Growth and Nitrogen Fixation Dynamics of Azotobacter Chroococcum in Nitrogen-Free and Omw Containing Medium
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Bacteria Belonging to Pseudomonas Typographi Sp. Nov. from the Bark Beetle Ips Typographus Have Genomic Potential to Aid in the Host Ecology
insects Article Bacteria Belonging to Pseudomonas typographi sp. nov. from the Bark Beetle Ips typographus Have Genomic Potential to Aid in the Host Ecology Ezequiel Peral-Aranega 1,2 , Zaki Saati-Santamaría 1,2 , Miroslav Kolaˇrik 3,4, Raúl Rivas 1,2,5 and Paula García-Fraile 1,2,4,5,* 1 Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; [email protected] (E.P.-A.); [email protected] (Z.S.-S.); [email protected] (R.R.) 2 Spanish-Portuguese Institute for Agricultural Research (CIALE), 37185 Salamanca, Spain 3 Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01 Prague, Czech Republic; [email protected] 4 Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic 5 Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain * Correspondence: [email protected] Received: 4 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Simple Summary: European Bark Beetle (Ips typographus) is a pest that affects dead and weakened spruce trees. Under certain environmental conditions, it has massive outbreaks, resulting in attacks of healthy trees, becoming a forest pest. It has been proposed that the bark beetle’s microbiome plays a key role in the insect’s ecology, providing nutrients, inhibiting pathogens, and degrading tree defense compounds, among other probable traits. During a study of bacterial associates from I. typographus, we isolated three strains identified as Pseudomonas from different beetle life stages. In this work, we aimed to reveal the taxonomic status of these bacterial strains and to sequence and annotate their genomes to mine possible traits related to a role within the bark beetle holobiont. -
Response of Azotobacter , Pseudomonas and Trichoderma on Growth of Apple Seedling
2012 International Conference on Biological and Life Sciences IPCBEE vol.40 (2012) © (2012) IACSIT Press, Singapore Response of Azotobacter , Pseudomonas and Trichoderma on Growth of Apple Seedling + Jayant Raman Department of Botany and Microbiology, Gurukul Kangri Vishwavidyalaya, Hardwar-249404, Uttarakhand Abstract. The investigation on the efficacy of biofertilizers (Azotobacter chroococcum, Pseudomonas striata and Trichoderma viride) considering different aspects of seedling growth under apple nursery conditions enabled to reach the positive conclusions. Azotobacter chroococcum and Trichoderma viride increased the maximum germination per cent of seeds while the maximum survival of seedlings was observed on inoculation with Azotobacter chroococcum and Trichoderma viride. Azotobacter chroococcum and Pseudomonas striata was found beneficial in promoting the growth of seedling by increasing the growth rate of length and diameter of seedlings. Trichoderma viride also helped against the pests and diseases at the same time provided sufficient moisture in dry spell. The highest growth rate of length and diameter of seedling was observed on inoculation with Azotobacter chroococcum + Pseudomonas striata + Trichoderma viride. The maximum initiation and increase rate in production of number of leaves was observed on inoculation with Azotobacter chroococcum and Pseudomonas striata. This treatment also produced large sized leaves. The highest content of N,P,K, Zn and Cu in leaves was analyzed on inoculation with Azotobacter chroococcum + Pseudomonas striata + Trichoderma viride. The highest reduction of the pests attack was observed on inoculation with Pseudomonas striata and Trichoderma viride, while the infestation was least in seedling due to antifungal fungistatic organic compounds and toxins on inoculation with Azotobacter chroococcum + Pseudomonas striata + Trichoderma viride. The good growth of root in seedlings was observed on inoculation with Azotobacter chroococcum + Pseudomonas striata + Trichoderma viride. -
Archaea, Bacteria and Termite, Nitrogen Fixation and Sustainable Plants Production
