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CAPITAL UNIVERSITY OF SCIENCE AND TECHNOLOGY, ISLAMABAD Chromium Reduction and Plant Growth Promotion by Staphylococcus arlettae in Wheat by Iqra Nisar A thesis submitted in partial fulfillment for the degree of Master of Science in the Faculty of Health and Life Sciences Department of Bioinformatics and Biosciences 2020 i Copyright © 2020 by Iqra Nisar All rights reserved. No part of this thesis may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, by any information storage and retrieval system without the prior written permission of the author. ii Dedicated to ALLAH Almighty, Hazrat Muhammad (PBUH) and my brother Mohsin Raza who has been a constant source of motivation and encouragement during the challenges and supporting me spiritually throughout my life. CERTIFICATE OF APPROVAL Chromium Reduction and Plant Growth Promotion by Staphylococcus arlettae in Wheat by Iqra Nisar (MBS183001) THESIS EXAMINING COMMITTEE S. No. Examiner Name Organization (a) External Examiner Dr. Nosheen Akhter NUMS, Rawalpindi (b) Internal Examiner Dr. Syeda Marriam Bakhtiar CUST, Islamabad (c) Supervisor Dr. Erum Dilshad CUST, Islamabad Dr. Erum Dilshad Thesis Supervisor October, 2020 Dr. Sahar Fazal Dr. Muhammad Abdul Qadir Head Dean Dept. of Biosciences & Bioinformatics Faculty of Health & Life Sciences October, 2020 October, 2020 iv Author's Declaration I, Iqra Nisar hereby state that my MS thesis titled \Chromium Reduction and Plant Growth Promotion by Staphylococcus arlettae in Wheat" is my own work and has not been submitted previously by me for taking any degree from Capital University of Science and Technology, Islamabad or anywhere else in the country/abroad. At any time if my statement is found to be incorrect even after my graduation, the University has the right to withdraw my MS Degree. (Iqra Nisar) Registration No: MBS183001 v Plagiarism Undertaking I solemnly declare that research work presented in this thesis titled \Chromium Reduction and Plant Growth Promotion by Staphylococcus arlettae in Wheat" is solely my research work with no significant contribution from any other person. Small contribution/help wherever taken has been dully acknowledged and that complete thesis has been written by me. I understand the zero tolerance policy of the HEC and Capital University of Science and Technology towards plagiarism. Therefore, I as an author of the above titled thesis declare that no portion of my thesis has been plagiarized and any material used as reference is properly referred/cited. I undertake that if I am found guilty of any formal plagiarism in the above titled thesis even after award of MS Degree, the University reserves the right to with- draw/revoke my MS degree and that HEC and the University have the right to publish my name on the HEC/University website on which names of students are placed who submitted plagiarized work. (Iqra Nisar) Registration No: MBS183001 vi Acknowledgements To start with the greatest name of Allah Almighty. Most gracious and merciful, whose bounties are unbounded, whose benevolence is eternal, whose blessings are uncountable, whose being everlasting, whose mercy is limitless, whose provisions are un-ending, and whose Love is our life, whose worship is our faith. Words seem too little to express my gratitude to Allah Almighty who has bestowed me with more than I deserve. Foremost, I would like to express my sincere gratitude to my supervisor Dr. Erum Dilshad for her continuous support during my research. Her patience, motivation, guidance and immense knowledge helped me in all the time of research and writing of this thesis. I could not have imagined having a better advisor and mentor for my MS thesis. I cannot thank her for her support. I owe a deep sense of gratitude to my teachers Dr. Sahar Fazal, Dr. Shaukat Iqbal Malik, Dr. Syeda Marriam Bakhtiar and Dr Arshia Amin for their insightful encouragement motivation and extraordinary kindness throughout my studies. I am so grateful to my mother for her utter support and pure trust that allowed me to chase my dreams and always being there to pray for me. I would like to thanks my husband, Faisal Faraz for his unconditional support, love and care. I would also like to thanks my friend Ms. Samiya Yasin for always helping me out and standing by my side through my thick and thin. I express my profound gratitude to my brothers and sister. Last but not the least, I would like to thank my loving and caring brother Mohsin Raza for supporting me spiritually throughout my life. This accomplishment have not been possible without their support and prayers. Thanks to all. (Iqra Nisar) Registration No: MBS183001 vii Abstract Wheat is a crop extensively cultivated for its seed, a cereal grain which is a world- wide staple food. It is the most tremendous health-building food. Microbial habitations are severely damaged by the indiscriminate use of organic fertilizers to meet the increasing demand of food supply. For supportable food production development bio fertilizers are used as a hopeful tool in different subdivisions com- prising farming, ecosystem and remediation. A substantial environmental concern is the high concentration of heavy metal pollutants in soil and water bodies re- sultant from industrial development remains. S. arlettae strains were isolated from textile and tannery industries with azo dye degradation potential and plant growth promoting property from sewages. Essential bacterial strain of Staphylo- coccus arlettae was used to check its influence on growth of wheat plant (Triticum aestivum .L). The impact of plant growth promoting bacteria on numerous pa- rameters on crop