"exponential/ logarithmic growth"
when they're actively growing, the culture conditions are continuously changing.
the bacteria cant keep up with the dilution rate. the
Study questions for lecture 5
How would you grow a methanogen or an acetogen? What conditions would you
use and what would you provide as nutrients or substrates for growth?
Methane is a greenhouse gas. What effect does it have today, and what effe
Study questions for lecture 4
Contrast the heterotrophic view of the origin of life with the
How can the oxidation of H2 on the outside of the cell lead to the generatio
Study questions for lecture 2
In catabolism, are the products generally more or less ordered than the substrates?
How does this relate to energy generation and G?
The products of anabolism are cell material.
Study questions for lecture 7
The first step in sulfate reduction is to activate sulfate by converting it to
adenosylphosphosulfate (APS), hydrolyzing ATP. Why is this necessary?
Hydrogen cycling is apparently used by sulfate reducers to gain par
Study questions for lecture 1
What is the connection between what an organism eats (uses as electron donor) and
breathes (uses as electron acceptor) and nutrient cycles? Are all steps in nutrient
cycles due to organisms catabolism, or are some biosyn
Reviews and Resources
Philosophy of Microbiology
Maureen OMalley. Cambridge University
Press, 2014, 269 p., $31.99 (paperback).
Is there really such an animal as a philosophy of microbiology? I am not convinced, but fortunately that is not wh
INSIGHTS | B O O K S
Maureen A. OMalley
Cambridge University Press,
2014. 279 pp.
and the extensive cooperation between microbes has provided a unique perspective
on the units of selection debate. Other
INSIGHTS | P E R S P E C T I V E S
REFERENCES AND NOTES
1. K. Henle et al., Agric. Ecosyst. Environ. 124, 60 (2008).
2. European Environment Agency, EU 2010 Biodiversity
Baseline (Tech. Rep. No. 12/2010, EEA, Copenhagen,
3. L. G. Carvalheiro et al.
by W. Ford Doolittle
_ harles Darwin contended more than a century
ago that all modern species diverged from a
more limited set of ancestral groups, which
themselves evolved from still fewer progeni-
tors and so on back to the beginning of l
Recalcitrant substanceshard to degrade
Naturale.g. lignin (a complex polyaromatic substance in wood etc.)
Xenobioticforeign to nature
Many are toxic, mutagenic, carcinogenic
Biomagnification can occurhydrophobic substance
Lecture 12Aerobic Organotrophs
Accumulation of O2 in the atmospherewhy?
Biochemical properties of O2
Excellent electron acceptor
The metabolism of aerobic organotrophs
Complete oxidation of electron donor generates lo
Chemostats and Steady-State Growth
We have considered bacterial growth experiments in batch culture
where the microbes continually change their environment during the
course of an experiment. The cultures start at a low population density
Lecture 15 Methylotrophy
Methylotrophs: Organisms that derive all carbon and energy from reduced carbon
substrates with no carbon-carbon bonds.
Methylotrophs use specialized enzymatic machinery and assimilation pathways to grow
on C1 compounds.
Study questions for lecture 3
In molecular phylogeny, what do we mean by evolutionary distance?
What would an unrooted tree of only two organisms look like? (Answer is below).
Add a midpoint root. Now what
Study questions for lecture 6
In the methanogenic pathway, which steps are energy-yielding (have a negative G)
and which steps are energy-requiring (have a positive G)?
What is the difference between hydrogenotrophi
Study questions for lecture 9
In the anaerobic ecosystem of sediments, bioreactors, etc., what is the difference
between having sulfate as electron acceptor and having CO2 as electron acceptor?
What are sulfate redu
Lectures 12 and 13Aerobic Organotrophs and Bioremediation
The metabolism of aerobic organotrophs
Complete oxidation of electron donor generates lots of electrons
Various pathways to pyruvate
Citric acid cycle (pyruvate to CO2
Lectures 10 and 11, phototrophs
Photosynthesisa major event in the history of life on earth
The progression from early respiration to photosynthesis to later respiration
Nature of the electron transport chain
Study questions for lecture 12
What are two reasons aerobes generate lots of ATP? Think in terms of electrons and
thermodynamics (redox potentials).
What is denitrification? What organisms carry it out?
photosynthesis requires light-sensitive pigments: chorophyll.
sunlgiht reaches the phototrophic organisms in packets of
absorption of light energy by chorophylls begins the process of
Dividing the world on salinity-The salinity of natural environments
varies over a wide range.
The largest saline environment-the worlds oceansaverage salinity 3.5% (fresh water, sweet water <0.5%)
methylotrophs and methylotrophy
bacteria and archaea able to use reduced carbon substrates with no C-C
bonds as their sole source of carbon and energy
Bioluminescence is broadly distributed among plants, animals and
bacteria (not described in an Achaea as yet).
Convergent evolutionneed oxygen in order to glow
dimer-substrates oxygen, reduced FMN and
Lecture 21Rhizobium-legume symbiosis
How does a legume plant form a root nodule?
How do rhizobia invade the nodule and become nitrogen-fixing bacteroids?
Why does this make everybody happy?
Host specificity: rhizobial species (or biovars) an
!June 2, 2014!
Social cheaters vs parasites!
lux mutants in light organ symbioses !
Secondary endosymbionts in aphids!
!Hamiltonella and bacteriophage APSE!
!Parasitoid wasps as a selective pressure!
Nitrogen fixation: a
microbial magic trick
Dr. Kathryn Fixen
N2 + 3H2
+ high pressure (~200 atm)
+ high tem
Ed Wilson-the father of sociobiology
Sociality from the biologists perpective
Interaction between two or more individuals
Interactions are measurable as either cooperation or conflict
This is a dispassionate view of sociality
conict- one person suffers
!May 30, 2014!
Introduction / denition of terms!
Symbionts as a source of carbon!
!Utilization of recalcitrant substrates!
!Chemosynthetic CO2 xation!
!Photosynthetic CO2 xation!
Symbionts as a source
May 9th, 2016
Dont drink moonshine.
Organisms that derive all carbon and energy from reduced carbon
substrates containing no carbon-carbon bonds