Sun W et al . (2021) Notulae Botanicae Horti Agrobotanici Cluj-Napoca Volume 49, Issue 2, Article number 12172 Notulae Botanicae Horti AcademicPres DOI:10.15835/nbha49212172 Agrobotanici Cluj-Napoca Re view Article Archaea, bacteria and termite, nitrogen fixation and sustainable plants production Wenli SUN 1a , Mohamad H. SHAHRAJABIAN 1a , Qi CHENG 1,2 * 1Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Beijing 100081, China; [email protected] ; [email protected] 2Hebei Agricultural University, College of Life Sciences, Baoding, Hebei, 071000, China; Global Alliance of HeBAU-CLS&HeQiS for BioAl-Manufacturing, Baoding, Hebei 071000, China; [email protected] (*corresponding author) a,b These authors contributed equally to the work Abstract Certain bacteria and archaea are responsible for biological nitrogen fixation. Metabolic pathways usually are common between archaea and bacteria. Diazotrophs are categorized into two main groups namely: root- nodule bacteria and plant growth-promoting rhizobacteria. Diazotrophs include free living bacteria, such as Azospirillum , Cupriavidus , and some sulfate reducing bacteria, and symbiotic diazotrophs such Rhizobium and Frankia . Three types of nitrogenase are iron and molybdenum (Fe/Mo), iron and vanadium (Fe/V) or iron only (Fe). The Mo-nitrogenase have a higher specific activity which is expressed better when Molybdenum is available. The best hosts for Rhizobium legumiosarum are Pisum , Vicia , Lathyrus and Lens ; Trifolium for Rhizobium trifolii ; Phaseolus vulgaris , Prunus angustifolia for Rhizobium phaseoli ; Medicago, Melilotus and Trigonella for Rhizobium meliloti ; Lupinus and Ornithopus for Lupini, and Glycine max for Rhizobium japonicum . Termites have significant key role in soil ecology, transporting and mixing soil. Termite gut microbes supply the enzymes required to degrade plant polymers, synthesize amino acids, recycle nitrogenous waste and fix atmospheric nitrogen. -
Electron Flow and Management in Living Systems: Advancing Understanding of Electron Transfer to Nitrogenase
Utah State University DigitalCommons@USU All Graduate Theses and Dissertations Graduate Studies 8-2018 Electron Flow and Management in Living Systems: Advancing Understanding of Electron Transfer to Nitrogenase Rhesa N. Ledbetter Utah State University Follow this and additional works at: https://digitalcommons.usu.edu/etd Part of the Biochemistry Commons Recommended Citation Ledbetter, Rhesa N., "Electron Flow and Management in Living Systems: Advancing Understanding of Electron Transfer to Nitrogenase" (2018). All Graduate Theses and Dissertations. 7197. https://digitalcommons.usu.edu/etd/7197 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@USU. It has been accepted for inclusion in All Graduate Theses and Dissertations by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. ELECTRON FLOW AND MANAGEMENT IN LIVING SYSTEMS: ADVANCING UNDERSTANDING OF ELECTRON TRANSFER TO NITROGENASE by Rhesa N. Ledbetter A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biochemistry Approved: ______________________ ______________________ Lance C. Seefeldt, Ph.D. Scott A. Ensign, Ph.D. Biochemistry Biochemistry Major Professor Committee Member ______________________ ______________________ Bruce Bugbee, Ph.D. Sean J. Johnson, Ph.D. Plant Physiology Biochemistry Committee Member Committee Member ______________________ ______________________ Nicholas E. Dickenson, Ph.D. Mark R. McLellan, Ph.D. Biochemistry Vice President for Research and Committee Member Dean of the School of Graduate Studies UTAH STATE UNIVERSITY Logan, Utah 2018 ii Copyright © Rhesa N. Ledbetter 2018 All Rights Reserved iii ABSTRACT Electron Flow and Management in Living Systems: Advancing Understanding of Electron Transfer to Nitrogenase by Rhesa N. -
A Web-Based 3D Molecular Structure Editor and Visualizer Platform
Mohebifar and Sajadi J Cheminform (2015) 7:56 DOI 10.1186/s13321-015-0101-7 SOFTWARE Open Access Chemozart: a web‑based 3D molecular structure editor and visualizer platform Mohamad Mohebifar* and Fatemehsadat Sajadi Abstract Background: Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimen- sional structures of molecules. Results: With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user- friendly interface is composed. More than 30 packages are used to compose this application which adds enough flex- ibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Conclusions: Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (applica- tion programming interface). JavaScript libraries which allow creation of web pages containing interactive three- dimensional molecular structures has also been made available. -
Diversity and Characterization of Azotobacter Isolates Obtained from Rice Rhizosphere Soils in Taiwan
Ann Microbiol (2018) 68:17–26 https://doi.org/10.1007/s13213-017-1312-0 ORIGINAL ARTICLE Diversity and characterization of Azotobacter isolates obtained from rice rhizosphere soils in Taiwan Syuan-Lu Chen 1 & Meng-Ke Tsai1 & Yuh-Ming Huang1 & Cheng-Hua Huang1 Received: 4 March 2017 /Accepted: 7 November 2017 /Published online: 15 December 2017 # Springer-Verlag GmbH Germany, part of Springer Nature and the University of Milan 2017 Abstract Azotobacter species, free-living nitrogen-fixing A. chroococcum CHB 869 may be used to develop bacteria, have been used as biofertilizers to improve the pro- biofertilizers for rice cultivation because they significantly ductivity of non-leguminous crops, including rice, due to their promoted rice growth. This study contributes to the selection