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Nutrient Utilisation by Trichodesmium Characterisation of Molecular and Physiological Processes

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Nutrient Utilisation by Trichodesmium Characterisation of Molecular and Physiological Processes UNIVERSITY OF SOUTHAMPTON FACULTY OF NATURAL AND ENVIRONMENTAL SCIENCES SCHOOL OF OCEAN AND EARTH SCIENCES NUTRIENT UTILISATION BY TRICHODESMIUM CHARACTERISATION OF MOLECULAR AND PHYSIOLOGICAL PROCESSES by DESPO POLYVIOU Thesis for the degree of Doctor of Philosophy August 2016 Despo Polyviou: Nutrient utilisation by Trichodesmium Characterisation of Molecular and Physiological Processes Supervised by: Prof. Thomas S. Bibby, Prof. C. Mark Moore, Dr Andrew Hitchcock, Dr Martha Gledhill and Prof. Matt Mowlem I dedicate this book to the three people who have made me who I am today: My brother, who taught me that shoes need to be taken for walks and that you can be anyone you like to be (be that a fairy tale character or a cool animal. My mum, the strongest person I know, who taught me what love is, what patience is, and who believed in me when no one else did (not even me). My dad, who inspired my love for the sea, and taught me to never cease searching both inside and around me. “I ca’n’t believe that!” said Alice “Ca’n’t you?” the Queen said in a pitying tone. “Try again: draw a long breath, and shut your eyes.” Alice laughed. “There’s no use trying,” she said: “one ca’n’t believe impossible things.” “I daresay you haven’t had much practice,” said the Queen. “When I was your age, I always did it for half-an-hour a day. Why, sometimes I’ve believed as many as six impossible things before breakfast.” Through the Looking-Glass Lewis Carroll UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF NATURAL AND ENVIRONMENTAL SCIENCES School of Ocean and Earth Science Doctor of Philosophy NUTRIENT UTILISATION BY TRICHODESMIUM: Characterisation of Molecular and Physiological Processes By Despo Polyviou The activity of photosynthetic cyanobacteria capable of nitrogen (N2) fixation (diazotrophs) strongly influences oceanic primary production and global biogeochemical cycles. The niche of these organisms extends mainly across low latitude oligotrophic oceans, largely deficient in nitrate, where they introduce ‘new’ nitrogen (N) to the system. In these regions the abundant marine cyanobacterium Trichodesmium spp. accounts for a significant proportion of the fixed N flux. Despite fixation of N, the availability of phosphorus (P) and iron (Fe) remain a constraint to the activity and biogeography of diazotrophs. The genome of Trichodesmium has therefore been shaped to provide intricate adaptive strategies optimising growth under both P and Fe depletion. Characterisation of these strategies can provide information that will enhance the understanding of the organism’s biogeography in the contemporary and future ocean. In this work, molecular and physiological techniques are employed to study nutrient uptake pathways, and the metabolic response of Trichodesmium erythraeum IMS101 (Trichodesmium hereafter) to nutrient limitation. The current lack of an established system for genetic manipulation of this organism inhibits direct functional characterisation of proteins. To circumvent this, the model cyanobacteria Synechocystis sp. PCC 6803 (Synechocystis hereafter) is used as a vehicle for the heterologous expression of Trichodesmium genes. Using this technique, the suggested contribution of Trichodesmium to an emerging oceanic P redox cycle is first explored. A four-gene cluster (ptxABCD), that encodes a putative ABC transporter (ptxABC) and NAD-dependent dehydrogenase (ptxD), is demonstrated to be responsible for the organism’s ability to utilise the reduced inorganic compound phosphite. The presence and expression of this gene cluster is also confirmed in diverse field metagenomic and metatranscriptomic datasets further confirming its role in Trichodesmium species. Pathways of Fe utilisation are also investigated. Through heterologous expression the function of a currently employed Fe stress biomarker, protein Tery_3377 (IdiA), which is homologous to both Fe3+ transporters (FutA2-like) and intracellular proteins with protective function under Fe stress (FutA1-like), is elucidated. Fusing the signal sequence of this protein to GFP revealed its periplasmic localisation, and its expression in Synechocystis mutants of both futA1 and futA2 paralogues further supported involvement in Fe3+ uptake, providing evidence for its function as an Fe transporter in Trichodesmium. Finally, a physiological experiment was performed to determine the significance of direct physical contact with Saharan desert dust for acquisition of Fe by Trichodesmium. It is demonstrated that cell surface processes are fundamental in dust- Fe utilisation by this organism and transcriptomic analysis identifies a number of unique genes regulated under different Fe and dust regimes including putative cell- surface proteins not previously studied in Trichodesmium. Combined, these studies have revealed a diverse array of molecular and physiological strategies potentially employed by Trichodesmium to survive and thrive on the ephemeral supplies of nutrients encountered in oligotrophic oceans, an attribute that facilitates its significant contribution to biogeochemical cycles. i Table of Contents Chapter 1 ........................................................................................................................................................... 1 1.1 The importance of marine primary production .................................................. 1 1.2 Nutrients in the ocean .............................................................................................. 3 1.2.1 Phosphorus .......................................................................................................... 6 1.2.2 Iron ........................................................................................................................ 8 1.2.3 Paradigms of nutrient limitation .................................................................... 9 1.3 Marine Diazotrophy ................................................................................................ 10 1.3.1 The players ........................................................................................................ 10 1.3.2 Oxygen avoidance............................................................................................. 16 1.4 Living with less- lessons from marine microorganisms .................................. 18 1.4.1 Cellular strategies to cope with P stress ...................................................... 18 1.4.2 Cellular strategies to cope with Fe stress .................................................... 22 1.4.3 Trophic life strategies- Genomic minimalism or maximalism? .............. 27 1.5 Omics and Detection of stress responses............................................................ 28 1.6 Significance of molecular data in ocean science ............................................... 31 1.7 Thesis plan ................................................................................................................ 32 Chapter 2 ........................................................................................................................................................ 35 2.1 Strains and growth conditions .............................................................................. 35 2.1.1 E. coli ................................................................................................................... 35 2.1.2 Trichodesmium.................................................................................................. 35 2.1.3 Synechocystis ..................................................................................................... 39 2.2 Physiological measurements ................................................................................ 40 2.2.1 Photosynthetic physiology ............................................................................. 40 2.2.2 Growth ................................................................................................................ 41 2.2.3 Chlorophyll a ..................................................................................................... 42 2.2.4 Statistical analysis ............................................................................................ 42 2.3 Methods for molecular analysis............................................................................ 42 2.3.1 Nucleic acid extractions and quality control .............................................. 42 2.3.2 DNase Treatment and cDNA synthesis ......................................................... 44 iii 2.3.3 Polymerase Chain Reaction (PCR) conditions ............................................ 45 2.3.4 Agarose gel electrophoresis ........................................................................... 46 2.4 Generation of genetically modified strains ........................................................ 48 2.4.1 Approaches ........................................................................................................ 48 2.4.2 Techniques ......................................................................................................... 53 2.5 Protein Immunoblotting and Crystallisation ..................................................... 55 2.5.1 Immunoblotting ................................................................................................ 55 2.5.2 Purification and crystallisation ..................................................................... 55 2.6 RNA sequencing ........................................................................................................ 57 2.6.1
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