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Showing papers in "Systematic and Applied Microbiology in 2019"


Journal ArticleDOI
TL;DR: Assessment of experiments that assessed how endophytic Pseudomonas stutzeri A1501 inoculated on maize improved plant growth and plant nitrogen content using a 15N dilution technique under two water regime conditions revealed that soil compartment and A 1501 inoculation treatments were the main factors affecting the distribution of the diazotrophic community.

73 citations


Journal ArticleDOI
TL;DR: Genome quality standards need to be considered to ensure unambiguous assignment of type material and nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code is proposed.

67 citations


Journal ArticleDOI
TL;DR: This study presents the first robust Bradyrhizobium species phylogeny based on genome sequence information for investigating the evolution of this important assemblage of bacteria.

53 citations


Journal ArticleDOI
TL;DR: Based on phylogenetic, physiological and genomic data, Ncl-1 and NZ3T represent novel genera in the Nanoarchaeota and the Desulfurococcaceae, respectively, with the proposed names Candidatus Nanoclepta minutus and Zestosphaera tikiterensis.

48 citations


Journal ArticleDOI
TL;DR: The multispecies inoculum of PGPRs containing Rhizobium phaseoli, SinorhizOBium americanum and Azospirillum brasilense nitrogen-fixing strains and other plant-growth promoting bacteria exerted a beneficial effect on maize plants that was greater than that obtained with single-bacteria.

44 citations


Journal ArticleDOI
TL;DR: Analysis of the 16S rRNA, 23S r RNA and whole genome sequences as well as MLST, ANIb and TETRA values reveal that C. abortus are the closest relatives of RSHA, suggesting a phylogenetic intermediate position between these two species.

40 citations


Journal ArticleDOI
TL;DR: The genome sequencing of the strains 2M, 9M and DPMP600 and their comparison with whole genome sequences of other Pectobacterium type strains confirmed their distinctiveness and separate species status within the genus based on parameters of in silico DNA-DNA hybridization and average nucleotide identity (ANI) values.

36 citations


Journal ArticleDOI
TL;DR: The results support the proposal of two novel species Bifidobacterium xylocopae sp.

33 citations


Journal ArticleDOI
TL;DR: 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 thenomenclatural code, and the roles of an official or computer-assisted taxonomy.

33 citations


Journal ArticleDOI
TL;DR: Fluorescence in situ hybridization was applied to confirm their high abundance, filamentous morphology, and contribution to the interfloc bridging that characterizes filamentous bulking, and genome-centric metagenomics using both Illumina and Oxford Nanopore sequencing was used to obtain a near complete population genome of the Ca.

33 citations



Journal ArticleDOI
TL;DR: The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches, to tackle microbial population diversity in extreme environments.

Journal ArticleDOI
TL;DR: Phylogenetic analyses provided evidence of horizontal transfer for PMU-like elements from various phytoplasmas, including distantly related ones, and the availability of this high-quality draft genome provided a foundation for genome-scale genotypic analysis and molecular phylogenetic analysis.

Journal ArticleDOI
Jiwen Liu1, Chun-Xu Xue1, Hao Sun1, Yanfen Zheng1, Zhe Meng1, Xiao-Hua Zhang1 
TL;DR: The discovery of higher glycoside hydrolase dissimilarities among Flavobacteriia, compared to peptidases and transporters, suggested variation in polysaccharide utilization related traits as an important ecophysiological factor in response to environmental alterations, such as decreased labile organic carbon in hadal waters.

Journal ArticleDOI
TL;DR: Metabolic reconstruction indicates this highly abundant species most likely degrades proteins and the polysaccharide laminarin, and for the most abundant and well characterised of the three species the name Candidatus Prosiliicoccus vernus.

Journal ArticleDOI
TL;DR: It is shown that rumen/hindgut Prevotella generally possess extensive repertoires of polysaccharide utilization loci (PULs) and carbohydrate active enzymes targeting various plant poly Saccharides and that finer diversity among generalists is evident too, both in range of substrates targeted and in PUL combinations targeting the same broad substrate classes.

Journal ArticleDOI
TL;DR: Phylogenetic analyses, average nucleotide identity data and digital DNA hybridizations, combined to phenotypic characteristics, resulted in the proposition and description of four new species i.e. Pseudomonas alloputida Kh7 T (= LMG 29756 T = CFBP 8484 T) sp.

Journal ArticleDOI
TL;DR: The collection of freshwater IIIb representatives is expanded and a new IIIb species of the genus "Ca. Fonsibacter" is described, proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems.


Journal ArticleDOI
TL;DR: Concerns are raised regarding the reliability and stability of nomenclature, the technological and conceptual limitations as well as availability of reference genomes, the information content of in silico functional predictions, and the recognition of evolutionary units of microbial diversity.

Journal ArticleDOI
TL;DR: In this article, the authors 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.

Journal ArticleDOI
TL;DR: Nine slow-growing rhizobia isolated from effective nodules on peanut were characterized to clarify the taxonomic status using a polyphasic approach and genotypic and phenotypic characteristics including sole carbon sources and growth features supported the phylogenetic results.

Journal ArticleDOI
TL;DR: A pluralistic approach to prokaryotic species recognition is required to accommodate the unique evolutionary ages and tendencies, population dynamics, and evolutionary fates of individual prokARYotic species.

Journal ArticleDOI
TL;DR: Phylogenetic analysis indicated that the isolates form an independent genus-level lineage within the family Natrialbaceae with 3 species-level subgroups, and it is suggested that the obligate alkaliphilic AArcht isolates with an identical phenotype are classified into a new genus and species.

Journal ArticleDOI
TL;DR: Cryobacterium and Arthrobacter are members of Actinobacteria, and are often found in cold environments, and in this study, 48 Cryobacteria strains, including 9 type strains and 39 new isolates collected from glaciers in China were subjected to multilocus sequence analysis (MLSA).

Journal ArticleDOI
TL;DR: The rhizobia isolated from nodules of these two legumes in Spain showed that, due its high promiscuity degree, P. vulgaris is able to establish symbiosis with local symbiovars well established in the soil after centuries of cultivation with other legumes.

Journal ArticleDOI
TL;DR: It is concluded that the name A. lwoffii pertains to GS9 and not to GS8 as originally assumed and that these groups represent two species.


Journal ArticleDOI
TL;DR: Assessment of the putative global distribution pattern of this novel lineage suggests its preference to anoxic marine, terrestrial, hydrocarbon-impacted, and freshwater habitats.

Journal ArticleDOI
TL;DR: The adapted and efficient rhizobial strains reported here were promising candidates for inoculant development and represent a contribution towards successful cultivation of L. albus in Tunisia, especially the most promising Mekna variety.