Soil Microorganisms
Lecture 3 Sep 13th
TODAY:
1. Discussion Questions
2. 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
Outline
A. Bacterial Morphology
1. Cell Structure
2. Cell Motility
3. Cell Wall Structures
a. Odd Soil and Water Bacteria
B. Intro to Bacterial Growth
C. Intro to Bacterial Genetics
1. Central Dogma
2. Gene Exchange
New Course Schedule
9/12
9/19
9/26
10/03
10/10
10/17
10/24
10/31
11/7
11/14
11/21
11/28
12/5
12/14
Intro to Bacteria and Viruses – Structure and Genetics
Bacterial Diversity, Metabolism, and Viruses
Bacterial-mediated Nitrogen Cycling
Exam 1
Bacterial-mediated Sulfur and Phosphorus Cycling
Plant-Bacteria Interactions
Methods of Assessment of Soil Bacteria
Soil Fungi – Diversity, Function, and Competition
Mycorrhizae and N Fixation
Exam 2
Soil Microfauna
Soil Mesofauna
Soil Macrofauna
Frontiers of Research in Soil Biology
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 world
1023 stars in the observable universe
1027 bacteria in tropical rain forest soils
1030 bacteria on earth
biomass exceeds that of all plants and animals
1013 cells in human body
1014 bacterial cells on and in the human body
Can persist for eons
8 million yr old bacteria revived from Antarctic ice
Bacterial Morphology
cocci
(spheres)
filamentous
spirilla
bacilli (rods)
Bacterial Morphology
Pili “Walking”
Polar flagella motility
Bacterial Morphology
Gliding
Slime Layer Capsule
• Slime layer capsule
• Polysaccharide layer
• Antibiotics, dessication, chemical attack
• Endospore
• Long-term survival
• Dormant state
• Nutrient deficiency
Bacterial Morphology
Gram + and Gram • Two main sub-groups of bacteria
• Based on differences in the structure of the ________
Bacterial Morphology
Bacteria vs. Archaea
Eukaryota
Archaea
Bacteria
Strange Bacteria
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
• Actinobacteria (phylum)
• Used to be classified as a fungus, Actinomycetes
• Some form branching filaments
• Geosmin
• Petrichor Frankia – N2 Fixing Bacteria
Oldest living thing on Earth? 500,000 yo
Nocardia – Lignin and Gingival Pockets
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?
Mass of Earth = 5.98*1024 kg
272 = 4.7*1021
10-12 g/cell
= 4.72* 106 kg
Would actually take about 40 hours
• Factors affecting growth are:
•1.
•2.
•3.
• Limiting nutrient:
CLASSIC GROWTH CURVE
Killham and Prosser, 2007
umax A
umax B
Copiotrophy (r-strategists) vs. oligotrophy (K-strategists)
umax A
½ umax A
Ks
Higher Ks:
Lower KS:
umax B
½ umax B
Ks B Ks A
Bacterial Evolution – Niching
Everyone 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
Everyone Competes……But Will Also Cooperate
• Bacterial Crosstalk
• “Please pass the sugar”
• Rhizobia inoculation
• Quorom Sensing
• Is everyone ready?
• Putting relatives first
• Bacterial “suicide
bombers”
C. Intro to Bacterial Genetics
1. Central Dogma
2. Gene Exchange
3. Examples in Soil
CENTRAL DOGMA
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
A
T
G
C
CENTRAL DOGMA
CENTRAL DOGMA
Ribonucleic Acid – Secondary Structure
CENTRAL DOGMA
The Ribosome
• 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
16S rRNA gene
• 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
2. Gene Exchange
• 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
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
2. Gene Exchange
• 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