Understanding marine microbial diversity: How bioinformatics can promote ecological knowledge

and biotechnological applications

Dr. Johanna B. Wesnigk,EMPA Bremen

On behalf of Prof. Frank Oliver Glöckner, Coordinator of Micro B3

Issues at Stake: Why Does it Matter

•Lack of understanding of microbial marine diversity, now combined with genomic dataexplosion:

• Who is out there, … and what are they doing ?•Our Approach:

• Genomic knowledge helps to get a grip on• black box of unknown but potentially important

microorganisms, • their functions in ecology & for biotechnology

• Knowing the environmental conditions helps• to relate diversity to function• to develop new biotechnological applications

Environmental Bioinformatics

EnvironmentOrganisms

Function

Ecosystem Biology

Statistics Key parameters

Modelling Predictions

Ecosystem Ecosystem functioningfunctioningMarine micro-algae: �responsible for45% of global netprimary production

Micro-organisms:Main recyclers of organic carbon

How do marine foodwebs adapt to global warming and ocean acidification?

How can we useknowledge to feed& fuel human population ?

WP 1Management

& Coordination

JacobsUni

WP 2Ocean Sampling

DayUOXS

WP 3Oceanography

& Environmental Data

MARIS

WP 5Bioinformatics

& Data Integration

MPIMM

WP 7Function

&Biotechnology

UGRO

WP 8Intellectual

PropertyManagement

UCL

Start: 1 January 2012; Duration: 4 years;32 partners (Involvement of stakeholders PharmaMar, SMEs, IGOs)

WP 9Dissemination

&TrainingEMPA

WP 6Exploring

Ecosystems BiologyCNRS

WP 4Standards andInteroperability

EMBL-EBI

Biodiversity Bioinformatics Biotechnology

Predicted (bio-)diversity hotspots from:de Monte eta al. 2013; The ISME Journal 7, 2054-2056 (October 2013) | doi:10.1038/ismej.2013.72

Routes of Tara Oceans and Malaspina Cruises, focusing on marine micro-organisms

www.oceansamplingday.org

Including Citizen Science

Legal Framework

From Visualising Bacteria to Understanding Genomes

Micro B3 deliveries:• Multidisciplinary

communication• Informatics services & tools

for Big Data (geo&bio)• IPR models for researchers,

policy and industry• Bioinformatics prediction

through our integratedMicro B3 Information System

Genomics

Oceanography

Biodi

vers

ity

13

Micro B3 publications

What can Bioinformatics do forDiversity & Functions?

Poster: Unraveling the unknown unknowns in the metagenomic protein universe using graphical modelsA. Fernàndez-Guerra et al. (Cork, 2012)

From Harvesting to Data Mining► Mining genomic data is efficient and

environmental friendly alternative

► Building capacity in bioinformatics:training,TT and KT for next generation of researchers• able to understand multidisciplinary needs• with skill set to work across disciplines

• Bridge information gap to biotechnologicalresearch and application• Proving activity of bioinformatic predictions,

embedded into environmental context• Marine Micr’Omics for Biotech Applications,

Industry Expert Workshop: • PharmaMar headquarters near Madrid, 3-4

November 2014

Bioinformatics systems & services help scientiststo keep their heads above the surface !

Thank you for your attentionj.wesnigk@empa-bremen.de

GATC

Drowning in an ocean of (sequence) data ??