GeoChip for microbial community analysis

1
GeoChip for microbial community analysis Zhili
He Institute for Environmental
Genomics Department of Botany and
Microbiology University of Oklahoma Email
zhili.he_at_ou.edu Phone [phone] March 23,
2007
2
An example of problems Carbon transformation and
transport in soil
http//www.climatescience.gov/
Global climate change

• C, N, P, and S cyclings
• Microbial structure and function
• Metabolic cooperation
• Plant-microbe interactions

The scientific evidence is clear global climate
change caused by human activities is occurring
now, and it is a growing threat to society.
Released on the AAAS Annual Meeting in December
2006.
3
Objective 4 Understanding rhizosphere microbial
communities and plant-microbe interactions

• Isolation of cellulose-degrading and
  ethanol-producing microbes
• Metagenomic analysis of rhizosphere microbial
  communities
• Development and application of functional gene
  microarrays for microbial community analysis
• Prediction of effects of changes in plant-microbe
  interactions on the environment, such as global
  warming

4
Fundamental scientific questions

• How does plant diversity (LIHD vs HILD) affect
  microbial function, diversity and stability?
• How do microbial communities affect feedstock
  productivity and stability/sustainability?
• Can microbial communities improve feedstock
  productivity and stability/sustainability?
• Will changes in plant-microbe interactions have
  significant impacts on the environment, such as
  global warming?

LIHD low-input and high-diversity HILD
high-input and low-diversity
5
Challenges for microbial community studies

• Small in size
• Extremely high diversity and complexity, 5000
  species/g soil
• 99 of the microbial species are uncultured
• Rapid adaptation to environmental changes
• Metabolic versatility and flexibility

6
Main approaches

• Metagenomics and community sequencing
• Functional gene microarrays
• Stable isotope probing (SIP)
• Evolution

7
Metagenomics

• Knowledge
• Structure and functions
• Metabolic co-operations
• Plant-microbe interactions

• Biotechnology
• Novel biocatalysts
• Natural drug compounds
• Novel genes/enzymes

Daniel. 2004. Curr Opin Biotechnol 5 199-204.
8
454 pyrosequencing
Soil samples
DNA extraction

• 20-100 Mb/run, and 5,000-10,000/run.
• An average microbial genome size 4.0 Mb.
• Finish in a half day.

Margulies et al. 2005. Nature 437 376-380.
9
Summary of GeoChip 3.0 probe and sequence
information by category
10
Generic and specific applications

• Survey for any environmental samples soil,
  water, sediments, oil fields, deep sea, animal
  guts, etc.
• Linking microbial structures to
  functions/activities.
• Detection of functional genes and/or organisms
  in a particular environment.
• Geochemical cyclings C, N, S and P.
• Estimation of gene abundance and activity.

11
GeoChip monitoring in situ bioremediation of
uranium
He et al., 2007, ISME (in press).
12
What are expected from this study?
Knowledge of microbial ecology and systems
biology microbial and plant diversity, metabolic
co-operation, plant-microbe interaction, and
global climate change.
Resources for biotechnology a discovery of novel
genes/enzymes (e.g. cellulase) and natural
metabolites (e.g. drugs), and biofules (e.g.
ethanol).
Training 10 graduates, 20 undergraduate, and
10 postdocs.
Deliverables 5-10 highly-profile publications,
useful research resources (e.g. metagenomic
libraries), and a new version of GeoChip.