various plant growth-promoting traits. The purposes of this of suitable Azotobacter strains for developing biofertilizer for- study were to characterize Azotobacter species isolated from mulations and soil management strategies of Azotobacter for rice rhizospheres in Taiwan and to determine the relationship paddy fields. between the species diversity of Azotobacter and soil proper- ties. A total of 98 Azotobacter isolates were isolated from 27 Keywords Nitrogen-fixing bacteria . Rice . Diazotropic paddy fields, and 16S rRNA gene sequences were used to bacteria . Nitrogenase . Diversity identify Azotobacter species. The characteristics of these Azotobacter strains were analyzed including carbon source utilization and plant growth-promoting traits such as nitrogen Introduction fixation activity, indole acetic acid production, phosphate- solubilizing ability, and siderophore secretion. Of the 98 Rice is one of the main food crops in the world, being con- strains isolated in this study, 12 were selected to evaluate their sumed by about 50% of world and 85% of Asian populations effects on rice growth. -
Genome-Wide Identification of Azospirillum Brasilense Sp245
Koul et al. BMC Genomics (2020) 21:821 https://doi.org/10.1186/s12864-020-07212-7 RESEARCH ARTICLE Open Access Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions Vatsala Koul1,2†, Divya Srivastava2†, Pushplata Prasad Singh2* and Mandira Kochar2* Abstract Background: Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. Results: Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. Conclusions: Differential expression of 468 A. -
Respiration in Azotobacter Vinelandii and Its Relationship with the Synthesis of Biopolymers
Electronic Journal of Biotechnology 48 (2020) 36–45 Contents lists available at ScienceDirect Electronic Journal of Biotechnology Review Respiration in Azotobacter vinelandii and its relationship with the synthesis of biopolymers Tania Castillo a,AndrésGarcíab, Claudio Padilla-Córdova c, Alvaro Díaz-Barrera c,CarlosPeñaa,⁎ a Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Post. 510-3, Cuernavaca 62250, Morelos, Mexico b Laboratorio de Biotecnología Ambiental, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico c Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2147, Casilla 4059, Valparaíso, Chile article info abstract Article history: Azotobacter vinelandii is a gram-negative soil bacterium that produces two biopolymers of biotechnological Received 20 April 2020 interest, alginate and poly(3-hydroxybutyrate), and it has been widely studied because of its capability to fix Accepted 27 August 2020 nitrogen even in the presence of oxygen. This bacterium is characterized by its high respiration rates, which Available online 4 September 2020 are almost 10-fold higher than those of Escherichia coli and are a disadvantage for fermentation processes. On the other hand, several works have demonstrated that adequate control of the oxygen supply in A. vinelandii Keywords: cultivations determines the yields and physicochemical characteristics of alginate and poly(3-hydroxybutyrate). poly(3-hydroxybutyrate) Azotobacter vinelandii Here, we summarize a review of the characteristics of A. vinelandii related to its respiration systems, as well as Alginate some of the most important findings on the oxygen consumption rates as a function of the cultivation Biopolymers parameters and biopolymer production. -
Diversity of Free-Living Nitrogen Fixing Bacteria in the Badlands of South Dakota Bibha Dahal South Dakota State University
South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Theses and Dissertations 2016 Diversity of Free-living Nitrogen Fixing Bacteria in the Badlands of South Dakota Bibha Dahal South Dakota State University Follow this and additional works at: http://openprairie.sdstate.edu/etd Part of the Bacteriology Commons, and the Environmental Microbiology and Microbial Ecology Commons Recommended Citation Dahal, Bibha, "Diversity of Free-living Nitrogen Fixing Bacteria in the Badlands of South Dakota" (2016). Theses and Dissertations. 688. http://openprairie.sdstate.edu/etd/688 This Thesis - Open Access is brought to you for free and open access by Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange. For more information, please contact [email protected]. DIVERSITY OF FREE-LIVING NITROGEN FIXING BACTERIA IN THE BADLANDS OF SOUTH DAKOTA BY BIBHA DAHAL A thesis submitted in partial fulfillment of the requirements for the Master of Science Major in Biological Sciences Specialization in Microbiology South Dakota State University 2016 iii ACKNOWLEDGEMENTS “Always aim for the moon, even if you miss, you’ll land among the stars”.- W. Clement Stone I would like to express my profuse gratitude and heartfelt appreciation to my advisor Dr. Volker Brӧzel for providing me a rewarding place to foster my career as a scientist. I am thankful for his implicit encouragement, guidance, and support throughout my research. This research would not be successful without his guidance and inspiration. -
