scholarly journals Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping

2020 ◽  
Vol 12 (12) ◽  
pp. 2521-2534
Author(s):  
Camilla Fagorzi ◽  
Alexandru Ilie ◽  
Francesca Decorosi ◽  
Lisa Cangioli ◽  
Carlo Viti ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Comparative Genomics ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Phenotypic Differences ◽  
Genetic Features ◽  
Alkaline Conditions ◽  
High Throughput Phenotyping ◽  
Acidic Conditions

Abstract Rhizobium–legume symbioses serve as paradigmatic examples 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 interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer 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 “nonsymbiotic” 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 nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic 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, the tested 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 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 Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov.

2019 ◽  
Vol 202 (2) ◽  
pp. 309-322 ◽  
Author(s):  
Guadalupe Rocha ◽  
Antoine Le Queré ◽  
Arturo Medina ◽  
Alma Cuéllar ◽  
José-Luis Contreras ◽  
...  
Keyword(s):  
High Temperatures ◽  
Sand Dune ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Wild Bean ◽  
Northern Mexico ◽  
Desert Sand ◽  
Wide Range ◽  
Alkaline Conditions ◽  
Strain Type

Abstract In northern Mexico, aridity, salinity and high temperatures limit areas that can be cultivated. To investigate the nature of nitrogen-fixing symbionts of Phaseolus filiformis, an adapted wild bean species native to this region, their phylogenies were inferred by MLSA. Most rhizobia recovered belong to the proposed new species Ensifer aridi. Phylogenetic analyses of nodC and nifH show that Mexican isolates carry symbiotic genes acquired through horizontal gene transfer that are divergent from those previously characterized among bean symbionts. These strains are salt tolerant, able to grow in alkaline conditions, high temperatures, and capable of utilizing a wide range of carbohydrates and organic acids as carbon sources for growth. This study improves the knowledge on diversity, geographic distribution and evolution of bean-nodulating rhizobia in Mexico and further enlarges the spectrum of microsymbiont with which Phaseolus species can interact with, including cultivated bean varieties, notably under stressed environments. Here, the species Ensifer aridi sp. nov. is proposed as strain type of the Moroccan isolate LMR001T (= LMG 31426T; = HAMBI 3707T) recovered from desert sand dune.

Characterization of Azomonas macrocytogenes strains isolated from Alberta soils

1987 ◽  
Vol 33 (9) ◽  
pp. 830-833 ◽  
Author(s):  
William J. Page ◽  
S. Karen Collinson
Keyword(s):  
Nitrogen Fixation ◽  
Agrobacterium Tumefaciens ◽  
Cell Morphology ◽  
Carbon Sources ◽  
Erwinia Carotovora ◽  
Growth Conditions ◽  
Dihydroxybenzoic Acid ◽  
Fluorescent Compound ◽  
Good Agreement

Five strains of Azomonas macrocytogenes were identified from a collection of aerobic nitrogen-fixing organisms obtained from Alberta soils. The cell morphology, colony appearance, and growth conditions of these five isolates and their use of nitrogen and carbon sources were in good agreement with four standard Azomonas macrocytogenes strains. The new strains did not produce N,N,N′,N′-tetramethyl-p-phenylenediamine-dependent cytochrome oxidase, were unable to form true cysts, formed blue–white fluorescent compound(s) under iron-limited conditions, and excreted 3,4-dihydroxybenzoic acid into culture fluids. The detection of this catechol proved to be more reliable and convenient than the observation of the red–violet colour of its ferrated form, which was a variable occurrence in older cultures. Four of the new strains were antagonistic to Agrobacterium tumefaciens and two strains stimulated Erwinia carotovora growth. The new strains also demonstrated nitrogen fixation under molybdate-deficient conditions, which suggested the presence of an alternative molybdate-independent nitrogenase.

scholarly journals Novel divergent nidovirus in a python with pneumonia

2014 ◽  
Vol 95 (11) ◽  
pp. 2480-2485 ◽  
Author(s):  
Rogier Bodewes ◽  
Charlotte Lempp ◽  
Anita C. Schürch ◽  
Andre Habierski ◽  
Kerstin Hahn ◽  
...  
Keyword(s):  
Animal Species ◽  
Phylogenetic Analyses ◽  
Disease Association ◽  
Necrotizing Pneumonia ◽  
Ribosomal Frameshift ◽  
Enveloped Viruses ◽  
Genetic Features ◽  
Python Molurus ◽  
Partial Genome

The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin–neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales.

scholarly journals Functional and Molecular Characterization of the Halomicrobium sp. IBSBa Inulosucrase

2021 ◽  
Vol 9 (4) ◽  
pp. 749
Author(s):  
Gülbahar Abaramak ◽  
Jaime Ricardo Porras-Domínguez ◽  
Henry Christopher Janse van Rensburg ◽  
Eveline Lescrinier ◽  
Ebru Toksoy Öner ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Halophilic Archaea ◽  
Maximum Activity ◽  
Physiological Relevance ◽  
Health Related ◽  
Specific Alternative ◽  
Binding Groove ◽  
Native Host

