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ScienceDirect Editorial overview: Microbial environmental biotechnology Irene Sanchez-Andrea and Mike Jetten Current Opinion in Biotechnology 2018, 50:vii–ix For a complete overview see the Issue https://doi.org/10.1016/j.copbio.2018.03.004 0958-1669/ã 2018 Published by Elsevier Ltd.
Irene Sanchez-Andrea1,2
In 2015, the United Nations formulated several sustainable development goals in which Microbial Environmental Biotechnology could play an important role. In line with those goals, access to sufficient clean (fresh) water and development of a sustainable biobased economy are of significant relevance for this special issue of Current Opinion of Biotechnology. As editors, we are delighted to put the contributing papers into a broader perspective. Before doing so, we first would like to thank all participating authors for their critical opinions and synthesizing the relevant literature on their topic of expertise.
1 Soehngen Institute of Anaerobic Microbiology, Netherlands2 Laboratory of
Microorganisms have inhabited our planet for billions of years, colonizing nearly every corner of the Earth. In the first 2 billion years, this was done in the absence of oxygen and still today many ecosystems and processes operate best under anaerobic conditions. In these systems, microorganisms are the key sources and sinks of greenhouse gases (i.e. methane, carbon dioxide and nitrous oxide) and thus strong influencers of climate change. As so, microorganisms remain the dominant drivers of the biogeochemical cycles despite strong anthropogenic influences. In the past 50 years, we have continually expanded the use of the microbial potential, especially in the recycling or clean-up of biological and waste materials. In the next 10 years, an accelerated exploration of our biosphere using various (meta) genomics and novel high throughput culture approaches leading to the discovery of new metabolisms will further propel the use of biotechnology. In addition, the experimental creation of new more effective metabolic routes by synthetic biology will play a more important role in the near future. Nevertheless, it is estimated that more than 90% of microbial diversity still remains to be discovered. This new microbial biodiversity represents an enormous wealth of novel and improved environmental biotechnological applications. With all the human pressure on the Earth’s limited resources, research on microbial biotechnologies which can mitigate or reverse the effect of anthropogenic pollution is essential for the future survival of our society. The large metabolic, yet under explored diversity of microorganisms offers enormous possibilities for technological exploitation.
Microbiology, Wageningen University, Netherlands e-mail:
[email protected]
Irene Sanchez-Andrea obtained her PhD in Microbiology in 2012 at the autonomous University of Madrid (Spain). She performed internships in laboratories in The Netherlands, Germany and USA. Afterwards she started her PostDoc in Wageningen University (NL) where she continues as an Assistant Professor nowadays. Her expertise focuses on microbial physiology and ecology of anaerobes and acidophiles with special attention on the sulfur cycle.
Mike Jetten1,2
1 Soehngen Institute of Anaerobic Microbiology, Netherlands2 Department of
Microbiology, Radboud University, Nijmegen, Netherlands e-mail:
[email protected]
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In this special issue, the state of the art on several of those relatively new microbial biotechnologies are summarized and critically evaluated. Profound knowledge on the ecophysiology of microorganisms can greatly expand their application. In the last decades, our knowledge of the microbial nitrogen cycle has increased tremendously with the discovery of several novel processes: ammonium oxidation by Thaumarchaea, complete ammonium oxidation to nitrate by comammox Nitrospira bacteria, and anaerobic ammonium oxidation (anammox) by planctomycetes bacteria. The anammox process has the potential to make nitrogen removal much more Current Opinion in Biotechnology 2018, 50:vii–ix
viii Microbial environmental biotechnology
Mike Jetten obtained his PhD in Anaerobic Microbiology in 1991 at the Wageningen University, Netherlands. After a PostDoc at MIT, Cambridge MA, USA, he moved to Delft University of Technology in 1994 as assistant professor. In 2000, he became full professor of Microbiology at Radboud University, Nijmegen, Netherlands. He received the Spinozapremie in 2012 and two ERC Advanced Grants. His team studies the anaerobic oxidation of methane and ammonium.
