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Systematic and Applied Microbiology | Page 2

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https://read.qxmd.com/read/30679000/shifts-in-the-anammox-bacterial-community-structure-and-abundance-in-sediments-from-the-changjiang-estuary-and-its-adjacent-area
#21
Lulu Fu, Yangyang Chen, Siqi Li, Hui He, Tiezhu Mi, Yu Zhen, Zhigang Yu
Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria...
January 7, 2019: Systematic and Applied Microbiology
https://read.qxmd.com/read/30612723/nodule-bacteria-from-the-cultured-legume-phaseolus-dumosus-belonging-to-the-phaseolus-vulgaris-cross-inoculation-group-with-common-tropici-phenotypic-characteristics-and-symbiovar-but-distinctive-phylogenomic-position-and-chromid
#22
Shamayim T Ramírez-Puebla, Marco A Rogel Hernández, Gabriela Guerrero Ruiz, Ernesto Ormeño-Orrillo, Julio C Martinez-Romero, Luis Eduardo Servín-Garcidueñas, Alejandra Núñez-de la Mora, Guadalupe Amescua-Villela, Simoneta Negrete-Yankelevich, Esperanza Martínez-Romero
Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI)...
December 23, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30718035/flavobacterium-circumlabens-sp-nov-and-flavobacterium-cupreum-sp-nov-two-psychrotrophic-species-isolated-from-antarctic-environmental-samples
#23
Stanislava Králová, Hans-Jürgen Busse, Pavel Švec, Ivana Mašlaňová, Eva Staňková, Miloš Barták, Ivo Sedláček
A taxonomic study of 24 Gram-stain-negative rod-shaped bacteria originating from the Antarctic environment is described. Phylogenetic analysis using 16S rRNA gene sequencing differentiated isolated strains into two groups belonging to the genus Flavobacterium. Group I (n=20) was closest to Flavobacterium aquidurense WB 1.1-56T (98.3% 16S rRNA gene sequence similarity) while group II (n=4) showed Flavobacterium hydatis DSM 2063T as its nearest neighbour (98.5-98.9% 16S rRNA gene sequence similarity). Despite high 16S rRNA gene sequence similarity, these two groups represented two distinct novel species as shown by phenotypic traits and low genomic relatedness assessed by rep-PCR fingerprinting, DNA-DNA hybridization and whole-genome sequencing...
December 21, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30685079/oenococcus-sicerae-sp-nov-isolated-from-french-cider
#24
Fabien J Cousin, Rozenn Le Guellec, Caroline Chagnot, Didier Goux, Marion Dalmasso, Jean-Marie Laplace, Marina Cretenet
Two Gram-stain-positive, small ellipsoidal cocci, non-motile, oxidase- and catalase-negative, and facultative anaerobic strains (UCMA15228T and UCMA17102) were isolated in France, from fermented apple juices (ciders). The 16S rRNA gene sequence was identical between the two isolates and showed 97 % similarity with respect to the closest related species Oenococcus oeni and O. kitaharae. Therefore, the two isolates were classified within the genus Oenococcus. The phylogeny based on the pheS gene sequences also confirmed the position of the new taxon...
December 21, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30616913/discovery-and-ecogenomic-context-of-a-global-caldiserica-related-phylum-active-in-thawing-permafrost-candidatus-cryosericota-phylum-nov-ca-cryosericia-class-nov-ca-cryosericales-ord-nov-ca-cryosericaceae-fam-nov-comprising-the-four-species-cryosericum-septentrionale
#25
Miguel A Martinez, Ben J Woodcroft, Julio C Ignacio Espinoza, Ahmed A Zayed, Caitlin M Singleton, Joel A Boyd, Yueh-Fen Li, Samuel Purvine, Heather Maughan, Suzanne B Hodgkins, Darya Anderson, Maya Sederholm, Ben Temperton, Benjamin Bolduc, Scott R Saleska, Gene W Tyson, Virginia I Rich, Scott R Saleska, Gene W Tyson, Virginia I Rich
The phylum Caldiserica was identified from the hot spring 16S rRNA gene lineage 'OP5' and named for the sole isolate Caldisericum exile, a hot spring sulfur-reducing chemoheterotroph. Here we characterize 7 Caldiserica metagenome-assembled genomes (MAGs) from a thawing permafrost site in Stordalen Mire, Arctic Sweden. By 16S rRNA and marker gene phylogenies, and average nucleotide and amino acid identities, these Stordalen Mire Caldiserica (SMC) MAGs form part of a divergent clade from C. exile. Genome and meta-transcriptome and proteome analyses suggest that unlike Caldisericum, the SMCs (i) are carbohydrate- and possibly amino acid fermenters that can use labile plant compounds and peptides, and (ii) encode adaptations to low temperature...
