MICROBIAL PROCESSES CONTRIBUTING

TO BIOGEOCHEMICAL CYCLES
Dr. Gede Suantika
 Introduction
Biogeochemistry 
Atmospheric
the scientific discipline that Science Geo
involves the study of
Oceanography Micro
the chemical, physical,
biology
geological,and biological
processes and reactions that
govern the composition of the Chemical
Geology
Element
natural environment
Biogeochemistry
Geomicrobiology 
the study of microorganisms
Environmental
Soil Science
as influenced by the geologic Science

environment and geochemical

processes
Biology Ecology
 Introduction
Microorganisms have considerable influence on the biogeochemical cycling of
elements in both aerobic and anaerobic environments
 Energy Flow
• All life forms, including microorganisms, require energy to
grow and the processing of energy from surrounding
environment  follows the laws of thermodynamics, ∆G
(free energy)
• Enegry-yielding reactions consist :
– Enzymes involved in catalyzing the oxidation a substrate
– Enzymes that participating in the reduction of different
substrate
With hundreds of
possible substrates as
electron donors and
hundreds of possible
electron acceptors,
there is tremendous
potential for interactions
of nutrients from different
biogeochemical process
 Oxygen and Carbon Cycling
• Large numbers of
microorganisms interface with
the oxygen cycle through
redox reactions
• There is an interconnection
between the oxygen and
carbon cycle because oxygen
reserves are found in organic
compound and CO2
 Microbial Metabolism of Carbon under
Aerobic and Anaerobic Conditions
• New organic compounds are
biologically synthesized only by
CO2 fixation by phototrophs and
chemolithotrophs

• Most organic compounds originate

in photosynthesis and thus
phototrophic organisms are the
foundation of the carbon cycle

• Anoxygenic phototrophs and

chemolithotrophs also produce
excess organic compounds, but in
most environments the
contributions of these organisms to
the accumulation of organic matter
are trivial compared to that of
oxygenic phototrophs
 Nitrogen Cycling

Blue green algae

in the oceans

Organism Nitrogen Denitrifying bacteria in

proteins fixing bacteria Nitrate taken up Plant and animal Dead organisms
boggy soil
in soil and by plant roots proteins and faeces
root nodule
Artificial inorganic Ammonium salts
Dead organisms fertilizer
and faeces
Soil Nitrifying bacteria

Lost in marine
nitrate
sediment

Microorganisms require nitrogen to make up 10% of their cellular

composition  considerable influence on the nitrogen cycle
 Nitrogen Fixation
One important aspect of the
nitrogen cycle is biological
nitrogen fixation  the
conversion of atmospheric N2
to ammonia by prokaryotes
Exp : Azotobacter,
Cyanobacter, Rhizobium,
Bradyrhizobium, Frankia
etc.
Nitrification and Denitrification
 Nitrogen Assimilation

• After N2 is fixed  most

microorganisms can readily
assimilate NH3 and nitrate
into amino acids and other
organic compounds
(immobilization)

• Mineralization  the
release of NH3 from
organic nitrogen
compounds that is
attributed to enzymatic
deamination reactions
 Sulfur Cycling
Sulfur  an element with multiple oxidation state
 Phosphorus Cycling
• Phosphorus is essential
for microbial systems
beacuse it is a required
component for sugar
phosphates, DNA, RNA,
and high energy molecule
(ATP)

• Phosphonate and
organophosphate esters
are common source for
phosphat in the
environment
 Iron Cycling
• Iron is the fourth most
abundant element in
Earth’s crust
• Most biological systems
can catalyze the redox
reactions of iron functions
as Fe3+/Fe2+ in
cytochrome
• Iron is also used by
microbial systems for
various other activities
 Siderophores
• Siderophores  relatively
low molecular weight,
ferric ion specific chelating
agents elaborated by
bacteria and fungi growing
under low iron stress

• Each microbial species

has its own unique Fe3+-
chelating molecular
structures

Siderophore in Gram-negative bacteria

 Ferritin and Magnetosomes
• Acquisition of iron by
microorganisms must be tightly
regulated to prevent
overaccumulation of soluble iron
in cytoplasma  Fe2+ will be
detrimental if it react with H2O2
that produce free radical (HO•)

• Ferritin  consists of protein

plus several thousand atoms of
ionic iron
• Magnetosomes  membranous
structure which contains various
iron substances (magnetite,
greigite, FeS, etc)
Magnetosomes in Aquaspirillum magnetotacticum
 Cycling of Manganese
• Some chemolithotrophic bacteria can obtain
energy fro the reduction of Mn4+ to Mn2+ of
from oxidation of Mn2+ to Mn4+
• Three different activities :
– oxidation of soluble manganese  is
attributed to enzymes produced by
Leptothrix, Pseudomonas, Citrobacter,
Bacillus, Arthrobacter, and Hypomicrobium
– oxidation of immobilized manganese 
the enzyme associated with this activity is
considered to be at the surface of the cell,
including Vibrio, Arthrobacter,
Oceanospirillum
– production of hydrogen peroxide
resulting in oxidation manganese  such
as Geobacter and Swanella
 Cycling of Selenium
• Selenium is similar to sulfur
 oxidation state ranging
from -2 to +6
• Selenium is required by
microorganisms at relatively
low levels for the formation of
selenomethionine (Se2+),
where selenium replaces
sulfur in methionine
• Selenomethionine  Figure 10.18. Global selenium cycle with microbial
interactions. Solid lines indicate reduction;
require for dehydrogenase dashed lines, oxidation; dotted lines, no change in
enzymatic activity in some oxidation state of Se. Microorganisms of
bacteria various genera are associated with the reactions
shown in the diagram.
 Cycling of Hydrogen
• The role of hydrogen in microbial systems is important  the
principal reservoir for hydrogen is water, yielding proton plus a
hydroxyl ion
• Proton are used by cell to generate ATP synthesis, flagellar
movement, nutrient uptake, and solute export
• Hydrogen cycle also occurs in :
– photosynthetic activity (convert into sugar and sugar to energy)
– anaerobic heterotrophic bacteria (produce H2 which is done by
hydrogenase)
– Methanogen that used H2 to generate methane
 Transformation of Mercury
• One of the most toxic metal is mercury, and microorganisms have
unique processes that enable cells to grow in mercury-contaminated
environment
• Various Gram-positive and Gram-negative bacteria are capable of
reducing Hg2+ to elemental mercury (Hg0) using mer operon
Thank You 