Antonie van Leeuwenhoek (Antonie Leeuwenhoek)

Publications in this journal

• Article: Identification of the rhizobial symbiont of Astragalus glombiformis in Eastern Morocco as Mesorhizobium camelthorni.

  Kamal Guerrouj, Eduardo Pérez-Valera, Rajaa Chahboune, Hanaa Abdelmoumen, Eulogio J Bedmar, Mustapha Missbah El Idrissi
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  ABSTRACT: Astragalus gombiformis is a desert symbiotic nitrogen-fixing legume of great nutritional value as fodder for camels and goats. However, there are no data published on the rhizobial bacteria that nodulate this wild legume in northern Africa. Thirty-four rhizobial bacteria were isolated from root nodules of A. gombifomis grown in sandy soils of the South-Eastern of Morocco. Twenty-five isolates were able to renodulate their original host and possessed a nodC gene copy. The phenotypic and genotypic characterizations carried out illustrated the diversity of the isolates. Phenotypic analysis showed that isolates used a great number of carbohydrates as sole carbon source. However, although they were isolated from arid sandy soils, the isolates do not tolerate drought stress applied in vitro. The phenotypic diversity corresponded mainly to the diversity in the use of some carbohydrates. The genetic analysis as assessed by repetitive extragenic palindromic (REP)-polymerase chain reaction (PCR) showed that the isolates clustered into 3 groups at a similarity coefficient of 81 %. The nearly-complete 16S rRNA gene sequence from a representative strain of each PCR-group showed they were closely related to members of the genus Mesorhizobium of the family Phyllobactericeae within the Alphaproteobacteria. Sequencing of the housekeeping genes atpD, glnII and recA, and their concatenated phylogenetic analysis, showed they are closely related to Mesorhizobium camelthorni. Sequencing of the symbiotic nodC gene from each strain revealed they had 83.53 % identity with the nodC sequence of the type strain M. camelthorni CCNWXJ 40-4(T.)
  Antonie van Leeuwenhoek 05/2013;
• Article: Jejudonia soesokkakensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the junction between the ocean and a freshwater spring, and emended description of the genus Aureitalea Park et al. 2012.

  Sooyeon Park, Jung-Sook Lee, Kenu-Chul Lee, Jung-Hoon Yoon
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  ABSTRACT: A Gram-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated SSK1-1(T), was isolated from the junction between the ocean and a freshwater spring at Jeju island of South Korea. Strain SSK1-1(T) was found to grow optimally at 30 °C, at pH 7.0-7.5 and in the presence of 2 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK1-1(T) is phylogenetically most closely related to members of the genera Ulvibacter and Aureitalea, with which it exhibited 16S rRNA gene sequence similarities of 93.1-95.3 %. The results of chemotaxonomic analyses distinguish strain SSK1-1(T) from the genera Ulvibacter and Aureitalea. Strain SSK1-1(T) was determined to contain MK-6 as the predominant menaquinone and iso-C15:0, anteiso-C15:0 and iso-C16:0 as the major fatty acids. The major polar lipids of strain SSK1-1(T) were identified as phosphatidylethanolamine and one unidentified lipid. The DNA G + C content of strain SSK1-1(T) was determined to be 39.9 mol%. The phylogenetic analysis, chemotaxonomic data and other phenotypic properties revealed that the strain SSK1-1(T) can be distinguished from the members of previously known genera of the family Flavobacteriaceae. On the basis of the data presented, strain SSK1-1(T) is considered to represent a novel genus and species, for which the name Jejudonia soesokkakensis gen. nov., sp. nov. is proposed. The type strain is SSK1-1(T) (=KCTC 32325(T) = CCUG 63830(T)). An emended description of the genus Aureitalea is also proposed.
  Antonie van Leeuwenhoek 05/2013;
• Article: Small chromosomes among Danish Candida glabrata isolates originated through different mechanisms.

