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Transcriptional Landscapes of Lipid Producing Microalgae Benoît M

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Transcriptional landscapes of lipid producing microalgae Benoît M. Carrères 2019 Transcriptional landscapes of lipid producing microalgae Benoî[email protected]:~$ ▮ Transcriptional landscapes of lipid producing microalgae Benoît Manuel Carrères Thesis committee Promotors Prof. Dr Vitor A. P. Martins dos Santos Professor of Systems and Synthetic Biology Wageningen University & Research Prof. Dr René H. Wij$els Professor of Bioprocess Engineering Wageningen University & Research Co-promotors Dr Peter J. Schaa% Associate professor* Systems and Synthetic Biology Wageningen University & Research Dr Dirk E. Martens Associate professor* Bioprocess Engineering Wageningen University & Research ,ther mem-ers Prof. Dr Alison Smith* University of Cam-ridge Prof. Dr. Dic+ de Ridder* Wageningen University & Research Dr Aalt D.). van Di#+* Wageningen University & Research Dr Ga-ino Sanche/(Pere/* Genetwister* Wageningen This research 0as cond1cted under the auspices of the .rad1ate School V2A. 3Advanced studies in Food Technology* Agro-iotechnology* Nutrition and Health Sciences). Transcriptional landscapes of lipid producing microalgae Benoît Manuel Carrères Thesis su-mitted in ful8lment of the re9uirements for the degree of doctor at Wageningen University -y the authority of the Rector Magnificus, Prof. Dr A.P.). Mol* in the presence of the Thesis' ommittee a%%ointed by the Academic Board to be defended in pu-lic on Wednesday 2; Novem-er 2;<= at 1.>; p.m in the Aula. Benoît Manuel Carrères 5ranscriptional landsca%es of lipid producing microalgae* :AB pages PhD thesis, Wageningen University* Wageningen, The Netherlands (:;<=7 With references* with summary in English CSB6D 9EF(=G(B>=A(<F>(F D,CD 1;.<F<EGHA;GE:B Contents Chapter 1 Introduction and thesis outline 7 Chapter 2 Algal omics: the functional annotation challenge 21 Chapter 3 A systems approach to explore triacylglycerol production in Neochloris oleoabundans 39 Chapter 4 Neochloris oleoabundans is worth its salt: Transcriptomic analysis under salt and nitrogen stress 77 Chapter 5 Draft Genome Sequence of the Oleaginous Green Alga Tetradesmus obliquus UTEX 393 103 Chapter 6 The diurnal transcriptional landscape of the microalga Tetradesmus obliquus 107 Chapter 7 Evaluation of diurnal responses of Tetradesmus obliquus under nitrogen limitation 145 Chapter 8 Discussion 181 Summary 211 Citations 219 Acknowledgments 241 Curriculum vitae 251 Publication list 253 Overview of completed training activities 255 Chapter 1 Introduction and thesis outline Introduction and thesis outline 1.1 Microalgae to produce biofuels Microalgae are unicell1lar microscopic and photosynthetic organisms. Due to their long evolutionary history* their -iodiversity is very -road* -oth phenotypically and genetically I<J. They can live individually as single cells* in clusters or communities, or in sym-iosis 0ith -acteria. They are found in all sorts of environments ranging from fresh0ater to hy%er(saline conditions, nutrient rich and nutrient limited conditions, and in environments that di$er largely in tem%erature and %" I:J. )ust like other micro(organisms, their importance 0ithin the planet’s ecosystem 0as overlooked for a long time. Among the many im%ortant roles algae play and have played on the planet are that they are in the origin of the planet’s oLygen rich atmosphere that %aved the road for the evolution of other e1+aryotes* and they are currently still accounted for producing half of the atmospheric oLygen I>J. Microalgae have -een the main contri-utors of the fossil fuels 0e 1se in everyday life* and they are no0 seen as a hope to reduce our de%endence on these same fossil fuels I>MEJ. Cndeed* 0hile they have -een studied for their outstanding ca%acity to clean 0ater from eLcessive content in nitrogen, phosphorus, and metals, the interest has no0 shifted to0ards -iotechnological production of valua-le products IF* =J. Microalgae* and nota-ly green algae* are valua-le candidates for diverse -iotechnological