Roundtables

Selected Roundtables for ISME16 are: 

Model communities: can we use them to discover generalizable principles in microbial ecology?

Convenors:  Alexander S. Beliaev, Stephen R. Lindemann, Biological Sciences Division, Pacific Northwest National Laboratory, USA

Speakers: Kelly Wrighton, The Ohio State University, USA, Ed DeLong, University of Hawaii, Manoa, USA, and Ian Head, Newcastle University, UK; Manuel Liebeke, Max Planck Institute for Marine Microbiology, Germany; Liping Zhao, Shanghai Jiao Tong University, China; Victoria Orphan, CALTech, USA; Kathryn Holt, University of Melbourne, Australia; Jillian Petersen, Max Planck Institute for Marine Microbiology, Germany.

Natural microbial communities are known to be highly biologically diverse – estimates exceed 104 species in just one average gram of soil. Furthermore, microbial communities in the field are subject to typically unknown, mostly uncontrollable, and sometimes extreme variations in environmental conditions. This complexity in the both the biological and environmental parameters makes it difficult to identify the mechanisms that govern community dynamics and from which higher-order properties (e.g. resistance to stress) emerge in natural microbial communities. The result is that patterns of community behavior can inexplicably vary between ostensibly-similar systems (perhaps the most obvious example being the human gut). Some have proposed the use of model systems to mechanistically understand the behavior of microbial interactions and their impacts upon community behavior, which have taken various forms like microcosms, stable enrichment cultures, and synthetic communities of isolated organisms. Others argue that such reductionistic, laboratory systems divorce microbes from their habitats in ways that make the knowledge gained poorly – if at all – applicable to the behavior of microbial communities in the field.

The advent of new techniques that allow nearly-complete genomes of uncultivated microbes to be accurately reconstructed from metagenomes coupled with global measurement techniques (e.g., transcriptomics, proteomics, and metabolomics) now permit us to examine the behavior of microbial populations in communities. These approaches applied to enriched consortia have revealed maintenance of extensive genomic diversity, suggesting that such cultures may be helpful in determining the mechanisms that maintain such diversity in nature. Laboratory cultivation of model communities allows parameters to be varied to identify genotype-phenotype-environment interactions in community behavior. Furthermore, the relative simplicity of model communities offers the promise of more holistic understanding of these systems that might uncover principles that help explain the behavior of more diverse microbial communities in nature, for which complexity prevents such complete examination. All of these characteristics suggest simple communities are highly attractive systems to understand the behavior of microbial communities in the field – but only if they are faithful, trustworthy models.


Soil metagenomics - deciphering big data

Convenors: Martin Hartmann, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Switzerland, Zhongjun Jia, Chinese Academy of Sciences, China, James M. Tiedje, Michigan State University, USA

Speakers: Martin Hartmann, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Switzerland, James Tiedje, Michigan State University, USA, Folker Meyer, Argonne National Lab, USA, Josh Neufeld, University of Waterloo, Canada, Mary Firestone, University of California, USA, Zhongjun Jia, Chinese Academy of Science, China

A fingernail-sized patch of soil contains billions of microbial cells, the genetic resource of which is collectively termed soil metagenome and suggestively ~1,000 times more rich than the human genome. Interdependent constituents of this community form intrinsic networks that drive   ecosystem functioning, but the majority of these members have escaped cultivation so far and their functions remain poorly understood. The advent of next-generation sequencing technologies has completely revolutionized our understanding of this genetic resource and this  groundbreaking change is ongoing. As our abilities grow to apply these technologies at the larger scale, bioinformatic problems on deciphering these data at the system level are mounting rapidly, preventing us from harnessing the full potential of these technologies. Novel pioneering  approaches are required to unravel big metagenomic data and integrate this information at the system level in order better understand what is driving ecosystem functioning. This Roundtable aims at identifying and compiling the newest promising approaches and bioinformatic tools for 1) inferring meaningful information from big metagenomic datasets, 2) linking this information to other variables at the systems level, and 3) narrowing down the sequence space by targeting the active part of the community. With the help of the audience, we will identify and collect promising approaches and tools in order to compile them as a resource available on the TerraGenome website. Having this information in one place will facilitate usage of these approaches and advance soil metagenomics research. 


