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Systematic and Applied Microbiology

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https://www.readbyqxmd.com/read/29342414/bacilli-community-of-saline-alkaline-soils-from-the-ararat-plain-armenia-assessed-by-molecular-and-culture-based-methods
#1
Hovik Panosyan, Anna Hakobyan, Nils-Kåre Birkeland, Armen Trchounian
The bacterial community composition in the A horizon of a natural saline-alkaline soil located in Ararat Plain (Armenia) was studied using molecular and culture-based methods The sequence analysis of a 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE) profiles indicated dominance of Firmicutes populations. The majority of the sequences of the bacterial 16S rRNA gene library were close relatives of representatives belonging to the genera Halobacillus (41.2%), Piscibacillus (23.5%), Bacillus (23...
January 5, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29336852/brazilian-species-of-calliandra-benth-tribe-ingeae-are-nodulated-by-diverse-strains-of-paraburkholderia
#2
Verônica Cordeiro Silva, Patricia Alves Casaes Alves, Mariana Ferreira Kruschewsky Rhem, José Miguel Ferreira Dos Santos, Euan K James, Eduardo Gross
The Chapada Diamantina in NE of Brazil is a biodiversity hotspot and a center of radiation for many Neotropical legume genera, such as Calliandra and Mimosa. The present study aimed to evaluate nodulation in Calliandra species endemic to various environments, and to characterize the diversity of their symbiotic rhizobia using housekeeping (16S rRNA, recA) and plasmid-borne, symbiosis-related (nifH and nodC) genes. The nodulation ability of selected isolates was assessed. All of the 126 bacterial isolates from 18 Calliandra species collected in six different vegetation types were identified as Paraburkholderia according to their housekeeping and symbiosis gene phylogenies...
January 5, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29310897/vicia-faba-l-in-the-bejaia-region-of-algeria-is-nodulated-by-rhizobium-leguminosarum-sv-viciae-rhizobium-laguerreae-and-two-new-genospecies
#3
Djellali Belhadi, Philippe de Lajudie, Nacer Ramdani, Christine Le Roux, Farida Boulila, Pierre Tisseyre, Abdelghani Boulila, Amar Benguedouar, Yahia Kaci, Gisèle Laguerre
Fifty-eight rhizobial strains were isolated from root nodules of Vicia faba cv. Equina and Vicia faba cv. Minor by the host-trapping method in soils collected from eleven sites in Bejaia, Eastern Algeria. Eleven genotypic groups were distinguished based on the combined PCR/RFLP of 16S rRNA, 16S-23S rRNA intergenic spacer and symbiotic (nodC and nodD-F) genes and further confirmed by multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and rpoB), the 16S rRNA gene and the nodulation genes nodC and nodD...
December 27, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29325988/arboriscoccus-pini-gen-nov-sp-nov-an-endophyte-from-a-pine-tree-of-the-class-alphaproteobacteria-emended-description-of-geminicoccus-roseus-and-proposal-of-geminicoccaceae-fam-nov
#4
Diogo N Proença, William B Whitman, Neha Varghese, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Paula V Morais
Bacterial strain B29T1T was isolated from the endophytic microbial community of a Pinus pinaster tree trunk and characterized. Strain B29T1T stained Gram-negative and formed diplococci that grew optimally at 26-30°C and at pH 6.0-7.0. The G+C content of the DNA was 61.6mol%. The respiratory quinone was ubiquinone 10 (UK-10), and the major fatty acids were C16:0, cyclo-C19:0ω8c and C18:0 12-methyl, representing 64% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain B29T1T within the order Rhodospirillales in a distinct lineage that also included the genus Geminicoccus...
