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

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.

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

Genome Biology and Evolution ◽

10.1093/gbe/evaa221 ◽

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.

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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.

Archives of Microbiology ◽

10.1007/s00203-019-01744-7 ◽

2019 ◽

Vol 202 (2) ◽

pp. 309-322 ◽

Cited By ~ 1

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.

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Adsorptive removal of trace oxytetracycline from water by acid-modified zeolite: influencing factors

Water Science & Technology ◽

10.2166/wst.2013.505 ◽

2013 ◽

Vol 68 (11) ◽

pp. 2473-2478 ◽

Cited By ~ 6

Author(s):

Wenhao An ◽

Hua Xiao ◽

Man Yu ◽

Xiaoyang Chen ◽

Yuxin Xu ◽

...

Keyword(s):

Humic Acid ◽

Removal Efficiency ◽

Natural Zeolite ◽

Opposite Effect ◽

Swine Wastewater ◽

Adsorption Efficiency ◽

Tetracycline Antibiotics ◽

Modified Zeolite ◽

Alkaline Conditions ◽

Acidic Conditions

Because of the wide use of antibiotics in the livestock industry, trace tetracycline antibiotics are frequently detected in swine wastewater and water bodies near pig farms. Based on natural zeolite, modified zeolite was synthesized by treatment with nitric acid. As one kind of typical tetracyclines, oxytetracycline (OTC) was chosen as the target adsorbate. Removal of trace OTC by modified zeolite and the effects of several main water matrices on OTC adsorption were studied in detail. OTC removal efficiency by acid-modified zeolite was about 90%, compared to less than 20% by natural zeolite. In general, in acidic conditions the removal efficiency of OTC by modified zeolite was about 90%, which was much higher than 20–35% in alkaline conditions. An increase in ionic strength from 0.01 to 1.0 M led to a decrease in adsorption efficiency from 90 to 27%. The presence of 10.0 mg L−1 dissolved humic acid accelerated sorption of OTC on modified zeolite, while 100.0 mg L−1 humic acid resulted in the opposite effect. An increase in temperature contributed to enhancing the adsorption efficiency.

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Bioactive Compounds from Sponge Associated Bacteria: Anticancer Activity and NRPS-PKS Gene Expression in Different Carbon Sources

American Journal of Biochemistry and Biotechnology ◽

10.3844/ajbbsp.2017.148.156 ◽

2017 ◽

Vol 13 (4) ◽

pp. 148-156

Author(s):

Jepri Agung Priyanto ◽

Rika Indri Astuti ◽

Jun Nomura ◽

Aris Tri Wahyudi

Keyword(s):

Gene Expression ◽

Anticancer Activity ◽

Bioactive Compounds ◽

Carbon Sources ◽

Associated Bacteria ◽

Sponge Associated Bacteria

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Effect of Carbon Sources on Growth and Nitrogen Fixation of Aulosira fertilisssima Ghose

Biochemie und Physiologie der Pflanzen ◽

10.1016/s0015-3796(88)80069-6 ◽

1988 ◽

Vol 183 (1) ◽

pp. 51-58

Author(s):

Meenakshi Banerjee ◽

H.D. Kumar

Keyword(s):

Nitrogen Fixation ◽

Carbon Sources

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Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts

Genes & Genomics ◽

10.1007/s13258-018-0693-1 ◽

2018 ◽

Vol 40 (8) ◽

pp. 857-864 ◽

Cited By ~ 4

Author(s):

Hongsheng Cai ◽

Yan Bai ◽

Changhong Guo

Keyword(s):

Comparative Genomics ◽

Specific Interactions ◽

Associated Bacteria ◽

Plant Hosts

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Effect of acidity on the properties of silica-aluminas synthesized by sol-gel method

Butlerov Communications ◽

10.37952/roi-jbc-01/20-63-7-126 ◽

2020 ◽

Vol 63 (7) ◽

pp. 126-132

Author(s):

Lyubov V. Furda ◽

◽

Evgenia A. Tarasenko ◽

Sofya N. Dudina ◽

Olga E. Lebedeva ◽

...