Natural vs synthetic microbial communities

Convenor: Mike Jetten, Soehngen Institute of Anaerobic Microbiology, Radboud University Nijmegen, the Netherlands

Speakers: Mike Jetten & Cornelia Welte, Radboud University Nijmegen, the Netherlands, Holger Daims, University of Vienna, Austria, Peer Bork, EMBL, Germany, David Berry, University of Vienna, Austria

About ten years ago the field of synthetic microbiology emerged and has expanded ever since. Within the field of synthetic microbiology, the blueprint of the microorganisms is genetically modified in order to reprogram them to perform new tasks. There is also a more natural way of engineering of microorganisms. In such cases specific conditions are provided that microbes are performing or catalyzing the desired reactions. Synthetic vs natural selection of communities both make use of the power of microorganisms, hereby contributing to a bio based economy. But what are the differences between synthetic & natural engineered microbial communities?
In our roundtable session two presentations are given with clear examples of natural and synthetic microbial communities. This will be the basis for a discussion where the following topics play an important role: We only have explored 1% of the microbial diversity; is it faster to screen for new microbes, or should we design them? What is the impact of synthetic microbiology on our society? Can synthetic & natural systems reinforce each other and what does this mean for future applications using microorganisms and microbial communities. The discussion plays an important role in our session; we cordially invite you to share your thoughts with us!


Engaging the casual microbiologist from the oceans to outer space

Convenor: Federico M. Lauro, Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore

Speakers: Federico M. Lauro, Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Julia Schnetzer, Max Planck Institute for Marine Microbiology, Germany, Russel Y. Neches, University of California, Davis, USA, Rob Knight, University of California, San Diego, USA, Elizabeth Henaff, Weill Cornell Medical College in New York City, USA, Jay Cullen, University of Victoria, Canada.

Following a successful debate on citizen microbiology at the ASM meeting in Colorado in 2013, the world has seen an upward trend in the number of projects that engage non-professional scientists in collecting, analyzing and interpreting microbiological data. Because of their small size, abundance and role in every aspect of life, microbes are well suited for citizen science projects. In fact, technological advancements are making the involvement of everyday citizens easier and more cost-effective. However, the scientific community has raised serious concerns over the validity of the results and the personal agenda driving individuals in becoming involved in projects (1). Moreover, the availability of funding for citizen science projects through traditional routes is still limited. This roundtable will take a closer look at some of the approaches employed, highlight successes and pitfalls and engage the participants in a discussion on how to create cost-effective but scientifically-sound projects, redefining the scope of citizen microbiology for the future.


Standards towards a genome-based taxonomy that will encompass the "uncultivated majority"

Convenors: Kostas Konstantinidis, Georgia Institute of Technology, USA, Ramon Rossello-Mora, Grup de Microbiologia Marina, IMEDEA (CSIC-UIB), Spain

Speakers: Kostas Konstantinidis, Georgia Tech, USA, Aharon Oren, Hebrew University of Jerusalem, Israel, Nikos Kyrpides, Joint Genome Institute, USA, Ramon Rossello-Mora, IMEDEA, Spain.

In the advent of genomics, prokaryotic taxonomy is undergoing an important shift in the major parameters used to circumscribe species. The genome sequence can be used for: (i) calculating inter-genome identities (ANI) that had shown the existence of discrete units with borders in the range of 93-96% identity; and (ii) the inference of physiologic and genealogic relations with high confidence. It is foreseeable that the future of taxonomy of cultured organisms will mainly rely on genomic data accompanied with metabolic tests as a proof of the detected diagnostic properties observed. However, the exact genomic measurements and standards to use are not well-defined currently.

