DOCSLIB.ORG

Evolution of Gene Blocks in Bacteria Using an Event-Based Model

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Evolution of Gene Blocks in Bacteria Using an Event-Based Model Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2020 Evolution of gene blocks in bacteria using an event-based model Huy Nguyen Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Nguyen, Huy, "Evolution of gene blocks in bacteria using an event-based model" (2020). Graduate Theses and Dissertations. 18368. https://lib.dr.iastate.edu/etd/18368 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Evolution of gene blocks in bacteria using an event-based model by Huy Nguyen A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Computer Science Program of Study Committee: Oliver Eulenstein, Co-major Professor Iddo Friedberg, Co-major Professor David Fernandez-Baca Dennis V. Lavrov Xiaoqiu Huang The student author, whose presentation of the scholarship herein was approved by the program of the study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2020 Copyright © Huy Nguyen, 2020. All rights reserved. ii DEDICATION To my parents, Danh Nguyen and Hoa Tran, who have encouraged, inspired, and enabled me to pursue my educational studies, and my family and friends for their support throughout my studies at home and abroad. iii TABLE OF CONTENTS Page LIST OF TABLES . .v LIST OF FIGURES . vi ACKNOWLEDGMENTS . ix ABSTRACT . .x CHAPTER 1. INTRODUCTION . .1 CHAPTER 2. RELATED WORKS . .4 2.1 Gene Block Evolution Models . .4 2.2 Finding Orthologous Gene Blocks in Bacteria . .8 2.3 Ancestral Reconstruction of Gene Blocks in Bacteria . .9 CHAPTER 3. PRELIMINARIES . 13 3.1 Event-based model . 13 3.2 Phylogenetic tree . 16 CHAPTER 4. FINDING ORTHOLOGOUS GENE BLOCKS IN BACTERIA: THE COM- PUTATIONAL HARDNESS OF THE PROBLEM AND NOVEL METHODS TO AD- DRESS IT . 18 4.1 The Relevant-Gene-Block problem . 19 4.2 The RGB problem is Hard . 20 4.3 Solving the RGB problem . 23 4.3.1 Greedy Algorithm . 24 4.3.2 Integer Linear Programming . 25 4.4 Results and Discussion . 26 4.4.1 Scalability Study . 27 4.4.2 Accuracy Study . 28 4.4.3 Concluding Discussion . 30 4.5 Conclusion . 31 CHAPTER 5. TRACING THE ANCESTRY OF OPERONS IN BACTERIA . 32 5.1 The Ancestral-Reconstruction-Gene-Block problem . 32 5.2 Solving the ARGB problems . 33 5.2.1 Local Algorithm . 33 5.2.2 Global Algorithm . 38 iv 5.3 Results and Discussion . 41 5.3.1 Operons using Escherichia coli as a reference taxon . 41 5.3.2 Operons using Bacillus subtilis as a reference taxon . 45 5.4 Conclusions . 48 CHAPTER 6. UNRAVELING A TANGLED SKEIN: EVOLUTIONARY ANALYSIS OF THE BACTERIAL GIBBERELLIN BIOSYNTHETIC OPERON . 50 6.1 Gene clusters analysis . 51 6.2 Results and Discussion . 59 6.3 Appendix: Supplementary Materials . 69 CHAPTER 7. DISCUSSION AND FUTURE DIRECTIONS . 85 7.1 Finding Orthologous Gene Blocks in Bacteria: the Computational Hardness of the Problem and Novel Methods to Address It . 85 7.1.1 Discussions . 85 7.1.2 Future directions . 86 7.2 Tracing the Ancestry of Operons in Bacteria . 88 7.2.1 Discussions . 88 7.2.2 Future directions . 89 7.3 Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthesis Operon . 90 7.3.1 Discussions . 90 7.3.2 Future directions . 91 BIBLIOGRAPHY . 93 v LIST OF TABLES Page Table 2.1 Pairwise events for the orthoblocks shown A-E . .8 Table 6.1 Pairwise alignments of GGPS2 proteins and representative GGPS proteins. Protein sequences were aligned using the MUSCLE algorithm (Geneious Prime; default settings). The GGPS proteins included in this analysis were selected due to the relatively close phylogenetic relationship between the core operon of this strain and that of the ggps2-containing strains, which lack a full-length ggps gene (i.e. Rhizobium etli bv. mimosae str. Mim1 has the most similar core operon to the ggps2-containing Rhizobium strains and Bradyrhizobium sp. WSM1417 has the most similar core operon to ggps2- containing Bradyrhizobium strains). Sequences with greater 90% amino acid identity are highlighted in dark blue, while those with greater 80% but less than 90% amino acid identity are highlighted in light blue . 69 Table 6.2 List of strains used within the ancestral reconstruction analyses. Shown for each strain is the corresponding GenBank genome accession, the legume host from which it was isolated, and the nodule type (D = determinate, I = indeterminate, * = neither). Note that the legume host and nodule type are irrelevant for the gammaproteobacteria plant pathogens analyzed in these reconstructions. 70 Table 6.3 Strains containing a CYP 114 − F dGA gene fusion. 