PhD Thesis 2012 - University of the Wit Authors: Sumaiya F. Jamal-Allyab*#, Stuart Rutherfordb, Colin

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  • A R B U S C U L A R M Y C O R R H I Z A A N D S O I L M I C R O B I A L

    I N T E R A C T I O N S I N S U G A R C A N E A G R I C U L T U R E I N

    K W A Z U L U – N A T A L, S O U T H A F R I C A

    SUMAIYA FAIZAL JAMAL–ALLY

    2013

    PHD THESIS

    FACULTY OF SCIENCE

  • A R B U S C U L A R M Y C O R R H I Z A A N D S O I L M I C R O B I A L

    I N T E R A C T I O N S I N S U G A R C A N E A G R I C U L T U R E I N

    K W A Z U L U – N A T A L, S O U T H A F R I C A

    SUMAIYA FAIZAL JAMAL-ALLY

    A Thesis, submitted to the Faculty of Science, University of the Witwatersrand, in

    fulfilment of the requirements for the degree of Doctor of Philosophy.

    Johannesburg, 2013

  • ii

    In the Name of God Most Gracious, Most Beneficent:

    I declare that this Thesis is my own, unaided work.

    The information used in my Thesis, has been obtained whilst working as a PhD

    student under the aegis of the South African Sugarcane Research Institute,

    Mount Edgecombe, and was subsequently completed (p/t) whilst employed as a

    lecturer in Microbiology, School of Life Sciences, University of KwaZulu-Natal,

    Pietermaritzburg, South Africa.

    This material was financially supported by the National Research Foundation,

    Thuthuka (RiT) - any opinion, findings and conclusions or recommendations

    expressed in this material are those of the author(s) and therefore the NRF does

    not accept any liability in regard thereto.

    My Thesis is being submitted for the Degree of Doctor of Philosophy at the

    University of the Witwatersrand, Johannesburg. It has not been submitted

    before for any degree or examination at any other University.

    SUMAIYA FAIZAL JAMAL-ALLY

    Signed on this 30 day of April 2013 in Pietermaritzburg, KwaZulu-Natal.

  • iii

    ABSTRACT

    A novel holistic approach was used to study the mycotrophic nature of

    commercial sugarcane varieties grown in KwaZulu-Natal, South Africa. All five

    varieties were mycotrophic, but N12 had the highest overall mycorrhization and

    was selected for a pot study to assess the growth response of sugarcane to

    inoculation with indigenous arbuscular mycorrhizal (AM) fungi and microflora.

    The pot study suggested that sugarcane will respond positively to inoculation

    with AM fungi, but the effects are most clear in the early phase of growth and

    less obvious in later elongation phases. This observation, taken together with the

    ability of sugarcane to grow well in sterile soil without microflora additions

    suggests that the plant may be facultatively mycotrophic. A multivariate analysis

    determined the nutrient relationships between soil and corresponding leaf

    nutrient levels on 72 sugarcane field plants, categorised according to either high

    or low percentage colonisation. Highly colonised plants were found to have more

    positive nutrient correlations compared to lower percentage colonised plants.

    AM fungi were identified from spore morphology and associated mycorrhizal

    bacteria (AMB) were identified by 16s rDNA analysis. Partial molecular

    identification was conducted using a universal eukaryotic forward NS31 primer

    and general fungal AM1 primers confirming the spores to be of AM fungi origin.

    A nested PCR was performed, using the universal fungal primers, NS5 and ITS4,

    followed by primer combinations to target sequences of specific Glomalean

    groups. Only partial molecular identification was conducted, as RFLPs were not

    successfully optimised. DNA from the Acaulospora gerdemannii/Acaulospora

    trappei group, Glomus occultum/Glomus brasilianum group, Glomus

    mosseae/Glomus intraradices group, Glomus etunicatum/ Glomus clariodeum

    group and Acaulosporaceae sensu stricto were detected, indicating AM fungi

    diversity. Bacteria, Brevibacillus reuszeri isolated from Scutellospora nigra,

    Bacillus megaterium and Stenotrophomonas maltophilia isolated from Glomus

    geosporum, Paenibacillus chitinolyticus and Bacillus cereus isolated from

    Acaulospora mellea and Gigaspora margarita spores respectively, were tested

  • iv

    for biocontrol capability against pathogenic nematodes of Paratrichodorus,

    Meloidogyne and Pratylenchus genera. Meloidogyne was the least susceptible to

    associated mycorrhizal bacteria biocontrol and Paratrichodorus the most

    susceptible. These studies have contributed to understanding the role of AM in

    sugarcane agriculture in South Africa.

