Soil Microorganisms Lecture 3 Sep 13th

TODAY:

1. Discussion Questions2. Reading Assignments from last week

1. Smith et al. (Eutrophication) – will discuss beginning of N lecture (9-26)2. Condron et al. 98-108 – will discuss beginning of metabolism lecture (9-19)

3. Lecture

OutlineA. Bacterial Morphology

1. Cell Structure2. Cell Motility3. Cell Wall Structures

a. Odd Soil and Water Bacteria

B. Intro to Bacterial Growth

C. Intro to Bacterial Genetics1. Central Dogma2. Gene Exchange

New Course Schedule

9/12 Intro to Bacteria and Viruses – Structure and Genetics9/19 Bacterial Diversity, Metabolism, and Viruses9/26 Bacterial-mediated Nitrogen Cycling10/03 Exam 110/10 Bacterial-mediated Sulfur and Phosphorus Cycling Plant-Bacteria Interactions10/17 Methods of Assessment of Soil Bacteria10/24 Soil Fungi – Diversity, Function, and Competition10/31 Mycorrhizae and N Fixation11/7 Exam 211/14 Soil Microfauna11/21 Soil Mesofauna11/28 Soil Macrofauna12/5 Frontiers of Research in Soil Biology12/14 Final Exam

I. Bacteria & Archaea

• Prokaryotic• Lack organelles• No true nucleus

• Unicellular

• Range in size from 0.1 um to > um• Why would it be disadvantageous for bacteria to be large?

• Most abundant “living” organisms in soil

Prokaryotes: The unseen majority

~108 – 1010 bacteria g-1 soil

1019 grains of sand in the world1023 stars in the observable universe1027 bacteria in tropical rain forest soils1030 bacteria on earth

biomass exceeds that of all plants and animals

1013 cells in human body1014 bacterial cells on and in the human body

Can persist for eons8 million yr old bacteria revived from Antarctic ice

Bacterial Morphology

spirilla bacilli (rods)

filamentous

cocci(spheres)

Pili “Walking”

Polar flagella motility

Bacterial Morphology

Gliding

• Slime layer capsule• Polysaccharide layer• Antibiotics, dessication, chemical attack

• Endospore• Long-term survival• Dormant state• Nutrient deficiency

Slime Layer Capsule

Bacterial Morphology

Gram + and Gram -

• Two main sub-groups of bacteria• Based on differences in the structure of the ________

Bacterial Morphology

Bacteria vs. Archaea

Archaea

EukaryotaBacteria

Bacterial Morphology

Beggiatoa (genus)

2H2S + O2 → 2S + 2H2O

• Oxidize Hydrogen Sulfide to S• Store S intracellular (golden granules)

• Visible with naked eye• Marine sediments

• Move up and down for optimum balance• Single cells or in filaments

Strange Bacteria

Pseudomonas fluorescens

• 1 um short rods

• Siderophore producing

Strange Bacteria

Strange Bacteria

• Actinobacteria (phylum)• Used to be classified as a fungus, Actinomycetes• Some form branching filaments• Geosmin

• Petrichor -

Oldest living thing on Earth? 500,000 yo Nocardia – Lignin and Gingival Pockets

Frankia – N2 Fixing Bacteria

Strange Bacteria

• Burkholderia (genus)• ~35 species• Cystic Fibrosis • Chloroorganic pesticides

• PCB

• Agricultural• Biocontrol Agents• PGP

• Biowarfare Agents

Strange Bacteria

• Deinococcus radiodurans• Soil bacteria• Toughest bacteria on Earth• Radiation, acid, dehydration, vacuum

• 5 gy kills human, 800 gy kill E. coli, 5000 kills radiodurans• Conan the bacterium

Tetrads, 4 cells sticking together

II. Bacterial Growth

"The mathematics of uncontrolled growth are frightening. A single cell of the bacterium E. coli would, under ideal circumstances, divide every twenty minutes. That is not particularly disturbing until you think about it, but the fact is that bacteria multiply geometrically: one becomes two, two become four, four become eight, and so on. In this way it can be shown that in a single day, one cell of E. coli could produce a super-colony equal in size and weight to the entire planet Earth."

