Microbial Environmental Genomics
Environmental Microbial Ecology in An ‘omics’ Era

http://www.nioo.knaw.nl/PROJECTS/microengen/

Initiator: Hans van Veen (The Netherlands), George Kowalchuk (The Netherlands)

Summary report of MicroEnGen-II (Shanghai, June 12-15, 2006)

After the first MicroEnGen workshop (Wageningen, The Netherlands, April 2004), which examined the potential impact of emerging technologies in microbial ecology, it was agreed that MicroEnGen-II would place its primary focus on the implementation of ‘-omics’ technologies within integrated programs of environmental microbiology. The workshop was expertly hosted by Liping Zhao, Xiaojun Zhang and colleagues of the Shanghai Jiao Tong University and was held at the Manhang Campus Conference Center Hotel on June 12th-15th, 2005. The summary report of the meeting is published in Microbial Biology, Vol. 53, Number 3/April 2007 (Springer New York)

The workshop’s focus on putting ‘omics’ technologies into action was immediately realized in the opening keynote address by Gary Sayler (USA) entitled “Functionalizing Genomics for Environmental Assessment and Monitoring”. This opening address highlighted the usefulness of evolving genomics methodologies when incorporated within a robust toolbox of quantitative molecular methods and biosensor technologies. This address showed that ‘omics’ approaches are not only trendy, but can be applied to practical environmental assessment issues.

The body of the workshop was organized according to environmental research topics with sessions in nutrient cycling and eutrophication, waste management and pollution, and changing land use and sustainable agriculture. The presentations in the nutrient cycle session were provided by Colin Murrell (UK), Philippe Lemanceau (France), and Jizhong Zhou (USA), who highlighted the usefulness of stable isotope probing, proteomics and functional microarrays, respectively, to assess the functional responses of microbial communities to nutrient inputs. Highlights of the waste management pollution session included an examination of microbial adaptation to lindane by Tim Vogel (France), a metagenomic perspective to a variety of complex communities by Liping Zhao (China) and a study of genomic islands of degradation genes by Stéphan Lacour (Switzerland). In the session on land use and sustainable agriculture, George Kowalchuk (the Netherlands) described patterns of microbial diversity in the rhizosphere, Barbara Reinhold-Hurek (Germany) examined the diversity and activity of root-associated diazotrophs via microarray and Q-PCR analyses, Mark Bailey (UK) again highlighted advances in stable isotope probing methods that are helping to link microbial identity and function, and James Borneman (USA) identified microorganisms involved in suppressing plant pathogens.

A number of sessions were also designed to draw attention to technological and scientific issues of particular interest. Unearthing and describing microbial diversity remains a daunting task and Gary Andersen (USA) and Yvan Moenne-Loccoz (France) described the implementation of microarray technologies to assess bacterial diversity in diverse habitats. In addition, Paola Bonfante (Italy) described a unique microbial sequencing project, namely that of Candidatus Glomeribacter Gigasporarum, an endobacterium of a mycorrhizal fungus. With the rapid increase in sequence data from genome and metagenomic projects, data curation and annotation has become a serious issue as discussed by Dawn Field (UK) and Nikos Kyrpides (USA). Also, sequencing technologies are evolving rapidly both in terms of throughput, as well as the scale of biological material that can be used to generate genomic and metagenomic sequences.

These breakthroughs are leading toward the sequencing of individual microbial cells, as exemplified by the Ploning technologies presented by Kun Zhang (USA). Andrew Spiers (UK) also highlighted the power of Raman spectroscopy for metabolic analysis at the level of microbial cells. The rapid increase in molecular information concerning the distribution of microorganisms in the environment is also fueling developments of ecological theory to explain and predict patterns of microbial diversity. These issues were central to the discussions put forth by Claire Horner-Divine (USA) and Bill Sloan (UK).

The workshop was concluded by a session devoted to contributions by Chinese scientists, followed by the closing keynote address by Jim Tiedje (USA). The session of Chinese contributions covered a wide range of topics within microbial ecology and put the spotlight on the rapid progress being gained within Chinese microbiology. This session served as a valuable springboard to discussions of common interests and possible collaborations between Chinese scientists and their western colleagues. The closing keynote examined the whole genome approach to microbial classification and evolution. The availability of complete genome sequences is providing insight into the forces that shape microbial genomes and determine their ecological niches. Burkholderia was highlighted as an example of a diverse, adaptive and rapidly evolving genus.

The focus of the MicroEnGen workshops has been to not only present emerging science, but also to discuss and synthesize research priorities and directions for the future. The contents of the first two workshops (Wageningen and Shanghai) were therefore bundled into approximately 15 manuscripts for submission to a special issue of Microbial Ecology on the topic of microbial eco-genomics. This special issue will mirror the MicroEnGen focus, with a combination of forward-reaching position papers, notes on the potential impact of emerging techniques and full-length original scientific contributions highlighting novel applications of ‘-omics’ methodologies within integrated research projects.

The third and final workshop within the initial MicroEnGen series was to have been be hosted by TIGR and held in Rockville, Maryland USA in September of 2006. However, it was postponed to December 2007 and was convened at Laboratoire Ampère of the French CNRS in Lyon. This interactive meeting sought to broaden the focus of microbial ecogenomics beyond the technology and case studies to address key environmental issues on local and global scales. The main environmental topics on the agenda included the application of ecogenomics to 1) bioremediation strategies to promote the assessment and clean up of polluted environments, 2) monitoring and mitigating global climate change 3) effects of land use demands, especially with respect to reclamation and sustainable agriculture, and 4) the ecology and emergence of diseases in humans and animals.

MicroEnGen was initiated to foster international cooperation in the integrated fields of microbial ecogenomics so as to maximize current collective research efforts and provide direction for future applications of microbial genomics in environmental sciences. Obviously, these efforts will not solve all issues in microbial eco-genomics, but by putting together key players from different sides of this dynamic field, the initial steps of this process have been put into motion, as evidenced by the collection of manuscripts highlighted in this issue. The challenge to the community of microbial ecologists will be to continue these efforts to fruition in the future.

Up-dated in May 2008