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Systematic and Applied Microbiology

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https://www.readbyqxmd.com/read/28284522/in-depth-analysis-of-rumen-microbial-and-carbohydrate-active-enzymes-profile-in-indian-crossbred-cattle
#1
V Lyju Jose, Ravi P More, Thulasi Appoothy, A Sha Arun
Rumen houses a plethora of symbiotic microorganisms empowering the host to hydrolyze plant lignocellulose. In this study, NGS based metagenomic approach coupled with bioinformatic analysis was employed to gain an insight into the deconstruction of lignocellulose by carbohydrate-active enzymes (CAZymes) in Indian crossbred Holstein-Friesian cattle. Cattle rumen metagenomic DNA was sequenced using Illumina-MiSeq and 1.9 gigabases of data generated with an average read length of 871 bp. Analysis of the assembled sequences by Pfam-based Carbohydrate-active enzyme Analysis Toolkit identified 17,164 putative protein-encoding CAZymes belonging to different families of glycoside hydrolases (7574), glycosyltransferases (5185), carbohydrate-binding modules (2418), carbohydrate esterases (1516), auxiliary activities (434) and polysaccharide lyases (37)...
February 28, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28249694/introducing-a-digital-protologue-a-timely-move-towards-a-database-driven-systematics-of-archaea-and-bacteria
#2
EDITORIAL
Ramon Rosselló-Móra, Martha E Trujillo, Iain C Sutcliffe
No abstract text is available yet for this article.
February 17, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28237188/identification-of-acetic-acid-bacteria-through-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-and-report-of-gluconobacter-nephelii-kommanee-et-al-2011-and-gluconobacter-uchimurae-tanasupawat-et-al-2012-as-later-heterotypic-synonyms
#3
Leilei Li, Ilse Cleenwerck, Luc De Vuyst, Peter Vandamme
The classification and identification of acetic acid bacteria (AAB) underwent much change during the last two decades. However, several closely related AAB species are difficult to differentiate and rapid and correct species level identification remains challenging. In the present study, 281 well-characterized AAB strains representing AAB species of the family Acetobacteraceae were used to construct a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification database...
February 15, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28238475/mesorhizobium-delmotii-and-mesorhizobium-prunaredense-are-two-new-species-containing-rhizobial-strains-within-the-symbiovar-anthyllidis
#4
Roba Mohamad, Anne Willems, Antoine Le Quéré, Géraldine Maynaud, Marjorie Pervent, Maurine Bonabaud, Emeric Dubois, Jean-Claude Cleyet-Marel, Brigitte Brunel
Eight mesorhizobial symbiotic strains isolated from Anthyllis vulneraria root-nodules were studied and compared taxonomically with defined Mesorhizobium species. All strains presented identical 16S rDNA sequences but can be differentiated by multilocus sequence analysis of housekeeping genes (recA, atpD, glnII and dnaK). Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analyses separate these strains in two groups and a separate strain. Levels of DNA-DNA relatedness were less than 55% between representative strains and their closest Mesorhizobium reference relatives...
February 12, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28216096/alkalinity-of-lanzarote-soils-is-a-factor-shaping-rhizobial-populations-with-sinorhizobium-meliloti-being-the-predominant-microsymbiont-of-lotus-lancerottensis
#5
Milagros León-Barrios, Juan Pérez-Yépez, Paola Dorta, Ana Garrido, Concepción Jiménez
Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp...
February 2, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28214058/phylogenetic-multilocus-sequence-analysis-of-indigenous-slow-growing-rhizobia-nodulating-cowpea-vigna-unguiculata-l-in-greece
#6
Anastasia P Tampakaki, Christos T Fotiadis, Georgia Ntatsi, Dimitrios Savvas
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...
February 2, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28209394/ensifer-shofinae-sp-nov-a-novel-rhizobial-species-isolated-from-root-nodules-of-soybean-glycine-max
#7
Wen Hao Chen, Sheng Hui Yang, Zhao Hu Li, Xiao Xia Zhang, Xin Hua Sui, En Tao Wang, Wen Xin Chen, Wen Feng Chen
Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167(T) and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90...
