Available online at www.sciencedirect.com
ScienceDirect Editorial overview: Environmental Biotechnology Hauke Harms and Howard Junca Current Opinion in Biotechnology 2014, 27:vii–ix For a complete overview see the Issue Available online 26th April 2014 0958-1669/$ – see front matter, # 2014 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.copbio.2014.04.002
Hauke Harms
Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany e-mail: [email protected] Hauke Harms obtained his diploma in biology and his PhD degree from the University of Hamburg (Germany). He pursued his career as long-term fellow of the European Environmental Research Organization in Wageningen (The Netherlands), as research group leader at the Swiss Federal Institute for Environmental Sciences (EAWAG) and as assistant professor for soil microbiology at the Swiss Federal Institute of Technology Lausanne (EPFL). Since 2004, he is full professor at the University of Leipzig and head of the Department of Environmental Microbiology at the Helmholtz Centre for Environmental Research - UFZ. In 2010, he was awarded the Erwin Schro¨dinger Price.
Howard Junca1,2
1 Program of Applied Biology, Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, UMNG, Colombia2 Head of Research Group Microbial
Ecology: Metabolism, Genomics and Evolution – CorpoGen, Bogota DC, Colombia e-mail: [email protected]
Howard Junca (Bogota, 1975) is B.Sc. (Microbiology, 1997) from Universidad de los Andes, Colombia, M.Sc. (Biology, 2001) from www.sciencedirect.com
Research into the fate of environmental chemicals has come a long way since its early days. Approximately four decades ago, the scientific discovery and public perception of rising concentrations of poisonous chemicals in the environment triggered a wave of attempts to prevail upon microbes to transform or degrade these pollutants. Despite this concern, the global industrialization has resulted in a higher overall disposal of organic and metallic contaminants in open environments, evidenced by the accumulation of novel, emergent or derived, recalcitrant pollutants. Some specific chemicals are highly regulated, under strict control or ban, and their concentrations are decreasing due to dispersion or degradation. For many others, this is not the case, so that new means of eliminating them by stimulating bioremediation processes in the environments need to be developed. Many astonishingly successful trials using individual pollutants and pure cultures of microorganisms once fuelled the hope that a robust bioremediation industry could be founded on laboratory-derived knowledge and superbugs. However, the transfer of results obtained in experimental settings inherited from medical microbiology to the real world often failed. It appeared that Koch’s postulates of simple causal relationships did not apply to microbial pollutant degradation in the environment. Contaminated sites turned out to be too large and hostile, environmental matrices and pollutant mixtures too complex, ecological communities too undefined and interwoven, and environmental conditions too unreliable for a remediation technology that was mostly based on knowledge of pollutant biochemistry. The awareness grew that pollutant degradation is a microbial trait that sometimes disappears on its way from the lab to nature. But at the same time, new hope arose with the contrasting perception that pollutant degradation can be understood as an ecosystem service that sometimes simply emerges when environments are managed the right way. Today environmental biotechnology development is driven by methodological and conceptual advances bridging the gap between the biochemistry, physicochemistry and ecology of pollutant degradation and the requirements of conscious management of microbial communities in natural environments. Nowadays (i) microbial communities can be analyzed comprehensively, for example, by high resolution technologies such as omicsbased approaches or by labelling and sorting of cells to reach near to realtime assessments, (ii) communities can be typed and their compositional and functional patterns can be used to assess their potentials and predict their behaviors when facing pollution, (iii) plants, fungal networks and predators can be utilized to help bacteria remediate the environment or unfold other beneficial activities, and (iv) even complicated natural and technical environments are about to become manageable. For more than 20 years Current Opinion in Biotechnology has been publishing a section dedicated to Environmental Biotechnology. It is our great Current Opinion in Biotechnology 2014, 27:vii–ix
viii Environmental biotechnology
Universidad Complutense, Spain, and Ph.D. summa cum laude (2004) from TU Braunschweig, Germany. Doctoral thesis and postdoctoral work under Prof. Dr. Dietmar H. Pieper supervision at GBF, Helmholtz Society, Germany. Following positions in GeBiX research network and Universidad Nacional de Colombia, since 2010 he is the Head of RG Microbial Ecology at CorpoGen and appointed, from 2013 on, as Full Professor of Universidad Militar Nueva Granada UMNG, Colombia. Current President 2012–2014 of the Latin American Association for Microbiology ALAM.
