Nitrogen Fixation for Agriculture and Environment
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Large‐Scale Genomic Sequence Data Resolve the Deepest Divergences in the Legume Phylogeny and Support a Near‐Simultaneous Evolutionary Origin of All Six Subfamilies
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2020 Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies Koenen, Erik J M ; Ojeda, Dario I ; Steeves, Royce ; Migliore, Jérémy ; Bakker, Freek T ; Wieringa, Jan J ; Kidner, Catherine ; Hardy, Olivier J ; Pennington, R Toby ; Bruneau, Anne ; Hughes, Colin E Abstract: Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear‐encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coa- lescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as ‘basal’ or ‘early‐diverging’ with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. -
Evolution of Angiosperm Pollen. 7. Nitrogen-Fixing Clade1
Evolution of Angiosperm Pollen. 7. Nitrogen-Fixing Clade1 Authors: Jiang, Wei, He, Hua-Jie, Lu, Lu, Burgess, Kevin S., Wang, Hong, et. al. Source: Annals of the Missouri Botanical Garden, 104(2) : 171-229 Published By: Missouri Botanical Garden Press URL: https://doi.org/10.3417/2019337 BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Complete website, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/terms-of-use. Usage of BioOne Complete content is strictly limited to personal, educational, and non - commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Downloaded From: https://bioone.org/journals/Annals-of-the-Missouri-Botanical-Garden on 01 Apr 2020 Terms of Use: https://bioone.org/terms-of-use Access provided by Kunming Institute of Botany, CAS Volume 104 Annals Number 2 of the R 2019 Missouri Botanical Garden EVOLUTION OF ANGIOSPERM Wei Jiang,2,3,7 Hua-Jie He,4,7 Lu Lu,2,5 POLLEN. 7. NITROGEN-FIXING Kevin S. Burgess,6 Hong Wang,2* and 2,4 CLADE1 De-Zhu Li * ABSTRACT Nitrogen-fixing symbiosis in root nodules is known in only 10 families, which are distributed among a clade of four orders and delimited as the nitrogen-fixing clade. -
Revised Taxonomy of the Family Rhizobiaceae, and Phylogeny of Mesorhizobia Nodulating Glycyrrhiza Spp
Division of Microbiology and Biotechnology Department of Food and Environmental Sciences University of Helsinki Finland Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp. Seyed Abdollah Mousavi Academic Dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public examination in lecture hall 3, Viikki building B, Latokartanonkaari 7, on the 20th of May 2016, at 12 o’clock noon. Helsinki 2016 Supervisor: Professor Kristina Lindström Department of Environmental Sciences University of Helsinki, Finland Pre-examiners: Professor Jaakko Hyvönen Department of Biosciences University of Helsinki, Finland Associate Professor Chang Fu Tian State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University, China Opponent: Professor J. Peter W. Young Department of Biology University of York, England Cover photo by Kristina Lindström Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae ISSN 2342-5423 (print) ISSN 2342-5431 (online) ISBN 978-951-51-2111-0 (paperback) ISBN 978-951-51-2112-7 (PDF) Electronic version available at http://ethesis.helsinki.fi/ Unigrafia Helsinki 2016 2 ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain “Bacteria”, which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated. -
Multi?Host Ectomycorrhizal Fungi Are Predominant in a Guinean Tropical
Environmental Microbiology (2010) 12(8), 2219–2232 doi:10.1111/j.1462-2920.2010.02183.x Multi-host ectomycorrhizal fungi are predominant in a Guinean tropical rainforest and shared between canopy trees and seedlingsemi_2183 2219..2232 Abdala Gamby Diédhiou,1,2*† Marc-André Selosse,3 lings harboured a similar fungal community. These Antoine Galiana,1 Moussa Diabaté,1,4 findings suggest that there was a potential for the Bernard Dreyfus,1 Amadou Moustapha Bâ,1,5 formation of common mycorrhizal networks in close Sergio Miana de Faria6 and Gilles Béna1 vicinity. However, no significant difference was 1Laboratoire des Symbioses Tropicales