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Systematic and Applied Microbiology

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
Alexandr Nemec, Lenka Radolfová-Křížová, Martina Maixnerová, Matěj Nemec, Dominique Clermont, Jaroslav Bzdil, Petr Ježek, Petra Španělová
In 1986, Bouvet and Grimont delineated two related taxa of the genus Acinetobacter termed genospecies (GS) 8 and 9. They proposed the name Acinetobacter lwoffii for GS8, which included the supposed type strain (CIP 64.10). As the authenticity of CIP 64.10 was later questioned, this study aimed at reassessing the taxonomy of these genospecies. We investigated 52 strains of GS8 or GS9, including CIP 64.10 and the genuine type strain of A. lwoffii (NCTC 5866T ). All strains were subjected to the genus-wide comparative analyses of MALDI-TOF whole-cell mass spectra, rpoB gene sequences and metabolic traits while whole-genome sequences were analysed for 16 strains...
October 12, 2018: Systematic and Applied Microbiology
Zhaojun Ji, Tianyan Liu, Jixing Zhang, Hui Yan, Entao Wang, Qingguo Cui, Wenxin Chen, Wenfeng Chen
Distribution of rhizobial species is affected by geographical isolation and selected by leguminous hosts, however, little is known about the molecular evolution of rhizobia nodulating the same legume in different eco-environments. In present study, the microevolution of Bradyrhizobium associated with the leguminous grass Kummerowia grown in exurban areas and cultivated in urban areas in China was investigated. Total 14 genospecies, including seven new groups, were identified based on a concatenated sequence analysis of taxonomic markers (SMc00019, truA and thrA) for 94 representative strains...
October 12, 2018: Systematic and Applied Microbiology
Marike Palmer, Stephanus N Venter, Martin P A Coetzee, Emma T Steenkamp
Many gene flow barriers associated with genetic isolation during eukaryotic species divergence, are lacking in prokaryotes. In these organisms the processes associated with horizontal gene transfer (HGT) may provide both the homogenizing force needed for genetic cohesion and the genetic variation essential to speciation. This is because HGT events can broadly be grouped into genetic conversions (where endogenous genetic material are replaced with homologs acquired from external sources) and genetic introductions (where novel genetic material is acquired from external sources)...
October 11, 2018: Systematic and Applied Microbiology
Jörg Böllmann, Steffen Engelbrecht, Marion Martienssen
An enrichment culture of Candidatus Brocadia fulgida was identified by three independent methods: analysis of autofluorescence using different microscope filter blocks and a fluorescence spectrometer, fluorescence in situ hybridization (FISH) with anammox-specific probes and partial sequencing of the 16S rDNA, hydrazine synthase hzsA and hydrazine oxidoreductase hzo. The filter block BV-2A (400-440, 470 LP, Nikon) was suitable for preliminary detection of Ca. B. fulgida. An excitation-emission matrix revealed three pairs of excitation-emission maxima: 288-330 nm, 288-478 nm and 417-478 nm...
September 20, 2018: Systematic and Applied Microbiology
Amalia Soenens, Margarita Gomila, Juan Imperial
We describe for the first time a non-symbiotic species of the recently described genus Neorhizobium, lacking nodulation or nitrogen fixation genes. The strains were isolated from a dryland agricultural soil in southern Spain where no record of legume cultivation is available, thus we propose the name Neorhizobium tomejilense sp. nov. (type strain T17_20T , LMG 30623T and CECT 9621T ). N. tomejilense exhibit a clear distinct lineage from the other Neorhizobium species, Neorhizobium galegae, Neorhizobium alkalisoli and Neorhizobium huautlense, based on polyphasic evidence...
September 17, 2018: Systematic and Applied Microbiology
Vitaly V Kadnikov, Andrey V Mardanov, Alexey V Beletsky, Andrey L Rakitin, Yulia A Frank, Olga V Karnachuk, Nikolai V Ravin
Candidate bacterial phylum BRC1 has been identified in a broad range of mostly organic-rich oxic and anoxic environments through molecular analysis of microbial communities. None of the members of BRC1 have been cultivated and only a few draft genome sequences have been obtained from metagenomes or as a result of single-cell sequencing. We have reconstructed complete genome of BRC1 bacterium, BY40, from metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia, and used it for metabolic reconstruction and comparison with existing genomic data...
September 3, 2018: Systematic and Applied Microbiology
Pascal Bartling, John Vollmers, Jörn Petersen
Many marine Alphaproteobacteria of the Roseobacter group show a characteristic swim-or-stick lifestyle, for which motility is a crucial trait. Three phylogenetically distinct flagellar gene clusters (FGCs) have been identified in Rhodobacteraceae that have been named fla1, fla2 and fla3 according to their relative abundance. In addition to the flagellar-dependent swimming and swarming motility, pilus-dependent twitching mediates bacterial locomotion. Furthermore, filament independent modes of motility, namely gliding and sliding, have been described for various microorganisms...
September 1, 2018: Systematic and Applied Microbiology
Jun-Lian Gao, Pengbo Sun, Xiao-Hong Sun, Shuai Tong, Hui Yan, Mei-Lin Han, Xiao-Jie Mao, Jian-Guang Sun
Four bacterial strains designated 410T , 441, 695T and 736 were isolated from maize root in Beijing, P. R. China. Based on 16S rRNA gene phylogeny, the four strains formed two clusters in the genus Caulobacter. Since strain 441 was a clonal variety of strain 410T , only three strains were selected for further taxonomic studies. The whole genome average nucleotide identity (ANI) value between strains 410T and 695T was 94.65%, and both strains shared less than 92.10% ANI values with their close phylogenetic neighbors Caulobacter vibrioides DSM 9893T , Caulobacter segnis ATCC 21756T and Caulobacter flavus CGMCC 1...
