bar-like blocks which have ridge and groove pattern oriented along or at high angles to the faults. The first approach to the surface block deformation is an assumption of initial parallel shear faulting followed by a chocolate tablet boudinage. Major faults which cut Meshkenet Tessera into rectangular blocks have been active repetitively while two progressive or superposed boudinage set formations have taken place at high angles during the relaxational or flattening type deformation of the area. Chocolate tablet boudinage is caused by a layer-parallel two-dimensional extension resulting in fracturing of the competent layer. Such structures, defined by two sets of boudin neck lines at right angles to each other, have been described by a number of authors. They develop in a flattening type of bulk deformation or during superposed deformation where the rock is elongated in two dimensions parallel to the surface. This is an attempt to describe and understand the formation and development of structures of Meshkenet Tessera which has complicated fault structures.

Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle.

PubMed

Gu, Chun Tao; Li, Chun Yan; Yang, Li Jie; Huo, Gui Cheng

2013-11-01

A Gram-stain-positive bacterial strain, S4-3(T), was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, DNA-DNA hybridization and an analysis of phenotypic features. Strain S4-3(T) showed 97.9-98.7 % 16S rRNA gene sequence similarities, 84.4-94.1 % pheS gene sequence similarities and 94.4-96.9 % rpoA gene sequence similarities to the type strains of Lactobacillus nantensis, Lactobacillus mindensis, Lactobacillus crustorum, Lactobacillus futsaii, Lactobacillus farciminis and Lactobacillus kimchiensis. dnaK gene sequence similarities between S4-3(T) and Lactobacillus nantensis LMG 23510(T), Lactobacillus mindensis LMG 21932(T), Lactobacillus crustorum LMG 23699(T), Lactobacillus futsaii JCM 17355(T) and Lactobacillus farciminis LMG 9200(T) were 95.4, 91.5, 90.4, 91.7 and 93.1 %, respectively. Based upon the data obtained in the present study, a novel species, Lactobacillus heilongjiangensis sp. nov., is proposed and the type strain is S4-3(T) ( = LMG 26166(T) = NCIMB 14701(T)).

Methylobacterium populi VP2: Plant Growth-Promoting Bacterium Isolated from a Highly Polluted Environment for Polycyclic Aromatic Hydrocarbon (PAH) Biodegradation

PubMed Central

Piccolo, Alessandro; Carotenuto, Rita; Pepe, Olimpia

2014-01-01

The use of microorganisms to accelerate the natural detoxification processes of toxic substances in the soil represents an alternative ecofriendly and low-cost method of environmental remediation compared to harmful incineration and chemical treatments. Fourteen strains able to grow on minimal selective medium with a complex mixture of different classes of xenobiotic compounds as the sole carbon source were isolated from the soil of the ex-industrial site ACNA (Aziende Chimiche Nazionali Associate) in Cengio (Savona, Italy). The best putative degrading isolate, Methylobacterium populi VP2, was identified using a polyphasic approach on the basis of its phenotypic, biochemical, and molecular characterisation. Moreover, this strain also showed multiple plant growth promotion activities: it was able to produce indole-3-acetic acid (IAA) and siderophores, solubilise phosphate, and produce a biofilm in the presence of phenanthrene and alleviate phenanthrene stress in tomato seeds. This is the first report on the simultaneous occurrence of the PAH-degrading ability by Methylobacterium populi and its multiple plant growth-promoting activities. Therefore, the selected indigenous strain, which is naturally present in highly contaminated soils, is good candidate for plant growth promotion and is capable of biodegrading xenobiotic organic compounds to remediate contaminated soil alone and/or soil associated with plants. PMID:25152928

Phenotypic and Genotypic Characteristics of Members of the Genus Streptobacillus

PubMed Central

Eisenberg, Tobias; Nicklas, Werner; Mauder, Norman; Rau, Jörg; Contzen, Matthias; Semmler, Torsten; Hofmann, Nicola; Aledelbi, Khayrieh; Ewers, Christa

2015-01-01

The genus Streptobacillus (S.) remained monotypic for almost 90 years until two new species were recently described. The type species, S. moniliformis, is one of the two etiological agents of rat bite fever, an under-diagnosed, worldwide occurring zoonosis. In a polyphasic approach field isolates and reference strains of S. moniliformis, S. hongkongensis, S. felis as well as divergent isolates were characterized by comparison of molecular data (n = 29) and from the majority also by their physiological as well as proteomic properties (n = 22). Based on growth-independent physiological profiling using VITEK2-compact, API ZYM and the Micronaut system fastidious growth-related difficulties could be overcome and streptobacilli could definitively be typed despite generally few differences. While differing in their isolation sites and dates, S. moniliformis isolates were found to possess almost identical spectra in matrix-assisted laser desorption ionization—time of flight mass spectrometry and Fourier transform infrared spectroscopy. Spectroscopic methods facilitated differentiation of S. moniliformis, S. hongkongensis and S. felis as well as one divergent isolate. Sequencing of 16S rRNA gene as well as functional genes groEL, recA and gyrB revealed only little intraspecific variability, but generally proved suitable for interspecies discrimination between all three taxa and two groups of divergent isolates. PMID:26252790

Diversity of predominant lactic acid bacteria associated with cocoa fermentation in Nigeria.

PubMed

Kostinek, Melanie; Ban-Koffi, Louis; Ottah-Atikpo, Margaret; Teniola, David; Schillinger, Ulrich; Holzapfel, Wilhelm H; Franz, Charles M A P

2008-04-01

The fermentation of cocoa relies on a complex succession of bacteria and filamentous fungi, all of which can have an impact on cocoa flavor. So far, few investigations have focused on the diversity of lactic acid bacteria involved in cocoa fermentation, and many earlier investigations did not rely on polyphasic taxonomical approaches, which take both phenotypic and genotypic characterization techniques into account. In our study, we characterized predominant lactic acid bacteria from cocoa fermentations in Nigeria, using a combination of phenotypic tests, repetitive extragenic palindromic PCR, and sequencing of the 16S rRNA gene of representative strains for accurate species identification. Thus, of a total of 193 lactic acid bacteria (LAB) strains isolated from common media used to cultivate LAB, 40 (20.7%) were heterofermentative and consisted of either L. brevis or L. fermentum strains. The majority of the isolates were homofermentative rods (110 strains; 57% of isolates) which were characterized as L. plantarum strains. The homofermentative cocci consisted predominantly of 35 (18.1% of isolates) Pediococcus acidilactici strains. Thus, the LAB populations derived from these media in this study were accurately described. This can contribute to the further assessment of the effect of common LAB strains on the flavor characteristics of fermenting cocoa in further studies.

Microbial species delineation using whole genome sequences

PubMed Central

Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T.; Mavrommatis, Kostas; Kyrpides, Nikos C.; Pati, Amrita

2015-01-01

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. PMID:26150420

Comparative Genomics of Burkholderia singularis sp. nov., a Low G+C Content, Free-Living Bacterium That Defies Taxonomic Dissection of the Genus Burkholderia

PubMed Central

Vandamme, Peter; Peeters, Charlotte; De Smet, Birgit; Price, Erin P.; Sarovich, Derek S.; Henry, Deborah A.; Hird, Trevor J.; Zlosnik, James E. A.; Mayo, Mark; Warner, Jeffrey; Baker, Anthony; Currie, Bart J.; Carlier, Aurélien

2017-01-01

Four Burkholderia pseudomallei-like isolates of human clinical origin were examined by a polyphasic taxonomic approach that included comparative whole genome analyses. The results demonstrated that these isolates represent a rare and unusual, novel Burkholderia species for which we propose the name B. singularis. The type strain is LMG 28154T (=CCUG 65685T). Its genome sequence has an average mol% G+C content of 64.34%, which is considerably lower than that of other Burkholderia species. The reduced G+C content of strain LMG 28154T was characterized by a genome wide AT bias that was not due to reduced GC-biased gene conversion or reductive genome evolution, but might have been caused by an altered DNA base excision repair pathway. B. singularis can be differentiated from other Burkholderia species by multilocus sequence analysis, MALDI-TOF mass spectrometry and a distinctive biochemical profile that includes the absence of nitrate reduction, a mucoid appearance on Columbia sheep blood agar, and a slowly positive oxidase reaction. Comparisons with publicly available whole genome sequences demonstrated that strain TSV85, an Australian water isolate, also represents the same species and therefore, to date, B. singularis has been recovered from human or environmental samples on three continents. PMID:28932212

Methylobacterium tarhaniae sp. nov., isolated from arid soil.

PubMed

Veyisoglu, Aysel; Camas, Mustafa; Tatar, Demet; Guven, Kiymet; Sazak, Anil; Sahin, Nevzat

2013-08-01

A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211(T), isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211(T) belonged to the genus Methylobacterium. Strain N4211(T) was most closely related to Methylobacterium aquaticum GR16(T) (98.56 %), Methylobacterium platani PMB02(T) (97.95 %) and Methylobacterium variabile GR3(T) (97.2 %), and the phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C18 : 1 cis11/t9/t6). The DNA G+C content was 67.3 mol%. DNA-DNA relatedness of strain N4211(T) and the most closely related strains M. aquaticum DSM 16371(T) and M. platani KCTC 12901(T) were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA-DNA hybridization data, strain N4211(T) is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium tarhaniae sp. nov. is proposed. The type strain is N4211(T)( = KCTC 23615(T) = DSM 25844(T)).

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses

PubMed Central

Stagnari, Fabio; Perpetuini, Giorgia; Tofalo, Rosanna; Campanelli, Gabriele; Leteo, Fabrizio; Della Vella, Umberto; Schirone, Maria; Suzzi, Giovanna; Pisante, Michele

2014-01-01

In the present study, long-term organic and conventional managements were compared at the experimental field of Monsampolo del Tronto (Marche region, Italy) with the aim of investigating soil chemical fertility and microbial community structure. A polyphasic approach, combining soil fertility indicators with microbiological analyses (plate counts, PCR-denaturing gradient gel electrophoresis [DGGE] and phospholipid fatty acid analysis [PLFA]) was applied. Organic matter, N as well as some important macro and micronutrients (K, P, Mg, Mn, Cu, and Zn) for crop growth, were more available under organic management. Bacterial counts were higher in organic management. A significant influence of management system and management x crop interaction was observed for total mesophilic bacteria, nitrogen fixing bacteria and actinobacteria. Interestingly, cultivable fungi were not detected in all analyzed samples. PLFA biomass was higher in the organic and Gram positive bacteria dominated the microbial community in both systems. Even if fungal biomass was higher in organic management, fungal PCR-DGGE fingerprinting revealed that the two systems were very similar in terms of fungal species suggesting that 10 years were not enough to establish a new dynamic equilibrium among ecosystem components. A better knowledge of soil biota and in particular of fungal community structure will be useful for the development of sustainable management strategies. PMID:25540640

Microbial minorities modulate methane consumption through niche partitioning.

PubMed

Bodelier, Paul L E; Meima-Franke, Marion; Hordijk, Cornelis A; Steenbergh, Anne K; Hefting, Mariet M; Bodrossy, Levente; von Bergen, Martin; Seifert, Jana

2013-11-01

Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating γ-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.

Optimization of water curing for the preservation of chestnuts (Castanea sativa Mill.) and evaluation of microbial dynamics during process.

PubMed

Blaiotta, Giuseppe; Di Capua, Marika; Romano, Annalisa; Coppola, Raffaele; Aponte, Maria

2014-09-01

Chestnuts are very perishable fruits, whose quality may be compromised during postharvest handling. Damage can be caused both by insects and fungi. Water curing, a commonly used postharvest method, is based on soaking fruits in water typically for about one week. Factors that affect effectiveness of water curing have only been explained partially. A decrease in pH, likely imputable to a light fermentation caused by lactic acid bacteria, may inhibit the growth of moulds. In this study a Lactobacillus pentosus strain was selected for its ability to inhibit fungi, and used as a starter culture during water curing. As second goal, a reduction of the environmental impact of the process was evaluated by using water that had been re-cycled from a previous curing treatment. Experiments were performed on pilot as well as on farm scale. In all trials, microbial dynamics were evaluated by means of a polyphasic approach including conventional and molecular-based analyses. According to results, the employment of an adjunct culture appears as a very promising opportunity. Even if no reduction in the duration of the process was achieved, waters exhibited a minor microbial complexity and fruits did not lose the natural lustre after the process. Copyright © 2014 Elsevier Ltd. All rights reserved.

Streptomyces kronopolitis sp. nov., an actinomycete that produces phoslactomycins isolated from a millipede (Kronopolites svenhedind Verhoeff).

PubMed

Liu, Chongxi; Ye, Lan; Li, Yao; Jiang, Shanwen; Liu, Hui; Yan, Kai; Xiang, Wensheng; Wang, Xiangjing

2016-12-01

A phoslactomycin-producing actinomycete, designated strain NEAU-ML8T, was isolated from a millipede (Kronopolites svenhedind Verhoeff) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain NEAU-ML8T belongs to the genus Streptomyces with the highest sequence similarities to Streptomyces lydicus NBRC 13058T (99.39 %) and Streptomyces chattanoogensis DSM 40002T (99.25 %). The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with NBRC 13058T and S. chattanoogensis DSM 40002T. This branching pattern was also supported by the tree rconstructed with the neighbour-joining method. A combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain NEAU-ML8T and its phylogenetically closely related strains, which further clarified their relatedness and demonstrated that NEAU-ML8T could be distinguished from NBRC 13058T and S. chattanoogensis DSM 40002T. Therefore, it is concluded that strain NEAU-ML8T can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces kronopolitis sp. nov. is proposed. The type strain is NEAU-ML8T (=DSM 101986T=CGMCC 4.7323T).

'Streptomyces caelicus', an antibiotic-producing species of the genus Streptomyces, and Streptomyces canchipurensis Li et al. 2015 are later heterotypic synonyms of Streptomyces muensis Ningthoujam et al. 2014.

PubMed

Wink, Joachim; Schumann, Peter; Atasayar, Ewelina; Klenk, Hans-Peter; Zaburannyi, Nestor; Westermann, Martin; Martin, Karin; Glaeser, Stefanie P; Kämpfer, Peter

2017-04-01

'Streptomyces caelicus' DSM 40835 was first reported as the producer of the antibiotic griselimycin by some coworkers of Rhone Poulenc in 1971. The project on isolation of the antibiotic compound was stopped because of the bad solubility and selectivity of the compound towards Mycobacteria. At Sanofi-Aventis, Germany, the project was re-evaluated in 2007 and the gene cluster of griselimycin could be identified, characterized and was patented in 2013. At this time, 'S. caelicus' was an invalid name. During the strain characterization work, it was found that 'S. caelicus' belongs to the group of species of the genus Streptomyces which show an unusual heterogeneity of the 16S rRNA gene sequences. However, high 16S rRNA gene sequence similarities to Streptomyces muensis JCM 17576T and Streptomyces canchipurensis JCM 17575T were obvious. Here, we present a comparative description of 'Streptomyces caelicus' DS 9461 (=DSM 40835=NCCB 100592) with S. muensis and S. canchipurensis by use of a polyphasic taxonomy approach and additional comparison of some housekeeping genes by multilocus sequence analysis (MLSA). An emended description of Streptomyces muensis is provided as a result of this work.

Evolution of the Mount Woods Inlier, northern Gawler Craton, Southern Australia: an integrated structural and aeromagnetic analysis

NASA Astrophysics Data System (ADS)

Betts, Peter G.; Valenta, Rick K.; Finlay, Jim

2003-05-01

Structural mapping integrated with interpretation and forward modelling of aeromagnetic data form complimentary and powerful tools for regional structural analysis because both techniques focus on architecture and overprinting relationships. This approach is used to constrain the geometry and evolution of the sparsely exposed Mount Woods Inlier in the northern Gawler Craton. The Mount Woods Inlier records a history of poly-phase deformation, high-temperature metamorphism, and syn- and post-orogenic magmatism between ca. 1736 and 1584 Ma. The earliest deformation involved isoclinal folding, and the development of bedding parallel and axial planar gneissic foliation (S 1). This was accompanied by high-temperature, upper amphibolite to granulite facies metamorphism at ca. 1736 Ma. During subsequent north-south shortening (D 2), open to isoclinal south-southeast-oriented F 2 folds developed as the Palaeoproterozoic successions of the inlier were thrust over the Archaean nuclei of the Gawler Craton. The syn-D 2 Engenina Adamellite was emplaced at ca. 1692 Ma. The post-D 2 history involved shear zone development and localised folding, exhumation of metamorphic rocks, and deposition of clastic sediments prior to the emplacement of the ca. 1584 Ma Granite Balta Suite. The Mount Woods Inlier is interpreted as the northern continuation of the Kimban Orogen.

New approaches to provide ride-through for critical loads in electric power distribution systems

NASA Astrophysics Data System (ADS)

Montero-Hernandez, Oscar C.

2001-07-01

The extensive use of electronic circuits has enabled modernization, automation, miniaturization, high quality, low cost, and other achievements regarding electric loads in the last decades. However, modern electronic circuits and systems are extremely sensitive to disturbances from the electric power supply. In fact, the rate at which these disturbances happen is considerable as has been documented in recent years. In response to the power quality concerns presented previously, this dissertation is proposing new approaches to provide ride-through for critical loads during voltage disturbances with emphasis on voltage sags. In this dissertation, a new approach based on an AC-DC-AC system is proposed to provide ride-through for critical loads connected in buildings and/or an industrial system. In this approach, a three-phase IGBT inverter with a built in Dc-link voltage regulator is suitably controlled along with static by-pass switches to provide continuous power to critical loads. During a disturbance, the input utility source is disconnected and the power from the inverter is connected to the load. The remaining voltage in the AC supply is converted to DC and compensated before being applied to the inverter and the load. After detecting normal utility conditions, power from the utility is restored to the critical load. In order to achieve an extended ride-through capability a second approach is introduced. In this case, the Dc-link voltage regulator is performed by a DC-DC Buck-Boost converter. This new approach has the capability to mitigate voltage variations below and above the nominal value. In the third approach presented in this dissertation, a three-phase AC to AC boost converter is investigated. This converter provides a boosting action for the utility input voltages, right before they are applied to the load. The proposed Pulse Width Modulation (PWM) control strategy ensures independent control of each phase and compensates for both single-phase or poly-phase voltage sags. Algorithms capable of detecting voltage disturbances such as voltage sags, voltage swells, flicker, frequency change, and harmonics in a fast and reliable way are investigated and developed in this dissertation as an essential part of the approaches previously described. Simulation and experimental work has been done to validate the feasibility of all approaches under the most common voltage disturbances such as single-phase voltage sags and three-phase voltage sags.

RDBE Development and Progress

NASA Astrophysics Data System (ADS)

Neill, A.; Bark, M.; Beaudoin, C.; Brisken, W.; Ben Frej, H.; Doeleman, S.; Durand, S.; Guerra, Ml; Hinton, A.; Luce, M.; McWhirter, R.; Morris, K.; Peck, G.; Revnell, M.; Rogers, A.; Romney, J.; Ruszczyk, C; Taveniku, M.; Walker, R.; Whitney, A.

2010-12-01

A digital backend based on the ROACH board has been developed jointly by the National Radio Astronomy Observatory and MIT Haystack Observatory. The RDBE will have both Polyphase Filterbank and Digital Downconverter personalities. The initial configuration outputs sixteen 32-MHz channels, comprised of half the channels from the PFB processing of the two IF inputs, for use in the VLBI2010 geodetic system and in the VLBA sensitivity upgrade project. The output rate is 2x10^9 bits/second (1x10^9 bits/sec = 1 Gbps) over a 10 GigE connection to the Mark 5C with the data written in Mark 5B format on disk.

Fundamentals of electric power conversion

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

Umans, S.D.

1992-12-01

Its rugged nature and straightforward design make the induction motor the most commonly used type of electric motor. This motor ranges in size from the fractional-horsepower, single-phase motors found in household appliances to polyphase motors rated at thousands of horsepower for industrial applications. Volume 1 of this report describes the function of induction motors, their characteristics, and induction motor testing. Volume 2 describes the characteristics of high-efficiency induction motors, with emphasis on the techniques used to obtain high efficiency. This two-volume report is written in nontechnical language and is intended for readers who require background from an applications, marketing, motormore » planning, or managerial perspective.« less

Fundamentals of electric power conversion

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

Umans, S.D.

1992-12-01

Its rugged nature and straightforward design make the induction motor the most commonly used type of electric motor. This motor ranges in size fro the fractional-horsepower, single-phase motors found in household appliances to polyphase motors rated at thousands of horsepower for industrial applications. Volume 1 of this report describes the function of induction motors, their characteristics, and induction motor testing. Volume 2 describes the characteristics of high-efficiency induction motors, with emphasis on the techniques used to obtain high efficiency. This two-volume report is written in nontechnical language and is intended for readers who require background from applications, marketing, motor planning,more » or managerial perspective.« less

RDBE Development and Progress

NASA Technical Reports Server (NTRS)

Niell, A.; Bark, M.; Beaudoin, C.; Brisken, W.; Frej, H. Ben; Doeleman, S.; Durand, S.; Guerra, M.; Hinton, A.; Luce, M.;

Graded pitch electromagnetic pump for thin strip metal casting systems

DOEpatents

Kuznetsov, S.B.

1986-04-01

A metal strip casing system is provided with an electromagnetic pump which includes a pair of primary blocks having a graded pole pitch, polyphase ac winding and being arranged on opposite sides of a movable heat sink. A nozzle is provided for depositing liquid metal on the heat sink such that the resulting metal strip and heat sink combination is subjected to a longitudinal electromagnetic field which increases in wavelength in the direction of travel of the heat sink, thereby subjecting the metal and heat sink to a longitudinal force having a magnitude which increases in the direction of travel. 4 figs.

POWTEX Neutron Diffractometer at FRM II - New Perspectives in Rock Deformation and Recrystallisation Analysis

NASA Astrophysics Data System (ADS)

Walter, J. M.; Stipp, M.; Ullemeyer, K.; Klein, H.; Leiss, B.; Hansen, B.; Kuhs, W. F.

2011-12-01

Neutron diffraction has become a routine method in Geoscience for the quantitative analysis of crystallographic preferred orientations (CPOs) and for (experimental) powder diffraction. Quantitative texture analysis is a common tool for the investigation of fabric development in mono- and polyphase rocks, their deformation histories and kinematics. Furthermore the quantitative characterization of anisotropic physical properties by bulk texture measurements can be achieved due to the high penetration capabilities of neutrons. To cope with increasing needs for beam time at neutron diffraction facilities with the corresponding technical characteristics and equipment, POWTEX (POWder and TEXture Diffractometer) is designed as a high-intensity diffractometer at the neutron research reactor FRM II in Garching, Germany by groups from the RWTH Aachen, Forschungszentrum Jülich and the University of Göttingen. Complementary to existing neutron diffractometers (SKAT at Dubna, Russia; GEM at ISIS, UK; HIPPO at Los Alamos, USA; D20 at ILL, France; and the local STRESS-SPEC and SPODI at FRM II) the layout of POWTEX is focused on fast (texture) measurements for either time-resolved experiments or the measurement of larger sample series as necessary for the study of large scale geological structures. By utilizing a range of neutron wavelengths simultaneously (TOF-technique), a high flux (~1 x 107 n/cm2s) and a high detector coverage ( 9.8 sr) effective texture measurements without sample tilting and rotation are possible. Furthermore the instrument and the angular detector resolution is sufficient for strong recrystallisation textures as well as weak textures of polyphase rocks. Thereby large sample environments will be implemented at POWTEX allowing in-situ time-resolved texture measurements during deformation experiments on rocksalt, ice and other materials. Furthermore a furnace for 3D-recrystallisation analysis of single grains will be realized complementary to the furnace that already exists for fine grained materials at the synchrotron beamline BW5 at HASYLAB, Germany (e.g. Klein et al. 2009). The in-situ triaxial deformation apparatus is operated by a uniaxial spindle drive with a maximum axial load of 200 kN, which will be redesigned to minimize shadowing effects on the detector. The HT experiments will be carried out in uniaxial compression or extension and an upgrade to triaxial deformation conditions is envisaged. The load frame can alternatively be used for ice deformation by inserting a cryostat cell for temperatures down to 77 K with a triaxial apparatus allowing also simple shear experiments on ice. Strain rates range between 10-8 and 10-3 s-1 reaching to at least 50 % axial strain. The furnace for the recrystallization analysis will be a mirror furnace with temperatures up to 1500° C, which will be rotatable around a vertical axis to obtain the required stereologic orientation information.

Potamolinea gen. nov. (Oscillatoriales, Cyanobacteria): a phylogenetically and ecologically coherent cyanobacterial genus.

PubMed

Martins, Mariéllen Dornelles; Branco, Luis Henrique Zanini

2016-09-01

Phormidium Kützing ex Gomont, a common genus of the Cyanobacteria, is widely known as a problematic group. Its simple morphology is not congruent with its genetic heterogeneity and several new generic entities have been described based on 16S rRNA gene sequence analyses from populations with similar morphology. During a study of the diversity of Phormidioideae (Phormidiaceae, Oscillatoriales) in Brazil, ten Phormidium-like strains from south-eastern and mid-western regions were isolated in monospecific cultures and submitted to polyphasic evaluation (morphological, ecological and molecular studies). The populations studied presented homogeneous morphology (trichomes straight, not attenuated and apical cell rounded or obtuse), differing mainly in cell length from the type species of the genus Phormidium (Phormidium lucidum Agardh ex Gomont) and occurring as three morphotypes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the populations studied, with European Phormidium aerugineo-caeruleum (Gomont) Anagnostidis & Komárek 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 Potamolinea Martins et Branco with two species: Potamolinea magna as the type species (strains 47PC and 48PC) and Potamolinea aerugineo-caerulea (Gomont) Martins et Branco (strains 1PC, 2PC and 38PC). These two species plus one still undetermined lineage,Potamolinea sp., are morphologically and genetically distinguishable, whereas the secondary structures of the D1-D1', box-B and V3 regions were conserved within each one. The generic name and specific epithets of the new taxa are proposed under the provisions of the International Code of Nomenclature for algae, fungi and plants.

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)).

Halobacillus alkaliphilus sp. nov., a halophilic bacterium isolated from a salt lake in Fuente de Piedra, southern Spain.

PubMed

Romano, Ida; Finore, Ilaria; Nicolaus, Giancarlo; Huertas, F Javier; Lama, Licia; Nicolaus, Barbara; Poli, Annarita

2008-04-01

A Gram-positive, spore-forming, halophilic bacterial strain, FP5T, was isolated from a salt lake in southern Spain and subjected to a polyphasic taxonomic study. Strain FP5T was strictly aerobic. Cells were coccoidal, occurring singly or in clusters. The cell-wall peptidoglycan type of strain FP5T was A4 beta based on l-Orn-d-Asp. Strain FP5T was characterized chemotaxonomically by having MK-7 as the major menaquinone and anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0 as the main fatty acids. The isolate grew optimally at 37 degrees C and in presence of 10 % NaCl; no growth was observed in the absence of NaCl. The DNA G+C content was 43.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FP5T falls within the evolutionary radiation of species of the genus Halobacillus. Levels of 16S rRNA gene sequence similarity between strain FP5T and the type strains of nine recognized Halobacillus species were in the range 97.0-99.0 %. Levels of DNA-DNA relatedness indicated that strain FP5T represents a genomic species that is distinct from recognized Halobacillus species. Strain FP5T could be differentiated from recognized Halobacillus species based on several phenotypic characteristics. On the basis of phenotypic, phylogenetic and genomic data, strain FP5T is considered to represent a novel species of the genus Halobacillus, for which the name Halobacillus alkaliphilus sp. nov. is proposed. The type strain is FP5T (=DSM 18525T =ATCC BAA-1361T).

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.

Enterobacter mori sp. nov., associated with bacterial wilt on Morus alba L.

PubMed

Zhu, Bo; Lou, Miao-Miao; Xie, Guan-Lin; Wang, Guo-Fen; Zhou, Qin; Wang, Fang; Fang, Yuan; Su, Ting; Li, Bin; Duan, Yong-Pin

2011-11-01

Two isolates of mulberry-pathogenic bacteria isolated from diseased mulberry roots were investigated in a polyphasic taxonomic study. Comparative 16S rRNA gene sequence analysis combined with rpoB gene sequence analysis allocated strains R18-2(T) and R3-3 to the genus Enterobacter, with Enterobacter asburiae, E. amnigenus, E. cancerogenus, E. cloacae subsp. cloacae, E. cloacae subsp. dissolvens and E. nimipressuralis as their closest relatives. Cells of the isolates were Gram-negative, facultatively anaerobic rods, 0.3-1.0 µm wide and 0.8-2.0 µm long, with peritrichous flagella, showing a DNA G+C content of 55.1 ± 0.5 mol%. Calculation of a similarity index based on phenotypic features and fatty acid methyl ester (FAME) analysis suggested that these isolates are members of E. cancerogenus or E. asburiae or a closely related species. Biochemical data revealed that the isolates could be differentiated from their nearest neighbours by the presence of lysine decarboxylase activity and their ability to utilize d-arabitol. DNA-DNA relatedness also distinguished the two isolates from phylogenetically closely related Enterobacter strains. Based on these data, it is proposed that the isolates represent a novel species of the genus Enterobacter, named Enterobacter mori sp. nov. The type strain is R18-2(T) ( = CGMCC 1.10322(T) = LMG 25706(T)).

Aminiphilus circumscriptus gen. nov., sp. nov., an anaerobic amino-acid-degrading bacterium from an upflow anaerobic sludge reactor.

PubMed

Díaz, C; Baena, S; Fardeau, M-L; Patel, B K C

2007-08-01

Strain ILE-2(T) was isolated from an upflow anaerobic sludge bed reactor treating brewery wastewater. The motile, non-sporulating, slightly curved cells (2-4 x 0.1 microm) stained Gram-negative and grew optimally at 42 degrees C and pH 7.1 with 0.5 % NaCl. The strain required yeast extract for growth and fermented Casamino acids, peptone, isoleucine, arginine, lysine, alanine, valine, glutamate, histidine, glutamine, methionine, malate, fumarate, glycerol and pyruvate to acetate, propionate and minor amounts of branched-chain fatty acids. Carbohydrates, formate, acetate, propionate, butyrate, isovalerate, methanol, ethanol, 1-propanol, butanol, lactate, succinate, starch, casein, gelatin, xylan and a number of other amino acids were not utilized. The DNA G+C content of strain ILE-2(T) was 52.7 mol%. 16S rRNA gene sequence analysis revealed that ILE-2(T) was distantly related to members of the genera Aminobacterium (83 % similarity) and Aminomonas (85 % similarity) in the family Syntrophomonadaceae, order Clostridiales, phylum Firmicutes. On the basis of the results of our polyphasic analysis, strain ILE-2(T) represents a novel species and genus within the family Syntrophomonadaceae, for which the name Aminiphilus circumscriptus gen. nov., sp. nov. is proposed. The type strain of Aminiphilus circumscriptus is ILE-2(T) (=DSM 16581(T) =JCM 14039(T)).

Circadian factor BMAL1 in histaminergic neurons regulates sleep architecture.

PubMed

Yu, Xiao; Zecharia, Anna; Zhang, Zhe; Yang, Qianzi; Yustos, Raquel; Jager, Polona; Vyssotski, Alexei L; Maywood, Elizabeth S; Chesham, Johanna E; Ma, Ying; Brickley, Stephen G; Hastings, Michael H; Franks, Nicholas P; Wisden, William

2014-12-01

Circadian clocks allow anticipation of daily environmental changes. The suprachiasmatic nucleus (SCN) houses the master clock, but clocks are also widely expressed elsewhere in the body. Although some peripheral clocks have established roles, it is unclear what local brain clocks do. We tested the contribution of one putative local clock in mouse histaminergic neurons in the tuberomamillary nucleus to the regulation of the sleep-wake cycle. Histaminergic neurons are silent during sleep, and start firing after wake onset; the released histamine, made by the enzyme histidine decarboxylase (HDC), enhances wakefulness. We found that hdc gene expression varies with time of day. Selectively deleting the Bmal1 (also known as Arntl or Mop3) clock gene from histaminergic cells removes this variation, producing higher HDC expression and brain histamine levels during the day. The consequences include more fragmented sleep, prolonged wake at night, shallower sleep depth (lower nonrapid eye movement [NREM] δ power), increased NREM-to-REM transitions, hindered recovery sleep after sleep deprivation, and impaired memory. Removing BMAL1 from histaminergic neurons does not, however, affect circadian rhythms. We propose that for mammals with polyphasic/nonwake consolidating sleep, the local BMAL1-dependent clock directs appropriately timed declines and increases in histamine biosynthesis to produce an appropriate balance of wake and sleep within the overall daily cycle of rest and activity specified by the SCN. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

A GPU-Based Wide-Band Radio Spectrometer

NASA Astrophysics Data System (ADS)

Chennamangalam, Jayanth; Scott, Simon; Jones, Glenn; Chen, Hong; Ford, John; Kepley, Amanda; Lorimer, D. R.; Nie, Jun; Prestage, Richard; Roshi, D. Anish; Wagner, Mark; Werthimer, Dan

2014-12-01

The graphics processing unit has become an integral part of astronomical instrumentation, enabling high-performance online data reduction and accelerated online signal processing. In this paper, we describe a wide-band reconfigurable spectrometer built using an off-the-shelf graphics processing unit card. This spectrometer, when configured as a polyphase filter bank, supports a dual-polarisation bandwidth of up to 1.1 GHz (or a single-polarisation bandwidth of up to 2.2 GHz) on the latest generation of graphics processing units. On the other hand, when configured as a direct fast Fourier transform, the spectrometer supports a dual-polarisation bandwidth of up to 1.4 GHz (or a single-polarisation bandwidth of up to 2.8 GHz).

Substantially parallel flux uncluttered rotor machines

DOEpatents

Hsu, John S.

2012-12-11

A permanent magnet-less and brushless synchronous system includes a stator that generates a magnetic rotating field when sourced by polyphase alternating currents. An uncluttered rotor is positioned within the magnetic rotating field and is spaced apart from the stator. An excitation core is spaced apart from the stator and the uncluttered rotor and magnetically couples the uncluttered rotor. The brushless excitation source generates a magnet torque by inducing magnetic poles near an outer peripheral surface of the uncluttered rotor, and the stator currents also generate a reluctance torque by a reaction of the difference between the direct and quadrature magnetic paths of the uncluttered rotor. The system can be used either as a motor or a generator

Colwellia aquaemaris sp. nov., isolated from the Cynoglossus semilaevis culture tank in a recirculating mariculture system.