et detected for the d13C and d15N values between seed- Méditerranéennes, UMR113 – INRA/AGRO- lings and adults of each ECM plant, and no ECM M/CIRAD/IRD/UM2 – TA10/J, Campus International de species exhibited signatures of mixotrophy. Our Baillarguet, 34398 Montpellier Cedex 5, France. results revealed (i) variation in ECM fungal diversity 2Laboratoire Commun de Microbiologie, according to the seedling versus adult development IRD/UCAD/ISRA, BP 1386 Dakar, Sénégal. stage of trees and (ii) low host specificity of ECM 3Centre d’Ecologie Fonctionnelle et Evolutive (CNRS, fungi, and indicated that multi-host fungi are more UMR 5175), Equipe Interactions Biotiques, 1919 Route abundant than single-host fungi in this forest stand. de Mende, 34293 Montpellier Cedex 5, France. 4Institut de Recherche Agronomique de Guinée, Division Introduction des Cultures Pérennes, Programme Recherche Forestière, BP 1523, Conakry, République de Guinée. Ectomycorrhizal (ECM) symbiosis involves soil fungi and 5Laboratoire de Biologie et Physiologie Végétales, tree roots. It provides mineral nutrients, water and protec- Faculté des Sciences Exactes et Naturelles, Université tion against pathogens to the plant which, as a reward, des Antilles et de la Guyane, BP 592, 97159 provides carbon to its fungal partner (Smith and Read, Pointe-à-Pitre, Guadeloupe, France. -
Ecological Niche Divergence Associated with Species and Populations Differentiation Inerythrophleum (Fabaceae, Caesalpinioideae)
Plant Ecology and Evolution 152 (1): 41–52, 2019 https://doi.org/10.5091/plecevo.2019.1543 REGULAR PAPER Ecological niche divergence associated with species and populations differentiation in Erythrophleum (Fabaceae, Caesalpinioideae) Anaïs-Pasiphaé Gorel1,*, Jérôme Duminil2, 3, 4, Jean-Louis Doucet1 & Adeline Fayolle1 1Terra Teaching and Research Center, Forest is life, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés, 5030 Gembloux, Belgium 2Evolutionary Biology and Ecology, CP160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 Av. F. Roosevelt, 1050 Brussels, Belgium 3DIADE, IRD, Univ Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier, France 4Bioversity International, Forest Genetic Resources and Restoration Programme, Sub-Regional Office for Central Africa, P.O. Box 2008 Messa, Yaoundé, Cameroon *Author for correspondence: [email protected] Background and aims – The isolation of populations inside forest refugia during past climate changes has widely been hypothesized as a major driver of tropical plant diversity. Environmental conditions can also influence patterns of diversity by driving divergent selection leading to local adaptation and, potentially, ecological speciation. Genetic and phylogenetic approaches are frequently used to study the diversification of African tree clades. However, the environmental space occupied by closely related species or intra- specific gene pools is barely quantified, though needed to properly test hypotheses on diversification processes. Methods – Using species distribution models, we determined the bioclimatic constraints on the distribution of closely related species and intra-specific gene pools. Our study model, Erythrophleum (Fabaceae – Caesalpinioideae), is a tropical tree genus widespread across Africa, and vastly investigated for genetics. Here, we combined the available phylogenetic data with information on niche divergence to explore the role of ecology into diversification at the species and gene pool levels. -
Marina Murillo Torres