  Khadija Mohamed Ahmad, Olena P Ishchuk, Linda Hellborg, Gloria Jørgensen, Miha Skvarc, Jørgen Stenderup, Dorte Jørck-Ramberg, Silvia Polakova, Jure Piškur
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  ABSTRACT: We analyzed 192 strains of the pathogenic yeast Candida glabrata from patients, mainly suffering from systemic infection, at Danish hospitals during 1985-1999. Our analysis showed that these strains were closely related but exhibited large karyotype polymorphism. Nine strains contained small chromosomes, which were smaller than 0.5 Mb. Regarding the year, patient and hospital, these C. glabrata strains had independent origin and the analyzed small chromosomes were structurally not related to each other (i.e. they contained different sets of genes). We suggest that at least two mechanisms could participate in their origin: (i) through a segmental duplication which covered the centromeric region, or (ii) by a translocation event moving a larger chromosome arm to another chromosome that leaves the centromere part with the shorter arm. The first type of small chromosomes carrying duplicated genes exhibited mitotic instability, while the second type, which contained the corresponding genes in only one copy in the genome, was mitotically stable. Apparently, in patients C. glabrata chromosomes are frequently reshuffled resulting in new genetic configurations, including appearance of small chromosomes, and some of these resulting "mutant" strains can have increased fitness in a certain patient "environment".
  Antonie van Leeuwenhoek 05/2013;
• Article: Isolation and characterization of novel ginsenoside-hydrolyzing glycosidase from Microbacterium esteraromaticum that transforms ginsenoside Rb2 to rare ginsenoside 20(S)-Rg3.

  Lin-Hu Quan, Chao Wang, Yan Jin, Ting-Rui Wang, Yeon-Ju Kim, Deok Chun Yang
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  ABSTRACT: Ginsenoside Rb2 was transformed by recombinant glycosidase (Bgp2) into ginsenosides Rd and 20(S)-Rg3. The bgp2 gene consists of 2,430 bp that encode 809 amino acids, and this gene has homology to the glycosyl hydrolase family 2 protein domain. SDS-PAGE was used to determine that the molecular mass of purified Bgp2 was 87 kDa. Using 0.1 mg ml(-1) of enzyme in 20 mM sodium phosphate buffer at 40 °C and pH 7.0, 1.0 mg ml(-1) ginsenoside Rb2 was transformed into 0.47 mg ml(-1) ginsenoside 20(S)-Rg3 within 120 min, with a corresponding molar conversion yield of 65 %. Bgp2 hydrolyzed the ginsenoside Rb2 along the following pathway: Rb2 → Rd → 20(S)-Rg3. This is the first report of the biotransformation of ginsenoside Rb2 to ginsenoside 20(S)-Rg3 using the recombinant glycosidase.
  Antonie van Leeuwenhoek 05/2013;
• Article: Paracoccus zhejiangensis sp. nov., isolated from activated sludge in wastewater-treatment system.

  Zhi-Guo Wu, Dao-Feng Zhang, Ya-Long Liu, Fang Wang, Xin Jiang, Chao Li, Shun-Peng Li, Qing Hong, Wen-Jun Li
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  ABSTRACT: A bacterial strain, designated J6(T), was isolated from activated sludge, collected from a chemical wastewater treatment system in Zhejiang Province of China. The cells stained Gram-negative, were aerobic, pale-yellow, and non-motile short rods. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the closest relative of this organism was Paracoccus aminophilus KACC 12262(T) = JCM 7686(T) (97.4 % sequence similarity). Strain J6(T) grew at 10-37 °C (optimum 30 °C), at pH 6.0-8.0 (optimum pH 7.0) and with 0-5 % NaCl (optimum 3 %, w/v). The predominant cellular fatty acid found was summed feature 8(C18:1 ω7c and/or C18:1 ω6c; 82.8 %). The major respiratory quinone-detected was Q-10 and the DNA G+C content was 61.9 mol %. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and several unknown polar lipids. Strain J6(T) showed low DNA-DNA relatedness values with P. aminophilus KACC 12262(T) (28 ± 3 %). The phylogenetic analysis, DNA-DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics allowed clear differentiation of the isolate from the other type strains of already described Paracoccus species. It is evident from the genotypic, phenotypic and chemotaxonomic analyses that strain J6(T) should be classified as a novel species of the genus Paracoccus, for which the name P. zhejiangensis sp. nov. is proposed. The type strain is J6(T) (KACC 16703(T) = CCTCC AB 2012031(T)).
  Antonie van Leeuwenhoek 05/2013;
• Article: Microlunatus cavernae sp. nov., a novel actinobacterium isolated from Alu ancient cave, Yunnan, south-west China.

