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Systematic and Applied Microbiology

Yuan Gong, Juan-Luan Bai, Huan-Ting Yang, Wen-Di Zhang, You-Wei Xiong, Peng Ding, Sheng Qin
Actinobacteria from special habitats are of interest due to their producing of bioactive compounds and diverse ecological functions. However, little is known of the diversity and functional traits of actinobacteria inhabiting coastal salt marsh soils. We assessed actinobacterial diversity from eight coastal salt marsh rhizosphere soils from Jiangsu Province, China, using culture-based and 16S rRNA gene high throughput sequencing (HTS) methods, in addition to evaluating their plant growth-promoting (PGP) traits of isolates...
June 12, 2018: Systematic and Applied Microbiology
Markus Santhosh Braun, Erjia Wang, Stefan Zimmermann, Michael Wink
Two strains (pedersoliT and girotti) of a new species of bacteria were isolated from the preen glands of wild Egyptian geese (Alopochen aegyptiacus) from the river Neckar in southern Germany in two subsequent years. The strains were lipophilic, fastidious, Gram-positive rods and belonged to the genus Corynebacterium. Phylogenetically, the isolates were most closely related to Corynebacterium falsenii DSM 44353T which has been found to be associated with birds before. 16S rRNA gene sequence similarity to all known Corynebacterium spp...
June 8, 2018: Systematic and Applied Microbiology
David R Singleton, Janice Lee, Allison N Dickey, Aaron Stroud, Elizabeth H Scholl, Fred A Wright, Michael D Aitken
Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced. Their 16S rRNA genes were highly similar to those previously recovered during stable-isotope probing (SIP) of one of the soils with the polycyclic aromatic hydrocarbon (PAH) phenanthrene. Heterotrophic growth of all strains occurred with a number of organic acids, as well as phenanthrene, but no other tested PAHs...
June 8, 2018: Systematic and Applied Microbiology
Adouda Salmi, Farida Boulila, Yasmina Bourebaba, Christine Le Roux, Djellali Belhadi, Philippe de Lajudie
Fifty-two slow-growing strains were isolated from root nodules of Calicotome spinosa grown in the Northeast of Algeria and grouped in 24 rep-PCR clusters. One representative strain for each profile was further phylogenetically characterized. The nearly complete 16S rRNA gene sequence indicated that all strains were affiliated to Bradyrhizobium. Multi-Locus Sequence Analysis (MLSA) of the atpD, glnII and recA genes and of the 16S-23S rRNA internal transcribed spacer (ITS) showed that these strains formed four divergent clusters: one close to Bradyrhizobium canariense and Bradyrhizobium lupini and three others separate from all the described species, representing three putative new Bradyrhizobium species...
May 31, 2018: Systematic and Applied Microbiology
Woon-Jong Yu, Jae-Won Lee, Ngoc-Loi Nguyen, Sung-Keun Rhee, Soo-Je Park
Methanotrophic bacteria are widespread and use methane as a sole carbon and energy source. They also play a crucial role in marine ecosystems by preventing the escape of methane into the atmosphere from diverse methane sources, such as methane seeps and hydrothermal vents. Despite their importance for methane carbon cycling, relatively few marine methanotrophic bacteria have been isolated and studied at the genomic level. Herein, we report the genome of a marine methanotrophic member of the genus Methylomicrobium, metagenome-assembled genome (MAG) wino1, which was obtained through enrichment using methane as the sole carbon source...
May 29, 2018: Systematic and Applied Microbiology
Alejandro M Labella, M Dolores Castro, Manuel Manchado, Teresa Lucena, David R Arahal, Juan J Borrego
Three strains, H01100409BT , H01100413B, and H27100402HT , were isolated from several internal organs of diseased redbanded seabream (Pagrus auriga) reared in Andalusia (Southern Spain). All strains were studied by phenotypic, including chemotaxonomy, and genomic characteristics. Phylogenetic analysis based on concatenated sequences of six housekeeping genes (gyrB, ftsZ, topA, mreB, gapA, and 16S rRNA) supported the inclusion of the strains within the clade Phosphoreum of the genus Photobacterium, and two of the strains (H27100402HT and H01100409BT ) formed a tight group separated from the closest species P...