Facultad de Biología Departamento de Microbiología Grado en Biología Implicación de las N-acil homoserina lactonas en el fenotipo y las propiedades simbióticas de Ensifer meliloti SVQ747 y su mutante en el sistema RND NolG Trabajo de Fin de Grado Marina Murillo Torres Tutora: María del Rosario Espuny Gómez Codirectora: Cynthia Victoria Alías Villegas Sevilla, junio de 2020 ÍNDICE Resumen ........................................................................................................................... 1 Introducción ..................................................................................................................... 1 Objetivos ........................................................................................................................... 6 Materiales y métodos ....................................................................................................... 7 Bacterias, medios y condiciones de cultivo ................................................................... 7 Obtención de estirpes portadoras de los plásmidos pME6000 y pME6863 .................. 9 Métodos utilizados en el estudio de las bacterias ........................................................ 10 Ensayo de difusión en placa para determinar la producción de AHL ................. 10 Movilidad, morfología de las colonias y producción de EPS .............................. 11 Métodos utilizados para los estudios con alfalfa (Medicago sativa cv. Aragón) ........ 11 Desinfección y germinación de semillas ............................................................ -
Fieldtrip Manual for Plant Biodiversity
Fieldtrip manual for Plant Biodiversity Ana Juan, Mª Ángeles Alonso, Alejandro Terrones, Joaquín Moreno, Joan Pérez & José Carlos Cristóbal Department of Environmental Sciences and Natural Resources Fieldtrip manual for Plant Biodiversity Introduction Plant Biodiversity is a subject taught during the second year of the Undergraduate Degree in Biology at the University of Alicante. The main principles about the diversity and morphology of the plants are mostly given during the theoretical classes. This fieldtrip practical manual, together with the laboratory sessions, gives the students an opportunity to see our most common wild plant species. Their direct observations allow them to identify properly the main botanical families, genera and species of our wild flora. This Fieldtrip manual for Plant Biodiversity has been written to enhance the understanding of plant diversity and to identify the different ecological conditions for plant species. Students have to understand that “plants do not grow everywhere”. Most of our natural flora, and specially the endemic one, requires specific environmental conditions to grow. So, the objectives of these fieldtrips are to identify wild flora and to recognise the ecological habitats where many of the identified plant species live. According to the official organisation of the subject Plant Biodiversity at the University of Alicante, nine hours correspond to two field practical sessions, which last 4 and 5 hours, respectively. This manual has been organised in only two chapters. Each chapter includes the description of the places to visit: - Chapter 1. Fieldtrip “Urbanova”: study of coastal sand dunes and salt marshes. - Chapter 2. Fieldtrip “Estación Biológica de Torretes”: study of mountain habitats. -
Combined Phylogenetic Analyses Reveal Interfamilial Relationships and Patterns of floral Evolution in the Eudicot Order Fabales
Cladistics Cladistics 1 (2012) 1–29 10.1111/j.1096-0031.2012.00392.x Combined phylogenetic analyses reveal interfamilial relationships and patterns of floral evolution in the eudicot order Fabales M. Ange´ lica Belloa,b,c,*, Paula J. Rudallb and Julie A. Hawkinsa aSchool of Biological Sciences, Lyle Tower, the University of Reading, Reading, Berkshire RG6 6BX, UK; bJodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; cReal Jardı´n Bota´nico-CSIC, Plaza de Murillo 2, CP 28014 Madrid, Spain Accepted 5 January 2012 Abstract Relationships between the four families placed in the angiosperm order Fabales (Leguminosae, Polygalaceae, Quillajaceae, Surianaceae) were hitherto poorly resolved. We combine published molecular data for the chloroplast regions matK and rbcL with 66 morphological characters surveyed for 73 ingroup and two outgroup species, and use Parsimony and Bayesian approaches to explore matrices with different missing data. All combined analyses using Parsimony recovered the topology Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). Bayesian analyses with matched morphological and molecular sampling recover the same topology, but analyses based