Microbial occurrence and

activities in the
environment
Carbon turnover in the environment (a)
Carbon turnover in the environment (b)
 Static aquatic ecosystems (a)
Surface:
cianobacteria and
algae
Deeper: anaerobic
(phototrophic)
bacteria

Lakes, Lagoons. etc

Overall
activities/microbial
mediated processes
change with:
•light availability
•O2 availability
•Temperature
•Osmotic pressure
•Etc.
Static aquatic ecosystems (b)
Static aquatic ecosystems (c)
Static aquatic ecosystems (d)
Dynamic aquatic ecosystems (a)
Dynamic aquatic ecosystems (b)
Terrestrial ecosystems
Microbial metabolisms of
biogenic compounds in
the environment
Microbial metabolism: sources of energy and of carbon

Sources of
energy

e- e-

Sources of Carbon: CO2, autotrophy; organic compounds, etherotrophy

 Metabolism of organic matter, used as carbon
and energy sources

Electron donor

(Carbon)

CO2
Electron acceptor

Fermentation: anaerobic processes by which some defined organic

compounds are partially oxydized with the production of electrons that are
used by intracellular intermediates of the process with the production of
reduced compounds, which are excreted by the cells as final product of the
fermentation.
 Metabolism of organic matter: catabolic and
anabolic pathways
Biogenic Cellular
compounds constituents
Polysaccharides
Polysaccharides
Proteins,
Proteins
Lipids,
Lipids
DNA, RNA

Chemical
Catabolism energy Anabolism
(esoergonic)
Esoergonico (endoergonic)
Endoergonico

NADH
Oxidized FADH2 Partially oxydized
chemicals chemicals
Simple and
oxydized Monosaccharides,
organic aminoacids, fatty
compounds acids, nitrogen
bases, etc
Metabolism: free energy carriers

kcal/mol

-14.8

-7.3
-7.3

-3.4
-3.3
Aerobic Respiration
Main steps of aerobic respiration of biogenic compounds
Occuring in aerobic:
1. Bacteria and
actinomycetes;
2. Yeasts, fungi, protozoi
algae;

Electron donor: biogenic

organic compounds;
Source of C: biogenic
organic compounds
Electron acceptor : O2
ATP production:
substrate
phosphorilation+
Carbon oxidative
phosphorylation
Energy
 Aerobic respiration: basic Glycolysis (a)
It occurs in the cytoplam and consists of two phases: i.e., the
“preparatory phase” and the “energy recovery phase”, 5 steps each.

1 Glucose  2 Pyruvic acid +

2 NADH+H+
+ 2ATP
 Aerobic respiration: basic Glycolysis (b)
Maltose
Maltase

amilases
Aerobic Respiration: Pyruvic acid oxidation (Krebs cycle)

In Eukaryotic cells it occurs in

the mitocondrium which has a
double membranes; the
internal one is impermeable to
H+. In Prokaryotic cells it takes
place at the level of the internal
part of the cytoplasmic
membrane, also impermeable
to H+.

2 Pyruvic acid 
6 CO2 + 8 NADH + 8 H+
+ 2 FADH2
+ 2 ATP
Aerobic Respiration: Krebs cycle as an amphibolic route
Aerobic Respiration: oxydative Phosphorylation (a)

NADH+H+/ NADPH+H+
FADH2

HH 2H+ + 2e-
Aerobic Respiration: oxydative Phosphorylation (b)
 Aerobic Respiration: oxydative Phosphorylation (c)
NADH+H+/ NADPH+H+

FADH2
H+
ATP
G°= -n F E° (E°=1.14 V)

e- ATP
G°= 52,6 kcal/mol
7ATP2.5 ATP.
e- 1.5 ATP when the 2H come
from FADH2 and are released
to Quinone.
ATP
e-