  Juan Cheng, Wei Chen, Bing Huo-Zhang, Salam Nimaichand, En-Min Zhou, Xin-Hua Lu, Hans-Peter Klenk, Wen-Jun Li
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  ABSTRACT: A Gram-positive, coccoid, non-endospore-forming actinobacterium, designated YIM C01117(T), was isolated from a soil sample collected from Alu ancient cave, Yunnan province, south-west China. Based on the 16S rRNA gene sequence analysis, strain YIM C01117(T) was shown to belong to the genus Microlunatus, with highest sequence similarity of 97.4 % to Microlunatus soli DSM 21800(T). The whole genomic DNA relatedness as shown by the DNA-DNA hybridization study between YIM C01117(T) and M. soli DSM 21800(T) had a low value (47 ± 2 %). Strain YIM C01117(T) was determined to contain LL-diaminopimelic acid with Gly, Glu and Ala amino acids (A3γ' type) in the cell wall. Whole-cell hydrolysates were found to contain glucose, galactose, mannose and ribose. The major polar lipids were determined to be phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinone system present is MK-9(H4), while the major fatty acids were identified to be anteiso-C15:0 (24.1 %), iso-C16:0 (22.3 %) and iso-C15:0 (11.4 %). The G+C content of the genomic DNA was determined to be 65.9 mol%. The chemotaxonomic and genotypic data support the affiliation of the strain YIM C01117(T) to the genus Microlunatus. The results of physiological and biochemical tests allow strain YIM C01117(T) to be differentiated phenotypically from recognized Microlunatus species. Strain YIM C01117(T) is therefore considered to represent a novel species of the genus Microlunatus, for which the name Microlunatus cavernae sp. nov. is proposed. The type strain is YIM C01117(T) (= DSM 26248(T) = JCM 18536(T)).
  Antonie van Leeuwenhoek 05/2013;
• Article: Cryptococcus lacticolor sp. nov. and Rhodotorula oligophaga sp. nov., novel yeasts isolated from the nasal smear microbiota of Queensland koalas kept in Japanese zoological parks.

  Kazuo Satoh, Mari Maeda, Yoshiko Umeda, Miho Sugamata, Koichi Makimura
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  ABSTRACT: A total of 515 yeast strains were isolated from the nasal smears of Queensland koalas and their breeding environments in Japanese zoological parks between 2005 and 2012. The most frequent species in the basidiomycetous yeast biota isolated from koala nasal passages was Cryptococcus neoformans, followed by Rhodotorula minuta. R. minuta was the most frequent species in the breeding environments, while C. neoformans was rare. Seven strains representing two novel yeast species were identified. Analyses of the 26S rDNA (LSU) D1/D2 domain and nuclear ribosomal DNA internal transcribed spacer region sequences indicated that these strains represent new species with close phylogenetic relationships to Cryptococcus and Rhodotorula. A sexual state was not found for either of these two novel yeasts. Key phenotypic characters confirmed that these strains could be placed in Cryptococcus and Rhodotorula. The names Cryptococcus lacticolor sp. nov. (type strain TIMM 10013(T) = JCM 15449(T) = CBS 10915(T) = DSM 21093(T), DDBJ/EMBL/Genbank Accession No.; AB375774 (ITS) and AB375775 (26S rDNA D1/D2 region), MycoBank ID; MB 802688, Fungal Barcoding Database ID; 3174), and Rhodotorula oligophaga sp. nov. (type strain TIMM 10017(T) = JCM 18398(T) = CBS 12623(T) = DSM 25814(T), DDBJ/EMBL/Genbank Accession No.; AB702967 (ITS) and AB702967 (26S rDNA D1/D2 region), MycoBank ID; MB 802689, Fungal Barcoding Database ID; 3175) are proposed for these new species.
  Antonie van Leeuwenhoek 05/2013;
• Article: Characterisation of the first actinobacterial group isolated from a Mexican extremophile environment.