High quality metagenomics (i.e. deep sequencing and careful binning and annotation) offers nearly equal information and comparable traits as genomics of cultured organisms. The discreteness and uniqueness of putative taxa can be proven by comparing bins with other similar bins/populations and with type strain genomes available in public databases. This amount of information could, to a large extent, overcome the problems of the lack of cultures, and allow a stable classification framework for uncultured organisms with no conspicuous properties. However, there is a need to establish a common procedure to classify and name candidate taxa reminiscent of that for cultured microorganisms. Further, there is a need to convince taxonomists that the rank of Candidatus should obtain status in the formal nomenclature system and be included in the rules of the International Code of Nomenclature of Prokaryotes. If both goals are achieved, microbial ecology could have a stable classification and nomenclature system that may be recognized by the scientific community.

This roundtable will discuss the issues outlined above, with special focus on what specific genome-derived measurements and standards should be employed in order to advance the current taxonomic practice, and how to best incorporate uncultivated organisms into such a genome-based system. A major objective of the roundtable will be to solicit input from the scientific community on a specific proposal for Candidatus descriptions and for incorporating new omics-derived features into taxonomic classifications.


The rapidly changing technology landscape of microbial systems research:  How can you most effectively identify and apply recent advances in your science?

Convenors: David A. Stahl, University of Washington and Pacific Northwest National Laboratory, USA, David W. Koppenaal,Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, USA

Speakers: Lili Pasa-Tolic, Vanessa Baily, Aaron Wright, Pacific Northwest National Laboratory, USA.

This roundtable will complement the oral session entitled “Cutting-edge methods in microbial ecology”. Microbial ecologists know their science is being profoundly changed by recent advances in analytical and computational capability. However, they are less certain about how to access and properly apply the emerging technology to answer their research questions. This roundtable will bring together technology leads and scientists that have worked together productively in applying the most recent technology advances to address fundamental questions in microbial ecology. Their success stories, and the capabilities and technological assistance offered by major federal user facilities will be highlighted.


Are humans accelerating the development of antibiotic resistance in the environment?

Convenor: Ed Topp, Agriculture and Agri-Food Canada, Satoru Suzuki, Center for Marine Environmental Studies, Ehime University, Japan

Speakers: Ed Topp, Agriculture and Agri-Food Canada, Tong Zhang, University of Hong Kong, Hong Kong, Elizabeth M. H. Wellington, The University of Warwick, UK, Satoru Suzuki, Ehime University, Japan.

Increased prevalence of antibiotic resistance genes (ARGs) is a serious public health issue, now widely recognized by numerous National governments and the World Health Organization. We can consider this problem as resulting from the complex interactions between human and natural environments. A roundtable discussion was held during ISME15 in Seoul on this issue, but it concerned only the aquatic environment. Here, we propose a broader discussion of antibiotic resistance, in particular with respect to anthropogenic impacts on the selection, enrichment and dissemination of ARGs within the environmental “resistome”. Examples of human activities which may be potentiating the environmental resistome include the emissions of wastes from agriculture, aquaculture, and wastewater treatment plants (WWTPs) that contain antibiotics, other chemicals that may co-select for resistance, and ARGs that are selected for in the digestive tracts of medicated animals and people.


Integrating protists into a universal taxonomic framework and genetic reference databases for eukaryotic biology, ecology, and evolution

Convenors: Cédric Berney, CNRS and UPMC, Station Biologique, France, Pelin Yilmaz, Max Planck Institute for Marine Microbiology, Germany, Virginia Edgcomb, Woods Hole Oceanographic Institution, USA, Eunsoo Kim, American Museum of Natural History, USA, Sina Adl, University of Saskatchewan, Canada, Guy Cochrane, EMBL-EBI / ENA, Wellcome Trust Genome Campus, UK, Javier del Campo, University of British Columbia, Canada, Frank Oliver Glöckner, Jacobs University Bremen, Germany, Alastair Simpson, Dalhousie University, Canada, Colomban de Vargas, CNRS and UPMC, Station Biologique, France

Speakers: Cédric Berney, CNRS and UPMC, Station Biologique, France, Pelin Yilmaz, Max Planck Institute for Marine Microbiology, Germany, Virginia Edgcomb, Woods Hole Oceanographic Institution, USA, Connie Lovejoy, Université Laval, Canada, Ramon Massana, Institut de Ciències del Mar, Spain, Alexandra Worden, Monterey Bay Aquarium Research Institute, USA.

