Fundamentals of Microbiology

EVA VLKOVÁ
FANFR ground floor 29
(consulting hours: Tuesday 1 -3 p.m.)
or lab 2 nd floor 230
vlkova@af.czu.cz
Fundamentals of Microbiology

12 lectures, FANFR 220

EXAM:
 written report on selected
microbiological theme
 10 minutes presentation on 5 th
January 2012
 written test
 Literature to study

 Prescott et al.: Microbiology, Wm. C.

Brown Publishers, 1996
 any other textbook of fundamentals of
microbiology or general microbiology
 http://kmvd.agrobiologie.cz/index.php?obsah
=skripta
 Lectures topics

1. Introduction, history of microbiology

2. Viruses
3. Bacteria, prokaryotic cell structure and function
4. Fungi, eukaryotic cell structure and function
5. Microbial nutrition and growth
6. Control of microorganisms by physical and chemical agents
7. Metabolism and enzymes
8. Generation of energy, respiration
9. Fermentations, catabolism of carbohydrates and polymers,
carbon cycle
10. Lipid and protein catabolism, biosynthesis
11. Nitrogen, phosphorus, and sulphur cycles
12. Microbial genetic
 Written report

 5 – 10 pages
 literature overview
 minimum 5 literature sources (textbooks, research
papers, http://portal.isiknowledge.com,
http://portal.isiknowledge.com)

Content:
 introduction
 main part
 conclusions
 list of references
 (enclosures)
 Fundamentals of Microbiology

24 hours of laboratory exercises

FA N F R 2 2 0

C R E D I T:
 2 written protocols on chosen laboratory
t r a i n i n g t h e m e ( e . g . AT B t e s t , i d e n t i f i c a t i o n o f
b a c t e r i a , w a t e r e x a m i n a t i o n ) , t i l l 1 5 th
D e c e m b e r 2 0 11 ( c o n t e n t : p r i n c i p l e ,
m e t h o d o l o g y, r e s u l t s , c o n c l u s i o n s )
 attendance on trainings
 Microbiology

 is defined as the science studying organisms or agents

which cannot be seen by eye and must be examined by
microscope (objects less than about 1 mm)
 its subjects are viruses, bacteria, many algae and fungi,
and protozoa
 can be divided into virology, bacteriology, algeology,
mycology etc.
 or on general, systematic, applied microbiology
 Microorganisms

 are necessary for the production of bread,

cheese, beer, antibiotics, vaccines, vitamins,
enzymes...
 they make possible the cycles of carbon,
oxygen, nitrogen, sulphur....
 they also caused many diseases
 History of Microbiology

Fracastorius
 medical doctor
 1546 – declared, that
small nonvisible
organisms exist and
are responsible for
diseases
 History of Microbiology

1665 – 1670 – microbiology as a science starts

 construction of first microscopes by Robert
Hooke and Antony van Leeuwenhoek –
described cocci and rods, blood cells and protozoa
 Louis Pasteur (1822-1895)

 discovered fermentations
 discovered anaerobic life
 sterilization,
pasteuratization
 vaccination (smallpox)
 isolation and identification
of causers of some
infection diseases
Robert Koch (1843-1910)

 solidifying of liquid cultivation

media (gelatine, agar)
 construction of Petri dish
 new cultivation media
 colouring of bacteria by
aniline colours
 isolation and identification of
causers of cholera, anthrax
and tuberculosis
 Koch‘s postulates

 the microorganism must be present in all ill

objects and absent in all healthy objects
 the causer of disease must be isolated and
grown in pure culture
 when the isolated microorganism is inoculated
into healthy host, the same disease will
developed
 the same microorganism must be isolated
again from the host
Some important historical facts

1786 – Muller – first classification of microorganisms

1867 – Lister – antiseptic surgery
1884 – Metchnikoff – phagocytosis
1884 – Gram – Gram colouring
1892 – Ivanowsky – viruses
1907 – Metchnikoff – probiotics
1923 – first edition of Bergey‘s manual
1928 – Fleming – penicillin
1937 – procaryotes x eucaryotes
1953 – Watson and Crick – structure of DNA
1983 – HIV identification
1984 – PCR
 Five kingdom system