December 14, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30587382/hymenobacter-amundsenii-sp-nov-resistant-to-ultraviolet-radiation-isolated-from-regoliths-in-antarctica
#26
Ivo Sedláček, Roman Pantůček, Stanislava Králová, Ivana Mašlaňová, Pavla Holochová, Eva Staňková, Veronika Vrbovská, Pavel Švec, Hans-Jürgen Busse
A group of thirteen bacterial strains was isolated from rock samples collected in a deglaciated northern part of James Ross Island, Antarctica. The cells were rod-shaped, Gram-stain-negative, non-motile, catalase positive, and produced moderately slimy, ultraviolet light (UVC)-irradiation-resistant and red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, extensive biotyping, fatty acid profile, chemotaxonomy analyses, and whole genome sequencing were applied in order to clarify the taxonomic position of these isolates...
December 14, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30551955/corrigendum-to-natronobiforma-cellulositropha-gen-nov-sp-nov-a-novel-haloalkaliphilic-member-of-the-family-natrialbaceae-class-halobacteria-from-hypersaline-alkaline-lakes-syst-appl-microbiol-41-2018-355-362
#27
Dimitry Y Sorokin, Tatiana V Khijniak, Nadezhda A Kostrikina, Alexander G Elcheninov, Stepan V Toshchakov, Nicole J Bale, Jaap S Sinninghe Damsté, Ilya V Kublanov
No abstract text is available yet for this article.
December 11, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30558959/moving-the-cataloguing-of-the-uncultivated-majority-forward
#28
EDITORIAL
Konstantinos T Konstantinidis, Ramon Rossello-Mora, Rudolf Amann
No abstract text is available yet for this article.
December 10, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30554810/reflections-on-the-introduction-of-the-digital-protologue-database-a-partial-success
#29
EDITORIAL
Ramon Rossello-Mora, Iain C Sutcliffe
No abstract text is available yet for this article.
December 10, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30551956/bifidobacterium-xylocopae-sp-nov-and-bifidobacterium-aemilianum-sp-nov-from-the-carpenter-bee-xylocopa-violacea-digestive-tract
#30
Daniele Alberoni, Francesca Gaggìa, Loredana Baffoni, Monica Marianna Modesto, Bruno Biavati, Diana Di Gioia
Social bees harbor a community of gut mutualistic bacteria, among which bifidobacteria occupy an important niche. Recently, four novel species have been isolated from guts of different bumblebees, thus allowing to suppose that a core bifidobacterial population may be present in wild solitary bees. To date there is sparse information about bifidobacteria in solitary bees such as Xylocopa and Osmia spp., this study is therefore focused on the isolation and characterization of bifidobacterial strains from solitary bees, in particular carpenter bee (Xylocopa violacea), builder bee (Osmia cornuta), and red mason bee (Osmia rufa)...
