1. Microbiology Why study Microbiology ? Evolution of life
Brock 13th edition: chapters 1, 16
Why study Microbiology ?
Evolution of life
Microbial evolution
Examples for universal importance of bacteria in biology, environment and health

2. a. Evolution of life Mammals Humans Vascular plants
Shelly invertebrates
Origin of Earth (4.6 bya)
Present
 20% O2
Figure 1.6 A summary of life on Earth through time and origin of the cellular domains.
From >1bio years BC, there is only evidence from stomatolites (fossilized bacterial mats) and high contents of light carbon isotopes in these formations
1 bya
Origin of cellular life
4 bya O2
Anoxygenic phototrophic bacteria
Algal diversity
Mic
only
rob ms
ial
life
for
2 bya
3 bya
Anoxic Earth
Earth is slowly oxygenated
Modern eukaryotes
Origin of cyanobacteria
Figure 1.6a

3. Evolution of life Early Bacteria Early Archaea
Mound: precipitates of clay, metal sulfides, silica, and carbonates
Figure 16.4 Submarine mounds and their possible link to the origin of life.
Pyrite, silicates etc precipitate and form montmorillionite clays
These serve as adsorptive surfaces and form catalytic surface for formation of simple organic molecules (“serpentinization”)
Phosphate from seawater then yielded nucleotides,… RNA
First energy sources were probably H2 and H2S
1st big step: self replicating RNA; this is possible, because RNA can bind small organic molecules (amino acids, nucleotides) and catalyze their polymerization (Ribozymes = RNA enzymes)
2nd big step: DNA as genetic storage molecule
3rd big step: lipid membrane; in water, lipids + proteins can form spontaneously proteolipid membrane vesicles
4th big step: LUCA forms… this “fixes” the use of DNA, RNA and proteins as main building blocks of biology and biological information processing
Mound: Aufschüttung, Hügel
Ocean water (20°C, containing metals, CO2 and PO42)
Flow of substances up through mound
Nitrogen bases
Amino acids
Sugars
Ocean crust
Nutrients in hot hydrothermal vent water
Figure 16.4

4. Evolution of life 6. Dispersal (other habitats)
Time
(0.3 to 0.5 billion years)
1. Prebiotic chemistry
2. “RNA world”
3. proteolipid membrane
4. LUCA (last universal common ancestor)
5. diversification, interaction
6. Dispersal (other habitats)
Figure 16.4 Submarine mounds and their possible link to the origin of life.
Pyrite, silicates etc precipitate and form montmorillionite clays
These serve as adsorptive surfaces and form catalytic surface for formation of simple organic molecules (“serpentinization”)
Phosphate from seawater then yielded nucleotides,… RNA
First energy sources were probably H2 and H2S
1st big step: self replicating RNA; this is possible, because RNA can bind small organic molecules (amino acids, nucleotides) and catalyze their polymerization (Ribozymes = RNA enzymes)
2nd big step: DNA as genetic storage molecule
3rd big step: lipid membrane; in water, lipids + proteins can form spontaneously proteolipid membrane vesicles
4th big step: LUCA forms… this “fixes” the use of DNA, RNA and proteins as main building blocks of biology and biological information processing
Mound: Aufschüttung, Hügel
Figure 16.4

5. LUCA’s energy metabolism
e--acceptor
e--donor
S + H2  H2S ΔG0’ = -20,6 kJ
Primitive ATPase
Primitive hydrogenase
Out
pyrite
Figure 16.7 A possible energy-generating scheme for primitive cells.
Early earth was anaerobic
Energy metabolism: probably H2 = fuel (e- source); most early branching clades still use H2.
H2 probably from pyrite + H2S (ΔG0’ = -42kJ; exergonic, occurs spontaneously), or from Fe2+ and UV light
H+ gradient
Cytoplasmic membrane In
S0 reductase
Figure 16.7

6. LUCA’s C-metabolism S + H2  H2S ΔG0’ = -20,6 kJ 4-4.3 x109 years BC
CO2 fixation  organic compounds (i.e. acetate)
accumulate
LUCA’s C-metabolism: probably autotrophic, using CO2 as C-source (still seen in ancient clades, e.g. Aquifex (bacteria) or Pyrolobus (Archaea)
Chemoorganotrophic bacteria:
Electrons from organic compounds
C-source: organic compounds (e.g.: a methyl group and carbon monoxide are derived from CO2; these are condensed by coenzyme A enzymatically to generate acetate; e.g. John W. Peters, Science 298, 552, (2002); DOI: /science anaerobic COaaaaccc
Chemoorganotrophic bacteria
“metabolic diversification”

