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 .
Hector Garcia Martin
Microbial Ecology Program
10x more nutrients (N and P) than plants.
Present on Earth longer than multicellular organisms:
Most important biogeochemical agents.
Billions of years ago
MicrobesMicrobes: the unseen majority
Accelerated precipitation over geological time suggested as source of formation of ore deposits (ZnS, Au and Fe).Geomicrobiology
Kashefi et al.(2001)
100m x 33210m2Geomicrobiology
(30 stories x
6 football fields)
Taken from “Smithsonian Earth”
Understanding the microbiological details will enable us to improve the process.Wastewater treatment
Image by Victor Kunin
Image by Linda Blackall’s lab
Being bioengineered to eliminate organic radioactive waste.Radioactive waste cleanup
Image by M. Daly.
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.
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
This widespread Lateral Gene Transfer allows antibiotic resistance to spread extremely fast.Antibiotic resistance
Image by Ralph A. Clevenger
- 16S rRNA phylogenetics.
- Genomics and metagenomics.New tools for microbial study
Everything you know is here
16S rRNA gene allows classification of all known life on earth based on gene similarity (no need for cultivation)
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
Metagenomics: study of genomes recovered from environmental samples.
no need for cultivation.
genomic information from interacting ecosystems.Genomics/Metagenomics
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
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