Call for Roundtables

Convener:	Ashley E. Franks, Amherst, USA
Co-Convener:	Sarah M. Strycharz, Amherst, USA
Speakers:	Derek R. Lovley, Amherst, USA
	Jurg Keller, Brisbane, Australia
	Kornel Rabaey,  Brisbane, Australia
	Kenneth H. Williams, Berkeley, USA

Description:
While much research has focused on the production of power in microbial fuel cells, the ability of bacteria to transfer electrons to and from a conductive surface has many environmentally favorable applications. In addition to electron transfer onto an insoluble electron acceptor, Geobacter species have been shown to use negatively poised electrodes as electron donors for reduction of fumarate, nitrate, and U(VI). Additionally, dechlorinating micro-organisms (Geobacter lovleyi and Anaeromyxobacter dehalogenans), capable of metal-reduction, have now been shown to reduce chlorinated ethenes and chlorinated aromatic compounds using a negatively poised electrode as the electron donor. These processes have important implications for bioremediation, particularly where electron donor limitations are inhibiting for source zone remediation of dense nonaqueous-phase liquids (DNAPL), and biostimulation by the addition of fermentable organic substrates has deleterious effects on the subsurface, such as increased methane production. Furthermore extracellular electron transfer processes have shown a high versatility for the energy-efficient treatment of organics in wastewater, cathode-driven denitrification and anode driven sulfide removal. These applications use both the transfer of electrons to and from a conductive surface to allow environmentally favorable biological mediated reactions. As demonstrated by the success of different trials, this technology is becoming quite close to practical commercial use. In this round table we wish to discuss the implementation of current microbial-electrode systems for beneficial environmental processes, including the hurdles to be overcome (scientific, legislative, governmental and industry) as well as speculation on future applications of microbial-electrode systems that may have yet to gain much attention.
Roundtable Schedule:

12:30-12:35:	Microbial-electrode systems – Introduction to the topic Sarah M. Strycharz, Amherst, USA
12:35-12:50:	Enhancing bioremediation of organic and metal contaminants with electrodes Derek R. Lovley, Amherst, USA
12:50-13:00:	The role of bio-electrochemical systems in resource recovery processes Jurg Keller, Brisbane, Australia
13:00-13:15:	Electrodes beyond the benchtop: Field scale approaches for monitoring     and mediating subsurface microbial processes Kenneth H. Williams, Berkeley, USA
13:15-14:00:	Discussion at large

Convenor:	Terry C. Hazen, Berkeley, USA
Speakers:	Jillian F. Banfield, Berkeley, USA Mark J. Bailey, Oxford, UK Jizhong (Joe) Zhou, Norman, USA Phil Hugenholtz, Walnut Creek, USA Gary L. Andersen, Berkeley, USA

Description:
Ecogenomic methods are developing at explosive rates and include, clone libraries, metagenomics, proteogenomics, functional gene arrays, and phylochip arrays.  These techniques are revolutionizing the way that we do, and think about microbial ecology.  Clearly some investigators prefer one over the other.  This roundtable is meant to stimulate discussion on the differences and applications and perhaps hint at developmental needs for these techniques and maybe even new research directions.  An expert in each of the areas will briefly try to convince the audience why their technique is best.  The experts will then debate each other with the participation of the audience and the moderator.

Roundtable Schedule:

12:30-12:35:	Emerging Ecogenomic methods - Introduction Terry C. Hazen, Berkeley, USA
12:35-12:45:	Proteogenomics Jillian F. Banfield, Berkeley, USA
12:45-12:55:	Clone Libraries Mark J. Bailey, Oxford, UK
12:55-13:05:	Functional Gene Arrays Jizhong (Joe) Zhou, Norman, USA
13:05-13:15:	Metagenomics Phil Hugenholtz, Walnut Creek, USA
13:15-13:25:	PhyloChip Microarray Gary L. Andersen, Berkeley, USA
13:25-14:00:	Discussion at large

Convenor:	Nianzhi Jiao, Xiamen, China
Co-Convenor:	Farooq Azam, San Diego, USA
Speakers:	Gerhard J. Herndl, Den Burg, The Netherlands Feng Chen, Baltimore, USA

Description:
Marine biological pump, a key mechanism for atmospheric CO2 fixation by the ocean, is based on particulate organic carbon (POC) transportation from surface to deep sea and sediment. Recent studies have revealed that dissolved organic carbon (DOC) can also be an important mechanism for carbon sequestration in the ocean. Labile DOC (LDOC) can be picked up by heterotrophic bacteria and then transported to upper trophic levels through “microbial loop” and consequently forming sinkable POC. Refractory DOC (RDOC) left or produced by microbial processes can remain in the ocean without returning back to atmosphere for thousands of years. In contrast to the “sinking biological pump”, DOC is not sinkable, and such newly recognized mechanisms can be called “non-sinking biological pump”. Since DOC is the largest organic carbon pool in the ocean, and RDOC is the majority of total DOC, non-sinking biological pump is one of the keys to understanding of carbon sink of the ocean.
This session will focus on the following processes:
1) Microbial transformation of DOC to POC (microbial loop related issue pump);  
2)Microbial transformation of DOC to RDOC (toward non-sinking biological pump) and
3) Microbial transformation of POC to DOC and RDOC (including virus lysis).
One of the outputs of the discussion would be to form a SCOR（Scientific Committee for Ocean Research）Working Group on the topic of “Microbial pumping of carbon in the ocean”. Related and interested ISME 12 participants are all welcome to the round table session.