PubMed

Liu, Ying; Liu, Liang-Zi; Zhong, Zhi-Ping; Zhou, Yu-Guang; Liu, Ying; Liu, Zhi-Pei

2014-12-01

A Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated S1(T), was isolated from the Cynoglossus semilaevis culture pond in a recirculating mariculture system in Tianjin, China. The taxonomy of strain S1(T) was studied by using a polyphasic approach. Cells of strain S1(T) were non-spore-forming, curved rods, 0.4-0.6 µm wide and 1.2-2.0 µm long, and motile by means of a single polar flagellum. The strain was positive for oxidase and catalase activities. Strain S1(T) was able to grow at 4-30 °C (optimum, 25 °C), at pH 5.5-10.0 (optimum, pH 6.5-7.5) and in the presence of 1-5 % (w/v) NaCl (optimum, 2 %). Strain S1(T) contained Q-8 as the sole respiratory quinone and C16 : 1ω7c/C16 : 1ω6c and C16 : 0 as the predominant cellular fatty acids. The genomic DNA G+C content was 40.1 mol% (Tm). Phylogenetic analysis based on 16S rRNA gene sequences placed strain S1(T) in the genus Colwellia, and it formed a distinct lineage in the phylogenetic tree together with Colwellia meonggei MA1-3(T), Colwellia aestuarii SMK-10(T), Colwellia polaris 537(T) and Colwellia chukchiensis BCw111(T), with 97.7, 96.1, 95.9 and 95.0 % 16S rRNA gene sequence similarity to these strains, respectively. DNA-DNA relatedness of strain S1(T) to Colwellia meonggei MA1-3(T) was 23.5±3.6 %. On the basis of the phylogenetic and phenotypic evidence, strain S1(T) is considered to represent a novel species of the genus Colwellia, for which the name Colwellia aquaemaris sp. nov. is proposed. The type strain is S1(T) ( = CGMCC 1.12165(T) = JCM 18479(T)). © 2014 IUMS.

Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae.

PubMed

Ruckmani, Arunachalam; Kaur, Ishwinder; Schumann, Peter; Klenk, Hans-Peter; Mayilraj, Shanmugam

2011-10-01

During the course of a study on the bacterial diversity in Western Ghats, India, an actinobacterial strain, designated PC IW02(T), was isolated and characterized by a polyphasic taxonomic approach. Strain PC IW02(T) was a non-motile, Gram-positive, short rod that formed creamish white to yellow coloured colonies. 16S rRNA gene sequence analysis showed that the novel strain showed highest sequence similarity with type strains of members of the genus Dermacoccus: Dermacoccus barathri (96.6 %), Dermacoccus profundi (96.5 %), Dermacoccus abyssi (96.4 %) and Dermacoccus nishinomiyaensis (95.9 %). The phylogenetic tree suggested that strain PC IW02(T) could represent a member of a new genus of the family Dermacoccaceae with the genus Demetria as closest clade. Pairwise sequence alignment with Demetria terragena HKI 0089(T) and Kytococcus sedentarius DSM 20547(T) showed similarities of 94.2 and 93.7 %, respectively. Strain PC IW02(T) had MK-8(H(4)) as the major menaquinone. The major fatty acids were iso-C(16 : 0) (43.4 %), iso-C(16 : 1) H (17.2 %) and anteiso-C(17 : 0) (9.9 %). The diagnostic cell-wall amino acid at position 3 of the peptide subunit was lysine; the interpeptide bridge consisted of Gly-Ser-Asp. The polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and phosphatidylserine, along with two unknown phospholipids. The genomic DNA G+C content of the isolate was 77 mol%. On the basis of phenotypic characteristics, including chemotaxonomic data, and 16S rRNA gene sequence similarities, strain PC IW02(T) represents a novel species in a new genus of the family Dermacoccaceae for which the name Calidifontibacter indicus gen. nov., sp. nov. is proposed. The type strain of Calidifontibacter indicus is PC IW02(T) ( = MTCC 8338(T) = DSM 22967(T) = JCM 16038(T)). An emended description of the family Dermacoccaceae is provided.

Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae.

PubMed

Cole, Jessica K; Morton, Beau R; Cardamone, Hayley C; Lake, Hannah R R; Dohnalkova, Alice C; Kim, Young-Mo; Kyle, Jennifer E; Maezato, Yukari; Dana, Karl L; Metz, Thomas O; Romine, Margaret F; Nelson, William C; Lindemann, Stephen R

2018-06-01

There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109 T , was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109 T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109 T (=JCM 31876 T =DSM 102886 T ). In addition, examination of the phylogenetics of strain HL-109 T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).

PyXRD v0.6.7: a free and open-source program to quantify disordered phyllosilicates using multi-specimen X-ray diffraction profile fitting

NASA Astrophysics Data System (ADS)

Dumon, M.; Van Ranst, E.

2016-01-01

This paper presents a free and open-source program called PyXRD (short for Python X-ray diffraction) to improve the quantification of complex, poly-phasic mixed-layer phyllosilicate assemblages. The validity of the program was checked by comparing its output with Sybilla v2.2.2, which shares the same mathematical formalism. The novelty of this program is the ab initio incorporation of the multi-specimen method, making it possible to share phases and (a selection of) their parameters across multiple specimens. PyXRD thus allows for modelling multiple specimens side by side, and this approach speeds up the manual refinement process significantly. To check the hypothesis that this multi-specimen set-up - as it effectively reduces the number of parameters and increases the number of observations - can also improve automatic parameter refinements, we calculated X-ray diffraction patterns for four theoretical mineral assemblages. These patterns were then used as input for one refinement employing the multi-specimen set-up and one employing the single-pattern set-ups. For all of the assemblages, PyXRD was able to reproduce or approximate the input parameters with the multi-specimen approach. Diverging solutions only occurred in single-pattern set-ups, which do not contain enough information to discern all minerals present (e.g. patterns of heated samples). Assuming a correct qualitative interpretation was made and a single pattern exists in which all phases are sufficiently discernible, the obtained results indicate a good quantification can often be obtained with just that pattern. However, these results from theoretical experiments cannot automatically be extrapolated to all real-life experiments. In any case, PyXRD has proven to be useful when X-ray diffraction patterns are modelled for complex mineral assemblages containing mixed-layer phyllosilicates with a multi-specimen approach.

Investigating the effect of plate-mantle interaction in basin creation and associated drainage systems: insights from the North West Shelf of Australia

NASA Astrophysics Data System (ADS)

Morón, S.; Gallagher, S. J.; Moresi, L. N.; Salles, T.; Rey, P. F.; Payenberg, T.

2016-12-01

The effect of plate-mantle dynamics on surface topography has increasingly being recognized. This concept is particularly useful for the understanding of the links between plate-mantle dynamics, continental break up and the creation of sedimentary basins and their associated drainage systems. To unravel these links back in time we present an approach that uses numerical models and the geological record. The sedimentary basins of the North West Shelf (NWS) of Australia contain an exceptional record of the Permian to early Cretaceous polyphased rifting of Australia from Greater India, which is in turn associated with the breakup of Gondwana. This record and the relative tectonic quiescence of the Australian Continent since the Late Cretaceous make the NWS a great natural laboratory for investigating the interaction between mantle dynamics, plate tectonics and drainage patterns. Furthermore, as a result of the extensive petroleum exploration and production in the area a uniquely large dataset containing seismic, lithologic, biostratigraphic and detrital zircon information is already available. This study will first focus on augmenting zircon datasets to refine the current conceptual models of paleodrainage systems associated with the NWS. Current conceptual models of drainage patterns suggest the previous existance of large transcontinental rivers that transported sediments from Antarctica and India, rather than from more proximal Australian sources. From a mass-balance point of view this model seems reasonable, as large transcontinental rivers would be required to transport the significant volume of sediments that are deposited in the thick (15km) sedimentary sequences of the NWS. Coupling of geodynamic (Underworld) and landscape-dynamics (Badlands) models will allow us to numerically test the likelihood of this conceptual model and also to present and integrated approach to investigate the link between deep Earth processes and surficial processes.

Chromobacterium haemolyticum sp. nov., a strongly haemolytic species.

PubMed

Han, Xiang Y; Han, Faye S; Segal, Jonathan

2008-06-01

A Gram-negative bacterium, strain MDA0585(T), isolated from a sputum culture, was characterized by a polyphasic approach. The 16S rRNA gene and a conserved portion of the DNA gyrase A gene were sequenced and analysed phylogenetically. Strain MDA0585(T) showed the closest relationships with Chromobacterium violaceum ATCC 12472(T) and Chromobacterium subtsugae PRAA4-1(T) (96.1 % and 96.3 % 16S rRNA gene sequence similarity, respectively). The cellular fatty acids of strain MDA0585(T) consisted mainly of C(16 : 0), C(16 : 1)omega7c and C(16 : 1)omega6c (summed feature 3) and C(18 : 1)omega7c and C(18 : 1)omega6c (summed feature 8), a profile that was similar to, but distinguishable from, those of C. violaceum ATCC 12472(T) and C. subtsugae PRAA4-1(T). In culture, strain MDA0585(T) differed from C. violaceum and C. subtsugae in several ways: lack of violet pigmentation, the ability to haemolyse sheep blood, differences in several biochemical reactions and higher resistance to antibiotics. The culture supernatant of strain MDA0585(T) also caused remarkable haemolysis of human erythrocytes. These results suggest that strain MDA0585(T) represents a novel species within the genus Chromobacterium, for which the name Chromobacterium haemolyticum sp. nov. is proposed. The type strain is MDA0585(T) (=CCUG 53230(T)=JCM 14163(T)=DSM 19808(T)).

Low-temperature anaerobic digestion is associated with differential methanogenic protein expression.

PubMed

Gunnigle, Eoin; Siggins, Alma; Botting, Catherine H; Fuszard, Matthew; O'Flaherty, Vincent; Abram, Florence

2015-05-01

Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tenacibaculum aiptasiae sp. nov., isolated from a sea anemone Aiptasia pulchella.

PubMed

Wang, Jih-Terng; Chou, Yi-Ju; Chou, Jui-Hsing; Chen, Chaolun Allen; Chen, Wen-Ming

2008-04-01

A novel bacterial strain, designated a4T, isolated from a sea anemone (Aiptasia pulchella) in Taiwan, was characterized using a polyphasic taxonomic approach. Strain a4T was aerobic, Gram-negative, pale-yellow-pigmented and rod-shaped. It grew optimally at 30-35 degrees C, in the presence of 3-4 % (w/v) NaCl and at pH 8.0. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes). The closest neighbours were Tenacibaculum lutimaris TF-26T (97.6 % similarity) and Tenacibaculum aestuarii SMK-4T (97.7 % similarity). The novel isolate could be distinguished from all Tenacibaculum species by several phenotypic characteristics. The major fatty acids were summed feature 3 (comprising C16 : 1 omega 7c and/or iso-C15 : 0 2-OH, 19.6 %), iso-C15 : 0 (12.9 %), iso-C16 : 0 3-OH (10.2 %), iso-C17 : 0 3-OH (9.9 %) and iso-C15 : 1 (9.5 %). The DNA G+C content was 35.0 mol%. Hence, genotypic and phenotypic data demonstrate that strain a4(T) should be classified as a representative of a novel species in the genus Tenacibaculum, for which the name Tenacibaculum aiptasiae sp. nov. is proposed. The type strain is a4T (=BCRC 17655T =LMG 24004T).

Gaetbulimicrobium brevivitae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat of the Yellow Sea in Korea.

PubMed

Yoon, Jung-Hoon; Kang, So-Jung; Jung, Seo-Youn; Oh, Hyun Woo; Oh, Tae-Kwang

2006-01-01

A Gram-negative, non-spore-forming and rod-shaped gliding bacterium, designated strain SMK-19T, was isolated from a tidal flat sediment of the Yellow Sea, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain SMK-19T grew optimally at 37 degrees C, in the presence of 2-3 % (w/v) NaCl and at pH 7.0-8.0. It contained MK-6 as the predominant menaquinone, and iso-C(17 : 0) 3-OH and iso-C(15 : 0) as the major fatty acids. Major polar lipids were phosphatidylethanolamine, unidentified phospholipids and an amino-group-containing lipid that is ninhydrin-positive. The DNA G+C content was 36.0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain SMK-19T formed a distinct evolutionary lineage within the family Flavobacteriaceae. The 16S rRNA gene sequence of strain SMK-19T exhibited similarity values of <94.4 % to those of other members of the family Flavobacteriaceae. Strain SMK-19T was distinguished from phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic, phylogenetic and chemotaxonomic data, SMK-19T (= KCTC 12390T = DSM 17196T) was classified at the type strain of a novel genus and species, Gaetbulimicrobium brevivitae gen. nov., sp. nov.

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil.

PubMed

Leite, Jakson; Passos, Samuel Ribeiro; Simões-Araújo, Jean Luiz; Rumjanek, Norma Gouvêa; Xavier, Gustavo Ribeiro; Zilli, Jerri Édson

2017-03-31

The leguminous inoculation with nodule-inducing bacteria that perform biological nitrogen fixation is a good example of an "eco-friendly agricultural practice". Bradyrhizobium strains BR 3267 and BR 3262 are recommended for cowpea (Vigna unguiculata) inoculation in Brazil and showed remarkable responses; nevertheless neither strain was characterized at species level, which is our goal in the present work using a polyphasic approach. The strains presented the typical phenotype of Bradyrhizobium with a slow growth and a white colony on yeast extract-mannitol medium. Strain BR 3267 was more versatile in its use of carbon sources compared to BR 3262. The fatty acid composition of BR 3267 was similar to the type strain of Bradyrhizobium yuanmingense; while BR 3262 was similar to Bradyrhizobium elkanii and Bradyrhizobium pachyrhizi. Phylogenetic analyses based on 16S rRNA and three housekeeping genes placed both strains within the genus Bradyrhizobium: strain BR 3267 was closest to B. yuanmingense and BR 3262 to B. pachyrhizi. Genome average nucleotide identity and DNA-DNA reassociation confirmed the genomic identification of B. yuanmingense BR 3267 and B. pachyrhizi BR 3262. The nodC and nifH gene analyses showed that strains BR 3267 and BR 3262 hold divergent symbiotic genes. In summary, the results indicate that cowpea can establish effective symbiosis with divergent bradyrhizobia isolated from Brazilian soils. Published by Elsevier Editora Ltda.

Novel microbiological and spatial statistical methods to improve strength of epidemiological evidence in a community-wide waterborne outbreak.

PubMed

Jalava, Katri; Rintala, Hanna; Ollgren, Jukka; Maunula, Leena; Gomez-Alvarez, Vicente; Revez, Joana; Palander, Marja; Antikainen, Jenni; Kauppinen, Ari; Räsänen, Pia; Siponen, Sallamaari; Nyholm, Outi; Kyyhkynen, Aino; Hakkarainen, Sirpa; Merentie, Juhani; Pärnänen, Martti; Loginov, Raisa; Ryu, Hodon; Kuusi, Markku; Siitonen, Anja; Miettinen, Ilkka; Santo Domingo, Jorge W; Hänninen, Marja-Liisa; Pitkänen, Tarja

2014-01-01

Failures in the drinking water distribution system cause gastrointestinal outbreaks with multiple pathogens. A water distribution pipe breakage caused a community-wide waterborne outbreak in Vuorela, Finland, July 2012. We investigated this outbreak with advanced epidemiological and microbiological methods. A total of 473/2931 inhabitants (16%) responded to a web-based questionnaire. Water and patient samples were subjected to analysis of multiple microbial targets, molecular typing and microbial community analysis. Spatial analysis on the water distribution network was done and we applied a spatial logistic regression model. The course of the illness was mild. Drinking untreated tap water from the defined outbreak area was significantly associated with illness (RR 5.6, 95% CI 1.9-16.4) increasing in a dose response manner. The closer a person lived to the water distribution breakage point, the higher the risk of becoming ill. Sapovirus, enterovirus, single Campylobacter jejuni and EHEC O157:H7 findings as well as virulence genes for EPEC, EAEC and EHEC pathogroups were detected by molecular or culture methods from the faecal samples of the patients. EPEC, EAEC and EHEC virulence genes and faecal indicator bacteria were also detected in water samples. Microbial community sequencing of contaminated tap water revealed abundance of Arcobacter species. The polyphasic approach improved the understanding of the source of the infections, and aided to define the extent and magnitude of this outbreak.

Occurrence of Aspergillus section Flavi and aflatoxins in Brazilian rice: From field to market.

PubMed

Katsurayama, Aline M; Martins, Ligia M; Iamanaka, Beatriz T; Fungaro, Maria Helena P; Silva, Josué J; Frisvad, Jens C; Pitt, John I; Taniwaki, Marta H

2018-02-02

The guarantee of the high quality of rice is of utmost importance because any toxic contaminant may affect consumer health, especially in countries such as Brazil where rice is part of the daily diet. A total of 187 rice samples, from field, processing and market from two different production systems, wetland from the state of Rio Grande do Sul, dryland, from the state of Maranhão and market samples from the state of São Paulo, were analyzed for fungi belonging to Aspergillus section Flavi and the presence of aflatoxins. Twenty-three soil samples from wetland and dryland were also analyzed. A total of 383 Aspergillus section Flavi strains were isolated from rice and soil samples. Using a polyphasic approach, with phenotypic (morphology and extrolite profiles) and molecular data (beta-tubulin gene sequences), five species were identified: A. flavus, A. caelatus, A. novoparasiticus, A. arachidicola and A. pseudocaelatus. This is the first report of these last three species from rice and rice plantation soil. Only seven (17%) of the A. flavus isolates produced type B aflatoxins, but 95% produced kojic acid and 69% cyclopiazonic acid. Less than 14% of the rice samples were contaminated with aflatoxins, but two of the market samples were well above the maximum tolerable limit (5μg/kg), established by the Brazilian National Health Surveillance Agency. Copyright © 2017 Elsevier B.V. All rights reserved.

Technological properties of Lactobacillus plantarum strains isolated from grape must fermentation.

PubMed

Berbegal, Carmen; Peña, Nuria; Russo, Pasquale; Grieco, Francesco; Pardo, Isabel; Ferrer, Sergi; Spano, Giuseppe; Capozzi, Vittorio

2016-08-01

Malolactic fermentation (MLF) is a secondary fermentation in wine that usually takes place during or at the end of alcoholic fermentation. Lactobacillus plantarum is able to conduct MLF (particularly under high pH conditions and in co-inoculation with yeasts), and some strains are commercially used as MLF starter cultures. Recent evidences suggest a further use of selected L. plantarum strains for the pre-alcoholic acidification of grape must. In this study, we have carried out an integrated (molecular, technological, and biotechnological) characterization of L. plantarum strains isolated from Apulian wines in order to combine the two protechnological features (MLF performances and must acidification aptitudes). Several parameters such as sugar, pH and ethanol tolerance, resistance to lyophilisation and behaviour in grape must were evaluated. Moreover, the expression of stress gene markers was investigated and was linked to the ability of L. plantarum strains to grow and perform MLF. Co-inoculation of Saccharomyces cerevisiae and L. plantarum in grape must improves the bacterial adaptation to harsh conditions of wine and reduced total fermentation time. For the first time, we applied a polyphasic approach for the characterization of L. plantarum in reason of the MLF performances. The proposed procedure can be generalized as a standard method for the selection of bacterial resources for the design of MLF starter cultures tailored for high pH must. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mycobiota and Mycotoxins in Traditional Medicinal Seeds from China

PubMed Central

Chen, Amanda Juan; Jiao, Xiaolin; Hu, Yongjian; Lu, Xiaohong; Gao, Weiwei

2015-01-01

The multi-mycotoxin occurrence for internal and superficial fungi contamination were comprehensively assessed in medicinal seeds used as food or beverage. Based on a polyphasic approach using morphological characters, β-tubulin and ITS gene blast, a total of 27 species belonging to 12 genera were identified from surface-sterilized seeds. Chaetomium globosporum was most predominant (23%), followed by Microascus trigonosporus (12%) and Alternaria alternata (9%). With respect to superficial mycobiota, thirty-four species belonging to 17 genera were detected. Aspergillus niger and Penicillium polonicum were predominant (12% and 15%, respectively). Medicinal seed samples and potential toxigenic fungi were tested for ochratoxin A (OTA) and aflatoxins (AFB1, AFB2, AFG1, AFG2) using UPLC-MS/MS. Platycladi seeds were contaminated with AFB1 (52.0 µg/kg) and tangerine seed was contaminated with OTA (92.3 µg/kg). Subsequent analysis indicated that one A. flavus strain isolated from platycladi seed was able to synthesize AFB1 (102.0 µg/kg) and AFB2 (15.3 µg/kg). Two P. polonicum strains isolated from tangerine and lychee seeds were able to synthesize OTA (4.1 µg/kg and 14.8 µg/kg, respectively). These results identify potential sources of OTA and aflatoxins in medicinal seeds and allude to the need to establish permitted limits for these mycotoxins in these seeds that are commonly consumed by humans. PMID:26404373

Characterization of Xenorhabdus isolates from La Rioja (Northern Spain) and virulence with and without their symbiotic entomopathogenic nematodes (Nematoda: Steinernematidae).

PubMed

Campos-Herrera, R; Tailliez, P; Pagès, S; Ginibre, N; Gutiérrez, C; Boemare, N E

2009-10-01

Eighteen Xenorhabdus isolates associated with Spanish entomopathogenic nematodes of the genus Steinernema were characterized using a polyphasic approach including phenotypic and molecular methods. Two isolates were classified as Xenorhabdus nematophila and were associated with Steinernema carpocapsae. Sixteen isolates were classified as Xenorhabdus bovienii, of which fifteen were associated with Steinernema feltiae and one with Steinernema kraussei. Two X. bovienii Phase II were also isolated, one instable phase isolated from S. feltiae strain Rioja and one stable phase from S. feltiae strain BZ. Four representative bacterial isolates were chosen to study their pathogenicity against Spodoptera littoralis with and without the presence of their nematode host. The four bacterial isolates were pathogenic for S. littoralis leading to septicemia 24h post-injection and killing around 90% of the insect larvae 36 h post-injection, except for that isolated from S. kraussei. After 48 h of injection, this latter isolate showed a lower final population in the larval hemolymph (10(7) instead of 10(8)CFU per larvae) and a lower larval mortality (70% instead of 95-100%). The virulence of the nematode-bacteria complexes against S. littoralis showed similar traits with a significant insect larvae mortality (80-90%) 5 days post-infection except for S. kraussei, although this strain reached similar of larval mortality at 7 days after infection.

Mycobiota and Mycotoxins in Traditional Medicinal Seeds from China.

PubMed

Chen, Amanda Juan; Jiao, Xiaolin; Hu, Yongjian; Lu, Xiaohong; Gao, Weiwei

2015-09-24

The multi-mycotoxin occurrence for internal and superficial fungi contamination were comprehensively assessed in medicinal seeds used as food or beverage. Based on a polyphasic approach using morphological characters, β-tubulin and ITS gene blast, a total of 27 species belonging to 12 genera were identified from surface-sterilized seeds. Chaetomium globosporum was most predominant (23%), followed by Microascus trigonosporus (12%) and Alternaria alternata (9%). With respect to superficial mycobiota, thirty-four species belonging to 17 genera were detected. Aspergillus niger and Penicillium polonicum were predominant (12% and 15%, respectively). Medicinal seed samples and potential toxigenic fungi were tested for ochratoxin A (OTA) and aflatoxins (AFB1, AFB2, AFG1, AFG2) using UPLC-MS/MS. Platycladi seeds were contaminated with AFB1 (52.0 µg/kg) and tangerine seed was contaminated with OTA (92.3 µg/kg). Subsequent analysis indicated that one A. flavus strain isolated from platycladi seed was able to synthesize AFB1 (102.0 µg/kg) and AFB2 (15.3 µg/kg). Two P. polonicum strains isolated from tangerine and lychee seeds were able to synthesize OTA (4.1 µg/kg and 14.8 µg/kg, respectively). These results identify potential sources of OTA and aflatoxins in medicinal seeds and allude to the need to establish permitted limits for these mycotoxins in these seeds that are commonly consumed by humans.

Capturing biodiversity: linking a cyanobacteria culture collection to the “scratchpads” virtual research environment enhances biodiversity knowledge

PubMed Central

Panou, Manthos

2016-01-01

Abstract Background Currently, cyanobacterial diversity is examined using a polyphasic approach by assessing morphological and molecular data (Komárek 2015). However, the comparison of morphological and genetic data is sometimes hindered by the lack of cultures of several cyanobacterial morphospecies and inadequate morphological data of sequenced strains (Rajaniemi et al. 2005). Furthermore, in order to evaluate the phenotypic plasticity within defined taxa, the variability observed in cultures has to be compared to the range in natural variation (Komárek and Mareš 2012). Thus, new tools are needed to aggregate, link and process data in a meaningful way, in order to properly study and understand cyanodiversity. New information An online database on cyanobacteria has been created, namely the Cyanobacteria culture collection (CCC) (http://cyanobacteria.myspecies.info/) using as case studies cyanobacterial strains isolated from lakes of Greece, which are part of the AUTH culture collection (School of Biology, Aristotle University of Thessaloniki). The database hosts, for the first time, information and data such as morphology/morphometry, biogeography, phylogeny, microphotographs, distribution maps, toxicology and biochemical traits of the strains. All this data are structured managed, and presented online and are publicly accessible with a recently developed tool, namely “Scratchpads”, a taxon-centric virtual research environment allowing browsing the taxonomic classification and retrieving various kinds of relevant information for each taxon. PMID:27226753

Xanthomonas prunicola sp. nov., a novel pathogen that affects nectarine (Prunus persica var. nectarina) trees.

PubMed

López, María M; Lopez-Soriano, Pablo; Garita-Cambronero, Jerson; Beltrán, Carmen; Taghouti, Geraldine; Portier, Perrine; Cubero, Jaime; Fischer-Le Saux, Marion; Marco-Noales, Ester

2018-06-01

Three isolates obtained from symptomatic nectarine trees (Prunus persica var. nectarina) cultivated in Murcia, Spain, which showed yellow and mucoid colonies similar to Xanthomonas arboricola pv. pruni, were negative after serological and real-time PCR analyses for this pathogen. For that reason, these isolates were characterized following a polyphasic approach that included both phenotypic and genomic methods. By sequence analysis of the 16S rRNA gene, these novel strains were identified as members of the genus Xanthomonas, and by multilocus sequence analysis (MLSA) they were clustered together in a distinct group that showed similarity values below 95 % with the rest of the species of this genus. Whole-genome comparisons of the average nucleotide identity (ANI) of genomes of the strains showed less than 91 % average nucleotide identity with all other species of the genus Xanthomonas. Additionally, phenotypic characterization based on API 20 NE, API 50 CH and BIOLOG tests differentiated the strains from the species of the genus Xanthomonas described previously. Moreover, the three strains were confirmed to be pathogenic on peach (Prunus persica), causing necrotic lesions on leaves. On the basis of these results, the novel strains represent a novel species of the genus Xanthomonas, for which the name Xanthomonas prunicola is proposed. The type strain is CFBP 8353 (=CECT 9404=IVIA 3287.1).

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

PubMed Central

Kubo, Kyoko; Lloyd, Karen G; F Biddle, Jennifer; Amann, Rudolf; Teske, Andreas; Knittel, Katrin

2012-01-01

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes. PMID:22551871

Microbial species delineation using whole genome sequences.

PubMed

Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

2015-08-18

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Diversity of yeasts associated with the sea surface microlayer and underlying water along the northern coast of Taiwan.

PubMed

Chang, Chin-Feng; Lee, Ching-Fu; Lin, Kao-Yung; Liu, Shiu-Mei

2016-01-01

Yeast communities inhabiting the sea surface microlayer (SSML) on the northern coast of Taiwan were examined using a cultivation method and compared with those inhabiting the underlying water (UW) at a 50-cm depth. Culturable yeasts were recovered from the SSML and UW samples collected in the morning during 4 field campaigns, and 420 strains were isolated. The 420 isolates were grouped into 43 species using a polyphasic molecular approach, including sequence analysis of the 26S rDNA D1/D2 domain and 5.8S-ITS region. From the SSML samples, 12 genera and 39 species, including 7 new species of Cryptococcus sp. (1), Candida spp. (4), and Rhodotorula spp. (2), were isolated. From the UW samples, 10 genera and 21 species, including one new species of Rhodotorula sp. (1), were isolated. Rhodotorula mucilaginosa was the most abundant species present in the yeast community in SSML (37.6%) and UW (21.6%) samples. Basidiomycetous yeasts (63.6%) and pigmented yeasts (64.5%) comprised the major yeast population. The yeast community in the SSML had a higher species number and abundance than the UW. Moreover, although the majority of yeast community species were from the SSML, individual species distribution in the SSML was unequal. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

PubMed Central

Röling, Wilfred F. M.; Kerler, Josef; Braster, Martin; Apriyantono, Anton; Stam, Hein; van Verseveld, Henk W.

2001-01-01

The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans. PMID:11319073

Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods.

PubMed

Yan, Yin-zhuo; Qian, Yu-lin; Ji, Feng-di; Chen, Jing-yu; Han, Bei-zhong

2013-05-01

Koji-making is a key process for production of high quality soy sauce. The microbial composition during koji-making was investigated by culture-dependent and culture-independent methods to determine predominant bacterial and fungal populations. The culture-dependent methods used were direct culture and colony morphology observation, and PCR amplification of 16S/26S rDNA fragments followed by sequencing analysis. The culture-independent method was based on the analysis of 16S/26S rDNA clone libraries. There were differences between the results obtained by different methods. However, sufficient overlap existed between the different methods to identify potentially significant microbial groups. 16 and 20 different bacterial species were identified using culture-dependent and culture-independent methods, respectively. 7 species could be identified by both methods. The most predominant bacterial genera were Weissella and Staphylococcus. Both 6 different fungal species were identified using culture-dependent and culture-independent methods, respectively. Only 3 species could be identified by both sets of methods. The most predominant fungi were Aspergillus and Candida species. This work illustrated the importance of a comprehensive polyphasic approach in the analysis of microbial composition during soy sauce koji-making, the knowledge of which will enable further optimization of microbial composition and quality control of koji to upgrade Chinese traditional soy sauce product. Copyright © 2013 Elsevier Ltd. All rights reserved.

Requalification of a Brazilian Trichoderma Collection and Screening of Its Capability to Decolourise Real Textile Effluent

PubMed Central

Silva Lisboa, Dianny; Santos, Cledir; Barbosa, Renan N.; Magalhães, Oliane; Paiva, Laura M.; Moreira, Keila A.; Lima, Nelson; Souza-Motta, Cristina M.

2017-01-01

Water contamination with large amounts of industrial textile coloured effluents is an environmental concern. For the treatment of textile effluents, white-rot fungi have received extensive attention due to their powerful capability to produce oxidative (e.g., ligninolytic) enzymes. In addition, other groups of fungi, such as species of Aspergillus and Trichoderma, have also been used for textile effluents treatment. The main aim of the present study was to requalify a Brazilian Trichoderma culture collection of 51 Trichoderma strains, isolated from different sources in Brazil and preserved in the oldest Latin-American Fungal Service Culture Collection, The Micoteca URM WDCM 804 (Recife, Brazil). Fungal isolates were re-identified through a polyphasic approach including macro- and micro-morphology and molecular biology, and screened for their capability to decolourise real effluents collected directly from storage tanks of a textile manufacture. Trichoderma atroviride URM 4950 presented the best performance on the dye decolourisation in real textile effluent and can be considered in a scale-up process at industrial level. Overall, the potential of Trichoderma strains in decolourising real textile dye present in textile effluent and the production of the oxidative enzymes Lac, LiP and MnP was demonstrated. Fungal strains are available in the collection e-catalogue to be further explored from the biotechnological point of view. PMID:28368305

Pseudomonas aestusnigri sp. nov., isolated from crude oil-contaminated intertidal sand samples after the Prestige oil spill.

PubMed

Sánchez, David; Mulet, Magdalena; Rodríguez, Ana C; David, Zoyla; Lalucat, Jorge; García-Valdés, Elena

2014-03-01

Strains VGXO14(T) and Vi1 were isolated from the Atlantic intertidal shore from Galicia, Spain, after the Prestige oil spill. Both strains were Gram-negative rod-shaped bacteria with one polar inserted flagellum, strictly aerobic, and able to grow at 18-37°C, pH 6-10 and 2-10% NaCl. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus but were distinct from any known Pseudomonas species. A polyphasic taxonomic approach including phylogenetic, chemotaxonomic, phenotypic and genotypic data confirmed that the strains belonged to the Pseudomonas pertucinogena group. In a multilocus sequence analysis, the similarity of VGXO14(T) and Vi1 to the closest type strain of the group, Pseudomonas pachastrellae, was 90.4%, which was lower than the threshold of 97% established to discriminate species in the Pseudomonas genus. The DNA-DNA hybridisation similarity between strains VGXO14(T) and Vi1 was 79.6%, but below 70% with the type strains in the P. pertucinogena group. Therefore, the strains should be classified within the genus Pseudomonas as a novel species, for which the name Pseudomonas aestusnigri is proposed. The type strain is VGXO14(T) (=CCUG 64165(T)=CECT 8317(T)). Copyright © 2013 Elsevier GmbH. All rights reserved.

Cryobacterium aureum sp. nov., a psychrophilic bacterium isolated from glacier ice collected from the ice tongue surface.

PubMed

Liu, Qing; Xin, Yu-Hua; Chen, Xiu-Ling; Liu, Hong-Can; Zhou, Yu-Guang; Chen, Wen-Xin

2018-04-01

A psychrophilic, Gram-stain-positive, rod-shaped bacterium, designated strain Hh31 T , was isolated from Xinjiang No. 1 Glacier in China. Strain Hh31 T was catalase-positive, oxidase-negative and able to grow at between 0-18 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh31 T belonged to the genus Cryobacterium and was most closely related to the type strains of Cryobacterium levicorallinum, Cryobacterium luteum and Cryobacterium flavum. DNA-DNA hybridization, calculation of average nucleotide identity and digital DNA-DNA hybridization revealed that strain Hh31 T was distinct from its closest phylogenetic neighbours. The major cellular fatty acids of strain Hh31 T were anteiso-C15 : 0, anteiso-C15 : 1, iso-C15:0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinones of strain Hh31 T were MK-9 and MK-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, one unidentified glycolipid and another unidentified lipid. Physiological tests such as carbon source utilization, showed phenotypic differentiation of strain Hh31 T from the closest related phylogenetic neighbours. Based on a polyphasic approach, a novel species, Cryobacterium aureum sp. nov., is proposed, with Hh31 T (=NBRC 107882 T =CGMCC 1.11213 T ) as the type strain.

Arthrobacter ruber sp. nov., isolated from glacier ice.

PubMed

Liu, Qing; Xin, Yu-Hua; Chen, Xiu-Ling; Liu, Hong-Can; Zhou, Yu-Guang; Chen, Wen-Xin

2018-05-01

A Gram-stain-positive strain designated MDB1-42 T was isolated from ice collected from Midui glacier in Tibet, PR China. Strain MDB1-42 T was catalase-positive, oxidase-negative and grew optimally at 25-28 °C and pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that MDB1-42 T represented a member of the genus Arthrobacter. The highest level of 16S rRNA gene sequence similarity (99.86 %) was found with Arthrobacter agilis NBRC 15319 T . Multilocus sequence analysis revealed low similarity of 91.93 % between MDB1-42 T and Arthrobacter agilis NBRC 15319 T . Average nucleotide identity and digital DNA-DNA hybridization values between MDB1-42 T and the most closely related strain, Arthrobacter agilis DSM 20550 T , were 81.36 and 24.5 %, respectively. The genomic DNA G+C content was 69.0 mol%. The major cellular fatty acids of MDB1-42 T were anteiso-C15 : 0 and anteiso-C17:0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid and one unidentified lipid. The predominant menaquinone was MK-9(H2). On the basis of results obtained using a polyphasic approach, a novel species Arthrobacter ruber sp. nov. is proposed, with MDB1-42 T (=CGMCC 1.9772 T =NBRC 113088 T ) as the type strain.

Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus.

PubMed

Giaj Merlera, G; Muñoz, S; Coelho, I; Cavaglieri, L R; Torres, A M; Reynoso, M M

2015-10-01

Aspergillus section Nigri is a heterogeneous fungal group including some ochratoxin A producer species that usually contaminate raisins. The section contains the Series Carbonaria which includes the toxigenic species Aspergillus carbonarius and nontoxigenic Aspergillus ibericus that are phenotypically undistinguishable. The aim of this study was to examine the diversity of black aspergilli isolated from raisins and to develop a specific genetic marker to distinguish A. ibericus from A. carbonarius. The species most frequently found in raisins in this study were Aspergillus tubingensis (35.4%) and A. carbonarius (32.3%), followed by Aspergillus luchuensis (10.7%), Aspergillus japonicus (7.7%), Aspergillus niger (6.2%), Aspergillus welwitschiae (4.6%) and A. ibericus (3.1%). Based on inter-simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Nigri members, a sequence-characterized amplified region (SCAR) marker was identified. Primers were designed based on the conserved regions of the SCAR marker and were utilized in a PCR for simultaneous identification of A. carbonarius and A. ibericus. The detection level of the SCAR-PCR was found to be 0.01 ng of purified DNA. The present SCAR-PCR is rapid and less cumbersome than conventional identification techniques and could be a supplementary strategy and a reliable tool for high-throughput sample analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice.

PubMed

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

2009-01-01

A pink-pigmented, aerobic, facultatively methylotrophic bacterial strain, CBMB27T, isolated from leaf tissues of rice (Oryza sativa L. 'Dong-Jin'), was analysed using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence-based phylogenetic analysis placed the strain in a clade with the species Methylobacterium oryzae, Methylobacterium fujisawaense and Methylobacterium mesophilicum; strain CBMB27T showed sequence similarities of 98.3, 98.5 and 97.3 %, respectively, to the type strains of these three species. DNA-DNA hybridization experiments revealed low levels (<38 %) of DNA-DNA relatedness between strain CBMB27T and its closest relatives. The sequence of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) in strain CBMB27T differed from those of close relatives. The major fatty acid of the isolate was C(18 : 1)omega7c and the G+C content of the genomic DNA was 66.8 mol%. Based on the results of 16S rRNA gene sequence analysis, DNA-DNA hybridization, and physiological and biochemical characterization, which enabled the isolate to be differentiated from all recognized species of the genus Methylobacterium, it was concluded that strain CBMB27T represents a novel species in the genus Methylobacterium for which the name Methylobacterium phyllosphaerae sp. nov. is proposed (type strain CBMB27T =LMG 24361T =KACC 11716T =DSM 19779T).

Mesozoic contractile and extensional structures in the Boyer Gap area, northern Dome Rock Mountains, Arizona

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

Boettcher, S.S.

1993-04-01

Mesozoic polyphase contractile and superposed ductile extensional structures affect Proterozoic augen gneiss, Paleozoic metasedimentary rocks, and Jurassic granitoids in the Boyer Gap area of the northern Dome Rock Mtns, W-central Arizona. The nappe-style contractile structures are preserved in the footwall of the Tyson Thrust shear zone, which is one of the structurally lowest thrust faults in the E-trending Jurassic and Cretaceous Maria fold and thrust belt. Contractile deformation preceded emplacement of Late Cretaceous granite (ca 80 Ma, U-Pb zircon) and some may be older than variably deformed Late Jurassic leucogranite. Specifically, detailed structural mapping reveals the presence of a km-scalemore » antiformal syncline that apparently formed as a result of superposition of tight to isoclinal, south-facing folds on an earlier, north-facing recumbent fold. The stratigraphic sequence of metamorphosed Paleozoic cratonal strata is largely intact in the northern Dome Rock Mtns, such that overturned and upright stratigraphic units can be distinguished. A third phase of folding in the Boyer Gap area is distinguished by intersection lineations that are folded obliquely across the hinges of open to tight, sheath folds. The axial planes of the sheet folds are subparallel to the mylonitic foliation in top-to-the-northeast extensional shear zones. The timing of ductile extensional structures in the northern Dome Rock is constrained by [sup 40]Ar/[sup 39]Ar isochron ages of 56 Ma and 48 Ma on biotite from mylonitic rocks in both the hanging wall and footwall of the Tyson Thrust shear zone. The two early phases of folding are the dominant mechanism by which shortening was accommodated in the Boyer Gap area, as opposed to deformation along discrete thrust faults with large offset. All of the ductile extensional structures are spectacularly displayed at an outcrop scale but are not of sufficient magnitude to obliterate the km-scale Mesozoic polyphase contractile structures.« less

Structural analysis and tectonic evolution of the eastern Binalud Mountains, NE Iran

NASA Astrophysics Data System (ADS)

Sheikholeslami, M. R.; Kouhpeyma, M.

2012-10-01

The Binalud Mountains are situated in the south of the Kopeh Dagh as a transitional zone between the Alborz and Central Iran zones. The Palaeotethys suture of the north Iran is located in this area. The Binalud Mountains consists of relatively thick successions of sedimentary, metamorphic and igneous rocks. The earliest deformation, a polyphase synmetamorphic deformation which occurred entirely in ductile conditions, is distinguished in the metamorphic rocks of the eastern part. D1, D2 and D3 deformation phases are related to this deformation. The D4 deformation affected the area after a period of sedimentation and erosion. The thrust faults of the central and southern part of the eastern Binalud were classified as structures related to the D5 tectonic event. From the geodynamic point of view, in Late Palaeozoic times the studied area formed an oceanic trench generated by the subduction of the Palaeotethys oceanic lithosphere beneath the Turan Plate. In the Late Triassic, the Early Cimmerian Event resulted in a collisional type orogeny generating a transpression polyphase deformation and the metamorphism of Permian and older sediments. Following this collision, granite intrusions were emplaced in the area and caused contact metamorphism. The exhumation and erosion of the rocks deformed and metamorphosed during Early Cimmerian Event caused the formation of molassic type sediments in a Rhaetian-Lias back arc basin. The continuation of convergence between the Turan and Iran Plates caused the metamorphism of these sediments and their transformation to phyllite and meta-sandstone. During Late Mesozoic and Early Cenozoic times, the convergence between Central Iran and Turan Plates continued and a NE compression caused folding of the Cretaceous and older rocks in the Kopeh Dagh area. In the Binalud area this deformation caused the generation of several thrust fault systems with S to SW vergence, resulting in a thrusting of Palaeozoic and Mesozoic successions on each other and on the Neogene sediments at the southern border of the Binalud Mountains.

The grand tour of the Ruby-East Humboldt metamorphic core complex, northeastern Nevada: Part 1 - Introduction & road log

USGS Publications Warehouse

Snoke, A.W.; Howard, K.A.; McGrew, A.J.; Burton, B.R.; Barnes, C.G.; Peters, M.T.; Wright, J.E.

1997-01-01

The purpose of this geological excursion is to provide an overview of the multiphase developmental history of the Ruby Mountains and East Humboldt Range, northeastern Nevada. Although these mountain ranges are commonly cited as a classic example of a Cordilleran metamorphic core complex developed through large-magnitude, mid-Tertiary crustal extension, a preceding polyphase Mesozoic contractional history is also well preserved in the ranges. An early phase of this history involved Late Jurassic two-mica granitic magmatism, high-temperature but relatively low-pressure metamorphism, and polyphase deformation in the central Ruby Mountains. In the northern Ruby Mountains and East Humboldt Range, a Late Cretaceous history of crustal shortening, metamorphism, and magmatism is manifested by fold-nappes (involving Archean basement rocks in the northern East Humboldt Range), widespread migmatization, injection of monzogranitic and leucogranitic magmas, all coupled with sillimanite-grade metamorphism. Following Late Cretaceous contraction, a protracted extensional deformation partially overprinted these areas during the Cenozoic. This extensional history may have begun as early as the Late Cretaceous or as late as the mid-Eocene. Late Eocene and Oligocene magmatism occurred at various levels in the crust yielding mafic to felsic orthogneisses in the deep crust, a composite granitic pluton in the upper crust, and volcanic rocks at the surface. Movement along a west-rooted, extensional shear zone in the Oligocene and early Miocene led to core-complex exhumation. The shear zone produced mylonitic rocks about 1 km thick at deep crustal levels, and an overprint of brittle detachment faulting at shallower levels as unroofing proceeded. Megabreccias and other synextensional sedimentary deposits are locally preserved in a tilted, upper Eocene through Miocene stratigraphic sequence. Neogene magmatism included the emplacement of basalt dikes and eruption of rhyolitic rocks. Subsequent Basin and Range normal faulting, as young as Holocene, records continued tectonic extension.

Vibration energy harvesting with polyphase AC transducers

NASA Astrophysics Data System (ADS)

McCullagh, James J.; Scruggs, Jeffrey T.; Asai, Takehiko

2016-04-01

Three-phase transduction affords certain advantages in the efficient electromechanical conversion of energy, especially at higher power scales. This paper considers the use of a three-phase electric machine for harvesting energy from vibrations. We consider the use of vector control techniques, which are common in the area of industrial electronics, for optimizing the feedback loops in a stochastically-excited energy harvesting system. To do this, we decompose the problem into two separate feedback loops for direct and quadrature current components, and illustrate how each might be separately optimized to maximize power output. In a simple analytical example, we illustrate how these techniques might be used to gain insight into the tradeoffs in the design of the electronic hardware and the choice of bus voltage.

Fundamentals of electric power conversion. Volume 1, Operating characteristics and testing of AC induction motors, final report

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

Umans, S.D.

1992-12-01

Its rugged nature and straightforward design make the induction motor the most commonly used type of electric motor. This motor ranges in size from the fractional-horsepower, single-phase motors found in household appliances to polyphase motors rated at thousands of horsepower for industrial applications. Volume 1 of this report describes the function of induction motors, their characteristics, and induction motor testing. Volume 2 describes the characteristics of high-efficiency induction motors, with emphasis on the techniques used to obtain high efficiency. This two-volume report is written in nontechnical language and is intended for readers who require background from an applications, marketing, motormore » planning, or managerial perspective.« less

Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.

PubMed

Martínez-Aguilar, Lourdes; Salazar-Salazar, Corelly; Méndez, Rafael Díaz; Caballero-Mellado, Jesús; Hirsch, Ann M; Vásquez-Murrieta, María Soledad; Estrada-de los Santos, Paulina

2013-12-01

During a survey of Burkholderia species with potential use in agrobiotechnology, a group of 12 strains was isolated from the rhizosphere and rhizoplane of tomato plants growing in Mexico (Nepantla, Mexico State). A phylogenetic analysis of 16S rRNA gene sequences showed that the strains are related to Burkholderia kururiensis and Burkholderia mimosarum (97.4 and 97.1 %, respectively). However, they induced effective nitrogen-fixing nodules on roots of Phaseolus vulgaris. Based on polyphasic taxonomy, the group of strains represents a novel species for which the name Burkholderia caballeronis sp. nov. is proposed. The type species is TNe-841(T) (= LMG 26416(T) = CIP 110324(T)).

An SCR inverter for electric vehicles

NASA Technical Reports Server (NTRS)

Latos, T.; Bosack, D.; Ehrlich, R.; Jahns, T.; Mezera, J.; Thimmesch, D.

1980-01-01

An inverter for an electric vehicle propulsion application has been designed and constructed to excite a polyphase induction motor from a fixed propulsion battery source. The inverter, rated at 35kW peak power, is fully regenerative and permits vehicle operation in both the forward and reverse directions. Thyristors are employed as the power switching devices arranged in a dc bus commutated topology. This paper describes the major role the controller plays in generating the motor excitation voltage and frequency to deliver performance similar to dc systems. Motoring efficiency test data for the controller are presented. It is concluded that an SCR inverter in conjunction with an ac induction motor is a viable alternative to present dc vehicle propulsion systems on the basis of performance and size criteria.

Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species.

PubMed

Caballero-Mellado, Jesús; Martínez-Aguilar, Lourdes; Paredes-Valdez, Guadalupe; Santos, Paulina Estrada-De los

2004-07-01

It was shown recently that the genus Burkholderia is rich in N2-fixing bacteria that are associated with plants. A group of these diazotrophic isolates with identical or very similar 16S rDNA restriction patterns [designated amplified rDNA restriction analysis (ARDRA) genotypes 13, 14 and 15] was selected and a polyphasic taxonomic study was performed, which included new isolates that were recovered from rhizospheres, rhizoplanes or internal tissues of maize, sugarcane and coffee plants. Morphological, physiological and biochemical features, as well as multi-locus enzyme electrophoresis profiles and whole-cell protein patterns, of 20 strains were analysed. In addition, analysis of cellular fatty acid profiles, 16S rDNA sequence analysis and DNA-DNA reassociation experiments were performed with representative strains. The taxonomic data indicated that the strains analysed belong to a novel diazotrophic Burkholderia species, for which the name Burkholderia unamae sp. nov. is proposed. Strain MTl-641T (=ATCC BAA-744T=CIP 107921T), isolated from the rhizosphere of maize, was designated as the type strain. B. unamae was found as an endophyte of plants grown in regions with climates ranging from semi-hot subhumid to hot humid, but not from plants grown in regions with semi-hot or hot dry climates. Moreover, B. unamae was isolated from rhizospheres and plants growing in soils with pH values in the range 4.5-7.1, but not from soils with pH values higher than 7.5.

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

PubMed

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

2011-05-01

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

Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster.

PubMed

Baek, Chaeyun; Kim, Eunji; Shin, Su-Kyoung; Choi, Sungmi; Yi, Hana

2017-10-01

A Gram-negative, motile, rod-shaped, and aerobic bacterial strain, designated LPB0072 T , was isolated from a Pacific oyster (Crassostrea gigas). Autotrophic growth with hydrogen gas was not observed. Cells oxidized thiosulfate to sulfate and reduced nitrate to nitrite. The complete genome sequence of strain LPB0072 T (CP017476) is 4.94 Mb in length and contains 4459 protein-coding genes, with a G+C content of 61.3 mol%. Analysis of the 16S rRNA gene sequence indicated that strain LPB0072 T belongs to the genus Hydrogenophaga, with greatest sequence similarity to the type strain of Hydrogenophaga taeniospiralis (97.5 %). The isoprenoid quinone (Q-8) and the major cellular fatty acids (C16 : 1ω7c and/or C16 : 1ω6c, C16 : 0 and C17 : 1ω6c) identified were concordant with the chemotaxonomic properties of the genus Hydrogenophaga. The average nucleotide identities with closely related species were below the suggested boundary for species delineation, indicating that the isolate is a novel species. Numerous physiological and biochemical features also distinguished the isolate from other known Hydrogenophaga species. Based on the polyphasic data presented in this study, strain LPB0072 T should be classified as a novel species in the genus Hydrogenophaga, and the name Hydrogenophaga crassostreae sp. nov. is proposed. The type strain is LPB0072 T (=KACC 18705 T =JCM 31188 T ).

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

PubMed

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

2015-02-01

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

Hymenobacter aquatilis sp. nov., isolated from a mesotrophic artificial lake.

PubMed

Kang, Heeyoung; Cha, Inseong; Kim, Haneul; Joh, Kiseong

2018-06-01

A novel strain, designated HMF3095 T , isolated from freshwater of a mesotrophic artificial lake in the Republic of Korea, was characterized by polyphasic taxonomy. The cells were Gram-stain-negative, aerobic, non-motile, straight rods and formed reddish colonies. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain HMF3095 T fell within the cluster of the genus Hymenobacterand was most closely related to Hymenobacter seoulensis 16F7G T and Hymenobacter tenuis POB6 T (96.7 % sequence similarity). Sequence similarities to all other type strains were 96.3 % or less. The major fatty acids were iso-C15 : 0, C16 : 1ω5c, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and anteiso-C15 : 0. The major isoprenoid quinone was menaquinone 7. The major polar lipids were phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified phospholipid. The DNA G+C content was 58.9 mol%. On the basis of the evidence presented in this study, strain HMF3095 T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter aquatilis sp. nov. is proposed. The type strain is HMF3095 T (=KCTC 52398 T =NBRC 112669 T ).

Nesterenkonia pannonica sp. nov., a novel alkaliphilic and moderately halophilic actinobacterium.

PubMed

Borsodi, Andrea K; Szili-Kovács, Tibor; Schumann, Peter; Spröer, Cathrin; Márialigeti, Károly; Tóth, Erika

2017-10-01

An alkaliphilic and moderately halophilic bacterial strain characterized by optimal growth at pH 9.0-10.0 and with 5-7 % (w/v) NaCl, designated BV-35 T , was isolated from water of a soda pan located in Kiskunság National Park, Hungary. Cells of the orange-pigmented colony were Gram-stain-positive, non-motile and non-endospore-forming coccoid rods. The isolate was strictly aerobic, catalase-positive and oxidase-negative. Strain BV-35 T displayed a peptidoglycan similar to type A4α, l-Lys-l-Glu (A11.54 according to www.peptidoglycan-types.info) but containing additionally 4-aminobutyric acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were its major cellular fatty acids. The DNA G+C content of strain BV-35 T was 65.4 mol%. Based on 16S rRNA gene sequence similarities, the novel isolate showed the closest relationship to Nesterenkonia populi GP 10-3 T (97.9 %). The DNA-DNA relatedness between BV-35 T and N. populi was 46.7 %. The distinguishing phenotypic and genetic results of this polyphasic study revealed that strain BV-35 T represents a novel member of the genus Nesterenkonia, for which the name Nesterenkonia pannonica sp. nov. is proposed. The type strain is BV-35 T (=DSM 29786 T =NCAIM B 02606 T ).

Streptomyces kalpinensis sp. nov., an actinomycete isolated from a salt water beach.

PubMed

Ma, Guo-Quan; Xia, Zhan-Feng; Wan, Chuan-Xing; Zhang, Yao; Luo, Xiao-Xia; Zhang, Li-Li

2017-12-01

A novel actinobacterium designated TRM 46509 T was isolated from a salt water beach at Kalpin, Xinjiang, north-west China. The strain was aerobic and Gram-stain-positive, with an optimum NaCl concentration for growth of 1 % (w/v). The isolate formed sparse aerial mycelium and produced spiral spores at the end of the aerial mycelium on Gauze's No. 1 medium. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid and ribose as the major whole-cell sugar. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified phospholipid. The predominant menaquinones were MK-9(H2), MK-9(H6) and MK-9(H8). The major fatty acids were C16:0, iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0. The G+C content of the DNA was 69.3 mol%. Phylogenetic analysis showed that strain TRM 46509 T shared 16S rRNA gene sequence similarity of 97.6 % with the closest described species Streptomyces tacrolimicus ATCC 55098 T . On the basis of evidence from this polyphasic study, strain TRM 46509 T should be designated as representing a novel species of the genus Streptomyces, for which the name Streptomyces kalpinensis sp. nov. is proposed. The type strain is TRM 46509 T (=CCTCC AA 2015028 T =KCTC 39667 T ).

Mucilaginibacter pedocola sp. nov., isolated from a heavy-metal-contaminated paddy field.

PubMed

Tang, Jingwei; Huang, Jing; Qiao, Zixu; Wang, Rui; Wang, Gejiao

2016-10-01

Strain TBZ30T was isolated from soil of a heavy-metal-contaminated paddy field. Cells of strain TBZ30T were Gram-staining-negative, rod-shaped, non-motile and non-spore-forming. The isolate was strictly aerobic, pink-pigmented, catalase- and oxidase-positive and produced exopolysaccharides. On the basis of 16S rRNA gene phylogeny, strain TBZ30T belonged to the genus Mucilaginibacter and appeared most closely related to Mucilaginibacter gynuensis YC7003T (95.8 %), Mucilaginibacter litoreus BR-18T (95.4 %) and Mucilaginibacter mallensis MP1X4T (95.4 %). Strain TBZ30T contained menaquinone-7 as the only ubiquinone. The main cellular fatty acids included summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and C16 : 1ω5c. The polar lipids were phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, four unidentified aminolipids, three unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 49.0 mol%. On the basis of polyphasic taxonomy analyses, strain TBZ30T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter pedocola sp. nov. is proposed. The type strain is TBZ30T (=KCTC 42833T=CCTCC AB 2015301T).

Lindane degradation by Candida VITJzN04, a newly isolated yeast strain from contaminated soil: kinetic study, enzyme analysis and biodegradation pathway.

PubMed

Salam, Jaseetha Abdul; Das, Nilanjana

2014-04-01

A new yeast strain was isolated from sugarcane cultivation field which was able to utilize lindane as sole carbon source for growth in mineral medium. The yeast was identified and named as Candida sp. VITJzN04 based on a polyphasic approach using morphological, biochemical and 18S rDNA, D1/D2 and ITS sequence analysis. The isolated yeast strain efficiently degraded 600 mg L⁻¹ of lindane within 6 days in mineral medium under the optimal conditions (pH 7; temperature 30 °C and inoculum dosage 0.06 g L⁻¹) with the least half-life of 1.17 days and degradation constant of 0.588 per day. Lindane degradation was tested with various kinetic models and results revealed that the reaction could be described best by first-order and pseudo first-order models. In addition, involvement of the enzymes viz. dechlorinase, dehalogenase, dichlorohydroquinone reductive dechlorinase, lignin peroxidase and manganese peroxidase was noted during lindane degradation. Addition of H2O2 in the mineral medium showed 32 % enhancement of lindane degradation within 3 days. Based on the metabolites identified by GC-MS and FTIR analysis, sequential process of lindane degradation by Candida VITJzN04 was proposed. To the best of our knowledge, this is the first report of isolation and characterization of lindane-degrading Candida sp. and elucidation of enzyme systems during the degradation process.

622-Mbps Orthogonal Frequency Division Multiplexing (OFDM) Digital Modem Implemented

NASA Technical Reports Server (NTRS)

Kifle, Muli; Bizon, Thomas P.; Nguyen, Nam T.; Tran, Quang K.; Mortensen, Dale J.

2002-01-01

Future generation space communications systems feature significantly higher data rates and relatively smaller frequency spectrum allocations than systems currently deployed. This requires the application of bandwidth- and power-efficient signal transmission techniques. There are a number of approaches to implementing such techniques, including analog, digital, mixed-signal, single-channel, or multichannel systems. In general, the digital implementations offer more advantages; however, a fully digital implementation is very difficult because of the very high clock speeds required. Multichannel techniques are used to reduce the sampling rate. One such technique, multicarrier modulation, divides the data into a number of low-rate channels that are stacked in frequency. Orthogonal frequency division multiplexing (OFDM), a form of multicarrier modulation, is being proposed for numerous systems, including mobile wireless and digital subscriber link communication systems. In response to this challenge, NASA Glenn Research Center's Communication Technology Division has developed an OFDM digital modem (modulator and demodulator) with an aggregate information throughput of 622 Mbps. The basic OFDM waveform is constructed by dividing an incoming data stream into four channels, each using either 16- ary quadrature amplitude modulation (16-QAM) or 8-phase shift keying (8-PSK). An efficient implementation for an OFDM architecture is being achieved using the combination of a discrete Fourier transform (DFT) at the transmitter to digitally stack the individual carriers, inverse DFT at the receiver to perform the frequency translations, and a polyphase filter to facilitate the pulse shaping.

Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome

PubMed Central

Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

2015-01-01

Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health. PMID:25714833

Novel Microbiological and Spatial Statistical Methods to Improve Strength of Epidemiological Evidence in a Community-Wide Waterborne Outbreak

PubMed Central

Jalava, Katri; Rintala, Hanna; Ollgren, Jukka; Maunula, Leena; Gomez-Alvarez, Vicente; Revez, Joana; Palander, Marja; Antikainen, Jenni; Kauppinen, Ari; Räsänen, Pia; Siponen, Sallamaari; Nyholm, Outi; Kyyhkynen, Aino; Hakkarainen, Sirpa; Merentie, Juhani; Pärnänen, Martti; Loginov, Raisa; Ryu, Hodon; Kuusi, Markku; Siitonen, Anja; Miettinen, Ilkka; Santo Domingo, Jorge W.; Hänninen, Marja-Liisa; Pitkänen, Tarja

2014-01-01

Failures in the drinking water distribution system cause gastrointestinal outbreaks with multiple pathogens. A water distribution pipe breakage caused a community-wide waterborne outbreak in Vuorela, Finland, July 2012. We investigated this outbreak with advanced epidemiological and microbiological methods. A total of 473/2931 inhabitants (16%) responded to a web-based questionnaire. Water and patient samples were subjected to analysis of multiple microbial targets, molecular typing and microbial community analysis. Spatial analysis on the water distribution network was done and we applied a spatial logistic regression model. The course of the illness was mild. Drinking untreated tap water from the defined outbreak area was significantly associated with illness (RR 5.6, 95% CI 1.9–16.4) increasing in a dose response manner. The closer a person lived to the water distribution breakage point, the higher the risk of becoming ill. Sapovirus, enterovirus, single Campylobacter jejuni and EHEC O157:H7 findings as well as virulence genes for EPEC, EAEC and EHEC pathogroups were detected by molecular or culture methods from the faecal samples of the patients. EPEC, EAEC and EHEC virulence genes and faecal indicator bacteria were also detected in water samples. Microbial community sequencing of contaminated tap water revealed abundance of Arcobacter species. The polyphasic approach improved the understanding of the source of the infections, and aided to define the extent and magnitude of this outbreak. PMID:25147923

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.

Streptomyces capitiformicae sp. nov., a novel actinomycete producing angucyclinone antibiotics isolated from the head of Camponotus japonicus Mayr.

PubMed

Jiang, Shanwen; Piao, Chenyu; Yu, Yang; Cao, Peng; Li, Chenxu; Yang, Fan; Li, Mutong; Xiang, Wensheng; Liu, Chongxi

2018-01-01

A novel actinomycete, designated strain 1H-SSA4 T , was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce angucyclinone antibiotics. A polyphasic approach was used to determine the taxonomic status of strain 1H-SSA4 T . The DNA G+C content of the draft genome sequence, consisting of 11.4 Mbp, was 70.0 mol%. 16S rRNA gene sequence similarity studies showed that strain 1H-SSA4 T belongs to the genus Streptomyces with the highest sequence similarity to Streptomyces hygroscopicus subsp. ossamyceticus NBRC 13983 T (98.9 %), and phylogenetically clustered with this species, Streptomyces torulosus LMG 20305 T (98.8 %), Streptomyces ipomoeae NBRC 13050 T (98.5 %) and Streptomyces decoyicus NRRL 2666 T (98.4 %). The morphological and chemotaxonomic properties of the strain were also consistent with those members of the genus Streptomyces. A combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-SSA4 T and the above-mentioned strains, which further clarified their relatedness and demonstrated that strain 1H-SSA4 T could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces capitiformicae sp. nov. is proposed. The type strain is 1H-SSA4 T (=CGMCC 4.7403 T =DSM 104537 T ).

Aquimarina salinaria sp. nov., a novel algicidal bacterium isolated from a saltpan.

PubMed

Chen, Wen-Ming; Sheu, Fu-Sian; Sheu, Shih-Yi

2012-02-01

A bacterial strain designated antisso-27(T), previously isolated from saltpan in Taiwan while screening for bacteria for algicidal activity, was characterized using the polyphasic taxonomic approach. Strain antisso-27(T) was Gram-negative, aerobic, brownish yellow colored, rod-shaped, non-flagellated and non-gliding. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain antisso-27(T) belonged to the genus Aquimarina within the family Flavobacteriaceae with relatively low sequence similarities of 94.0-96.6% to other valid Aquimarina spp. It contained iso-C(17:0) 3-OH, iso-C(15:0), iso-C(16:0), iso-C(15:1) and iso-C(15:0) 3-OH as the main fatty acids and contained a menaquinone with six isoprene units (MK-6) as the major isoprenoid quinone. Major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, an uncharacterized aminolipid and five uncharacterized phospholipids. Strain antisso-27(T) employed direct mode of algicidal lysis to Chlorella vulgaris strain 211-31; nevertheless, it released an algicidal substance against M. aeruginosa strain MTY01. This is the first study that the Aquimarina species possesses both direct and indirect algicidal activities. On the basis of the phylogenetic and phenotypic data, strain antisso-27(T) should be classified as representing a novel species, for which the name A. salinaria sp. nov. is proposed. The type strain is A. salinaria antisso-27(T) (= BCRC 80080(T) = LMG 25375(T)).

The DBBC environment for millimeter radioastronomy

NASA Astrophysics Data System (ADS)

Tuccari, Gino; Comoretto, Giovanni; Melis, Andrea; Buttaccio, Salvo

2012-09-01

The Digital Base Band Converter project developed in the last decade produced a general architecture and a class of boards, firmware and software, giving the possibility to build a general purpose back-end system for VLBI or single-dish observational activities. Such approach suggests the realization of a digital radio system, i.e. a receiver with conversion not realized with analogue techniques, maintaining only amplification stages in the analogue domain. This solution can be applied until a maximum around 16 GHz, the present limit for the instantaneous input band in the latest version of the DBBC project, while in the millimeter frequency range this maximum limit of 0.5-2 GHz of the previous versions allows the intermediate frequency to be processed in the digital domain. A description of the elements developed in the DBBC project is presented, with their use in different environments. The architecture is composed of a PC controlled mainframe, and of different modules that can be combined in a very flexible way in order to realize different instruments. The instrument can be expanded or retrofitted to meet increasing observational demands. Available modules include ADC converters, processing boards, physical interfaces (VSI and 10G Ethernet). Several applications have already been implemented and used in radioastronomic observations: a DDC (Direct Digital Conversion) for VLBI observations, a Polyphase Digital Filter Bank, and a Multiband Scansion Spectrometer. Other applications are currently studied for additional functionalities like a spectropolarimeter, a linear-to-circular polarization converter, a RFI-mitigation tool, and a phase-reference holographic tool-kit.

A reappraisal of the Pleurotus eryngii complex - new species and taxonomic combinations based on the application of a polyphasic approach, and an identification key to Pleurotus taxa associated with Apiaceae plants.

PubMed

Zervakis, Georgios I; Ntougias, Spyridon; Gargano, Maria Letizia; Besi, Maria I; Polemis, Elias; Typas, Milton A; Venturella, Giuseppe

2014-01-01

The Pleurotus eryngii species-complex comprises choice edible mushrooms growing on roots and lower stem residues of Apiaceae (umbellifers) plants. Material deriving from extensive sampling was studied by mating compatibility, morphological and ecological criteria, and through analysis of ITS1-5.8S-ITS2 and IGS1 rRNA sequences. Results revealed that P. eryngii sensu stricto forms a diverse and widely distributed aggregate composed of varieties elaeoselini, eryngii, ferulae, thapsiae, and tingitanus. Pleurotuseryngii subsp. tuoliensis comb. nov. is a phylogenetically sister group to the former growing only on various Ferula species in Asia. The existence of Pleurotusnebrodensis outside of Sicily (i.e., in Greece) is reported for the first time on the basis of molecular data, while P. nebrodensis subsp. fossulatus comb. nov. is a related Asiatic taxon associated with the same plant (Prangos ferulacea). Last, Pleurotusferulaginis sp. nov. grows on Ferulago campestris in northeast Italy, Slovenia and Hungary; it occupies a distinct phylogenetic position accompanied with significant differences in spore size and mating incompatibility versus other Pleurotus populations. Coevolution with umbellifers and host/substrate specificity seem to play key roles in speciation processes within this fungal group. An identification key to the nine Pleurotus taxa growing in association with Apiaceae plants is provided. Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Influence of Storage Conditions on the Growth of Pseudomonas Species in Refrigerated Raw Milk▿ †

PubMed Central

De Jonghe, Valerie; Coorevits, An; Van Hoorde, Koenraad; Messens, Winy; Van Landschoot, Anita; De Vos, Paul; Heyndrickx, Marc

2011-01-01

The refrigerated storage of raw milk throughout the dairy chain prior to heat treatment creates selective conditions for growth of psychrotolerant bacteria. These bacteria, mainly belonging to the genus Pseudomonas, are capable of producing thermoresistant extracellular proteases and lipases, which can cause spoilage and structural defects in pasteurized and ultra-high-temperature-treated milk (products). To map the influence of refrigerated storage on the growth of these pseudomonads, milk samples were taken after the first milking turn and incubated laboratory scale at temperatures simulating optimal and suboptimal preprocessing storage conditions. The outgrowth of Pseudomonas members was monitored over time by means of cultivation-independent denaturing gradient gel electrophoresis (DGGE). Isolates were identified by a polyphasic approach. These incubations revealed that outgrowth of Pseudomonas members occurred from the beginning of the dairy chain (farm tank) under both optimal and suboptimal storage conditions. An even greater risk for outgrowth, as indicated by a vast increase of about 2 log CFU per ml raw milk, existed downstream in the chain, especially when raw milk was stored under suboptimal conditions. This difference in Pseudomonas outgrowth between optimal and suboptimal storage was already statistically significant within the farm tank. The predominant taxa were identified as Pseudomonas gessardii, Pseudomonas gessardii-like, Pseudomonas fluorescens-like, Pseudomonas lundensis, Pseudomonas fragi, and Pseudomonas fragi-like. Those taxa show an important spoilage potential as determined on elective media for proteolysis and lipolysis. PMID:21115713

Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of Inquilinus limosus gen. nov., sp. nov.

PubMed

Coenye, Tom; Goris, Johan; Spilker, Theodore; Vandamme, Peter; LiPuma, John J

2002-06-01

Using a polyphasic approach (including cellular protein and fatty acid analysis, biochemical characterization, 16S ribosomal DNA sequencing, and DNA-DNA hybridizations), we characterized 51 bacterial isolates recovered from respiratory secretions of cystic fibrosis (CF) patients. Our analyses showed that 24 isolates belong to taxa that have so far not (or only rarely) been reported from CF patients. These taxa include Acinetobacter sp., Bordetella hinzii, Burkholderia fungorum, Comamonas testosteroni, Chryseobacterium sp., Herbaspirillum sp., Moraxella osloensis, Pandoraea genomospecies 4, Ralstonia gilardii, Ralstonia mannitolilytica, Rhizobium radiobacter, and Xanthomonas sp. In addition, one isolate most likely represents a novel Ralstonia species, whereas nine isolates belong to novel taxa within the alpha-PROTEOBACTERIA: Eight of these latter isolates are classified into the novel genus Inquilinus gen. nov. as Inquilinus limosus gen. nov., sp. nov., or as Inquilinus sp. The remaining 17 isolates are characterized as members of the family ENTEROBACTERIACEAE: The recovery of these species suggests that the CF lung is an ecological niche capable of supporting the growth of a wide variety of bacteria rarely seen in clinical samples. Elucidation of the factors that account for the association between these unusual species and the respiratory tract of CF patients may provide important insights into the pathophysiology of CF infection. Because accurate identification of these organisms in the clinical microbiology laboratory may be problematic, the present study highlights the utility of reference laboratories capable of identifying unusual species recovered from CF sputum.

