Crystal ball – 2009

Abstract

Environmental Microbiology ReportsVolume 1, Issue 1 p. 3-26 Free Access Crystal ball – 2009 First published: 05 February 2009 https://doi.org/10.1111/j.1758-2229.2008.00010.xCitations: 4AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL In this feature, leading researchers in the field of environmental microbiology speculate on the technical and conceptual developments that will drive innovative research and open new vistas over the next few years. How to use a crystal ball in environmental microbiology: developing new ways to explore complex datasets Alban Ramette and Antje Boetius, Max Planck Institute for Marine Microbiology, Bremen, Germany A crystal ball is an instrument which – when used properly – helps to gain information on the past, present or future by other means than common human senses and the standard technologies supporting them, with the purpose to use this information to generate knowledge and to aid decision making. Hence, it could be a very useful tool in environmental microbiology, which deals with an enormous number and diversity of unknown populations, processes and habitats, many of which escape human scales, and almost all of which are not traceable in the past – if we would only know how to use the crystal ball. Esoteric handbooks say that: (i) one must have a specific question to ask, (ii) one must be able to completely concentrate on this question and be very patient until the fog goes away and some information-containing images develop, then (iii) one must accept what one sees and not be blocked by preconceived opinions, finally (iv) the crystal ball is a sensitive tool that must be well maintained, cultivated and surrounded by positive energies. So, doesn't this sound like the good advices we get from our statistics experts and data base managers in how to deal with large and complex data sets? Let us face it, the big challenges in environmental microbiology – such as estimating total microbial diversity and its temporal and spatial patterns in a given habitat, studying evolution and succession of populations, recording and predicting the effects of global change, deciphering biological interactions, understanding the links between genomes and metabolomes in organisms – can only be solved by supernatural clairvoyance, or by a painstaking effort to improve observation, data recording, data accessibility and availability. In other words, the urgent questions in environmental microbiology are known, the methods and technologies are largely available, but the culture and art of retrieving and dealing with large multidisciplinary data sets have remained under-developed in our field, and are still largely missing from the education of new generations of scientists. The coming years will be associated with dramatic changes in the way we hitherto have approached microbial diversity and functions in natural environments. The drivers of these profound changes are already noticeable. First, major environmental issues (think global warming, ocean acidification, species extinction, altered land use) create a number of real-life, large-scale natural experiments with uncertain outcome, and increase the pressure to provide more predictive knowledge. Second, neighbouring disciplines such as oceanography and the geosciences have already prepared for new scales of global earth observation to which environmental microbiology could be hooked in many advantageous ways. Third, powerful sequencing tools are now offering a more detailed snapshot of the extensive diversity in natural environments. Fourth, the current revolution in single-cell imaging is just starting to open new dimensions in our understanding of what microbial life is about. Not only can we now look at who is there, but also at what and when they do it on an individual basis. Microbial ecology is showing the signs of a profound mutation of concepts, approaches and methods because microbial diversity and functions can now be questioned routinely over a huge range of spatial, temporal scales and environmental gradients, just as macrobial studies. From those simultaneously occurring scientific revolutions that describe the infinitely small and immensely big patterns of microbial life, exciting progress will logically come from the merging of those fields, so that butterfly effects at the single-cell level can be detected in their complex and ecosystem-sustaining context. Although successful results have been obtained by the description of specific cells to ecosystems, it will be also needed to place the pieces of the big puzzle back together: the understanding of the ever-increasing -omics databases will not be fully comprehended if we impose our compartmentalized vision of the world to the objects of our research: Terrestrial and marine realms, sediment, water column and atmosphere are all interconnected. Moreover, macro- and microorganisms are also connected in ways we have not understood. More studies are needed that investigate biological interactions and compare diversity patterns across taxa, not only to determine whether the same scaling rules apply, but also to identify common structuring factors, and the taxonomic levels at which comparisons are meaningful. Furthermore, the under-explored topics of intra-community dynamics, community turnover and functional complementarities within habitats and communities require further effort. Intra-community dynamics could indeed be the unsuspected keys to the many bizarreries of microbial communities that make them appear so structurally and functionally unpredictable. So, at first sight, our crystal ball shows us, looking into the crystal ball. The closer we get to the real world with all its complexity, the larger our databases