Aims and Goal
Information about diversity in terms of what kind of microorganisms exist in which part of the earth forms the basis for understanding the role of microbial ecosystem. Information on microbial diversity that has been pushed into black box so far is gradually revealed by the techniques of environmental meta-genomics. This information includes diversity of functions in addition to diversity of the system. This information about diversity also becomes a major clue to learn how the foundation of ecosystem has been sustained. At the microbial diversity group we are working on creating microbial habitat map of the ecosystem of Japan through consortium activities for supporting research collaboration across the fields and information exchange between researchers.
Details of Activities
1) Microbial Habitat Map
Habitat map is not only used for visually understanding the habitat distribution, but it is also used as a tool for understanding the status of ecosystem by superimposing the environmental information. Data of individual researcher is completed once he presents a paper, and in many cases, primary data used in the paper or data not directly used in the paper remains stored on the hard disk of the researcher’s computer. By collecting individual data concerning each habitat distribution lying in the dead storage and by doing re-analysis, it should be possible to create a habitat map of a wide area. In fact, in flora and fauna, such analysis based on habitat map is used for understanding the status of habitat distribution and changes in it, and for assessing the impact of environmental changes.
In the case of Habitat map of microorganisms, it is not just a distribution map, it rather reflects that basic functions of ecosystems. So far, using only past data of flora and fauna as a reference, only final results based on just analysis were observed. However, if environmental impact assessment is done by consolidating data of microbial communities that respond very rapidly, it should be possible to assess by capturing small changes.
In this group, for promoting research of microbial ecosystem using environmental metagenomics, we share information of surveys and sample analysis, we locate data of environmental metagenome and habitat distribution that would lead to creating a wide area habitat map of microbial communities, and we share information that would lead to making project proposals.
We would also like student members to share ideas and information that would lead to creating habitat map of microorganisms. We would provide support so that such information becomes basis and leads to new research projects.
2) Environmental Metagenomics and Bioinformatics
Environmental metagenomics is one of the power tools that provides basic data needed to visualize the microbial ecosystem. Expense incurred on sequencing has declined, and it has become possible for anyone to read the gene sequence information. From this data, not only systems, but it is also possible to extract and identify functions such as physiological metabolism. However, for this analysis, not only database, but it is also necessary to use metabolism map and bioinformatics where metabolic functions are allocated from genes. In metabolic function analysis, metabolic functions like KEGG (Kyoto Encyclopedia of Gens and Genomes: http://www.genome.jp/kegg/ )and MetaCyc (http://metacyc.org/), and database that link the responsible genes are mainly used. However, such database still has many imperfections, and therefore, for using them in the research of microbial ecosystem, rather than just using them as a user, it is necessary to convert data and knowledge available with each research about metabolic functions into database for creating a database that is more accurate and that covers wider range of functions.
Therefore, this committee acts as a bridge for exchanging information with the researchers of KEGG, etc., and cooperating with the field of informatics. Please contact us if you have any ideas and proposals for cooperation.
3) Activities so far:
It started its activities as a committee in 2009. At that time, because the Convention of Biological Diversity / Convention of Parties（CBD COP10）was going to be held in Nagoya in 2010, diverse ideas were being debated in many areas. Unfortunately, with regard to diversity of microorganisms, while recognizing that it is important, it appeared that its scope of discussion was limited. In order to change this situation, study meetings and symposiums are organized by the Ecological Society of Japan and Japanese Society of Microbial Ecology, and the group has been debating the status and significance of investigative research of biodiversity from the standpoint of microorganisms.
Contact for joining:
Committee Representative: Hiroyuki Yamamoto
e-mail: kyama @ jamstec. go. jp
