Cyanobacteria Biotechnology by Paul Hudson

Cyanobacteria Biotechnology



Edited by
Paul Hudson







Logo: Wiley

Foreword: Cyanobacteria Biotechnology

Dear reader,

This book comes on the heels of a first era of development of photosynthetic cyanobacteria as microbial catalysts. We are now poised for the beginning of a second one.

Cyanobacteria have been studied for decades as model organisms for various aspects of photosynthesis, such as water oxidation, light sensing, harvesting and conversion, regulation of the Calvin–Benson–Bassham cycle, the circadian rhythm, and nutrient starvation. Although cyanobacteria have traditionally been cultivated at large scale as supplemental foodstuffs or sources of antioxidants, it was only 20 years ago that reliable genetic engineering was developed for model strains in a demonstration of ethanol biosynthesis by Synechococcus elongatus. It is fitting in the foreword of such a book to ask where does the field of cyanobacteria metabolic engineering stand today?

From an industrial perspective, the use of light to power CO2 fixation and conversion is attractive, as both substrates are abundant and cheap. Furthermore, microbial cells are regenerative catalysts and already a proven and accepted technology for some products. However, microbial conversion of light energy to a desired chemical comes with, to borrow from an old proverb, “many a slip ‘twixt the cup and the lip.” There is an energy loss at each step of the conversion process, including light capture, electron transport, and within the stoichiometry of the native metabolic network. Introduction of additional conversion steps to a target chemical brings more inefficiency. Thus, from the same industrial perspective that prioritizes low costs, it is clear that a potential cyanobacteria process must be made to operate near the theoretical energy conversion limit, or perhaps, the conversion limit must be increased, to ensure adoption. Metabolic engineering and biotechnology aim to elucidate the mechanisms of these inefficiencies, as well as devise and test designs for mitigating them. To date, advances in these areas are not sufficient for cyanobacteria to have widespread industrial use.

However, there is hope. As this book will show, our capabilities in studying and manipulating cyanobacteria is now highly advanced and include facile gene editing, rapid design and implementation of biosynthetic pathways, and powerful techniques for mapping metabolic fluxes and photosynthetic processes. Application of these tools within basic research continuously reveals new features of cyanobacteria metabolism, which become new targets for optimization. The discovery of novel, fast-growing strains has shown that photosynthesis can power CO2 uptake and cell growth at rates significantly higher than previously thought, and many metabolic engineering strategies described in this book can now be ported to such strains. Bold, novel designs for engineering light harvesting, atmospheric nitrogen fixation, and bioreactors will also lead to improvements in productivity in the medium term. Interestingly, our efforts will likely aid by advances in crop engineering, where the chloroplast metabolism is often a target. As cyanobacteria serve as models for the chloroplast of C3 plants, plant scientists are also studying (and engineering) cyanobacteria.

This book should serve as a guide for engineering cyanobacteria and is thus intended for multiple audiences. Researchers at the beginning of their careers, such as graduate students, should find the book useful to learn what has been achieved to date, and for a given specialization, where the most lucrative research lines lie. Cyanobacteria are understood well enough to make rational modifications for purpose, but mechanisms for regulation of key pathways are not yet known. This book is also useful for non-academics, such as biotechnologists seeking to exploit photosynthesis for industrial use. There are several chapters detailing metabolism of cyanobacteria for certain chemical classes, as well as descriptions of state-of-the-art methodologies for creating new strains, analyzing them, and even scale-up.

This book is divided into three parts: Core Cyanobacteria Processes, Concepts in Metabolic Engineering, and Frontiers of Cyanobacteria Biotechnology. Each chapter is written by experts and makes extensive reference to recent literature and patent filings. The initial chapters describe key metabolic processes unique to cyanobacteria, namely, CO2 uptake and fixation (Chapter 1 by Hagemann et al.), the photosynthetic electron transport chain (Chapter 2 by Lea-Smith and Hanke), and light harvesting (Chapter 3 by Branco dos Santos and colleagues). In keeping with the theme of this book, these chapters also describe engineering strategies to improve efficiencies of these processes.

