Download Table 3.1

Table 3.1
A sampling of completed prokaryotic genomes. (Modified from US Department of Environment
Joint Genome Institute)
Organism
Genome
size (Mb)
ORFs
Phenotype/habitat
Bacteria
Acinetobacter sp. ADPI
3.59
3425
Agrobacterium tumefaciens C58
Dupont
Anabaena variabilis ATCC29413
5.67
5467
7.10
5720
Bacillus cereus ATCC 14579
Bradyrhizobium japonicum
USDA 110
Buchnera aphidicola APS
Burkholderia xenovorans LB400
5.42
9.10
5397
8371
0.655
9.73
609
8784
Candidatus Tremblaya princeps
0.139
110
Carsonella rudii
0.160
182
Clostridium acetobutylicum
ATCC 824
Dechloromonas aromatica RCB
Deinococcus radiodurans R1
4.13
3955
4.50
3.28
4247
3239
Desulfovibrio desulfuricans G20
3.73
3853
Dehalococcoides ethenogenes strain
195 (now D. mccartyi)
Escherichia coli K12
1.47
1629
4.64
4359
Escherichia coli O157:H7 EDL933
5.62
5622
Geobacter metallireducens GS‐15
4.01
3587
Mesotoga prima MesG1.Ag 4.2
2.97
2736
Methylococcus capsulatus Bath
Mycoplasma genitalium
3.30
0.580
3012
516
Aerobic chemoheterotroph and human
pathogen/water, soil, human skin
Aerobic chemoheterotroph/soil, plant
pathogen
Oxygenic photosynthesis, nitrogen fixation/
water, soil
Aerobic spore‐forming heterotroph/soil
Aerobic heterotroph, nitrogen‐fixing
symbiont on soybean roots/soil
Insect endosymbiont
Aerobic heterotroph, metabolizes
polychlorinated biphenyl/soil
Obligate endosymbiont of a citrus‐feeding
mealy bug; this bacterium harbors an
endosymbiont
Obligate endosymbiont of a psyllid, a plant
sap‐feeding insect
Obligate anaerobic spore‐forming
chemoorganotroph/soil
Facultative benzene degrader/water, soil
Chemoheterotroph, aerobe, highly radiation
resistant/soil
Strict anaerobe, chemoorganotroph using
substrate as electron acceptors/sediment
Strict anaerobe using chlorinated solvents as
final electron acceptor/sewage, groundwater
Facultative chemoheterotroph/human
intestine
Facultative chemoautotroph, human
pathogen/intestine, food
Anaerobic chemoheterotroph using metal
anions as electron acceptors/water,
subsurface sediment
Strict anaerobe containing a reductive
dehalogenase gene; isolated from
polychlorinated biphenyl (PCB)‐
contaminated sediment
Aerobic methanotroph/soil water
Intracellular human parasite of urogenital
tract
Table 3.1 Continued
Organism
Genome
size (Mb)
ORFs
Phenotype/habitat
Nitrobacter winogradskyi Nb‐255
3.40
3174
Pelagibacter ubique (SARII) HTCC
1062
Pelagibacter ubique (SAR 11)
HIMB59
Polaromonas naphthalenivorans
CJ2
Prochlorococcus marinus MIT 9312
Prochlorococcus marinus MIT 9313
Pseudomonas fluorescens Pf‐5
Pseudomonas putida KT2440
Rhodopseudomonas palustris
CGA009
Shewanella oneidensis MR‐1
1.309
1394
1.410
1532
5.34
5022
1.70
2.41
7.07
6.18
5.86
1852
2321
6223
5446
4897
5.13
4601
Silicibacter pomeroyi DSS‐3
4.60
4314
Sorangium cellulosum So ce 56
13.0
9700
Streptomyces avermitilis MA‐4680
9.11
7759
Synechococcus elongatus PCC 7942
Thermotoga maritima MSB8
2.74
1.86
2712
1907
Trichodesmium erythraeum
ImS101
7.75
4494
Facultative autotroph, CO2 fixation, nitrite
oxidizer/soil
Aerobic marine heterotroph/coastal
temperate NE Pacific
Aerobic marine heterotroph/coastal tropical
N Pacific
Chemoorgano‐ and lithotrophic aerobe/
terrestrial sediment
Photosynthetic bacterioplankton/ocean
Photosynthetic bacterioplankton/ocean
Aerobic chemoheterotroph/soil
Aerobic chemoautotroph/soil
Physiologically versatile‐facultative
photosynthetic organism/water, soil
Metabolically versatile chemoheterotroph,
metal reduction/lake sediment
Aerobic heterotroph important in the sulfur
cycle/seawater
Aerobic hterotroph with complex
developmental life cycle (member of the
myxobacteria)
Aerobic chemoheterotroph, filamentous
spore former/soil