  Erika T Quintana, Ricardo Flores Badillo, Luis A Maldonado
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  ABSTRACT: The "Cave of Crystals" (aka 'Naica') in Chihuahua Mexico is a natural unique subterranean ecosystem which mainly consists of crystals made of calcium sulfate. The main system of caves are found at a depth of 300 meters (m) below sea level with crystals that range in size from a few centimeters to 15 m. The crystals date from nearly 400,000 years old and are thought to be formed when the cave was fully covered by water. At present time, this place shows a nearly constant temperature of 55 °C over the year and a humidity of 100 % which makes this place incomparable and unbearable to animal and/or human life. In the present study, two actinobacterial groups were isolated from within this system of caves and subjected to a systematic study to establish their phylogenetic relationship to microorganisms belonging to this vast group of Gram positive bacteria. Phenotypic properties, chemotaxonomic and 16S rRNA gene sequencing show that the microorganisms are members of the family Pseudonocardiaceae and are most closely related to the genus Prauserella. The present study is the first to report the isolation and presence of Actinobacteria or any other microbial form of life in this exceptional place. Moreover, this unexpected biodiversity can also provide an insight of the antibiotic resistome present in the isolates reported in this study.
  Antonie van Leeuwenhoek 05/2013;
• Article: An integrated study reveals diverse methanogens, Thaumarchaeota, and yet-uncultivated archaeal lineages in Armenian hot springs.

  Brian P Hedlund, Jeremy A Dodsworth, Jessica K Cole, Hovik H Panosyan
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  ABSTRACT: Culture-independent and enrichment techniques, with an emphasis on members of the Archaea, were used to determine the composition and structure of microbial communities inhabiting microbial mats in the source pools of two geothermal springs near the towns of Arzakan and Jermuk in Armenia. Amplification of small-subunit rRNA genes using "universal" primers followed by pyrosequencing (pyrotags) revealed highly diverse microbial communities in both springs, with >99 % of pyrosequences corresponding to members of the domain Bacteria. The spring in Arzakan was colonized by a photosynthetic mat dominated by Cyanobacteria, in addition to Proteobacteria, Bacteroidetes, Chloroflexi, Spirochaeta and a diversity of other Bacteria. The spring in Jermuk was colonized by phylotypes related to sulfur, iron, and hydrogen chemolithotrophs in the Betaproteobacteria and Epsilonproteobacteria, along with a diversity of other Bacteria. Analysis of near full-length small subunit rRNA genes amplified using Archaea-specific primers showed that both springs are inhabited by a diversity of methanogens, including Methanomicrobiales and Methanosarcinales and relatives of Methanomassiliicoccus luminyensis, close relatives of the ammonia-oxidizing archaeon (AOA) "Candidatus Nitrososphaera gargensis", and the yet-uncultivated Miscellaneous Crenarchaeotal Group and Deep Hydrothermal Vent Crenarchaeota group 1. Methanogenic enrichments confirmed the predicted physiological diversity, revealing methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis at 45 and 55 °C, but not 65 °C. This is one of only a few studies combining cultivation-independent and -dependent approaches to study archaea in moderate-temperature (37-73 °C) terrestrial geothermal environments and suggests important roles for methanogenic archaea and AOA in the carbon and nitrogen biogeochemical cycles in these environments.
  Antonie van Leeuwenhoek 04/2013;
• Article: Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov.

  Amanda L Jones, Iain C Sutcliffe, Michael Goodfellow
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  ABSTRACT: Recently we proposed that Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 be transferred to a novel genus, Prescottia, as Prescottia equi comb. nov. However, in accordance with Principle 2 and Rule 51b(4) of the Bacteriological Code (1990 Revision), the bacterial genus name Prescottia Jones et al. 2013 is deemed illegitimate as this name has been used previously for a plant genus within the family Orchidaceae. Consequently, a new genus name, Prescottella gen. nov. is proposed for the bacterial taxon and a new combination Prescottella equi comb. nov. is proposed for the type species.
  Antonie van Leeuwenhoek 04/2013;
• Article: Salinicola peritrichatus sp. nov., isolated from deep-sea sediment.