4H+
2 H O
 Aerobic Respiration: overall energy balance
Basic Glycolysis  2ATP + 2NADH/H+
AcCoA production and Krebs Cycle  2ATP + 8NADH/H+ + 2
FADH2
Considering that 1 NADH/H+ corresponds at 2.5 ATP and that 1 FADH2
corresponds to 1.5 ATP, the complete oxydation of 1 mole of Glucose results
in the production of 32 ATP, i.e., at under the standard conditions, of -233.6
kcal/mol.
The oxydation of 1 mole of Glucose via chimical-physical pathways
produces, under standard conditions, 686 kcal/mole; thus, the cell
apparentely recovers about 30% of the overall Energy obtainable from by
the Glucose. The energy not accumulated by the cell is released as heat.
Under real conditions, the cell recovers over than 60% of the energy
theoretically obtainable from one mole of glucose.
The overall arobic respiration is controlled at the glycolysis and Krebs cycle
level by the concentration of energy indicators, like ATP and ADP, but also of
key intermediate of the Krebs cycle, precursors of anabolic pathways
starting from Krebs intermediates.
Aerobic Respiration: hydrocarbons as substrates (a)
In several aerobic Gram– and
Gram+ bacteria and in yeasts

Electron Donors:
hydrocarbons
Carbon source:
hydrocarbons
Electron acceptor:
O2
ATP production:
oxidative
phosphorylation

TCC
Aerobic Respiration: hydrocarbons as substrates (b)
In several aerobic Gram– e Gram+
bacteria

é donors and Carbon

sources : hydrocarbons
é acceptor: O2
ATP production:
oxidative
TCC phosphorylation
Aerobic Respiration: hydrocarbons as substrates (c)

TCC
Aerobic Respiration: Gram- bacteria that use it (a)
(Rods)
 Aerobic Respiration: Gram- bacteria that use it (b)
(Cocci)

Aerobic Respiration: Gram+ bacteria that use it (a)

(Cocci)
(Cocci)
Aerobic Respiration: Gram+ bacteria that use it (b)
 Aerobic Respiration: Gram+ bacteria that use it (a)

Further, “respire aerobically ” biogenic organic matter also yeasts, fungi,

protozoi and several autotrophic mixotrophes
Anaerobic Respiration
Anaerobic Respiration of biogenic compounds (a)
The organic compounds occurring in
anaerobic habitats can act as source
of energy and carbon for local
microorganisms. They are oxidized
through pathways identical or different
from those typical of aerobic
respiration but the electrons are in this
case used by inorganic or organic
electron acceptors imported by the cell
from the local environment. The
reduced products are then excreted.
Anaerobic respiration is mainly
adopted by bacteria, which are the
most prominent microbes in the
anaerobic environment.
The anaerobic respiration is less
esoergonic than the aerobic
respiration.
 Anaerobic Respiration of biogenic compounds (b)
Electron
donor

Carbon for
the
anabolism

Energy

Electron
acceptor
Anaerobic Respiration: Nitrate-reduction (denitrification)
By Gram– anaerobic and aerobic bacteria, often form the genera
Pseudomonas, Alcaligenes, Ralstonia, etc.
Inhibited by O2 Electron donor :
organic compouds
(processed as
indicated for the
aerobic respiration)
Source of C: same
organic comounds
Electron acceptor:
NO3- (O2)
ATP Production: as
mentioned for the
aerobic respiration
NADH Production :
from C oxidation
 Anaerobic Respiration: Sulfate-reduction (a)
By Gram– anaerobic bacteria able normally tolerating oxygen. Group I: not
oxydizing acetate (i.e., Desulfovibrio, Desulfomonas, Desulfotomaculum -
sporigen-, etc.); Group II: oxydizing acetate, H2 (i.e.,
Desulfobacter,Desulfococcus,Desulfonema -G+- etc).

Electon donors : organic

acids (acetate, Grup II), fatty
acids, alchools, H2 (litotrophy)
C sources: organic
compounds listed above;
CO2(autotrophy)
Electron aceptors: SO4= (S,
Desulforomonas)
ATP production: transport of
e-, protonic gradient

NADH production:
Oxidation of organic
compounds or H2.
 Anaerobic Respiration: Sulfate-reduction (b)
Chemiolitotrophy Electron donors
(Type II)
Organotrophy (Type I)

Alcohols, Organic
acids, Fatty acids:
Krebs cycle (Type
I)
NADH/NAPDH+H+
Anaerobic Respiration: Sulfate-reduction (c)

Acetate (modified
Krebs cycle) (Type
II)
NADH/NAPDH+H+
Anaerobic Respiration: Sulfate-reduction (d)

AcCoA cycle as a
mechanism for the
a) acetate oxydation
(pathway indicated
by the blue arrows in
the scheme) (Type
II)
and/or
b) The preparation
of cell constituents
from CO2 (Type II)

Anabolic
pathways
 Anaerobic
Respiration:
main sulfate-
reducing
bacteria (a)
In addition, there
are the So
reducing bacteria:
Desulfuromonas sp.
Desulfurella sp.
Sulfurospirillum sp.
Campylobacter sp.