1. MONERA = PROCARYOTAE
SUBCELLULATA – Vira – viruses
PROTOCELLULATA – Bacteria – bacteria
Cyanophyta – cyanophytes
2. PROTISTA – eucaryotic cell
- algae, protozoa, some simple fungi
3. FUNGI – fungi and mashrooms
4. PLANTAE – plants
5. ANIMALIA – animals
 Main differences between microorganisms

criterion viruses bacteria fungi protozoa

cell type no procaryotic eucaryotic eucaryotic
cell wall no yes yes no
size 20-400 nm 1-2 (10) μm 5-10 μm 50-300 μm
 Differences between procaryotic and
eucaryotic cell
procaryotic eucaryotic
criterion
cell cell

nucleus
- +
membrane

size usually
- +
>2 μm

mitochondria - +

endoplasmic
- +
reticulum (ER)
free in
placing of
cytoplasmic on ER
ribosomes
matrix
chromosomes circular linear
Viruses
 General properties of viruses

 simple acellular organization

 virion = complete virus particle
 one or more molecules of DNA or RNA (absence of both in
the same virion)
 enclosed in protein capside, sometimes other layers
(carbohydrates, lipids, additional proteins)
 exist in two phases: extracellular and intracellular
 obligatory intracellular parasites (intracellular phase,
replicating nucleic acid, induce host metabolism to
synthesize virion components)
 inability to reproduce independently on the host cells
 few or no enzymes (extracellular phase)
 without own metabolism
 Virion

 size: 10 – 300 (400) nm

 nucleic acid in central part
 DNA or RNA, single- or double-stranded, linear or circular
 capsid = protein coat composed from capsomers
 morphological types of capsides: helical and icosahedral
Virion structure
Size and morphology of viruses
 Virus taxonomy

 lack of knowledge of viruses origin and

evolution
 viruses are separated into large groups
based on their host preferences: animal and
plant viruses, bacteriophages
 divided into 73 families by:
a) nucleic acid type
b) nucleic acid strandedness
c) presence or absence of an envelope
Bacteriophage structure
Bacteriophage adsorption
Animal virus entry into the host cell
Lysogenic and lytic cycle of bacteriophage
Lytic cycle of bacteriophage
Bacteria
 Differences between procaryotic and
eucaryotic cell
procaryotic eucaryotic
criterion
cell cell

cell wall - +

size usually
- +
>2 μm

mitochondria - +

endoplasmic
- +
reticulum (ER)
free in
placing of
cytoplasmic on ER
ribosomes
matrix
chromosomes circular linear
 Bacterial size and shape

cocci – roughly spherical cells, 1 μm

rods (bacilli) – rod shape, 1 x 2-4 (10) μm
actinomycetes – filamentous bacteria, filaments
are 1 μm width and several mm long
Morphology of bactrerial cell
G+ cell wall structure
G- cell wall structure
 Glycocalyx

o adherence, enzyme storage

o polysaccharides filaments

bacterial cell
 Pili and Fimbriae

o attachment to surfaces
o sex-pili – conjugation
o protein filaments
 Flagella

o movement, antigens
o proteins (flagellin)
o monotricha
o lofotricha
o amfitricha
o peritricha
 Plasma membrane

o contain proteins and phospholipids

o lipids forms bilayer, hydrophilic x hydrophobic ends
o thin structure, thick 5-10 nm
o peripheral x integral proteins
o selectively permeable barrier
o nutrient and water transport
o metabolic processes
 Nutrient transport

o main role play cell wall and plasma membrane

Passive (simple) diffusion
o concentration gradient
o no energy consumption
o ions, glycerol, O2, CO2
Osmosis
 Facilitated diffusion

o carriers proteins – permeases

o by concentration gradient
o no energy use
o limited in procaryotes, typical for eucaryotes
 Active transport

o against concentration gradient

o use of energy
o membrane proteins
 Group translocation

o against concentration
gradient
o use of energy
o membrane proteins
o molecules are modified
during the transport
o typical for eucaryotes
 Mesosome

o internal membrane system

o invagination of plasma
membrane
o function is unknown
o involved in cell wall
formation during division
o chromosome replication
o energy metabolism
o artefacts generated during
the fixation for electron
microscopy
 Cytoplasmic matrix

o protoplast
o inclusion bodies
o granules
o enzymes
o ribosomes
(synthesizing
proteins)
o nucleoid (DNA
and associated
proteins)
 Nucleoid

o one circle chromosome

o single- or double-stranded DNA
o about 3 500 genes
o no membrane
o enzymes
DNA replication
 Plasmids

o circle double-stranded DNA

o can exist and replicate independently of the
chromosome or may be integrated with it
o are not required, genes that give advatages
 Ribosomes

o protein synthesis
o rRNA, mRNA, tRNA
o proteins
 Endospores

o resistant dormant structure

o no reproduction
o Clostridium, Bacillus
o viable for over 500 years
o multilayered (central core,
membrane, cortex, coat,
exosporium)
o low water content,
metabolism and ribosome
number reduction
 Bacteria identification

