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Systematic and Applied Microbiology

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https://www.readbyqxmd.com/read/29747878/development-of-a-16s-rrna-targeted-fluorescence-in-situ-hybridization-probe-for-quantification-of-the-ammonia-oxidizer-nitrosotalea-devanaterra-and-its-relatives
#1
C X Restrepo-Ortiz, S N Merbt, J Barrero-Canossa, B M Fuchs, E O Casamayor
The Thaumarchaeota SAGMCG-1 group and, in particular, members of the genus Nitrosotalea have high occurrence in acidic soils, the rhizosphere, groundwater and oligotrophic lakes, and play a potential role in nitrogen cycling. In this study, the specific oligonucleotide fluorescence in situ hybridization probe SAG357 was designed for this Thaumarchaeota group based on the available 16S rRNA gene sequences in databases, and included the ammonia-oxidizing species Nitrosotalea devanaterra. Cell permeabilization for catalyzed reporter deposition fluorescence in situ detection and the hybridization conditions were optimized on enrichment cultures of the target species N...
April 28, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29752017/natronobiforma-cellulositropha-gen-nov-sp-nov-a-novel-haloalkaliphilic-member-of-the-family-natrialbaceae-class-halobacteria-from-hypersaline-alkaline-lakes
#2
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
Six strains of extremely halophilic and alkaliphilic euryarchaea were enriched and isolated in pure culture from surface brines and sediments of hypersaline alkaline lakes in various geographical locations with various forms of insoluble cellulose as growth substrate. The cells are mostly flat motile rods with a thin monolayer cell wall while growing on cellobiose. In contrast, the cells growing with cellulose are mostly nonmotile cocci covered with a thick external EPS layer. The isolates, designated AArcel, are obligate aerobic heterotrophs with a narrow substrate spectrum...
April 27, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29752018/the-microbial-community-in-a-moving-bed-biotrickling-filter-operated-to-remove-hydrogen-sulfide-from-gas-streams
#3
Cesira Giordano, Francesco Spennati, Gualtiero Mori, Giulio Munz, Claudia Vannini
The information available on the microbial communities responsible for pollutant degradation is increasingly accessible. Its use to optimize process design and operation is an important challenge in the field of effluent treatment research. Therefore, a prototype of a moving bed biotrickling filter (MBBTF) reactor was designed and, for the first time, operated at full-scale for the removal of sulfides desorbing from tannery industrial wastewater. The bacterial community operating in this innovative reactor was studied, and its composition and response to different operating conditions were characterized...
April 25, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29759899/integrated-diversity-analysis-of-the-microbial-community-in-a-reverse-osmosis-system-from-a-brazilian-oil-refinery
#4
Daiane R B Belgini, Virgínia M Siqueira, Douglas M Oliveira, Samantha G Fonseca, Viviane Piccin-Santos, Roberto S Dias, Larissa Quartaroli, Rodrigo S Souza, Ana Paula R Torres, Maíra P Sousa, Cláudio M Silva, Cynthia C Silva, Sérgio O De Paula, Valéria M Oliveira
Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality...
April 13, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29752019/pseudomonas-laurylsulfatovorans-sp-nov-sodium-dodecyl-sulfate-degrading-bacteria-isolated-from-the-peaty-soil-of-a-wastewater-treatment-plant
#5
Ewa M Furmanczyk, Michal A Kaminski, Leszek Lipinski, Andrzej Dziembowski, Adam Sobczak
Pseudomonas are known from their flexible degradation capabilities and their engagement in xenobiotic biotransformation and bioremediation in habitats like soil, active sludge, plant surfaces, and freshwater or marine environments. Here we present taxonomic characterization of three efficient sodium dodecyl sulfate degrading strains: AP3_10, AP3_20 and AP3_22T belonging to the genus Pseudomonas, recently isolated from peaty soil used in a biological wastewater treatment plant. Sequence analyses of 16S rRNA and housekeeping genes: gyrB, rpoD and rpoB showed that the three closely related isolates classify within the Pseudomonas jessenii subgroup...