on other data recover a different Bayesian topology: ((Polygalaceae + Leguminosae) (Quillajaceae + Surianaceae)). We explore the evolution of floral characters in the context of the more consistent topology: Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). This reveals synapomorphies for (Leguminosae (Quillajaceae + Suri- anaceae)) as the presence of free filaments and marginal ⁄ ventral placentation, for (Quillajaceae + Surianaceae) as pentamery and apocarpy, and for Leguminosae the presence of an abaxial median sepal and unicarpellate gynoecium. An octamerous androecium is synapomorphic for Polygalaceae. The development of papilionate flowers, and the evolutionary context in which these phenotypes appeared in Leguminosae and Polygalaceae, shows that the morphologies are convergent rather than synapomorphic within Fabales. -
Molecular Plant-Microbe Interacfions
GET ENGAGED. GROW YOUR KNOWLEDGE. MAKE CONNECTIONS. Publish your work and submit to Molecular Plant-Microbe Interactions (MPMI) Grow your career with the Career Center Read the latest IS-MPMI member news in Interactions Find a colleague and start collaborating using the Member Directory Network with over 1,500 IS-MPMI members ismpmi.org/welcome Get all the latest updates! Follow IS-MPMI. Welcome to Glasgow and the XVIII International Congress on Molecular Plant-Microbe Interactions! We have created a wide-reaching program that showcases emerging topics in plant-microbe interactions; new concurrent sessions on topics such as post- translational modifications, long-distance/systemic signaling, invertebrate-plant interactions, and environmental impacts on microbial infection; and established popular sessions on symbiosis and mutualism, microbial manipulation of the host, molecular recognition, and cell biology. A diverse selection of satellite meetings will be offered on Sunday, July 14, and a workshop on Tuesday, July 16, will highlight the importance of scientific reproducibility. We are proud to have achieved gender balance in our slate of plenary speakers and to have speakers for the scheduled talks that represent the full diversity of the scientists working in our field. More than 1,400 delegates from 52 countries have registered to attend the meeting to discuss the current breakthroughs and future directions of research on plant-microbe interactions. Seventy early career researchers have received travel awards to attend the congress; -
Cleavage of the SYMBIOSIS RECEPTOR-LIKE KINASE
Current Biology 24, 422–427, February 17, 2014 ª2014 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2013.12.053 Report Cleavage of the SYMBIOSIS RECEPTOR- LIKE KINASE Ectodomain Promotes Complex Formation with Nod Factor Receptor 5 Meritxell Antolı´n-Llovera,1 Martina K. Ried,1 leaf cells expressing L. japonicus SYMRK (Figures 1A and and Martin Parniske1,* 1B). SYMRK cleavage is thus either mediated by proteases 1Genetics, Faculty of Biology, University of Munich (LMU), present in both L. japonicus roots and N. benthamiana leaves Großhaderner Straße 4, 82152 Martinsried, Germany or, alternatively, is an intrinsic activity of the ectodomain. Upon expression in N. benthamiana leaf cells, most of the fluores- cently tagged protein was observed at the plasma membrane Summary (Figures S2 and S3). Moreover, most of the tagged protein as judged by protein blots (Figures 1, S1, and S4) is in the full- Plants form root symbioses with fungi and bacteria to length state. This observation, together with the observed gly- improve their nutrient supply. SYMBIOSIS RECEPTOR- codecoration of the MLD fragment, makes a cleavage at the LIKE KINASE (SYMRK) is required for phosphate-acquiring plasma membrane a likely scenario, but does not exclude arbuscular mycorrhiza, as well as for the nitrogen-fixing the possibility that it occurs already en route through the root nodule symbiosis of legumes [1] and actinorhizal plants secretory pathway. [2, 3], but its precise function was completely unclear. Here we show that the extracytoplasmic region of SYMRK, which The GDPC Motif Connects the LRRs with the MLD and Is comprises three leucine-rich repeats (LRRs) and a malectin- Critical for MLD Release and Symbiosis like domain (MLD) related to a carbohydrate-binding protein The symrk-14 mutant suffered from abnormal epidermal infec- from Xenopus laevis [4], is cleaved to release the MLD in the tion after inoculation with either arbuscular mycorrhiza (AM) absence of symbiotic stimulation. -