7. Metabolic diversification
S + H2  H2S ΔG0’ = -20,6 kJ
4-4.3 x109 years BC
CO2 fixation  organic compounds
accumulate
Bacteria
Archaea
methanogenesis
3.7 x109 years BC
H2, CO2  acetate
4 H2 + CO2  CH4 + 2H2O
H3CCOO- + H2O  CH4 + HCO3-

8. Bacteria: evolve phototrophy
S + H2  H2S ΔG0’ = -20,6 kJ
4-4.3 x109 years BC
CO2 fixation  organic compounds
accumulate
Phototrophy only arose in bacteria
With exception of some early branching bacteria (Aquifex, Thermotoga), all contemporary bacteria seem to derive from a common bacterial ancestor which was an anaerobic prototroph
Original strategy: anaerobic phototrophy
H2S is oxidized to S; electrons are transferred to NAD(P), thus generating NAD(P)H; the NAD(P)H is subsequently used to convert ADP to ATP
2.7-3 Bio years ago: cyanobacteria evolved a photosystem using H2O (instead of H2S) for photosynthetic reduction of CO2: this released O2 (instead of S) (for details, see chapter 13)
Bacteria
Archaea
methanogenesis
3.7 x109 years BC
H2, CO2  acetate
4 H2 + CO2  CH4 + 2H2O
H3CCOO- + H2O  CH4 + HCO3-
CO2 fixation
3.3 x109 years BC
Anaerobic phototrophy (H2S S)
2.7 x109 years BC
Oxygen generating phototrophy (H2O O2)
CO2 fixation

9. Organisms, events O2 level
Eon
BYA
Organisms, events
O2 level
Metabolic highlights
O2 toxicity
New metabolic pathways:
- sulfate reduction
- nitrification
- chemolithotrophy
- O2 respiration (grow fast)
Extinction of the dinosaurs
Phanaerozoic
Cambrian
0.5
Early animals
Precambrian
Multicellular eukaryotes
20%
1.0
10%
Proterozoic
1.5
First eukaryotes with organelles
First: Fe-oxidation
Figure 16.6 Major landmarks in biological evolution, Earth’s changing geochemistry, and microbial metabolic diversification.
First O2 consumed by oxydation of FeS and FeS2  banded iron formations (geology)
It took approx 300 mio years to reach 0.1% oxygen levels
Ozone shield: absorbs light of <300nm  enables life on land 1%
2.0
Endosymbiosis?
Ozone shield
Great oxidation event
0.1%
Aerobic respiration
2.5
Cyanobacteria
Oxygenic photosynthesis
(2H2O  O2  4H)
3.0
Archaean
Sulfate reduction Fe3 reduction
Precambrian Fe3+ sediments
Purple and green bacteria
Anoxygenic photosynthesis
3.5
Anoxic
Bacteria/Archaea divergence
Acetogenesis
4.0
Methanogenesis
First cellular life; LUCA
Hadean
Formation of crust and oceans
Sterile Earth
4.5
Formation of Earth
Figure 16.6 and 8

10. Endosymbiont theory of Eukaryote evolution
a) From nucleated Archaeon
b) Hydrogen hypothesis
Bacteria
Eukarya
Archaea
Bacteria
Eukarya
Archaea
Animals
Plants
Animals
Plants
Figure 16.9 Endosymbiotic models for the origin of the eukaryotic cell.
The hydrogen theory seems to be more compatible with the Eukaryotic cell makeup:
The first endosymbiont had:
DNA for lipid biosynthesis and glycolytic enzymes (cytoplasm) from Archaea and Bacteria (kept the one from Bacteria)
DNA for replication and gene expression machinery from Archaea and Bacteria (kept the one from Archaea)
The nuclear envelope has formed some time in between
Mitochondria: respiration (enzymes in inner membrane) and oxidative phosphorylation (ATP generation; enzymes in inner membrane), citric acid cycle enzymes (in matrix= space engulved by the inner membrane)
nucleus formed
Archaeon
with nucleus
cyanobacterium
cyanobacterium
Ancestor of mitochondrion
(Bacteria)
Engulfment of a H2-producing cell of Bacteria by a H2-consuming cell of Archaea
Figure 16.9

11. Table 16.1 Major characteristics of Bacteria, Archaea, and Eukarya

12. three take home messages
Bacteria are the ancient form of life. All other organisms evolved from this. LUCA existed probably 4.3 Bio years ago.
All forms of life had extreme effects on their environment... and mediated dramatic change
Intense interactions. All organisms have interacted with each other (directly or indirectly). E.g. Eukaryotes have always been interacting intensely with bacteria throughout their evolution. The evolution and function of one cannot be understood in the absence of the other.