April 11, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29673864/pseudomonas-gallaeciensis-sp-nov-isolated-from-crude-oil-contaminated-intertidal-sand-samples-after-the-prestige-oil-spill
#6
Magdalena Mulet, David Sánchez, Ana C Rodríguez, Balbina Nogales, Rafael Bosch, Antonio Busquets, Margarita Gomila, Jorge Lalucat, Elena García-Valdés
Strains V113T , V92 and V120 have been isolated from sand samples taken at the Atlantic intertidal shore in Galicia, Spain, after the Prestige oil spill. A preliminary analysis of the 16S rRNA and the partial rpoD gene sequences indicated that these strains belonged to the Pseudomonas genus, but they were distinct from any known Pseudomonas species. They were extensively characterized by a polyphasic taxonomic approach and phylogenetic data that confirmed that these strains belonged to the Pseudomonas pertucinogena group...
April 11, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29759900/detection-of-the-type-iii-secretion-system-and-its-phylogenetic-and-symbiotic-characterization-in-peanut-bradyrhizobia-isolated-from-guangdong-province-china
#7
Huaqin Ruan, Meijuan Hu, Jingyu Chen, Xue Li, Ting Li, Yongxiu Lai, En Tao Wang, Jun Gu
The distribution of rhcRST and rhcJ-C1 fragments located in different loci of the type III secretion system (T3SS) gene cluster in the peanut-nodulating bradyrhizobia isolated from Guangdong Province, China was investigated by PCR-based sequencing. T3SS was detected in approximately one-third of the peanut bradyrhizobial strains and the T3SS-harboring strains belonging to different Bradyrhizobium genomic species. Diverse T3SS groups corresponding to different symbiotic gene types were defined among the 23 T3SS-harboring strains...
April 8, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29655875/acetobacter-oryzifermentans-sp-nov-isolated-from-korean-traditional-vinegar-and-reclassification-of-the-type-strains-of-acetobacter-pasteurianus-subsp-ascendens-henneberg-1898-and-acetobacter-pasteurianus-subsp-paradoxus-frateur-1950-as-acetobacter-ascendens
#8
Kyung Hyun Kim, Ga Youn Cho, Byung Hee Chun, Stefan Weckx, Ji Young Moon, Soo-Hwan Yeo, Che Ok Jeon
Twelve Acetobacter pasteurianus-related strains with publicly available genomes in GenBank shared high 16S rRNA gene sequence similarity (>99.59%), but average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values and multilocus sequence- and genome-based relatedness analyses suggested that they were divided into four different phylogenetic lineages. Relatedness analyses based on multilocus sequences, 1,194 core genes and whole-cell MALDI-TOF profiles supported that strains LMG 1590T and LMG 1591 (previously classified as the type strains of A...
April 5, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29656850/bradyrhizobium-algeriense-sp-nov-a-novel-species-isolated-from-effective-nodules-of-retama-sphaerocarpa-from-northeastern-algeria
#9
Hadjira Ahnia, Yasmina Bourebaba, David Durán, Farida Boulila, José M Palacios, Luis Rey, Tomás Ruiz-Argüeso, Abdelghani Boulila, Juan Imperial
We have characterized genetic, phenotypic and symbiotic properties of bacterial strains previously isolated from nitrogen-fixing nodules of Retama sphaerocarpa from Northern Algeria. Phylogenetic analyses of 16S rRNA genes and three concatenated housekeeping genes, recA, atpD and glnII, placed them in a new divergent group that is proposed to form a new Bradyrhizobium species, Bradyrhizobium algeriense sp. nov. (type strain RST89T , LMG 27618 and CECT 8363). Based on these phylogenetic markers and on genomic identity data derived from draft genomic sequences, Bradyrhizobium valentinum LmjM3T , Bradyrhizobium lablabi CCBAU 23086T , Bradyrhizobium retamae Ro19T , and Bradyrhizobium jicamae PAC68T are the closest relatives of B...