November 29, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30528643/alteromonas-flava-sp-nov-and-alteromonas-facilis-sp-nov-two-novel-copper-tolerating-bacteria-isolated-from-a-sea-cucumber-culture-pond-in-china
#31
Jing Zhang, Chong Wang, Ji-Ru Han, Guan-Jun Chen, Zong-Jun Du
Two bacterial strains, P0211T and P0213T , were isolated from a sea cucumber culture pond in China. The strains were able to resist high copper levels. These two strains were characterized at the phenotypic, chemotaxonomic, and genomic level. They were completely different colors, but the 16S rRNA genes showed 99.30% similarity. Phylogenetic analysis based on the sequences of the 16S rRNA gene and five housekeeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) supported the inclusion of these strains within the genus Alteromonas, and the two isolated strains formed a group separated from the closest species Alteromonas aestuariivivens KCTC 52655T ...
November 29, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30514593/kocuria-tytonicola-new-bacteria-from-the-preen-glands-of-american-barn-owls-tyto-furcata
#32
Markus Santhosh Braun, Erjia Wang, Stefan Zimmermann, Sébastien Boutin, Hermann Wagner, Michael Wink
Although birds are hosts to a large number of microorganisms, microbes have rarely been found in avian oil glands. Here, we report on two strains of a new bacterial species from the preen oil of American barn owls (Tyto furcata). Phenotypic as well as genotypic methods placed the isolates to the genus Kocuria. Strains are non-fastidious, non-lipophilic Gram-positive cocci and can be unambiguously discriminated from their closest relative Kocuria rhizophila DSM 11926T . In phylogenetic trees, the owl bacteria formed a distinct cluster which was clearly separated from all other known Kocuria species...
November 20, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30528275/a-study-of-three-bacteria-isolated-from-marine-sediment-and-description-of-micromonospora-globispora-sp-nov
#33
Lorena Carro, Aysel Veyisoglu, Demet Cetin, José M Igual, Hans-Peter Klenk, Martha E Trujillo, Nevzat Sahin
During a study looking for the isolation of new actinobacteria strains with potential for antibiotic production from deep marine sediment, three strains were collected with a morphology similar to the one described for the Micromonospora genus. A polyphasic study was designed to determine the taxonomic affiliation of the strains S2901T , S2903, and S2904. All the strains showed chemotaxonomic properties in line with their classification in the genus Micromonospora, meso-diaminopimelic acid in the wall peptidoglycan, a tetrahydrogenated menaquinone with nine isoprene units as major respiratory quinone, iso-C15:0 and iso-C16:0 as major fatty acids and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids...
November 16, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30528276/recovering-microbial-genomes-from-metagenomes-in-hypersaline-environments-the-good-the-bad-and-the-ugly
#34
María Dolores Ramos-Barbero, Ana-B Martin-Cuadrado, Tomeu Viver, Fernando Santos, Manuel Martinez-Garcia, Josefa Antón
Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity...
November 15, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30477901/candidatus-krumholzbacterium-zodletonensis-gen-nov-sp-nov-the-first-representative-of-the-candidate-phylum-krumholzbacterota-phyl-nov-recovered-from-an-anoxic-sulfidic-spring-using-genome-resolved-metagenomics
#35
Noha H Youssef, Ibrahim F Farag, C Ryan Hahn, Hasitha Premathilake, Emily Fry, Matthew Hart, Krystal Huffaker, Edward Bird, Jimmre Hambright, Wouter D Hoff, Mostafa S Elshahed
The accumulation of genomes of uncultured organisms has highlighted the need for devising a taxonomic and nomenclature scheme to validate names and prevent redundancies. We here report on the recovery and analysis of four phylogenetically related genomes recovered from an anoxic sulfide and sulfur-rich spring (Zodletone spring) in southwestern Oklahoma. Phylogenetic analysis based on 120 single copy markers attested to their position as a novel distinct bacterial phylum. Genomic analysis suggests Gram-negative flagellated organisms that possess type IV pili...