13. b. Bacteria and Archaea evolution
Very high rate of evolution!!
Haploid genomes
Rapid growth
Large populations

14. Bacteria/ Archaea evolution
Wild-type cell Pigment mutants Light Dark
Mutants lost in light
Mutant selected in dark
Cell populations
Pigment mutants
Wild type
Subculture number
Bacteriochlorophyll a/ml of culture 15 10 5 20 4 3 2 1
Rhodobacter capsulatus
Figure Survival of the fittest and natural selection in a population of phototrophic purple bacteria.
Figure 16.10

15. Phylogenetic analysis of Bacteria, Archaea
Small ribosomal subunit RNA sequence: “long distance” relationships
Ribosomal RNA genes
Figure Ribosomal RNA (rRNA).
Ribosomal data base:
Variable…….conserved
16S (bacteria), 18S (Eukaryotes)
Ubiquitous and essential
Ancient
Easy RNA isolation
Conserved and variable regions
Sufficiently long
16S rRNA
Base position in 16S RNA gene

16. Phylogenetic analysis of Bacteria, Archaea
conserved protein-coding genes: “long distance” and strain differentiation
EF-Tu (protein biosynth.)
Hsp60
aatRNA synthetases …
Figure Ribosomal RNA (rRNA).
Ribosomal data base:

17. Phylogenetic analysis
via 16S rDNA
Isolate DNA
16 S gene
Amplify 16S gene by PCR
Run on agarose gel; check for correct size
Kilo- bases 1 2 3 4 5
3.0–
2.0–
Figure PCR amplification of the 16S rRNA gene.
1.5–
1.0–
0.5–
Sequence
Before alignment
After alignment
Species 1
Species 2
Nonidentities
Gaps 9 15
A C G G T
Align sequences; generate tree
Distinct species
Ancestral cell
Distinct species
Figure 16.12, 13

18. Display phylogenetic relationship
Cladistics = grouping by common features (absent in more distant relatives)
Parsimony = assumes least number of steps
Rooted trees
node
Figure Phylogenetic trees.
“cladistics” methods are used for tree construction
Phylogenetic tree = cladogram
Parsimony = assumption that the correct evolutionary path is the one requiring the least number of genetic changes
Unrooted tree
Relative relationships
Defines unique paths of evolution
Employs “outgroup”
Figure 16.14

19. Universal phylogenetic tree
3 “domains”
PROKARYOTES
EUKARYOTES
Bacteria
Archaea
Eukarya
> 80 phyla
> 10 Mio species??
2 major phyla
8 Mio species ?
Animals (7.7 Mio species)
Entamoebae
Slime molds
Green nonsulfur bacteria
Figure Universal phylogenetic tree as determined from comparative SSU rRNA gene sequence analysis.
This is also consistent with 30 other “house keeping” genes
Formerly, biologists were classifying organisms into five “kingdoms”: plants, animals, fungi, protists, bacteria…. This is not consistent with sequence data!!!!
Bacteria: > 80 phyla; however, each phylum can harbor species with very distinct physiology; e.g. the proteobacteria display species of all known physiologies
Bacteria: based on microbial community analysis, there are > 10 Mio bacterial species
Eukaryonten: 8.7 Mio Species
7.7 Mio animal species
plant species
fungi species
protozoa etc.
Reference: Science 338, (2012)
Euryarchaeota
Fungi (0.6 Mio species)
Mitochondrion
Methanosarcina
Methano- bacterium
Gram- positive bacteria
Crenarchaeota
Extreme halophiles
Plants (0.3 Mio spec.)
Proteobacteria
Thermoproteus
Methano- coccus
Ciliates
Chloroplast
Pyrodictium
Thermoplasma
Cyanobacteria
Thermococcus
Flavobacteria
Flagellates
Marine Crenarchaeota
Pyrolobus
Methanopyrus
Trichomonads
Thermotoga
Thermodesulfobacterium
Microsporidia
Aquifex
Diplomonads (Giardia)
LUCA
Extensive genetic
exchange??
Figure 16.16