pleasure to introduce the 2014 edition. We did a careful effort to compile reviews on a variety of topics we deem at the conceptual and technical research forefront since they provide a broad perspective of the interaction of ecological communities with environmental chemicals. This collection of twelve excellent opinion papers is reflecting and representing four general recent trends we could identify in Environmental Biotechnology. One of these trends is the application of cutting edge technologies and advanced analysis methods to the diagnosis and management of microbial ecological functioning. In this context, Mu¨ller et al. give an overview of advances in flow-cytometric single cell analysis providing further insights in how this strategy can play a key determinative role for microbial resource management in environmental biotechnology. Gieg et al. draw our attention to the importance of syntrophic consortia, which formerly escaped in-depth analysis, for the biodegradation of hydrocarbons in anaerobic subsurface environments and how state-of-the-art methods can be used to unravel their collaboration. Jacobsen and Hjelmsø show how methodological developments, such as mRNA quantification have generated new possibilities for assessing pesticide effects on microbial community structures. A second trend is the recognition of novel classes of pollutants. In this respect, Holden et al. present five reasons to advocate the use of bacteria for the assessment of the environmental risks arising from manufactured nanoparticles, whereas Kolvenbach et al. describe how biochemical, physiological and environmental constraints jointly control evolutionary processes leading to functional degradation pathways for emerging pollutants. A third trend is the focus on environments that traditionally have not been regarded as subject of environmental biotechnology. Ho¨hener and Ponsin give an overview of recent advances regarding the remediation of vadose zone environments contaminated by a wide range of organic and inorganic pollutants. The focus of the contribution by McGenity is on intertidal wetlands. He gives various intriguing and timely examples on how these highly active and fragile environments suffer from and respond to contamination with complex petroleum mixtures. In the same context, Ron and Rosenberg revive the notion of optimized nitrogen and phosphorous fertilization regimes as a way to maintain and boost autochthonous hydrocarbonoclastic bacteria for the enhanced remediation of marine petroleum pollution. The fourth trend consists in regarding pollutant degradation as an ecosystem service relying on biochemically active degraders as a part of an interacting multiorganism guild, mostly composed of bacteria, which, however, require the support and empowerment by an ecological network of non-degrader organisms. Griebler et al. impressively synthesize in a unifying framework how the integrity and functioning of groundwater ecosystems relies on evolutionary and ecological principles and how its stewardship and conservation requires approaches of corresponding comprehensiveness. Wick et al. show that interactions between plants and microorganisms are crucial for the biotransformation of organic chemicals and that bioremediation approaches, for example, in constructed wetlands, should encompass measures to ensure joint and complementary functionality between vegetation and microbial communities. Brader et al. shed light on the metabolic potential of endophytic bacteria, its role for specific interaction and communication with the plant host anticipate biotechnological uses. Finally, Jurkevitch et al. review in a comprehensive way the current knowledge regarding the roles of bacterial micro-predators to control densities, composition and abundance of bacterial communities.
Current Opinion in Biotechnology 2014, 27:vii–ix
www.sciencedirect.com
Editorial overview: Environmental Biotechnology Harms and Junca ix
Pointing at their effects and possible applications in contaminated environments, they encourage further integrative studies including protists, bacteria and phages with such features.
www.sciencedirect.com
We thank all the authors for their excellent contributions to this issue and we are confident that the readers will be enlightened and entertained as much as we were during the editorial process.