83 Table 6.4 Strains containing a F dGA − SDRGA gene fusion. 83 vi LIST OF FIGURES Page Figure 2.1 Species C has an experimentally determined operon (Black arrows), and serves as the reference taxon. The orthologs in species A, B, D, and E were determined as explained in the text. The events between C and all other species for this orthoblock are A{C: deletion (of gene c); B{C: split (of gene c), C{D: duplication (of b) and split (jagged line); C{E: duplication (of b).7 Figure 2.2 Given a tree rooted at node x and the leaf nodes are labeled with nucleotides, the reconstruction problem finds nucleotide assignment for each inner node. Figure 2.2b is an example of such assignment. 12 Figure 4.1 The x-axis is the operon/ gene block names, we sort the gene blocks in ascending order according to the number of genes in each block. From left to right: operon ast to operon ygb has 5 genes in the gene block, operon cai to operon ydh has 6 genes in the gene block, operon cas to operon tdc has 7 genes in the gene block, operon bam to operon ydg has 8 genes in the gene block, operon atp to operon yje has 9 genes in the gene block, operon paa to operon yrb has 11 genes, operon hyf has 12 genes, operon nuo has 13 genes. The y-axis is the running time of the method in a log10-scale second 27 Figure 4.2 The x-axis is the same as Figure 2. The y-axis is the number of event count for the orthologous gene block in each species compared to the reference gene block. In Figure 3a,3b,3c, a dot represent the deletion events, split events, sum of deletion events, and split events respectively. Red dots represent the Heuristic method. Blue dots represent the Greedy method. Green dots represent the ILP method. 30 Figure 5.1 Ancestral reconstruction of operon atpIBEFHAGDC using the global op- timization approach.The lower-case letters in each tree node represent the genes in the orthoblock (e.g. \a" represents \atpA", see legend in blue bar, top). A `j' designates a split (i.e. a distance ≥500bp between the genes to either side of the `j'). The green bar on top shows the total number of events that took place in this reconstruction. The numbers in the brackets in the inner nodes are a 3-tuple showing the cumulative count of events going from the leafnodes to the tree root in the following order: [deletions, duplica- tions, splits]. No orthologus gene blocks were found in species labeled with an asterisk (∗). The reference genome E. coli is marked with a box. These naming and color conventions persist through this study. 42 Figure 5.2 Ancestral gene block reconstruction of operon paaABCDEFGHIJK using the global reconstruction approach. 44 Figure 5.3 Ancestral reconstruction of lepA-hemN-hrcA-grpE-dnaK-dnaJ-prmA-yqeU- rimO......................................... 46 vii Figure 5.4 Ancestral reconstruction of mmgABCDE-prpB................. 47 Figure 6.1 Diversity among GA biosynthetic operons in divergent bacterial lineages. The core operon genes are defined as cyp112, cyp114, fd, sdr, cyp117, ggps, cps, and ks, as these are almost always present within the GA operon. Other genes, including cyp115, idi, and ids2, exhibit a more limited distribution among GA operon-containing species. The tandem diagonal lines in the Mesorhizobium loti MAFF303099 operon indicates that cyp115 is not lo- cated adjacent to the rest of the operon. 51 Figure 6.2 Pipeline of the method to reconstruct the ancestral state of gibberellin operon . 52 Figure 6.3 Reduced ancestral reconstruction of the GA biosynthetic operon using rpoB for phylogenetic analysis. A phylogenetic tree was constructed with align- ments of rpoB protein sequences from 118 α-rhizobia species and two gammapro- teobacteria using the Neighbor-Joining method as a measure of the distance between species. The number of analyzed species was reduced to 64 with the Phylogenetic Diversity Analyzer software, and ROAGUE was then applied to create the ancestral operon reconstruction. Annotations are defined in section 6.1..................................... 54 Figure 6.4 Reduced ancestral reconstruction of the GA biosynthetic operon using the concatenated operon for phylogenetic analysis. A phylogenetic tree was constructed with alignments of concatenated proteins from core GA operon genes (cyp112-cyp114-fd-sdr-cyp117-cps-ks) from 118 α-rhizobia species and two gammaproteobacteria using the Neighbor-Joining method. The num- ber of analyzed species was reduced to 64 with the Phylogenetic Diversity Analyzer software, and ROAGUE was then applied to create the ancestral operon reconstruction.