Evolution Et Adaptation Fonctionnelle Des Arbres Tropicaux : Le Cas Du Genre Guibourtia Benn
EVOLUTION ET ADAPTATION FONCTIONNELLE DES ARBRES TROPICAUX : LE CAS DU GENRE GUIBOURTIA BENN. FELICIEN TOSSO COMMUNAUTE FRANÇAISE DE BELGIQUE UNIVERSITE DE LIEGE – GEMBLOUX AGRO-BIO TECH EVOLUTION ET ADAPTATION FONCTIONNELLE DES ARBRES TROPICAUX : LE CAS DU GENRE GUIBOURTIA BENN. Dji-ndé Félicien TOSSO Dissertation originale présentée en vue de l’obtention du grade de docteur en sciences agronomiques et ingénierie biologique Co-Promoteurs : Prof. Jean-Louis Doucet et Dr. Olivier J. Hardy Année 2018 Copyright Cette œuvre est sous licence Creative Commons. Vous êtes libre de reproduire, de modifier, de distribuer et de communiquer cette création au public selon les conditions suivantes : - paternité (BY) : vous devez citer le nom de l'auteur original de la manière indiquée par l'auteur de l'œuvre ou le titulaire des droits qui vous confère cette autorisation (mais pas d'une manière qui suggérerait qu'ils vous soutiennent ou approuvent votre utilisation de l'œuvre) ; - pas d'utilisation commerciale (NC) : vous n'avez pas le droit d'utiliser cette création à des fins commerciales ; - partage des conditions initiales à l'identique (SA) : si vous modifiez, transformez ou adaptez cette création, vous n'avez le droit de distribuer la création qui en résulte que sous un contrat identique à celui-ci. À chaque réutilisation ou distribution de cette création, vous devez faire apparaitre clairement au public les conditions contractuelles de sa mise à disposition. Chacune de ces conditions peut être levée si vous obtenez l'autorisation du titulaire des droits sur cette œuvre. Rien dans ce contrat ne diminue ou ne restreint le droit moral de l’auteur. -
Intracellular Accommodation of Microbes by Plants: a Common Developmental Program for Symbiosis and Disease? Martin Parniske
320 Intracellular accommodation of microbes by plants: a common developmental program for symbiosis and disease? Martin Parniske Plant cells engage in mutualistic and parasitic endosymbioses leading to resistance (see the review by Jeff Ellis et al. in with a wide variety of microoganisms, ranging from Gram- this issue [1]). In contrast, surprisingly little is known negative (Rhizobium, Nostoc) and Gram-positive bacteria about the molecular processes that allow these fungi to (Frankia), to oomycetes (Phytophthora), Chytridiomycetes, infect and exploit living plant cells during disease in Zygomycetes (arbuscular mycorrhizal fungi) and true fungi compatible interactions. (Erysiphe, ascomycete; Puccinia, basidiomycete). Endosymbiosis is characterised by the 'symbiosome', a Although the common feature of endosymbioses is the compartment within host cells in which the symbiotic penetration of the plant cell wall and the apparent coloni- microorganism is either partially or completely enclosed by a sation of the plant cell, the invading microorganisms are host-derived membrane. The analysis of plant mutants separated from the cytoplasm by a plant membrane, the indicates that the genetic requirements for the interaction with symbiosome membrane (SM), which is, at least initially, rhizobia and arbuscular mycorrhiza fungi are partially in continuum with the plasmamembrane (Figure 1). Often, overlapping. The extent to which plants use similar or identical cell-wall-like matrix material is deposited between the SM developmental programs for the intracellular accommodation of and the microorganism. Thus, the microsymbiont may be different microorganisms is, however, not clear. For example, intracellular, but it is always extracytoplasmatic because of plant cells actively weaken their cell wall to facilitate bacterial the integrity of the SM.