Photosynthetic bacterioplankton/ocean
Hyperthermophilic anaerobe/geothermal
marine sediment
Photosynthetic nitrogen‐fixing filamentous
cyanobacteria/ocean water
Archaea
Archaeoglobus fulgidus DSM 4304
2.18
2519
Cenarchaeum symbiosum A
2.0
2066
Halobacterium salinarum NRC‐1
2.57
2726
Haloferax volcanii DS2, ATCC
29605
Methanopyrus kandleri AV19
4,0
4064
1.69
1765
Methanosarcina barkeri Fusaro
4.87
3854
Nanoarchaeum equitans Kin4‐M
0.49
608
Strict anaerobe, hyperthermophilic, sulfate
reduction/hot springs
Aerobe, psychrophile, obligate symbiont
within marine sponge
Chemoorganotrophic aerobe/highly saline
ponds and lakes
Chemoorganotrophic aerobe, mesophilic/
salty shore of the Dead Sea
Strict anaerobe hyperthermophilic,
methanogenesis/hot springs
Strict anaerobe, methanogenesis, cellulose
metabolism/marine mud, sludge
Intracellular parasite, anaerobic
hyperthermophile/hot springs
Table 3.1 Continued
Organism
Genome
size (Mb)
ORFs
Phenotype/habitat
Nitrosopulilus maritinus SCM1
1.64
1842
Pyrococcus furiosus DSM 3638
1.90
2179
Sulfolobus solfataricus P2
2.99
3141
Thermoplasma volcanium GSS1
1.58
1610
Aerobic, mesophile, autotrophic ammonia
oxidizer/marine
Strict anaerobe hyperthermophilic, radiation
resistant, sulfur respiration/hot springs
Strict aerobe hyperthermophilic, acidophile,
sulfur oxidizer/hot springs
Facultative acidophilic thermophile/
hydrothermal vent
Mb, mega bases, 106 base pairs; ORF, open reading frame; Integrated Microbial Genomes website: http://img.jgi.doe
.gov/cgi‐bin/w/main.cgi.
Table 3.2
Framework for categorizing and organizing open reading frames (ORFs) found during genome‐
sequencing projects. Twenty‐five gene categories (cluster of orthologous groups of proteins:
COGs) and their respective contributions to the sequenced genome of Pseudomonas putida
KT2240 are listed. (From US Department of Environment Joint Genome Institute)
Functional group of genes (COG)
Example genome (Pseudomonas putida
KT2440): number of genes in each
functional group (% of total)
Information storage and processing
J Translation, ribosomal structure and biogenesis
A RNA processing and modification
K Transcription
L DNA replication, recombination and repair
B Chromatin structure and dynamics
  187 (3.4)
   3 (0.05)
  440 (8.1)
  221 (4.0)
   2 (0.04)
Cellular processes
D Cell cycle control, cell division and chromosome
partitioning
Y Nuclear structure
V Defense mechanisms
T Signal transduction mechanisms
M Cell wall/membrane/envelope biogenesis
N Cell motility
Z Cytoskeleton
W Extracellular structures
U Intracellular trafficking, secretion, and
vesicular transport
O Posttranslational modification, protein
turnover, chaperones
Metabolism
C Energy production and conversion
G Carbohydrate transport and metabolism
E Amino acid transport and metabolism
F Nucleotide transport and metabolism
H Coenzyme transport and metabolism
I Lipid transport and metabolism
P Inorganic ion transport and metabolism
Q Secondary metabolites biosynthesis, transport
and catabolism
Poorly characterized
R General function prediction only
S Function unknown
  42 (0.77)
   –
  63 (1.2)
  330 (6.1)
  266 (4.9)
  127 (2.3)
   –
   –
  123 (2.3)
  174 (3.2)
  293 (5.4)
  228 (4.2)
  516 (9.5)
  91 (1.7)
  186 (3.4)
  181 (3.3)
  275 (5.1)
  128 (2.3)
  564 (10.4)
1014 (18.6)
Table 3.3
Physiological classification of life forms based on energy source and carbon source. The five
categories assist in understanding both individual microorganisms and biogeochemical systems
Carbon
source
Fixed
organic
Gaseous
CO2
Energy source
Chemical, organic
Chemical, inorganic
Light
Chemosynthetic
organoheterotroph
(Example: humans,
fungi, Pseudomonas)
Chemosynthetic
lithoheterotroph
(Example: Beggiatoa sp.)