Load more

Recommended publications
  • The Diversity of Cultivable Hydrocarbon-Degrading
    THE DIVERSITY OF CULTIVABLE HYDROCARBON-DEGRADING BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL AND SLUDGE FROM ARZEW REFINERY IN ALGERIA Sonia Sekkour, Abdelkader Bekki, Zoulikha Bouchiba, Timothy Vogel, Elisabeth Navarro, Ing Sonia To cite this version: Sonia Sekkour, Abdelkader Bekki, Zoulikha Bouchiba, Timothy Vogel, Elisabeth Navarro, et al.. THE DIVERSITY OF CULTIVABLE HYDROCARBON-DEGRADING BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL AND SLUDGE FROM ARZEW REFINERY IN ALGERIA. Journal of Microbiology, Biotechnology and Food Sciences, Faculty of Biotechnology and Food Sci- ences, Slovak University of Agriculture in Nitra, 2019, 9 (1), pp.70-77. 10.15414/jmbfs.2019.9.1.70-77. ird-02497490 HAL Id: ird-02497490 https://hal.ird.fr/ird-02497490 Submitted on 3 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THE DIVERSITY OF CULTIVABLE HYDROCARBON-DEGRADING BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL AND SLUDGE FROM ARZEW REFINERY IN ALGERIA Sonia SEKKOUR1*, Abdelkader BEKKI1, Zoulikha BOUCHIBA1, Timothy M. Vogel2, Elisabeth NAVARRO2 Address(es): Ing. Sonia SEKKOUR PhD., 1Université Ahmed Benbella, Faculté des sciences de la nature et de la vie, Département de Biotechnologie, Laboratoire de biotechnologie des rhizobiums et amélioration des plantes, 31000 Oran, Algérie.
    [Show full text]
  • Developing a Genetic Manipulation System for the Antarctic Archaeon, Halorubrum Lacusprofundi: Investigating Acetamidase Gene Function
    www.nature.com/scientificreports OPEN Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: Received: 27 May 2016 Accepted: 16 September 2016 investigating acetamidase gene Published: 06 October 2016 function Y. Liao1, T. J. Williams1, J. C. Walsh2,3, M. Ji1, A. Poljak4, P. M. G. Curmi2, I. G. Duggin3 & R. Cavicchioli1 No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
    [Show full text]
  • Caracterización Fenotípica Y Genotípica De Doce Rizobios Aislados De Diversas Regiones Geográficas De Venezuela
    Caracterización fenotípica y genotípica de doce rizobios aislados de diversas regiones geográficas de Venezuela María Eugenia Marquina, Néstor Enrique González & Yulimar Castro Laboratorio de Fijación Biológica de Nitrógeno y Cultivos de Tejidos Vegetales in vitro, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes. Núcleo Pedro Rincón Gutiérrez, Edificio A, 2º piso, La Hechicera, Mérida, Venezuela; [email protected], [email protected], [email protected] Recibido 10-VIII-2010. Corregido 08-I-2011. Aceptado 08-II-2011. Abstract: Phenotypic and genotypic characterization of twelve rhizobial isolates from different regions of Venezuela. Rhizobial taxonomy and systematics have progressed substantially, nevertheless, few studies have been developed on venezuelan species. This study evaluated the phenotypic and genetic variation between 12 venezuelan indigenous rhizobial isolates and 10 international referential strains, by phenotypical traits and DNA molecular markers. In this regard, a PCR-RFLP of the 16S rDNA gene, the presence of large plasmids, metabolic assays in solid media, salinity resistance, pH and temperature growth conditions, and intrinsic antibiotic resis- tance were assayed. In reference to the phenotypic attributes, we recognized three main groups: A group I, which comprised all the strains metabolizing between 67.5%-90% of the C and N sources. They were also acid-tolerant, as well as acid producers, capable of growing at 40ºC and in high salinity conditions (2-2.5% NaCl). With regard to the antibiotic sensitivity, this group was susceptible to a 30% of the antibiotic assayed. Strains belonging to Group II exhibited a lower salt tolerance (0.1-1.5%NaCl), as well as a lower acid tolerance, since they grew well at pH values equal or higher than 5.0.