  Ying-Yi Huo, Fan-Xu Meng, Lin Xu, Chun-Sheng Wang, Xue-Wei Xu
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  ABSTRACT: A Gram stain-negative, aerobic and rod-shaped bacterium, strain DY22(T), was isolated from a deep-sea sediment collected from the east Pacific Ocean. The isolate was found to grow in the presence of 0-20.0 % (w/v) NaCl and at pH 4.5-8.5; optimum growth was observed with 0.5-2.0 % (w/v) NaCl and at pH 5.0-7.0. Chemotaxonomic analysis showed the presence of ubiquinone-9 as predominant respiratory quinone and C16:0, C19:0 ω8c cyclo and C12:0 3-OH as major cellular fatty acids. The genomic DNA G+C content was determined to be 59.6 mol%. Comparative 16S rRNA gene sequence analysis revealed that the novel isolate belongs to the genus Salinicola. Strain DY22(T) exhibited the closest phylogenetic affinity to the type strain of Salinicola salarius with 97.2 % sequence similarity and less than 97 % sequence similarity with respect to other Salinicola species with validly published names. The DNA-DNA reassociation values between strain DY22(T) and S. salarius DSM 18044(T) was 52 ± 4 %. On the basis of phenotypic, chemotaxonomic and genotypic data, strain DY22(T) represents a novel species of the genus Salinicola, for which the name Salinicola peritrichatus sp. nov. (type strain DY22(T) = CGMCC 1.12381(T) = JCM 18795(T)) is proposed.
  Antonie van Leeuwenhoek 04/2013;
• Article: Marinobacter persicus sp. nov., a moderately halophilic bacterium from a saline lake in Iran.

  Maryam Bagheri, Mohammad Ali Amoozegar, Maryam Didari, Ali Makhdoumi-Kakhki, Peter Schumann, Cathrin Spröer, Cristina Sánchez-Porro, Antonio Ventosa
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  ABSTRACT: A Gram-negative, non-endospore-forming, rod shaped, strictly aerobic, moderately halophilic bacterium, designated strain M9B(T), was isolated from the hypersaline lake Aran-Bidgol in Iran. Cells of strain M9B(T) were found to be motile and produce colonies with an orange-yellow pigment. Growth was determined to occur between 5 and 20 % (w/v) NaCl and the isolate grew optimally at 7.5-10 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were determined to be pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of 6-8 and 25-45 °C, respectively. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain M9B(T) is a member of the genus Marinobacter. The closest relative to this strain was found to be Marinobacter hydrocarbonoclasticus MBIC 1303(T) with a similarity level of 97.7 %. DNA-DNA hybridization between the novel isolate and this phylogenetically related species was 13 ± 2 %. The major cellular fatty acids of the isolate were identified as C16:0, C19:1 ω6c, C18:1 ω9c and C16:1 ω9c. The polar lipid pattern of strain M9B(T) was determined to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and three phospholipids. Ubiquinone 9 (Q-9) was the only lipoquinone detected. The G+C content of the genomic DNA of this strain was determined to be 58.6 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Marinobacter, for which the name Marinobacter persicus sp. nov. is proposed. The type strain of Marinobacter persicus is strain M9B(T) (=IBRC-M 10445(T) = CCM 7970(T) = CECT 7991(T) = KCTC 23561(T)).
  Antonie van Leeuwenhoek 04/2013;
• Article: A biochemical correlate of dimorphism in a zygomycete Benjaminiella poitrasii: characterization of purified NAD-dependent glutamate dehydrogenase, a target for antifungal agents.

  C V Joshi, E K Pathan, N S Punekar, S G Tupe, B P Kapadnis, M V Deshpande
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  ABSTRACT: The fungal organisms, especially pathogens, change their vegetative (Y, unicellular yeast and H, hypha) morphology reversibly for survival and proliferation in the host environment. NAD-dependent glutamate dehydrogenase (NAD-GDH, EC 1.4.1.2) from a non-pathogenic dimorphic zygomycete Benjaminiella poitrasii was previously reported to be an important biochemical correlate of the transition process. The enzyme was purified to homogeneity and characterized. It is a 371 kDa native molecular weight protein made up of four identical subunits. Kinetic studies showed that unlike other NAD-GDHs, it may act as an anabolic enzyme and has more affinity towards 2-oxoglutarate than L-glutamate. Chemical modifications revealed the involvement of single histidine and lysine residues in the catalytic activity of the enzyme. The phosphorylation and dephosphorylation study showed that the NAD-GDH is present in active phosphorylated form in hyphal cells of B. poitrasii. Two of the 1,2,3 triazole linked β-lactam-bile acid conjugates synthesized in the laboratory (B18, B20) were found to be potent inhibitors of purified NAD-GDH which also significantly affected Y-H transition in B. poitrasii. Furthermore, the compound B20 inhibited germ tube formation during Y-H transition in Candida albicans strains and Yarrowia lipolytica. The possible use of NAD-GDH as a target for antifungal agents is discussed.
  Antonie van Leeuwenhoek 04/2013;
• Article: Mucilaginibacter calamicampi sp. nov., a member of the family Sphingobacteriaceae isolated from soil at a field of reeds.