of sequences and contextual parameters become, the more we need to focus on specific questions, to develop tools for data exploration and visualization, and to be able to retrieve images representing knowledge from the fog – just as the successful fortune teller who knows how to handle the crystal ball. And here is a deeper look into our funky crystal ball for future developments in environmental microbiology: analytical methods will be borrowed from fields as distant as astrophysics or climate research, as they are the closest to deal with the same types of computer-intensive challenges we are facing. Both positive and negative results of analyses will be reported so that redundant work will be avoided, especially in the context of the limited computer power and time available for each analysis. As computing power becomes more available, Bayesian statistics, for instance, will be favoured by environmental microbial ecologists who wish to assess the likelihood of all competing hypotheses within the space of all possible models that would apply to a given dataset. Analytical pipelines will automatically data mine and produce new information, available for the participating scientific community, and this reward is high enough to make the effort worthwhile. The growing knowledge of the whole field will be represented in a unique, constantly updated and well-curated, publicly available instrument. The current lab-centred approaches will be replaced by something more structured, bigger and transparent – a giant crystal ball maintained by a global community effort. Living organisms are information traps: making Synthetic Biology innocuous Antoine Danchin, Genetics of Bacterial Genomes/CNRS URA2171, Institut Pasteur, Paris, France Synthetic Biology aims at reconstructing life de novo. This asks for construction of two chemically distinct components: the cell factory and the program running it. An experiment of whole genome transplantation has been produced by one laboratory, driving a recipient host to give birth to a cell of a different species, that of the transplanted genome (Lartigue et al., 2007). In the cell, the program is separated from the machine, exactly as it is in computers. We expect that this feat will be reproduced elsewhere, and that variations on this theme will clarify the idiosyncrasies of the operating systems that drive organisms into life (we already recognize three of them, in Archaea, Bacteria and Eukarya). Analysis of genome channelling will help the model of the cell-as-a-computer to develop further (Mingorance et al., 2004). Thus, information is placed at the heart of all our scientific exploration. We can now conjecture that Information will be considered as an authentic category of Nature, on a par with Matter, Energy, Space and Time. Indeed, with the present reader, I share some exchange of information: this uses some of the four standard categories, but not much! Information per se is therefore an essential category. It will soon be accepted generally that information cannot be derived from the classical ones. An entirely novel mathematical formalism will be invented to represent information, as well as experiments aiming at decyphering the articulation between Information and the four standard categories: we need the equivalent of Einstein's E = mc2, with information at its core. Leaving the abstract world of mathematics, we will soon push this conjecture much further, and understand that living organisms are information traps. This will have enormous consequences on our understanding of several major processes associated to life. Ageing for one, and of course initiation of cancer. But we will also begin to see evolution, and learning or memory, as directly associated to the capacity of living organisms to trap information, whatever its source. This knowledge will reshape our view of Synthetic Biology. Babies are born very young Not convinced? Here is the short argument. Aged organisms make young ones: to perpetuate life requires creation of information. Making a progeny is ubiquitous, and there must be genes involved in the process. Creation of information does not require energy (Landauer, 1961). Yet accumulation of valuable information needs to make room, and energy is needed there to prevent destruction of already accumulated information (Landauer, 1961; Bennett, 1988). We will identify biochemical degradative processes, and energy sources, that implement the process in vivo. We will also understand how orthogonal processes, using different enzymes and energy sources, permit locally autonomous accumulation of information (learning should not be too much affected by general metabolism, for example). This ability to trap information has considerable consequences for Synthetic Biology: while we wish to make factories which produce fine chemicals, depollute our environment or synthesize biofuels, we will face a terrible dilemma. Either we will make the equivalent of our classical factories, and omit in our cell constructs the genes that permit accumulation of information – and this will result in cells that will multiply only for some time, then die. Or, aiming at perennial factories, we may wish to include genes that are used to catch and hold information. We will then end up with cells that, contrary to our desire, will begin to act according to whatever information has been created, rapidly forgetting the goal for which the cell factories have been constructed. In this context ‘scaling up’ will be a nightmare. But it will be a rosy dream for those who are afraid by genetically modified organisms and the like: the only dangerous organisms will be those that already exist, having evolved so as to harness information capture in a very efficient way. This will put us back to reason: the really dangerous bugs to come are not domestic, they are those transplanted from foreign countries to virgin ones (Xie et al., 2000; Global invasive species database: http://www.issg.org/database/species/search.asp?st=100ss; National invasive species information centre: http://www.invasivespeciesinfo.gov/). References Bennett, C. (1988) Notes on the history of reversible computation. IBM J Res Dev 44: 270– 277. Landauer, R. (1961) Irreversibility and heat generation in the computing process. IBM J Res Dev 3: 184– 191. Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison, C.A., 3rd, et al. (2007) Genome transplantation in bacteria: changing one species to another. Science 317: 632– 638. Mingorance, J., Tamames, J., and Vicente, M. (2004) Genomic channeling in bacterial cell division. J Mol Recognit 17: 481– 487. Xie, Y., Li, Z.Y., Gregg, W.P., and Li, D.M. (2000) Invasive species in China – an overview. Biodivers Conserv 10: 1317– 1341. C-MORE/Agouron Institute young investigators perspective on the future of microbial oceanography Emiley Eloe, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA Mauro Celussi, Istituto Nazionale di Oceanografia e Geofisica Sperimentale, Dipartimento di Oceanografia Biologica, Trieste, Italy Laura Croal, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Scott Gifford, Department of Marine Sciences, University of Georgia, Athens, GA, USA Laura Gómez-Consarnau, Marine Microbiology, School of Pure and Applied Natural Sciences, University of Kalmar, Kalmar, Sweden Yuan Liu, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA Ryan Paerl, Department of Ocean Science, University of California, Santa Cruz, CA, USA Daniela Böttjer, Université Pierre et Marie Curie-Paris 6, Laboratoire Arago & CNRS, UMR 7621, Laboratoire d'Océanographie Biologique de Banyuls, Observatoire Océanologique, Avenue Fontaulé, Banyuls-sur-Mer, France During the 2007 summer training course ‘Microbial Oceanography: from Genomes to Biomes’, hosted by the Center for Microbial Oceanography: Research and Education (C-MORE) and sponsored by the Agouron Institute, 16 international students (graduate as well as post-doctoral) were given the opportunity to improve their knowledge in microbial oceanography. Some of the leading microbial ecologists and oceanographers in the world were recruited to participate as faculty for this course and offered an exceptionally interactive environment. Three major topics were addressed during the course: (i) Microbial Control of Biogeochemistry, (ii) Microbial Growth and Metabolism and (iii) Biodiversity and Evolution of Microbial Physiology. Dr Alexandra Worden (Monterey Bay Aquarium Research Institute) led a colloquium focusing on the Environmental Microbiology 2005 ‘crystal ball’ article in which leading researchers describe their vision of what practical and theoretical developments will drive the field of environmental microbiology in the coming years. Students were encouraged to think about and articulate what intellectual and technological advances they believed would shape innovative research in microbial oceanography in the coming years. The following contributions are the opinions and ideas developed by some of the students during the research training course that highlight what we believe will take centre stage in microbial oceanography in the near future. Ecosystem metabolism: realizing prokaryotic physiology and growth While it would seem microbial production and respiration might simply be a game of addition and subtraction, the end result of determining metabolic balance in the sea remains one of the more elusive topics in microbial oceanography. The reasons for this are complex, with the focal point of the issue being our inability to accurately determine ecosystem balance: Are aquatic ecosystems net heterotrophic or net autotrophic? How flexible are microbial physiologies and how does this flexibility influence biochemical stoichiometry? How applicable is Redfield stoichiometry over large temporal and spatial scales, and how will the changing atmospheric CO2 regime influence cellular stoichiometries? Are there spatial and temporal decouplings in the net system metabolism and what processes underlie such dynamics? One of the first steps to addressing these questions would be to identify and characterize the full breadth of extant prokaryotic metabolisms. Knowledge of environmental prokaryotic diversity and functioning has grown exponentially in the last 30 years. Historically, the central dogma has been that organic carbon production was separated over some time and space scales from organic carbon decomposition, which reflected the conceptual framework of autotrophy versus heterotrophy. In the early 2000s, views of carbon fluxes and energy budgets were changed by the realization that a significant number of the previously defined heterotrophic marine bacterioplankton may actually grow photoheterotrophically, obtaining energy from sunlight and reducing power and nutritional substrates from organic matter. Two almost contemporaneous discoveries contributed to changing views of marine bacterioplankton physiology and its contributions to oceanic carbon flux and energy budget. One was the discovery of the global presence of bacteria containing bacteriochlorophyll (e.g. Kolber et al., 2001); the other was the discovery of bacterial rhodopsins, proteorhodopsins (Béjàet al., 2000). The phototrophy conferred by such mechanisms has the potential to supplement energy derived from respiration in fueling essential functions such as cellular maintenance and active growth (Béjàet al., 2000; Gómez-Consarnau et al., 2007). On the other hand, more than a decade before, what was believed then to be strictly