February 2, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28094097/diverse-genotypes-of-bradyrhizobium-nodulate-herbaceous-chamaecrista-moench-fabaceae-caesalpinioideae-species-in-brazil
#8
José Miguel Ferreira Dos Santos, Patricia Alves Casaes Alves, Verônica Cordeiro Silva, Mariana Ferreira Kruschewsky Rhem, Euan K James, Eduardo Gross
The genus Chamaecrista comprises more than 330 species which are mainly distributed across tropical America, especially in Brazil (256 spp.), the main center of radiation. In this study, nodulation of herbaceous Chamaecrista species that are commonly found growing in different vegetation types in the north eastern Brazilian state of Bahia was assessed together with the diversity of rhizobia isolated from their root nodules. Genetic characterization of the isolates was performed using molecular markers to examine the phylogeny of their "core" (16S rRNA, ITS, recA, glnII, dnaK and gyrB) and symbiosis-related (nifH, nodC) genomes...
March 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28081924/physiological-and-gene-expression-responses-to-nitrogen-regimes-and-temperatures-in-mastigocladus-sp-strain-chp1-a-predominant-thermotolerant-cyanobacterium-of-hot-springs
#9
M Estrella Alcamán, Jaime Alcorta, Birgitta Bergman, Mónica Vásquez, Martin Polz, Beatriz Díez
Cyanobacteria are widely distributed primary producers with significant implications for the global biogeochemical cycles of carbon and nitrogen. Diazotrophic cyanobacteria of subsection V (Order Stigonematales) are particularly ubiquitous in photoautotrophic microbial mats of hot springs. The Stigonematal cyanobacterium strain CHP1 isolated from the Porcelana hot spring (Chile) was one of the major contributors of the new nitrogen through nitrogen fixation. Further morphological and genetic characterization verified that the strain CHP1 belongs to Stigonematales, and it formed a separate clade together with other thermophiles of the genera Fischerella and Mastigocladus...
March 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28081923/analysis-of-rhizobial-endosymbionts-of-vicia-lathyrus-and-trifolium-species-used-to-maintain-mountain-firewalls-in-sierra-nevada-national-park-south-spain
#10
Pablo J Villadas, Ana V Lasa, Pilar Martínez-Hidalgo, José David Flores-Félix, Eustoquio Martínez-Molina, Nicolás Toro, Encarna Velázquez, Manuel Fernández-López
Forest fires lead to the annual disappearance of many natural formations that require the creation of firewall areas. They can be maintained by enriching their pastures with attractive plants for grazing livestock, mainly legumes, which have a high protein content and low dependence on N fertilizers due to their ability to establish nitrogen-fixing symbiosis with rhizobia. In this study, the rhizobia isolated from the nodules of six legumes from the genera Vicia, Lathyrus and Trifolium were analysed in a firewall zone established in Lanjarón (Granada) close to the Sierra Nevada National Park (Spain)...
March 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28063627/competition-between-rhizobia-under-different-environmental-conditions-affects-the-nodulation-of-a-legume
#11
Zhao Jun Ji, Hui Yan, Qing Guo Cui, En Tao Wang, Wen Feng Chen, Wen Xin Chen
Mutualistic symbiosis and nitrogen fixation of legume rhizobia play a key role in ecological environments. Although many different rhizobial species can form nodules with a specific legume, there is often a dominant microsymbiont, which has the highest nodule occupancy rates, and they are often known as the "most favorable rhizobia". Shifts in the most favorable rhizobia for a legume in different geographical regions or soil types are not well understood. Therefore, in order to explore the shift model, an experiment was designed using successive inoculations of rhizobia on one legume...