Bacterial diversity characterization in petroleum samples from Brazilian reservoirs

PubMed Central

de Oliveira, Valéria Maia; Sette, Lara Durães; Simioni, Karen Christina Marques; dos Santos Neto, Eugênio Vaz

2008-01-01

This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments. PMID:24031244

Eiseniicola composti gen. nov., sp. nov., with antifungal activity against plant pathogenic fungi.

PubMed

Yasir, Muhammad; Aslam, Zubair; Song, Geun Cheol; Jeon, Che Ok; Chung, Young Ryun

2010-01-01

A Gram-negative, short rod-shaped bacterial strain, YC06271T, was isolated from the vermicompost (VC) collected at Masan, Korea and its taxonomic position was investigated by a polyphasic taxonomic approach. Strain YC06271T grew optimally at 28-30 degrees C and at pH 7.0-9.0. The 16S rRNA gene sequence of strain YC06271T was most closely related to members of the genera Bordetella (96.4-95.8 %), Achromobacter (96.0-95.7 %), Alcaligenes (96.0-94.2 %), Pusillimonas noertemannii (95.9 %), Pigmentiphaga (95.8-95.5 %) and less than 95.5 % similarity with the members of the other genera of the family Alcaligenaceae. Strain YC06271T contained ubiquinone-8 (Q-8) as the major respiratory quinone system and putrescine as the major polyamine. The major fatty acids of strain YC06271T were C16:1omega7c and/or C15:0 iso 2-OH and C16:0. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 55.4 mol%. Phylogenetic analysis, biochemical, chemotaxonomic and phenotypic characteristics strongly supported the differentiation of strain YC06271T from the validly published genera of the family Alcaligenaceae. Therefore, it is proposed that strain YC06271T represents a novel species within a novel genus, with the name Eiseniicola composti gen. nov., sp. nov. The type strain is YC06271T (= KCTC 22250T = DSM 21045T).

The predominance of Lactobacillus sanfranciscensis in French organic sourdoughs and its impact on related bread characteristics.

PubMed

Lhomme, Emilie; Orain, Servane; Courcoux, Philippe; Onno, Bernard; Dousset, Xavier

2015-11-20

Fourteen bakeries located in different regions of France were selected. These bakers use natural sourdough and organic ingredients. Consequently, different organic sourdoughs used for the manufacture of French bread were studied by the enumeration of lactic acid bacteria (LAB) and 16S rRNA sequencing of the isolates. In addition, after DNA extraction the bacterial diversity was assessed by pyrosequencing of the 16S rDNA V1-V3 region. Although LAB counts showed significant variations (7.6-9.5log10CFU/g) depending on the sourdough studied, their identification through a polyphasic approach revealed a large predominance of Lactobacillus sanfranciscensis in all samples. In ten sourdoughs, both culture and independent methods identified L. sanfranciscensis as the dominant LAB species identified. In the remaining sourdoughs, culture methods identified 30-80% of the LAB as L. sanfranciscensis whereas more than 95% of the reads obtained by pyrosequencing belonged to L. sanfranciscensis. Other sub-dominant species, such as Lactobacillus curvatus, Lactobacillus hammesii, Lactobacillus paralimentarius, Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus sakei, were also identified. Quantification of L. sanfranciscensis by real-time PCR confirmed the predominance of this species ranging from 8.24 to 10.38log10CFU/g. Regarding the acidification characteristics, sourdough and related bread physico-chemical characteristics varied, questioning the involvement of sub-dominant species or L. sanfranciscensis intra-species diversity and/or the role of the baker's practices. Copyright © 2015 Elsevier B.V. All rights reserved.

Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes.

PubMed

Rivera-Posada, J A; Pratchett, M; Cano-Gomez, A; Arango-Gomez, J D; Owens, L

2011-09-09

We used a polyphasic approach for precise identification of bacterial flora (Vibrionaceae) isolated from crown-of-thorns starfish (COTS) from Lizard Island (Great Barrier Reef, Australia) and Guam (U.S.A., Western Pacific Ocean). Previous 16S rRNA gene phylogenetic analysis was useful to allocate and identify isolates within the Photobacterium, Splendidus and Harveyi clades but failed in the identification of Vibrio harveyi-like isolates. Species of the V harveyi group have almost indistinguishable phenotypes and genotypes, and thus, identification by standard biochemical tests and 16S rRNA gene analysis is commonly inaccurate. Biochemical profiling and sequence analysis of additional topA and mreB housekeeping genes were carried out for definitive identification of 19 bacterial isolates recovered from sick and wild COTS. For 8 isolates, biochemical profiles and topA and mreB gene sequence alignments with the closest relatives (GenBank) confirmed previous 16S rRNA-based identification: V. fortis and Photobacterium eurosenbergii species (from wild COTS), and V natriegens (from diseased COTS). Further phylogenetic analysis based on topA and mreB concatenated sequences served to identify the remaining 11 V harveyi-like isolates: V. owensii and V. rotiferianus (from wild COTS), and V. owensii, V. rotiferianus, and V. harveyi (from diseased COTS). This study further confirms the reliability of topA-mreB gene sequence analysis for identification of these close species, and it reveals a wider distribution range of the potentially pathogenic V. harveyi group.

Micromonospora zeae sp. nov., a novel endophytic actinomycete isolated from corn root (Zea mays L.).

PubMed

Shen, Yue; Zhang, Yuejing; Liu, Chongxi; Wang, Xiangjing; Zhao, Junwei; Jia, Feiyu; Yang, Lingyu; Yang, Deguang; Xiang, Wensheng

2014-11-01

A novel actinomycete, designated strain NEAU-gq9(T), was isolated from corn root (Zea mays L.) and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora. On the basis of 16S rRNA gene sequence similarity studies, strain NEAU-gq9(T) was most closely related to Micromonospora zamorensis CR38(T) (99.3%), Micromonospora jinlongensis NEAU-GRX11(T) (99.2%), Micromonospora saelicesensis Lupac 09(T) (99.2%), Micromonospora chokoriensis 2-19(6)(T) (98.9%), Micromonospora coxensis 2-30-b(28)(T) (98.6%) and Micromonospora lupini Lupac 14N(T) (98.5%). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that strain NEAU-gq9(T) is a member of the genus Micromonospora and supported the closest phylogenetic relationship to M. zamorensis CR38(T), M. jinlongensis NEAU-GRX11(T), M. saelicesensis Lupac 09(T), M. chokoriensis 2-19(6)(T) and M. lupini Lupac 14N(T). A combination of DNA-DNA hybridization, morphological and physiological characteristics indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. Therefore, it is proposed that strain NEAU-gq9(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora zeae sp. nov. is proposed. The type strain is NEAU-gq9(T) (=CGMCC 4.7092(T)=DSM 45882(T)).

Two new aflatoxin producing species, and an overview of Aspergillus section Flavi

PubMed Central

Varga, J.; Frisvad, J.C.; Samson, R.A.

2011-01-01

Aspergillus subgenus Circumdati section Flavi includes species with usually biseriate conidial heads, in shades of yellow-green to brown, and dark sclerotia. Several species assigned to this section are either important mycotoxin producers including aflatoxins, cyclopiazonic acid, ochratoxins and kojic acid, or are used in oriental food fermentation processes and as hosts for heterologous gene expression. A polyphasic approach was applied using morphological characters, extrolite data and partial calmodulin, β-tubulin and ITS sequences to examine the evolutionary relationships within this section. The data indicate that Aspergillus section Flavi involves 22 species, which can be grouped into seven clades. Two new species, A. pseudocaelatus sp. nov. and A. pseudonomius sp. nov. have been discovered, and can be distinguished from other species in this section based on sequence data and extrolite profiles. Aspergillus pseudocaelatus is represented by a single isolate collected from Arachis burkartii leaf in Argentina, is closely related to the non-aflatoxin producing A. caelatus, and produces aflatoxins B & G, cyclopiazonic acid and kojic acid, while A. pseudonomius was isolated from insects and soil in the USA. This species is related to A. nomius, and produces aflatoxin B1 (but not G-type aflatoxins), chrysogine and kojic acid. In order to prove the aflatoxin producing abilities of the isolates, phylogenetic analysis of three genes taking part in aflatoxin biosynthesis, including the transcriptional regulator aflR, norsolonic acid reductase and O-methyltransferase were also carried out. A detailed overview of the species accepted in Aspergillus section Flavi is presented. PMID:21892243

Streptomyces lasiicapitis sp. nov., an actinomycete that produces kanchanamycin, isolated from the head of an ant (Lasius fuliginosus L.).

PubMed

Ye, Lan; Zhao, Shanshan; Li, Yao; Jiang, Shanwen; Zhao, Yue; Li, Jinmeng; Yan, Kai; Wang, Xiangjing; Xiang, Wensheng; Liu, Chongxi

2017-05-01

During a screening for novel and biotechnologically useful actinobacteria in insects, a kanchanamycin-producing actinomycete with antifungal activity, designated strain 3H-HV17(2)T, was isolated from the head of an ant (Lasius fuliginosus L.) and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain 3H-HV17(2)T belongs to the genus Streptomyces with the highest sequence similarities to Streptomyces spectabilis NBRC 13424T (98.90 %, with which it phylogenetically clustered, Streptomyces alboflavus NRRL B-2373T (98.65 %) and Streptomyces flavofungini NBRC 13371T (98.36 %). Phylogenetic analysis based on the gyrB gene also supported the close relationship of these strains. The morphological and chemotaxonomic properties of the strain are also consistent with those members of the genus Streptomyces. A combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 3H-HV17(2)T and its phylogenetically closely related strains, which further clarified their relatedness and demonstrated that strain 3H-HV17(2)T could be distinguished from these strains. Therefore, strain 3H-HV17(2)T is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces lasiicapitis sp. nov. is proposed. The type strain is 3H-HV17(2)T (=CGMCC 4.7349T=DSM 103124T).

Streptomyces formicae sp. nov., a novel actinomycete isolated from the head of Camponotus japonicus Mayr.

PubMed

Bai, Lu; Liu, Chongxi; Guo, Lifeng; Piao, Chenyu; Li, Zhilei; Li, Jiansong; Jia, Feiyu; Wang, Xiangjing; Xiang, Wensheng

2016-02-01

During a screening for novel and biotechnologically useful actinobacteria in insects, a novel actinomycete with antifungal activity, designated strain 1H-GS9(T), was isolated from the head of a Camponotus japonicus Mayr ant, which were collected from Northeast Agricultural University (Harbin, Heilongjiang, China). Strain 1H-GS9(T) was characterised using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain 1H-GS9(T) belongs to the genus Streptomyces with high sequence similarities to Streptomyces scopuliridis DSM 41917(T) (98.8 %) and Streptomyces mauvecolor JCM 5002(T) (98.6 %). However, phylogenetic analysis based on the 16S rRNA gene sequence indicated that it forms a monophyletic clade with Streptomyces kurssanovii JCM 4388(T) (98.6 %), Streptomyces xantholiticus JCM 4282(T) (98.6 %) and Streptomyces peucetius JCM 9920(T) (98.5 %). Thus, a combination of DNA-DNA hybridization experiments and phenotypic tests were carried out between strain 1H-GS9(T) and the above-mentioned five strains, which further clarified their relatedness and demonstrated that strain 1H-GS9(T) could be distinguished from these strains. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces formicae sp. nov. is proposed. The type strain is 1H-GS9(T) (=CGMCC 4.7277(T) = DSM 100524(T)).

Biotic stress shifted structure and abundance of Enterobacteriaceae in the lettuce microbiome.

PubMed

Erlacher, Armin; Cardinale, Massimiliano; Grube, Martin; Berg, Gabriele

2015-01-01

Lettuce cultivars are not only amongst the most popular vegetables eaten raw, they are also involved in severe pathogen outbreaks world-wide. While outbreaks caused by Enterobacteriaceae species are well-studied, less is known about their occurrence in natural environments as well as the impact of biotic stress. Here, we studied the ecology of the human health-relevant bacterial family Enterobacteriaceae and assessed the impact of biotic disturbances by a soil-borne phytopathogenic fungus and Gastropoda on their structure and abundance in mesocosm and pot experiments. Using a polyphasic approach including network analyses of 16S rRNA gene amplicon libraries, quantitative PCR and complementary fluorescence in situ hybridization (FISH) microscopy we found substantial yet divergent Enterobacteriaceae communities. A similar spectrum of 14 genera was identified from rhizo- and phyllospheres but the abundance of Enterobacteriaceae was on average 3fold higher in phyllosphere samples. Both stress factors shifted the bacterial community of the leaf habitat, characterized by increases of species abundance and diversity. For the rhizosphere, we observed significant structural shifts of Enterobacteriaceae communities but also a high degree of resilience. These results could be confirmed by FISH microscopy but it was difficult to visualize phyllosphere communities. Additional inoculation experiments with Escherichia coli as model revealed their presence below the wax layer as well as in the endosphere of leaves. The observed presence influenced by stress factors and the endophytic life style of Enterobacteriaceae on lettuce can be an important aspect in relation to human health.

Pseudoclavibacter caeni sp. nov., isolated from sludge of a sewage disposal plant.

PubMed

Srinivasan, Sathiyaraj; Kim, Hyun Sook; Kim, Myung Kyum; Lee, Myungjin

2012-04-01

A Gram-positive, strictly aerobic, rod-shaped, non-motile bacterial strain, designated MJ28T, was isolated from a sludge sample from the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ28T. Strain MJ28T showed highest 16S rRNA gene sequence similarity to Pseudoclavibacter soli KP02T (95.2 %). Levels of 16S rRNA gene sequence similarity to the type strains of other Pseudoclavibacter species were less than 94.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ28T belonged to the clade formed by members of the genus Pseudoclavibacter in the family Microbacteriaceae. The G+C content of the genomic DNA of strain MJ28T was 65.8 mol%. The chemotaxonomic characteristics of strain MJ28T showed features typical of the genus Pseudoclavibacter, with MK-9 as the predominant respiratory quinone, 2,4-diaminobutryic acid as the diamino acid in the peptidoglycan, and anteiso-C17:0 (44.6 %), anteiso-C15:0 (35.7 %) and C16:0 (9.5 %) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ28T is considered to represent a novel species of the genus Pseudoclavibacter, for which the name Pseudoclavibacter caeni sp. nov. is proposed. The type strain is MJ28T (=KCTC 19773T=JCM 16921T).

Larkinella harenae sp. nov., Isolated from Korean Beach Soil.

PubMed

Park, Su-Jin; Lee, Jae-Jin; Lee, Seung-Yeol; Lee, Dae Sung; Kim, Myung Kyum; Ten, Leonid N; Jung, Hee-Young

2017-07-01

A Gram-negative, short rod-shaped, gliding motile, and pale pink-pigmented bacterial strain, designated 15J9-9 T , was isolated from the soil of Iho Tewoo Beach, Jeju Island, Korea, and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 15J9-9 T belonged to the family Cytophagaceae and was related to Larkinella bovis M2T2B15 T (96.5% similarity), Larkinella arboricola Z0532 T (95.3% similarity), and Larkinella insperata LMG 22510 T (95.2% similarity). The DNA G+C content of strain 15J9-9 T was 48 mol%. The detection of phosphatidylethanolamine, phosphatidylserine, two unknown aminophospholipids (APL 1 and APL 2 ), and two unknown polar lipids (L 1 and L 2 ) in polar lipid profile, menaquinone-7 as the predominant quinone, and a fatty acid profile of C 16:1 ω5c, iso-C 15:0 , and iso-C 17:0 3-OH as the major fatty acids supported the affiliation of strain 15J9-9 T to the genus Larkinella. Based on its phenotypic properties and phylogenetic distinctiveness, strain 15J9-9 T should be classified in the genus Larkinella as a representative of a novel species, for which the name Larkinella harenae sp. nov. is proposed. The type strain is 15J9-9 T (=KCTC 42999 T  = JCM 31656 T ).

Design Techniques for Uniform-DFT, Linear Phase Filter Banks

NASA Technical Reports Server (NTRS)

Sun, Honglin; DeLeon, Phillip

1999-01-01

Uniform-DFT filter banks are an important class of filter banks and their theory is well known. One notable characteristic is their very efficient implementation when using polyphase filters and the FFT. Separately, linear phase filter banks, i.e. filter banks in which the analysis filters have a linear phase are also an important class of filter banks and desired in many applications. Unfortunately, it has been proved that one cannot design critically-sampled, uniform-DFT, linear phase filter banks and achieve perfect reconstruction. In this paper, we present a least-squares solution to this problem and in addition prove that oversampled, uniform-DFT, linear phase filter banks (which are also useful in many applications) can be constructed for perfect reconstruction. Design examples are included illustrate the methods.

Fluid inclusions in minerals from the geothermal fields of Tuscany, Italy

USGS Publications Warehouse

Belkin, H.; de Vivo, B.; Gianelli, G.; Lattanzi, P.

1985-01-01

A reconnaissance study on fluid inclusions from the geothermal fields of Tuscany indicates that the hydrothermal minerals were formed by fluids which were, at least in part, boiling. Four types of aqueous inclusions were recognized: (A) two-phase (liquid + vapor) liquid rich, (B) two-phase (vapor + liquid) vapor rich, (C) polyphase hypersaline liquid rich and (D) three phase-H2O liquid + CO2 liquid + CO2-rich vapor. Freezing and heating microthermometric determinations are reported for 230 inclusions from samples from six wells. It is suggested that boiling of an originally homogeneous, moderately saline, CO2-bearing liquid phase produced a residual hypersaline brine and a CO2-rich vapor phase. There are indications of a temperature decrease in the geothermal field of Larderello, especially in its peripheral zones. ?? 1985.

Sphingomonas pituitosa sp. nov., an exopolysaccharide-producing bacterium that secretes an unusual type of sphingan.

PubMed

Denner, E B; Paukner, S; Kämpfer, P; Moore, E R; Abraham, W R; Busse, H J; Wanner, G; Lubitz, W

2001-05-01

Strain EDIVT, an exopolysaccharide-producing bacterium, was subjected to polyphasic characterization. The bacterium produced copious amounts of an extracellular polysaccharide, forming slimy, viscous, intensely yellow-pigmented colonies on Czapek-Dox (CZD) agar. The culture fluids of the liquid version of CZD medium were highly viscous after cultivation for 5 d. Cells of strain EDIVT were Gram-negative, catalase-positive, oxidase-negative, nonspore-forming, rod-shaped and motile. Comparisons of 16S rDNA gene sequences demonstrated that EDIVT clusters phylogenetically with the species of the genus Sphingomonas sensu stricto. The G+C content of the DNA (64.5 mol%), the presence of ubiquinone Q-10, the presence of 2-hydroxymyristic acid (14:0 2-OH) as the major hydroxylated fatty acid, the absence of 3-hydroxy fatty acids and the detection of sym-homospermidine as the major component in the polyamine pattern, together with the presence of sphingoglycolipid, supported this delineation. 16S rDNA sequence analysis indicated that strain EDIVT is most closely related (99.4% similarity) to Sphingomonas trueperi LMG 2142T. DNA-DNA hybridization showed that the level of relatedness to S. trueperi is only 45.5%. Further differences were apparent in the cellular fatty acid profile, the polar lipid pattern, the Fourier-transform infrared spectrum and whole-cell proteins and in a number of biochemical characteristics. On the basis of the estimated phylogenetic position derived from 16S rDNA sequence data, DNA-DNA reassociation and phenotypic differences, strain EDIVT (= CIP 106154T = DSM 13101T) was recognized as a new species of Sphingomonas, for which the name Sphingomonas pituitosa sp. nov. is proposed. A component analysis of the exopolysaccharide (named PS-EDIV) suggested that it represents a novel type of sphingan composed of glucose, rhamnose and an unidentified sugar. Glucuronic acid, which is commonly found in sphingans, was absent. The mean molecular mass of PS-EDIV was approximately 3 x 10(6) Da.

Sphaerisporangium dianthi sp. nov., an endophytic actinomycete isolated from a root of Dianthus chinensis L.

PubMed

Xing, Jia; Liu, Chongxi; Zhang, Yuejing; He, Hairong; Zhou, Ying; Li, Lianjie; Zhao, Junwei; Liu, Shuanghe; Wang, Xiangjing; Xiang, Wensheng

2015-01-01

A novel actinomycete, designated strain NEAU-CY18(T), was isolated from the root of a Chinese medicinal plant Dianthus chinensis L and subjected to a polyphasic taxonomic study. The novel strain was found to develop spherical sporangia with non-motile spores on aerial mycelium. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The whole-cell sugars were identified as madurose, mannose, ribose, galactose and glucose. The phospholipid profile was found to contain diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified phospholipid. The predominant menaquinones were identified as MK-9(H4), MK-9(H2) and MK-9(H6). The major fatty acids were identified as C17:0 10-methyl, iso-C16:0 and C16:0. EzTaxon-e analysis of the 16S rRNA gene sequence indicated that the strain belongs to the genus Sphaerisporangium and was most closely related to Sphaerisporangium cinnabarinum JCM 3291(T) (98.9 %) and Sphaerisporangium melleum JCM 13064(T) (98.3 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain NEAU-CY18(T) forms a monophyletic clade with S. cinnabarinum JCM 3291(T), an association that was supported by a bootstrap value of 97 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. Comparisons of some phenotypic properties and low DNA-DNA relatedness values enabled the strain to be differentiated from S. cinnabarinum JCM 3291(T) and S. melleum JCM 13064(T). Therefore, it is concluded that strain NEAU-CY18(T) represents a novel Sphaerisporangium species, for which the name Sphaerisporangium dianthi sp. nov. is proposed. The type strain is NEAU-CY18(T) ( = CGMCC 4.7132(T) = DSM 46736(T)).

Domibacillus tundrae sp. nov., isolated from active layer soil of tussock tundra in Alaska, and emended description of the genus Domibacillus.

PubMed

Gyeong, Hye Ryeon; Baek, Kiwoon; Hwang, Chung Yeon; Park, Key Hun; Kim, Hye Min; Lee, Hong Kum; Lee, Yoo Kyung

2015-10-01

A novel Gram-stain-positive, spore-forming, aerobic, motile and rod-shaped bacterium designated strain PAMC 80007T was isolated from an active layer soil sample of Council, Alaska. Optimal growth of strain PAMC 80007T was observed at 30 °C, pH 7.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain PAMC 80007T belonged to the genus Domibacillus. This strain was closely related to Domibacillus enclensis (98.3 %), Domibacillus robiginosus (98.3 %) and Domibacillus indicus (97.2 %). Genomic DNA G+C content was 43.5 mol% and genomic relatedness analyses based on the average nucleotide identity and the genome-to-genome distance showed that strain PAMC 80007T is clearly distinguished from the closely related species of the genus Domibacillus. The major fatty acids (>5 %) were iso-C15 : 0 (24.7 %), C16 : 1ω11c (16.8 %), anteiso-C15 : 0 (16.5 %), C16 : 0 (15.6 %) and anteiso-C17 : 0 (8.7 %). The major respiratory isoprenoid quinones were menaquinone-6 (MK-6) and menaquinone-7 (MK-7), and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, phospholipid and two unidentified lipids. meso-Diaminopimelic acid (type A1γ) was present in the cell-wall peptidoglycan, and the major whole-cell sugar was ribose with a minor quantity of glucose. Results from a polyphasic study suggested that strain PAMC 80007T represents a novel species of the genus Domibacillus for which the name Domibacillus tundrae sp. nov. is proposed. The type strain is PAMC 80007T ( = JCM 30371T = KCTC 33549T = DSM 29572T). An emended description of the genus Domibacillus is also provided.

[Vitamin B12-independent strains of Methylophaga marina isolated from Red Sea algae].

PubMed

Li, Ts D; Doronina, N V; Ivanova, E G; Trotsenko, Iu A

2007-01-01

Two strains (KM3 and KM5) of halophilic methylobacteria isolated from Red Sea algae do not require vitamin B12 for growth and can use methanol, methylamine, dimethylamine, trimethylamine, dimethyl sulfide, and fructose as sources of carbon and energy. The cells of these strains are gram-negative motile monotrichous (strain KM3) or peritrichous (strain KM5) rods. The strains are strictly aerobic and require Na+ ions but not growth factors for growth. They are oxidase- and catalase-positive and reduce nitrates to nitrites. Both strains can grow in a temperature range of 4 to 37 degrees C (with optimal growth at 29-34 degrees C), at pH between 5.5 and 8.5 (with optimal growth at pH 7.5-8.0), and in a range of salt concentrations between 0.5 and 15% NaCl (with optimal growth at 5-9% NaCl). The phospholipids of these strains are dominated by phosphatidylethanolamine and phosphatidylglycerol and also include phosphatidylcholine, phosphatidylserine, and cardiolipin. The dominant fatty acids are C(16:1omega7c) and C(16:0). The major ubiquinone is Q8. The cells accumulate ectoin, glutamate, and sucrose as intracellular osmoprotectants. The strains implement the 2-keto-3-deoxy-6-phosphogluconate-dependent variant of the ribulose monophosphate pathway. The G+C content of the DNA is 44.4-44.7 mol %. Analysis of the 16S rRNA genes showed that both strains belong to Gammaproteobacteria and have a high degree of homology (99.4%) to Methylophaga marina ATCC 35842T . Based on the data of polyphasic taxonomy, strains KM3 and KM5 are identified as new strains M. marina KM3 (VKM B-2386) and M. marina KM5 (VKM B-2387). The ability of these strains to produce auxins (indole-3-acetic acid) suggests their metabolic association with marine algae.

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 and phylogenetic analysis of one actinomycete strain YIM 90022 exhibiting anticancer activity].

PubMed

Chen, Yi-Guang; Li, Wen-Jun; Cui, Xiao-Long; Jiang, Cheng-Lin; Xu, Li-Hua

2006-10-01

One facultative alkaliphilic actinomycete strain YIM 90022 was isolated from hypersaline alkaline soil in Qinghai province, China. An almost-complete 16S rRNA gene sequence (1500 bp) for strain YIM 90022 was obtained. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 90022 was closely related to four members of the genus Nocardiopsis with 16S rRNA gene sequence similarity values of 98.8% (N. exhalans DSM 44407T), 98.5% (N. prasina DSM 43845T), 98.4% (N. metallicus DSM 44598T) and 97.8% (N. listeri DSM 40297T), but represented a distinct phylogenetic lineage. Repetitive element sequence-based PCR (rep-PCR) genomic fingerprinting was evaluated on strain YIM 90022 and its closest relatives to investigate their genetic relatedness. The analysis of the rep-PCR genomic fingerprints showed that strain YIM 90022 was distinguishable from its closest relatives. The polyphasic taxonomic data presented in this study, including its morphology, physiological and biochemical characteristics, chemotaxonomy, 16S rRNA gene sequence-based phylogenetic analysis and rep-PCR genomic fingerprinting, supported the view that strain YIM 90022 represented a potential new species of the genus Nocardiopsis. The fermentation broth of strain YIM 90022 strongly inhibited growth of cell series of gastric cancer, lung cancer, mammary cancer, melanoma cancer, renal cancer and uterus cancer. Strain YIM 90022 grew well on most tested media, producing exuberant vegetative hyphae and aerial hyphae. The vegetative hyphae are long and fragmented. Light yellow to deep brown diffusible pigments were produced on ISP 2, ISP 3 and ISP 6. Growth of the strain occurred in the pH range 6.0-12.0, with optimal pH8.5. The NaCl tolerate range was 0-15% (W/V). Cell walls contain meso-diaminopimelic acid and have no diagnostic sugars. Polar lipids are phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine. Major menaquinones are MK-10 (H4, H6). The DNA G + C content is 71.5 mol %.

Inversion of calcite twin data for paleostress (1) : improved Etchecopar technique tested on numerically-generated and natural data

NASA Astrophysics Data System (ADS)

Parlangeau, Camille; Lacombe, Olivier; Daniel, Jean-Marc; Schueller, Sylvie

2015-04-01

Inversion of calcite twin data are known to be a powerful tool to reconstruct the past-state of stress in carbonate rocks of the crust, especially in fold-and-thrust belts and sedimentary basins. This is of key importance to constrain results of geomechanical modelling. Without proposing a new inversion scheme, this contribution reports some recent improvements of the most efficient stress inversion technique to date (Etchecopar, 1984) that allows to reconstruct the 5 parameters of the deviatoric paleostress tensors (principal stress orientations and differential stress magnitudes) from monophase and polyphase twin data sets. The improvements consist in the search of the possible tensors that account for the twin data (twinned and untwinned planes) and the aid to the user to define the best stress tensor solution, among others. We perform a systematic exploration of an hypersphere in 4 dimensions by varying different parameters, Euler's angles and the stress ratio. We first record all tensors with a minimum penalization function accounting for 20% of the twinned planes. We then define clusters of tensors following a dissimilarity criterion based on the stress distance between the 4 parameters of the reduced stress tensors and a degree of disjunction of the related sets of twinned planes. The percentage of twinned data to be explained by each tensor is then progressively increased and tested using the standard Etchecopar procedure until the best solution that explains the maximum number of twinned planes and the whole set of untwinned planes is reached. This new inversion procedure is tested on monophase and polyphase numerically-generated as well as natural calcite twin data in order to more accurately define the ability of the technique to separate more or less similar deviatoric stress tensors applied in sequence on the samples, to test the impact of strain hardening through the change of the critical resolved shear stress for twinning as well as to evaluate the possible bias due to measurement uncertainties or clustering of grain optical axes in the samples.

Stress and strain partitioning during high PT deformation of polyphase aggregates

NASA Astrophysics Data System (ADS)

Bejina, F.; Bystricky, M.; Ingrin, J.

2013-12-01

Previous experimental studies on the rheology of the upper mantle have mostly focused on the deformation properties of olivine. Yet minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO, at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases (up to 50 vol% of MgO) were sintered by spark plasma sintering at temperatures of 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Deformation experiments on samples 1.2 mm in diameter and 1.2 mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. The harder phase, forsterite, sustains significantly higher stress levels than MgO, as predicted by numerical models for two-phase flow. Microstructural analysis by SEM reveals equilibrated microstructures in the starting samples, with well-mixed forsterite and MgO layers alternating with forsterite-rich layers. In the deformed samples, this compositional banding is accentuated, with more intense deformation in the well-mixed layers. Results on stress and strain partitioning in polyphase aggregates in the context of existing models of two-phase flow will be discussed.

Experimental Deformation of Polyphase Aggregates at Pressures and Temperatures of the Upper Mantle

NASA Astrophysics Data System (ADS)

Bejina, F.; Bystricky, M.; Ingrin, J.

2011-12-01

Modelling the solid-state flow of the upper mantle requires a thorough understanding of its rheology and therefore necessitates to perform deformation experiments on mantle rocks (or analogues) at very high pressures and temperatures. Minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. Nevertheless, most experimental studies to date have focused on the deformation properties of olivine single crystals or monomineralic olivine aggregates. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases were sintered by spark plasma sintering (SPS) at 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Microstructural analysis by SEM reveals equilibrated microstructures with forsterite and MgO grain sizes of a few microns. Deformation experiments on samples 1.2 mm in diameter and ~1.2mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens, respectively a monomineralic and a polymineralic aggregate, were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. As expected, the harder phase, forsterite, sustains much higher stress levels than MgO, in agreement with numerical models for two-phase flow. Results on stress and strain partitioning in polyphase aggregates and on the effect of the presence of a weak phase on the rheology of forsterite-rich aggregates will be discussed.

Polyphase enrichment and redistribution processes in silver-rich mineral associations of the hydrothermal fluorite-barite-(Ag-Cu) Clara deposit, SW Germany

NASA Astrophysics Data System (ADS)

Keim, Maximilian F.; Walter, Benjamin F.; Neumann, Udo; Kreissl, Stefan; Bayerl, Richard; Markl, Gregor

2018-03-01

The silver-copper sulfide mineralization associated with the fluorite-barite vein system at the Clara deposit in SW Germany shows large scale vertical zoning. Low to moderate silver contents prevail in the upper 350 m, whereas high silver contents occur in the subsequent 450 m of the currently known vein system. This change in Ag tenor is related to conspicuous mineralogical changes with depth. A detailed petrographic and fluid inclusion study identifies evidence for five subsequent hydrothermal and one alteration stage—all contributing to mineralogical diversity. The vertical Ag zoning, however, is attributed only to the first of these stages. During this first stage, increasing oxidation of ascending hydrothermal fluids (90-160 °C, 24.2-26.7 wt% NaCl+CaCl2) led to the formation of high-Ag tetrahedrite-tennantite in the lower parts and basically Ag-free enargite in the upper parts of the vein system. The subsequent hydrothermal stage led to significant mineralogical changes, but inherited the pre-existing Ag zonation. In this second hydrothermal stage, which was related to fluids similar in composition to those of the first stage (70-125 °C, 23.1-26.5 wt% NaCl+CaCl2), dissolution of high Ag-tetrahedrite-tennantite resulted in the formation of complex Ag-sulfosalts together with moderately Ag-bearing tetrahedrite-tennantite and chalcopyrite. The first two stages were formed by fluid mixing of a sedimentary and a hot basement fluid. The influx of fluids with high Ag, Bi and Pb activity during stage 3 and 5 resulted in the local replacement of earlier Ag-sulfosalts by galena and Ag-(Bi)-sulfosalts. The fourth stage is marked by partial dissolution of sulfides and sulfosalts by a late, hot, undiluted basement fluid (250 °C, 18.7-20.9 wt% NaCl+CaCl2) precipitating fluorite, barite and quartz. Finally, supergene alteration lead to the dissolution of silver-bearing phases and the precipitation of acanthite and native silver. The study illustrates, how metal tenor and mineralogy are decoupled in vertically extensive, polyphase hydrothermal vein systems. This may be pertinent to similarly zoned polymetallic vein systems.

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)).

The M6 1799 Vendée intraplate earthquake (France) : characterizing the active fault with a multidisciplinary approach.

NASA Astrophysics Data System (ADS)

Kaub, C.; Perrot, J.; Le Roy, P., Sr.; Authemayou, C.; Bollinger, L.; Hebert, H.; Geoffroy, L.

2017-12-01

The coastal Vendee (France) is located to the south of the intraplate Armorican area. This region is affected by a system of dominantly NW-SE trending shear zones and faults inherited from a long and poly-phased tectonic history since Variscan times. This area currently presents a moderate background seismic activity, but was affected by a significant historical earthquake (magnitude M 6) on the 1799 January 25th. This event generated particularly strong site effects in a Neogene basin located along a major onshore/offshore discontinuity bounding the basin, the Machecoul fault. The objective of this study is to identify and qualify active faults potentially responsible for such major seismic event in order to better constrain the seismic hazard of this area. We adopt for this purpose a multidisciplinary approach including an onshore seismological survey, high-resolution low-penetration offshore seismic data (CHIRP echo sounder, Sparker source and single channel streamer), high-resolution interferometric sonar bathymetry (GeoSwath), compilation of onshore drilling database (BSS, BRGM), and quantitative geomorphology In the meantime, the seismicity of the area was characterized by a network of 10 REFTEK stations, deployed since January 2016 around the Bay of Bourgneuf (MACHE network). About 50 local earthquakes, with coda magnitudes ranging from 0.5 to 3.1 and local magnitude ranging from 0.2 to 2.9 were identified so far. This new database complement a local earthquake catalog acquired since 2011 from previous regional networks. We surveyed the fault segments offshore, in the Bay of Bourgneuf, analyzing 700 km of high-resolution seismic profiles and 40 km² of high-resolution bathymetry acquired during the RETZ1 (2016) and RETZ2 (2017) campaigns, in addition to HR-bathymetry along the fault scarp. Those data are interpreted in conjunction with onshore wells to determine if (and since when) the Machecoul fault controlled tectonically the Neogene sedimentation.

