scholarly journals Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species

2020 ◽  
Vol 21 (14) ◽  
pp. 4922
Author(s):  
Artur Pinski ◽  
Joanna Zur ◽  
Robert Hasterok ◽  
Katarzyna Hupert-Kocurek
Keyword(s):  
Comparative Genomics ◽  
Stenotrophomonas Maltophilia ◽  
Growth Promotion ◽  
Genetic Differences ◽  
Cold Shock Protein ◽  
Promising Alternative ◽  
Genetic Features ◽  
Characteristic Features ◽  
Stenotrophomonas Rhizophila ◽  
Chitin Binding Protein

Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.

scholarly journals Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

2021 ◽  
Vol 9 (4) ◽  
pp. 757
Author(s):  
Qing-Mei Li ◽  
Ying-Li Zhou ◽  
Zhan-Fei Wei ◽  
Yong Wang
Keyword(s):  
Comparative Genomics ◽  
Deep Sea ◽  
Binding Protein ◽  
Glycerol Metabolism ◽  
Metabolic Reconstruction ◽  
Type Ii Secretion ◽  
Phylogenetic Groups ◽  
Genes Encoding ◽  
Epipelagic Zone ◽  
Chitin Binding Protein

Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

scholarly journals Symbiotic and non-symbiotic members of the genus Ensifer (syn. Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping

2020 ◽  
Author(s):  
Camilla Fagorzi ◽  
Alexandru Ilie ◽  
Francesca Decorosi ◽  
Lisa Cangioli ◽  
Carlo Viti ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Comparative Genomics ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Associated Bacteria ◽  
Phenotypic Differences ◽  
Genetic Features ◽  
Alkaline Conditions ◽  
High Throughput Phenotyping ◽  
Acidic Conditions

ABSTRACTRhizobium – legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF emerged several times within the genus Ensifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “non-symbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of ten Ensifer strains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

scholarly journals Comparative Genomics Reveals Potential Mechanisms of Plant Beneficial Effects of a Novel Bamboo-Endophytic Bacterial Isolate Paraburkholderia sacchari Suichang626

2021 ◽  
Vol 12 ◽  
Author(s):  
Kai Wang ◽  
Ying Wu ◽  
Mengyuan Ye ◽  
Yifan Yang ◽  
Fred O. Asiegbu ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Plant Growth ◽  
Growth Promotion ◽  
Moso Bamboo ◽  
Associated Bacteria ◽  
Beneficial Effects ◽  
Genome Wide ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Genome Information

Plant-beneficial microbes have drawn wide attention due to their potential application as bio-control agents and bio-fertilizers. Moso bamboo, which is among the monocots with the highest growth rate, lives perennially with abundant microbes that may benefit annually growing crops. Genome information of moso bamboo associated bacteria remains underexplored. We isolated and identified a novel Paraburkholderia strain Suichang626 from moso bamboo roots. Growth promoting effects of Suichang626 on both moso bamboo and seedlings of the model dicot Arabidopsis thaliana were documented in laboratory conditions. To gain insight into the genetic basis of this growth promotion effect, we sequenced the genome of Suichang626. Evidenced by genome-wide phylogeny data, we propose that Suichang626 is a novel strain of Paraburkholderia sacchari. Gene homologs encoding biosynthesis of the plant growth-promoting chemicals, acetoin and 2,3-butanediol, were identified in the genome of Suichang626. Comparative genomics was further performed with plant-beneficial and plant/animal pathogenic species of Paraburkholderia and Burkholderia. Genes related to volatile organic compounds, nitrogen fixation, and auxin biosynthesis were discovered specifically in the plant growth-promoting species of both genera.

scholarly journals Phylogenomic insights into distribution and adaptation of Bdellovibrionota in marine waters

2020 ◽  
Author(s):  
Qing-Mei Li ◽  
Ying-Li Zhou ◽  
Zhan-Fei Wei ◽  
Yong Wang
Keyword(s):  
Comparative Genomics ◽  
Marine Environment ◽  
Deep Sea ◽  
Binding Protein ◽  
Glycerol Metabolism ◽  
Metabolic Reconstruction ◽  
Gram Negative Bacteria ◽  
Phylogenetic Groups ◽  
Gram Negative ◽  
Chitin Binding Protein

AbstractBdellovibrionota is composed of obligate predators that can consume some gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies on 82 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ABC transporters and penicillin-binding protein were necessary for predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, meanwhile, all the marine genomes have a number of related genes for adapting marine environment. The chitinase and chitin-binding protein encoding genes were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey a wider spectrum of microbes. This study expanded our knowledge on adaption strategies of Bdellovibrionota inhabiting deep sea and their potential usage for biological control.ImportanceBdellovibrionota can prey gram-negative bacteria proposed as biocontrol agent. Available Bdellovibrionota genomes showed that most are from marine environment. However, vertical distribution and adaption of Bdellovibrionota in deep sea has not been reported. Our study of Bdellovibrionota revealed four groups (Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia) and their distribution pattern in oceans. We also identified the genes for different phases of predation and adaptation in deep-sea environment. Moreover, Oligoflexia genomes contain more genes for carbohydrates utilization and particularly those encoding chitin-binding protein and chitinase. Our analyses of Bdellovibrionota genomes may help understand their special lifestyle and deep-sea adaptation.