March 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28057375/description-of-a-new-anaerobic-thermophilic-bacterium-thermoanaerobacterium-butyriciformans-sp-nov
#12
G López, S J Cañas-Duarte, A M Pinzón-Velasco, N E Vega-Vela, M Rodríguez, S Restrepo, S Baena
Strain USBA-019(T), an anaerobic and thermophilic strain, was identified as a new member of the genus Thermoanaerobacterium. USBA-019(T) cells are gram-positive, strictly anaerobic, thermophilic, chemoorganotrophic, moderately acidophilic, non-motile, endospore-forming, slightly curved, and rod-shaped. Cells measure 0.4×3.0-7.0μm. Optimal growth occurs at 50-55°C (35-65°C). Optimum pH is 5.0-5.5 (4.0-8.5). Thiosulfate, elemental sulfur and nitrate were utilized as electron acceptors. Fermentation of glucose, lactose, cellobiose, galactose, arabinose, xylose, starch and xylan primarily produced acetate and butyrate...
March 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28040300/neptuniibacter-pectenicola-sp-nov-and-neptuniibacter-marinus-sp-nov-two-novel-species-isolated-from-a-great-scallop-pecten-maximus-hatchery-in-norway-and-emended-description-of-the-genus-neptuniibacter
#13
Ana L Diéguez, Sabela Balboa, Thorolf Magnesen, Jesús L Romalde
Nine isolates obtained from a great scallop hatchery in Norway were characterized using a polyphasic approach. Strains were Gram-negative, aerobic and motile rods with oxidative metabolism. Phylogenetic analysis based on the sequences of 16S rRNA and rpoB genes showed that these strains formed two different groups associated with members of the genus Neptuniibacter. DNA-DNA hybridization (DDH) and Average Nucleotide Identity (ANI) demonstrated that the isolates constituted two novel species of this genus, which can be phenotypically differentiated from their closest relatives...
March 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28292625/-candidatus-dichloromethanomonas-elyunquensis-gen-nov-sp-nov-a-dichloromethane-degrading-anaerobe-of-the-peptococcaceae-family
#14
Sara Kleindienst, Steven A Higgins, Despina Tsementzi, Gao Chen, Konstantinos T Konstantinidis, E Erin Mack, Frank E Löffler
Taxonomic assignments of anaerobic dichloromethane (DCM)-degrading bacteria remain poorly constrained but are important for understanding the microbial diversity of organisms contributing to DCM turnover in environmental systems. We describe the taxonomic classification of a novel DCM degrader in consortium RM obtained from pristine Rio Mameyes sediment. Phylogenetic analysis of full-length 16S rRNA gene sequences demonstrated that the DCM degrader was most closely related to members of the genera Dehalobacter and Syntrophobotulus, but sequence similarities did not exceed 94% and 93%, respectively...
December 21, 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27776911/genomic-characterization-of-a-fructophilic-bee-symbiont-lactobacillus-kunkeei-reveals-its-niche-specific-adaptation
#15
Shintaro Maeno, Yasuhiro Tanizawa, Yu Kanesaki, Eri Kubota, Himanshu Kumar, Leon Dicks, Seppo Salminen, Junichi Nakagawa, Masanori Arita, Akihito Endo
Lactobacillus kunkeei is classified as a sole obligate fructophilic lactic acid bacterium that is found in fructose-rich niches, including the guts of honeybees. The species is differentiated from other lactobacilli based on its poor growth with glucose, enhanced growth in the presence of oxygen and other electron acceptors, and production of high concentrations of acetate from the metabolism of glucose. These characteristics are similar to phylogenetically distant Fructobacillus spp. In the present study, the genomic structure of L...
