Microbial Physiology & Diversity

Prof. Kristen DeAngelisdeangelis@microbio.umass.edu

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