    Keywords: arbuscular mycorrhiza, sugarcane varieties, multivariate analysis,

    nutrient relationships, associated mycorrhizal bacteria, biocontrol, nematodes

  • v

    I LOVINGLY DEDICATE MY THESIS TO

    My Creator, for making all things possible;

    My wonderful husband Hassen Ally, for his eternal love and encouragement;

    My beautiful son Muhammad-Suhayl, for his little fingers “helping mom type”,

    My amazing parents Rasheeda and Faizal Jamal, for your continuous love and

    dedication to our family;

    My sister Naasiha Jamal, my brother Yacoob Jamal and sister-in-law Nazeefa

    Jamal, for your continuous love and support.

  • vi

    ACKNOWLEDGEMENTS

    I would like to sincerely thank my supervisor Prof CJ Straker (Wits) for patience

    and guidance throughout this study and especially encouraging me to continue

    with my PhD even after my paralysis.

    I sincerely thank my co-supervisor Dr RS Rutherford (SASRI) for support and

    advice throughout this study.

    I sincerely thank Mufti Ismail Ibn Musa Menk, and Qaris Haroon Taylor, for

    spiritual guidance, wisdom and oceans of knowledge.

    Sincere thanks to the National Research Foundation (Thuthuka – RiT) for

    financially supporting this material.

    Special thanks to:

     Dr Sackey Yobo (UKZN), for help and advice with using the SAS

    programmes.

     Dr Patrice Cadet (SASRI/CIRAD), for advice during the field trials and the

    ADE-4 statistical analysis.

     Dr Shaun Berry (SASRI), for providing the nematodes and technical staff

    during sample collection and processing.

     Prof Mark Laing, for being an inspiration and a wonderful mentor.

     Dr Unathi Kolanisi, for her moral support.

     Jayson Kuppusamy from Merck, for invaluable advice.

     My colleagues and students, for support and encouragement.

     SASRI and the University of KwaZulu-Natal, for granting me the

    opportunity and facilities to complete my PhD.

  • vii

    RESEARCH OUTPUTS

    1. Original publication submitted to Journal of Plant Nutrition

    Title: Multivariate Analysis of Plant-Soil Nutrient Relationships in Arbuscular

    Mycorrhizal Sugarcane Grown in KwaZulu-Natal, South Africa

    Authors: Sumaiya F. Jamal-Allyab*#, Stuart Rutherfordb, Colin J. Strakera

    a Mycology Research Laboratory, School of Molecular and Cell Biology,

    University of the Witwatersrand, Private Bag 3, Wits 2050, Johannesburg,

    South Africa

    b Crop Protection, South African Sugar Research Institute, Private Bag

    X02, Mount Edgecombe 4300, South Africa

    *Corresponding author: Sumaiya F Jamal-Ally

    #Present address: Microbiology, School of Life Sciences, University of

    KwaZulu-Natal, Private Bag X01, Scottville, Pietermaritzburg 3209, South

    Africa

    Email: jamal@ukzn.ac.za ; Telephone: +27 829737496;

    Facsimile: +27 33 2606209

    2. Conference poster presentation

    Sumaiya F. Jamal-Ally; Stuart Rutherford; Colin J. Straker. "Arbuscular

    Mycorrhizas and Soil Microbial Interactions in Sugarcane Agriculture in KwaZulu-

    Natal, South Africa". The 7th International Conference on Mycorrhiza (ICOM 7),

    The Energy and Resources Institute; India Habitat Centre, New Delhi, 6 to 11

    January 2013.

  • viii

    3. Conference oral presentation

    Jamal, S. F.; Cadet, P.; Rutherford, R. S.; Straker, C. J. "Effect of mycorrhiza on the

    nutrient uptake of sugarcane". Proceedings of the 78th Annual Congress of South

    African Sugar Technologists' Association, held at Kwa-Shukela, Mount

    Edgecombe, South Africa, 27-30 July 2004. pp 343-347. (paper)

    4. Seminars

     Sumaiya F. Jamal-Ally. "Arbuscular Mycorrhizas: An Under Earth Revolution."

    School of Life Sciences Seminar Series, held at the University of KwaZulu-

    Natal, Agricultural Campus, Pietermaritzburg, South Africa, 24 August 2012.

     Sumaiya F. Jamal- Ally. "Enhanced Uptake of Nutrients In Arbuscular

    Mycorrhizal Sugarcane Grown in the North Coast Region of Kwazulu-Natal".

    School of Biochemistry, Genetics and Microbiology Research Day, held at the

    University of KwaZulu-Natal, Agricultural Campus, Pietermaritzburg, South

    Africa, 14 June 2011.

  • ix

    TABLE OF CONTENTS

    DECLARATION…..….…………………………………………………………………………………..………………