Classification = arrangement of organisms into

groups or taxa
Identification – process of determining that a
particular isolate belongs to recognized taxon
Nomenclature – names for taxonomic groups
Basic taxon = species (binomial system)
Species = set of cells with the same
characteristics
Strain = set of cells which grew from one cell

Classification systems:
 phylogenetic
 numerical taxonomy
 phenetic
 An example of taxonomic ranks and names

Rank Example
Kingdom Procaryotae
Phytum Actinobacteria
Class Actinobacteria
Order Bifidobacteridae
Family Bifidobacteriales
Genus Bifidobacterium
Species Bifidobacterium animalis
Subspecies Bifidobacterium animalis ssp. lactis
 Morphological characteristics

o cell shape
o cell size
o staining behavior
o cilia and flagella
o endospore shape and location
Cultivation characteristics

o morphology of colonies
o colour of colonies
o growth in liquid media
 Physiological characteristics

o growth temperature optimum and range

o osmotic tolerance
o oxygen relationships
o pH optimum and growth rang
o salt requirements and tolerance
o sensitivity to metabolic inhibitors and antibiotics
 Metabolic characteristics

o carbon and nitrogen sources

o energy sources
o fermentation products
o mechanisms of energy conversion
o secondary metabolites formed
o storage inclusions
 Molecular characteristics

o comparison of proteins
o nucleic acid base composition – G+C content
o nucleid acid hybridization
o nucleic acid sequencing
o polymerase chain reaction
Micromycetes

Yeasts and Moulds

Micromycetes - introduction

 eucaryotic, filamentous or holocarpic

 haploid, except zygotes
 hyphae with or without cross walls
(septa)
 diameter of hyphae 5-10 μm, length from
μm to hundreds mm
 mycelium – network of hyphae
 cell wall with chitin or cellulose
 mono-, di-, polycaryotic structure
 Kingdom: Mycota (Fungi)

Division: Eumycota (True fungi)

Subdivision: Zygomycotina
Genus: Mucor, Rhizopus
Subdivision: Ascomycotina
Genus: Aspergillus, Penicillium,
Saccharomyces
Subdivision: Deuteromycotina
(Fungi imperfecti)
Genus: Candida, Monilia
Micromycetes

Yeasts and Moulds

Scheme of yeast cell
Life cycle of yeast
Saccharomyces
cerevisiae

Reproduction of
yeasts:
 buding(vegetative)
 ascospores
(sexual spores)
Cell-division cycle in a
yeast Saccharomyces
cerevisiae
Buding and Pseudomycelia
 Important yeast genera

Saccharomyces – ethanol fermentation, vitamin

production, bakery yeasts, food spoilage
(honey, jam, ketchup)
Kluyveromyces – milk products (kefir), feed
mixtures, spoilage of cheeses
Candida – some are pathogenic, food spoilage
(beer, milk products, meet, vegetable), feed
mixtures, cocoa bean fermentation
Torulopsis – feed mixtures
 Methylene blue staining

 this method distinguish live (colourless)

and dead (coloured) cell
 Saccharomyces cerevisiae
 a drop of yeast is placed in the centre of
a slide
 one drop of methylene blue is added
 cover glass
 examine with dry objectives (10x, 45x)
 Moulds
Nonseptated hyphae Septated hyphae

Fructification organs
Sporangiophore
Connidiophore
 Reproduction of Moulds

 Vegetative – disintegration of mycelium

 Sexual spores – zygospores, ascospores
 Asexual spores – fructification organs
- sporangiophore
- conidiophore
Asexual spores of moulds

Mucor Penicillium
 Zygomycota

 nonseptated mycelia
 sexual zygospres, asexual
sporangiospores
 saprophytic
 soil, fruits, food spoilage,
decomposition of
polysaccharides (pectin)
 Rhizopus, Mucor
Life cycle of Zygomycota
 Ascomycota

 sexual ascospores,
asexual conidiospores
 moulds with septated
mycelia
 sporogenic yeasts
 Penicillium, Aspergillus,
Candida, Saccharomyces
Life cycle of Ascomycota
Deuteromycota (Fungi imperfecti)

 conidial stages of Ascomycota

 sexual reproduction has not been
primarily observed
 two names for one genera – one
genera placed into both groups
Ascomycota and Deuteromycota
 food spoilage, plant pathogens,
decomposition of organic matter
Penicilin – antibiotic, P. notatum, Sir Alexander
Flemming 1929
P. expansum – patulin
P. roquefortii and P. camembertii
P. marneffei – pathogenic for immunodeficient people
 soil, decomposition of organic matter
 food spoilage – bread, vegetable
Aspergilus flavus 1961 – aflatoxins
(mycotoxins)
food spoilage – vegetable, meat,
dried meat, crops, jams
production of enzymes (amylases,
lipases and pectinases),
soya sauce
Asp. niger – production of citric acid
Blacks, wet walls of
food factories
Tokay wines
vegetable pathogen
Microbial nutrition requirements