growth and development was examined. Staphylococcus arlettae has the ability of Staphylococcus arlettae to simultaneously produce PGPP and reduce Cr cytotoxicity seed showed increased proportion of germination, length of radicle, coleoptile length of coleoptile, wet and dry weight. It is also exposed that in absence as well as presence of Cr S. arlettae treated seeds showed increased percentage of germination. S. arlettae treatment resulted in an increase in shoot length over control untreated seeds in the absence of Cr and also showed healthier rooting response. Hence the progression of the bio fertilizers and the promotion of bacterial inoculation of S. arlettae in the field is an ecologically approachable way to meet the worldwide necessity to uplift crops harvests. Additionally, develop- ments in new technologies leading to the enhancement of biofertilizer shelf-lives, facilitation of distribution and application in the fields, are essential for their use to be extended in the future. Contents Author's Declaration iv Plagiarism Undertakingv Acknowledgements vi Abstract vii List of Figures xi List of Tables xii Abbreviations xiii 1 Introduction1 1.1 Background...............................1 1.2 Aims of Research Study........................4 1.3 Objectives of Research Study.....................4 2 Literature Review5 2.1 Wheat Plant...............................5 2.1.1 Nutritional Value........................5 2.1.2 Crop Development.......................7 2.1.3 Conditions for Growth.....................7 2.1.3.1 Ecology and Climatic Requirements........7 2.1.3.2 Sowing Date.....................8 2.1.3.3 Seed Treatment....................8 2.1.3.4 Land Preparation...................8 2.1.4 Crop Water Requirement (CWR)...............9 2.1.4.1 Climate........................9 2.1.4.2 Crop Type......................9 2.1.4.3 Crop Growth Stages.................9 2.2 Bio Fertilizers.............................. 10 2.2.1 Fungal Bio Fertilizers...................... 11 2.2.1.1 Types of Fungal Bio Fertilizers........... 11 viii ix 2.2.1.1.1 Arbuscular Mycorrhizal Fungi....... 11 2.2.1.1.2 Mycorrhizal Fungi............. 11 2.2.1.1.3 Ectomycorrhizae (ECM) and Arbuscular Mycorrhizae (AM)............. 11 2.2.2 Classification of Bio Fertilizers................. 12 2.2.2.1 Rhizobium...................... 12 2.2.2.2 Azotobacter...................... 12 2.2.2.3 Azospirillum..................... 12 2.2.2.4 Cyanobacteria.................... 13 2.2.2.5 Azolla......................... 14 2.2.2.6 Phosphate Solubilizing Microorganisms (PSM).. 15 2.3 Rhizobacteria (Plant Growth Promoting)............... 15 2.3.1 Mechanisms of Plant Growth-Promoting Rhizobacteria.......................... 16 2.4 Nitrogen Fixation............................ 17 2.5 Phosphate Solubilization........................ 19 2.6 Staphylococcus arlettae ......................... 21 2.6.1 Origin.............................. 22 2.6.2 Previous Studies........................ 23 2.6.2.1 Arsenic Hyper Tolerance............... 23 2.6.2.2 Decolorizing Azo Dyes................ 23 2.6.2.3 Lipase Activity.................... 24 2.6.2.4 Extremophilic Lipase Activity............ 24 2.6.2.5 Degradation of Phenolic and Non-Phenolic Com- pounds........................ 24 2.6.2.6 Triglyceride Removing Ability............ 25 2.6.3 Genome Sequencing....................... 25 2.7 Chromium Cytotoxicity........................ 26 2.8 Sources.................................. 27 2.8.1 Effects of Chromium...................... 27 2.8.2 Mechanism of Toxicity..................... 28 2.8.3 Microbial Detoxification Mechanism by Heavy Metal.... 29 2.8.3.1 Bio Sorption..................... 30 2.8.3.1.1 Metal Dependent Bio Accumulation... 30 2.8.3.1.2 Metal Independent Bio Accumulation... 30 2.8.3.1.3 Example................... 30 3 Material and Methods 31
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  • Staphylococcus Sciuri C2865 from a Distinct Subspecies Cluster As Reservoir of the Novel Transferable Trimethoprim Resistance Ge

    Staphylococcus Sciuri C2865 from a Distinct Subspecies Cluster As Reservoir of the Novel Transferable Trimethoprim Resistance Ge

    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.30.320143; this version posted September 30, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Novel trimethoprim resistance gene and mobile elements in distinct S. sciuri C2865 1 Staphylococcus sciuri C2865 from a distinct subspecies cluster as reservoir of 2 the novel transferable trimethoprim resistance gene, dfrE, and adaptation 3 driving mobile elements 4 Elena Gómez-Sanz1,2*, Jose Manuel Haro-Moreno3, Slade O. Jensen4,5, Juan José Roda-García3, 5 Mario López-Pérez3 6 1 Institute of Food Nutrition and Health, ETHZ, Zurich, Switzerland 7 2 Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 8 Logroño, Spain 9 3 Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 10 Apartado 18, San Juan 03550, Alicante, Spain 11 4 Infectious Diseases and Microbiology, School of Medicine, Western Sydney University, Sydney, 12 New South Wales, Australia. 13 5 Antimicrobial Resistance and Mobile Elements Group, Ingham Institute for Applied Medical 14 Research, Sydney, New South Wales, Australia. 15 * Corresponding author: Email: [email protected] (EGS) 16 17 Short title: Novel trimethoprim resistance gene and mobile elements in distinct S. sciuri C2865 18 Keywords: methicillin-resistant coagulase negative staphylococci; Staphylococcus sciuri; 19 dihydrofolate reductase; trimethoprim; dfrE; multidrug resistance; mobile genetic elements; 20 plasmid; SCCmec; prophage; PICI; comparative genomics; S. sciuri subspecies; intraspecies 21 diversity; adaptation; evolution; reservoir.