Tag Archives: earth microbiome project

Sequencing meta-analysis workshop, Manchester, 18-20 May 2015

We are organizing a workshop to bring together ecologists and bioinformaticians to work on a meta-analysis of sequencing data with the aim of exploring patterns in belowground biodiversity.

The description and biogeography of belowground biodiversity is severely lagging behind that of aboveground diversity. This is despite increasing recognition of the importance of soil organisms for ecosystem functioning, including carbon and nitrogen cycling, and feedbacks to plant community composition, which underlie ecosystem services such as food production and climate mitigation. Moreover, recent evidence suggests that patterns of belowground biodiversity might not follow those of aboveground biodiversity. Thus, belowground biodiversity offers a unique opportunity to test and develop ecological theory. However, bringing together soil biodiversity data is challenging, especially when it comes to sequencing data, because pipelines and metadata are not standardized.

Confirmed speakers/leaders of the workshop are:

Dr Kelly Ramirez, Netherlands Institute of Ecology, the Netherlands and GSBI

Dr Rob Griffiths, CEH Wallingford, UK

Dr Jennifer Talbot, Boston University, USA

-Dr Hyun Soon Gweon, CEH Wallingford, UK

Dr John Davison, University of Tartu, Estonia

The aim of this workshop is to bring together ecologists and bioinformaticians to do a meta-analysis of sequencing data of soil microbial communities. Both publicly available data and participants’ data will be used, and the anticipated outcome is a publication in a peer-reviewed journal. The workshop will consist of lectures by our invited speakers to highlight recent advances, and participants will be expected to give a short presentation about their background and expertise. The majority of time will be spent identifying ecological questions to address with the data, analyzing the data in novel ways, and drafting a manuscript.

Spaces for this workshop are limited, and we are seeking motivated ecologists and bioinformaticians of all career stages to participate in, and contribute to, the workshop. Participants are expected to bring their own dataset of soil microbial (principally bacterial) community sequencing data (including metadata), and to have some experience in analyzing sequencing data.

The call for participants is now open. Applications should consist of a one-page CV, description of the dataset(s) that the applicant will bring to the workshop, and a statement (500 words maximum) of what the applicant will contribute to, and hopes to get out of, the workshop, including proposed hypotheses to be explored during the workshop.

Send your application to besplantsoileco@gmail.com before April the 10th 5pm. Applicants will be notified whether they have been selected for the workshop by April the 17th. For questions email Franciska de Vries: franciska.devries@manchester.ac.uk

Registration fee: £75 (students)/£100 (BES members)/£125 (others)

 

Flyer

You, me, and the EMP (Earth Microbiome Project)

In this guest post, Dr. Dorota Porazinska of the University of Colorado introduces the Earth Microbiome Project (EMP), an initiative to understand microbial communities, their diversity and function at the global scale, and explains how researchers can help the EMP as part of their own research projects. Communities like Plants-Soils-Ecosystems provide great environments for connecting like-minded researchers and encouraging collaboration – if you’re interested, read on, and get in touch! Now, over to Dorota:

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 future.

emp-logo

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.

emp-wordle

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
  • 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. 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 dot porazinska at colorado dot edu