December 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27771162/multi-locus-sequence-analysis-and-symbiotic-characterization-of-novel-ensifer-strains-nodulating-tephrosia-spp-in-the-indian-thar-desert
#16
Nisha Tak, Esha Awasthi, Garima Bissa, Raju Ram Meghwal, Euan K James, Janet S Sprent, Hukam S Gehlot
Phylogenetically diverse Ensifer strains associated with five species of Tephrosia growing in alkaline soils of semi-arid regions of the Thar Desert were characterized using multi locus sequence analysis. Based on 16S rRNA and four protein-coding housekeeping gene (recA, atpD, glnII and dnaK) sequences, the Tephrosia-Ensifer strains were genetically different from the type strains of Ensifer saheli, Ensifer kostiensis, Ensifer terangae (African origin) and Ensifer psoraleae (Asiatic origin). One strain, Ensifer sp...
December 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27745752/varibaculum-anthropi-sp-nov-represented-by-three-genetically-different-genomovars-isolated-from-clinical-material-and-emended-description-of-the-genus-varibaculum
#17
Stefanie P Glaeser, Swapnil Doijad, Muaz Hijazin, Trinad Chakraborty, Enevold Falsen, Val Hall, Peter Kämpfer
During the years 1994-2011 five strictly anaerobic, Gram-stain-positive, diphtheroid bacteria (strains CCUG 31793(T), CCUG 44221, CCUG 61255, CCUG 45114, and CCUG 44993) were isolated from different clinical samples in Sweden and the United Kingdom. Comparative analysis of 16S rRNA gene sequences showed that the five strains shared 99-100% 16S rRNA gene sequence similarity among each other and 98.3-98.6% sequence similarity to Varibaculum cambriense DSM 15806(T). Genomic fingerprint patterns generated with ERIC-, BOX-, and RAPD-PCR, and whole genome sequence (WGS) based comparison by in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) analysis and six housekeeping gene (atpA, rpoB, pgi, metG, gltA and gyrA) based multilocus sequence analysis (MLSA) showed that the strains could be differentiated from V...
December 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27729171/discrimination-and-divergence-among-lactobacillus-plantarum-group-lpg-isolates-with-reference-to-their-probiotic-functionalities-from-vegetable-origin
#18
Sundru Manjulata Devi, Subramanian Aishwarya, Prakash M Halami
The present study was aimed to evaluate the diversity and probiotic properties of Lactobacillus plantarum-group cultures from vegetable origin. First, genotypic diversity of L. plantarum (n=34) was achieved by PCR of Random Amplified Polymorphic DNA and recA gene-specific multiplex PCR. The isolates were segregated into five groups namely, Lactobacillus pentosus, Lactobacillus paraplantarum, Lactobacillus arizonensis, Lactobacillus plantarum subsp. plantarum and argentoratensis. Further discrimination was achieved by restriction fragment length polymorphism of probiotic adhesion genes viz...
December 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27726901/phylogenomic-re-assessment-of-the-thermophilic-genus-geobacillus
#19
Habibu Aliyu, Pedro Lebre, Jochen Blom, Don Cowan, Pieter De Maayer
Geobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA-DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness...
December 2016: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/27720237/novel-volatiles-of-skin-borne-bacteria-inhibit-the-growth-of-gram-positive-bacteria-and-affect-quorum-sensing-controlled-phenotypes-of-gram-negative-bacteria
#20
Marie Chantal Lemfack, Srinivasa Rao Ravella, Nicola Lorenz, Marco Kai, Kirsten Jung, Stefan Schulz, Birgit Piechulla
The skin microbiota is import for body protection. Here we present the first comprehensive analysis of the volatile organic compound (VOC) profiles of typical skin-resident corynebacterial and staphylococcal species. The VOC profile of Staphylococcus schleiferi DSMZ 4807 was of particular interest as it is dominated by two compounds, 3-(phenylamino)butan-2-one and 3-(phenylimino)butan-2-one (schleiferon A and B, respectively). Neither of these has previously been reported from natural sources. Schleiferon A and B inhibited the growth of various Gram-positive species and affected two quorum-sensing-dependent phenotypes - prodigiosin accumulation and bioluminescence - of Gram-negative bacteria...
December 2016: Systematic and Applied Microbiology
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