Roundtable Schedule:

12:30-12:40:	Microscale interactions of bacteria with organic matter and its influence on carbon export flux in the ocean Farooq Azam, Scripps Institution of Oceanography, San Diego, USA
12:40-12:45:	Discussion
12:45-12:55:	Non-sinkable biological pump and microbial carbon sequestration in the ocean Nianzhi Jiao, Xiamen, China
12:55-13:00:	Discussion
13:00-13:10:	Autotrophic versus heterotrophic carbon processing in the meso- and bathypelagic realm of the ocean Gerhard J. Herndl, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
13:10-13:15:	Discussion
13:15-13:25:	Marine viruses and their impacts on ocean's carbon cycling Feng Chen, University of Maryland Biotechnology Institute , Baltimore, USA
13:25-13:30	Discussion
13:30-14:00	Discussion at large on Microbial Pumping of Carbon in the Ocean

Convenor:	Victor de Lorenzo, Madrid, Spain
Speakers:	Roberto Kolter, Boston, USA Steve Lindow, Berkley, USA

Description:
From the mid-80s up to the late 90s, numerous attempts were made to design genetically modified micro-organisms for environmental release as agents for bioremediation and control of organic pollutants. Yet, the field eventually came to a standstill after recurrent failures to program bacteria to behave in a non-natural fashion in scenarios quite different of the controlled conditions of the Laboratory. Part of the problem can be traced to the naivety of the genetic engineers of the time, who uncared for design principles for complex systems and circuits that are routine in e.g. electric engineering. The situation is changing after the advent of Synthetic Biology and its emphasis in robust design concepts, modularization, abstraction, orthogonality (ie. context-independency) and definition of systems boundaries. The question at stake in this Round Table is whether Synthetic Biology -and the possibility to design bacteria á la carte may provide a solution to many of the intractable problems encountered in the past that prevented the application of genetic engineering for bioremediation of polluted sites -or for agronomical applications. Will these organisms be efficacious? Will their use be ethical? Will they pose risks? Will there be a revival of the GMO controversies of the early 90s? What is the research agenda that we have to adopt? These topics will be introduced from various perspectives by 3 researchers with a record of involvement not only in the scientific foundations of genetic engineering and its biotechnological applications, but also as participants in the ensuing wider debates on risk assessment and governance of bacteria destined for the environment.

Roundtable Schedule:

12:30-12:35:	Introduction on Synthetic Biology Victor de Lorenzo, Madrid, Spain
12:35-12:45:	Refactoring Microorganisms for the Environment: Something Old and Something New Victor de Lorenzo, Madrid, Spain
12:45-12:55:	The Birth of Genetic Engineering vs. the Birth of Synthetic Biology  Roberto Kolter, Boston, USA
12:55-13:05:	Releasing Genetically Modified Bacteria: Where we are 20 Years Later Steve Lindow, Berkley, USA
13:05-14:00:	Discussion at large

Convenor:	Henry Müller, Styrian, Austria
Speakers:	Katja Opelt, Neuherberg, Germany Jana Lottmann, Lincoln, New Zealand

Description:
Plants provide several ecological niches to a large number of bacteria. These niches are located outside the plant (rhizosphere, phyllosphere, carposphere) as well as within the plant tissue (endorhiza, endosphere). Because of particular prevailing abiotic and biotic conditions microbial life in each of the micro-ecosystems requires specific capacities for e.g. adaptation, colonisation, communication and utilisation of nutrient sources. Thus, plants harbour bacterial communities with a high degree of phylogenetic and functional diversity. The wide variety of capacities exhibited by plant-associated bacteria offers numerous options for human purpose. Currently, bacteria originated from plants are exploited in different fields of biotechnology, such as plant protection, biocatalysis and production of pharmaceutical compounds. To exploit the abilities of bacteria in more extent, innovative areas to employ their potential are needed. On the other hand, novel resources e.g. exotic plant species in extreme environments and information about the ecological background of microbial communities have to be considered in future research. In the frame of the present round table the utilisation of Methylobacteria to enhance the aroma synthesis in strawberries and the specific occurrence of polyhydroxyalkanoate-producing bacteria associated with plant roots will be presented. Additionally, bryophytes, the oldest group of land plants, will be introduced as an excellent source for bioactive bacteria.