Description of Mycobacterium chelonae subsp. bovis subsp. nov., isolated from cattle (Bos taurus coreanae), emended description of Mycobacterium chelonae and creation of Mycobacterium chelonae subsp. chelonae subsp. nov.

PubMed

Kim, Byoung-Jun; Kim, Ga-Na; Kim, Bo-Ram; Jeon, Che Ok; Jeong, Joseph; Lee, Seon Ho; Lim, Ji-Hun; Lee, Seung-Heon; Kim, Chang Ki; Kook, Yoon-Hoh; Kim, Bum-Joon

2017-10-01

Three rapidly growing mycobacterial strains, QIA-37 T , QIA-40 and QIA-41, were isolated from the lymph nodes of three separate Korean native cattle, Hanwoo (Bos taurus coreanae). These strains were previously shown to be phylogenetically distinct but closely related to Mycobacterium chelonae ATCC 35752 T by taxonomic approaches targeting three genes (16S rRNA, hsp6 and rpoB) and were further characterized using a polyphasic approach in this study. The 16S rRNA gene sequences of all three strains showed 99.7 % sequence similarity with that of the M. chelonae type strain. A multilocus sequence typing analysis targeting 10 housekeeping genes, including hsp65 and rpoB, revealed a phylogenetic cluster of these strains with M. chelonae. DNA-DNA hybridization values of 78.2 % between QIA-37 T and M. chelonae indicated that it belongs to M. chelonae but is a novel subspecies distinct from M. chelonae. Phylogenetic analysis based on whole-genome sequences revealed a 95.44±0.06 % average nucleotide identity (ANI) value with M. chelonae, slightly higher than the 95.0 % ANI criterion for determining a novel species. In addition, distinct phenotypic characteristics such as positive growth at 37 °C, at which temperature M. chelonae does not grow, further support the taxonomic status of these strains as representatives of a novel subspecies of M. chelonae. Therefore, we propose an emended description of Mycobacterium chelonae, and descriptions of M. chelonae subsp. chelonae subsp. nov. and M. chelonae subsp. bovis subsp. nov. are presented; strains ATCC 35752 T (=CCUG 47445 T =CIP 104535 T =DSM 43804 T =JCM 6388 T =NCTC 946 T ) and QIA-37 T (=KCTC 39630 T =JCM 30986 T ) are the type strains of the two novel subspecies.

PAPR reduction in FBMC using an ACE-based linear programming optimization

NASA Astrophysics Data System (ADS)

van der Neut, Nuan; Maharaj, Bodhaswar TJ; de Lange, Frederick; González, Gustavo J.; Gregorio, Fernando; Cousseau, Juan

2014-12-01

This paper presents four novel techniques for peak-to-average power ratio (PAPR) reduction in filter bank multicarrier (FBMC) modulation systems. The approach extends on current PAPR reduction active constellation extension (ACE) methods, as used in orthogonal frequency division multiplexing (OFDM), to an FBMC implementation as the main contribution. The four techniques introduced can be split up into two: linear programming optimization ACE-based techniques and smart gradient-project (SGP) ACE techniques. The linear programming (LP)-based techniques compensate for the symbol overlaps by utilizing a frame-based approach and provide a theoretical upper bound on achievable performance for the overlapping ACE techniques. The overlapping ACE techniques on the other hand can handle symbol by symbol processing. Furthermore, as a result of FBMC properties, the proposed techniques do not require side information transmission. The PAPR performance of the techniques is shown to match, or in some cases improve, on current PAPR techniques for FBMC. Initial analysis of the computational complexity of the SGP techniques indicates that the complexity issues with PAPR reduction in FBMC implementations can be addressed. The out-of-band interference introduced by the techniques is investigated. As a result, it is shown that the interference can be compensated for, whilst still maintaining decent PAPR performance. Additional results are also provided by means of a study of the PAPR reduction of the proposed techniques at a fixed clipping probability. The bit error rate (BER) degradation is investigated to ensure that the trade-off in terms of BER degradation is not too severe. As illustrated by exhaustive simulations, the SGP ACE-based technique proposed are ideal candidates for practical implementation in systems employing the low-complexity polyphase implementation of FBMC modulators. The methods are shown to offer significant PAPR reduction and increase the feasibility of FBMC as a replacement modulation system for OFDM.

Ochratoxin production and taxonomy of the yellow aspergilli (Aspergillus section Circumdati)

PubMed Central

Visagie, C.M.; Varga, J.; Houbraken, J.; Meijer, M.; Kocsubé, S.; Yilmaz, N.; Fotedar, R.; Seifert, K.A.; Frisvad, J.C.; Samson, R.A.

2014-01-01

Aspergillus section Circumdati or the Aspergillus ochraceus group, includes species with rough walled stipes, biseriate conidial heads, yellow to ochre conidia and sclerotia that do not turn black. Several species are able to produce mycotoxins including ochratoxins, penicillic acids, and xanthomegnins. Some species also produce drug lead candidates such as the notoamides. A polyphasic approach was applied using morphological characters, extrolite data and partial calmodulin, β-tubulin and ITS sequences to examine the evolutionary relationships within this section. Based on this approach the section Circumdati is revised and 27 species are accepted, introducing seven new species: A. occultus, A. pallidofulvus, A. pulvericola, A. salwaensis, A. sesamicola, A. subramanianii and A. westlandensis. In addition we correctly apply the name A. fresenii (≡ A. sulphureus (nom. illeg.)). A guide for the identification of these 27 species is provided. These new species can be distinguished from others based on morphological characters, sequence data and extrolite profiles. The previously described A. onikii and A. petrakii were found to be conspecific with A. ochraceus, whilst A. flocculosus is tentatively synonymised with A. ochraceopetaliformis, despite extrolite differences between the two species. Based on the extrolite data, 13 species of section Circumdati produce large amounts of ochratoxin A: A. affinis, A. cretensis, A. fresenii, A. muricatus, A. occultus, A. ochraceopetaliformis (A. flocculosus), A. ochraceus, A. pseudoelegans, A. pulvericola, A. roseoglobulosus, A. sclerotiorum, A. steynii and A. westerdijkiae. Seven additional species produce ochratoxin A inconsistently and/or in trace amounts: A. melleus, A. ostianus, A. persii, A. salwaensis, A. sesamicola, A. subramanianii and A. westlandensis. The most important species regarding potential ochratoxin A contamination in agricultural products are A. ochraceus, A. steynii and A. westerdijkiae. PMID:25492980

Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater.

PubMed

Xing, Defeng; Ren, Nanqi; Li, Qiubo; Lin, Ming; Wang, Aijie; Zhao, Lihua

2006-04-01

Two strictly anaerobic bacterial strains (YUAN-3T and X-29) were isolated from anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor. The strains were Gram-positive, non-spore-forming, mesophilic and motile. Cells were regular rods (0.4-0.8 x 1.5-8.0 microm) and occurred singly, in pairs and sometimes in chains of up to eight. Autoaggregative and autofluorescent growth of strain YUAN-3T and non-aggregative growth of strain X-29 were observed at 20-44 degrees C and pH 3.5-9.0. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. Fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids iso-C(16 : 0) (44.18 %) and iso-C(12 : 0) (26.67 %). The DNA G+C contents of strains YUAN-3T and X-29 were 47.8 and 49.0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a novel phyletic sublineage within the Clostridium cellulosi rRNA cluster, with <92 % 16S rRNA gene sequence similarity to currently known species. On the basis of polyphasic evidence from this study, it is proposed that the unknown bacterium should be classified in a new genus as a novel species, Ethanoligenens harbinense gen. nov., sp. nov. The type strain of Ethanoligenens harbinense is YUAN-3T (=JCM 12961T = CGMCC 1.5033T).

Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng.

PubMed

Lee, Do-Hoon; Cha, Chang-Jun

2017-11-01

A novel bacterial strain, designated CJ661 T , was isolated from soil of ginseng in Anseong, South Korea. Cells of strain CJ661 T were white-coloured, Gram-staining-negative, non-motile, aerobic and rod-shaped. Strain CJ661 T grew optimally at 30 °C and pH 7.0. The analysis of 16S rRNA gene sequence of strain CJ661 T showed that it belongs to the genus Ramlibacter within the family Comamonadaceae and was most closely related to Ramlibacter ginsenosidimutans KCTC 22276 T (98.1 %), followed by Ramlibacter henchirensis DSM 14656 T (97.1 %). DNA-DNA relatedness levels of strain CJ661 T were 40.6 % to R. ginsenosidimutans KCTC 22276 T and 25.0 % to R. henchirensis DSM 14656 T . The major isoprenoid quinone was ubiquinone (Q-8). The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids of strain CJ661 T were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The G+C content of the genomic DNA was 65.4 mol%. On the basis polyphasic taxonomic data, strain CJ661 T represents a novel species in the genus Ramlibacter, for which name Ramlibacter alkalitolerans sp. nov. is proposed; the type strain is CJ661 T (=KACC 19305 T =JCM 32081 T ).

Streptomyces canalis sp. nov., an actinomycete isolated from an alkali-removing canal.

PubMed

Xie, Yu-Xuan; Han, Xiao-Xue; Luo, Xiao-Xia; Xia, Zhan-Feng; Wan, Chuan-Xing; Zhang, Li-Li

2016-08-01

A novel actinomycete strain, designated TRM 46794-61T, was isolated from an alkali-removing canal in 14th Farms of Xinjiang Production and Construction Corps, north-west China. The isolate contained ll-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugar patterns of the isolate contained ribose, mannose and glucose. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The predominant menaquinones were MK-9(H2), MK-9(H4), MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The G+C content of the DNA was 70.4 mol%. Phylogenetic analysis showed that strain TRM 46794-61T had a 16S rRNA gene sequence similarity of 97.6 % with the most closely related species with a validly published name, Streptomyces aidingensis TRM 46012T, and it could be distinguished from all species in the genus Streptomyces based on data from this polyphasic taxonomic study. However, DNA-DNA hybridization studies between strain TRM 46794-61T and S.aidingensis TRM 46012T showed only 45.4 % relatedness. On the basis of these data, strain TRM 46794-61T should be designated as a representative of a novel species of the genus Streptomyces, for which the name Streptomyces canalis sp. nov. is proposed. The type strain is TRM 46794-61T (=CCTCC AA 2015006T=KCTC 39568T).

Aeromicrobium halotolerans sp. nov., isolated from desert soil sample.

PubMed

Yan, Zheng-Fei; Lin, Pei; Chu, Xiao; Kook, MooChang; Li, Chang-Tian; Yi, Tae-Hoo

2016-07-01

A Gram-positive, aerobic, and non-motile, rod-shaped actinomycete strain, designated YIM Y47(T), was isolated from soils collected from Turpan desert, China, and subjected to a polyphasic taxonomic study. Phylogenetic analysis indicated that strain YIM Y47(T) belonged to the genus Aeromicrobium. YIM Y47(T) shared highest 16S rRNA gene sequence similarities with Aeromicrobium massiliense JC14(T) (96.47 %). Growth occurs at 20-45 °C (optimum at 30 °C), pH 6.0-8.0 (optimum at pH 7.0), and salinities of 0-7.0 % NaCl (optimum at 4.0 %). The strain YIM Y47(T) exhibits chemotaxonomic features with menaquinone-7 (MK-7) as the predominant quinone, C16:0, C18:1 ω9c and 10-methyl C18:0 (>10 %) as major fatty acids. The cell-wall peptidoglycan of strain YIM Y47(T) contained LL-diaminopimelic acid as the diagnostic diamino acid. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and unknown phospholipids. The G+C content of the genomic DNA of strain YIM Y47(T) was found to be 44.7 mol%. On the basis of phylogenetic analyses and phenotypic data, it is proposed that strain YIM Y47(T) should be classified as representing a novel species of the genus Aeromicrobium, with the name Aeromicrobium halotolerans sp. nov. The type strain is YIM Y47(T) (=KCTC 39113(T)=CGMCC 1.15063(T)=DSM 29939(T)=JCM 30627(T)).

Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.

PubMed

Kim, Yoon-Gon; Jin, Yeon-A; Hwang, Chung Yeon; Cho, Byung Cheol

2008-01-01

A Gram-negative, strictly aerobic, marine bacterium, designated strain CL-YJ9(T), was isolated from sediment closely associated with the roots of a plant (Suaeda japonica) inhabiting a coastal tidal flat. Cells of the novel strain were straight and rod-shaped and were motile by means of monopolar flagella. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CL-YJ9(T) belongs to the genus Marinobacterium and was most closely related to Marinobacterium halophilum mano11(T) (94.1% sequence similarity) and to other members of the genus Marinobacterium (92.5-93.7% sequence similarity). The strain grew with 1-5% NaCl (optimum, 3%) and at 5-30 degrees C (optimum, approx. 25 degrees C) and pH 6.0-9.0 (optimum, pH 7.0). The predominant cellular fatty acids were summed feature 3 (C(16:1)omega7c and/or iso-C(15:0) 2-OH, 40.3%), C(18:1)omega7c (26.6%), C(16:0) (16.6%) and C(10:0) 3-OH (7.1%). The major isoprenoid quinone was Q-8. The G+C content of the genomic DNA was 61 mol%. On the basis of the data from this polyphasic study, strain CL-YJ9(T) belongs to the genus Marinobacterium but is distinguishable from the recognized species. Strain CL-YJ9(T) therefore represents a novel species, for which the name Marinobacterium rhizophilum sp. nov. is proposed. The type strain is CL-YJ9(T) (=KCCM 42386(T) =DSM 18822(T)).

Rheumatoid myositis, myth or reality? A clinical, imaging and histological study.

PubMed

Ancuţa, Codrina; Pomîrleanu, Daniela Cristina; Anton, Carmen Rodica; Moraru, Eovelina; Anton, Emil; Chirieac, Rodica Marieta; Ancuţa, Eugen

2014-01-01

Rheumatoid myositis (RM) is still poorly characterized, albeit the concept of muscle involvement in rheumatoid arthritis (RA) is well-recognized as being driven by a wide range of causes including inflammation, drugs, impaired joint flexibility, sedentarism. To describe clinical, serological, imaging and histological pattern of RM. This is a retrospective study on eight RM selected from a cohort of one hundred and three RA systematically assessed for skeletal muscle involvement. Data collected included clinical, serum muscle enzymes, muscle imaging and biopsy (Hematoxylin-Eosin, modified Gömöri trichrome staining). Routine muscle histology indicated both non-specific muscle fiber damage (changes in fiber size and internal structure: pleomorphic mitochondria, dilated sarcotubular system, multiple internal or subsarcommal nuclei; abnormal fiber types distribution: trend towards type II; atrophy; degenerative/regenerative modifications) and the presence of inflammatory deposits in all patients (mild to moderate, patchy B- and T-cells infiltrates, mainly perivascular and endomysial, but also in the perimysial region classified as polymyositis-like deposits). High levels of serum muscle enzymes, abnormal EMG (short duration, small amplitude, polyphasic motor unit action potentials) without insertional activity and fibrillations, active inflammation on both Doppler ultrasound and MRI were commonly reported. Traditional analysis of muscle biopsy specimens (Hematoxylin-Eosin, modified Gömöri trichrome staining) is faraway unsatisfactory, only documenting changes in muscle fibers size, architecture, internal structure, and, possibly, detecting perivascular, perimysial or endomysial inflammatory deposits. Upcoming research should address the value of muscle imaging for the diagnosis and evaluation of treatment response and muscle function in rheumatoid myositis.

Streptomyces fuscichromogenes sp. nov., an actinomycete from soil.

PubMed

Zhang, Hao; Zheng, Jimei; Zhuang, Junli; Xin, Yuhua; Zheng, Xiaowei; Zhang, Jianli

2017-01-01

A novel actinomycete, designated strain m16T, was isolated from a soil sample collected from the tropical rain forest of Xishuangbanna, a prefecture in Yunnan Province, south-west China, and characterized by using polyphasic taxomomy. Cells were aerobic and Gram-reaction-positive, and spore chains were observed to be of the helical type, with elliptical spores and smooth spore surfaces. The novel strain grew over a temperature range of 15-35 °C, at pH 5.0-11.0 and in the presence of 0-3 % (w/v) NaCl. The DNA G+C content of strain m16T was 70.0 mol%. The main fatty acids were iso-C16 : 0 (29.3 %), iso-C15: 0 (15.4 %) and anteiso-C15:0 (14.6 %), and the predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). Comparative 16S rRNA gene sequence analysis showed that strain m16T was most closely related to Streptomyces jiujiangensis KCTC 29262T (98.7 %), Streptomyces panaciradicis KACC 17632T (98.7 %), Streptomyces rhizophilus NBRC 108885T (98.5 %), Streptomyces shenzhenensis DSM 42034T (98.4 %), Streptomyces graminisoli JR-19T (98.4 %) and Streptomyces gramineus JR-43T (98.3 %). Phylogenetic, chemotaxonomic and phenotypic analyses indicated that strain m16T represents a novel species within the genus Streptomyces, for which the name Streptomyces fuscichromogenes is proposed. The type strain is m16T (=CGMCC 4.7110T=KCTC 29195T).

POWTEX - A new High-Intensity Powder and Texture Diffractometer at FRM II, Garching Germany

NASA Astrophysics Data System (ADS)

Walter, J. M.; Brückel, T.; Dronskowski, R.; Hansen, B. T.; Houben, A.; Klein, H.; Leiss, B.; Vollbrecht, A.; Sowa, H.

2009-05-01

In recent years, neutron diffraction has become a routine tool in Geoscience for experimental high-field (HP/HT/HH) powder diffraction and for the quantitative analysis of the crystallographic preferred orientation (CPO). Quantitative texture analysis is e.g. involved in the research fields of fabric development in mono- and polyphase rocks, deformation histories and kinematics during mountain building processes and the characterization of flow kinematics in lava flows. Secondly the quantitative characterization of anisotropic physical properties of both rock and analogue materials is conducted by bulk texture measurements of sometimes larger sample volumes. This is easily achievable by neutron diffraction due to the high penetration capabilities of the neutrons. The resulting geoscientific need for increased measuring time at neutron diffraction facilities with the corresponding technical characteristics and equipment will in future be satisfied by this high-intensity diffractometer at the neutron research reactor FRM II in Garching, Germany. It will be built by a consortium of groups from the RWTH Aachen, Forschungszentrum Jülich and the University of Göttingen, who will also operate the instrument. The diffractometer will be optimized to high intensities (flux) with an equivalent sufficient resolution for polyphase rocks. Furthermore a broad range of d-values (0.5 to 15 Å) will be measurable. The uniqueness of this instrument is the geoscientific focus on different sample environments for in situ-static and deformation experiments (stress, strain and annealing/recrystallisation) and (U)HP/(U)HT experiments. A LP/LT or atmospheric-P deformation rig for in situ-deformation experiments on ice, halite or rock analogue materials is planned, to allow in situ-measurements of the texture development during deformation and annealing. Additionally a uniaxial HT/MP deformation apparatus for salt deformation experiments and an adapted Griggs- type deformation rig are also designated. Furthermore an uniaxial stress frame for in situ stress investigations is planned to conduct simultaneous measurements of stress, elastic or plastic deformation and texture. Other sample environments for geoscientific application will be HP/HT furnaces and pressure cells for powder diffraction investigations. Furthermore the diffractometer will be built in combination with a high-pressure multi anvil up to 25 GPa and 2500 K built by the University of Bayreuth at the same beam line. The detector concept allows single shot texture measurements and therefore the measurement of larger geological sample series as necessary for the investigations of complete geological structures. This concept is complementary to the geoscience neutron texture diffractometer in Dubna, Russia and the stress diffractometer STRESS-SPEC located also at the Garching research reactor. For powder diffraction the diffractometer will be complementary to the existing high-resolution powder diffractometer SPODI at the FRM-II. It will offer the possibility of short, high-intensity parametric powder diffraction measurements in dependency of temperature, electrical, magnetic and stress fields due to the higher flux at the sample. The optimization to high-intensities and therefore short measuring times will also allow time-resolved measurements of kinetic reactions even of small sample volumes.

The analysis of decimation and interpolation in the linear canonical transform domain.

PubMed

Xu, Shuiqing; Chai, Yi; Hu, Youqiang; Huang, Lei; Feng, Li

2016-01-01

Decimation and interpolation are the two basic building blocks in the multirate digital signal processing systems. As the linear canonical transform (LCT) has been shown to be a powerful tool for optics and signal processing, it is worthwhile and interesting to analyze the decimation and interpolation in the LCT domain. In this paper, the definition of equivalent filter in the LCT domain have been given at first. Then, by applying the definition, the direct implementation structure and polyphase networks for decimator and interpolator in the LCT domain have been proposed. Finally, the perfect reconstruction expressions for differential filters in the LCT domain have been presented as an application. The proposed theorems in this study are the bases for generalizations of the multirate signal processing in the LCT domain, which can advance the filter banks theorems in the LCT domain.

A polyphasic study on the taxonomic position of industrial sour dough yeasts.

PubMed

Mäntynen, V H; Korhola, M; Gudmundsson, H; Turakainen, H; Alfredsson, G A; Salovaara, H; Lindström, K

1999-02-01

The sour dough bread making process is extensively used to produce wholesome palatable rye bread. The process is traditionally done using a back-slopping procedure. Traditional sour doughs in Finland comprise of lactic acid bacteria and yeasts. The yeasts present in these doughs have been enriched in the doughs due to their metabolic activities, e.g. acid tolerance. We characterized the yeasts in five major sour bread bakeries in Finland. We found that most of the commercial sour doughs contained yeasts which were similar to Candida milleri on the basis of 18S rDNA and EF-3 PCR-RFLP patterns and metabolic activities. Some of the bakery yeasts exhibited extensive karyotype polymorphism. The minimum growth temperature was 8 degrees C for C. milleri and also for most of sour dough yeasts.

[The influence of ultrahigh-frequency electromagnetic radiation and low-intensity laser radiation on the body core temperature and basal metabolism in rats with systemic inflammation].

PubMed

Zhavoronok, I P; Molchanova, A Iu; Ulashik, V S

2012-01-01

The effects of ultrahigh-frequency electromagnetic radiation (UHF EMR) and low-intensity laser irradiation (LILI) on the body and skin temperature, oxygen consumption, production of carbon dioxide and heat release were investigated in the experiments on intact rats and during LPS-induced polyphasic fever. It was found that UHF EMR with the wavelength of 4,9 mm, 5,6 mm or 7,1 mm and LILI with the wavelength of 0.47 microm, 0.67 microm and 0.87 microm caused modulation of basal metabolism and thermal response to systemically administered lipopolysaccharide (LPS). These findings suggest that the most pronounced antipyretic and hypometabolic effects were observed after the treatment with UHF EMR at 7,1 mm and LILI at 470 microm.

Geology of the world-class Kiaka polyphase gold deposit, West African Craton, Burkina Faso

NASA Astrophysics Data System (ADS)

Fontaine, Arnaud; Eglinger, Aurélien; Ada, Koumangdiwè; André-Mayer, Anne-Sylvie; Reisberg, Laurie; Siebenaller, Luc; Le Mignot, Elodie; Ganne, Jérôme; Poujol, Marc

2017-02-01

The Kiaka gold deposit is a major resource in West Africa, with measured and indicated resources of 124 Mt at 1.09 g/t Au (3.9 Moz) and inferred resources of 27 Mt at 0.83 g/t Au (0.8 Moz). Located within the Manga-Fada N'Gourma greenstone and plutonic belt in south of the Burkina Faso, the deposit is hosted by a metamorphosed volcano-sedimentary sequence of lithic-, quartz-biotite metagreywackes, aluminosilicate-bearing metapelites and garnet-orthopyroxene-bearing schists and volcanic units. Structural observations indicate four local deformation events: DK1, DK2 and DK3 and DK4. Respectively, these events are linked to regional D1 E-W compression, D2 NW-SE compression and lastly, D3- and D4-related reactivations along D2 shear zones. The S2 foliation and D2 shear zones are developed during lower amphibolite facies metamorphism whereas retrogression occurs during D3-4 reactivations along these shear zones at upper greenschist facies conditions. The emplacement of a dioritic intrusion, dated at 2140 ± 7 Ma (Concordia U-Pb age on magmatic zircon), is interpreted to be contemporaneous with sinistral displacement along mineralized, NE-trending D2 shear zones. The intersection of these shears zones and the Markoye shear zone (dextral-reverse D1 and sinistral-reverse D2 reactivations) controlled the final geometry of the host rocks and the ore zones. Four subparallel elongated ore bodies are mainly hosted within D2-related shear zones and some are developed in an apparent axial plane of a F2 isoclinal fold. Detailed petrographic studies have identified two main types of hydrothermal alteration associated with two stages of gold mineralization. The stage (1) corresponds to replacement zones with biotite and clinozoisite during the D2 event associated with pyrrhotite ± pyrite, chalcopyrite (disseminated gold stage). The stage (2) occurs during reactivations of the D2-related auriferous shear zones (vein stage) and is characterized by diopside ± actinolite D3 veins and veinlets and D4 pervasive muscovite, ± chlorite, ± calcite in quartz-carbonate vein selvages and associated with pyrrhotite + arsenopyrite ± electrum, ± native gold and tellurobismuthite. The latter stage (2) could be divided into two sub-stages based on mineralogy and crosscutting relationship. A weighted average Re-Os pyrrhotite age at 2157 ± 24 Ma (Re-Os age based on 3 replicates) constraints the timing of the disseminated gold stage and represents the first absolute age for gold mineralization in the Manga Fada N'Gourma area. The timing of gold at Kiaka may be also coeval with one of the two lode gold event at ∼ ca. 2.16-2.15 Ga and occurred concomitant with tectono-thermal activity during Eo-Eburnean orogeny. The study of the Kiaka gold deposit emphasizes the importance of a multi-scale and multidisciplinary approach (field observations, petrography geothermobarometry and geochronology) to decipher the polyphase character of some Paleoproterozoic gold deposits.

Azospirillum zeae sp. nov., a diazotrophic bacterium isolated from rhizosphere soil of Zea mays.

PubMed

Mehnaz, Samina; Weselowski, Brian; Lazarovits, George

2007-12-01

Two free-living nitrogen-fixing bacterial strains, N6 and N7(T), were isolated from corn rhizosphere. A polyphasic taxonomic approach, including morphological characterization, Biolog analysis, DNA-DNA hybridization, and 16S rRNA, cpn60 and nifH gene sequence analysis, was taken to analyse the two strains. 16S rRNA gene sequence analysis indicated that strains N6 and N7(T) both belonged to the genus Azospirillum and were closely related to Azospirillum oryzae (98.7 and 98.8 % similarity, respectively) and Azospirillum lipoferum (97.5 and 97.6 % similarity, respectively). DNA-DNA hybridization of strains N6 and N7(T) showed reassociation values of 48 and 37 %, respectively, with A. oryzae and 43 % with A. lipoferum. Sequences of the nifH and cpn60 genes of both strains showed 99 and approximately 95 % similarity, respectively, with those of A. oryzae. Chemotaxonomic characteristics (Q-10 as quinone system, 18 : 1omega7c as major fatty acid) and G+C content of the DNA (67.6 mol%) were also similar to those of members of the genus Azospirillum. Gene sequences and Biolog and fatty acid analysis showed that strains N6 and N7(T) differed from the closely related species A. lipoferum and A. oryzae. On the basis of these results, it is proposed that these nitrogen-fixing strains represent a novel species. The name Azospirillum zeae sp. nov. is suggested, with N7(T) (=NCCB 100147(T)=LMG 23989(T)) as the type strain.

Spirosoma jeollabukense sp. nov., isolated from soil.

PubMed

Li, Weilan; Ten, Leonid N; Lee, Seung-Yeol; Lee, Dong Hoon; Jung, Hee-Young

2018-04-01

A Gram-negative, non-motile, rod-shaped, aerobic bacterial strain, designated S2-3-6 T , was isolated from soil in Jeollabuk-do province, South Korea, and was characterized taxonomically using a polyphasic approach. According to a comparative 16S rRNA gene sequence analysis, strain S2-3-6 T belonged to the family Cytophagaceae and was most closely related to Spirosoma endophyticum EX36 T (98.2%), Spirosoma fluviale MSd3 T (96.0%), and Spirosoma linguale DSM 74 T (95.7%). Strain S2-3-6 T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and C16:0 N alcohol as major cellular fatty acids, MK-7 as the predominant respiratory quinone, and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain S2-3-6 T was 47.8%. Phenotypic and chemotaxonomic data supported the affiliation of strain S2-3-6 T to the genus Spirosoma. However, the DNA-DNA relatedness between strain S2-3-6 T and Spirosoma endophyticum KACC 17920 T was 27%, clearly showing that the isolate constitutes a new genospecies. Strain S2-3-6 T could be clearly differentiated from its closest neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, strain S2-3-6 T represents a novel species of the genus Spirosoma, for which the name Spirosoma jeollabukense sp. nov. is proposed. The type strain is S2-3-6 T (= KCTC 52725 T  = JCM 32129 T ).

Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea.

PubMed

Jung, Seo-Youn; Kang, So-Jung; Lee, Mi-Hwa; Lee, Soo-Young; Oh, Tae-Kwang; Yoon, Jung-Hoon

2005-09-01

Three Gram-negative, yellow-pigmented, rod-shaped bacterial strains, SMK-12(T), SMK-36 and SMK-45, were isolated from a tidal flat sediment of the Yellow Sea in Korea, and their taxonomic positions were investigated by a polyphasic approach. The three strains grew optimally at 25-30 degrees C and in the presence of 2-3% (w/v) NaCl. They contained MK-6 as the predominant menaquinone. The major cellular fatty acids were iso-C(15:0), iso-C(17:0) 3-OH, iso-C(15:1), anteiso-C(15:0), iso-C(15:0) 3-OH and C(16:1)omega7c and/or iso-C(15:0) 2-OH. The DNA G+C contents of the three strains were 34.7-34.9 mol%. The phylogenetic tree based on 16S rRNA gene sequences revealed that the three strains form one distinct evolutionary lineage supported by a bootstrap value of 100 % within the family Flavobacteriaceae. The three strains exhibited 16S rRNA gene sequence similarity levels of 93.8-94.9% to the nearest phylogenetic neighbours, the genera Algibacter, Bizionia and Formosa. On the basis of differences in phenotypic characteristics and phylogenetic distinctiveness, strains SMK-12(T), SMK-36 and SMK-45 were classified in a novel genus and species, for which the name Gaetbulibacter saemankumensis gen. nov., sp. nov. is proposed. The type strain for the novel species is SMK-12(T) (=KCTC 12379(T)=DSM 17032(T)).

Functional Basis of Microorganism Classification.

PubMed

Zhu, Chengsheng; Delmont, Tom O; Vogel, Timothy M; Bromberg, Yana

2015-08-01

Correctly identifying nearest "neighbors" of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent.

Anoxybacillus vitaminiphilus sp. nov., a strictly aerobic and moderately thermophilic bacterium isolated from a hot spring.

PubMed

Zhang, Xin-Qi; Zhang, Zhen-Li; Wu, Nan; Zhu, Xu-Fen; Wu, Min

2013-11-01

A strictly aerobic, Gram-stain-positive, motile and spore-forming bacterium, strain 3nP4(T), was isolated from the Puge hot spring located in the south-western geothermal area of China. Strain 3nP4(T) grew at 38-66 °C (optimum 57-60 °C), at pH 6.0-9.3 (optimum 7.0-7.5) and with 0-4 % (w/v) NaCl (optimum 0-0.5 %). Phylogenetic analysis of 16S rRNA gene sequences, as well as DNA-DNA relatedness values, indicated that the isolate represents a novel species of the genus Anoxybacillus, related most closely to Anoxybacillus voinovskiensis DSM 12111(T). Strain 3nP4(T) had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid as major polar lipids and iso-C15 : 0 and iso-C17 : 0 as major fatty acids, which are both typical chemotaxonomic characteristics of the genus Anoxybacillus. The mean DNA G+C content of strain 3nP4(T) was 39.2±0.95 mol% (HPLC). A distinctive characteristic of the novel isolate was its extreme reliance on vitamin mixture or yeast extract for growth. Based on data from this taxonomic study using a polyphasic approach, strain 3nP4(T) is considered to represent a novel species of the genus Anoxybacillus, for which the name Anoxybacillus vitaminiphilus sp. nov. is proposed. The type strain is 3nP4(T) ( = CGMCC 1.8979(T) = JCM 16594(T)).

Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils.

PubMed

Martina, Pablo; Leguizamon, Mariana; Prieto, Claudia I; Sousa, Silvia A; Montanaro, Patricia; Draghi, Walter O; Stämmler, Maren; Bettiol, Marisa; de Carvalho, Carla C C R; Palau, Juliana; Figoli, Cecilia; Alvarez, Florencia; Benetti, Silvina; Lejona, Sergio; Vescina, Cecilia; Ferreras, Julián; Lasch, Peter; Lagares, Antonio; Zorreguieta, Angeles; Leitão, Jorge H; Yantorno, Osvaldo M; Bosch, Alejandra

2018-01-01

Bacteria from the Burkholderia cepacia complex (Bcc) are capable of causing severe infections in patients with cystic fibrosis (CF). These opportunistic pathogens are also widely distributed in natural and man-made environments. After a 12-year epidemiological surveillance involving Bcc bacteria from respiratory secretions of Argentinean patients with CF and from hospital settings, we found six isolates of the Bcc with a concatenated species-specific allele sequence that differed by more than 3 % from those of the Bcc with validly published names. According to the multilocus sequence analysis (MLSA), these isolates clustered with the agricultural soil strain, Burkholderia sp. PBP 78, which was already deposited in the PubMLST database. The isolates were examined using a polyphasic approach, which included 16S rRNA, recA, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), DNA base composition, average nucleotide identities (ANIs), fatty acid profiles, and biochemical characterizations. The results of the present study demonstrate that the seven isolates represent a single novel species within the Bcc, for which the name Burkholderia puraquae sp. nov. is proposed. Burkholderia puraquae sp. nov. CAMPA 1040 T (=LMG 29660 T =DSM 103137 T ) was designated the type strain of the novel species, which can be differentiated from other species of the Bcc mainly from recA gene sequence analysis, MLSA, ANIb, MALDI-TOF MS analysis, and some biochemical tests, including the ability to grow at 42 °C, aesculin hydrolysis, and lysine decarboxylase and β-galactosidase activities.

