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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
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
Yuyin Yang, Jianfei Chen, Baoqin Li, Yong Liu, Shuguang Xie
Nitrite-dependent anaerobic methane oxidation (n-damo), mainly carried out by n-damo bacteria, is an important pathway for mitigating methane emission from freshwater lakes. Although n-damo bacteria have been detected in a variety of freshwater lakes, their potential and distribution, and associated environmental factors, remain unclear. Therefore, the current study investigated the potential and distribution of anaerobic methanotrophs in sediments from Erhai Lake and Dianchi Lake, two adjacent freshwater lakes in the Yunnan Plateau with different trophic status...
August 13, 2018: Systematic and Applied Microbiology
Ramya Krishnan, Elke Lang, Samriti Midha, Prabhu B Patil, N Rameshkumar
Three novel strains namely, L1E11T , L1E4 and 228 were isolated as a part of an ongoing study on 1-aminocyclopropane-1-carboxylate (ACC) deaminase expressing rhizobacteria from crops cultivated in saline affected coastal agro-ecosystems of Kerala, India. The novel strains were positive for many properties that are beneficial to plant growth including ACC deaminase (ACCd) activity that ranged from 1.87±0.27 to 2.88±0.71μmol of α-ketobutyrate/hr/mg of total protein. Presence of other traits such as biofilm formation, siderophore production, phosphate solubilisation, utilisation of root derived compounds and ability to colonise host roots indicates its plant-associated life style...
August 11, 2018: Systematic and Applied Microbiology
Sofie E De Meyer, Katinka X Ruthrof, Tom Edwards, Anna J M Hopkins, Giles Hardy, Graham O'Hara, John Howieson
Given that phosphate supplies may diminish and become uneconomic to mine after 2020, there is a compelling need to develop alternative industries to support the population on Christmas Island. Former mine sites could be turned into productive agricultural land, however, large-scale commercial agriculture has never been attempted, and, given the uniqueness of the island, the diversity of rhizobia prior to introducing legumes needed evaluation. Therefore, 84 rhizobia isolates were obtained from nine different hosts, both crop and introduced legumes, located at seven sites across the island...
August 4, 2018: Systematic and Applied Microbiology
Maria Chuvochina, Christian Rinke, Donovan H Parks, Michael S Rappé, Gene W Tyson, Pelin Yilmaz, William B Whitman, Philip Hugenholtz
Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum...
July 18, 2018: Systematic and Applied Microbiology
Ramon Rosselló-Móra, William B Whitman
The application of next generation sequencing and molecular ecology to the systematics and taxonomy of prokaryotes offers enormous insights into prokaryotic biology. This discussion explores some major disagreements but also considers the opportunities associated with the nomenclature of the uncultured taxa, the use of genome sequences as type material, the plurality of the nomenclatural code, and the roles of an official or computer-assisted taxonomy.
July 7, 2018: Systematic and Applied Microbiology
Di Fan, Timothy Schwinghamer, Donald L Smith
Plants are chronically associated with microorganisms, residing all tissues. Holonomic analysis of diversity of established rhizobacteria in uncultivated plants is scarce. Thus, the present study was conducted to access the root-associated bacterial diversity of 6 crops (maize, canola, soybean, reed canarygrass, alfafa, and miscanthus) and 20 uncultivated plant species in the region of Sainte-Anne-de-Bellevue, Québec, Canada, using pure-culture methods. Based on 16S rRNA gene sequence analysis, 446 bacterial isolates were distributed onto four phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes), 32 families and 90 genera...
July 3, 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
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...
September 2018: Systematic and Applied Microbiology
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