    [Show full text]
  • Specificity in Legume-Rhizobia Symbioses
    International Journal of Molecular Sciences Review Specificity in Legume-Rhizobia Symbioses Mitchell Andrews * and Morag E. Andrews Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand; [email protected] * Correspondence: [email protected]; Tel.: +64-3-423-0692 Academic Editors: Peter M. Gresshoff and Brett Ferguson Received: 12 February 2017; Accepted: 21 March 2017; Published: 26 March 2017 Abstract: Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N2) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga).
    [Show full text]
  • The Diversity of Cultivable Hydrocarbon-Degrading Bacteria Isolated from Crude Oil Contaminated Soil and Sludge from Arzew Refinery in Algeria
    THE DIVERSITY OF CULTIVABLE HYDROCARBON-DEGRADING BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL AND SLUDGE FROM ARZEW REFINERY IN ALGERIA Sonia SEKKOUR1*, Abdelkader BEKKI1, Zoulikha BOUCHIBA1, Timothy M. Vogel2, Elisabeth NAVARRO2 Address(es): Ing. Sonia SEKKOUR PhD., 1Université Ahmed Benbella, Faculté des sciences de la nature et de la vie, Département de Biotechnologie, Laboratoire de biotechnologie des rhizobiums et amélioration des plantes, 31000 Oran, Algérie. 2Environmental Microbial Genomics Group, Laboratoire Ampère, Centre National de la Recherche Scientifique, UMR5005, Institut National de la Recherche Agronomique, USC1407, Ecole Centrale de Lyon, Université de Lyon, Ecully, France. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2019.9.1.70-77 ARTICLE INFO ABSTRACT Received 27. 3. 2018 The use of autochtonious bacterial strains is a valuable bioremediation strategy for cleaning the environment from hydrocarbon Revised 19. 2. 2019 pollutants. The isolation, selection and identification of hydrocarbon-degrading bacteria is therefore crucial for obtaining the most Accepted 14. 3. 2019 promising strains for decontaminate a specific site. In this study, two different media, a minimal medium supplemented with petroleum Published 1. 8. 2019 and with oil refinery sludge as sole carbon source, were used for the isolation of native hydrocarbon-degrading bacterial strains from crude oil contaminated soils and oil refinery sludges which allowed isolation of fifty-eight strains.The evalution of diversity of twenty- two bacterials isolates reveled a dominance of the phylum Proteobacteria (20/22 strains), with a unique class of Alphaproteobacteria, Regular article the two remaining strains belong to the phylum Actinobacteria. Partial 16S rRNA gene sequencing performed on isolates showed high level of identity with known sequences.
    [Show full text]
  • High-Quality Permanent Draft Genome Sequence of Ensifer
    Mhamdi et al. Standards in Genomic Sciences (2015) 10:34 DOI 10.1186/s40793-015-0005-1 SHORT GENOME REPORT Open Access High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris Ridha Mhamdi1, Julie Ardley2, Rui Tian2, Rekha Seshadri3, T.B.K. Reddy3, Amrita Pati3, Tanja Woyke3, Victor Markowitz4, Natalia Ivanova3, Nikos Kyrpides3,5 and Wayne Reeve2* Abstract Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal. Keywords: Root-nodule bacteria, Nitrogen fixation, Alphaproteobacteria, Ensifer, Phaseolus vulgaris Introduction root nodules of common bean grown in sandy, slightly Common bean (Phaseolus vulgaris) represents a very alkaline soil from the oasis of Rjim-Maatoug in South valuable source of proteins for low-income populations Tunisia [9].