Plasmid Transformation of Azotobacter Vinelandii OP by JAMES L
Journal of General Microbiology (1987), 133, 2059-2072. Printed in Great Britain 2059 Plasmid Transformation of Azotobacter vinelandii OP By JAMES L. DORAN, WADE H. BINGLE, KENNETH L. ROY, KOJI HIRATSUKA AND WILLIAM J. PAGE* Department of Microbiology, University of Alberta, Edmonton, Alberta, Canada T6G 2E9 (Received 19 December 1986; revised 19 March 1987) Azotobacter vinelandii OP which had been naturally induced to competence by growth in iron- and molybdenum-limited medium was transformed with the broad-host-range cloning vector pKT210. However, the transformation frequency at nearly saturating levels of DNA was 1000- fold lower for pKT210 than for a single chromosomal DNA marker (nif+). Plasmid- and chromosomal-DN A-mediated transformation events were competitive, magnesium-dependent, 42 "C-sensitive processes specific to double-stranded DNA, suggesting a common mechanism of DNA binding and uptake. The low frequency of plasmid transformation was not related to restriction of transforming DNA or to the growth period allowed for phenotypic expression. Covalently-closed-circular and open-circular forms of pKT2 10 transformed cells equally well whereas EcoRI- or HindIII-linearized pKT210 transformed cells with two to three times greater efficiency. Genetic transformation was enhanced 10- to 50-fold when pKT210 contained an insert fragment of A. vinelandii nif DNA, indicating that A. vinelandii possessed a homology- facilitated transformation system. However, all transformants failed to maintain the plasmid- encoded antibiotic resistance determinants, and extrachromosomal plasmid DNA was not recovered from these cells. Flush-ended pKT210 was not active in transformation; however, competent cells were transformed to Nif+ by HincII-digested plasmid DNA containing the cloned A. -
Integrated Multi-Selection Schemes for Complex Molecular Structures
Workshop on Molecular Graphics and Visual Analysis of Molecular Data (MolVA) (2019) J. Byška, M. Krone, and B. Sommer (Editors) MolFind – Integrated Multi-Selection Schemes for Complex Molecular Structures Robin Skånberg1;2, Mathieu Linares1;2, Martin Falk1;2, Ingrid Hotz1;2, and Anders Ynnerman1;2 1Scientific Visualization Group, Linköpings University, Sweden 2Swedish e-Science Research Centre (SeRC) Figure 1: Growing an initial selection of two residues along covalent bonds in a protein fibril. Abstract Selecting components and observing changes of properties and configurations over time is an important step in the analysis of molecular dynamics (MD) data. In this paper, we present a selection tool combining text-based queries with spatial selection and filtering. Morphological operations facilitate refinement of the selection by growth operators, e.g. across covalent bonds. The combination of different selection paradigms enables flexible and intuitive analysis on different levels of detail and visual depiction of molecular events. Immediate visual feedback during interactions ensures a smooth exploration of the data. We demonstrate the utility of our selection framework by analyzing temporal changes in the secondary structure of poly-alanine and the binding of aspirin to phospholipase A2. 1 Introduction In this paper, we present a selection framework for molecu- lar substructures embedded in the visual analytics tool VIA-MD “It is through the interactive manipulation of a visual in- [SLK∗18, KSH∗18]. The work is mostly targeted toward expert terface – the analytic discourse – that knowledge is con- users from the molecular simulation domain. The user-driven de- structed, tested, refined and shared.”[PSCO09] sign of the framework combines a large set of selection paradigms This is also true for the analysis of molecular dynamics (MD) in a flexible way while maintaining a simple and intuitive interface data and the generation of expressive visualization. -
Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea
microorganisms Article Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea Amrit Koirala 1 and Volker S. Brözel 1,2,* 1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA; [email protected] 2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa * Correspondence: [email protected]; Tel.: +1-605-688-6144 Abstract: The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico predic- tion of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocu- Citation: Koirala, A.; Brözel, V.S. mented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes Phylogeny of Nitrogenase Structural and Assembly Components Reveals are currently supported by biochemical evidence of diazotrophy.