You, the EMP, and the GSBI: aligning stars of the soil biodiversity universe

Written by Dr. Dorota Porazinska    

 

It has been one month since the First Global Soil Biodiversity Conference and I still catch myself going back to the many inspiring talks and posters diligently recording the progress of soil ecology, to a place where soil biodiversity was on everybody’s top list. It was impressive to see not only the huge leaps in understanding how soil biodiversity affects ecosystem services, but also how this knowledge can influence the value that people place on soils or how it can help shape new policies relevant to land and climate.  While most of us work on a tiny piece of the soil biodiversity puzzle, the First Global Soil Biodiversity Conference provided a forum and a framework to successfully bring the pieces into place. In a pre-conference workshop on data synthesis, the Soil Biodiversity Curation Working Group was formed with the goal of linking all existing soil biodiversity resources and databases.   This would be a milestone step towards building a larger context to our individual research projects.

The Earth Microbiome Project (EMP) offers to the GSBI community three core components: a resource, a database, and a framework. The EMP was initiated in 2010 to understand patterns in microbial communities across different spatial, temporal and evolutionary scales, to understand the functional basis for these patterns, and to provide a portal for the analysis and visualization of the data. The EMP has primarily generated data from amplicon sequencing of Bacteria and Archaea to date, although expansion to other taxa including eukaryotes and viruses, and other forms of data generation including metagenomics, metatranscriptomics, and metabolomics, is anticipated in the future. By participating in the EMP, the GSBI members would be providing much needed expansion of the biodiversity data necessary for guiding scientists in the development of new research initiatives.  This would ultimately assist managers, farmers, and politicians to more accurately predict the effects of land management and to inform policy.

The EMP is a massively collaborative project. Individual projects are stand-alone, hypotheses-driven studies contributed by PIs from around the world. The EMP has generated 16S rRNA profiles for >30,000 samples representing >40 ecological biomes, including oceans, sediments, rivers, lakes, human, plant- and animal-associated ecosystems. Soils constitute <10% of these samples, and although many project contributions to date have been from agricultural sites from the North American meridian, the EMP results to date confirm our expectations of these ecosystems: high diversity, many novel taxa, and limited community overlap among biomes and geographic locations. By joining the EMP project, the GSBI members can further improve our understanding of the soil ecosystems in the global biodiversity context. 

The success of the EMP depends on your participation.

If you join the EMP, we will: 

  • Extract DNA and sequence 16S rRNA amplicons free of charge using standardized protocols (http://www.earthmicrobiome.org/emp-standard-protocols/)
  • Archive the data and make it publically available
  • Perform initial analysis of the sequencing data (quality-filtering, OTU-clustering, taxonomy assignment, and beta diversity analyses integrated with a vast database of other studies)

To join the EMP, we ask that you submit:

  • A one-paragraph proposal that describes your study, focusing on what the samples are and what spatial, temporal or evolutionary questions your sample set addresses in the microbial world
  • Information about each sample (“sample metadata”) that must be provided in standardized format (the EMP will assist with this) prior to sample receipt

For detailed information about goals and protocols, please visit the EMP website:  http://www.earthmicrobiome.org. Note the EMP data release policy, which is that all data are made freely available to the community upon sequencing.

For specific questions about submission of the proposal and the mandatory metadata, please email: dorota.porazinska@colorado.edu.