20. c. Current topics of interest
Methods: for analyzing microorganisms
Philosophy: the bacterial species problem
health: effects of the microbiota
health: what is a pathogen? How to kill bacteria?
environment: metabolic effects on C, N, P, S… cycles
Industry/safety: genetic engineering

21. Analyzing Bacteria and Archea
Physiology: << 5 % of all bacteria have been cultured
phenotype (motility, morphology, metabolism…)
FISH (Fluorecence in situ hybridization): DNA-oligo binding rRNA
Bacillus
Figure Fluorescently labeled rRNA probes: Phylogenetic stains.
Yeast
Universal probe
eukaryal probe
DNA sequencing (fast evolving field!!):
- 16S “community sequencing”
- “metagenome sequencing”
 predict genes/metabolism
 predict physiology

22. Costs of DNA sequencing

23. DNA sequencing for microbial community analysis
Community sampling approach
Environmental genomics approach
Outcomes
Single-gene phylogenetic tree
Total gene pool of the community
1. Identification of all gene categories
2. Discovery of new genes
3. Linking of genes to phylotypes
Phylogenetic snapshot of most members of the community 1.
Identification of novel phylotypes 2.
Amplify single gene, for example, gene encoding 16S rRNA
Restriction digest total DNA and then shotgun sequence, OR sequence directly (without cloning) using a “next generation” DNA sequencer
Extract total community DNA
Microbial community
Sequence and generate tree
Assembly and annotation
DNA
Partial genomes
Figure Single-gene versus environmental genomic approaches to microbial community analysis.
Figure 22.16

24. Example 1: The gut microbiota Role in health and diseases
Animal evolution
Gut: somewhere between the cnidarians (Quallen) and deuterostomes ()
Early Animal Evolution: Emerging Views from Comparative Biology and Geology
Andrew H. Knoll 1* and Sean B. Carroll 2
Fig. 3. Anatomical, developmental, and genetic innovations in the evolution of Bilateria. Inferences about the evolution of bilaterian features have been drawn from comparisons of developmental mechanisms and genetics among sponges, cnidarians, ctenophores, and selected protostomes and deuterostomes and mapped onto one presumed phylogeny [figure modified from (69)]. We note that the relationships among lower metazoans and bilaterians and the evolution of particular characters (highlighted in blue) are both uncertain and of central importance. Characteristics shared between protostomes and deuterstomes are deduced to have existed in some form in their last common ancestor, Urbilateria. The evolution of gene functions in controlling specific developmental features are shown in red. Figure based on references (34, 39, 40, 50, 52, 63, 69), and text

25. Example 1: The gut microbiota Role in health and diseases
Animal evolution
Gut: somewhere between the cnidarians (Quallen) and deuterostomes ()
Early Animal Evolution: Emerging Views from Comparative Biology and Geology
Andrew H. Knoll 1* and Sean B. Carroll 2
Fig. 3. Anatomical, developmental, and genetic innovations in the evolution of Bilateria. Inferences about the evolution of bilaterian features have been drawn from comparisons of developmental mechanisms and genetics among sponges, cnidarians, ctenophores, and selected protostomes and deuterostomes and mapped onto one presumed phylogeny [figure modified from (69)]. We note that the relationships among lower metazoans and bilaterians and the evolution of particular characters (highlighted in blue) are both uncertain and of central importance. Characteristics shared between protostomes and deuterstomes are deduced to have existed in some form in their last common ancestor, Urbilateria. The evolution of gene functions in controlling specific developmental features are shown in red. Figure based on references (34, 39, 40, 50, 52, 63, 69), and text
=>>
A long history of co-evolution