Functional Basis of Microorganism Classification

PubMed Central

Zhu, Chengsheng; Delmont, Tom O.; Vogel, Timothy M.; Bromberg, Yana

2015-01-01

Correctly identifying nearest “neighbors” of a given microorganism is important in industrial and clinical applications where close relationships imply similar treatment. Microbial classification based on similarity of physiological and genetic organism traits (polyphasic similarity) is experimentally difficult and, arguably, subjective. Evolutionary relatedness, inferred from phylogenetic markers, facilitates classification but does not guarantee functional identity between members of the same taxon or lack of similarity between different taxa. Using over thirteen hundred sequenced bacterial genomes, we built a novel function-based microorganism classification scheme, functional-repertoire similarity-based organism network (FuSiON; flattened to fusion). Our scheme is phenetic, based on a network of quantitatively defined organism relationships across the known prokaryotic space. It correlates significantly with the current taxonomy, but the observed discrepancies reveal both (1) the inconsistency of functional diversity levels among different taxa and (2) an (unsurprising) bias towards prioritizing, for classification purposes, relatively minor traits of particular interest to humans. Our dynamic network-based organism classification is independent of the arbitrary pairwise organism similarity cut-offs traditionally applied to establish taxonomic identity. Instead, it reveals natural, functionally defined organism groupings and is thus robust in handling organism diversity. Additionally, fusion can use organism meta-data to highlight the specific environmental factors that drive microbial diversification. Our approach provides a complementary view to cladistic assignments and holds important clues for further exploration of microbial lifestyles. Fusion is a more practical fit for biomedical, industrial, and ecological applications, as many of these rely on understanding the functional capabilities of the microbes in their environment and are less concerned with phylogenetic descent. PMID:26317871

Streptomyces cameroonensis sp. nov., a Geldanamycin Producer That Promotes Theobroma cacao Growth.

PubMed

Boudjeko, Thaddée; Tchinda, Romaric Armel Mouafo; Zitouni, Mina; Nana, Joëlle Aimée Vera Tchatchou; Lerat, Sylvain; Beaulieu, Carole

2017-03-31

The taxonomy of an actinobacterial strain, designated JJY4 T , was established using a polyphasic approach. JJY4 T was isolated from the rhizosphere of Chromolaena odorata in Yaoundé (Cameroon) during a project for the selection of biological control agents. Strain JJY4 T exhibited antimicrobial activities against bacteria, fungi, and oomycetes. Strain JJY4 T also exhibited the traits of plant growth-promoting rhizobacteria such as the solubilization of inorganic phosphate, production of siderophores and indole-3-acetic acid, and 1-aminocyclopropane-1-carboxylate deaminase activity. In planta assays performed on cocoa plantlets confirmed that strain JJY4 T exhibited strong abilities to promote plant growth and protect against Phytophthora megakarya, the main causal agent of cocoa pod rot. The formation of rugose-ornamented spores in spiral spore chains by strain JJY4 T is a typical feature of members found in the Streptomyces violaceusniger clade and, similar to some members of the clade, strain JJY4 T produces geldanamycin. A phylogenetic analysis based on 16S rRNA gene sequences confirmed this classification and suggests that strain JJY4 T be added to the subclade constituted of the type strains Streptomyces malaysiensis DSM 41697 T and Streptomyces samsunensis DSM 42010 T . However, DNA-DNA relatedness and physiological characteristics allowed for the differentiation of strain JJY4 T from its closest phylogenetic relatives. Based on these results, strain JJY4 T (=NRRL B-65369, =NBRC 112705) appears to represent a novel species in the S. violaceusniger clade for which the proposed name is Streptomyces cameroonensis sp. nov.

Serratia oryzae sp. nov., isolated from rice stems.

PubMed

Zhang, Cai-Wen; Zhang, Jun; Zhao, Juan-Juan; Zhao, Xia; Zhao, Dong-Fang; Yin, Hua-Qun; Zhang, Xiao-Xia

2017-08-01

A novel endophytic bacterium, strain J11-6T, was isolated from rice stems. Its taxonomic position was investigated using a polyphasic approach. The novel strain was Gram-staining-negative, facultatively anaerobic, motile and rod-shaped. Although the results of phylogenetic analysis based on 16S rRNA gene sequences indicated that J11-6T represented a member of the genus Rahnella, multilocus sequence analysis (MLSA) on the basis of concatenated partial atpD, gyrB, rpoB and infB gene sequences showed a clear distinction of J11-6T from the type strains of species of the genus Rahnella but indicated that it lay within the clade of the genus Serratia. The phylogenetically closest species were Serratia fonticola and Serratia aquatilis on the basis of the results of the MLSA phylogenetic analysis. The predominant cellular fatty acids were C16 : 1ω7c (38.7 %) and C16 : 0 (25.0 %). The DNA G+C content was 53.2 mol%. The DNA-DNA relatedness was 17.4 % between J11-6T and Rahnella aquatilis CIP 78.65T, and 29.2 % between J11-6T and S. fonticola LMG 7882T which indicates that this strain represents a novel species of the genus Serratia. Characterization by genotypic and phenotypic analysis indicated that J11-6T (=ACCC 19934T=KCTC 52529T) represents a novel species of the genus Serratia, for which the name Serratia oryzae sp. nov. is proposed.

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

PubMed

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

2016-05-01

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

Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization.

PubMed

Tambong, James T; Xu, Renlin; Bromfield, Eden S P

2017-04-01

The bacterial strain 2-92T, isolated from a field plot under long-term (>40 years) mineral fertilization, exhibited in vitro antagonistic properties against fungal pathogens. A polyphasic approach was undertaken to verify its taxonomic status. Strain 2-92T was Gram-reaction-negative, aerobic, non-spore-forming, motile by one or more flagella, and oxidase-, catalase- and urease-positive. The optimal growth temperature of strain 2-92T was 30 °C. 16S rRNA gene sequence analysis demonstrated that the strain is related to species of the genus Pseudomonas. Phylogenetic analysis of six housekeeping genes (dnaA, gyrB, recA, recF, rpoB and rpoD) revealed that strain 2-92T clustered as a distinct and well separated lineage with Pseudomonassimiae as the most closely related species. Polar lipid and fatty acid compositions corroborated the taxonomic position of strain 2-92T in the genus Pseudomonas. Phenotypic characteristics from carbon utilization tests could be used to differentiate strain 2-92T from closely related species of the genus Pseudomonas. DNA-DNA hybridization values (wet laboratory and genome-based) and average nucleotide identity data confirmed that this strain represents a novel species. On the basis of phenotypic and genotypic characteristics, it is concluded that this strain represents a separate novel species for which the name Pseudomonas canadensis sp. nov. is proposed, with type strain 2-92T (=LMG 28499T=DOAB 798T). The DNA G+C content is 60.30 mol%.

Transfer, composition and technological characterization of the lactic acid bacterial populations of the wooden vats used to produce traditional stretched cheeses.

PubMed

Scatassa, Maria Luisa; Gaglio, Raimondo; Macaluso, Giusi; Francesca, Nicola; Randazzo, Walter; Cardamone, Cinzia; Di Grigoli, Antonino; Moschetti, Giancarlo; Settanni, Luca

2015-12-01

The biofilms of 12 wooden vats used for the production of the traditional stretched cheeses Caciocavallo Palermitano and PDO Vastedda della valle del Belìce were investigated. Salmonella spp. and Listeria monocytogenes were never detected. Total coliforms were at low numbers with Escherichia coli found only in three vats. Coagulase-positive staphylococci (CPS) were below the enumeration limit, whereas lactic acid bacteria (LAB) dominated the surfaces of all vats. In general, the dominance was showed by coccus LAB. Enterococci were estimated at high numbers, but usually between 1 and 2 Log cycles lower than other LAB. LAB populations were investigated at species and strain level and for their technological properties relevant in cheese production. Eighty-five strains were analysed by a polyphasic genetic approach and allotted into 16 species within the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus and Streptococcus. Enterococcus faecium was found in all wooden vats and the species most frequently isolated were Enterococcus faecalis, Lactococcus lactis, Leuconostoc mesenteroides, Pediococcus acidilactici and Streptococcus thermophilus. The study of the quantitative data on acidification rate, autolysis kinetics, diacetyl production, antibacterial compound generation and proteolysis by cluster and principal component analysis led to the identification of some strains with promising dairy characteristics. Interestingly, a consistent percentage of LAB was bacteriocin-like inhibitory substances (BLIS) producer. Thus, the microbial biofilms of the wooden vats analysed in this study might contribute actively to the stability of the final cheeses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbiological and physicochemical characterization of small-scale cocoa fermentations and screening of yeast and bacterial strains to develop a defined starter culture.

PubMed

Pereira, Gilberto Vinícius de Melo; Miguel, Maria Gabriela da Cruz Pedrozo; Ramos, Cíntia Lacerda; Schwan, Rosane Freitas

2012-08-01

Spontaneous cocoa bean fermentations performed under bench- and pilot-scale conditions were studied using an integrated microbiological approach with culture-dependent and culture-independent techniques, as well as analyses of target metabolites from both cocoa pulp and cotyledons. Both fermentation ecosystems reached equilibrium through a two-phase process, starting with the simultaneous growth of the yeasts (with Saccharomyces cerevisiae as the dominant species) and lactic acid bacteria (LAB) (Lactobacillus fermentum and Lactobacillus plantarum were the dominant species), which were gradually replaced by the acetic acid bacteria (AAB) (Acetobacter tropicalis was the dominant species). In both processes, a sequence of substrate consumption (sucrose, glucose, fructose, and citric acid) and metabolite production kinetics (ethanol, lactic acid, and acetic acid) similar to that of previous, larger-scale fermentation experiments was observed. The technological potential of yeast, LAB, and AAB isolates was evaluated using a polyphasic study that included the measurement of stress-tolerant growth and fermentation kinetic parameters in cocoa pulp media. Overall, strains L. fermentum UFLA CHBE8.12 (citric acid fermenting, lactic acid producing, and tolerant to heat, acid, lactic acid, and ethanol), S. cerevisiae UFLA CHYC7.04 (ethanol producing and tolerant to acid, heat, and ethanol), and Acetobacter tropicalis UFLA CHBE16.01 (ethanol and lactic acid oxidizing, acetic acid producing, and tolerant to acid, heat, acetic acid, and ethanol) were selected to form a cocktail starter culture that should lead to better-controlled and more-reliable cocoa bean fermentation processes.

Highly thermo-halo-alkali-stable β-1,4-endoxylanase from a novel polyextremophilic strain of Bacillus halodurans.

PubMed

Kumar, Vikash; Syal, Poonam; Satyanarayana, T

2013-05-01

A novel bacterial isolate, capable of producing extracellular highly thermostable, halo-alkali-stable and cellulase-free xylanase, was isolated from soil and identified as Bacillus halodurans TSPV1 by polyphasic approach. The Plackett-Burman design identified wheat bran, lactose, tryptone and NaCl as the factors that significantly affect xylanase production, and thus, these were optimized by response surface methodology. The data analysis suggested that optimum levels of wheat bran (15-20 g L(-1)), lactose (1.0-1.5 g L(-1)), tryptone (2-2.5 g L(-1)) and NaCl (7.0-8.0 g L(-1)) support 6.75-fold higher xylanase production than that in the un-optimized medium. The xylanase is optimally active at 90 °C and pH 10, and stable for 4 h at 90 °C (T 1/2 60 h) over a broad range of NaCl concentrations (0-29 %). This is the first report on the isolation of polyextremophilic B. halodurans strain that produces thermo-halo-alkali-stable xylanase in submerged fermentation. This enzyme efficiently saccharifies agro residues like wheat bran and corncobs. Fifty-six percent of hemicellulose of wheat bran could be hydrolyzed by xylanase (100 U g(-1) substrate) along with cellulase (22 U FPase and 50 U CMCase g(-1)). The xylanase, being thermo-alkali stable and cellulase free, can find applications in pre-bleaching of paper pulps and hydrolysis of xylan in agricultural residues.

Phylogeny of culturable cyanobacteria from Brazilian mangroves.

PubMed

Silva, Caroline Souza Pamplona; Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Fiore, Marli Fátima

2014-03-01

The cyanobacterial community from Brazilian mangrove ecosystems was examined using a culture-dependent method. Fifty cyanobacterial strains were isolated from soil, water and periphytic samples collected from Cardoso Island and Bertioga mangroves using specific cyanobacterial culture media. Unicellular, homocytous and heterocytous morphotypes were recovered, representing five orders, seven families and eight genera (Synechococcus, Cyanobium, Cyanobacterium, Chlorogloea, Leptolyngbya, Phormidium, Nostoc and Microchaete). All of these novel mangrove strains had their 16S rRNA gene sequenced and BLAST analysis revealed sequence identities ranging from 92.5 to 99.7% when they were compared with other strains available in GenBank. The results showed a high variability of the 16S rRNA gene sequences among the genotypes that was not associated with the morphologies observed. Phylogenetic analyses showed several branches formed exclusively by some of these novel 16S rRNA gene sequences. BLAST and phylogeny analyses allowed for the identification of Nodosilinea and Oxynema strains, genera already known to exhibit poor morphological diacritic traits. In addition, several Nostoc and Leptolyngbya morphotypes of the mangrove strains may represent new generic entities, as they were distantly affiliated with true genera clades. The presence of non-ribosomal peptide synthetase, polyketide synthase, microcystin and saxitoxin genes were detected in 20.5%, 100%, 37.5% and 33.3%, respectively, of the 44 tested isolates. A total of 134 organic extracts obtained from 44 strains were tested against microorganisms, and 26% of the extracts showed some antimicrobial activity. This is the first polyphasic study of cultured cyanobacteria from Brazilian mangrove ecosystems using morphological, genetic and biological approaches. Copyright © 2014 Elsevier GmbH. All rights reserved.

Novel green algal isolates from the Egyptian hyper-arid desert oases: a polyphasic approach with a description of Pharao desertorum gen. et sp. nov. (Chlorophyceae, Chlorophyta).

PubMed

Saber, Abdullah A; Fučíková, Karolina; McManus, Hilary A; Guella, Graziano; Cantonati, Marco

2018-03-30

The biodiversity of terrestrial algae is still grossly understudied, and African deserts in particular are barely touched in this respect. Here, four coccoid green algae from oases in the Western Desert of Egypt were characterized using a combination of morphotaxonomic, ecological and 18S rDNA data, with additional carotenoid and lipid analyses for two of the strains. Three strains were identified as affiliated with known taxa: Mychonastes sp., Asterarcys sp. (first report of this genus from a desert soil), and Stichococcus cf. deasonii. The fourth strain is proposed to represent a new cryptic genus Pharao gen. nov., with the type species P. desertorum sp. nov. The new taxon is sister to the clade of uncharacterized North American desert strains of Radiococcaceae (Chlorophyceae, Chlorophyta). The pigment profile of P. desertorum gen. et sp. nov. revealed carotenoids and chlorophylls typical of green algae. Bioorganic analysis showed a complex lipidome based on phospho- (PC), galacto- (MGDG and DGDG), betaine- (DGTS), and sulfoquinovosyl- (SQDG) membrane lipids, besides significant amounts of storage neutral lipids such as diacyl- (DAG) and triacylglycerols (TAG). The presence of saturated alkyl chains within all the membrane lipid classes in P. desertorum and Asterarcys sp. appears to reflect the need to maintain membrane fluidity and viscosity. In summary, African deserts likely still harbor new taxa to be described, and lipidomic analyses of such taxa may provide clues about their ability to survive in the extremely harsh desert habitats. © 2018 Phycological Society of America.

Microbiological and Physicochemical Characterization of Small-Scale Cocoa Fermentations and Screening of Yeast and Bacterial Strains To Develop a Defined Starter Culture

PubMed Central

Pereira, Gilberto Vinícius de Melo; Miguel, Maria Gabriela da Cruz Pedrozo; Ramos, Cíntia Lacerda

2012-01-01

Spontaneous cocoa bean fermentations performed under bench- and pilot-scale conditions were studied using an integrated microbiological approach with culture-dependent and culture-independent techniques, as well as analyses of target metabolites from both cocoa pulp and cotyledons. Both fermentation ecosystems reached equilibrium through a two-phase process, starting with the simultaneous growth of the yeasts (with Saccharomyces cerevisiae as the dominant species) and lactic acid bacteria (LAB) (Lactobacillus fermentum and Lactobacillus plantarum were the dominant species), which were gradually replaced by the acetic acid bacteria (AAB) (Acetobacter tropicalis was the dominant species). In both processes, a sequence of substrate consumption (sucrose, glucose, fructose, and citric acid) and metabolite production kinetics (ethanol, lactic acid, and acetic acid) similar to that of previous, larger-scale fermentation experiments was observed. The technological potential of yeast, LAB, and AAB isolates was evaluated using a polyphasic study that included the measurement of stress-tolerant growth and fermentation kinetic parameters in cocoa pulp media. Overall, strains L. fermentum UFLA CHBE8.12 (citric acid fermenting, lactic acid producing, and tolerant to heat, acid, lactic acid, and ethanol), S. cerevisiae UFLA CHYC7.04 (ethanol producing and tolerant to acid, heat, and ethanol), and Acetobacter tropicalis UFLA CHBE16.01 (ethanol and lactic acid oxidizing, acetic acid producing, and tolerant to acid, heat, acetic acid, and ethanol) were selected to form a cocktail starter culture that should lead to better-controlled and more-reliable cocoa bean fermentation processes. PMID:22636007

Flavobacterium cloacae sp. nov., isolated from waste water.

PubMed

Liu, Hongming; Lu, Peng; Zhu, Guoping

2017-04-01

A Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium, named wh15T, was isolated from the waste water of a municipal wastewater treatment plant in Wuhu, PR China. The taxonomic status of the strain was characterized using a polyphasic taxonomic approach. Growth occurred at 15-45 °C (optimum, 25-40 °C), at pH 5.0-8.0 (optimum, pH 7.0) and with 0-4 % NaCl (optimum, 1-2 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that wh15T represented a member of genus Flavobacterium and shared the highest similarity with Flavobacterium ummariense DS-12T (93.93 %), Flavobacterium ceti 454-2T (93.71 %) and Flavobacterium marinum SW105T (93.63 %). The major respiratory quinone of wh15T was MK-6 and major fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The DNA G+C content of wh15T was 32.3 mol%. Phenotypic, phylogenetic and chemotaxonomic evidence indicated that wh15T represents a novel species of the genus Flavobacterium, the name Flavobacterium cloacae is proposed. The type strain is wh15T (=CCTCC AB 2015420T=JCM 31173T).

Stratal stacking patterns and tectono-sedimentary evolution of hyperextended magma-poor rifted margins

NASA Astrophysics Data System (ADS)

Ribes, C.; Gillard, M.; Epin, M. E.; Ghienne, J. F.; Manatschal, G.; Karner, G. D.; Johnson, C. A.

2016-12-01

Research on the formation and evolution of deep-water rifted margins has undergone a major paradigm shift in recent years. An increasing number of studies of present-day and fossil rifted margins allow us to identify and characterize the structural architecture of the most distal parts of rifted margins, the so-called hyperextended, magma-poor rifted margins. However, at present, little is known about the depositional environments, sedimentary facies, stacking patterns, subsidence and thermal history within these domains. In this context, characterizing the stratal stacking patterns and understanding their spatial and temporal evolution is a new challenge. The major difficulty comes from the fact that the observed stratigraphic geometries and facies relationships are a result of the complex interplay between sediment supply and available accommodation, which is controlled by not only the regional generation of accommodation, but also by local tectono-magmatic processes. These parameters are poorly constrained or even sufficiently known in these tectonic settings. Indeed, the complex structural evolution of hyperextended magma-poor rifted margins, including the development of poly-phase in-sequence and out of sequence extensional detachment faults and associated mantle exhumation and magmatic activity, can generate complex accommodation patterns over a highly structured top basement. The presentation summarizes early results concerning the controlling parameters on ultra-deep water stratigraphic stacking patterns and to provide a conceptual framework. This observation-driven approach combines fieldwork from fossil Alpine Tethys margins exposed in the Alps and the analysis of seismic reflection data from present-day deep water rifted margins such as the Australian-Antarctic, East India and Iberia-Newfoundland margins.

Molecular typing of environmental and clinical strains of Vibrio vulnificus isolated in the northeastern USA.

PubMed

Reynaud, Yann; Pitchford, Steven; De Decker, Sophie; Wikfors, Gary H; Brown, Christopher L

2013-01-01

Vibrio vulnificus is a ubiquitous marine bacterium that is responsible for infections and some seafood-related illnesses and deaths in the United States, mainly in individuals with compromised health status in the Gulf of Mexico region. Most phylogenetic studies focus on V. vulnificus strains isolated in the southern United States, but almost no genetic data are available on northeastern bacterial isolates of clinical or environmental origin. Our goal in this study was to examine the genetic diversity of environmental strains isolated from commercially-produced oysters and in clinical strains of known pathogenicity in northeastern United States. We conducted analyses of a total of eighty-three strains of V. vulnificus, including 18 clinical strains known to be pathogenic. A polyphasic, molecular-typing approach was carried out, based upon established biotypes, vcg, CPS, 16S rRNA types and three other genes possibly associated with virulence (arylsulfatase A, mtlABC, and nanA). An established Multi Locus Sequence Typing (MLST) method was also performed. Phylogenetic analyses of these markers and MLST results produced similar patterns of clustering of strains into two main lineages (we categorized as 'LI' and 'LII'), with clinical and environmental strains clustering together in both lineages. Lineage LII was comprised primarily but not entirely of clinical bacterial isolates. Putative virulence markers were present in both clinical and environmental strains. These results suggest that some northeastern environmental strains of V. vulnificus are phylogenetically close to clinical strains and probably are capable of virulence. Further studies are necessary to assess the risk of human illness from consuming raw oysters harvested in the northeastern US.

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

PubMed Central

Alves, Ricardo J Eloy; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M; Schleper, Christa; Urich, Tim

2013-01-01

The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota–AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils. PMID:23466705

Rhodanobacter caeni sp. nov., isolated from sludge from a sewage disposal plant.

PubMed

Woo, Sung-Geun; Srinivasan, Sathiyaraj; Kim, Myung Kyum; Lee, Myungjin

2012-12-01

Two Gram-reaction-negative, motile bacteria, designated strains MJ01(T) and MJ14, were isolated from sludge collected from the Daejeon sewage disposal plant in South Korea. The taxonomic positions of both strains were determined using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strains MJ01(T) and MJ14 appeared indistinguishable and to be most closely related to members of the genus Rhodanobacter in the family Xanthomonadaceae of the Gammaproteobacteria (96.4-98.8% sequence similarity). Strain MJ01(T) exhibited a relatively high level of DNA-DNA relatedness with strain MJ14 (89.3 %) but relatively low DNA-DNA relatedness values with established species in the genus Rhodanobacter (<60 %). The genomic DNA G+C contents of strains MJ01(T) and MJ14 were 65.3 and 64.8 mol%, respectively. The major respiratory quinone of both novel strains was the ubiquinone Q-8. The major fatty acids of both strains were iso-C(15 : 0), iso-C(16 : 0), iso-C(17:0) and iso-C(17 : 1)ω9c, and the polar lipid profiles of the two strains contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and minor amounts of unidentified aminophospholipids and phospholipids. Based on the phenotypic, genotypic and phylogenetic evidence, strains MJ01(T) and MJ14 represent a single novel species in the genus Rhodanobacter, for which the name Rhodanobacter caeni sp. nov. is proposed. The type strain is MJ01(T) ( = KCTC 22449(T) = JCM 16242(T)), with MJ14 ( = KCTC 22460 = JCM 16243) as a reference strain.

Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.

PubMed

Ben Hania, Wajdi; Joseph, Manon; Schumann, Peter; Bunk, Boyke; Fiebig, Anne; Spröer, Cathrin; Klenk, Hans-Peter; Fardeau, Marie-Laure; Spring, Stefan

2015-01-01

During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2(T) had a size of 0.2 - 0.25 × 8-9 μm, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35°C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed.

The Butterflies of Principal Components: A Case of Ultrafine-Grained Polyphase Units

NASA Astrophysics Data System (ADS)

Rietmeijer, F. J. M.

1996-03-01

Dusts in the accretion regions of chondritic interplanetary dust particles [IDPs] consisted of three principal components: carbonaceous units [CUs], carbon-bearing chondritic units [GUs] and carbon-free silicate units [PUs]. Among others, differences among chondritic IDP morphologies and variable bulk C/Si ratios reflect variable mixtures of principal components. The spherical shapes of the initially amorphous principal components remain visible in many chondritic porous IDPs but fusion was documented for CUs, GUs and PUs. The PUs occur as coarse- and ultrafine-grained units that include so called GEMS. Spherical principal components preserved in an IDP as recognisable textural units have unique proporties with important implications for their petrological evolution from pre-accretion processing to protoplanet alteration and dynamic pyrometamorphism. Throughout their lifetime the units behaved as closed-systems without chemical exchange with other units. This behaviour is reflected in their mineralogies while the bulk compositions of principal components define the environments wherein they were formed.

Bi-directional four quadrant (BDQ4) power converter development

NASA Technical Reports Server (NTRS)

Schwarz, F. C.

1979-01-01

The feasibility for implementation of a concept for direct ac/dc multikilowatt power conversion with bidirectional transfer of energy was investigated. A 10 kHz current carrier was derived directly from a common 60 Hz three phase power system. This carrier was modulated to remove the 360 Hz ripple, inherent in the three phase power supply and then demodulated and processed by a high frequency filter. The resulting dc power was then supplied to a load. The process was implemented without the use of low frequency transformers and filters. This power conversion processes was reversible and can operate in the four quadrants as viewed from any of the two of the converter's ports. Areas of application include: power systems on air and spacecraft; terrestrial traction; integration of solar and wind powered systems with utility networks; HVDC; asynchronous coupling of polyphase networks; heat treatment; industrial machine drives; and power supplies for any use including instrumentation.

Schematic for efficient computation of GC, GC3, and AT3 bias spectra of genome

PubMed Central

Rizvi, Ahsan Z; Venu Gopal, T; Bhattacharya, C

2012-01-01

Selection of synonymous codons for an amino acid is biased in protein translation process. This biased selection causes repetition of synonymous codons in structural parts of genome that stands for high N/3 peaks in DNA spectrum. Period-3 spectral property is utilized here to produce a 3-phase network model based on polyphase filterbank concepts for derivation of codon bias spectra (CBS). Modification of parameters in this model can produce GC, GC3, and AT3 bias spectra. Complete schematic in LabVIEW platform is presented here for efficient and parallel computation of GC, GC3, and AT3 bias spectra of genomes alongwith results of CBS patterns. We have performed the correlation coefficient analysis of GC, GC3, and AT3 bias spectra with codon bias patterns of CBS for biological and statistical significance of this model. PMID:22368390

Schematic for efficient computation of GC, GC3, and AT3 bias spectra of genome.

PubMed

Rizvi, Ahsan Z; Venu Gopal, T; Bhattacharya, C

2012-01-01

Selection of synonymous codons for an amino acid is biased in protein translation process. This biased selection causes repetition of synonymous codons in structural parts of genome that stands for high N/3 peaks in DNA spectrum. Period-3 spectral property is utilized here to produce a 3-phase network model based on polyphase filterbank concepts for derivation of codon bias spectra (CBS). Modification of parameters in this model can produce GC, GC3, and AT3 bias spectra. Complete schematic in LabVIEW platform is presented here for efficient and parallel computation of GC, GC3, and AT3 bias spectra of genomes alongwith results of CBS patterns. We have performed the correlation coefficient analysis of GC, GC3, and AT3 bias spectra with codon bias patterns of CBS for biological and statistical significance of this model.

The Digital Data Acquisition System for the Russian VLBI Network of New Generation

NASA Technical Reports Server (NTRS)

Fedotov, Leonid; Nosov, Eugeny; Grenkov, Sergey; Marshalov, Dmitry

2010-01-01

The system consists of several identical channels of 1024 MHz bandwidth each. In each channel, the RF band is frequency-translated to the intermediate frequency range 1 - 2 GHz. Each channel consists of two parts: the digitizer and Mark 5C recorder. The digitizer is placed on the antenna close to the corresponding Low-Noise Amplifier output and consists of the analog frequency converter, ADC, and a device for digital processing of the signals using FPGA. In the digitizer the subdigitization on frequency of 2048 MHz is used. For producing narrow-band channels and to interface with existing data acquisition systems, the polyphase filtering with FPGA can be used. Digital signals are re-quantized to 2-bits in the FPGA and are transferred to an input of Mark 5C through a fiber line. The breadboard model of the digitizer is being tested, and the data acquisition system is being designed.

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

Reclassification of Xuhuaishuia manganoxidans Wang et al. 2015 as a later heterotypic synonym of Brevirhabdus pacifica Wu et al. 2015 and emendation of the species description.

PubMed

Liu, Yang; Lai, Qiliang; Xu, Xue-Wei; Wu, Yue-Hong; Cheng, Hong; Zhang, Xiao-Hua; Wang, Long; Shao, Zongze

2017-08-01

A polyphasic taxonomic study was undertaken to clarify the exact position of type strain DY6-4T of Xuhuaishuia manganoxidans. A combination of physiological properties of X. manganoxidans DY6-4T was consistent with those of type strain 22DY15T of Brevirhabdus pacifica. The 16S rRNA gene sequence analyses indicated that X. manganoxidans DY6-4T and B. pacifica 22DY15T shared 100 % similarity and formed a monophyletic group. The close relationship between the two strains was underpinned by the results of chemotaxonomic characteristics, including the fatty acids, quinone and polar lipids. The digital DNA-DNA hybridization and average nucleotide identity values between the two strains were 99.90 and 99.98 %, respectively. Based on these results, we propose that Xuhuaishuia manganoxidans is a later heterotypic synonym of Brevirhabdus pacifica.

Pseudo-membranes on internal organs associated with Rhodococcus qingshengii infection in Atlantic salmon (Salmo salar).

PubMed

Avendaño-Herrera, Rubén; Balboa, Sabela; Doce, Alejandra; Ilardi, Pedro; Lovera, Pablo; Toranzo, Alicia E; Romalde, Jesús L

2011-01-10

This paper describes a pathological condition in intensive reared Atlantic salmon (Salmo salar), restricted to the appearance of pseudo-membranes covering internal organs (i.e. spleen, liver, heart and others) associated with the presence of large numbers of a Gram-positive bacteria. Isolate 79043-3, obtained as pure culture from affected fish, was subjected to a polyphasic taxonomic study in order to determine its exact taxonomic position, as well as to experimental challenges leading to determine its pathogenic potential for cultured fish. Based on this characterization, we report the first isolation of Rhodococcus qingshengii, from a farmed population of Atlantic salmon in Chile. Virulence studies demonstrated that the isolate fulfilled the Koch's postulates, suggesting that this bacterial species could be considered as an opportunistic pathogen for Atlantic salmon. Copyright © 2010 Elsevier B.V. All rights reserved.

Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea.

PubMed

Xu, Yongle; Zhang, Rui; Li, Qipei; Liu, Keshao; Jiao, Nianzhi

2015-02-01

A novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000(T), was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T: were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000(T) was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000(T) formed a branch within the genus Marivirga, but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea. The 16S rRNA gene sequence similarity of strain JLT2000(T) with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000(T) had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). In addition, strain JLT2000(T) could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989(T) and Marivirga sericea NBRC 15983(T). Based on this polyphasic analysis, strain JLT2000(T) represents a novel species of the genus Marivirga, for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000(T) ( = JCM 18012(T) = CGMCC 1.10832(T)). © 2015 IUMS.

Altered Fecal Microbiota in Paediatric Inflammatory Bowel Disease.

PubMed

Maukonen, Johanna; Kolho, Kaija-Leena; Paasela, Monika; Honkanen, Jarno; Klemetti, Paula; Vaarala, Outi; Saarela, Maria

2015-12-01

Several factors support the view of inflammatory bowel disease [IBD] origin in the host responsiveness to intestinal bacteria, although no single bacterial species has been shown as a causative agent in the pathogenesis. Our aim was to analyse the fecal microbiota of paediatric IBD patients at different stages of the disease. In addition, the characteristics of immune response to the bacterial isolates showing very low abundance in IBD were studied. Fecal samples [1-3 samples/child] were collected from 10 paediatric patients with crohn's disease [CD], and 12 with ulcerative colitis [UC] and from 8 healthy children, for polyphasic microbiological analysis (culture, real-time polymerase chain reaction [PCR], and denaturing gradient gel electrophoresis). In addition, in vitro cytokine responses of peripheral blood mononuclear cells to the bacterial isolates, which showed very low abundance in IBD, were studied. Although predominant bacterial diversity was higher in IBD, the numbers of Lachnospiraceae and Coriobacteriaceae bacteria were lower in IBD patients as compared with control children [p < 0.05]. In addition, Ruminococcaceae population diversity was lower in IBD [p < 0.05] and correlated negatively with fecal calprotectin levels. Both abundance and diversity of bifidobacterial populations were lower in children with IBD [p < 0.05], and particularly low numbers of certain bifidobacterial isolates were detected. In CD, we found enhanced up-regulation of interleukin-6 transcripts and impaired RAR-related orphan receptor C response to bifidobacteria, whereas decreased interferon-gamma response was observed in both CD and UC. We demonstrate altered fecal microbiota in paediatric IBD, particularly low numbers and diversity of bifidobacterial populations. Interestingly, immunological response to bifidobacteria differed between paediatric CD patients and control children. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Chryseomicrobium imtechense gen. nov., sp. nov., a new member of the family Planococcaceae.

PubMed

Arora, Pankaj Kumar; Chauhan, Archana; Pant, Bhawana; Korpole, Suresh; Mayilraj, Shanmugam; Jain, Rakesh Kumar

2011-08-01

A Gram-stain-positive, rod-shaped, yellow, non-motile, non-spore-forming, strictly aerobic bacterial strain, designated MW 10(T), was isolated from seawater of the Bay of Bengal, India, and was subjected to a polyphasic taxonomic study. Analysis of the 16S rRNA gene sequence revealed that strain MW 10(T) showed highest similarity to the type strains of Psychrobacillus psychrodurans (96.15 %) and Psychrobacillus psychrotolerans (96.01 %) and showed less than 96 % similarity to members of the genera Paenisporosarcina, Planococcus, Sporosarcina and Planomicrobium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain MW 10(T) formed a clade separate from members of closely related genera. The morphological, physiological and chemotaxonomic characteristics of strain MW 10(T) differed from those of members of closely related genera. The major fatty acid in strain MW 10(T) was iso-C(15 : 0) and the menaquinones were MK-7 (48.4 %), MK-8 (32.3 %), MK-7(H(2)) (13.7 %) and MK-6 (5.6 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown phospholipid, an unknown lipid and an unknown glycolipid. The cell-wall peptidoglycan type was l-Lys-d-Asp. The genomic DNA G+C content (53.4 mol%) of strain MW 10(T) was significantly different from those of members of closely related genera. On the basis of its morphological, physiological and chemotaxonomic characteristics as well as our phylogenetic analysis, we conclude that strain MW 10(T) is a member of a novel genus and species, for which the name Chryseomicrobium imtechense gen. nov., sp. nov., is proposed. The type strain of Chryseomicrobium imtechense is MW 10(T) ( = MTCC 10098(T)  = JCM 16573(T)).

Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India.