Photosynthetic heterotroph
(Example: purple and green
bacteria; Rhodospirillum)
Chemosynthetic
lithoautotroph
(Example: ammonia‐,
hydrogen‐, and sulfur‐oxidizing
bacteria; Nitrosomonas, Aquifex)
Photosynthetic autotroph
Terminology:
• Autotroph: carbon from CO2 fixation
• Heterotroph: carbon assimilated from (fixed) organic compounds
• Photosynthetic: energy from light
• Chemosynthetic: energy from oxidizing reduced chemicals
• Chemolitho: energy from oxidizing inorganic reduced chemicals
• Chemoorgano: energy from oxidizing organic reduced chemicals.
(Example: plants, algae,
Prochlorococcus)
Table 3.4
Predominant ecological limitations for energy and growth for three physiological classes of
microorganisms in a variety of habitats
Habitat characteristics and nutrient limitations faced by three
physiological classes of microorganisms
Habitat type
Photoautotroph
Chemolithotroph
Chemoorganoheterotroph
Ocean water
Daily light cycle,
light penetration
depth; scarce iron
Flux of reduced inorganic
compounds, especially NH3,
H2S, H2, or CH4 from
nutrient turnover and
hydrothermal vents
Carbon flux from phototrophs,
dead biomass, and influent
waters
Lake water
Daily light cycle,
light penetration
depth; scarce
phosphorus
Flux of reduced inorganic
materials, especially NH3, H2,
and CH4 from nutrient
turnover
Carbon flux from phototrophs,
dead biomass and influent
waters
Sediment
(freshwater
and oceanic)
Daily light cycle,
light penetration
depth
Flux of reduced inorganic
materials, especially NH3 and
H2 from nutrient turnover or
H2, H2S, or CH4 from
hydrothermal vents
Flux of organic carbon from
phototrophs and dead biomass;
flux of final electron acceptors
to carbon‐rich anaerobic strata
Soil
Daily light cycle,
light penetration
depth
Flux of reduced gaseous
substrates, especially
methane from nutrient
turnover by anaerobes
Slow turnover of soil humus,
dead biomass, plant root
exudates; leaf fall from
vegetation
Subsurface
sediment
No light
Flux of reduced inorganic
materials, especially H2 and
CH4 from geothermal origin
Carbon flux from nutrient
turnover
Table 3.5
phoB (PhoB, response
regulator), phoR (PhoR,
sensor kinase), phoU,
and pstA, ‐B, ‐C, ‐S
(facilitate PhoR function)
Enteric
bacteria
Pho system
(acquisition of
inorganic
phosphate)
Phosphate
limitation
Multiple genes,
including those
controlling ammonia
assimilation
Klebsiella
aerogenes and
many others
glnB, glnD, glnG, glnL
(transcriptional
regulators and enzyme
modifiers)
Some enteric
bacteria
Ntr system
(enhances
ability to acquire
nitrogen from
organic sources
and from low
ammonia
concentrations)
Nif system
(nitrogen
fixation)
Ammonia
limitation
Ammonia
limitation
relA and spoT (enzymes
of (p)ppGpp metabolism)
Enteric
bacteria and
many others
Stringent
response
crp (transcription
activator CAP): cya
(adenylate cyclase)
Regulatory genes (and
their products)
Amino acid
or energy
limitation
Organism(s)
Enteric
bacteria
System
Nutrient utilization
Carbon
Catabolite
limitation
repression
Stimulus/
conditions
PhoA (alkaline
phosphatase) and ~40
other genes involved
in utilizing
organophosphates
Multiple genes
encoding nitrogenase
(for nitrogen fixation)
Genes encoding
catabolic enzymes (lac,
mal, gal, ara, tna, dsd,
hut, etc.)