26. Example 1: The gut microbiota Role in health and diseases
MAMP signaling/innate immunity
Microbiota enzyme/function
Health
Energy: acetate, butyrate
Innate defense: priming
Vitamins: K, B12, C, niacin,
panthotenic acid, biotin,
folic acid
GALT: maturation
Gut: somewhere between the cnidarians (Quallen) and deuterostomes ()
Early Animal Evolution: Emerging Views from Comparative Biology and Geology
Andrew H. Knoll 1* and Sean B. Carroll 2
Fig. 3. Anatomical, developmental, and genetic innovations in the evolution of Bilateria. Inferences about the evolution of bilaterian features have been drawn from comparisons of developmental mechanisms and genetics among sponges, cnidarians, ctenophores, and selected protostomes and deuterostomes and mapped onto one presumed phylogeny [figure modified from (69)]. We note that the relationships among lower metazoans and bilaterians and the evolution of particular characters (highlighted in blue) are both uncertain and of central importance. Characteristics shared between protostomes and deuterstomes are deduced to have existed in some form in their last common ancestor, Urbilateria. The evolution of gene functions in controlling specific developmental features are shown in red. Figure based on references (34, 39, 40, 50, 52, 63, 69), and text
Cancer: Infektionen und Krebs – eine Zweimillionen-Schnittmenge
Lange glaubte man, Krebs und Infektionen seien zwei völlig voneinander unabhängige Krankheitsfelder – und häufig ist diese Meinung noch immer anzutreffen: Infektionskrankheiten fängt man sich von außen ein, Krebs entsteht im Körper. Dass diese strikte Trennung längst nicht mehr gilt, zeigen die drei weltweit häufig auftretenden Tumorerkrankungen Magen-, Leber- und Gebärmutterhalskrebs.
Gebärmutterhalskrebs, oder fachsprachlich Zervixkarzinom, ist die Folge einer Infektion mit humanen Papillomaviren. Die Ursache von fast 80 Prozent aller Leberkrebs-Fälle ist eine Infektion mit Hepatitisviren. Etwa 75 Prozent der Magentumore gehen auf eine Infektion mit Helicobacter pylori zurück.
Und das ist nur die Spitze des Eisbergs: Weltweit erkranken jährlich etwa zwölf Millionen Menschen an Tumoren – zwei Millionen dieser Erkrankungen werden durch Erreger wie Viren oder Bakterien ausgelöst. Und natürlich sind Krebspatienten allgemein besonders anfällig für Infektionen. Infektionsforschung ist also im weiteren Sinne auch Krebsforschung – und umgekehrt.
Mucosa: maturation
Colonization resistance
Disease
Inflammatory bowel disease: stimulus
Th17 immune responses: stimulus
Host metabolism: stimulus
cancer: stimulus ?

27. Example 1: The gut microbiota Role in health and diseases
The microbial communities of humans are characteristic and complex mixtures of microorganisms that have
co-evolved with their human hosts. The species that make up these communities vary between hosts as a
result of restricted migration of microorganisms between hosts and strong ecological interactions within
hosts, as well as host variability in terms of diet, genotype and colonization history. The shared evolutionary
fate of humans and their symbiotic bacteria has selected for mutualistic interactions that are essential for
human health, and ecological or genetic changes that uncouple this shared fate can result in disease. In
this way, looking to ecological and evolutionary principles might provide new strategies for restoring and
maintaining human health.
Dethlefsen, 2008, Nature 448, pp. 811ff

28. Example 2: The “bacterial species problem”
Plants/animals: cross fertile offspring
Bacteria, Archaea: ??

29. Example 2: The “bacterial species problem”

30. The “bacterial species problem”
Phylogenetic tree
181 genomes
proteobacteriales
Phylogenomic tree
≥5 genes exchanged by «horizontal gene transfer»
Dagan et al., 2008, PNAS 105, pp ff.

31. The “bacterial species problem”
Streptococcus
As an example, Fig. 1A shows the relationships among multiple isolates of three closely related streptococcal species. Streptococcus pneumoniae is a major human pathogen, S. mitis is a commensal bacteria with a history of taxonomic uncertainty (11), and S. pseudopneumoniae is a recently described organism of uncertain status
that nonetheless corresponds to a distinct cluster in these data (12). There are striking differences in the amount of sequence diversity observed within homologous housekeeping genes in these named species, ranging from 1.2% for S. pneumoniae to 3.0% for S. pseudopneumoniae and up to 5.0%for S. mitis. The distance between two randomly selected S. mitis genotypes is similar to the average distance between S. pneumoniae and S. pseudopneumoniae genotypes (5.1%) (2). This implies that the use of a fixed level of sequence divergence for differentiating species would tend to either rejoin S. pneumoniae and S. pseudopneumoniae, or break up S. mitis so that nearly every isolate was a species of its own. This is clearly unsatisfactory.
Sympatric ancestral population? Population, deren Verbreitungsgebiete zumindest teilweise überlappt
Ecological radiation? Ausbreitung in neue Nieschen
Neutral diversity? Polymorphismen (non coding; synonyme Nukleotid-Austausche)
Effective population size? Die Grösse der Population einer Spezies, die ohne Selektionsdrücke zum selben Mass von neutraler Diversität führen würde. (10ex5 bis 10exp 9 ist typisch für Bakterien)
… aber: Bierdeckelkalkulation: es gibt 10exp 20 Vibrio-Bakterien auf der Erde (passt nicht zur gemessenen effektiven Populationsgrösse)
Fraser et al., 2009, Science 323, pp. 741ff