scholarly journals In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes

2020 ◽  
Vol 33 (2) ◽  
pp. 349-363 ◽  
Author(s):  
Susan Mosquito ◽  
Iris Bertani ◽  
Danilo Licastro ◽  
Stéphane Compant ◽  
Michael P. Myers ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Growth Promotion ◽  
Rice Seed ◽  
In Planta ◽  
Root Cortex ◽  
Knock Out ◽  
Colonization Ability ◽  
Secretory System ◽  
Secretome Profiling

Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant–bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant–bacteria interaction.

scholarly journals Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

2019 ◽  
Vol 222 (3) ◽  
pp. 1584-1598 ◽  
Author(s):  
Emmanuelle Morin ◽  
Shingo Miyauchi ◽  
Hélène San Clemente ◽  
Eric C. H. Chen ◽  
Adrian Pelin ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Rhizophagus Irregularis ◽  
Gigaspora Rosea ◽  
Genetic Features

scholarly journals A molecular biological protocol to distinguish potentially human pathogenic Stenotrophomonas maltophilia from plant-associated Stenotrophomonas rhizophila

2005 ◽  
Vol 7 (11) ◽  
pp. 1853-1858 ◽  
Author(s):  
Kathrin Ribbeck-Busch ◽  
Anja Roder ◽  
Dirk Hasse ◽  
Wietse de Boer ◽  
Jose Luis Martinez ◽  
...  
Keyword(s):  
Stenotrophomonas Maltophilia ◽  
Stenotrophomonas Rhizophila

scholarly journals The mode of action of plant associated Burkholderia against grey mould disease in grapevine revealed through traits and genomic analyses

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qassim Esmaeel ◽  
Cédric Jacquard ◽  
Lisa Sanchez ◽  
Christophe Clément ◽  
Essaid Ait Barka
Keyword(s):  
Growth Promotion ◽  
In Silico Analysis ◽  
Grey Mould ◽  
Transcript Level ◽  
Systemic Resistance ◽  
Mycelium Growth ◽  
Callose Deposition ◽  
Promising Alternative ◽  
Agricultural Applications ◽  
Biocontrol Potential

Abstract Plant-associated Burkholderia spp. have been shown to offer a promising alternative method that may address concerns with ecological issue associated with pesticide overuse in agriculture. However to date, little work has studied the role of Burkholderia species as biocontrol agents for grapevine pathogens. To this end, two Burkholderia strains, BE17 and BE24 isolated from the maize rhizosphere in France, were investigated to determine their biocontrol potential and their ability to induce systemic resistance against grey mould disease in grapevine. Results showed the capacity of both strains to inhibit spore germination and mycelium growth of Botrytis cinerea. Experimental inoculation with BE17 and BE24 showed a significant protection of bacterized-plantlets against grey mould compared to the non-bacterized control. BE17 and BE24-bacterized plants accumulated more reactive oxygen species and an increased callose deposition was observed in leaves of bacterized plantlets compared to the control plantlets. In bacterized plants, gene expression analysis subsequent to B. cinerea challenge showed that strains BE17 and BE24 significantly increased the relative transcript level of pathogenesis-related (PR) proteins PR5 and PR10, two markers involved in the Salicylic acid (SA)-signaling pathway. Furthermore, in silico analysis of strains revealed the presence of genes involved in plant growth promotion and biocontrol highlighting the attractiveness of these strains for sustainable agricultural applications.

Genetic Analysis Using Microsphere Arrays

2005 ◽  
Author(s):  
John P. Nolan ◽  
Alina Desphande
Keyword(s):  
Flow Cytometry ◽  
Genetic Analysis ◽  
Sequence Data ◽  
Genome Project ◽  
High Throughput Analysis ◽  
New Associations ◽  
Disease States ◽  
Genetic Features ◽  
Characteristic Features ◽  
New Perspective

The use of DNA microarrays to analyze simultaneously many genetic features from a sample is providing a new perspective on the effect of the genome on normal biological processes and disease states. The translation of this new perspective into new diagnostics and treatments will require development of microarray technology to enable cost-effective, high-throughput analysis of many samples. Microsphere arrays—sets of optically encoded microparticles—measured by flow cytometry are an experimentally flexible alternative to the flat-surface microarrays that are being used in a variety of biomedical analyses. In this chapter, we review the major areas where microsphere arrays are being used for genetic analysis and discuss the key experimental considerations that enable these and future applications. The human genome project and other genome projects have opened great new possibilities for biomedical research. Along with these new possibilities have come new technical challenges involving the conversion of raw DNA sequence data into useful information for basic research, diagnostic, and therapeutic applications. Applications include the discovery of new associations between diseases and specific genes, the evaluation of genetic predisposition to disease, and the prediction of the response of individual patients to drugs. In the areas of public health, addressing issues such as infectious disease, food safety, and bioterrorism can all be enhanced through molecular analysis. Perhaps the most daunting challenge involves the specific analysis of hundreds or thousands of genetic features in hundreds or thousands of individual samples. To address these challenges, a variety of analytical methods and platforms are being developed, ranging from laboratory methods such as mass spectrometry to portable microfluidic devices. Each of these assay platforms has characteristic features that determine sensitivity, throughput, and flexibility. Flow cytometry is among the most versatile of analytical platforms, providing sensitive and quantitative multiparameter fluorescence measurements of cells and microparticles with high analysis rates. These features underlie the development of several current and emerging genetic analysis tools. One of the earliest flow cytometric measurements was a genetic analysis of a sort— the measurement of relative DNA content in individual cells using fluorescent DNA binding dyes.

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