applications -ecause they are fast gro0ing photoautotrophic organisms that re9uire minimal nutrition, do not re9uire ara-le land to gro0 and thus do not com%ete 0ith feed production, have s1%erior areal productivity* and are more efficient at converting photons into -iomass than plants I<;M<:J. Many microalgae are categorized as oleaginous -ecause they can accumulate a large proportion of their dry(0eight in fatty(acids 3>;(B;O7 I<>M<AJ. The two species studied in this thesis are the oleaginous microalgae named Ettlia oleoa-undans* formally +no0n as 6eochloris oleoa-undans* and 5etradesmus o-liq1us* formally +no0n as Scenedesmus obliquus and Acutodesm1s obliq1us. 2ike other oleaginous microalgae* they can produce triacylglycerides 35A.7* 0hich can -e eLtracted and easily converted into -iodiesel IG* E* <<J. Besides, 5A.s are free of un0anted chemical constituents unlike the phospholipids and the glycolipids, leading to purer -iofuel I<GJ. The main interests here are the rene0a-le and sustaina-le aspects of gro0ing microalgae* leading to a carbon- neutral -iofuel production. While promising, the current state of -iofuel prod1ction using microalgae is not economically feasible I<BJ. Besides -iofuels, other products 0ith higher = Chapter 1 added value can -e produced* such as pigments, unsaturated fatty acids* -ioplastics and proteins IB* 1EM:;J. Despite of its %otential* the costs of lipid production in algae are currently still too high to ma+e -iofuel production 0ith microalgae economically feasible considering the current oil prices. Ct 0as recently estimated that the cost of microalgal -iomass could -e as lo0 as ;.A; euros %er Pg, and at this price level* -iofuel production 0ould -e profita-le I<BJ. 4or the moment, commercial -ioproduction from microalgae is still limited to high(value products. Applications for commodities such as -ul+ chemicals and -iofuels re9uire su-stantial improvements, such as the increase of the total solar-to-product conversion efficiency. ,ne direct 0ay to achieve this is to optimize the eLternal conditions and to maintain these during scale(1%. The production scale(1p difficulties are studied at the Algae Production And Research Center 3AlgaePARC) I:<* ::J. Another 0ay to increase efficiency is to modify the meta-olism of the algae to reach a higher solar efficiency 1nder production conditions. 4or this, a -etter understanding of algal meta-olism and underlying mechanisms is needed. This is precisely the topic of this thesis, in 0hich C analy/e the internal phenoty%es of microalgae in response to a num-er of gro0th conditions relevant to industrial applications. S%ecifically* C studied the e$ect of light-dark cycles, salt water* intense light, and nitrogen limited or depleted conditions. 1.2 Limiting factors for profitable bioproduction Microalgae can -e gro0n in very diverse ty%e of -ioreactors* each coming 0ith their o0n advantages and disadvantages. The most used reactors are race(0ay %onds, diverse configurations of t1-ular systems, rectangular %anels, and plastic foil -ased -ags. Relying on freely availa-le sunlight is an im%ortant factor to minimize costs. "o0ever* outdoor cultivation is s1-#ect to variations in tem%erature* light intensity* and a light-dark cycle. During the dark %eriod* cellular respiration occurs and can lead 1% to :AO loss in daily produced -iomass I:>J. Commonly* this loss is due to the usage of a storage com%ound like starch that accumulates during the light %eriod. Thus, starch is a transient energy and carbon storage com%ound that is used in the night for maintenance purposes and for pre%aration of the cells for the neLt day. As a result, mutants that cannot %roduce starch sho0 a decrease in the efficiency in diurnal gro0th condition I:GJ. 2ipids, another possible storage com%ound* are hardly used during the night* even by starchless m1tants. <; Introduction and thesis outline 4ig1re <.