Genes (>200) for
ribosomes, other
proteins involved in
translation and
biosynthetic enzymes
glnA (glutamine
synthetase), hut, and
others encoding
deaminases
Regulated genes
(and their products)
Complex; ammonia represses
activity of NtrC; under low
ammonia status, NtrC is active
and promotes transcription of
NifA, the activator protein for
nif transcription
Two‐component regulation;
transcriptional activation by
PhoB upon signal of low
phosphate from the sensor
kinase, PhoR
Complex
Activation by CAP protein
complexed with cAMP as a
signal of carbon source
limitations
(p)ppGpp thought to modify
promoter recognition by RNA
polymerase
Type of regulation
Prominent gene regulation systems that allow bacteria to sense and coordinate metabolism according to environmental conditions,
especially starvation‐related stresses. (From Schaechter, M., J.L. Ingram, and F.C. Niedhardt. 2006. Microbe. American Society for
Microbiology Press, Washington, DC. With permission from the American Society for Microbiology)
Sporulation
rpoS (sigma‐S), lrp (Lrp),
crp (CAP), dsrA, rprA,
and oxyS (regulatory
sRNA molecules), and
many other regulatory
genes
SpoOA (activator), spoOF
(modulator), and many
other regulatory genes
All bacteria
Bacillus
subtilis and
other spore
formers
fis (Fis), hns (H‐NS), relA
(RelA), and spoT (SpoT)
Unknown
ArcA (ArcA, repressor)
and arcB (ArcB,
modulator)
fnr (Fnr)
All bacteria
E. coli and
other
facultative
bacteria
E. coli
E. coli
Many (>100) genes
for spore formation
Hundreds of genes,
many involved in
macromolecule
synthesis
Hundreds of genes
affecting structure and
metabolism
Genes (>20) for
enzymes of
fermentation
pathways
Genes for nitrate
reductase and other
enzymes of anaerobic
respiration
Many genes (>30) for
aerobic enzymes
Complex; involves availability
of RNA polymerase/sigma‐70
holoenzyme influenced by
passive control
Multiple modes of regulation
in a complex network;
involves several global
regulatory systems, in addition
to selection of genes with
promoters recognized by σs
Complex; cells respond to
nutrient deprivation with
SpoOA phosphorelay; a
cluster of sigma factors assist
in controlling seven stages of
differentiation leading to
endospore formation and
release
Unknown
Repression of genes of aerobic
enzymes by ArcA upon signal
from ArcB of low oxygen
Transcriptional activation
by Fnr
cAMP, cyclic adenosine monophosphate; CAP, catabolite activator protein; (p)ppGpp; a mixture of guanosine tetra‐ and penta‐phosphate.