All of them are

anaerobic non
spore-forming
mesophilic Gram-
bacteria.
Desulfurella is a
thermophilic
bacterium
 Anaerobic
Respiration: main
sulfate-reducing
bacteria (b)
Desulfovibrio sp. Desulfonema sp.

Desulfobulbus sp. Desulfobacter sp.

Desulforosarcina sp. Desulforomonas sp.

 Anaerobic Respiration: acetogenesis, methanogenesis
Acetogenic bacteria: Gram– (Acetobacterium, etc.) or Gram+ (Clostridium),
obligate anaerobic. Methanogenic bacteria: Archea (Gram +/-), cocci and
rods, 7 groups: Methanobacterium, Methanothermus, Methanococcus,
Methanosarcina, Methanopyrus, Methanocorpusculum, obligate anaerobic.
e- donors: sugars
e- donors: methylated (glycolysis + acetate
compounds, acetate, H2 reduction), acetate (via
C sources: organic reversed AcCoA), H2
compounds; CO2 C source: organic
(biosynthesis via AcCoA) compounds; CO 2
e- acceptors: CO2 (biosynthesis via AcCoA)

ATP production: e- aceptor:CO2;

e- trasfer pyruvate
ATP production: e-
transfer
 Anaerobic Respiration: methanogenesis (a)

Production of energy from H2 and

CO2.
Cell constituents are produced
from H2 and CO2 via the AcCoA
cycle (up to Acetyl -CoA as
displayed before).
Anaerobic Respiration: methanogenesis (b)
Anaerobic Respiration: main methanogenic bacteria (a)
Anaerobic Respiration: main methanogenic bacteria (b)

Methanobacterium sp. (autoflorescenza da F420) Methanosarcina sp. (autoflorescenza da F420)

Methanobrevibacterium sp. Methanobacterium sp. Methanospirillum sp. Methanosarcina sp.

 Respiration of biogenic compounds: summary
Electron
donor

Carbon for
the
anabolism

Energy

Electron
acceptor
Anaerobic Respiration in estuarine sediments
Fermentation
Main fermentation pathways for biogenic compounds (a)
Main fermentation pathways for biogenic compounds(b)
Glycolysis

By anaerobic Gram+ and

Gram- bacteria, but also by
facultative anaerobic yeasts.

e- donor : sugars (with

glycolysis), organic acids
C sources: the same
compounds above
e- acceptors: intermediates
of the substrate metabolism
ATP production : substrate
phosphorylation
NADH production:
Substrate oxidation.
Clostridia:key biogenic compounds fermenting bacteria

Gram+, strictly anaerobic bacteria with rod shaped, spore forming cells.
Some are fermenting sugars towards acids and alcohols, other hydrolyzing
cellulose by fermenting glucose to ethanol, other are fermenting proteins
and aminoacids. Other are fixing N2. Rarely they are displaying more than
one of such abilities. Some are pathogens for humans and animals, such as
C. tetani, C. botulinum and C. perfringens.
Production of acids & alcohols from sugars

Fermentation aceton-
butylic by Clostridia.
In the first phase are
mainly produced acetic
and butyric acids (ratio
1:3); then, with the
medium acidification,
the production of
alcohols is becoming
prominent.
The production of
acids continues if the
pH of the medium is
controlled.
Main Clostridia fermenting bacteria
Anaerobic respiration & fermentation of organic matter(a)

In sediments, in the deep

portions of soils or landfills
fed with organic mater, in
the intestinal tracts, in
anaerobic digestors, etc.
(Acidogenesis)

(Acetogenesis)

SO4=

SO4=-reduction
(Methanogenesis)

S=
Anaerobic respiration & fermentation of organic matter(b)

Under standard
conditions (1 M, 1
atm)
Under real
conditions
Aerobic Respiration of
inorganic compounds
(Aerobic
Chemiolitotrophy)
Aerobic Respiration of biogenic inorganic compounds