    [Show full text]
  • Diversity and Distribution of Rhizobia Nodulated with Phaseolus Vulgaris in Two Ecoregions of China
    Soil Biology & Biochemistry 78 (2014) 128e137 Contents lists available at ScienceDirect Soil Biology & Biochemistry journal homepage: www.elsevier.com/locate/soilbio Diversity and distribution of rhizobia nodulated with Phaseolus vulgaris in two ecoregions of China * Ying Cao a, En-Tao Wang b, Liang Zhao a, Wei-Min Chen a, Ge-Hong Wei a, a State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, 712100 Yangling, Shaanxi, China b Departamento de Microbiología, Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, 11340 Mexico, D.F., Mexico article info abstract Article history: To reveal the diversity and geographic distribution of bean (Phaseolus vulgaris L.) rhizobia in China, a total Received 21 May 2014 of 226 strains of nodule bacteria were isolated from bean plants grown in fields of nine sites in northern Received in revised form (ecoregion I) and southern (ecoregion II) regions of China, with soil pH ranged from 8.06 to 4.97. Based 30 July 2014 upon the phylogenies of housekeeping and symbiotic genes, 96.9% of the isolates were Rhizobium cor- Accepted 31 July 2014 responding to four defined species and four unnamed genospecies, while the remaining were five Bra- Available online 12 August 2014 dyrhizobium genospecies. Rhizobium leguminosarum, Rhizobium etli and Rhizobium sp. II or IV were dominant in different ecoregions, with varied relative abundances. Therefore, diverse and distinctive Keywords: Rhizobia bean rhizobial communities exist in different ecoregions of China, demonstrating that the introduction of fi Common bean bean plants has driven the evolution of rhizobia to t the necessity to nodulate the host plant under the Phylogeny local conditions, mainly the soil pH and the nutrient availability.
    [Show full text]
  • Türkiye'nin Eskişehir Ilinden, Phaseolus Vulgaris L.'Den Izole
    www.biodicon.com Biological Diversity and Conservation ISSN 1308-8084 Online; ISSN 1308-5301 Print 11/2 (2018) 106-114 Research article/Araştırma makalesi Molecular identifications of rhizobial samples isolated from Phaseolus vulgaris L. in Eskişehir province of Turkey Cem Tolga GÜRKANLI *1, İbrahim ÖZKOÇ2, Merih KIVANÇ3 1 Ordu University, Fatsa Faculty of Marine Sciences, 52400, Fatsa, Ordu/Turkey 2Ondokuz Mayis University, Faculty of Arts and Science, Department of Biology, Atakum, Samsun/Turkey 3Anadolu University, Faculty of Science, Department of Biology, 26470, Eskişehir/Turkey Abstract In this study three rhizobial samples (R28, R51, R66) were anaysed using molecular phylogenetic methods. Rhizobial samples were isolated (from P. vulgaris L. root nodules collected from Eskişehir province of Turkey) and morphologically characterized in a previous study. Analyses were performed using a concatenated data set which composed of three housekeeping genes (recA, atpD and glnII). Additionally two symbiotic genes, nodA and nifH, were sequenced and analysed to determine the symbiotic plasmid type. As a result of housekeeping gene phylogeny, isolate R28 was found to be related to R. laguerreae. Although other two isolates, R51 and R66, placed in the same lineage with R. sophoriradicis, they showed enough divergence to be considered as a new species. But this presumption need to be confirmed with further investigations. Network analyses of nodA and nifH genes clearly showed that R28 has a unique symbiotic plasmid. On the other hand, symbiotic plasmids of R51 and R66 found to be related to p42d which is the most common symbiotic plasmid in rhizobia nodulating P. vulgaris L. in Europe and also Turkey.
    [Show full text]
  • Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments
    Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 491091, 17 pages http://dx.doi.org/10.1155/2013/491091 Research Article Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments Ramona Marasco,1 Eleonora Rolli,1 Marco Fusi,1 Ameur Cherif,2 Ayman Abou-Hadid,3 Usama El-Bahairy,3 Sara Borin,1 Claudia Sorlini,1 and Daniele Daffonchio1 1 Department of Food, Environment, and Nutritional Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy 2 Laboratory of Microorganisms and Active Biomolecules, University of Tunis El Manar, Campus Universitaire, Rommana 1068, Tunis BP 94, Tunisia and Laboratory BVBGR, ISBST, University of Manouba, La Manouba 2010, Tunisia 3 Department of Horticulture, Faculty of Agriculture, Ain Shams University, Shubra Elkheima, Cairo, Egypt Correspondence should be addressed to Daniele Daffonchio; [email protected] Received 13 March 2013; Revised 14 May 2013; Accepted 21 May 2013 Academic Editor: George Tsiamis Copyright © 2013 Ramona Marasco et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches.