Starvation
Miscellaneous global systems
Growth rate
Growth‐
control
supporting
property of
environment
Starvation or Stationary phase
inhibition
Energy metabolism
Presence of
Arc system
oxygen
(aerobic
respiration)
Anaerobic
Presence
respiration
of electron
acceptors
other than
oxygen
Fermentation
Absence of
usable
electron
acceptors
Table 3.6
Estimates of microbial growth rate, dormancy, and duration of dormancy and survival in nature
Habitat
Growth rate
Laboratory medium
Human intestine
Mouse
Rumen
Pond
Lake water
Ocean
Ocean
Soil
Shallow groundwater
Marine surface
sediments
Shallow subsurface
Deep subsurface
Deep marine
sediments
Organism
Doubling time (DT)
or survival time (ST)
E. coli
E. coli
Salmonella typhimurium
Heterotrophic bacteria
Heterotrophic bacteria
Heterotrophic bacteria
Heterotrophic bacteria
Autotroph, Prochlorococcus
Heterotrophs: α
Proteobacteria, rhizobia
Heterotrophs: Acidovorax,
Commamonas
Sulfate reducers
20 min DT
12 h DT
10–24 h DT
~12 h DT
2–10 h DT
10–280 h DT
20–200 h DT
~24 h DT
100 days DT
Geobacter
Heterotrophs
46 h DT
100 years DT
Sulfate reducers,
heterotrophs
200–3000 year DT
Duration of dormancy or survival
Laboratory test tube
Clostridium aceticum
endospore
Lake Vostok beneath
Dormant nitrifying
the Antarctic ice
prokaryotes
sheet
Gut of extinct bee
Heterotroph, spore‐
trapped in amber
forming Bacillus
Deeply buried clay
Dormant heterotrophs
and shale
Precambrian
Heterotroph, endospore
salt crystals
15 days DT
1 year DT
References
Koch, 1971
Koch, 1971
Brock, 1971
Brock, 1971
Brock, 1971
Brock, 1971
Jannasch, 1969
Vaulot et al., 1995
Gray and Williams,
1971
Mailloux and Fuller,
2003
Hoehler and Jorgensen,
2013
Holmes et al., 2013
Phelps et al., 1994;
Fredrickson and
Onstott, 2001
Hoehler and Jorgensen,
2013
34 years ST
Braun et al., 1981
>1.4 × 105 years ST
Sowers, 2001; Price and
Sowers, 2004
25–40 × 106 years ST
Cano and Borucki,
1995
Phelps et al., 1994;
Price and Sowers, 2004
Vreeland et al., 2000
100 × 106 years ST
250 × 106 years ST
Table 3.7
/2MnO2(s) + 1/2 HCO3− +3/2H+ + e
= 1/2MnCO3(s) + H2O
FeOOH(S) + HCO3− + 2H+ + e
= FeCO3(s) + 2H2O
+ H+ + e = 1/2CH3OH
Manganese reduction
Iron reduction
Fermentation
1
/4CO2(g) + H+ + e
= 1/8CH3COOH + 1/4H2O
=
Acetogenesis
H+ + e
+ 1/4H2O
1/
8CO2(g) +
1/ CH (g)
8
4
1/ SO 2− + 9/ H+ + e
4
8
8
= 1/8H2S(g) + 1/2H2O
1/ CH O
2
2
1
Methanogenesis
Sulfate reduction
/5 NO3− + 6/5H+ + e
= 1/10N2 + 3/5H2O
Denitrification
1
/4O2 (g) + H+ + e = 1/2H2O
1
Aerobic respiration
Process
−4.2
−4.13
−3.75
2CH2O → CH3COOH
2CH2O → CO2 + CH4
2CH2O + SO4 +
→ 2CO2 + H2S + 2H2O
2H+
 −22
 −23
 −25
 −27
 −42
CH2O + 4FeOOH + 8H+
→ CO2 + 4Fe2+ + 7H2O
−0.8
3CH2O → CO2 + CH3CH2OH
 −98
CH2O + 2MnO2 + 4H+
→ CO2 + 2Mn2+ + 3H2O
+8.9
−3.01
−119
5CH2O + 4NO3− + 4H+
→ 5CO2 + 2N2 + 7H2O
+12.65
−125
ΔG° (kJ/eq.)