phototrophic such as Cyanobacteria (Synechococcus and Prochlorococcus) were found to be capable of assimilating organic molecules (e.g. amino acids), thereby comprising an active component of secondary production and likely heterotrophic metabolism. We think that, despite the myth that metabolism is, in its holistic meaning, basically mapped out based on cultivated model cellular systems, the improvement of genomic techniques together with the effort in improving culture strategies will reveal still more diverse metabolic pathways that we are not fully aware of but have enormous potential for biotechnology and industry. Microbial biodiversity: molecular techniques and the need for creative culturing In the last decade, molecular techniques have dramatically shifted our understanding of the functional diversity found in microbial communities. However, many questions remain as to how this diversity relates to community function. A large portion of environmental sequences are annotated as hypothetical, and even those genes that have an annotation might be misidentified, particularly since a large portion of current databases are biased towards biomedical, rather than environmental sequences. Furthermore, it is unclear what components of a community's genetic pool are actively expressed, and how that expression varies on temporal and spatial scales. One method, metaproteomics, holds great potential, although current technological challenges restrict its widespread use in the very near future. On the other hand, the technology for isolation and sequencing of environmental RNA (metatranscriptomics) is readily available today. We believe as sequencing costs continue to decrease, the use of metatranscriptomics will become more widespread, offering researchers the opportunity to discern between a community's genetic potential and actual function. While molecular methods have enabled extensive insights into microbial diversity in various environments, a ‘physiological revolution’ is upon us that necessitates representative cultured isolates. Having culturable representatives of organisms containing genes found to be of interest from metagenomic surveys provides us the opportunity to functionally annotate the metagenome of the ocean and acquire information that can help refine our models of the biological contributions to geochemical cycles in the oceans. Moreover, such approaches have informed our understanding of microbial physiology and therefore lend themselves as potentially useful tools in our efforts to constrain ecosystem metabolism. We now have several technologies that have demonstrated success in allowing us to cultivate the ‘uncultivatable’ and a wealth of metagenomic data to draw from as we proceed with our cultivation efforts. Thus, our current challenge is to be creative in how we couple the information we gain from metagenomic studies and physiological investigations of novel organisms to better direct our future cultivation efforts using these technologies. A variety of approaches have been successful for the cultivation of novel organisms from the environment. A now classic example is the use of high-throughput methods that employ a dilution-to-extinction approach, which enabled the first cultivation of members of the ubiquitous SAR11 clade (Rappéet al., 2002). In the case of these SAR11 isolates, a dilution-to-extinction approach provided a means to eliminate competition by faster-growing organisms. In another example, a diffusion growth chamber was utilized to allow the exchange of chemicals between the chamber and the environment but restricted the movement of cells; this study revealed that isolation-based approaches may impede cultivation success by disrupting natural chemical interactions that occur between organisms (Kaeberlein et al., 2002). Thus, an important consideration for future cultivation studies and studies of marine microbes in general is how the dynamic chemical interactions between organisms in the marine environment may affect their growth and cultivatibility. Small but powerful: aquatic viruses The significance of viral-mediated processes for the understanding of global biogeochemical processes has become increasingly apparent over the past two decades. But what do we really know about aquatic viruses and their impact, what do we think we know and more important, what do the current methods allow us to think? Viruses are small, highly abundant (Bergh et al., 1989), have great potential to infect several autotrophic and heterotrophic bacteria, archaea and eukaryotes (Proctor and Fuhrman, 1990), and therefore great potential to shape the chemical composition and biological diversity of aquatic communities. By lysing prokaryotic and eukaryotic cells viruses can stimulate ecosystem respiration and nutrient regeneration, alter the transfer of energy and organic matter, and influence genetic exchange among microplanktonic members of aquatic environments. Determining whether cells are removed by grazing or viral lysis has important biogeochemical implications. Cells that undergo grazing can be channelled to higher trophic levels, while cells that undergo viral lysis may funnel more material into the dissolved phase, thereby reducing the flux of sinking particulate organic matter from the surface ocean to the seafloor (‘biological pump’), a significant issue in terms of global carbon cycling. Successful infection depends on the encounter between the virus and the host, partly explaining the fact that some groups of microorganisms and habitats are minimally affected by virus-induced processes. Heterotrophic bacterial mortality due to viral lysis is much better studied than that of phytoplankton and there exist even fewer reports on viruses infecting marine