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Why study microbes?. Hector Garcia Martin Microbial Ecology Program JGI. Account for >50% of living protoplasm on earth. 10x more nutrients (N and P) than plants. Present on Earth longer than multicellular organisms: Most important biogeochemical agents. Earth . Forms. Dinosaurs. 1st .

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why study microbes

Why study microbes?

Hector Garcia Martin

Microbial Ecology Program

JGI

microbes the unseen majority
Account for >50% of living protoplasm on earth.

10x more nutrients (N and P) than plants.

Present on Earth longer than multicellular organisms:

Most important biogeochemical agents.

Earth

Forms

Dinosaurs

1st

Arthropods

Microorganisms

2.0

1.5

1.0

4.5

4.0

3.5

3.0

2.5

0.5

Billions of years ago

3.5 million

Humans

Age Of

Microbes

Microbes: the unseen majority
atmosphere genesis
Creation of atmosphere as we know it:

- O2 levels: Photosynthesis initiated by cyanobacteria 2.3 billion years ago.

- 99% of O2 production in oceans.

- Rising levels of O2 gave rise to first well-documented glaciation.

Atmosphere genesis
geomicrobiology
Decomposition of organic material and determination of soil composition.

Accelerated precipitation over geological time suggested as source of formation of ore deposits (ZnS, Au and Fe).

Geomicrobiology

Kashefi et al.(2001)

AEM 67(7):3275

geomicrobiology5
Cave formation by microorganism on walls metabolizing sulfuric acid:

Carlsbad caves,

New Mexico

Big room:

100m x 33210m2

Geomicrobiology

(30 stories x

6 football fields)

Taken from “Smithsonian Earth”

wastewater treatment
Bacteria remove excess phosphorus and other pollutants from wastewater before it can be released back into the environment.

Understanding the microbiological details will enable us to improve the process.

Wastewater treatment

Image by Victor Kunin

Image by Linda Blackall’s lab

radioactive waste cleanup
The world’s toughest bacteria (Deinococcus radiodurans) can survive up to 1000 times the dose of radiation that would kill a human.

Being bioengineered to eliminate organic radioactive waste.

Radioactive waste cleanup

Image by M. Daly.

www.scifun.ed.ac.uk/card/facts.html

energy production
The microbial consortia in inside a termite’s gut allows it to be one of the few living beings able to digest wood.

Study of this community is expected to provide enzymes for industrial production of hydrogen for energetic purposes (e.g. hydrogen cars).

Energy production

Images from Diversa corp.

human gut bacterial community
Our adult bodies harbour 10 times more microbial than human cells.

The gut microbiome endows us with functional features that we need not evolve ourselves (e.g. synthesis of certain vitamins).

Understanding the gut microbiome will hopefully help understand dietary effects on health and cure diseases (e.g. Crohn’s disease)

Human gut bacterial community
antibiotic resistance
Many microbes adapt to their environment by exchanging genes rather than by just inheriting them from their parents (like we do).

This widespread Lateral Gene Transfer allows antibiotic resistance to spread extremely fast.

Antibiotic resistance

www.bioteach.ubc.ca

www.savetheantibiotic.com

why study microbes11
Driving force in geology and planet formation.

Applications in human health, bioremediation and energy production.

Unforeseen biotechnological applications.

Why study microbes?
how did we study microbes
Cultivate in lab environment.

Characterize physiological properties in controlled experiments.

How did we study microbes?

www.bio.waikato.ac.nz

culture bias
99% of organisms are not culturable with present methods.Culture bias

Culturable

Unculturable

Image by Ralph A. Clevenger

new tools for microbial study
In the last twenty years revolutionary new methods have been developed for understanding microbial ecology and studying the uncultured majority:

- 16S rRNA phylogenetics.

- Genomics and metagenomics.

New tools for microbial study
slide15

You are here

Everything you know is here

16S rRNA gene allows classification of all known life on earth based on gene similarity (no need for cultivation)

www.nhm.org

genomics metagenomics
Genome: whole hereditary information encoded in DNA. Allows to:

Assess the organism capabilities (can it live on oxygen? nitrate?)

Infer possible niches (does it live in the ocean? air? underwater vents?)

Hypothesize relationships with other organisms (Symbiosis? Synthropy?)

Genomics/Metagenomics
genomics metagenomics17
Genomics: study of an organism’s genomes (=genes + non-coding sequences) and use of genes.

Metagenomics: study of genomes recovered from environmental samples.

no need for cultivation.

genomic information from interacting ecosystems.

Genomics/Metagenomics
jgi s role
JGI has started a deep involvement in microbial sequencing:

141 out 566 (25%) of available microbial genomes (draft or finished) have been or are being sequenced here.

The Community Sequencing Program offers sequencing capability for free for projects selected on scientific merits.

JGI’s role
conclusions
Microbes drive a large amount of important processes.

New methods introduced in the last 20 years are revolutionizing our understanding of microbial ecology.

JGI is deeply involved in providing the genomes and tools to understand microbes.

Conclusions