sustainable with less oxygen demand, less use of chemicals and less greenhouse gas emissions. In 2002, the anammox process was introduced for removal of nitrogen in side stream and industrial wastewater treatment with relatively high nitrogen content and temperatures. It is now a wellestablished technology with hundreds of plants in operation worldwide. The next challenge for the biotechnological application of anammox is its introduction in the main stream of municipal water treatment in which low temperatures, low nitrogen content and competitions with heterotrophs are encountered. In this issue, Agrawal et al. critically evaluate how mainstream implementation of partial nitritation/anammox (PN/A) requires transferable and operable ways to steer microbial competition as to meet the stringent discharge requirements on a year-round basis. A stable PN/A should increase biogas (mainly methane) yields and contribute to an overall energy-positive sewage treatment. Van Kessel et al. focus on the use of such surplus biogas for the efficient removal of nitrogen from wastewater by a combination of newly discovered Methylomirabilis bacteria and Methanoperedens archaea. In specific cases the use of methane can make wastewater treatment systems even more sustainable, especially when they are introduced together with anammox bacteria. A treatment system based on these three anaerobic microbial processes will strongly depend on the regulation of oxygen-limited partial nitrification and thus need a very careful introduction of air for the production of nitrite. Too much oxygen could result in the production of nitrate by the recently discovered comammox Nitrospira bacteria, as it is further reviewed by Lawson and Luecker. They describe the discovery of the complete ammonium-oxidizers, and speculate on the conditions that may favour these organisms in engineered and natural ecosystems. Low ammonium and hypoxic conditions appear to be the key factors controlling comammox abundance and activity. Nitrogen metabolism is important not only in wastewater treatment, but also in agricultural soils as reviewed by Motte et al. Nitrification, the conversion of ammonium via nitrite to nitrate by soil archaea and bacteria can lead to nitrate leaching and the following production of the greenhouse gas nitrous oxide production. It is estimated that up to 50% of the applied nitrogen may be lost and is no longer available for crop growth. Inhibition of nitrification is frequently applied to reduce nitrogen losses, and may contribute to a more sustainable and environmental-friendly agricultural practice. How newly identified ammonia-oxidizing archaea and comammox bacteria do react to widely used inhibitors is currently not well explored. In their review, Motte et al. compare and contrast the different pathways in ammonia oxidation, with special attention to the interaction with nitrification inhibitors. In all of the previous examples, selection of specific microorganisms, mixtures of microorganism or stable microbial communities is a very important matter. In their contribution, Zerfass et al. argue that understanding and engineering of microbial communities requires a holistic approach that not only considers species–species interactions, but also species–environment and feedbacks between ecological and evolutionary dynamics. Their engineering approach is based on thermodynamics of microbial growth and microbial redox biochemistry. In this way, specific environmental conditions are enforced, with the help of electron accepting or providing redox agents and electrodes, to generate higher-level thermodynamic boundaries. The resulting end-state will be ecologically and evolutionarily stable, mimicking the natural states of complex communities. In addition to waste clean-up, microorganisms or microbial communities can be used to develop a more biobased economy. Three contributions in this
Current Opinion in Biotechnology 2018, 50:vii–ix
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Editorial overview Sanchez-Andrea and Jetten ix
issue discuss the possibilities and limitations of aerobic and anaerobic one-carbon metabolism as biotechnological platforms to produce biofuels and biochemical. Claassens et al. provide us with a general guide and decision basis how to choose electron donors for microbial carbon fixation in chemoautotrophic or methylotrophic microorganisms, and show hydrogen, carbon monoxide and formate as the most promising donors that are efficiently produced electrochemically and have reduction potentials low enough to directly reduce the main cellular electron carriers. Chistoserdova summarizes the biotechnological developments involving microbial conversion of single carbon compounds such as methane and methanol by different approaches. Native one-carbon microorganisms or robust industrial microorganisms such as Escherichia coli or yeast could be engineered to convert C1 compounds via introduction of specific metabolic modules. Also, the options to use defined microbial consortia for C1 conversion in industrial applications are discussed. Finally, the potential of C1 utilizers in biomining of rare Earth elements is reviewed. Cantera et al. focus on the bioconversion of methane into biomolecules with a high added value such as ectoine, feed proteins, biofuels, bioplastics and polysaccharides. Biotechnological approaches using both discontinuous and continuous bioreactors are reviewed. After reading about so many biotechnological applications, one get the idea that society is doing a pretty good job profiting from microbes. But there is way more out there to be discovered. Loureiro et al. deepen in the exploration of (meta)genomic sequences to identify novel biosynthethic clusters for the production of new drugs and the state of the art of the heterologous expression of these clusters.
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We get a feeling that Nature provides with sufficient metabolic diversity but sometimes humans need more efficient microorganisms, that is, efficiency in terms of faster production, better yield and easy to grow, just to adapt them to our needs. In that direction, research on metabolic and genetic engineering is essential to steer the metabolism of microorganisms to our needs. We can either overexpress convenient pathways in our bug, or take a pathway and ‘copy-paste’ it in another bug. The possibilities are large and the field moves fast. A big revolution which has occurred in the last decade is the application of the viral defense mechanism called Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to genome editing. The use of the CRISPR-related technologies to genetically modify model microorganisms like E. coli but also others like Bacilli, Streptomycetes, etc. is reviewed by Mougiakos et al. These technologies have added a new perspective for strain developing as optimized cell factories and by combining a number of different strategies such as pathway overexpression or chromosomal deletions/insertions/substitutions, the production of different terpenoids, alcohols, aminoacids or organic acids or the antibiotic resistance have been improved. The exploration of new environments could bring us new forms of nucleases that could expand the application threshold of the genome editing: exciting times to come . . . Taken together we hope these papers provide you with a state-of-the-art overview of important environmental biotechnological examples that will help to contribute to a biobased economy and provide us with clean water in the near future.
Acknowledgements ISA and MSMJ are funded by the SIAM gravitation grant of N.W.O./O.C. W. 024.002.002. MSMJ is supported by ERC AG 339880.
Current Opinion in Biotechnology 2018, 50:vii–ix