Current Opinion in Biotechnology 2014, 27:vii–ix
ScienceDirect Editorial overview: Environmental Biotechnology Hauke Harms and Howard Junca Current Opinion in Biotechnology 2014, 27:vii–ix For a complete overview see the Issue Available online 26th April 2014 0958-1669/$ – see front matter, # 2014 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.copbio.2014.04.002
Hauke Harms
Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany e-mail: [email protected] Hauke Harms obtained his diploma in biology and his PhD degree from the University of Hamburg (Germany). He pursued his career as long-term fellow of the European Environmental Research Organization in Wageningen (The Netherlands), as research group leader at the Swiss Federal Institute for Environmental Sciences (EAWAG) and as assistant professor for soil microbiology at the Swiss Federal Institute of Technology Lausanne (EPFL). Since 2004, he is full professor at the University of Leipzig and head of the Department of Environmental Microbiology at the Helmholtz Centre for Environmental Research - UFZ. In 2010, he was awarded the Erwin Schro¨dinger Price.
Howard Junca1,2
1 Program of Applied Biology, Faculty of Basic and Applied Sciences, Universidad Militar Nueva Granada, UMNG, Colombia2 Head of Research Group Microbial
Ecology: Metabolism, Genomics and Evolution – CorpoGen, Bogota DC, Colombia e-mail: [email protected]
Howard Junca (Bogota, 1975) is B.Sc. (Microbiology, 1997) from Universidad de los Andes, Colombia, M.Sc. (Biology, 2001) from www.sciencedirect.com
Research into the fate of environmental chemicals has come a long way since its early days. Approximately four decades ago, the scientific discovery and public perception of rising concentrations of poisonous chemicals in the environment triggered a wave of attempts to prevail upon microbes to transform or degrade these pollutants. Despite this concern, the global industrialization has resulted in a higher overall disposal of organic and metallic contaminants in open environments, evidenced by the accumulation of novel, emergent or derived, recalcitrant pollutants. Some specific chemicals are highly regulated, under strict control or ban, and their concentrations are decreasing due to dispersion or degradation. For many others, this is not the case, so that new means of eliminating them by stimulating bioremediation processes in the environments need to be developed. Many astonishingly successful trials using individual pollutants and pure cultures of microorganisms once fuelled the hope that a robust bioremediation industry could be founded on laboratory-derived knowledge and superbugs. However, the transfer of results obtained in experimental settings inherited from medical microbiology to the real world often failed. It appeared that Koch’s postulates of simple causal relationships did not apply to microbial pollutant degradation in the environment. Contaminated sites turned out to be too large and hostile, environmental matrices and pollutant mixtures too complex, ecological communities too undefined and interwoven, and environmental conditions too unreliable for a remediation technology that was mostly based on knowledge of pollutant biochemistry. The awareness grew that pollutant degradation is a microbial trait that sometimes disappears on its way from the lab to nature. But at the same time, new hope arose with the contrasting perception that pollutant degradation can be understood as an ecosystem service that sometimes simply emerges when environments are managed the right way. Today environmental biotechnology development is driven by methodological and conceptual advances bridging the gap between the biochemistry, physicochemistry and ecology of pollutant degradation and the requirements of conscious management of microbial communities in natural environments. Nowadays (i) microbial communities can be analyzed comprehensively, for example, by high resolution technologies such as omicsbased approaches or by labelling and sorting of cells to reach near to realtime assessments, (ii) communities can be typed and their compositional and functional patterns can be used to assess their potentials and predict their behaviors when facing pollution, (iii) plants, fungal networks and predators can be utilized to help bacteria remediate the environment or unfold other beneficial activities, and (iv) even complicated natural and technical environments are about to become manageable. For more than 20 years Current Opinion in Biotechnology has been publishing a section dedicated to Environmental Biotechnology. It is our great Current Opinion in Biotechnology 2014, 27:vii–ix
viii Environmental biotechnology
Universidad Complutense, Spain, and Ph.D. summa cum laude (2004) from TU Braunschweig, Germany. Doctoral thesis and postdoctoral work under Prof. Dr. Dietmar H. Pieper supervision at GBF, Helmholtz Society, Germany. Following positions in GeBiX research network and Universidad Nacional de Colombia, since 2010 he is the Head of RG Microbial Ecology at CorpoGen and appointed, from 2013 on, as Full Professor of Universidad Militar Nueva Granada UMNG, Colombia. Current President 2012–2014 of the Latin American Association for Microbiology ALAM.