CH2O + O2 → CO2 + H2O
Heterotrophic reactions
+13.75
(PE° ≈ log K)
PE regimes
Hierarchy of oxidation–reduction processes typical of carbon‐rich environments. When carbonaceous materials (CH2O) are
electron donors, individual microorganisms or consortia of populations can mediate electron transfer reactions. See also
Figures 3.10 and 3.12. (Modified from Stumm, W. and J.J. Morgan. 1996. Aquatic Chemistry: Chemical equilibria and rates in natural
waters, 3rd edn. John Wiley and Sons, Inc., New York. Reprinted with permission from John Wiley and Sons, Inc., New York)
Table 3.8
Well‐characterized chemolithotrophic and methanotrophic reactions and their respective energy
and growth yields. (Modified from Kelly, D.P. and A.P. Wood. 2013. The chemolithotrophic
prokaryotes. In: M.W. Dworkin, S. Falkow, E. Rosenberg, K.‐H. Schleifer, and E. Stackebrandt
(eds), The Prokaryotes, Vol. 2, 3rd edn, pp. 441–456. Springer‐Verlag, New York. With kind
permission of Springer Science and Business Media.)
Substrate
oxidized
Reaction
ΔG° (kJ/mol
substrate)
Estimated
number of mol
ATP synthesized/
mol substrate
H2 + 0.5O2 → H2O
5H2 + 2NO3 − + 2H+ → N2 + 6H2O
4H2 + CO2 → CH4 + 2H2O
NH4+ + 1.5O2 → NO2 − + H2O+ 2H+
NH4+ + 0.75O2 → 0.5 N2 + 1.5 H2O + H+
NH4+ + NO2− → N2 + 2 H2O
H2
H2
H2
NH4+
−237
−241
−35
−272
NH4+
−315
NH4+
−361
NH2OH + O2 → NO2− + H2O + H+
NH2OH
−288
2
NO2−
+ 0.5O2 → NO3−
H2S + 0.5O2 → S0 + H2O
NO2−
−73
1
H2S
−209
1?
S0 + 1.5O2 + H2O → H2SO4
S0
−519
1–3?
S0 + 6/5 NO3− + 2/5 H2O → SO42− + 3/5 N2 + 4/5 H+
S0
+515
S
0
−352
S0
−314
HS−
−733
1.5–4?
S2O32−
S2O32−
S4O62−
−739
−751
2.3
4–5
−1245
5
S4O62−
−1266
8–10
2+
Fe
FeS2
Cu2S
−47
−1210
−120
0.5
1?
+
+ H2O → 3 NO2− + SO42− +2H+
S0 + 6Fe + 4 H2O → HSO4− + 6Fe2+ + 7H+
HS− + 2O2 → SO42− + H+ + 7H+
S0
3 NO3−
3+
2H+
+ 2O2 + H2O →
+
5S2 O32− + 8 NO3− + H2O → 10 SO42− + 2H+ + 4N2
S2O32−
2SO42−
S4O62− + 3.5O2 + 3H2O → 4 SO42− + 6H+
5 S4O62−
+
14NO3−
+
+ 8H2O →
20 SO42−
+
16H+
+ 7N2
+ 2H + 0.5O2 → 2Fe + H2O
4FeS2 + 15O2 + 2H2O → 2Fe2(SO4)3 + 2H2SO4
Cu2S + 0.5O2 + H2SO4 → CuS + CuSO4 + H2O
(oxidation of Cu+ to Cu2+)
CuSe + 0.5O2 + H2SO4 → CuSO4 + Se0 + H2O
(oxidation of selenide to selenium)
CH4 + 2O2 → CO2 + 2H2O
CH4 + 4MnO2 + 7H+ → HCO3‐ + 4Mn2+ + 5H2O
CH4 + 8/3 NO2− + 8/3H+ → CO2 + 4/3N2 + 10/3H2O
CuSe
−124
CH4
CH4
CH4
−871
−556
−309
CH4 + 8Fe(OH)3 + 15H+ → HCO3‐ + 8Fe2+ + 21H2O
CH4
−270
CH4 + 8/5 NO3− + 8/5H+ → CO2 + 4/5N2 +14/5H2O
CH4
CH4 + SO42− → HCO3− + H2S− + H2O
CH4
2Fe2+
3+
2–3
<0.25?
1 or 2
1?
−153
−20 to −40
0.5?