April 4, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29653822/robust-frankia-phylogeny-species-delineation-and-intraspecies-diversity-based-on-multi-locus-sequence-analysis-mlsa-and-single-locus-strain-typing-slst-adapted-to-a-large-sample-size
#10
Adrien C Pozzi, Hector H Bautista-Guerrero, Sophie S Abby, Aude Herrera-Belaroussi, Danis Abrouk, Philippe Normand, Frédéric Menu, Maria P Fernandez
Diazotrophic Actinobacteria of the genus Frankia represent a challenge to classical bacterial taxonomy as they include many unculturable strains. As a consequence, we still have a poor understanding of their diversity, evolution and biogeography. In this study, a Multi-Locus Sequence Analysis (MLSA) using atpD, dnaA, ftsZ, pgk, and rpoB loci was done on a large set of cultured and uncultured strains, compared to 16S rRNA and correlated to Average Nucleotide Identity (ANI) from available Frankia genomes. MLSA provided a robust resolution of Frankia genus phylogeny and clarified the status of unresolved species and complex of species...
March 29, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29576402/genomic-insight-into-the-taxonomy-of-rhizobium-genospecies-that-nodulate-phaseolus-vulgaris
#11
Wenjun Tong, Xiangchen Li, Yunyun Huo, Lu Zhang, Ying Cao, Entao Wang, Weimin Chen, Shiheng Tao, Gehong Wei
Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA...
March 16, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29567394/consistent-associations-with-beneficial-bacteria-in-the-seed-endosphere-of-barley-hordeum-vulgare-l
#12
Md Mahafizur Rahman, Elias Flory, Hans-Werner Koyro, Zainul Abideen, Adam Schikora, Christian Suarez, Sylvia Schnell, Massimiliano Cardinale
The importance of the plant microbiome for host fitness has led to the concept of the "plant holobiont". Seeds are reservoirs and vectors for beneficial microbes, which are very intimate partners of higher plants with the potential to connect plant generations. In this study, the endophytic seed microbiota of numerous barley samples, representing different cultivars, geographical sites and harvest years, was investigated. Cultivation-dependent and -independent analyses, microscopy, functional plate assays, greenhouse assays and functional prediction were used, with the aim of assessing the composition, stability and function of the barley seed endophytic bacterial microbiota...
March 13, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29571921/genetic-diversity-and-symbiotic-effectiveness-of-phaseolus-vulgaris-nodulating-rhizobia-in-kenya
#13
George M Mwenda, Graham W O'Hara, Sofie E De Meyer, John G Howieson, Jason J Terpolilli
Phaseolus vulgaris (common bean) was introduced to Kenya several centuries ago but the rhizobia that nodulate it in the country remain poorly characterised. To address this gap in knowledge, 178 isolates recovered from the root nodules of P. vulgaris cultivated in Kenya were genotyped stepwise by the analysis of genomic DNA fingerprints, PCR-RFLP and 16S rRNA, atpD, recA and nodC gene sequences. Results indicated that P. vulgaris in Kenya is nodulated by at least six Rhizobium genospecies, with most of the isolates belonging to Rhizobium phaseoli and a possibly novel Rhizobium species...
March 9, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29555111/microbiota-composition-gene-pool-and-its-expression-in-gir-cattle-bos-indicus-rumen-under-different-forage-diets-using-metagenomic-and-metatranscriptomic-approaches
#14
Ramesh J Pandit, Ankit T Hinsu, Shriram H Patel, Subhash J Jakhesara, Prakash G Koringa, Fosso Bruno, Androniki Psifidi, S V Shah, Chaitanya G Joshi
Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes...