December 22, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29352612/biogeographical-patterns-of-bacterial-and-archaeal-communities-from-distant-hypersaline-environments
#5
M Del R Mora-Ruiz, A Cifuentes, F Font-Verdera, C Pérez-Fernández, M E Farias, B González, A Orfila, R Rosselló-Móra
Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to "species") using multivariate analysis revealed regionally distinct taxa compositions...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29338888/vibrio-communities-in-scleractinian-corals-differ-according-to-health-status-and-geographic-location-in-the-mediterranean-sea
#6
Esther Rubio-Portillo, Juan F Gago, Manuel Martínez-García, Luigi Vezzulli, Ramon Rosselló-Móra, Josefa Antón, Alfonso A Ramos-Esplá
The increase in seawater temperature associated with global warming is a significant threat to coral health and is linked to increasing mass mortality events and Vibrio-related coral diseases. In the Mediterranean Sea, the endemic Cladocora caespitosa and the invasive species Oculina patagonica are the main scleractinian corals affected by mass mortalities. In this study, culturable Vibrio spp. assemblages associated with healthy and unhealthy colonies of these two shallow coral species were characterized to assess the presence of Vibrio pathogens in tissue necrosis...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29331569/salinivibrio-kushneri-sp-nov-a-moderately-halophilic-bacterium-isolated-from-salterns
#7
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29325987/transfer-of-pectobacterium-carotovorum-subsp-carotovorum-strains-isolated-from-potatoes-grown-at-high-altitudes-to-pectobacterium-peruviense-sp-nov
#8
Malgorzata Waleron, Agnieszka Misztak, Michal Waleron, Martyna Franczuk, Bartosz Wielgomas, Krzysztof Waleron
Seven Gram-negative, rod-shaped pectinolytic bacteria strains designated as IFB5227, IFB5228, IFB5229, IFB5230, IFB5231, IFB5232, IFB5636, isolated from potato tubers cultivated in Peru at high altitude (2400-3800m) were subjected to polyphasic analyses that revealed their distinctiveness from the other Pectobacterium species. Phylogenetic analyses based on five housekeeping genes (gyrA, recA, recN, rpoA and rpoS) clearly showed strains separateness, simultaneously indicating Pectobacterium atrosepticum, Pectobacterium wasabiae, Pectobacterium parmentieri and Pectobacterium betavasculorum as the closest relatives...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29307475/rhizobium-laguerreae-is-the-main-nitrogen-fixing-symbiont-of-cultivated-lentil-lens-culinaris-in-morocco
#9
Kaoutar Taha, El Bekkay Berraho, Imane El Attar, Samia Dekkiche, Jamal Aurag, Gilles Béna
Genetic diversity and population structure of 268 Lens culinaris symbiotic rhizobia collected from 40 cultivated fields in the main lentil production regions in Morocco were estimated. Three chromosomal housekeeping genes (recA, glnII and atpD) and one common symbiotic gene (nodC) were sequenced and analyzed in order to identify the local symbionts of lentil. The molecular phylogeny of the concatenated housekeeping genes clustered more than 95% of the isolates in one main clade together with Rhizobium laguerreae species...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29306597/vagococcus-teuberi-sp-nov-isolated-from-the-malian-artisanal-sour-milk-f%C3%A3-n%C3%A3
#10
Stephan Wullschleger, Christoph Jans, Clelia Seifert, Sarah Baumgartner, Christophe Lacroix, Bassirou Bonfoh, Marc J A Stevens, Leo Meile
Ten bacterial isolates belonging to the genus Vagococcus were obtained from Malian sour milk fènè produced from spontaneously fermented cow milk. However, these isolates could not be assigned to a species upon initial comparative 16S rRNA gene sequence analysis and were therefore further characterized. Rep-PCR fingerprinting of the isolates yielded four strain clusters represented by strains CG-21T (=DSM 21459T), 24CA, CM21 and 9H. Sequence identity of the 16S rRNA gene of DSM 21459T to its closest relative species Vagococcus penaei was 97...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29305057/comparison-of-dna-extraction-methods-for-human-gut-microbial-community-profiling
#11
Mi Young Lim, Eun-Ji Song, Sang Ho Kim, Jangwon Lee, Young-Do Nam
The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29295750/ereboglobus-luteus-gen-nov-sp-nov-from-cockroach-guts-and-new-insights-into-the-oxygen-relationship-of-the-genera-opitutus-and-didymococcus-verrucomicrobia-opitutaceae
#12
Dorothee Tegtmeier, Alexandra Belitz, Renate Radek, Thomas Heimerl, Andreas Brune
We isolated a novel member of the phylum Verrucomicrobia from the hindgut of the cockroach Shelfordella lateralis. Strain Ho45 is a yellow-pigmented, motile coccus that represents a new genus-level lineage with less than 93% sequence similarity to the 16S rRNA genes of other species in the family Opitutaceae. Ultrastructural analysis revealed a Gram-negative cell envelope with an outer membrane and a periplasmic space. In its ability to ferment sugars to propionate and acetate as major products, strain Ho45 resembles its closest relative, Opitutus terrae...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29279139/photobacterium-carnosum-sp-nov-isolated-from-spoiled-modified-atmosphere-packaged-poultry-meat
#13
Maik Hilgarth, Sandra Fuertes, Matthias Ehrmann, Rudi F Vogel
Analysis of spoilage-associated microbiota of modified-atmosphere packaged poultry meat revealed four different bacterial isolates that could not be assigned to known species. They showed a Gram-negative staining behavior, were facultatively aerobic, non-motile with variable cell morphology. Phylogenetic analysis of 16S rDNA and gyrB, rpoD and recA revealed a distinct lineage within the genus Photobacterium with Photobacterium (P.) iliopiscarium DSM 9896T, P. phosphoreum DSM 15556T, P. kishitanii DSM 19954T, P...