<D Batch c1ltivation to increase 5A. yield for -iodiesel %rod1ction. Batch c1ltivation is done in t0o-step %rocess 0ith a Rgro0th %haseS and a Rstress %haseS. The stress %hase is ind1ced -y nitrogen depletion* res1lting in li%ids and 5A.s acc1m1lation. '1rrent sol1tions are not optimal for -iodiesel %rod1ction at a com%etitive %rice. Cn order to achieve high concentrations of lipids and 5A. 3>;(B;O7* microalgae need to -e eL%osed to adverse gro0th conditions. Commonly this is done -y applying nitrogen limitation or complete de%letion of nitrogen from the medium* 0hich results in overflo0 of the photon energy into carbon--ased molecules like starch and 5A. I:AJ. Starch and 5A. are the main forms of carbon and energy storage and serve as an electron sin+ 0hen the synthesis of reducing e9uivalents in the photosystems eLceeds the re9uirement for cell gro0th I<GJ. This mechanism has led to a simple t0o-ste% -atch strategy for 5A. production, starting 0ith a gro0th phase under replete conditions, follo0ed -y a stress phase during 0hich usually nitrogen is de%leted as displayed in 4igure <.< I:BJ. "o0ever* 1%on complete depletion of nitrogen the efficiency of photo(energy conversion decreases during the accumulation of 5A.* leading eventually to a decrease in the yield of TA. on photons. Therefore* instead of complete starvation* a less stressful condition of continuous nitrogen limitation 0as %roposed I:EJ. Cn such a system there is simultaneous gro0th and accumulation of 5A. for longer %eriods of time. 4urthermore* constant photosynthetic efficiency can -e maintained and the amount of do0n time for cleaning and restarting the system is much shorter. Additionally* such a condition allo0s more QeLibility to ad#1st the system 0ith the changing outdoor conditions. A recent com%arison against continuous production, -atch production displayed higher photon( to-5A. yield for -oth 0ild(ty%e and the starchless mutant 3slm<7. Even though the starchless mutant had :;O lo0er photo-to(5A. yield* it accumulated BAO more 5A. as %art of its dry 0eight than the wild(ty%e. Both strains were studied in this thesis in Chapters Error: Reference source not found and Error: Reference source not found I:FJ.
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  • DIMITAR VALEV: Wastewater Treatment with Algae Doctoral Dissertation, 118 Pp

    DIMITAR VALEV: Wastewater Treatment with Algae Doctoral Dissertation, 118 Pp

    ANNALES UNIVERSITATIS TURKUENSIS UNIVERSITATIS ANNALES AI 627 AI Dimitar Valev WASTEWATER TREATMENT WITH ALGAE Dimitar Valev Painosalama Oy, Turku, Finland 2020 Finland Turku, Oy, Painosalama ISBN 978-951-29-8094-9 (PRINT) – ISBN 978-951-29-8095-6 (PDF) TURUN YLIOPISTON JULKAISUJA ANNALES UNIVERSITATIS TURKUENSIS ISSN 0082-7002 (Print) SARJA – SER. AI OSA – TOM. 627 | ASTRONOMICA – CHEMICA – PHYSICA – MATHEMATICA | TURKU 2020 ISSN 2343-3175 (Online) WASTEWATER TREATMENT WITH ALGAE Dimitar Valev TURUN YLIOPISTON JULKAISUJA – ANNALES UNIVERSITATIS TURKUENSIS SARJA – SER. AI OSA – TOM. 627 | ASTRONOMICA – CHEMICA – PHYSICA – MATHEMATICA | TURKU 2020 University of Turku Faculty of Science and Engineering Department of Biochemistry / Molecular Plant Biology Doctoral programme in Molecular Life Sciences Supervised by Dr. Esa Tyystjärvi Dr. Taina Tyystjärvi Department of Biochemistry / Department of Biochemistry / Molecular Plant Biology, Molecular Plant Biology, University of Turku, FI-20014 University of Turku, FI-20014 Turku, Finland Turku, Finland Dr. Taras Antal Department of Botany and Plant Ecology Pskov State University Pskov 180000 Russia Reviewed by Professor Amit Bhatnagar Professor Koenraad Muylaert Water Chemistry & Microbiology Laboratory of Aquatic Biology University of Eastern Finland KU Leuven Kuopio, Finland Kortrijk, Belgium Opponent Professor Ondřej Prášil Centre Algatech Institute of Microbiology, The Czech Academy of Sciences Třeboň, Czech Republic The originality of this publication has been checked in accordance with the University of Turku quality assurance system using the Turnitin OriginalityCheck service. ISBN 978-951-29-8094-9 (PRINT) ISBN 978-951-29-8095-6 (PDF) ISSN 0082-7002 (Painettu/Print) ISSN 2343-3175 (Sähköinen/Online) Painosalama Oy, Turku, Finland 2020 UNIVERSITY OF TURKU Faculty of Science and Engineering Department of Biochemistry Molecular Plant Biology DIMITAR VALEV: Wastewater treatment with algae Doctoral Dissertation, 118 pp.