The next few years will represent a critical time to bridge the gap between centuries-old morphological and physiological knowledge of microbial eukaryotic diversity and the current deluge of novel eukaryotic sequence data (from environmental metabarcoding surveys, single-cell transcriptomics and genomics). In this roundtable we will present UniEuk, a community-based project to address the greatest challenge faced by protistology in this new age of environmental meta-barcoding/-genomics/-transcriptomics. It consists of two major components:

1. A standardized curation process of genetic data by active members of the protistology community (predominantly PhD students and post-docs) that will generate phylogenetically-informed reference databases of curated genetic markers with reference alignments and trees. The EukRef initiative (www.eukref.org) is driving this bottom-up process for the 18S rRNA gene.

2. Structuring the generated knowledge into a ‘universal’ taxonomic framework for eukaryotes, exhaustively covering the diversity of protists. The UniEuk taxonomic framework will integrate classical morphology-based data and information from relevant genetic markers, with top-down validation by a comprehensive network of taxonomy experts.

The outputs of UniEuk and the EukRef initiative will be publicly available and self-sustainable. The broad use and long-term preservation of the system will be achieved by direct implementation into EMBL-EBI/ENA, with the UniEuk taxonomic framework proposed as a complementary choice to the NCBI taxonomy. Overall, the UniEuk/EukRef endeavor will provide a much-needed common language for the fast-growing protistology community, bridging novel protistan genetic data from environmental and single-cell -omics to classical protistology knowledge that has effectively linked taxon names to morphological, physiological, behavioral, and ecological information.


Microbial feedbacks to climate change: current status, challenges and future perspectives

Convenors: Jizhong Zhou, University of Oklahoma, USA, Yunfeng Yang, Tsinghua University, China

Speakers: Brajesh Singh, University of Western Sydney, Australia, Gene Tyson, University of Queensland, Australia, Gangsheng Wang, Oak Ridge National Laboratory, USA, Jizhong Zhou, University of Oklahoma, USA.

Unraveling biological feedbacks to climate change faces several grand challenges. First, global climate change involves simultaneous alternations in multiple factors (e.g., elevated CO2, temperature, precipitation, nitrogen deposition, plant diversity, and land use change), which could  potentially trigger complex interactive influences on ecosystem structure and functions. Ecosystem responses to multiple global change factors are regulated by complex feedback processes. Second, ecosystem responses to climate change are likely to be nonlinear with thresholds  beyond which community structure and ecosystem functions are dramatically altered. Thus key system tipping points and their impacts on microbes have become important for understanding long-term ecosystem functioning. In addition, translation of the understanding of the  cellular-level processes to ecosystem-level knowledge of function and dynamics is challenging. It involves the difficulty of scaling across space, time and different organization levels, which is a critical issue in climate change biology.

The objective of this roundtable session is to highlight  the most recent advances in global change microbiology to address fundamental questions important to climate change biology, ecosystem ecology, microbial ecology and theoretical ecology. This session will benefit microbiologists interested in microbial ecology, systems biology,  bioinformatics, metagenomics, climate change, and biogeochemistry. After attending this session, it is expected that participants should be able to (i) recognize the most recent developments and progresses in microbial ecology related to climate change; (ii) identify the challenges,  opportunities, and future directions in climate change microbiology; (iii) obtain insights of several key long-term experimental manipulations of ecosystems important to climate change.