Transcript Document

Why is 454 important?
Benefits:
•Can detect and measure minor population members.
•Provides initial window on total diversity of microbes in the environment.
•Allows relative quantitative measures of species abundance.
•Efficiency and high throughput allows intensive sampling of all sites of interest.
•Offers a tool to finger-print microbial populations for correlations with
biogeochemical activity.
•Permits microbial population biology studies in natural environments.
•Makes possible biogeographical studies of microbial populations.
•Important complement to metagenomic investigations: i.e. Sorcerer II Expedition
Concept of the Rare Biosphere:
•Minor population members may serve as key-stone species
•Rare Biosphere may be source of genomic innovation being observed in new
microbial genome sequences.
•Under-represented microbial populations may become dominant in response to
environmental shifts.
•Rare biosphere may serve as sentinel for global change.
Societal Impacts of 454-Based studies
Microbial Population Structure of the World’s Oceans
•Human health
•Persistence and Distribution of human pathogens
•Monitoring and tracing of HABs (Harmful Algal Blooms)
•Improved prediction of global change and climate change
•Detecting and monitoring human disturbance of marine ecosystems
•Prediction and monitoring of consequences of ocean acidification and ocean
warming in a high-CO2 world
•Prediction and monitoring of ecosystem change by pollution with nutrients,
man-made chemicals, etc.
•Recognition of antibiotic-resistant bacteria in the environment
What’s next for ICoMM?
-Continuation of on-going activities:
a) Further explore 454 technology for environmental microbial
(and other) diversity
b) Build up MICROBIS sequence and lipid databases
(the latter in collaboration with LIPID MAPS)
c) Organize general ICoMM meeting to establish protocols
for sampling, sample selection, sample preparation,
extraction, sequencing, database management, etc.
d) Explore the possibility to act as a resource for 454 sequencing
for the marine microbial scientific community
e) Submit proposals to US, European and Dutch funding
agencies to extend ICoMM activities
f) Establish links with other programs and organizations
-Relation to other CoML programs
ICoMM could serve the CoML community as a central
resource for 454 sequence technology
Some examples:
-CenSeam (Seamounts) & ChEss (Vents and Seep)
The first 454 results of the two Axial Seamount samples
clearly describe the microbial communities and microbial
diversity of seamounts and vents
-CeDaMaR (Abyssal plains) & MAR-ECO (Mid-Ocean Ridges)
The microbial diversity of the East Pacific Rise will be
revisited through 454 sequencing
-NaGISA (Near shore)
In collaboration with the Woods Hole Center for Oceans and
Human Health (WH-COHH) 454 tag sequencing of near shore
samples will be performed to help to identify low-abundant
pathogenic bacteria, harmful algae, etc.
-Relation to other programs and organizations
• POGO (Partnership for the Observation of the Global Oceans)
- At the recent POGO meeting in India the directors of the large marine
institutes worldwide decided:
a) to develop a meta-database of past, present and future cruises of their
Research Vessels (RV’s)
b) to support requests for sampling, monitoring and berths during expeditions
of their RV’s (A successful example is the sampling performed for ICoMM
during an Atlantic meridional trip of an English RV crossing at least 7
biogeochemical provinces)
These decisions will enable ICoMM and many other CoML programmes to
obtain samples, make measurements and perform observations in (remote)
areas (e.g. polar regions) at low cost
-Relations to other programs and organizations
-SAHFOS (Sir Alister Hardy Foundation for Ocean Science)
For 75 years subsurface water samples have been filtered with
the so-called Continuous Plankton Recorder (CPR) by Ships of
Opportunity during frequent and repeated trajectories, mostly
in the Atlantic. Although these samples are stored in formalin at
Plymouth (UK), recent research indicates that DNA is partly
preserved.
This may open possibilities to study past diversity through 454
sequencing, which may be of interest for ICoMM, CMarZ
(Zooplankton) and HMAP (Past Oceans).
ICoMM is presently exploring this approach.
-Relations to other programmes and organisations
• GEO (Global Earth Observations)
The recently established international GEO serves as an catalyst
and umbrella for extant and future long term, comprehensive and
sustainable remote and in-situ observations of the Earth
(including the oceans!) and is driven by the social benefits of such
data. Biodiversity is one of these 9 social benefits and a firmer
relation between CoML and GEO would be highly beneficial for
both.
POGO has undertaken actions to implement a senior marine
scientist in the GEO secretariat at Geneva.
-Relations to other programs and organizations
• IODP (International Ocean Drilling Program)
The analysis of IODP or other sediment cores for DNA
and lipids opens the possibility to survey sub-seafloor
microbial diversity and community structure.
In collaboration with WHOI samples from different sites
will be subjected to 454 sequencing
Courtesy Jed Fuhrman