PubMed

Verma, Ashish; Mual, Poonam; Mayilraj, Shanmugam; Krishnamurthi, Srinivasan

2015-10-01

Two novel Gram-stain-negative, slow-growing, halotolerant strains with rod-shaped cells, designated as strains Mi-7T and Mi-8, which formed pin-point colonies on halophilic media were isolated during a study into the microbial diversity of a salt pan in the state of Tamilnadu, India. Both the strains had an obligate requirement for 1 % (w/v) NaCl for growth and were halotolerant, growing at NaCl concentrations of up to 20 % (w/v) in media. The strains, however, showed an inability to utilize the majority of substrates tested as sole carbon sources for growth and in fermentation reactions. Molecular phylogenetic analyses, based on 16S rRNA gene sequence revealed their closest phylogenetic neighbours to be members of the genus Marinobacter, with whom they showed the highest sequence similarity of 93.6 % and even less with the type strain of the type species, Marinobacter hydrocarbonoclasticus DSM 8798T (91.1 %). Similarities with other genera within the family Alteromonadaceae were below 91.0 %. However, the two strains were very closely related to each other with 99.9 % sequence similarity, and DNA–DNA hybridization analyses confirmed their placement in the same species. The DNA G+C content of both strains was 65 mol%. Using the polyphasic taxonomic data obtained from this study, strains Mi-7T and Mi-8 represent two strains of the same species of a novel genus for which the name Tamilnaduibacter salinus gen. nov., sp. nov., is proposed; the type strain of the novel species is Mi-7T ( = MTCC 12009T = DSM 28688T).

Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae).

PubMed

Bang, Byung-Ho; Rhee, Moon-Soo; Chang, Dong-Ho; Park, Doo-Sang; Kim, Byoung-Chan

2015-02-01

A novel, Gram-stain positive, facultative anaerobic, non-motile and straight to curve rod shaped bacterium, strain LV19(T) was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus, which was collected from Yeong-dong, Chuncheongbuk-do, South Korea. The colonies of the new isolate were convex, circular, cream white in color and 1-2 mm in diameter after 3 days incubation on Tryptic Soy Agar at 37 °C. Based on the 16S rRNA gene sequence similarity, the new isolate was most closely related to Erysipelothrix inopinata MF-EP02(T), E. rhusiopathiae ATCC 19414 (T) and E. tonsillarum T-305(T) (94.8, 93.8 and 93.7 % similarity, respectively). Strain LV19(T) grew optimally at 37 °C, at pH 8.0 and in the presence of 0.5 % (w/v) NaCl. Oxidase activity and catalase activity were negative. The major cellular fatty acids (>10 %) were C18:2 cis-9,12 (28.9 %), C18:1 cis-9 (22.3 %), C16:0 (22.2 %) and C18:0 (18.5 %). The cell-wall hydrolysates contained ribose as a major sugar. Major polar lipids were phosphatidylglycerol and three unidentified glycolipids. No quinone was detected. The G+C content of the genomic DNA was 36.3 mol%. The levels of DNA-DNA relatedness between strain LV19(T) and all the reference strains were less than 20 %. On the basis of polyphasic evidence from this study, the isolate is considered to represent a novel species of the genus Erysipelothrix, for which the name Erysipelothrix larvae sp. nov. is proposed; the type strain is LV19(T) (=KCTC 33523(T) = DSM 28480(T)).

Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate).

PubMed

Tanasupawat, Somboon; Takehana, Toshihiko; Yoshida, Shosuke; Hiraga, Kazumi; Oda, Kohei

2016-08-01

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped bacterium, designed strain 201-F6T, was isolated from a microbial consortium that degrades poly(ethylene terephthalate) (PET) collected in Sakai city, Japan, and was characterized on the basis of a polyphasic taxonomic study. The cells were motile with a polar flagellum. The strain contained cytochrome oxidase and catalase. It grew within the pH range 5.5-9.0 (optimally at pH 7-7.5) and at 15-42 ºC (optimally at 30-37 ºC). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). C16 : 0, C17 : 0 cyclo, C18 :1ω7c and C12 : 0 2-OH were the predominant cellular fatty acids. The major polar lipids were phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of genomic DNA was 70.4 mol%. Phylogenetic analysis using the 16S rRNA gene sequences showed that strain 201-F6T was affiliated to the genus Ideonella, and was closely related to Ideonella dechloratans LMG 28178T (97.7 %) and Ideonella azotifigens JCM 15503T (96.6 %). Strain 201-F6T could be clearly distinguished from the related species of the genus Ideonella by its physiological and biochemical characteristics as well as by its phylogenetic position and DNA-DNA relatedness. Therefore, the strain represents a novel species of the genus Ideonella, for which the name Ideonella sakaiensis sp. nov. (type strain 201-F6T=NBRC 110686T=TISTR 2288T) is proposed.

Streptomyces xylanilyticus sp. nov., isolated from soil.

PubMed

Moonmangmee, Duangtip; Kanchanasin, Pawina; Phongsopitanun, Wongsakorn; Tanasupawat, Somboon; Moonmangmee, Somporn

2017-10-01

A novel actinomycete, strain SR2-123 T , belonging to the genus Streptomyces, was isolated from a soil sample collected from the Sakaerat Environmental Research Station, Thailand Institute of Scientific and Technological Research, Nakhon Ratchasima Province, Thailand. The taxonomic position of the strain was characterized using a polyphasic study. Strain SR2-123 T contained ll-diaminopimelic acid, glucose, mannose and ribose in whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. Menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unknown phospholipid, unknown glycolipids, an unknown aminophospholipid, unknown lipids and an unknown aminolipid. The DNA G+C content was 74.8 mol%. The strain was closely related to Streptomyces coeruleorubidus JCM 4359 T (98.5 %), Streptomyces flavofungini JCM 4753 T (98.5 %), Streptomyces coerulescens NBRC 12758 T (98. 5 %) and Streptomyces alboflavus JCM 4615 T (98.4 %), based on 16S rRNA gene sequence similarities. The novel strain exhibited low DNA-DNA relatedness values with the type strains (11.4-25.0 %) of closely related species. On the basis of phenotypic and genotypic characteristics, strain SR2-123 T could be distinguished from closely related species of the genus Streptomyces and represents a novel species of the genus Streptomyces for which the name Streptomyces xylanilyticus sp. nov. is proposed. The type strain is SR2-123 T (=TISTR 2493 T =KCTC 39909 T ).

Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil.

PubMed

Sujarit, Kanaporn; Kudo, Takuji; Ohkuma, Moriya; Pathom-Aree, Wasu; Lumyong, Saisamorn

2016-10-01

Actinomycete strain CMU-AB204T was isolated from oil palm rhizosphere soil collected in Chiang Mai University (Chiang Mai, Thailand). Based on morphological and chemotaxonomic characteristics, the organism was considered to belong to the genus Streptomyces. Whole cell-wall hydrolysates consisted of ll-diaminopimelic acid, glucose, ribose and galactose. The predominant menaquinones were MK-9(H4), MK-9(H6), MK-9(H2) and MK-8(H4). The fatty acid profile contained iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 as major components. The principal phospholipids detected were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content of strain CMU-AB204T was 70.9 mol%. Based on 16S rRNA gene sequence similarity, strain CMU-AB204T was closely related to Streptomyces orinoci JCM 4546T (98.7 %), Streptomyces lilacinus NBRC 12884T (98.5 %), Streptomyces abikoensis CGMCC 4.1662T (98.5 %), Streptomyces griseocarneus JCM 4905T (98.4 %) and Streptomyces xinghaiensis JCM 16958T (98.3 %). Phylogenetic trees revealed that the new strain had a distinct taxonomic position from closely related type strains of the genus Streptomyces. Spiny to hairy spores clearly differentiated strain CMU-AB204T from the five most closely related Streptomyces species, which produced smooth spores. On the basis of evidence from this polyphasic study, it is proposed that strain CMU-AB204T represents a novel species of the genus Streptomyces, namely Streptomyces palmae sp. nov. The type strain is CMU-AB204T (=JCM 31289T=TBRC 1999T).

Streptosporangium minutum sp. nov., isolated from garden soil exposed to microwave radiation.

PubMed

Le Roes-Hill, Marilize; Durrell, Kim; Prins, Alaric; Meyers, Paul R

2018-06-01

The actinobacterium, strain M26 T , was isolated from garden soil that was pre-treated with microwave radiation. The soil sample was collected in Roodepoort, Gauteng Province, South Africa as part of an antibiotic-screening programme. The isolate produced branched vegetative mycelium with sporangiophores bearing small sporangia ranging from 3 to 6 μm in diameter. Rapid genus identification revealed that the isolate belongs to the genus Streptosporangium. To confirm this result, the strain was subjected to polyphasic taxonomic characterisation. Chemotaxonomic characteristics were as follows: meso-DAP in the peptidoglycan, the whole-cell hydrolysate yielded madurose, predominant menaquinones were MK9 (21%), MK9(H 2 ) (40%), MK9(H 4 ) (31%) and MK9(H 6 ) (3%); the polar lipid profile included an aminolipid, phosphoglycolipids, phosphatidylethanolamine, and phosphatidylmonomethylethanolamine. In addition, the fatty acid profile showed the presence of C 16:0 (12.8%), C 17:1 ω8c (14.2%), and 10-methyl-C 17:0 (15.8%). Furthermore, 16S rRNA gene sequence phylogenetic analysis showed that the strain is closely related to members of the genus Streptosporangium, which supports its classification within the family Streptosporangiaceae. Strain M26 T exhibited antibiosis against a range of pathogenic bacteria, including, but not limited to Acinetobacter baumannii ATCC 19606 T , Enterobacter cloacae subsp. cloacae ATCC BAA-1143, Enterococcus faecalis ATCC 51299 (vancomycin resistant), Escherichia coli ATCC 25922, Listeria monocytogenes ATCC 19111, Mycobacterium tuberculosis H37Rv T , Pseudomonas aeruginosa ATCC 27853, Salmonella enterica subsp. arizonae ATCC 13314 T , and the methicillin-resistant Staphylococcus aureus subsp. aureus ATCC 33591 (MRSA). The name Streptosporangium minutum is proposed with the type strain M26 T (=LMG 28850 T =NRRL B-65295 T ).

MARGATS cruise: investigation of the deep internal structure and the heterogeneous margins of the Demerara plateau reveals a polyphased volcanic history

NASA Astrophysics Data System (ADS)

Graindorge, D.; Museur, T.; Roest, W. R.; Klingelhoefer, F.; Loncke, L.; Basile, C.; Poetisi, E.; Deverchere, J.; Heuret, A.; Jean-Frederic, L.; Perrot, J.

2017-12-01

The MARGATS scientific cruise was carried out from October 20th to November 16th 2016 on board the R/V L'Atalante, offshore Suriname and French Guiana. This cruise is part of a program dedicated to the geological investigation of the continental margin, including the Demerara plateau, following the GUYAPLAC (2003), IGUANES (2013) and DRADEM (2016) cruises. The aim of MARGATS was to image the internal structure of the Demerara plateau and its different margins using coincident deep penetrating wide angle refraction and multi channel reflection seismic (MCS) methods. During the MARGATS experiment 171 OBS deployments were distributed along 4 wide-angle lines. Along each wide-angle line we also recorded coincident MCS data using a 3 km long 480 channel streamer. The dataset was completed by three MCS lines along the eastern part of the Demerara plateau. MCS MAR007 line which is coincident with line OBS MAR-3 was extended on land by 13 land stations deployed along the Maroni River. This line, together with MCS MAR001 and the coincident OBS MAR-1 line reveal the highly homogeneous deep structure of the internal part of the plateau. MCS MAR005 line, which is coincident with OBS MAR-2, MCS MAR006 line coincident with OBS MAR-4, MCS MAR002, MCS MAR003 and MCS MAR004 helps to elucidate the structural complexity of the northern transform margin and the eastern divergent margin of the plateau. These new datasets are highly complementary to the DRADEM dredge results which provide evidence for mid Jurassic volcanic rocks along the plateau and significant vertical displacements along the transform margin. These results allow to interpret the plateau as the remains of a huge jurassic volcanic divergent margin along the Central Atlantic ocean to the west, possibly remobilized during the cretaceous opening of the Equatorial Atlantic ocean as an highly oblique margin to the north and a divergent margin to the east in persistent presence of volcanism. This AGU session will be a great opportunity to present the exceptional quality of the seismic data, after the initial processing steps and how these data are conditioning a new understanding of the Demarara plateau and its margins which implies the hypothetic role of a new hot spot shaping the complex polyphased history of the structure.

Formation of an active thrust triangle zone associated with structural inversion in a subduction setting, eastern New Zealand

NASA Astrophysics Data System (ADS)

Barnes, Philip M.; Nicol, Andrew

2004-02-01

We analyze a thrust triangle zone, which underlies the continental shelf of Hawke Bay, eastern New Zealand, within the Hikurangi subduction margin. This triangle zone differs from many other examples in that it is active, 90 km from the leading edge of the overriding plate, and formed due to polyphase deformation involving opposed dipping thrust duplex and backthrust, with the later structure forming in response to inversion of an extensional graben. The component structures of the zone mainly developed sequentially rather than synchronously. High-quality marine seismic reflection lines, tied to well and seabed samples, reveal the three-dimensional structure of the zone, together with its 25 Myr evolution and late Quaternary activity. The triangle zone occurs in the lateral overlap between a stack of NW dipping blind thrusts, and a principal backthrust, the Kidnappers fault. The NW dipping thrusts initiated in the early-middle Miocene during the early stages of subduction, with subsequent thrust duplex formation producing major uplift and erosion in the late Miocene-early Pliocene. The active backthrust formed during the late Miocene to early Pliocene as a thin-skinned listric extensional fault confined to the cover sequence. Structural inversion of the extensional fault commenced in the early-middle Pliocene, produced the backthrust and marks the formation of the thrust triangle zone. The thrust duplex and backthrust accrued strain following inversion; however, the later structure accommodated most of the surface deformation in the Quaternary. Section balancing of the triangle zone together with a detailed analysis of reverse displacements along the backthrust reveal spatial and temporal variations of strain accumulation on the two principal components of the zone. Although the formation of the triangle zone is strongly influenced by regional tectonics of the subduction system, these variations may also, in part, reflect local fault interaction. For example, high Quaternary displacement rates on the backthrust accounts for ˜70% of the displacement loss that occurs on the southern segments of the overlapping, Lachlan fault. Understanding the tectonic evolution of such complex, polyphase thrust triangle zones requires the preservation of growth strata that record sequential deformation history. In the absence of such data, synchroneity of opposed dipping thrusts in triangle zones cannot be assumed.

Polyphase tectono-magmatic and fluid history related to mantle exhumation in an ultra-distal rift domain: example of the fossil Platta domain, SE Switzerland

NASA Astrophysics Data System (ADS)

Epin, Marie-Eva; Manatschal, Gianreto; Amann, Méderic; Lescanne, Marc

2017-04-01

Despite the fact that many studies have investigated mantle exhumation at magma-poor rifted margins, there are still numerous questions concerning the 3D architecture, magmatic, fluid and thermal evolution of these ultra-distal domains that remain unexplained. Indeed, it has been observed in seismic data from ultra-distal magma-poor rifted margins that top basement is heavily structured and complex, however, the processes controlling the morpho-tectonic and magmatic evolution of these domains remain unknown. The aim of this study is to describe the 3D top basement morphology of an exhumed mantle domain, exposed over 200 km2 in the fossil Platta domain in SE Switzerland, and to define the timing and processes controlling its evolution. The examined Platta nappe corresponds to a remnant of the former ultra-distal Adriatic margin of the Alpine Tethys. The rift-structures are relatively well preserved due to the weak Alpine tectonic and metamorphic overprint during the emplacement in the Alpine nappe stack. Detailed mapping of parts of the Platta nappe enabled us to document the top basement architecture of an exhumed mantle domain and to investigate its link to later, rift/oceanic structures, magmatic additions and fluids. Our observations show a polyphase and/or complex: 1) deformation history associated with mantle exhumation along low-angle exhumation faults overprinted by later high-angle normal faults, 2) top basement morphology capped by magmato-sedimentary rocks, 3) tectono-magmatic evolution that includes gabbros, emplaced at deeper levels and subsequently exhumed and overlain by younger extrusive magmatic additions, and 4) fluid history including serpentinization, calcification, hydrothermal vent, rodingitization and spilitization affecting exhumed mantle and associated magmatic rocks. The overall observations provide important information on the temporal and spatial evolution of the tectonic, magmatic and fluid systems controlling the formation of ultra-distal magma-poor rifted margins as well as the processes controlling lithospheric breakup. In this context, our field observations can help to better understand the tectono-magmatic processes associated to these, not yet drilled domains that may form in young, narrow rifted margins (e.g. Red Sea, Gulf of Aden) or may represent the Ocean-Continent Transition in more mature, magma-poor Atlantic type systems.

Microbial Burden Approach : New Monitoring Approach for Measuring Microbial Burden

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri; Vaishampayan, Parag; Barmatz, Martin

2013-01-01

Advantages of new approach for differentiating live cells/ spores from dead cells/spores. Four examples of Salmonella outbreaks leading to costly destruction of dairy products. List of possible collaboration activities between JPL and other industries (for future discussion). Limitations of traditional microbial monitoring approaches. Introduction to new approach for rapid measurement of viable (live) bacterial cells/spores and its areas of application. Detailed example for determining live spores using new approach (similar procedure for determining live cells). JPL has developed a patented approach for measuring amount of live and dead cells/spores. This novel "molecular" method takes less than 5 to 7 hrs. compared to the seven days required using conventional techniques. Conventional "molecular" techniques can not discriminate live cells/spores among dead cells/spores. The JPL-developed novel method eliminates false positive results obtained from conventional "molecular" techniques that lead to unnecessary delay in the processing and to unnecessary destruction of food products.

NK cell-based immunotherapy for malignant diseases

PubMed Central

Cheng, Min; Chen, Yongyan; Xiao, Weihua; Sun, Rui; Tian, Zhigang

2013-01-01

Natural killer (NK) cells play critical roles in host immunity against cancer. In response, cancers develop mechanisms to escape NK cell attack or induce defective NK cells. Current NK cell-based cancer immunotherapy aims to overcome NK cell paralysis using several approaches. One approach uses expanded allogeneic NK cells, which are not inhibited by self histocompatibility antigens like autologous NK cells, for adoptive cellular immunotherapy. Another adoptive transfer approach uses stable allogeneic NK cell lines, which is more practical for quality control and large-scale production. A third approach is genetic modification of fresh NK cells or NK cell lines to highly express cytokines, Fc receptors and/or chimeric tumor-antigen receptors. Therapeutic NK cells can be derived from various sources, including peripheral or cord blood cells, stem cells or even induced pluripotent stem cells (iPSCs), and a variety of stimulators can be used for large-scale production in laboratories or good manufacturing practice (GMP) facilities, including soluble growth factors, immobilized molecules or antibodies, and other cellular activators. A list of NK cell therapies to treat several types of cancer in clinical trials is reviewed here. Several different approaches to NK-based immunotherapy, such as tissue-specific NK cells, killer receptor-oriented NK cells and chemically treated NK cells, are discussed. A few new techniques or strategies to monitor NK cell therapy by non-invasive imaging, predetermine the efficiency of NK cell therapy by in vivo experiments and evaluate NK cell therapy approaches in clinical trials are also introduced. PMID:23604045

An approach for cell viability online detection based on the characteristics of lensfree cell diffraction fingerprint.

PubMed

Li, Guoxiao; Zhang, Rongbiao; Yang, Ning; Yin, Changsheng; Wei, Mingji; Zhang, Yecheng; Sun, Jian

2018-06-01

To overcome the drawbacks such as low automation and high cost, an approach for cell viability online detection is proposed, based on the extracted lensfree cell diffraction fingerprint characteristics. The cell fingerprints are acquired by a constructed large field-of-view (FOV) diffraction imaging platform without any lenses. The approach realizes distinguishing live and dead cells online and calculating cell viability index based on the number of live cells. With theoretical analysis and simulation, diffraction fingerprints of cells with different morphology are simulated and two characteristics are discovered to be able to reflect cell viability status effectively. Two parameters, fringe intensity contrast (FIC) and fringe dispersion (FD), are defined to quantify these two characteristics. They are verified to be reliable to identify live cells. In a cytotoxicity assay of different methyl mercury concentration on BRL cells, the proposed approach is used to detect cell viability. MTT method is also employed and the results of correlational analysis and Bland-Altman analysis prove the validity of the proposed approach. By comparison, it can be revealed that the proposed approach has some advantages over other present techniques. Therefore it may be widely used as a cell viability measurement method in drug screening, nutritional investigation and cell toxicology studies. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Modeling and analysis of cascade solar cells

NASA Technical Reports Server (NTRS)

Ho, F. D.

1986-01-01

A brief review is given of the present status of the development of cascade solar cells. It is known that photovoltaic efficiencies can be improved through this development. The designs and calculations of the multijunction cells, however, are quite complicated. The main goal is to find a method which is a compromise between accuracy and simplicity for modeling a cascade solar cell. Three approaches are presently under way, among them (1) equivalent circuit approach, (2) numerical approach, and (3) analytical approach. Here, the first and the second approaches are discussed. The equivalent circuit approach using SPICE (Simulation Program, Integrated Circuit Emphasis) to the cascade cells and the cascade-cell array is highlighted. The methods of extracting parameters for modeling are discussed.

Methanotroph Diversity in Landfill Soil: Isolation of Novel Type I and Type II Methanotrophs Whose Presence Was Suggested by Culture-Independent 16S Ribosomal DNA Analysis

PubMed Central

Wise, Mark G.; McArthur, J Vaun; Shimkets, Lawrence J.

1999-01-01

The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4.8 versus 6.8), air/CH4/CO2 headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1× nitrate minimal salts [NMS] versus 0.2× NMS). Screening of the isolates showed that the nutrient-rich 1× NMS selected for type I methanotrophs, while the nutrient-poor 0.2× NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobium group, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly published Methylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described. PMID:10543800

Structures Self-Assembled Through Directional Solidification

NASA Technical Reports Server (NTRS)

Dynys, Frederick W.; Sayir, Ali

2005-01-01

Nanotechnology has created a demand for new fabrication methods with an emphasis on simple, low-cost techniques. Directional solidification of eutectics (DSE) is an unconventional approach in comparison to low-temperature biomimetic approaches. A technical challenge for DSE is producing microstructural architectures on the nanometer scale. In both processes, the driving force is the minimization of Gibb's free energy. Selfassembly by biomimetic approaches depends on weak interaction forces between organic molecules to define the architectural structure. The architectural structure for solidification depends on strong chemical bonding between atoms. Constituents partition into atomic-level arrangements at the liquid-solid interface to form polyphase structures, and this atomic-level arrangement at the liquid-solid interface is controlled by atomic diffusion and total undercooling due to composition (diffusion), kinetics, and curvature of the boundary phases. Judicious selection of the materials system and control of the total undercooling are the keys to producing structures on the nanometer scale. The silicon-titanium silicide (Si-TiSi2) eutectic forms a rod structure under isothermal cooling conditions. At the NASA Glenn Research Center, directional solidification was employed along with a thermal gradient to promote uniform rods oriented with the thermal gradient. The preceding photomicrograph shows the typical transverse microstructure of a solidified Si-TiSi2 eutectic composition. The dark and light gray regions are Si and TiSi2, respectively. Preferred rod orientation along the thermal gradient was poor. The ordered TiSi2 rods have a narrow distribution in diameter of 2 to 3 m, as shown. The rod diameter showed a weak dependence on process conditions. Anisotropic etch behavior between different phases provides the opportunity to fabricate structures with high aspect ratios. The photomicrographs show the resulting microstructure after a wet chemical etch and a dry plasma etch. The wet chemical etches the silicon away, exposing the TiSi2 rods, whereas plasma etching preferentially etches the Si-TiSi2 interface to form a crater. The porous architectures are applicable to fabricating microdevices or creating templates for part fabrication. The porous rod structure can serve as a platform for fabricating microplasma devices for propulsion or microheat exchangers and for fabricating microfilters for miniatured chemical reactors. Although more work is required, self-assembly from DSE can have a role in microdevice fabrication.

Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil.

PubMed

Sheu, Shih-Yi; Chou, Jui-Hsing; Bontemps, Cyril; Elliott, Geoffrey N; Gross, Eduardo; James, Euan K; Sprent, Janet I; Young, J Peter W; Chen, Wen-Ming

2012-09-01

Four strains, designated JPY-345(T), JPY-347, JPY-366 and JPY-581, were isolated from nitrogen-fixing nodules on the roots of two species of Mimosa, Mimosa cordistipula and Mimosa misera, that are native to North East Brazil, and their taxonomic positions were investigated by using a polyphasic approach. All four strains grew at 15-43 °C (optimum 35 °C), at pH 4-7 (optimum pH 5) and with 0-2 % (w/v) NaCl (optimum 0 % NaCl). On the basis of 16S rRNA gene sequence analysis, strain JPY-345(T) showed 97.3 % sequence similarity to the closest related species Burkholderia soli GP25-8(T), 97.3 % sequence similarity to Burkholderia caryophylli ATCC25418(T) and 97.1 % sequence similarity to Burkholderia kururiensis KP23(T). The predominant fatty acids of the strains were C(18 : 1)ω7c (36.1 %), C(16 : 0) (19.8 %) and summed feature 3, comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c (11.5 %). The major isoprenoid quinone was Q-8 and the DNA G+C content of the strains was 64.2-65.7 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. DNA-DNA hybridizations between the novel strain and recognized species of the genus Burkholderia yielded relatedness values of <51.8 %. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data, the four strains represent a novel species in the genus Burkholderia, for which the name Burkholderia symbiotica sp. nov. is proposed. The type strain is JPY-345(T) (= LMG 26032(T) = BCRC 80258(T) = KCTC 23309(T)).

Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory.

PubMed

Zhang, Long; Zhou, Qing-Xin; Song, Man; Chen, Xiao-Long; Xu, Xi-Hui; Chen, Kai; Li, Shun-Peng; Jiang, Jian-Dong

2015-12-01

Two Gram-stain negative, coccoid to oval-shaped, non-spore-forming bacteria (LR4T and LR4-1), isolated from the soil of a pesticide factory in Nanjing, China, were investigated for their taxonomic allocation by using a polyphasic approach. Both strains grew optimally at pH 7.0, 30 °C and in the absence of NaCl. Both strains were positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major fatty acids (>10 % of the total fatty acids) were C18:1ω7c/C18:1ω6c (summed feature 8) and C17:1 iso I/C17:1 anteiso B (summed feature 4). Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct line within a clade containing the genera Chelatococcus, Bosea, Camelimonas, Salinarimonas, Psychroglaciecola, Microvirga, Methylobacterium, Albibacter, Hansschlegelia and Methylopila in the order Rhizobiales, with the highest 16S rRNA gene sequence similarity to Chelatococcus asaccharovorans TE2T (94.12 %), followed by Bosea thiooxidans DSM 9653T (93.25 %). Strains LR4T and LR4-1 were closely related on the basis of DNA-DNA reassociation and therefore represent a single novel species. Based on phenotypic, chemotaxonomic and phylogenetic data, strains LR4T and LR4-1 represent a novel species of a new genus in the order Rhizobiales, for which the name Qingshengfania soli gen. nov., sp. nov. is proposed. The type strain of the type species is LR4T ( = CCTCC AB 2015036T = KCTC 42463T).

Nonomuraea indica sp. nov., novel actinomycetes isolated from lime-stone open pit mine, India.

PubMed

Quadri, Syed Raziuddin; Tian, Xin-Peng; Zhang, Jing; Li, Jie; Nie, Guo-Xing; Tang, Shu-Kun; Al Ruwaili, Jamal; Agsar, Dayanand; Li, Wen-Jun; Dastager, Syed G

2015-08-01

A Gram-positive, aerobic, nonmotile actinomycete strain designated DRQ-2(T) was isolated from the soil sample collected from lime-stone open pit mine from the Gulbarga region, Karnataka province, India. Strain DRQ-2(T) was identified as a member of the genus Nonomuraea by a polyphasic approach. Strain DRQ-2(T) could be differentiated from other members of the genus Nonomuraea on the basis of physiology and 16S rRNA gene sequence analysis. The 16S rRNA gene sequence similarity of strain DRQ-2(T) showed highest sequence similarity to Nonomuraea muscovyensis DSM 45913(T) (99.1%), N. salmonea DSM 43678(T) (98.2%) and N. maheshkhaliensis JCM 13929(T) with 98.0%, respectively. Chemotaxonomic properties showing predominant menaquinones of MK-9 (H4), MK-9(H2) and MK-9(H6), major polar lipids comprised diphosphatidylglycerol, phosphatidylmono methyl ethanolamine (PME), phosphatidylethanolamine (PE), hydroxy-PME (OH-PME), hydroxy PE (OH-PEE), phosphatidylglycerol (PG), ninhydrin-positive phosphoglycolipid and unknown phospholipid, fatty acids with major amounts of i-C16:0, ai-C15:0 and ai-C17:0 supported allocation of the strain to the genus Nonomuraea. Results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of strain DRQ-2(T) from closely related species. The genomic DNA G+C content of the organism was 72.5 mol%. On the basis of phenotypic, chemotypic and molecular characteristics, strain DRQ-2(T) represents a novel species of the genus Nonomuraea, for which the name N. indica sp. nov. is proposed, with type strain DRQ-2(T) (=NCIM 5480(T)= CCTCC AA 209050(T)).

Erwinia teleogrylli sp. nov., a Bacterial Isolate Associated with a Chinese Cricket

PubMed Central

Liu, Bo; Luo, Jin; Li, Wei; Long, Xiu-Feng; Zhang, Yu-Qin; Zeng, Zhi-Gang; Tian, Yong-Qiang

2016-01-01

A bacterial isolate (SCU-B244T) was obtained in China from crickets (Teleogryllus occipitalis) living in cropland deserted for approximately 10 years. The isolated bacteria were Gram-negative, facultatively anaerobic, oxidase-negative rods. A preliminary analysis of the 16S rRNA gene sequence indicated that the strain belongs to either the genus Erwinia or Pantoea. Analysis of multilocus sequence typing based on concatenated partial atpD, gyrB and infB gene sequences and physiological and biochemical characteristics indicated that the strain belonged to the genus Erwinia, as member of a new species as it was distinct from other known Erwinia species. Further analysis of the 16S rRNA gene showed SCU-B244T to have 94.71% identity to the closest species of that genus, Erwinia oleae (DSM 23398T), which is below the threshold of 97% used to discriminate bacterial species. DNA-DNA hybridization results (5.78±2.52%) between SCU-B244T and Erwinia oleae (DSM 23398T) confirmed that SCU-B244T and Erwinia oleae (DSM 23398T) represent different species combined with average nucleotide identity values which range from 72.42% to 74.41. The DNA G+C content of SCU-B244T was 55.32 mol%, which also differs from that of Erwinia oleae (54.7 to 54.9 mol%). The polyphasic taxonomic approach used here confirmed that the strain belongs to the Erwinia group and represents a novel species. The name Erwinia teleogrylli sp. nov. is proposed for this novel taxon, for which the type strain is SCU-B244T (= CGMCC 1.12772T = DSM 28222T = KCTC 42022T). PMID:26800121

Chemotaxonomy of heterocystous cyanobacteria using FAME profiling as species markers.

PubMed

Shukla, Ekta; Singh, Satya Shila; Singh, Prashant; Mishra, Arun Kumar

2012-07-01

The fatty acid methyl ester (FAME) analysis of the 12 heterocystous cyanobacterial strains showed different fatty acid profiling based on the presence/absence and the percentage of 13 different types of fatty acids. The major fatty acids viz. palmitic acid (16:0), hexadecadienoic acid (16:2), stearic acid (18:0), oleic acid (18:1), linoleic (18:2), and linolenic acid (18:3) were present among all the strains except Cylindrospermum musicola where oleic acid (18:1) was absent. All the strains showed high levels of polyunsaturated fatty acid (PUFAs; 41-68.35%) followed by saturated fatty acid (SAFAs; 1.82-40.66%) and monounsaturated fatty acid (0.85-24.98%). Highest percentage of PUFAs and essential fatty acid (linolenic acid; 18:3) was reported in Scytonema bohnerii which can be used as fatty acid supplement in medical and biotechnological purpose. The cluster analysis based on FAME profiling suggests the presence of two distinct clusters with Euclidean distance ranging from 0 to 25. S. bohnerii of cluster I was distantly related to the other strains of cluster II. The genotypes of cluster II were further divided into two subclusters, i.e., IIa with C. musicola showing great divergence with the other genotypes of IIb which was further subdivided into two groups. Subsubcluster IIb(1) was represented by a genotype, Anabaena sp. whereas subsubcluster IIb(2) was distinguished by two groups, i.e., one group having significant similarity among their three genotypes showed distant relation with the other group having closely related six genotypes. To test the validity of the fatty acid profiles as a marker, cluster analysis has also been generated on the basis of morphological attributes. Our results suggest that FAME profiling might be used as species markers in the study of polyphasic approach based taxonomy and phylogenetic relationship.

Nafulsella turpanensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil.

PubMed

Zhang, Lei; Shen, Xihui; Liu, Yingbao; Li, Shiqing

2013-05-01

A Gram-staining-negative, rod-shaped, gliding and pale-pink-pigmented bacterium, designated strain ZLM-10(T), was isolated from a soil sample collected from an arid area in Xinjiang province, China, and characterized in a taxonomic study using a polyphasic approach. The novel strain grew optimally at 30-37 °C and in the presence of 2 % (w/v) sea salts. The only respiratory quinone detected was MK-7 and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified aminophospholipids. The DNA G+C content was 45.4 mol%. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZLM-10(T) was a member of the phylum Bacteroidetes and appeared most closely related to Cesiribacter roseus 311(T) (90.2 % sequence similarity), Marivirga sericea LMG 13021(T) (89.2 %), Cesiribacter andamanensis AMV16(T) (89.1 %) and Marivirga tractuosa DSM 4126(T) (89.1 %). On the basis of phenotypic and genotypic data and phylogenetic inference, strain ZLM-10(T) should be classified as a novel species of a new genus in the family Flammeovirgaceae, for which the name Nafulsella turpanensis gen. nov., sp. nov. is proposed. The type strain of the type species is ZLM-10(T) ( = CCTCC AB 208222(T) = KCTC 23983(T)).

Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat.

PubMed

Park, Sooyeon; Park, Ji-Min; Kang, Chul-Hyung; Yoon, Jung-Hoon

2014-06-01

A Gram-stain-negative, non-motile, aerobic, curved-to-spiral-rod-shaped bacterium, designated AH-MY2(T), was isolated from a tidal flat on Aphae island in the sea to the south-west of South Korea, and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain AH-MY2(T) grew optimally at 30 °C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain AH-MY2(T) clustered with the type strain of Terasakiella pusilla and that this cluster joined the clade comprising the type strains of species of the genus Thalassospira. Strain AH-MY2(T) exhibited 16S rRNA gene sequence similarity values of 90.6% to the type strain of Terasakiella pusilla and of less than 91.0% to the type strains of other species with validly published names. Strain AH-MY2(T) contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c as the major fatty acid. The major polar lipids detected in strain AH-MY2(T) were phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids and one unidentified glycolipid. The DNA G+C content of strain AH-MY2(T) was 56.0 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain AH-MY2(T) represented a novel genus and species within the family Rhodospirillaceae of the class Alphaproteobacteria, for which the name Aestuariispira insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariispira insulae is AH-MY2(T) ( = KCTC 32577(T) = CECT 8488(T)). © 2014 IUMS.