32. The “bacterial species problem”
Bacteria, Archaea: - no sexual cycle
- “long distance” gene exchange
 phylogenetic species concept
 niche occupation: “ecotype”
16S rRNA Gene Tree
Multigene Tree
Photobacterium damselae
FS-2.1
50 changes
FS-4.2
Photobacterium phosphoreum
Photobacterium leiognathi
FS-3.1
officially: >7000 registered species
- current definition: >70% DNA-DNA hybridization
< 3% 16S sequence difference
16S sequences: good for long distance comparison; no sufficient resolution at species- or strain-level
Multigene phylogenetic analysis much better suited at species- or strain-level
Species formation/maintenance: equilibrium between divergence (by mutation and horizontal gene transfer from distantly related species) and convergence by horizontal gene exchange between members of the species
FS-5.1
FS-2.2
Photobacterium mandapamensis
ATCC 11040T
FS-5.2
Photobacterium angustum
ATCC 51761
Photobacterium phosphoreum
NCIMB 13476
Photobacterium iliopiscarium
NCIMB 13478
Photobacterium iliopiscarium
NCIMB 13481
ATCC 51760T
Photobacterium kishitanii
chubb.1.1
ckamo.3.1
canat.1.2
hstri.1.1
Photobacterium kishitanii
calba.1.1
BAA-1194T
apros.2.1
ckamo.1.1
vlong.3.1

33. The “bacterial species problem”  ecotypes
One microbial habitat
Ecotype I
Ecotype II
Ecotype III
New species of Ecotype III
Cell containing an adaptive mutation
Population of mutant Ecotype III
Periodic selection
Adaptive mutant survives. Original Ecotype III wild-type cells out competed
Repeat process many times
Figure A model for bacterial speciation.
Ecotype: genetically “identical” species sharing the same ecological niche
Different ecotypes can coexist physically, but they do not compete for the same key nutrients/factors. Thus they can evolve independent from each other.
Figure 16.25

34. Classification: traditional approach
Taxonomic systems:
Bergey’s Manual of Systematic Bacteriology
The Prokaryotes
International Committee on Systematics of Prokaryotes
Table 16.5 Some national microbial culture collections

35. Example 3: global Carbon-cycle
, a greenhouse gas
CH4
CO2
Human activities
Respiration
Land plants
Animals and microorganisms
Figure 24.1 The carbon cycle.
Almost any organic carbon compound is eventually degraded biologically into CO2 and CH4.
CH4 is as greenhouse gas 20-fold more potent than CO2.
Atmosphere: 790 x 10exp9 tons Carbon
Biosphere:
terrestric 700 x 10exp9 tons Carbon
Marine organisms 3 x 10exp9 tons Carbon
Aquatic plants and phyto- plankton
CO2
Aquatic animals
Biological pump
Fossil fuels
Humus
CO2
Death and mineralization
CH4
CH4
Soil formation
Earth’s crust
Rock formation
Atmosphere
Figure 24.1

36. Example 3: global Carbon-cycle
(CH2O)n
Organic matter
Oxygenic photosynthesis
Respiration
Chemolithotrophy
Methanotrophy
Figure 24.1 The carbon cycle.
Oxic
CO2
Anoxic
Methanogenesis
Acetogenesis
Anaerobic respiration and fermentation
Syntroph assisted
Anoxygenic photosynthesis
Organic matter
(CH2O)n
Figure 24.2

37. Example 3: anaerobic methane oxidation
Marine sediments
Methanotrophic Archaea (ANME-types)
Sulfate-reducing Bacteria
Figure 24.1 The carbon cycle.
In marine sediments, AOM is catalyzed by cell aggregates of Bacteria and Archaea (called ANME, anorganic methanotroph):
The exact mechanism underlying the methane activation step are still under investigation
The electrons are directly shuttled to the sulfate reducing bacteria (e.g. via acetate, formate, organic sulfide)
Organic compounds
Figure 14.28

38. c. Current topics of interest
Methods: for analyzing microorganisms
Philosophy: the bacterial species problem
health: effects of the microbiota
health: what is a pathogen? How to kill bacteria?
environment: metabolic effects on C, N, P, S… cycles
Industry/safety: genetic engineering