Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode

Wu, Yanrui; Wang, Yilian; Li, Jishun; Hu, Jindong; Chen, Kai; Wei, Yanli; Bazhanov, D. P.; Bazhanova, A. A.; He-tong, Yang

doi:10.1128/genomea.00015-15

Cited by 9 publications

(6 citation statements)

References 18 publications

(16 reference statements)

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“…Several isolates belonging to this genus were demonstrated to possess plant-growth promoting properties (Calciolari and Silva, 2013;Islam et al, 2015). The same abilities were observed for a rhizospheric S. maltophilia strain and confirmed through genome sequencing (Wu et al, 2015). Furthermore, some plant-associated Stenotrophomonas strains were reported as able to degrade oil hydrocarbons (Ali et al, 2012) and phenanthrene (Muratova et al, 2015).…”

Section: Phylogenetic Diversitysupporting

confidence: 56%

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

Gandolfi

Canedoli

Imperato

et al. 2017

Environmental Pollution

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Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. The diversity of alkane hydroxylase (alkB) phylotypes harboured by phyllospheric bacteria associated to urban Platanus trees was also evaluated. Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. On the contrary, diversity of hydrocarbon-degrading populations increased over the months, although it resulted lower than that reported for other habitats. It was therefore hypothesized that atmospheric hydrocarbons might play a key role in the selection of phyllospheric populations in urban areas.

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Section: Phylogenetic Diversitysupporting

confidence: 56%

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

Gandolfi

Canedoli

Imperato

et al. 2017

Environmental Pollution

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“…Its sister group is Sm10. It holds 9 strains of contrasting geographic and ecological provenances, ranging from Chinese soil and plant-associated bacteria like the rice-root endophyte RR10 (Zhu et al, 2012 ), the grassland-soil tetracycline degrading isolate DT1 (Naas et al, 2008 ), and strain B418, isolated from a barley rhizosphere and displaying plant-growth promotion properties (Wu et al, 2015 ), to clinical isolates (22_SMAL, 179_SMAL, 453_SMAL, 517_SMAL) collected and studied in the context of a large genome sequencing project carried out at the University of Washington Medical Center (Roach et al, 2015 ). Cluster Sm11 tightly groups the well-characterized poplar endophyte R551-3, which is a model plant-growth-promoting bacterium (Ryan et al, 2009 ; Taghavi et al, 2009 ; Alavi et al, 2014 ) and SBo1, cultured from the gut of the olive fruit fly Bactrocera oleae (Blow et al, 2016 ).…”

Section: Resultsmentioning

confidence: 99%

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

2018

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The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

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“…These reactions are dependent to a large extent to VP2 and also VP5, which are the most variable proteins in BTV; VP2 especially contains the most epitopes that drive neutralizing antibodies production and therefore is the main determinant of the serotype [ 4 ]. To date, 27 serotypes have been identified, including BTV25 identified in Switzerland in 2007 [ 5 ], BTV26 from Kuwait in 2010 [ 4 ] and BTV27 detected in goats in Corsica (France) in 2014 [ 6 ]. In addition, two putative new serotypes, respectively BTV28 and BTV29 were recently detected [ 7 ].…”

Section: Introductionmentioning

confidence: 99%

Experimental bluetongue virus superinfection in calves previously immunized with bluetongue virus serotype 8

Martinelle

Pozzo

Sarradin

et al. 2016

Vet Res

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The effect of a superinfection with bluetongue virus serotype 1 (BTV1) was evaluated on two groups of four calves. One group received a commercial inactivated BTV serotype 8 (BTV8) vaccine. This group and the non-vaccinated group of calves were challenged twice (4 months apart) with the European BTV8 strain isolated during the 2006–2007 epidemics. Calves were then infected with a BTV1 inoculum which was found to be unexpectedly contaminated by BTV serotype 15 (BTV15). BTV1 and BTV15 single infections were performed on two other groups of three BTV naïve calves. A severe clinical picture was obtained after superinfection with BTV1/BTV15 in both vaccinated and non-vaccinated animals and after challenge with BTV8 in non-vaccinated animals. BTV1 and BTV15 single infection caused only very slight clinical signs. After superinfection and at the viraemic peak, there were an average of above 1000 times more BTV15 genomic copies than BTV1 ones. BTV1 RNA could be detected only in the spleen of one calf whereas BTV15 RNA was found in 15 organs of seven different animals. BTV8 immunization whether it was acquired through vaccination and challenges or challenges alone did not change BTV1 or BTV15 RNA detection in superinfected animals. However in these animals a partial cross neutralization between BTV8 and BTV1 might be involved in the lower BTV1 replication versus BTV15. Infection with different serotypes can occur also in the field. Interference between virus strains, genetic reassortment and cross-protection were considered as mechanisms to explain the clinical outcomes and the other virological and immunological findings in the course of BTV1/BTV15 superinfection.Electronic supplementary materialThe online version of this article (doi:10.1186/s13567-016-0357-6) contains supplementary material, which is available to authorized users.

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Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode

Cited by 9 publications

References 18 publications

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

Experimental bluetongue virus superinfection in calves previously immunized with bluetongue virus serotype 8

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