  Jung-Hoon Yoon, Sooyeon Park, Yong-Taek Jung
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  ABSTRACT: A Gram-negative, aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, designated WR-R1Y(T), was isolated from soil at a field of reeds in South Korea. Strain WR-R1Y(T) grew optimally at 30 °C, at pH 7.0-7.5 and in the absence of NaCl. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain WR-R1Y(T) fell within the clade comprising Mucilaginibacter species, coherently clustering with the type strain of Mucilaginibacter composti, with which it exhibited the highest 16S rRNA gene sequence similarity value of 97.6 %. Sequence similarities to the type strains of the other Mucilaginibacter species and the other species used in the phylogenetic analysis were 93.1-96.9 % and <91.1 %, respectively. Strain WR-R1Y(T) contained MK-7 as the predominant menaquinone and iso-C15:0, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:0 and iso-C17:0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified aminophospholipid. The DNA G+C content of strain WR-R1Y(T) was 43.1 mol% and its mean DNA-DNA relatedness value with M. composti KACC 14956(T) was 17 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain WR-R1Y(T) is separate from other Mucilaginibacter species. On the basis of the data presented, strain WR-R1Y(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter calamicampi sp. nov. is proposed. The type strain is WR-R1Y(T) (= KCTC 32214(T) = CCUG 63418(T)).
  Antonie van Leeuwenhoek 04/2013;
• Article: Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov.

  Mobolaji Adeolu, Radhey S Gupta
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  ABSTRACT: The species from the order Neisseriales are currently distinguished from other bacteria on the basis of branching in 16S rRNA gene trees. For this order containing a single family, Neisseriaceae, no distinctive molecular, biochemical, or phenotypic characters are presently known. We report here detailed phylogenetic and comparative analyses on the 27 genome sequenced species of the order Neisseriales. Our comparative genomic analyses have identified 54 conserved signature indels (CSIs) in widely distributed proteins that are specific for either all of the sequenced Neisseriales species or a number of clades within this order that are also supported by phylogenetic analyses. Of these CSIs, 11 are specifically present in all of the sequenced species from this order, but are not found in homologous proteins from any other bacteria. These CSIs provide novel molecular markers specific for, and delimiting, this order. Twenty-one CSIs in diverse proteins are specific for a group comprised of the genera Neisseria, Eikenella, Kingella, and Simonsiella (Clade I), which are obligate host-associated organisms, lacking flagella and exhibiting varied morphology. The species from these genera also formed a strongly supported clade in phylogenetic trees based upon concatenated protein sequences; a monophyletic grouping of these genera and other genera displaying similar morphological characteristics was also observed in the 16S rRNA gene tree. A second clade (Clade II), supported by seven of the identified CSIs and phylogenetic trees based upon concatenated protein sequences, grouped together species from the genera Chromobacterium, Laribacter, and Pseudogulbenkiania that are rod-shaped bacteria, which display flagella-based motility and are capable of free living. The remainder of the CSIs were uniquely shared by smaller groups within these two main clades. Our analyses also provide novel insights into the evolutionary history of the Neisseriales and suggest that the CSIs that are specific for the Clade I species may play an important role in the evolution of obligate host-association within this order. On the basis of phylogenetic analysis, the identified CSIs, and conserved phenotypic characteristics of different Neisseriales genera, we propose a division of this order into two families: an emended family Neisseriaceae (corresponding to Clade I) containing the genera Alysiella, Bergeriella, Conchiformibius, Eikenella, Kingella, Neisseria, Simonsiella, Stenoxybacter, Uruburuella and Vitreoscilla and a new family, Chromobacteriaceae fam. nov., harboring the remainder of the genera from this order (viz. Andreprevotia, Aquaspirillum, Aquitalea, Chitinibacter, Chitinilyticum, Chitiniphilus, Chromobacterium, Deefgea, Formivibrio, Gulbenkiania, Iodobacter, Jeongeupia, Laribacter, Leeia, Microvirgula, Paludibacterium, Pseudogulbenkiania, Silvimonas, and Vogesella).
  Antonie van Leeuwenhoek 04/2013;
• Article: Sphingomonas ginsenosidivorax sp. nov., with the ability to transform ginsenosides.