Fructans are fructose-based (poly)saccharides with inulin and levan being the best-known ones. Thanks to their health-related benefits, inulin-type fructans have been under the focus of scientific and industrial communities, though mostly represented by plant-based inulins, and rarely by microbial ones. Recently, it was discovered that some extremely halophilic Archaea are also able to synthesize fructans. Here, we describe the first in-depth functional and molecular characterization of an Archaeal inulosucrase from Halomicrobium sp. IBSBa (HmcIsc). The HmcIsc enzyme was recombinantly expressed and purified in Escherichia coli and shown to synthesize inulin as proven by nuclear magnetic resonance (NMR) analysis. In accordance with the halophilic lifestyle of its native host, the enzyme showed maximum activity at very high NaCl concentrations (3.5 M), with specific adaptations for that purpose. Phylogenetic analyses suggested that Archaeal inulosucrases have been acquired from halophilic bacilli through horizontal gene transfer, with a HX(H/F)T motif evolving further into a HXHT motif, together with a unique D residue creating the onset of a specific alternative acceptor binding groove. This work uncovers a novel area in fructan research, highlighting unexplored aspects of life in hypersaline habitats, and raising questions about the general physiological relevance of inulosucrases and their products in nature.

scholarly journals Molecular Characterization of PGC-1β (PPAR Gamma Coactivator 1β) and its Roles in Mitochondrial Biogenesis in Blunt Snout Bream (Megalobrama amblycephala)

2020 ◽  
Vol 21 (6) ◽  
pp. 1935 ◽  
Author(s):  
Kangle Lu ◽  
Tomas Policar ◽  
Xiaojun Song ◽  
Samad Rahimnejad
Keyword(s):  
Molecular Characterization ◽  
Mitochondrial Biogenesis ◽  
Phylogenetic Analyses ◽  
Ppar Gamma ◽  
Megalobrama Amblycephala ◽  
Fat Intake ◽  
High Fat ◽  
Blunt Snout Bream ◽  
Mitochondria Biogenesis

This study aimed at achieving the molecular characterization of peroxisome proliferator-activated receptor-gamma coactivator 1β (PGC-1β) and exploring its modulatory roles in mitochondria biogenesis in blunt snout bream (Megalobrama amblycephala). A full-length cDNA of PGC-1β was cloned from liver which covered 3110 bp encoding 859 amino acids. The conserved motifs of PGC-1β family proteins were gained by MEME software, and the phylogenetic analyses showed motif loss and rearrangement of PGC-1β in fish. The function of PGC-1β was evaluated through overexpression and knockdown of PGC-1β in primary hepatocytes of blunt snout bream. We observed overexpression of PGC-1β along with enhanced mitochondrial transcription factor A (TFAM) expression and mtDNA copies in hepatocytes, and its knockdown led to slightly reduced NRF1 expression. However, knockdown of PGC-1β did not significantly influence TFAM expression or mtDNA copies. The alterations in mitochondria biogenesis were assessed following high-fat intake, and the results showed that it induces downregulation of PGC-1β. Furthermore, significant decreases in mitochondrial respiratory chain activities and mitochondria biogenesis were observed by high-fat intake. Our findings demonstrated that overexpression of PGC-1β induces the enhancement of TFAM expression and mtDNA amount but not NRF-1. Therefore, it could be concluded that PGC-1β is involved in mitochondrial biogenesis in blunt snout bream but not through PGC-1β/NRF-1 pathway.

scholarly journals Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hongru Su ◽  
Eri Onoda ◽  
Hitoshi Tai ◽  
Hiromi Fujita ◽  
Shigetoshi Sakabe ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Housekeeping Genes ◽  
Pcr Screening ◽  
Taxonomic Profiling ◽  
Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

New perspectives on Aspersentis Megarhynchus (Acanthocephala: Heteracanthocephalidae) from Notothenia Coriiceps Richardson (Nototheniidae) in the West Antarctic, with emended generic diagnosis

2021 ◽  
Vol 95 ◽  
Author(s):  
O.M. Amin ◽  
R.A. Heckmann ◽  
S. Dallarés ◽  
M. Constenla ◽  
N.Yu. Rubtsova ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Original Description ◽  
Generic Diagnosis ◽  
West Antarctica ◽  
Dorsal Wall ◽  
West Antarctic ◽  
Notothenia Coriiceps ◽  
The Many ◽  
Dorsal Position

Abstract A number of variable descriptive accounts of Aspersentis megarhynchus (von Linstow, 1892) Golvan, 1960 have been reported from specimens collected from many species of fish in various locations off Antarctic islands. We have described a new population from Notothenia coriiceps Richardson (Nototheniidae) off Galindez Island, West Antarctica, and features not previously reported, resolved the taxonomic controversies and nomenclature, and emended and updated the generic diagnosis taking into account the newly observed structures. These are depicted in microscopic images and include the outer spiral wall of the proboscis receptacle, the thicker dorsal wall of the receptacle compared to the ventral wall, parts of the female reproductive system, the separate cement gland ducts, the dorsal position of the male gonopore and more detail of proboscis hooks and trunk spines. It is surprising that the newly observed features were missed from the many descriptions of A. megarhynchus created since the original description. The variability in A. megarhynchus is noted with a comparison of the morphometrics of our specimens vs. those in six other descriptions. We also analysed the metal composition of hooks and spines using energy-dispersive X-ray analysis and concluded a molecular characterization of the species based on 18S DNA gene, with related phylogenetic analyses.

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

Characterization of Alternative Carbon Sources for Denitrification

2011 ◽  
Vol 2011 (15) ◽  
pp. 1661-1672
Author(s):  
Annalisa Onnis-Hayden ◽  
Yunqing Du ◽  
Sylvia Yu ◽  
Samuel Ledwell ◽  
Paul Togna ◽  
...  
Keyword(s):  
Carbon Sources
Sign in / Sign up

Export Citation Format

Share Document