Keyword(s):

Surface Area ◽

Sol Gel ◽

Molar Ratio ◽

Active Centers ◽

Indicator Method ◽

Synthesis Conditions ◽

Alkaline Conditions ◽

Acidic Conditions ◽

Amphoteric Properties ◽

Hydrolysis Of

In the present work amorphous silica-aluminas were synthesized by the coprecipitation method during the hydrolysis of an alcohol solution of tetraethoxysilane (with a tetraethoxysilane: alcohol mass ratio of 1: 1) and 6% aqueous solution of aluminum nitrate at pH values of 1, 3, and 10. The Si/Al molar ratio for all synthesized samples were 4.72 (± 0.29). The amorphous character of the investigated materials was confirmed by X-ray phase analysis. According to the results of scanning electron microscopy, it was found that the resulting powders have particles with a size of 1-20 μm. It was shown that the conditions of synthesis affected the specific surface area and porosity of the materials under study. By the method of low-temperature adsorption-thermodesorption of nitrogen it was established that silica-aluminas obtained under acidic conditions were microporous materials. For the sample obtained under alkaline conditions (pH = 10), the contribution of macropores is very significant. A decrease in surface area is observed as the pH of the synthesis increases. The Hammett indicator method was used to identify and quantify surface centers of different acidity. All studied silica-aluminas are characterized by the presence of both Brønsted basic (pKax from 7 to 12.8) and acidic (pKax from 0 to 7) centers, and Lewis basic (pKax from -4.4 to 0) with a pronounced maximum at pKax = 1.02. It was found that the synthesis conditions had a significant effect on the concentration of active centers. The values of the Hammett function are practically the same for the 3 studied silica-aluminas and describe the studied samples as materials of medium acidity. The variety of Lewis and Brønsted centers on the surface indicates the amphoteric properties of the materials under study. This gives the samples the properties of polyfunctional sorbents and catalysts.

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Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains

Applied and Environmental Microbiology ◽

10.1128/aem.02873-19 ◽

2020 ◽

Vol 86 (6) ◽

Cited By ~ 3

Author(s):

Ebrahim Osdaghi ◽

Touraj Rahimi ◽

S. Mohsen Taghavi ◽

Maryam Ansari ◽

Sadegh Zarei ◽

...

Keyword(s):

Genetic Diversity ◽

Comparative Genomics ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Sensu Stricto ◽

Bacterial Canker ◽

Agricultural Crops ◽

Content Type ◽

Canker Disease

ABSTRACT Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections. IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.

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Biodegradation Potential and Diversity of Diclofenac-degrading Microbiota in an Immobilized Cell Biofilter

Processes ◽

10.3390/pr7090554 ◽

2019 ◽

Vol 7 (9) ◽

pp. 554 ◽

Cited By ~ 4

Author(s):

Efstathia Navrozidou ◽

Nikolaos Remmas ◽

Paraschos Melidis ◽

Dimitrios G. Karpouzas ◽

George Tsiamis ◽

...

Keyword(s):

Activated Sludge ◽

High Throughput Sequencing ◽

Rhodopseudomonas Palustris ◽

Carbon Sources ◽

High Strength ◽

Adaptation Period ◽

Immobilized Cell ◽

Wide Range ◽

Acidic Conditions ◽

Ph Decrease

Despite that diclofenac has been embodied to the European watch list of priority substances of concern, studies on diclofenac biodegradation are limited and the diversity of diclofenac-degrading microbiota remains unknown. In this work, an immobilized cell biofilter was constructed and operated to evaluate its effectiveness to depurate high strength diclofenac wastewater and to identify the diclofenac-degrading community accommodated in activated sludge by employing high-throughput sequencing techniques. After a two-month adaptation period, biofilter removal efficiencies reached values as high as 97.63 ± 0.62%, whereas utilization of diclofenac in the immobilized cell biofilter led to a drastic pH decrease. Based on Illumina sequencing, the major bacterial taxa identified in the immobilized cell biofilter were members of the species Granulicella pectinivorans and Rhodanobacter terrae, followed by members of the species Castellaniella denitrificans, Parvibaculum lavamentivorans, Bordetella petrii, Bryocella elongata and Rhodopseudomonas palustris. The ability of such taxa to utilize a wide range of carbon sources and to effectively adapt under acidic conditions seemed to be the main parameters, which favored their prevalence in the immobilized cell biofilter. In addition, Wickerhamiella was the predominant fungal taxon in the immobilized cell biofilter, which appears to be actively involved in diclofenac degradation in activated sludge systems.

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