November 15, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30477902/effect-of-inoculation-with-nitrogen-fixing-bacterium-pseudomonas-stutzeri-a1501-on-maize-plant-growth-and-the-microbiome-indigenous-to-the-rhizosphere
#36
Xiubin Ke, Shuai Feng, Jin Wang, Wei Lu, Wei Zhang, Ming Chen, Min Lin
Plant growth promoting diazotrophs with the ability to associate with plant roots are in common use as inoculants to benefit crop yield and to mitigate chemical nitrogen fertilization. However, limited information is available in understanding to what extent the plant growth-promoting effect of the inoculum has on the plant's nitrogen acquisition as well as on the impact of inoculation on the indigenous rhizosphere microbial population. Here we reported on experiments that assessed how endophytic Pseudomonas stutzeri A1501 inoculated on maize improved plant growth and plant nitrogen content using a 15 N dilution technique under two water regime conditions...
November 6, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30415881/phaseolus-vulgaris-is-nodulated-by-the-symbiovar-viciae-of-several-genospecies-of-rhizobium-laguerreae-complex-in-a-spanish-region-where-lens-culinaris-is-the-traditionally-cultivated-legume
#37
José David Flores-Félix, Fernando Sánchez-Juanes, Paula García-Fraile, Angel Valverde, Pedro F Mateos, José Manuel Gónzalez-Buitrago, Encarna Velázquez, Raúl Rivas
Phaseolus vulgaris and Lens culinaris are two legumes with different distribution centers that were introduced in Spain at different times, but in some regions L. culinaris has been traditionally cultivated and P. vulgaris did not. Here we analysed the rhizobia isolated from nodules of these two legumes in one of these regions. MALDI-TOF MS analysis showed that all isolated strains matched with Rhizobium laguerreae and the phylogenetic analysis of rrs, atpD and recA genes confirmed these results. The phylogenetic analysis of these core genes allowed the differentiation of several groups within R...
November 2, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30455068/the-genome-of-candidatus-phytoplasma-solani-strain-sa-1-is-highly-dynamic-and-prone-to-adopting-foreign-sequences
#38
Martina Seruga Music, Ivana Samarzija, Saskia A Hogenhout, Mindia Haryono, Shu-Ting Cho, Chih-Horng Kuo
Bacteria of the genus 'Candidatus Phytoplasma' are uncultivated intracellular plant pathogens transmitted by phloem-feeding insects. They have small genomes lacking genes for essential metabolites, which they acquire from either plant or insect hosts. Nonetheless, some phytoplasmas, such as 'Ca. P. solani', have broad plant host range and are transmitted by several polyphagous insect species. To understand better how these obligate symbionts can colonize such a wide range of hosts, the genome of 'Ca. P. solani' strain SA-1 was sequenced from infected periwinkle via a metagenomics approach...
November 1, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30447886/reorganising-the-order-bacillales-through-phylogenomics
#39
Pieter De Maayer, Habibu Aliyu, Don A Cowan
Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order...
October 26, 2018: Systematic and Applied Microbiology
https://read.qxmd.com/read/30384991/the-rhizosphere-of-the-halophytic-grass-sporobolus-robustus-kunth-hosts-rhizobium-genospecies-that-are-efficient-on-prosopis-juliflora-sw-dc-and-vachellia-seyal-del-p-j-h-hurter-seedlings
#40
Fatoumata Fall, Christine Le Roux, Amadou Mustapha Bâ, Dioumacor Fall, Niokhor Bakhoum, Mathieu Ndigue Faye, Aboubacry Kane, Ibrahima Ndoye, Diegane Diouf
The aim of this study was to survey the abundance and genetic diversity of legume-nodulating rhizobia (LNR) in the rhizosphere of a salt-tolerant grass, Sporobolus robustus Kunth, in the dry and rainy seasons along a salinity gradient, and to test their effectiveness on Prosopis juliflora (SW.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings. The results showed a significant decrease in LNR population density and diversity in response to salinity, particularly during the dry season. A phylogenetic analysis of the 16S-23S rRNA ITS region clustered the 232 rhizobium isolates into three genera and 12 distinct representative genotypes: Mesorhizobium (8 genotypes), Ensifer (2 genotypes) and Rhizobium (2 genotypes)...
October 26, 2018: Systematic and Applied Microbiology
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