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Why study microbes?

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?

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  1. Why study microbes? Hector Garcia Martin Microbial Ecology Program JGI

  2. 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

  3. 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

  4. 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

  5. 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”

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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

  11. Driving force in geology and planet formation. Applications in human health, bioremediation and energy production. Unforeseen biotechnological applications. Why study microbes?

  12. Cultivate in lab environment. Characterize physiological properties in controlled experiments. How did we study microbes? www.bio.waikato.ac.nz

  13. 99% of organisms are not culturable with present methods. Culture bias Culturable Unculturable Image by Ralph A. Clevenger

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

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