  Xue-Feng Jin, Jin-Kwang Kim, Qing-Mei Liu, Myung-Suk Kang, Dan He, Feng-Xie Jin, Sun-Chang Kim, Wan-Taek Im
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  ABSTRACT: A Gram-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain designated KHI67(T) was isolated from sediment of the Gapcheon River in South Korea and its taxonomic position was investigated by using a polyphasic approach. Strain KHI67(T) was observed to grow optimally at 25-30 °C and at pH 7.0 on nutrient and R2A agar. On the basis of 16S rRNA gene sequence similarity, strain KHI67(T) was shown to belong to the family Sphingomonadaceae and was related to Sphingomonas faeni MA-olki(T) (97.6 % sequence similarity), Sphingomonas aerolata NW12(T) (97.5 %) and Sphingomonas aurantiaca MA101b(T) (97.3 %). The G + C content of the genomic DNA was determined to be 65.6 %. The major ubiquinone was found to be Q-10, the major polyamine was identified as homospermidine and the major fatty acids identified were summed feature 8 (comprising C18:1 ω7c/ω6c; 37.0 %), C16:0 (13.0 %), summed feature 3 (comprising C16:1 ω7c/C16:1 ω6c; 12.8 %) and C14:0 2OH (9.3 %). DNA and chemotaxonomic data supported the affiliation of strain KHI67(T) to the genus Sphingomonas. The DNA-DNA relatedness values between strain KHI67(T) and its closest phylogenetic neighbours were below 15 %. Strain KHI67(T) could be differentiated genotypically and phenotypically from the recognised species of the genus Sphingomonas. The isolate therefore represents a novel species, for which the name Sphingomonas ginsenosidivorax sp. nov. is proposed, with the type strain KHI67(T) (=KACC 14951(T) = JCM 17076(T) = LMG 25801(T)).
  Antonie van Leeuwenhoek 04/2013;
• Article: Microbiology of hyper-arid environments: recent insights from the Atacama Desert, Chile.

  Alan T Bull, Juan A Asenjo
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  ABSTRACT: Interests in the Atacama Desert of northern Chile until very recently were founded on its mineral resources, notably nitrate, copper, lithium and boron. Now this vast desert, the oldest and most arid on Earth, is revealing a microbial diversity that was unimagined even a decade or so ago; indeed the extreme hyper-arid core of the Desert was considered previously to be completely devoid of life. In this Perspective article we highlight pioneering research that, to the contrary, establishes the Atacama as a combination of rich microbial habitats including bacteria that influence biogeochemical transformations in the desert and others that are propitious sources of novel natural products. Many of the Atacama's habitats are especially rich in actinobacteria, not necessarily as dense populations but extensive in taxonomic diversity and capacities to synthesize novel secondary metabolites. Among the latter, compounds have been characterized that express a range of antibiotic, anti-cancer and anti- inflammatory properties to which a variety of bioinformatics and metabolic engineering tools are being applied in order to enhance potencies and productivities. Unquestionably the Atacama Desert is a living desert with regard to which future microbiology and biotechnology research presents exciting opportunities.
  Antonie van Leeuwenhoek 04/2013;
• Article: Saccharopolyspora dendranthemae sp. nov. a halotolerant endophytic actinomycete isolated from a coastal salt marsh plant in Jiangsu, China.