    [Show full text]
  • Article in Press
    G Model SYAPM-25671; No. of Pages 5 ARTICLE IN PRESS Systematic and Applied Microbiology xxx (2015) xxx–xxx Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics Ernesto Ormeno-Orrillo,˜ Luis E. Servín-Garciduenas,˜ Marco A. Rogel, Víctor González, ∗ Humberto Peralta, Jaime Mora, Julio Martínez-Romero, Esperanza Martínez-Romero Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico a r t a b i c l e i n f o s t r a c t Article history: Phylogenomic analyses showed two major superclades within the family Rhizobiaceae that corresponded Received 23 September 2014 to the Rhizobium/Agrobacterium and Shinella/Ensifer groups. Within the Rhizobium/Agrobacterium group, Received in revised form 9 December 2014 four highly supported clades were evident that could correspond to distinct genera. The Shinella/Ensifer Accepted 11 December 2014 group encompassed not only the genera Shinella and Ensifer but also a separate clade containing the type T strain of Rhizobium giardinii. Ensifer adhaerens (Casida A ) was an outlier within its group, separated from Keywords: the rest of the Ensifer strains. The phylogenomic analysis presented provided support for the revival of Rhizobia Allorhizobium as a bona fide genus within the Rhizobiaceae, the distinctiveness of Agrobacterium and the Root nodule bacteria Systematics recently proposed Neorhizobium genus, and suggested that R. giardinii may be transferred to a novel genus. Phylogeny Genomics has provided data for defining bacterial-species limits from estimates of average nucleotide Genome identity (ANI) and in silico DNA–DNA hybridization (DDH).
    [Show full text]
  • Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments
    Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 491091, 17 pages http://dx.doi.org/10.1155/2013/491091 Research Article Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments Ramona Marasco,1 Eleonora Rolli,1 Marco Fusi,1 Ameur Cherif,2 Ayman Abou-Hadid,3 Usama El-Bahairy,3 Sara Borin,1 Claudia Sorlini,1 and Daniele Daffonchio1 1 Department of Food, Environment, and Nutritional Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy 2 Laboratory of Microorganisms and Active Biomolecules, University of Tunis El Manar, Campus Universitaire, Rommana 1068, Tunis BP 94, Tunisia and Laboratory BVBGR, ISBST, University of Manouba, La Manouba 2010, Tunisia 3 Department of Horticulture, Faculty of Agriculture, Ain Shams University, Shubra Elkheima, Cairo, Egypt Correspondence should be addressed to Daniele Daffonchio; [email protected] Received 13 March 2013; Revised 14 May 2013; Accepted 21 May 2013 Academic Editor: George Tsiamis Copyright © 2013 Ramona Marasco et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches.
    [Show full text]
  • Burkholderia Spp. Are the Most Competitive Symbionts of Mimosa, Particularly Under N-Limited Conditions
    Environmental Microbiology (2009) 11(4), 762–778 doi:10.1111/j.1462-2920.2008.01799.x Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions Geoffrey N. Elliott,1*† Jui-Hsing Chou,2 levels, rates of bacterial growth, rhizobia-rhizobia Wen-Ming Chen,2 Guido V. Bloemberg,3 growth inhibition or individual nodulation rate. Cyril Bontemps,4 Esperanza Martínez-Romero,5 However, the competitive domination of PAS44 over Encarna Velázquez,6 J. Peter W. Young,4 LMG19424 was reduced in the presence of nitrate for Janet I. Sprent1 and Euan K. James1 all three plant hosts. The largest significant effect was 1College of Life Sciences, University of Dundee, for M. pudica, in which LMG19424 formed 57% of the Dundee DD1 5EH, UK. nodules in the presence of 0.5 mM potassium nitrate. 2Laboratory of Microbiology, Department Seafood In this host, ammonium also had a similar, but lesser, Science, National Kaohsiung Marine University, effect. Comparable results were also found using an Kaohsiung City 811, Taiwan. N-containing soil mixture, and environmental N levels 3Leiden University, Institute of Molecular Plant Sciences, are therefore suggested as a factor in the competitive Wassenaarseweg 64, Leiden 2333 AL, the Netherlands. success of the bacterial symbiont in vivo. 4Department of Biology 3, University of York, PO Box 373, York YO10 5YW, England, UK. Introduction 5Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP 565A, Cuernavaca, Morelos, Nodulation in legumes occurs not only in symbiosis México. with members of the class a-Proteobacteria (including 6Departamento de Microbiología y Genética, Rhizobium, Sinorhizobium, Azorhizobium, Mesorhizo- Universidad de Salamanca, Salamanca, Spain.
    [Show full text]