December 19, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29169691/kocuria-uropygioeca-sp-nov-and-kocuria-uropygialis-sp-nov-isolated-from-the-preen-glands-of-great-spotted-woodpeckers-dendrocopos-major
#14
Markus Santhosh Braun, Erjia Wang, Stefan Zimmermann, Sébastien Boutin, Michael Wink
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...
November 15, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29129355/a-metagenomic-approach-to-dissect-the-genetic-composition-of-enterotypes-in-han-chinese-and-two-muslim-groups
#15
Jing Li, Ruiqing Fu, Yajun Yang, Hans-Peter Horz, Yaqun Guan, Yan Lu, Haiyi Lou, Lei Tian, Shijie Zheng, Hongjiao Liu, Meng Shi, Kun Tang, Sijia Wang, Shuhua Xu
Distinct enterotypes have been observed in the human gut but little is known about the genetic basis of the microbiome. Moreover, it is not clear how many genetic differences exist between enterotypes within or between populations. In this study, both the 16S rRNA gene and the metagenomes of the gut microbiota were sequenced from 48 Han Chinese, 48 Kazaks, and 96 Uyghurs, and taxonomies were assigned after de novo assembly. Single nucleotide polymorphisms were also identified by referring to data from the Human Microbiome Project...
November 9, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29113688/corrigendum-to-soybeans-inoculated-with-root-zone-soils-of-canadian-native-legumes-harbour-diverse-and-novel-bradyrhizobium-spp-that-possess-agricultural-potential-syst-appl-microbiol-40-october-7-2017-440-447
#16
Eden S P Bromfield, Sylvie Cloutier, James T Tambong, Thu Van Tran Thi
No abstract text is available yet for this article.
November 4, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29198596/phenotypic-and-genetic-diversity-of-moroccan-rhizobia-isolated-from-vicia-faba-and-study-of-genes-that-are-likely-to-be-involved-in-their-osmotolerance
#17
Loubna Benidire, Majida Lahrouni, Khalid Daoui, Zain El Abidine Fatemi, Ricardo Gomez Carmona, Michael Göttfert, Khalid Oufdou
Rhizobia are symbiotic nitrogen-fixing bacteria in root nodules of legumes. In Morocco, faba bean (Vicia faba L.), which is the main legume crop cultivated in the country, is often grown in marginal soils of arid and semi-arid regions. This study examines the phenotypic diversity of rhizobia nodulating V. faba isolated from different regions in Morocco for tolerance to some abiotic stresses. A total of 106 rhizobia strains isolated from nodules were identified at the species level by analysing 16S rDNA. Additionally, for selected strains recA, otsA, kup and nodA fragments were sequenced...
November 3, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29153257/pseudomonas-silesiensis-sp-nov-strain-a3-t-isolated-from-a-biological-pesticide-sewage-treatment-plant-and-analysis-of-the-complete-genome-sequence
#18
Michał A Kaminski, Ewa M Furmanczyk, Adam Sobczak, Andrzej Dziembowski, Leszek Lipinski
Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp...
November 3, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29150173/genetic-studies-to-re-affiliate-edwardsiella-tarda-fish-isolates-to-edwardsiella-piscicida-and-edwardsiella-anguillarum-species
#19
Noemí Buján, Haitham Mohammed, Sabela Balboa, Jesús L Romalde, Alicia E Toranzo, Cova R Arias, Beatriz Magariños
Until 2012, the genus Edwardsiella was composed by three species Edwardsiella tarda, Edwardsiella hoshinae and Edwardsiella ictaluri. In 2013, Edwardsiella piscicida, compiling fish pathogenic strains previously identified as E. tarda was described, and more recently a new species isolated from diseased eel was reported, namely Edwardsiella anguillarum. The incorporation of these species into the genus makes necessary a revision of the taxonomic position of the isolates previously identified as E. tarda. Using AFLP technique, MLSA studies and in silico DNA-DNA hybridization, 46 of 49 E...
November 3, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29129356/multilocus-sequence-analysis-of-homologous-recombination-and-diversity-in-arthrobacter-sensu-lato-named-species-and-glacier-inhabiting-strains
#20
Qing Liu, Yu-Hua Xin, Yu-Guang Zhou, Wen-Xin Chen
Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato...
November 3, 2017: Systematic and Applied Microbiology
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