heterotrophic protists. In addition, most data on virus inflection are for the marine surface waters rather than subsurface waters or sediments. Assessing (i) the impact of viruses on host populations and (ii) the fate of host cell material released remains a difficult but important challenge that is currently limited by methodological hurdles (Suttle, 2007). Results of viral-induced mortality of prokaryotic and eukaryotic organisms obtained from different approaches (e.g. modified dilution method, transmission electron microscopy) often produce variable and ambiguous results. Thus, we need more straightforward and reliable methods to assess viral-induced microbial mortality in order to include these processes in complex nutrient and energy cycle-based models. Combining existing approaches with advances in flow cytometry or molecular tools might reveal new and promising insights. Recognition of the pivotal role viruses may play in aquatic ecosystems has undoubtedly been fruitful to our knowledge of processes in microbial oceanography but still ‘the unknown appears to beat the known’. In the past two decades, much research had been devoted to the understanding of marine viruses and we foresee that much more progress will be made in the near future. Ecological theory and the all-important hypothesis Microbial processes are essential for ecosystem sustainability and understanding these processes appears to be best achieved by generating a theory that is based on existing observations and subsequent experimental validation. In the face of the new ‘-omics’ age, the integration of novel technologies into classical ecological concepts should occupy a central position for future research in microbial oceanography, and both general ecologists and microbial ecologists need to become more interested in bridging the gap between these two disciplines. The concept of ecological theory applied to microbial oceanography is not new – and yet we still struggle to develop theories to encompass patterns and observations. When it comes to microbial ecological theory: does one apply to all? Are there perhaps multiple theories to explain different environments? Or are we pressed to develop a new, all-encompassing theory? Nevertheless, much can be learned from classical whole-ecosystem approaches, where investigations of the patterns of species abundance, distribution and biomass, community composition and food web structure can yield insight on the feedback mechanisms between marine ecosystems and the atmosphere. Also, we must always be cognizant of the importance of hypothesis-driven research. Discovery-based science is valuable in and of itself, but proceeding without a clear purpose to meet a relevant conclusion will not propel this field forward. The goals of the study must dictate: Are relevant data collected and what are the relevant data? Perhaps one of the most outstanding hurdles to overcome rests in determining the appropriate scale at which to sample and test based on the particular question of interest. How do microbial oceanographers extrapolate microscale transformations, interactions and diversity to ocean-basin, or even global, processes? Is such extrapolation necessary in the context of a question that seeks to investigate the micro- or even nanoscale? Continuous monitoring and time-series programmes will be invaluable, since they link changes in physical, chemical and biological aspects of marine systems and facilitate the microbial contribution to the global climate change. Events are more easily digested and described in hindsight, but predicting their impacts on microbial community structure and function, and larger-scale ecosystem and biome impacts will be a real challenge. Our hope is that targeted monitoring and hypothesis-oriented research, accompanied by modelling efforts that are well informed by sound experimental data, will continue to improve and better focus our predictive abilities, allowing us to make critical decisions concerning the management of our current environment for future generations. Acknowledgements We would like to extend special thanks to the Agouron Institute, the C-MORE, and the School of Ocean and Earth Science at the University of Hawaii at Mānoa. We are deeply grateful to the Agouron Institute, Dave Karl, Ed DeLong, Matt Church, Grieg Steward and Mike Rappé for inviting us to participate in the 2007 summer training course on ‘Microbial Oceanography: from Genomes to Biomes’. Many thanks also to the visiting faculty: K. Buesseler, P. Boyd, J. Cullen, P. del Giorgio, K. Johnson, Z. Johnson, M. Leinen, C. Pédros-Alío, G. Rocap, V. Smetacek, M. Sieracki, J. Thompson, P. JleB Williams and A. Worden, and to the other course participants: Angelo Bernadino, Scott Grant, Aaron Hartz, Laura Hmelo, Leo A. Procise, Regina Radan, Raquel Vaquer and Marcos Yoshinaga. References Béjà, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., et al. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 28: 1902– 1906. Bergh, O., Børsheim, K.Y., Bratbak, G., Heldal, M., et al. (1989) High abundance of viruses found in aquatic environments. Nature 340: 467– 468. Gómez-Consarnau, L., González, J.M., Coll-Lladó, M., Gourdon, P., Pascher, T., Neutze, R., et al. (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445: 210– 213. Kaeberlein, T., Lewis, K., and Epstein, S.S. (2002) Isolating uncultivable microorganisms in pure culture in a simulated natural environment. Science 296: 1127– 1129. Kolber, Z.S., Plumley, F.G., Lang, A.S., Beatty, J.T., Blankenship, R.E., VanDover, C.L., et al. (2001) Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292: 2492– 2495. Proctor, L.M., and Fuhrman, J.A. (1990) Viral mortality of marine bacteria and cyanobacteria. Nature 343: 60– 62. Rappé, M