Download - Lecture 14 (3 22-2016) slides
Microbial Physiology & Diversity
Prof. Kristen [email protected]
PhD Microbiologyhttp://www.micro.umass.edu/deangelis/
Schedule
Logistics
We will have a 2-3 minute break a bit more than half-way through our 75 minutes of class.
We will do some in-class exercises to help you digest the materials, including practice quizzes.
You will learn more if you do the reading assignments before class.
My lecture slides with additional notes will be posted to moodle just after class.
Grades are based on the four exams, which will cover lectures and reading materials.
Lecture 14: How to measure diversity
Objectives
Explain the ways in which the microbial world is diverse.
How can we can measure diversity? What are different kinds of diversity?
Name some factors that support the amount of observed diversity.
Why is diversity important? Who is Antonie van Leeuwenhoek? Louis
Pasteur? Robert Koch? Sergei Winogradski? Carl Woese?
Microbes are the foundation for all
of life.
What are microbes?
Any living thing you need a microscope to see...
Antonie van Leeuwenhoek“Father of Microbiology”Dutch trader & scientist(1632 –1723)Discovered the microbial world by developing the microscope
Figures of bacteria from the human mouth (letter 39, 17 Sept. 1683)
How many microbes are there?
106 per mL109 per g
101-3 per m3
How many microbes are there?
106 per mL109 per g
101-3 per m3
How many microbes are there?
1013 bacteria vs1013 human cells1-3% body mass
How many species are there?
How many species are there? If each 1 m3 of soil contains
only one unique species (by the 70% DNA-DNA hybridization measure defining a species), there are ~1017 prokaryotic species in the top 1 km of Earth’s crust.
Or, if there is one unique species in 1 km3, there are “only” ~108 species.
Taxonomic diversity
How can there be so much diversity?
What are the different kinds of diversity?
Taxonomic diversity – based on a marker gene usually, some way of splitting organisms into groups
Phylogenetic diversity – considers the degrees of relatedness, usually by a gene or family of genes
Genetic diversity – the complement of genes that mark an organism or community's potential function
Functional diversity – the range of actual functions of an organism or community
Early (wrong) trees of lifeWhittaker 1959 – five-kingdom treeErnst Haeckel 1866
Small subunit ribosomal RNA
The Central Dogma of Biology
DNA → RNA → Protein
Small subunit (16S) ribosomal RNA from Thermus thermophilus
Proteins in blue Single strand rRNA in orange
Small subunit ribosomal RNA
Small subunit rRNA & Carl WoeseWoese, Candler & Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. PNAS
The Domain Bacteria
SSU is a popular measure of diversity
Pace NR, Science 1997
For Woese et al., 1990
“Omics” Genomics – sequencing whole genomes Phylogenetics and phylogenomics – evolutionary
relatedness of organisms based on marker genes or whole sequences
Metagenomics – sequencing mixed communities Transcriptomics – sequencing RNA with the
intent of looking at messages (along for the ride) Proteomics – protein sequence (MS) Metabolomics – metabolites (NMR)
→ Trees based on rRNA largely match those based on genome sequences
Many phylogenetic markers
Ciccarelli et al., Towards automatic reconstruction of a highly resolved tree of life. Science 2006
Global phylogeny of fully sequenced organisms
concatenated alignment of 31 universal protein families
covers 191 species whose genomes have been fully sequenced
Reconstructing evolutionary time
Doolittle, 2000
BEWARE: Horizontal Gene Transfer (HGT)
What is diversity?
Diversity = Richness + evenness
Rarefaction analysis is a way to estimate total richness
The “rare biosphere” Most organisms exist at very low relative abundance A potentially bottomless well of diversity
Sogin et al 2006 Proc Natl Acad Sci USA 32:12125
How can we expand known diversity?
Cultivation and enrichment
Molecular techniques
Louis Pasteur French chemist & microbiologist
(1822-1895) Pasteurization Described anaerobic bacteria (butyric
acid, lactic acid fermentation) Role of yeast in alcohol fermentation Swan-necked flask experiments
conclusively disproved spontaneous generation
Robert Koch German scientist and
physician (1843-1910) Established causative
agents of disease Developed methods for
studying bacteria in pure culture using agar plates (named after his assistant, Julius Richard Petri)
Koch's postulates...
The cultured diversity is tiny
Wu et al., A phylogeny-drivengenomic encyclopaedia of Bacteria and Archaea. Nature 2009
GEBA project: sequence and analyse the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage
1%
Microbial metabolisms that define functional groups... or what we call microbes
Redox Ladder
Electron Tower
Redox Ladder
Sergei Winogradsky Russian microbiologist Discovered that microbes were
capable of geochemical transformations
Discovered chemolithotrophs Isolated anaerobic nitrogen
fixing bacteria
Why is diversity important? Direct link between plant and microbial diversity and
stress resistance Net N mineralization Microbial biomass Microbial activity
Zak et al., 2003;
Why is diversity important? Human
health!
Lozupone et al., Science 2012