Bacterial cell composition

Elements: C 50%, N 8%, H 8%, O 30%, P 3%, S 1%, K, Mg, Ca, Na,
Cl (all 0,4%), Fe, Cu, Mn, Co, I, F, Zn
Matter: water 80%, dry matter 20% (proteins 60%, DNA 3%, RNA
16%, polysaccharides 3%, lipids 15%, other compounds 3%)

Requirements
 macroelements: C, N, H, O, S, P, K, Ca, Mg, Fe
 microelements: Mn, Zn, Co, Mo, Cu, ......
 biosynthesis and source of energy (chemothrophs)
Carbon, Hydrogen and Oxygen

 often satisfied together

 the skeleton of organic molecules (saccharides,
peptides, lipids)
 CO2 or organic carbon (source of energy, are
reduced and donate electrons to other molecules
 saprophytes
 parasites
 Nitrogen

 amino acids, proteins, enzymes, purines,

pyrimidines (DNA, RNA)
 organic – amino acids, peptides (pepton, trypton,
yeast extract)
 inorganic – NH4+, NO3, N2 (reduction to NH4+)
 Phosphorus

 nucleic acids, phospholipids, ATP, ......

 inorganic – soluble forms of phosphate (H2PO4-,
HPO42-, PO43-)
 organic – phosphatase, nucleic acids, phospholipids
 Sulphur

 amino acids (methionine, cysteine)

 vitamins (biotin, thiamin)
 inorganic – usually preferable, SO42-
 organic – S amino acids
 Microbial growth

 usually the growth of microbial population

is studied, not the growth of individual cell
 changes in the population during
cultivation time describes growth curve
 batch and continual cultivation
 in bacteria, each cell separates into two
new cells in every generation
The Growth Curve in a Closed System
Measurement of microbial growth

 direct counting
 cultivation
 turbidity measurement
 Lag phase

 cells do not divide

 preparation for multiplication
 ribosomes, enzymes synthesis
 number of cells can decrease
 the length depends on the age of
inoculum and medium quality
 Exponential phase

 maximum growth and division rate

 the shortest generation time
 the highest consumption of nutrients
 the highest production of primary products
 determination of growth characeteristics (matematical
rules are valit at that phase)
 Stationary phase

 the total number of viable cells is constant

 balance between cell division and cell death
 nutrient limitation
 accumulation of metabolites
 maximum production of secondary
metabolites
 Death phase

 decreasing number of live cells

 nutrient deprivation
 toxic metabolites
 small number of cells resists in
anabiosis
 Mathematical characteristics of the growth

 lag phase duration

 generation time (time for each cell division, time
necessary for cell number doubling in population)
Microorganism Generation
time (h)
Streptococcus thermophilus 0.20 (12´)
Escherichia coli 0.35 (21´)
Bacillus subtilis 0.43 (26´)
Clostridium botulinum 0.58 (35´)
Mycobacterium tuberculosis 12
Saccharomyces cerevisiae 2
Protozoa 10
Mathematical characteristics of the growth

 specific growth rate (number of generation

per time unit, amount of biomass generated
per time unit, amount of cells...)

Microorganism specific growth rate (h-1)

Streptococcus thermophilus 3,47
Escherichia coli 1,98
Bacillus subtilis 1,61
Clostridium botulinum 1,19
Mycobacterium tuberculosis 0,06
Saccharomyces cerevisiae 0,35
Protozoa 0,07
 Continuous cultivation

 growth in open system

 population in
exponential phase
 chemostats – regulation
by constant chemical
composition of the
media
 turbidostat – constant
cell number
Factors influencing growth

(Staphylococcus aureus)

(Halobacterium)

(Lactobacillus)
(Escherichia)
(proteolytic bacteria)
 (Chlamydomonas nivalis)

(Pseudomonas florescens)
(E. coli)

(Thermus aquaticus)

(Sulfolobus, Pyrococcus)
obligate anaerobe: Micrococcus luteus, Pseudomonas, fungi
facultative anaerobe: E. coli, Enterococcus, Saccharomyces
aerotolerant anaerobe: Streptococcus pyogenes
obligate anaerobe: Clostridium, Bacteroides, Bifidobacteria
microarophile: Campylobacter, Lactobacillus
 Influence of nutrient
Growth of Bifidobacterium animalis on media
with glucose (Glu) or raffinose (Raf)
Influence of nutrient (diauxic growth)