Key concepts in metabolic engineering of cyanobacteria are introduced in the subsequent four chapters. Xiong and colleagues (Chapter 4) give an overview of how to measure and interpret metabolic fluxes, and how this technology has revealed new aspects of cyanobacteria metabolism. Hudson (Chapter 5) reviews the state of the art of synthetic biology in cyanobacteria, a rapidly growing sub-discipline, with perspective on what should be considered for an industrial process. In Chapter 6, Ducat and colleagues describe the source-sink balance in cyanobacteria and plants, namely, how do cells sense an imbalance in energy and adapt so as to dissipate it, and can this be exploited for bio-production? In Chapter 7, Ku and Lan compile examples of metabolic engineering in cyanobacteria to derive heuristics for future engineering regarding reaction driving forces, kinetics, and stability. The middle of the book explores in more detail metabolic pathways for the biosynthesis of compounds of industrial interest. The ethanol biosynthesis pathway (Chapter 8, Luan and Lu) is the most studied, has been deployed at pilot scale, and is a model for understanding limitations in large-scale production. Terpenes (Chapter 9, Rodrigues and Lindberg), storage polymers (Chapter 10, Koch and Forchhammer), and fatty acids (Chapter 11, Kawahara and Hihara) are higher value compounds that find use outside of biofuels. In Chapter 12, Oliveira and colleagues describe our current understanding of how cyanobacteria secrete or pump compounds outside of the cell and give perspective on future engineering of product export.

The third part begins by highlighting N2-fixing cyanobacteria (Chapter 13, Zhou and colleagues), strains that are underrepresented in the literature but have potential application for fertilizer, and production of nitrogen-rich chemicals. Chapter 14 by Wangikar and colleagues reports on recently discovered fast-growing cyanobacteria, their unique attributes in energy and carbon metabolism, and how CO2 fixation and growth rate could be enhanced in other strains. The book is concluded by two chapters on cultivation technology. In Chapter 15, Bühler and colleagues describe cyanobacteria biofilms as a new format for high-density cultivation, but one that comes with unique challenges in terms of mass transfer to and from the biocatalyst. In Chapter 16, Touloupakis and Carlozzi summarize their work on outdoor cultivation of photosynthetic bacteria, where the day/night cycle causes periodicity in cell growth and, in this case, hydrogen production.

The book highlights several “grand challenges,” in cyanobacteria biotechnology that awaits a new generation of scientists and engineers. Can we achieve a high, stable partitioning of carbon away from biomass and into a product of interest? What new metabolic pathways can mitigate the energetic costs of carbon fixation and photorespiration and can these be integrated with the native metabolism? How can we expand the PAR spectrum for cyanobacteria? How can we improve tolerance to “industrial stresses,” such as high light (compounded by eventual cultivation in atmospheric CO2), salt, and bio-contaminants? What is the optimal reactor configuration that balances cost with productivity?

One theme is that drawing parallels to heterotrophic bacteria will only take us so far in engineering cyanobacteria; these microbes have unique regulation mechanisms that we must continue to elucidate. To paraphrase a summation by Ducat in Chapter 6, cyanobacteria metabolism may be evolved and optimized to anticipate fluctuating conditions and not for continuous secretion of fixed carbon as biotechnologists would like. This book is meant to inform and inspire scientists to solve such challenges. We all are looking forward to the next era of cyanobacteria engineering.

Stockholm 2020

Paul Hudson, Editor


While editing this book, I relied heavily on my research group at KTH Royal Institute of Technology. I acknowledge them for reviewing drafts and for enlightening discussions about content: Ivana Cengic, Michael Jahn, Lun Yao, Kiyan Shabestary, Markus Janasch, Johannes Asplund-Samuelsson, and Jan Karlsen. I am also grateful to Matilda Klett for advice, support, and inspiration.

Part I
Core Cyanobacteria Processes