March 9, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29452714/genetic-diversity-and-structure-of-rhizobium-leguminosarum-populations-associated-with-clover-plants-are-influenced-by-local-environmental-variables
#15
Andrei Stefan, Jannick Van Cauwenberghe, Craita M Rosu, Catalina Stedel, Nikolaos E Labrou, Emmanouil Flemetakis, Rodica C Efrose
The identification and conservation of indigenous rhizobia associated with legume plants and their application as biofertilizers is becoming an agricultural worldwide priority. However, little is known about the genetic diversity and phylogeny of rhizobia in Romania. In the present study, the genetic diversity and population composition of Rhizobium leguminosarum symbiovar trifolii isolates from 12 clover plants populations located across two regions in Romania were analyzed. Red clover isolates were phenotypically evaluated and genotyped by sequencing 16S rRNA gene, 16S-23S intergenic spacer, three chromosomal genes (atpD, glnII and recA) and two plasmid genes (nifH and nodA)...
May 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29429564/genomic-comparison-between-members-of-the-salinibacteraceae-family-and-description-of-a-new-species-of-salinibacter-salinibacter-altiplanensis-sp-nov-isolated-from-high-altitude-hypersaline-environments-of-the-argentinian-altiplano
#16
Tomeu Viver, Luis Orellana, Pedro González-Torres, Sara Díaz, Mercedes Urdiain, María Eugenia Farías, Vladimir Benes, Peter Kaempfer, Azadeh Shahinpei, Mohammad Ali Amoozegar, Rudolf Amann, Josefa Antón, Konstantinos T Konstantinidis, Ramon Rosselló-Móra
The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability...
May 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29426637/agrobacterium-rosae-sp-nov-isolated-from-galls-on-different-agricultural-crops
#17
Nemanja Kuzmanović, Joanna Puławska, Kornelia Smalla, Xavier Nesme
The plant tumorigenic strain NCPPB 1650T isolated from Rosa×hybrida, and four nonpathogenic strains isolated from tumors on grapevine (strain 384), raspberry (strain 839) and blueberry (strains B20.3 and B25.3) were characterized by using polyphasic taxonomic methods. Based on 16S rRNA gene phylogeny, strains were clustered within the genus Agrobacterium. Furthermore, multilocus sequence analysis (MLSA) based on the partial sequences of atpD, recA and rpoB housekeeping genes indicated that five strains studied form a novel Agrobacterium species...
May 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29426636/phylogenetic-relationships-among-endosymbiotic-r-body-producer-bacteria-providing-their-host-the-killer-trait
#18
Martina Schrallhammer, Michele Castelli, Giulio Petroni
R-body producing bacterial endosymbionts of Paramecium spp. transform their hosts into "killer" paramecia and provide them a selective advantage. This killer trait is connected to the presence of R-bodies, which are peculiar, tightly coiled protein ribbons capable of rapid unrolling. Based mainly on those two characteristics the respective obligate intracellular bacteria have been comprised in the genus Caedibacter and additional traits such as host species, subcellular localization, and R-body dimensions and mode of unrolling were used for species discrimination...
May 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29402492/agrobacterium-bohemicum-sp-nov-isolated-from-poppy-seed-wastes-in-central-bohemia
#19
Jiří Zahradník, Jaroslav Nunvar, Hana Pařízková, Lucie Kolářová, Andrea Palyzová, Helena Marešová, Michal Grulich, Eva Kyslíková, Pavel Kyslík
Two non-pathogenic strains R89-1 and R90T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261T and Agrobacterium skierniewicense Ch11T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains...
May 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29395538/bacillus-onubensis-sp-nov-isolated-from-the-air-of-two-andalusian-caves
#20
Irene Dominguez-Moñino, Valme Jurado, Jose L Gonzalez-Pimentel, Ana Zelia Miller, Bernardo Hermosin, Cesareo Saiz-Jimenez
Two Gram-positive, catalase-positive, oxidase-negative, motile, endospore-forming, rod-shaped bacteria, designated as 0911MAR22V3T and 0911TES10J4, were isolated from air samples collected in two show caves, located in Andalusia, Southern Spain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains were indistinguishable and they were most closely related to Bacillus humi DSM 16318T (98%). DNA-DNA hybridization values of the strain 0911MAR22V3T with respect to strain 0911TES10J4 and B...
May 2018: Systematic and Applied Microbiology
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