  Yue-Ji Zhang, Wen-Di Zhang, Sheng Qin, Guang-Kai Bian, Ke Xing, Yun-Feng Li, Cheng-Liang Cao, Ji-Hong Jiang
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  ABSTRACT: A halotolerant actinomycete strain, designated strain KLBMP 1305(T), was isolated from a salt marsh plant Dendranthema indicum (Linn.) Des Moul collected from the coastal region of Nantong, Jiangsu Province, in east China and was studied in detail for its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain KLBMP 1305(T) is a member of the genus Saccharopolyspora. The 16S rRNA gene sequence similarity indicated that strain KLBMP 1305(T) was most closely related to 'Saccharopolyspora pathumthaniensis' S582(T) (99.31 %), 'Saccharopolyspora endophytica' YIM 61095(T) (99.17 %) and Saccharopolyspora tripterygii YIM 65359(T) (99.15 %); similarity to other type strains of the genus Saccharopolyspora was <97.2 %. The organism had chemical and morphological features consistent with its classification in the genus Saccharopolyspora such as meso-diaminopimelic acid as the diagnostic diamino acid in the cell wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The predominant menaquinone was MK-9(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown glycolipid and an unknown lipid. The major fatty acids were iso-C16:0, iso-C15:0, anteiso-C15:0, anteiso-C17:0 and sum in feature 8 (18:1ω7c/18:1ω6c). The G+C content of the genomic DNA of the type strain was 68.7 mol%. DNA-DNA relatedness data, together with phenotypic differences, clearly distinguished the isolate from its closest relatives. On the basis of these phenotypic and genotypic data, the isolate represents a novel species, for which the name Saccharopolyspora dendranthemae sp. nov. is proposed. The type strain is KLBMP 1305(T) (=KCTC 19889(T) = NBRC 108675(T)).
  Antonie van Leeuwenhoek 04/2013;
• Article: Penicillium subrubescens, a new species efficiently producing inulinase.

  S Mansouri, J Houbraken, R A Samson, J C Frisvad, M Christensen, D E Tuthill, S Koutaniemi, A Hatakka, P Lankinen
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  ABSTRACT: Inulin is a reserve carbohydrate in about 15 % of the flowering plants and is accumulated in underground tubers of e.g. chicory, dahlia and Jerusalem artichoke. This carbohydrate consists of linear chains of β-(2,1)-linked fructose attached to a sucrose molecule. Inulinases hydrolyse inulin into fructose and glucose. To find efficient inulin degrading fungi, 126 fungal strains from the Fungal Biotechnology Culture Collection (FBCC) at University of Helsinki and 74 freshly isolated strains from soil around Jerusalem artichoke tubers were screened in liquid cultures with inulin as a sole source of carbon or ground Jerusalem artichoke tubers, which contains up to 19 % (fresh weight) inulin. Inulinase and invertase activities were assayed by the dinitrosalicylic acid (DNS) method and a freshly isolated Penicillium strain originating from agricultural soil (FBCC 1632) was the most efficient inulinase producer. When it was cultivated at pH 6 and 28 °C in 2 litre bioreactors using inulin and Jerusalem artichoke as a carbon source, inulinase and invertase activities were on day 4 7.7 and 3.1 U mL(-1), respectively. The released sugars analysed by TLC and HPLC showed that considerable amounts of fructose were released while the levels of oligofructans were low, indicating an exoinulinase type of activity. Taxonomic study of the inulinase producing strain showed that this isolate represents a new species belonging in Penicillium section Lanata-divaricata. This new species produces a unique combination of extrolites and is phenotypically and phylogenetically closely related to Penicillium pulvillorum. We propose the name Penicillium subrubescens sp. nov. (CBS 132785(T) = FBCC 1632(T)) for this new species.
  Antonie van Leeuwenhoek 04/2013;
• Article: The bacteria and bacteriophages from a Mesquite Flats site of the Death Valley desert.

  Eric Prestel, Christophe Regeard, Sylvie Salamitou, Julie Neveu, Michael S Dubow
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  ABSTRACT: Arid zones cover over 30 % of the Earth's continental surface. In order to better understand the role of microbes in this type of harsh environment, we isolated and characterized the bacteriophages from samples of the surface sand of the Mesquite Flats region via electron microscopy and DNA sequencing of a select number of cloned phage DNAs. An electron microscopic analysis of the recovered virus-like particles revealed at least 11 apparently different morphotypes sharing structural characteristics of the Caudoviridae family of tailed phages. We found that 36 % of the sequences contained no significant identity (e-value >10(-3)) with sequences in the databases. Pilot sequencing of cloned 16S rRNA genes identified Bacteroidetes and Proteobacteria as the major bacterial groups present in this severe environment. The majority of the 16S rDNA sequences from the total (uncultured) bacterial population displayed ≤96 % identity to 16S rRNA genes in the database, suggesting an unexplored bacterial population likely adapted to a desert environment. In addition, we also isolated and identified 38 cultivable bacterial strains, the majority of which belonged to the genus Bacillus. Mitomycin-C treatment of the cultivable bacteria demonstrated that the vast majority (84 %) contained at least one SOS-inducible prophage.
  Antonie van Leeuwenhoek 04/2013;