Energy source C source

(electron source)
Organic compounds

Heterotrophy
Autotrophy
(Mixotrophy)

Fe3+
(obligated /facoltative)

Oxygen is the final electron acceptor

Aerobic Respiration of inorganics: electron donors

G°= -n F E°
Aerobic Respiration of inorganics: CO2 assimilation
by Calvin Cycle

(1)
(1) (2)

(3)

(2)

(3)
 Hydrogen-oxidizing chemolitotrophs
They are facultative chemotrophs, mixotrophs and strictly aerobic. The Calvin
cycle and their hydrogenases are inhibited by the presence of organic substrates
Aerobic Respiration of inorganics: electron donors

G°= -n F E°
H2 oxidation in Ralstonia eutropha

e- donors: H2, organic

substrates
C sources: CO2, CO
e- acceptors: O2
ATP production:
oxidative
phosphorylation +
substrate
phosphorylation
(under mixotrophy)
NADH is then NADH production:
converted into from oxidation of H2
NADPH requited or via the oxidation of
by the Calvin cycle organic substrates
(mixotrophy)
Aerobic Respiration of inorganics: electron donors

G°= -n F E°
 So and H2S-oxidizing chemolitotrophs (a)
Sulfobacteria: Gram- aerobic, strictly litotrophs. Sometimes mixotrophs.
They prefer acid pHs. Examples: Thiobacillus, Sulfolobus, Bacillus, etc.

e- donors : S, S=,
S2O3=
C sources: CO2;
organic compounds
e- acceptor: oxygen
ATP production:
oxidative
phosphorylation +
substrate
phosphorylation (in
mixotroph)
NADH production:
reverse e- transport

Decrease of pH!
 So and H2S-oxidizing chemolitotrophs (b)
Cell constituents are prepared from CO2 via the Calvin cycle. NADPH is
prepared via the reverse transport of electrons.

E0 -0.32 V
E0 -0.22 V
E0 +0.022 V E0 +0.82 V
 So, H2S and S2O3=-
oxidizing chemolitotrophs
Solfolobus: archaeabacterium
The others are Eubacteria, Gram-, with rod
shaped flagelled cells.
Aerobic Respiration of inorganics: electron donors

G°= -n F E°
 Fe2+-oxidizing chemolitotrophs (a)
Gram-, aerobic, strictly litotrophs.
Sometimes mixotrophs
Examples: Thiobacillus ferrooxidans,
Solfolobus (thermophilic archea)
e—donors: Fe++ (Fe+++ precipites as
hydroxyde)
C sources: CO2 (via Calvin
cycle)/organic compounds
e- acceptor: oxygen
ATP production: natural H+ gradient
+ oxidative phosphorylation
NADH production: reverse e- trasf.
Fe2+-oxidizing chemolitotrophs (b)
Fe++ is bioavailable only
under anaerobic or acid
environments. Due to this,
several Fe++ bacteria also
oxidize S to create the
required acidity (pH 2).
Thiobacillus ferrooxidans
exploits the H+ gradient
due to acid environment to
produce ATP. Extracellular
Fe++ is oxidized to
generate e- that then
neutralize intracellular H+.
Bacteria working at pH 7
cannot account on the
natural H+ gradient nor on
a high Fe++ availability.
Thus, they produce a little
energy.
Metals Bioleaching

Calcocite
Covellite
bacterial
oxidation (direct
role)
Bacterial
oxidation
(indirect role)
 NH3/NH4+-oxidizing chemolitotrophs (a)
NH4-oxidants & NO2-oxidants: Gram-, aerobic, strictly litotrophs. Also
mixotrophs. Exs.: Nitrosomonas, Nitrosococcus & Nitrobacter, Nitrococcus.

∆E° -275kJ/mole
∆E° -76kJ/mole, 1 ATP

Cell constituents are prepared via

Calvin cycle; NADH is produced via
reverse transfer of electrons.
NH3/NH4+-oxidizing chemolitotrophs (b)
Phothotropy
 Photosynthetic organisms and phototrophy
Prokaryotic microorganisms (bacteria) and uni and pluricellular eukaryotic
organisms (algae, plants).

Calvin
cycle