May 24, 2018: Systematic and Applied Microbiology
Francisca A Burgos, Candis L Ray, Covadonga R Arias
The acquisition of gut microbes does not occur randomly and is highly dependent on host factors, environmental cues, and self-assembly rules exerted by the microbes themselves. The main objective of this project was to characterize how the gut microbiome develops during the early life stages of Channel Catfish and to identify i) which bacteria are the main constituents of the gut microbiome at different ontogenesis stages, and ii) at which time point(s) the gut microbiome stabilizes. High-throughput Illumina Miseq DNA sequencing of the V4 domain of the 16S rRNA gene was used to assess the microbial community composition during the life stages of Channel Catfish along with water and feed samples...
May 23, 2018: Systematic and Applied Microbiology
Cynthia Gyogluu, Sanjay K Jaiswal, Stephen Kyei-Boahen, Felix D Dakora
Indigenous soybean rhizobial strains were isolated from root nodules sampled from farmers' fields in Mozambique to determine their identity, distribution and symbiotic relationships. Plant infection assays revealed variable nodulation and symbiotic effectiveness among the 43 bacterial isolates tested. Strains from Ruace generally promoted greater whole-plant growth than the others. 16S rRNA-RFLP analysis of genomic DNA extracted from the rhizobial isolates produced different banding patterns, a clear indication of high bacterial diversity...
May 20, 2018: Systematic and Applied Microbiology
Samanta Michelini, Monica Modesto, Gianfranco Filippini, Caterina Spiezio, Camillo Sandri, Bruno Biavati, Annamaria Pisi, Paola Mattarelli
No abstract text is available yet for this article.
May 18, 2018: Systematic and Applied Microbiology
Hassiba Belahbib, Zarath M Summers, Marie-Laure Fardeau, Manon Joseph, Christian Tamburini, Alain Dolla, Bernard Ollivier, Fabrice Armougom
The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universal tree of life. Recent reshaping of the Thermotogae taxonomy has led to the description of a new genus, Pseudothermotoga, a sister group of the genus Thermotoga within the order Thermotogales...
May 16, 2018: Systematic and Applied Microbiology
Cheng-Tai Huang, Kuan-Ting Hish, Chun-Neng Wang, Chi-Te Liu, Wen-Yuan Kao
In this study, the genetic diversity and identification of Bradyrhizobium symbionts of Crotalaria zanzibarica, the most widely-distributed invasive legume in Taiwan, and other sympatric legume species growing along riverbanks of Taiwan were evaluated for the first time. In total, 59 and 54 Bradyrhizobium isolates were obtained from C. zanzibarica and its coexisting legume species, respectively. Based on the multilocus sequence analysis (MLSA) of concatenated four housekeeping genes (dnaK-glnII-recA-rpoB gene sequences, 1901bp), the 113 isolates displayed 53 unique haplotypes and grouped into 21 clades...
May 7, 2018: Systematic and Applied Microbiology
Abdelhakim Msaddak, Mokhtar Rejili, David Durán, Luis Rey, José Manuel Palacios, Juan Imperial, Tomás Ruiz-Argüeso, Mohamed Mars
In this study, a polyphasic approach was used to analyze three representative strains (LmiH4, LmiM2 and LmiT21) from a collection of six previously described strains isolated in Tunisia from root nodules of Lupinus micranthus. The phylogenetic analysis of the concatenated rrs, recA and glnII genes showed that strain LmiH4 had 100% concatenated gene sequence identity with the type strain Bradyrhizobium retamae Ro19T. Similarly, strain LmiM2 shared 100% concatenated gene sequence identity with the species Bradyrhizobium valentinum LmjM3T...
May 4, 2018: Systematic and Applied Microbiology
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
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
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
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
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
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
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
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
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