Polyphasic approach for assessing changes in an autochthonous marine bacterial community in the presence of Prestige fuel oil and its biodegradation potential.

PubMed

Jiménez, Núria; Viñas, Marc; Guiu-Aragonés, Cèlia; Bayona, Josep M; Albaigés, Joan; Solanas, Anna M

2011-08-01

A laboratory experiment was conducted to identify key hydrocarbon degraders from a marine oil spill sample (Prestige fuel oil), to ascertain their role in the degradation of different hydrocarbons, and to assess their biodegradation potential for this complex heavy oil. After a 17-month enrichment in weathered fuel, the bacterial community, initially consisting mainly of Methylophaga species, underwent a major selective pressure in favor of obligate hydrocarbonoclastic microorganisms, such as Alcanivorax and Marinobacter spp. and other hydrocarbon-degrading taxa (Thalassospira and Alcaligenes), and showed strong biodegradation potential. This ranged from >99% for all low- and medium-molecular-weight alkanes (C(15)-C(27)) and polycyclic aromatic hydrocarbons (C(0)- to C(2)- naphthalene, anthracene, phenanthrene, dibenzothiophene, and carbazole), to 75-98% for higher molecular-weight alkanes (C(28)-C(40)) and to 55-80% for the C(3) derivatives of tricyclic and tetracyclic polycyclic aromatic hydrocarbons (PAHs) (e.g., C(3)-chrysenes), in 60 days. The numbers of total heterotrophs and of n-alkane-, aliphatic-, and PAH degraders, as well as the structures of these populations, were monitored throughout the biodegradation process. The salinity of the counting medium affects the counts of PAH degraders, while the carbon source (n-hexadecane vs. a mixture of aliphatic hydrocarbons) is a key factor when counting aliphatic degraders. These limitations notwithstanding, some bacterial genera associated with hydrocarbon degradation (mainly belonging to α- and γ-Proteobacteria, including the hydrocarbonoclastic Alcanivorax and Marinobacter) were identified. We conclude that Thalassospira and Roseobacter contribute to the degradation of aliphatic hydrocarbons, whereas Mesorhizobium and Muricauda participate in the degradation of PAHs.

Roseovarius albus sp. nov., a new Alphaproteobacterium isolated from the Mediterranean Sea.

PubMed

Lucena, Teresa; Ruvira, María A; Macián, M Carmen; Pujalte, María J; Arahal, David R

2014-04-01

Strain 4SM10(T), an aerobic marine, Gram-negative, heterotrophic and non pigmented bacterium isolated from seawater from Vinaroz in Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence placed the strain within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analyses also showed that strain 4SM10(T) forms a stable clade with species of the genus Roseovarius, being related to Roseovarius nubinhibens ISM(T) and Roseovarius aestuarii SMK-122(T) at 97.5 and 97.4 % 16S rRNA sequence similarity, respectively. Average Nucleotide Identity (ANI) values, determined as a measure of overall genomic resemblance, confirmed that strain 4SM10(T) does not belong to the same species as R. aestuarii CECT 7745(T) and Roseovarius nubinhibens CECT 7750(T) displaying ANI values well below the 95 % boundary for genomic species. Strain 4SM10(T) requires Na(+) plus a divalent cation (either Mg(2+) or Ca(2+)) to grow, reduces nitrate to nitrite and uses a large number of amino acids and organic acids (but no carbohydrates) as sole carbon sources. Enzymatic activities displayed in API ZYM tests are alkaline phosphatase, leucine arylamidase and acid phosphatase. The major cellular fatty acids were identified as C18:1 ω7c and/or C18:1 ω6c (67.1 %). The DNA G+C content was determined to be 54.27 mol%. Based on the genotypic and phenotypic data obtained, the name Roseovarius albus sp. nov. is proposed for this novel taxon, with the type strain 4SM10(T) (=CECT 7450(T) = KCTC 22653(T)).

Phylogenetic multilocus sequence analysis of indigenous slow-growing rhizobia nodulating cowpea (Vigna unguiculata L.) in Greece.

PubMed

Tampakaki, Anastasia P; Fotiadis, Christos T; Ntatsi, Georgia; Savvas, Dimitrios

2017-04-01

Cowpea (Vigna unguiculata) is a promiscuous grain legume, capable of establishing efficient symbiosis with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus Bradyrhizobium. Although much research has been done on cowpea-nodulating bacteria in various countries around the world, little is known about the genetic and symbiotic diversity of indigenous cowpea rhizobia in European soils. In the present study, the genetic and symbiotic diversity of indigenous rhizobia isolated from field-grown cowpea nodules in three geographically different Greek regions were studied. Forty-five authenticated strains were subjected to a polyphasic approach. ERIC-PCR based fingerprinting analysis grouped the isolates into seven groups and representative strains of each group were further analyzed. The analysis of the rrs gene showed that the strains belong to different species of the genus Bradyrhizobium. The analysis of the 16S-23S IGS region showed that the strains from each geographic region were characterized by distinct IGS types which may represent novel phylogenetic lineages, closely related to the type species of Bradyrhizobium pachyrhizi, Bradyrhizobium ferriligni and Bradyrhizobium liaoningense. MLSA analysis of three housekeeping genes (recA, glnII, and gyrB) showed the close relatedness of our strains with B. pachyrhizi PAC48 T and B. liaoningense USDA 3622 T and confirmed that the B. liaoningense-related isolate VUEP21 may constitute a novel species within Bradyrhizobium. Moreover, symbiotic gene phylogenies, based on nodC and nifH genes, showed that the B. pachyrhizi-related isolates belonged to symbiovar vignae, whereas the B. liaoningense-related isolates may represent a novel symbiovar. Copyright © 2017 Elsevier GmbH. All rights reserved.

A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata.

PubMed

Tampakaki, Anastasia P; Fotiadis, Christos T; Ntatsi, Georgia; Savvas, Dimitrios

2017-10-01

Cowpea (Vigna unguiculata) forms nitrogen-fixing root nodules with diverse symbiotic bacteria, mainly slow-growing rhizobial species belonging to the genus Bradyrhizobium, although a few studies have reported the isolation of fast-growing rhizobia under laboratory and field conditions. Although much research has been done on cowpea-nodulating bacteria in various countries around the world, very limited information is available on cowpea rhizobia in European soils. The aim of this study was to study the genetic and phenotypic diversity of indigenous cowpea-nodulating rhizobia in Greece. The genetic diversity of indigenous rhizobia associated with cowpea was investigated through a polyphasic approach. ERIC-PCR based fingerprinting analysis grouped the isolates into three groups. Based on the analysis of the 16S rRNA genes, IGS and on the concatenation of six housekeeping genes (recA, glnII, gyrB, truA, thrA and SMc00019), rhizobial isolates were classified within the species Ensifer fredii. However, symbiotic gene phylogenies, based on nodC, nifH and rhcRST genes, showed that the Ensifer isolates are markedly diverged from type and reference strains of E. fredii and formed one clearly separate cluster. The E. fredii strains were able to nodulate and fix nitrogen in cowpea but not in soybean and common bean. The present study showed that cowpea is nodulated under field conditions by fast-growing rhizobia belonging to the species E. fredii. Based on the phylogenies, similarity levels of symbiotic genes and the host range, the Ensifer isolates may constitute a new symbiovar for which the name 'aegeanense' is proposed. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Description of Kibdelosporangium banguiense sp. nov., a novel actinomycete isolated from soil of the forest of Pama, on the plateau of Bangui, Central African Republic.

PubMed

Pascual, Javier; González, Ignacio; Estévez, Mar; Benito, Patricia; Trujillo, Martha E; Genilloud, Olga

2016-05-01

A novel actinomycete strain F-240,109(T) from the MEDINA collection was isolated from a soil sample collected in the forest of Pama, on the plateau of Bangui, Central African Republic. The strain was identified according to its 16S rRNA gene sequence as a new member of the genus Kibdelosporangium, being closely related to Kibdelosporangium aridum subsp. aridum (98.6 % sequence similarity), Kibledosporangium phytohabitans (98.3 %), Kibdelosporangium aridum subsp. largum (97.7 %), Kibdelosporangium philippinense (97.6 %) and Kibledosporangium lantanae (96.9 %). In order to resolve its precise taxonomic status, the strain was characterised through a polyphasic approach. The strain is a Gram-stain positive, aerobic, non-motile and catalase-positive actinomycete characterised by formation of extensively branched substrate mycelia and sparse brownish grey aerial mycelia with sporangium-like globular structures. The chemotaxonomic characterisation of strain F-240,109(T) corroborated its affiliation into the genus Kibdelosporangium. The peptidoglycan contains meso-diaminopimelic acid; the major menaquinone is MK-9(H4); the phospholipid profile contains high amounts of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol and an unidentified phospholipid; and the predominant cellular fatty acid methyl esters are iso-C16:0, iso-C14:0, iso-C15:0 and 2OH iso-C16:0. However, some key phenotypic differences regarding to its close relatives and DNA-DNA hybridization values indicate that strain F-240,109(T) represents a novel Kibdelosporangium species, for which the name Kibdelosporangium banguiense sp. nov. is proposed. The type strain is strain F-240,109(T) (=DSM 46670(T), =LMG 28181(T)).

Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov.

PubMed

Busarakam, Kanungnid; Brown, Ros; Bull, Alan T; Tan, Geok Yuan Annie; Zucchi, Tiago D; da Silva, Leonardo José; de Souza, Wallace Rafael; Goodfellow, Michael

2016-02-01

The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).

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.

Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada

PubMed Central

Yu, Xiumei; Cloutier, Sylvie; Tambong, James T.

2014-01-01

Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium. To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230T. Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA–DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain OO99T elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99T ( = LMG 26739T = HAMBI 3284T) as the type strain. The DNA G+C content is 62.6 mol%. PMID:24969302

A plea for geometrical order in tectonics

NASA Astrophysics Data System (ADS)

Schmid, Stefan

2017-04-01

Ever since publishing his landmark book "Folding and Fracturing of Rocks" 50 years ago John G. Ramsay (Ramsay 1967) has fascinated many of us with his stringent mathematical-geometrical approach towards analyzing finite strain in rocks, in particular what the geometry and kinematics of folding are concerned. The figures in this early book, as well as John's drawings and photographs published in later books and articles, undoubtedly also impressed many of us by their sheer aesthetic value. This book and his later work conveyed the message that rock deformation behaves in an "orderly" way, a message that is shared by many, but not all, of John's colleagues in structural geology and tectonics. This contribution is a plea for careful structural analysis and extensive fieldwork, providing the indispensable base in any attempt to go further and also understand the physics of rock deformation and geological processes at all scales. Two large-scale examples will be discussed in this respect: (1) The problem of mélanges in an ophiolite-bearing unit of the Swiss Alps (Arosa Zone) showing that careful structural analysis leads to the view that such chaotic mélanges were postulated by some authors in the absence of a carful structural analysis, and that the geometry in fact is a result of polyphase deformation, and (2) the problem of orogen scale transects of across the Alps that reflect an amazing degree of order in the stacking of diverse paleogeographical units enabling geometrical-kinematic attempts of retrodeformation and contrasting with alternative and rather "chaotic" views. Reference: Ramsay, J.G. 1967: Folding and Fracturing of Rocks. McGraw-Hill New York, 568pp.

Fontibacillus aquaticus gen. nov., sp. nov., isolated from a warm spring.

PubMed

Saha, P; Krishnamurthi, S; Bhattacharya, A; Sharma, R; Chakrabarti, T

2010-02-01

A novel facultatively anaerobic strain, designated GPTSA 19(T), was isolated from a warm spring and characterized using a polyphasic approach. The strain behaved as Gram-negative in the Gram staining procedure but showed a Gram-positive reaction in the aminopeptidase test. The novel strain was a mesophilic rod with ellipsoidal endospores. On the basis of 16S rRNA gene sequence analysis, the strain showed closest similarity (96.0 %) with Paenibacillus motobuensis MC10(T). The gene sequence similarity of the novel strain with other species of the genus Paenibacillus was <95.8 %. The novel strain also had PAEN 515F and 682F signature sequence stretches in the 16S rRNA gene that are usually found in most species of the genus Paenibacillus. The strain possessed anteiso-C(15 : 0) as the major fatty acid and MK-7 as the predominant menaquinone. Polar lipids included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), six unknown phospholipids (PLs), one aminophospholipid (PN), three glycolipids (GLs), two aminolipids (ALs), one aminophosphoglycolipid (APGL) and three unknown lipids (ULs). The polar lipid profile of the novel strain, especially as regards ALs, GLs and PLs, distinguished it from the recognized type species of the genus Paenibacillus, Paenibacillus polymyxa, as well as from its closest relative P. motobuensis. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the new strain merits the rank of a novel genus for which the name Fontibacillus gen. nov. is proposed. The type species of the new genus is Fontibacillus aquaticus gen. nov., sp. nov. with the type strain GPTSA 19(T) (=MTCC 7155(T)=DSM 17643(T)).

Biodiversity of mycobiota throughout the Brazil nut supply chain: From rainforest to consumer.

PubMed

Taniwaki, Marta H; Frisvad, Jens C; Ferranti, Larissa S; de Souza Lopes, Aline; Larsen, Thomas O; Fungaro, Maria Helena P; Iamanaka, Beatriz T

2017-02-01

A total of 172 Brazil nut samples (114 in shell and 58 shelled) from the Amazon rainforest region and São Paulo state, Brazil was collected at different stages of the Brazil nut production chain: rainforest, street markets, processing plants and supermarkets. The mycobiota of the Brazil nut samples were evaluated and also compared in relation to water activity. A huge diversity of Aspergillus and Penicillium species were found, besides Eurotium spp., Zygomycetes and dematiaceous fungi. A polyphasic approach using morphological and physiological characteristics, as well as molecular and extrolite profiles, were studied to distinguish species among the more important toxigenic ones in Aspergillus section Flavi and A. section Nigri. Several metabolites and toxins were found in these two sections. Ochratoxin A (OTA) was found in 3% of A. niger and 100% of A. carbonarius. Production of aflatoxins B and G were found in all isolates of A. arachidicola, A. bombycis, A. nomius, A. pseudocaelatus and A. pseudonomius, while aflatoxin B was found in 38% of A. flavus and all isolates of A. pseudotamarii. Cyclopiazonic acid (CPA) was found in A. bertholletius (94%), A. tamarii (100%), A. caelatus (54%) and A. flavus (41%). Tenuazonic acid, a toxin commonly found in Alternaria species was produced by A. bertholletius (47%), A. caelatus (77%), A. nomius (55%), A. pseudonomius (75%), A. arachidicola (50%) and A. bombycis (100%). This work shows the changes of Brazil nut mycobiota and the potential of mycotoxin production from rainforest to consumer, considering the different environments which exist until the nuts are consumed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nonomuraea glycinis sp. nov., a novel actinomycete isolated from the root of black soya bean [Glycine max (L.) Merr].

PubMed

Li, Zhilei; Song, Wei; Zhao, Junwei; Zhuang, Xiaoxin; Zhao, Yue; Wang, Xiangjing; Xiang, Wensheng

2017-12-01

A novel actinomycete, designated strain NEAU-BB2C19 T , was isolated from the root of black soya bean [Glycine max (L.) Merr] collected from Harbin, Heilongjiang Province, China, and characterized using a polyphasic approach. The strain was an aerobic, Gram-stain-positive actinomycete that formed extensively branched substrate mycelium and aerial hyphae. The predominant menaquinones were MK-9(H2) and MK-9(H0). The major cellular fatty acid profile consisted of iso-C16 : 0, 10-methyl C17 : 0 and 10-methyl C18 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylglycerol and glycolipid. The DNA G+C content was 68.2±0.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-BB2C19 T should be assigned to the genus Nonomuraea and formed a distinct branch with its closest neighbour Nonomuraea guangzhouensis NEAU-ZJ3 T (98.75 % 16S rRNA gene sequence similarity). The morphological and chemotaxonomic properties of the strain were also consistent with those of members of the genus Nonomuraea. A combination of DNA-DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-BB2C19 T could be clearly differentiated from its closest phylogenetic relative. Thus, the strain is concluded to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea glycinis sp. nov. is proposed. The type strain is NEAU-BB2C19 T (=CGMCC 4.7430 T =DSM 104838 T ).

Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees.

PubMed

Degefu, Tulu; Wolde-Meskel, Endalkachew; Liu, Binbin; Cleenwerck, Ilse; Willems, Anne; Frostegård, Åsa

2013-05-01

A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.

A description of the lactic acid bacteria microbiota associated with the production of traditional fermented vegetables in Vietnam.

PubMed

Nguyen, Doan Thi Lam; Van Hoorde, Koenraad; Cnockaert, Margo; De Brandt, Evie; Aerts, Maarten; Binh Thanh, Le; Vandamme, Peter

2013-04-15

An important part of the daily nourishment in Vietnam constitutes of fermented vegetables. Bacteria and especially lactic acid bacteria play a central role in the production of many fermented vegetables. The current study was conducted to investigate the diversity of native lactic acid bacteria (LAB) populations in 'dua muoi' (mustard and beet fermentation) and 'ca muoi' (eggplant fermentation), three types of popular traditional fermented vegetables of Vietnamese origin. To this end a polyphasic approach combining matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and pheS gene sequence analysis was used. In addition, denaturing gradient gel electrophoresis was performed as a culture-independent method to complement the observed culturable diversity data. A total of 881 LAB isolates were recovered from 21 different samples. Predominant LAB associated with 'dua muoi' and 'ca muoi' were identified as Lactobacillus fermentum (56.6%), Lactobacillus pentosus (24.4%) and Lactobacillus plantarum (17.1%). Less abundant species were Pediococcus pentosaceus (1.0%) and Lactobacillus brevis (0.5%). Species present less than 0.1% included Lactobacillus paracasei, Lactobacillus pantheris and Pediococcus acidilactici. In contrast to fermented mustard and beet with the highest prevalence of L. fermentum, the species most recovered from fermented eggplant samples was L. pentosus. In addition, an important degree of genetic variability within the different predominant species was observed and strain dependency correlating with the type of fermented vegetable or location of production could be demonstrated using multivariate statistics. This research gives an extensive and detailed inventory of the LAB diversity associated with the production of diverse Vietnamese fermented vegetables and demonstrates the influence of type of raw material and/or production location and conditions on this diversity. Copyright © 2013 Elsevier B.V. All rights reserved.

Mucilaginibacter pocheonensis sp. nov., with ginsenoside-converting activity, isolated from soil of a ginseng-cultivating field.

PubMed

Zhao, Yan; Lee, Hyung-Gwan; Kim, Soo-Ki; Yu, Hongshan; Jin, Fengxie; Im, Wan-Taek

2016-09-01

A Gram-reaction-negative, aerobic, heterotrophic, non-motile, non-spore-forming, rod-shaped bacterial strain, designated Gsoil 032T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain Gsoil 032T grew at 10-42 °C and at pH 5.0-10.0 on R2A agar medium. Strain Gsoil 032T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to compound K. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 032T was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter sabulilitoris SMS-12T (97.6 % sequence similarity) and Mucilaginibacter lappiensis ANJLI2T (97.1 %) The G+C content of the genomic DNA was 44.4 mol%. The predominant respiratory quinone was menaquinone MK-7 and the major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipid detected was phosphatidylethanolamine, while the minor polar lipids were various unidentified aminophospholipids, unidentified phospholipids and unidentified polar lipids. DNA and chemotaxonomic data supported the affiliation of strain Gsoil 032T to the genus Mucilaginibacter. Strain Gsoil 032T could be differentiated genotypically and phenotypically from recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter pocheonensis sp. nov. is proposed, with the type strain Gsoil 032T (=KCTC 12641T=LMG 23495T).

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.

Sphingopyxis italica sp. nov., isolated from Roman catacombs.

PubMed

Alias-Villegas, Cynthia; Jurado, Valme; Laiz, Leonila; Saiz-Jimenez, Cesareo

2013-07-01

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71(T), was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71(T) belongs to the genus Sphingopyxis, and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889(T) (98.72 %), Sphingopyxis taejonensis DSM 15583(T) (98.65 %), Sphingopyxis ginsengisoli LMG 23390(T) (98.16 %), Sphingopyxis panaciterrae KCTC 12580(T) (98.09 %), Sphingopyxis alaskensis DSM 13593(T) (98.09 %), Sphingopyxis witflariensis DSM 14551(T) (98.09 %), Sphingopyxis bauzanensis DSM 22271(T) (98.02 %), Sphingopyxis granuli KCTC 12209(T) (97.73 %), Sphingopyxis macrogoltabida KACC 10927(T) (97.49 %), Sphingopyxis ummariensis DSM 24316(T) (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112(T) (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis. However, a polyphasic approach using physiological tests, DNA base ratios, DNA-DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71(T) belongs to a novel species within the genus Sphingopyxis, for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71(T) ( = DSM 25229(T) = CECT 8016(T)).

Impact of thistle rennet from Carlina acanthifolia All. subsp. acanthifolia on bacterial diversity and dynamics of a specialty Italian raw ewes' milk cheese.

PubMed

Cardinali, Federica; Osimani, Andrea; Taccari, Manuela; Milanović, Vesna; Garofalo, Cristiana; Clementi, Francesca; Polverigiani, Serena; Zitti, Silvia; Raffaelli, Nadia; Mozzon, Massimo; Foligni, Roberta; Franciosi, Elena; Tuohy, Kieran; Aquilanti, Lucia

2017-08-16

Caciofiore della Sibilla is an Italian specialty soft cheese manufactured with Sopravissana raw ewes' milk and thistle rennet prepared with young fresh leaves and stems of Carlina acanthifolia All. subsp. acanthifolia, according to an ancient tradition deeply rooted in the territory of origin (mountainous hinterland of the Marche region, Central Italy). In this study, the impact of thistle rennet on the bacterial dynamics and diversity of Caciofiore della Sibilla cheese was investigated by applying a polyphasic approach based on culture and DNA-based techniques (Illumina sequencing and PCR-DGGE). A control cheese manufactured with the same batch of ewes' raw milk and commercial animal rennet was analyzed in parallel. Overall, a large number of bacterial taxa were identified, including spoilage, environmental and pro-technological bacteria, primarily ascribed to Lactobacillales. Thistle rennet was observed clearly to affect the early bacterial dynamics of Caciofiore della Sibilla cheese with Lactobacillus alimentarius/paralimentarius and Lactobacillus plantarum/paraplantarum/pentosus being detected in the phyllosphere of C. acanthifolia All., thistle rennet and curd obtained with thistle rennet. Other bacterial taxa, hypothetically originating from the vegetable coagulant (Enterococcus faecium, Lactobacillus brevis, Lactobacillus delbrueckii, Leuconostoc mesenteroides/pseudomesenteroides), were exclusively found in Caciofiore della Sibilla cheese by PCR-DGGE. At the end of the maturation period, Illumina sequencing demonstrated that both cheeses were dominated by Lactobacillales; however curd and cheese produced with thistle rennet were co-dominated by Lactobacillus and Leuconostoc, whereas Lactoccous prevailed in curd and cheese produced with commercial animal rennet followed by Lactobacillus. Differences in the bacterial composition between the two cheeses at the end of their maturation period were confirmed by PCR-DGGE analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).

PubMed

Ma, Zhaoxu; Zhao, Shanshan; Cao, Tingting; Liu, Chongxi; Huang, Ying; Gao, Yuhang; Yan, Kai; Xiang, Wensheng; Wang, Xiangjing

2016-12-01

A novel actinobacterium, designated strain NEAU-QY3T, was isolated from the leaves of Sonchus oleraceus L. and examined using a polyphasic taxonomic approach. The organism formed single spores with smooth surface on substrate mycelia. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain had a close association with the genus Verrucosispora and shared the highest sequence similarity with Verrucosispora qiuiae RtIII47T (99.17 %), an association that was supported by a bootstrap value of 94 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. The strain also showed high 16S rRNA gene sequence similarities to Xiangella phaseoli NEAU-J5T (98.78 %), Jishengella endophytica 202201T (98.51 %), Micromonospora eburnea LK2-10T (98.28 %), Verrucosispora lutea YIM 013T (98.23 %) and Salinispora pacifica CNR-114T (98.23 %). Furthermore, phylogenetic analysis based on the gyrB gene sequences supported the conclusion that strain NEAU-QY3T should be assigned to the genus Verrucosispora. However, the DNA-DNA hybridization relatedness values between strain NEAU-QY3T and V. qiuiae RtIII47T and V. lutea YIM 013T were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA-DNA hybridization results, strain NEAU-QY3T was readily distinguished from its most closely related strains and classified as a new species, for which the name Verrucosispora sonchi sp. nov. is proposed. The type strain is NEAU-QY3T (=CGMCC 4.7312T=DSM 101530T).

Bacillus kyonggiensis sp. nov., isolated from soil of a lettuce field.

PubMed

Dong, Ke; Lee, Sangseob

2011-10-01

A Gram-positive, rod-shaped, motile, endospore-forming bacterial strain, designated NB22(T), was isolated from soil of a lettuce field in Kyonggi province, South Korea, and was characterized by using a polyphasic taxonomic approach. This novel isolate grew optimally at 30-37°C and pH 8-9. It grew in the presence of 0-4% NaCl (optimum, 1-2%). Comparative 16S rRNA gene sequence analysis showed that strain NB22(T) was closely related to members of the genus Bacillus and fell within a coherent cluster comprising B. siralis 171544(T) (98.1%) and B. korlensis ZLC-26(T) (97.3%). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.4%. Strain NB22(T) had a genomic DNA G+C content of 36.3 mol% and the predominant respiratory quinone was MK-7. The peptidoglycan contained meso-diaminopimelic acid. The major cellular fatty acids were iso-C(15:0), anteiso-C(15:0), C(14:0), and C(16:0). These chemotaxonomic results supported the affiliation of strain NB22(T) to the genus Bacillus, and the low DNA-DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain NB22(T) from recognized Bacillus species. On the basis of the evidence presented, strain NB22(T) is considered to represent a novel species of the genus Bacillus, for which the name Bacillus kyonggiensis sp. nov. is proposed. The type strain is NB22(T) (=KEMB 5401-267(T) =JCM 17569(T)).

Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant.

PubMed

Srinivasan, Sathiyaraj; Park, Giho; Yang, Hyejin; Hwang, Supyong; Bae, Yoonjung; Jung, Yong-An; Kim, Myung Kyum; Lee, Myungjin

2012-11-01

A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32(T)) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32(T). Strain MJ32(T) showed highest 16S rRNA gene sequence similarity to Gordonia hirsuta DSM 44140(T) (98.1%) and Gordonia hydrophobica DSM 44015(T) (97.0%); levels of sequence similarity to the type strains of other recognized Gordonia species were less than 97.0%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32(T) belonged to the clade formed by members of the genus Gordonia in the family Gordoniaceae. The G+C content of the genomic DNA of strain MJ32(T) was 69.2 mol%. Chemotaxonomically, strain MJ32(T) showed features typical of the genus Gordonia. The predominant respiratory quinone was MK-9(H(2)), the mycolic acids present had C(56)-C(60) carbon atoms, and the major fatty acids were C(16:0) (34.6%), tuberculostearic acid (21.8%), C(16:1)ω7c (19.5%) and C(18:1)ω9c (12.7%). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32(T) is considered to represent a novel species of the genus Gordonia, for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32(T) (=KCTC 19771(T)=JCM 16923(T)).

Phylogenomic and MALDI-TOF MS Analysis of Streptococcus sinensis HKU4T Reveals a Distinct Phylogenetic Clade in the Genus Streptococcus

PubMed Central

Tse, Herman; Chen, Jonathan H.K.; Tang, Ying; Lau, Susanna K.P.; Woo, Patrick C.Y.

2014-01-01

Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. PMID:25331233

Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus.

PubMed

Teng, Jade L L; Huang, Yi; Tse, Herman; Chen, Jonathan H K; Tang, Ying; Lau, Susanna K P; Woo, Patrick C Y

2014-10-20

Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the "sanguinis group." As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the "mitis group." On the basis of the findings, we propose a novel group, named "sinensis group," to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Cell delivery in regenerative medicine: the cell sheet engineering approach.

PubMed

Yang, Joseph; Yamato, Masayuki; Nishida, Kohji; Ohki, Takeshi; Kanzaki, Masato; Sekine, Hidekazu; Shimizu, Tatsuya; Okano, Teruo

2006-11-28

Recently, cell-based therapies have developed as a foundation for regenerative medicine. General approaches for cell delivery have thus far involved the use of direct injection of single cell suspensions into the target tissues. Additionally, tissue engineering with the general paradigm of seeding cells into biodegradable scaffolds has also evolved as a method for the reconstruction of various tissues and organs. With success in clinical trials, regenerative therapies using these approaches have therefore garnered significant interest and attention. As a novel alternative, we have developed cell sheet engineering using temperature-responsive culture dishes, which allows for the non-invasive harvest of cultured cells as intact sheets along with their deposited extracellular matrix. Using this approach, cell sheets can be directly transplanted to host tissues without the use of scaffolding or carrier materials, or used to create in vitro tissue constructs via the layering of individual cell sheets. In addition to simple transplantation, cell sheet engineered constructs have also been applied for alternative therapies such as endoscopic transplantation, combinatorial tissue reconstruction, and polysurgery to overcome limitations of regenerative therapies and cell delivery using conventional approaches.

Genomic taxonomy of vibrios

PubMed Central

Thompson, Cristiane C; Vicente, Ana Carolina P; Souza, Rangel C; Vasconcelos, Ana Tereza R; Vesth, Tammi; Alves, Nelson; Ussery, David W; Iida, Tetsuya; Thompson, Fabiano L

2009-01-01

Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding. PMID:19860885

Single-cell analysis of radiotracers' uptake by fluorescence microscopy: direct and droplet approach

NASA Astrophysics Data System (ADS)

Gallina, M. E.; Kim, T. J.; Vasquez, J.; Tuerkcan, S.; Abbyad, P.; Pratx, G.

2017-02-01

Radionuclides are used for sensitive and specific detection of small molecules in vivo and in vitro. Recently, radioluminescence microscopy extended their use to single-cell studies. Here we propose a new single-cell radioisotopic assay that improves throughput while adding sorting capabilities. The new method uses fluorescence-based sensor for revealing single-cell interactions with radioactive molecular markers. This study focuses on comparing two different experimental approaches. Several probes were tested and Dihydrorhodamine 123 was selected as the best compromise between sensitivity, brightness and stability. The sensor was incorporated either directly within the cell cytoplasm (direct approach), or it was coencapsulated with radiolabeled single-cells in oil-dispersed water droplets (droplet approach). Both approaches successfully activated the fluorescence signal following cellular uptake of 18F-fluorodeoxyglucose (FDG) and external Xrays exposure. The direct approach offered single-cell resolution and longtime stability ( > 20 hours), moreover it could discriminate FDG uptake at labelling concentration as low as 300 μCi/ml. In cells incubated with Dihydrorhodamine 123 after exposure to high radiation doses (8-16 Gy), the fluorescence signal was found to increase with the depletion of ROS quenchers. On the other side, the droplet approach required higher labelling concentrations (1.00 mCi/ml), and, at the current state of art, three cells per droplet are necessary to produce a fluorescent signal. This approach, however, is independent on cellular oxidative stress and, with further improvements, will be more suitable for studying heterogeneous populations. We anticipate this technology to pave the way for the analysis of single-cell interactions with radiomarkers by radiofluorogenic-activated single-cell sorting.

Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data.

PubMed

Tektonidis, Marco; Kim, Il-Han; Chen, Yi-Chun M; Eils, Roland; Spector, David L; Rohr, Karl

2015-01-01

The analysis of the motion of subcellular particles in live cell microscopy images is essential for understanding biological processes within cells. For accurate quantification of the particle motion, compensation of the motion and deformation of the cell nucleus is required. We introduce a non-rigid multi-frame registration approach for live cell fluorescence microscopy image data. Compared to existing approaches using pairwise registration, our approach exploits information from multiple consecutive images simultaneously to improve the registration accuracy. We present three intensity-based variants of the multi-frame registration approach and we investigate two different temporal weighting schemes. The approach has been successfully applied to synthetic and live cell microscopy image sequences, and an experimental comparison with non-rigid pairwise registration has been carried out. Copyright © 2014 Elsevier B.V. All rights reserved.

A Cell-Based Approach to Early Pancreatic Cancer Detection

DTIC Science & Technology

2016-10-01

Award Number: W81XWH-15-1-0457 TITLE: A Cell -Based Approach to Early Pancreatic Cancer Detection PRINCIPAL INVESTIGATOR: Dr. Ben Stanger...SUBTITLE 5a. CONTRACT NUMBER A Cell -Based Approach to Early Pancreatic Cancer Detection 5b. GRANT NUMBER W81XWH-15-1-0457 5c. PROGRAM ELEMENT NUMBER 6...tumor cells from mouse blood by depleting the sample of white blood cells (WBCs). Furthermore, the RNA profile of these cells can be assessed by

Tuning cell adhesion by direct nanostructuring silicon into cell repulsive/adhesive patterns

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

Premnath, Priyatha, E-mail: priyatha.premnath@ryerson.ca; Tavangar, Amirhossein, E-mail: atavanga@ryerson.ca; Tan, Bo, E-mail: tanbo@ryerson.ca

2015-09-10

Developing platforms that allow tuning cell functionality through incorporating physical, chemical, or mechanical cues onto the material surfaces is one of the key challenges in research in the field of biomaterials. In this respect, various approaches have been proposed and numerous structures have been developed on a variety of materials. Most of these approaches, however, demand a multistep process or post-chemical treatment. Therefore, a simple approach would be desirable to develop bio-functionalized platforms for effectively modulating cell adhesion and consequently programming cell functionality without requiring any chemical or biological surface treatment. This study introduces a versatile yet simple laser approachmore » to structure silicon (Si) chips into cytophobic/cytophilic patterns in order to modulate cell adhesion and proliferation. These patterns are fabricated on platforms through direct laser processing of Si substrates, which renders a desired computer-generated configuration into patterns. We investigate the morphology, chemistry, and wettability of the platform surfaces. Subsequently, we study the functionality of the fabricated platforms on modulating cervical cancer cells (HeLa) behaviour. The results from in vitro studies suggest that the nanostructures efficiently repel HeLa cells and drive them to migrate onto untreated sites. The study of the morphology of the cells reveals that cells evade the cytophobic area by bending and changing direction. Additionally, cell patterning, cell directionality, cell channelling, and cell trapping are achieved by developing different platforms with specific patterns. The flexibility and controllability of this approach to effectively structure Si substrates to cell-repulsive and cell-adhesive patterns offer perceptible outlook for developing bio-functionalized platforms for a variety of biomedical devices. Moreover, this approach could pave the way for developing anti-cancer platforms that selectively repel cancer cells while favoring the adhesion of normal cells. - Highlights: • Si platforms with cytophobic/philic patterns were developed to program cell growth. • Both nanotopography and chemistry contributed to the cytophobic property. • Cytophobic zones efficiently repel and drive HeLa cells to migrate to adhesive sites. • The approach enables cell patterning, directionality, channelling, and trapping. • This approach paves the way for developing anti-cancer platforms.« less