August 25, 2018: Systematic and Applied Microbiology
En-Min Zhou, Wen-Dong Xian, Jian-Yu Jiao, Lan Liu, Meng-Meng Li, Yi-Ping Ding, Yi-Rui Yin, Jiao Zhao, Salam Nimaichand, Min Xiao, Wen-Jun Li
Two closely related, thermophilic bacteria, designated strains YIM 76954T and YIM 76947, were isolated from the Rehai Geothermal Field, Tengchong, Yunnan province, south-west China. Polyphasic approach and whole genome sequencing were used to determine the taxonomy status and genomic profiles of the novel strains. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates were closely related to Thermus scotoductus SE-1T (97.1% sequence similarity), and T. amyloliquefaciens YIM 77409T (96...
August 25, 2018: Systematic and Applied Microbiology
Jörg Overmann, Sixing Huang, Ulrich Nübel, Richard L Hahnke, Brian J Tindall
To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species...
August 24, 2018: Systematic and Applied Microbiology
Yuyang Liu, Jiwen Liu, Peng Yao, Tiantian Ge, Yanlu Qiao, Meixun Zhao, Xiao-Hua Zhang
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) vary in their contribution to nitrification in different environments. The eastern China marginal seas (ECMS) are featured by complex river runoffs and ocean currents, forming different sediment patches. Here, via quantitative PCR and clone library analysis of the amoA genes, we showed that AOB were more abundant than AOA in ECMS sediments. The abundance, diversity and richness of AOA, but not AOB, were higher in the East China Sea (ECS) than in the Yellow Sea (YS) and Bohai Sea (BS)...
August 23, 2018: Systematic and Applied Microbiology
Monica Modesto, Edoardo Puglisi, Andrea Bonetti, Samanta Michelini, Caterina Spiezio, Camillo Sandri, Barbara Sgorbati, Lorenzo Morelli, Paola Mattarelli
Four novel Gram-stain-positive, non spore forming and fructose-6-phosphate phosphoketolase-positive strains were isolated from the faeces of a cotton top tamarin (Saguinus oedipus) and an emperor tamarin (Saguinus imperator). Phylogenetic analyses based on 16S rRNA revealed that bifidobacterial strains TRE 1T exhibit close phylogenetic relatedness to Bifidobacterium catulorum DSM 103154 (96.0%) and Bifidobacterium tissieri DSM 100201 (96.0%); TRE DT and TRE HT were closely related to Bifidobacterium longum subsp...
August 23, 2018: Systematic and Applied Microbiology
T Ben Francis, Karen Krüger, Bernhard M Fuchs, Hanno Teeling, Rudolf I Amann
Microbial degradation of algal biomass following spring phytoplankton blooms has been characterised as a concerted effort among multiple clades of heterotrophic bacteria. Despite their significance to overall carbon turnover, many of these clades have resisted cultivation. One clade known from 16S rRNA gene sequencing surveys at Helgoland in the North Sea, was formerly identified as belonging to the genus Ulvibacter. This clade rapidly responds to algal blooms, transiently making up as much as 20% of the free-living bacterioplankton...
August 20, 2018: Systematic and Applied Microbiology
Emily St John, Yitai Liu, Mircea Podar, Matthew B Stott, Jennifer Meneghin, Zhiqiang Chen, Kirill Lagutin, Kevin Mitchell, Anna-Louise Reysenbach
Three thermophilic Nanoarchaeota-Crenarchaeota symbiotic systems have been described. We obtained another stable anaerobic enrichment culture at 80°C, pH 6.0 from a New Zealand hot spring. The nanoarchaeote (Ncl-1) and its host (NZ3T ) were isolated in co-culture and their genomes assembled. The small (∼200nm) flagellated cocci were often attached to larger cocci. Based on 16S rRNA gene similarity (88.4%) and average amino acid identity (52%), Ncl-1 is closely related to Candidatus Nanopusillus acidilobi...
August 16, 2018: Systematic and Applied Microbiology
Jure Škraban, Ilse Cleenwerck, Peter Vandamme, Lijana Fanedl, Janja Trček
Strains T5K1 and AV446 isolated from apple cider vinegars during a submerged vinegar production in two separate vinegar facilities showed 94% 16S rRNA gene similarity to its closest neighbors Komagataeibacter maltaceti LMG 1529T and Gluconacetobacter entanii LTH 4560T . Further phylogenetic and phenotypic characterizations indicated that the isolates belonged to a novel species of the Komagataeibacter genus. Comparison based on 16S-23S rRNA gene ITS sequences and concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, grouped both strains to a single phylogenetic cluster well separated from the other species of the Komagataeibacter genus...
August 16, 2018: Systematic and Applied Microbiology
Martin H Andersen, Simon J McIlroy, Marta Nierychlo, Per H Nielsen, Mads Albertsen
Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. These filaments are often members of the phylum Chloroflexi, sometimes reaching abundances in excess of 30% of the biovolume. The uncultured Chloroflexi phylotype, Candidatus Amarolinea, has been observed in high abundances in Danish full-scale activated sludge systems by 16S rRNA gene amplicon surveys, where it has been associated with bulking. In this study, fluorescence in situ hybridization was applied to confirm their high abundance, filamentous morphology, and contribution to the interfloc bridging that characterizes filamentous bulking...
August 16, 2018: Systematic and Applied Microbiology
Habibu Aliyu, Pedro Lebre, Jochen Blom, Don Cowan, Pieter De Maayer
No abstract text is available yet for this article.
September 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...
September 2018: 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...
September 2018: Systematic and Applied Microbiology
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