Roundtable Schedule:

12:30-12:35:	Introduction on Plant-Associated Bacteria for Biotechnology Henry Müller, Styrian, Austria
12:35-12:45:	Flavour enhancement in strawberries by Methylobacteria and PHA-producers among plant associated bacteria Henry Müller, Styrian, Austria
12:45-12:55:	Potential of moss-associated bacteria for biotechnological applications Katja Opelt, Neuherberg, Germany
12:55-13:05:	Enhancement of plant health and plant growth by beneficial bacteria Jana Lottmann, Lincoln, New Zealand
13:05-14:00:	Discussion at large

Convenor:	Jennifer Pett-Ridge, Livermore, USA
Co-Convenor:	Marcel Kuypers, Breman, Germany
Speakers:	Alfred Spormann, Stanford, USA John Moreau, Middleton, USA Théodore Bouchez, Antony Cedex, France Claude Lechene, Cambridge, USA

Description:
Using nano-secondary ion mass spectrometry (NanoSIMS), the isotopic/elemental composition of single microbial cells can be measured at natural abundances or after stable isotope probing.  This imaging ion microprobe combines high sensitivity (e.g. detecting 1 out of every 20 nitrogen atoms in the sample), high spatial resolution, and a capacity to image multiple elements/isotopes simultaneously.  To date, the technique has been successfully used to measure single cell C and N fixation, interactions between microbial proteins and biomineralization, S and CH4 cycling and host-symbiont interactions. Using new approaches which combine SIMS and FISH methodology, microbiologists can also explore the ecophysiology of known and uncultured microorganisms in complex environments by simultaneously collecting functional and phylogenetic information from individual cells.  Ongoing research suggests that labeling of intracellular features, such as mRNA and proteins may be compatible with NanoSIMS analysis.  We will discuss the fertile potential in the field of SIMS microbial ecology along with the hurdles that remain to be overcome.

Roundtable Schedule:

12:30-12:35:	What Can NanoSIMS Do For Microbial Ecology? Jennifer Pett-Ridge, Livermore, United States of America
12:35-12:45	Imaging Metabolic Interactions in Microbial Communities A. Spormann Stanford University Chemical Engineering, Biological Sciences, Environmental Engineering, Stanford, United States of America
12:45-12:55:	NanoSIMS Reveals Protein-Nanoparticle Interactions in Sedimentary Sulfide Biominerals John Moreau, Middleton, United States of America
12:55-13:05:	Development and use of Nanosims-ish to Decipher Functional Networks of Uncultured Microbed in Complex Ecosystems Théodore Bouchez, Antony Cedex, France
13:05-13:15:	High-Resolution Quantitative Imaging of Mamalian and Bacterial Cells Using Stable Isotope Mass Soectrometry Claude Lechene, Cambridge, United States of America
13:15-13:20:	Experiences as a New NanoSIMS User Marcel Kuypers, Breman, Germany
13:20-14:00:	Discussion at large

Convenor:	Angela D. Kent, Urbana, USA
Co-Convenor:	Anthony C. Yannarell, Urbana, USA
Speakers:	Jed Fuhrman, Los Angeles, USA Rob Knight, Boulder, USA

Description:
The discipline of microbial ecology interfaces with many different fields, such as microbiology, population/community/landscape ecology, biogeochemistry, ecosystem science, and evolutionary biology. Thus, microbial ecology has a tremendous potential for synthesis across biological and environmental sciences. This synthesis can be facilitated through the strategic collection of datasets that may be utilized and repurposed by multiple research teams. For instance, linking microbial community fingerprints to DNA sequences can be used to characterize long-term community changes in a specific system, while simultaneously expanding the database of known DNA sequences, which may appear in future studies or in other systems. Providing the proper ecological context for these data will also greatly increase their value for cross-system synthesis, and standard documentation of simultaneously measured environmental variables is therefore important. The “long-view” in microbial ecology will embrace the variable nature of biological systems, and proper characterization of these systems requires careful, repeated observations. We believe that a synthetic understanding of microbial ecology can be advanced by collaborative efforts and a movement beyond the “single investigator, single system” model of research. The purpose of this roundtable is to discuss research strategies for the collection of samples and data that can be integrated with larger scale studies, address multiple research questions, and grow beyond their original purpose.
Relevance: Microbial activities are the keystones of sustainability, and moving towards a synthesis-oriented microbial ecology will bring us closer to a fundamental understanding of microbial “life-support” functions on multiple scales.

Roundtable Schedule:

12:30-12:40:	Broad studies, deep studies, and collaborative studies Anthony C. Yannarell, University of Illinois, Urbana, USA
12:40-12:50:	Taking the long view: time-series data for understanding microbial communities Jed Fuhrman, University of Southern California, Los Angeles, USA
12:50-13:00:	Challenges for global analyses of microbial diversity Rob D. Knight, University of Colorado, Boulder, USA
13:00-13:10:	Building collaborative bridges in microbial ecology Angela D. Kent, University of Illinois, Urbana, USA
13:10-14:00:	Large group discussion to develop a strategy for a synthetic research program/  summary