pleasure to introduce the 2014 edition. We did a careful effort to compile reviews on a variety of topics we deem at the conceptual and technical research forefront since they provide a broad perspective of the interaction of ecological communities with environmental chemicals. This collection of twelve excellent opinion papers is reflecting and representing four general recent trends we could identify in Environmental Biotechnology. One of these trends is the application of cutting edge technologies and advanced analysis methods to the diagnosis and management of microbial ecological functioning. In this context, Mu¨ller et al. give an overview of advances in flow-cytometric single cell analysis providing further insights in how this strategy can play a key determinative role for microbial resource management in environmental biotechnology. Gieg et al. draw our attention to the importance of syntrophic consortia, which formerly escaped in-depth analysis, for the biodegradation of hydrocarbons in anaerobic subsurface environments and how state-of-the-art methods can be used to unravel their collaboration. Jacobsen and Hjelmsø show how methodological developments, such as mRNA quantification have generated new possibilities for assessing pesticide effects on microbial community structures. A second trend is the recognition of novel classes of pollutants. In this respect, Holden et al. present five reasons to advocate the use of bacteria for the assessment of the environmental risks arising from manufactured nanoparticles, whereas Kolvenbach et al. describe how biochemical, physiological and environmental constraints jointly control evolutionary processes leading to functional degradation pathways for emerging pollutants. A third trend is the focus on environments that traditionally have not been regarded as subject of environmental biotechnology. Ho¨hener and Ponsin give an overview of recent advances regarding the remediation of vadose zone environments contaminated by a wide range of organic and inorganic pollutants. The focus of the contribution by McGenity is on intertidal wetlands. He gives various intriguing and timely examples on how these highly active and fragile environments suffer from and respond to contamination with complex petroleum mixtures. In the same context, Ron and Rosenberg revive the notion of optimized nitrogen and phosphorous fertilization regimes as a way to maintain and boost autochthonous hydrocarbonoclastic bacteria for the enhanced remediation of marine petroleum pollution. The fourth trend consists in regarding pollutant degradation as an ecosystem service relying on biochemically active degraders as a part of an interacting multiorganism guild, mostly composed of bacteria, which, however, require the support and empowerment by an ecological network of non-degrader organisms. Griebler et al. impressively synthesize in a unifying framework how the integrity and functioning of groundwater ecosystems relies on evolutionary and ecological principles and how its stewardship and conservation requires approaches of corresponding comprehensiveness. Wick et al. show that interactions between plants and microorganisms are crucial for the biotransformation of organic chemicals and that bioremediation approaches, for example, in constructed wetlands, should encompass measures to ensure joint and complementary functionality between vegetation and microbial communities. Brader et al. shed light on the metabolic potential of endophytic bacteria, its role for specific interaction and communication with the plant host anticipate biotechnological uses. Finally, Jurkevitch et al. review in a comprehensive way the current knowledge regarding the roles of bacterial micro-predators to control densities, composition and abundance of bacterial communities.
Current Opinion in Biotechnology 2014, 27:vii–ix
www.sciencedirect.com
Editorial overview: Environmental Biotechnology Harms and Junca ix
Pointing at their effects and possible applications in contaminated environments, they encourage further integrative studies including protists, bacteria and phages with such features.
www.sciencedirect.com
We thank all the authors for their excellent contributions to this issue and we are confident that the readers will be enlightened and entertained as much as we were during the editorial process.
Current Opinion in Biotechnology 2014, 27:vii–ix