Michael Crichton (1969) The Andromeda Strain, Dell, N.Y. p247

Is he correct?

272 = 4.7*1021

10-12 g/cell= 4.72* 106 kg

Mass of Earth = 5.98*1024 kg

Would actually take about 40 hours

• Factors affecting growth are:•1. •2.•3.

• Limiting nutrient:

CLASSIC GROWTH CURVE

Killham and Prosser, 2007

Copiotrophy (r-strategists) vs. oligotrophy (K-strategists)

umax A

umax B

umax A

½ umax A

Ks

umax B

½ umax B

Ks AKs B

Higher Ks:

Lower KS:

Bacterial Evolution – NichingEveryone Competes

• 12 identical populations of E. Coli over 23 years• 50,000 generations• After 20,000 grew 70% faster than parent strain• 120 mutations were fixed in the populations• Some could not repair DNA any more• Some could use citrate under aerobic conditions

• Never seen in the wild

• Bacterial Crosstalk• “Please pass the sugar”• Rhizobia inoculation

• Quorom Sensing• Is everyone ready?

• Putting relatives first• Bacterial “suicide

bombers”

Everyone Competes……But Will Also Cooperate

C. Intro to Bacterial Genetics

1. Central Dogma2. Gene Exchange3. Examples in Soil

The ability to extract DNA (deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) from cells within soils have given us great new insights into soil microbial communities

TA

G C

CENTRAL DOGMA

CENTRAL DOGMA

Ribonucleic Acid – Secondary Structure

CENTRAL DOGMA

The Ribosome

CENTRAL DOGMA

• Translates mRNA (gene transcript)• mRNA Protein

• Consists of protein and RNA• Active sites are conserved

• Genes encoding protein and RNA are conserved

Replication

Transcription

Translation

16S rRNA gene

16S rRNA

• Acts as scaffold for ribosomal proteins

• Conserved and hypervariable regions

• Basis of bacterial taxonomy

2. Gene Exchange

• Plasmid

• Extrachromosomal circular genetic structure that can reproduce autonomously but is not essential

• Generally 1-10% the size of the chromosome• Provides genetic diversity and enables bacteria to rapidly adapt to a wide range of ecological niches

• Some plasmid – encoded functions

• Antibiotic and toxin resistance• Enzymes for xenobiotic degradation• N2 fixation genes

• Transfer Method #1: Conjugation• Requires cell to cell contact, usually plasmid mediated• Most important mechanism• Uses pili• Does not have to be closely related• Does not involve the chromosome

2. Gene Exchange

SOUND

2. Gene Exchange

• Transfer Method #2: Transduction• Bacteriophage infection• Transfer by delivery of viral DNA• Sometimes species or strain specific due to attachment sites

• Phage attached to pili• Bacteria change their pili

• May become adsorbed to soil

SOUND

• Transfer Method #2: Transduction

• Lytic Phage: Inserted phage DNA is copied by cell machinery• Many copies are made• Phage components assemble themselves• Cell wall bursts and phage replicates are released

• Lysogenic Phage: Integration of phage DNA into host chromosome

• Replicated as part of chromosome• ~10% of human genome is ancient viruses• May enter lytic cycle

• Sometimes mistakes are made in copying viral DNA• Portion of host DNA integrated into viral DNA• Transfer of genes among hosts via viral infection

2. Gene Exchange

• Transfer Method #3: Transformation

• Uptake of naked extracellular DNA – closely related species• Incorporation into the genome• Originated as a way to obtain nutrients• Extracellular DNA can be stabilized onto soil• Least important of three genetic exchange mechanisms

2. Gene Exchange