Growth of E. coli on media with glucose (glukózy) and sorbitol

Antimicrobial substances

normal growth

time of
substance
addition bacterio- (microbi-) static substance

bacterio- (microbi-) cide substances

Metabolism, Carbon Cycle
Sources of energy for microorganism
 ATP – adenosine triphosphate

o energy carrier
o ATP breaks down to
ADP and orthoposphate
(Pi), energy is available
for work
o energy from
photosynthesis,
respiration and
fermentation is
accumulated in ATP
 The cell‘s energy cycle

Catabolism Anabolism
 Enzymes
o specific proteins catalyzing
metabolic reactions
o increase the rates of
reactions
o formation of the enzyme-
substrate complex
o its conversion to products
o cleavage of substrate
Allosteric regulation
o modulator binds to
regulatory site
o changes enzyme
conformation
o alteration in the shape of the
active site
o possibility to bind the
substrate
A general diagram of aerobic catabolism in a
chemoorganoheterotroph
 Glycolysis

o glucose degradation to
pyruvate
o (Embden-Meyerhof
pathway)
o cytoplasmic matrix
Carbon cycle in the environment
 Catabolism of Carbohydrates

polymers (starch, cellulose)

hydrolysis or phosphorolysis
monomers (glu, man, fru, gal)
glycolysis
pyruvate

fermentation respiration
Fermentations

o 2 ATP from glucose

o anaerobic processes
o electrons from
organic molecules
are donated to
organic electron
acceptors
o products of
fermentations are
simpler organic
molecules
 Alcoholic fermentation

o glycolysis → pyruvate decarboxylation

(acetaldehyde) → reduction to ethanol
o C6H12O6 → 2CH3CH2OH + 2CO2 (2ATP)
 Alcoholic fermentation

Saccharomyces
o bakery, alcoholic beverages, vitamins
o anaerobic – fermentation x aerobic – respiration
o mezophiles
o mono- or disaccharides

Candida
Zymomonas (bacteria)
 Lactic acid fermentation

o glycolysis → pyruvate + H+ → lactic acid

homolactic fermentation:
o main product is lactic acid (> 90 %)

heterolactic fermentation:
o about 50% lactic acid, acetic acid, ethanol, CO2,
other organic acids
 Lactic acid bacteria (LAB)

o anaerobic, facultative anaerobic, microaerophilic

o mesophilic, thermophilic
o acidotolerant
o mono or disaccharides, organic N, vitamins
 Lactic acid bacteria (LAB)

Homolactic fermenters
Lactococcus – milk, milk products, Lc. lactis, Lc. cremoris
Streptococcus – yogurt, Sc. thermophilus
Enterococcus – intestinal tract, probiotic, indicators of faecal
pollution, E. faecium, E. fecalis
Pediococcus – milk, silage, fermented meat products
Lactobacillus: homo as well as heterolactic
Lb. deslbrueckii ssp. bulgaricus – yogurt
Lb. acidophilus – milk, intestinal tract, probiotic
Lb. plantarum – plants, silage
 Lactic acid bacteria (LAB)

Heterolactic fermenters
Lactobacillus – Lb. fermentum, Lb. brevis – silage,
souerkraut, plants
Leuconostoc – milk, milk products (production of
polysaccharides), silage
 Fermentation by bifidobacteria

sugars (mono or oligosaccharides) → 60%

acetic acid + 40% lactic acids

Bifidobacterium
o anaerobes, mezophilic
o intestinal tract, probiotics
o B. bifidum
o B. animalis
o B. longum
 Propionic acid fermentation

monosaccharide or lactic acid → pyruvate → propionate +

acetic acid + CO2 + H2O

Propionibacterium
o facultative anaerobe, mezophilic
o skin (P. acne), Emmenthal chesses (flavour and holes),
intestinal tract
 Butyric acid fermentation

sugars (mono-, oligo- or polysaccharides) →

pyruvate → butyric acid + acetic acid + CO2 + H2
+ alcohols or other organic acids

Clostridium
o anaerobic, mezophilic, G+, sporeforming
o intestinal tract, soil, food spoilage
o C. perfringens
o C. butyricum
o C. botulinum
 Methanogenesis

o acetic acid or CO2 + H2 → CO2 + CH4

o methanogenic bacteria (Methanobacterium,
Methanococcus, Methanobrevibacter)
o biogas production
o greenhouse gas
 Mixed acid fermentation

pyruvate → ethanol + acetic acid + lactic acid +

succinic + formic acid + CO2 + H2

Escherichia
o facultative anaerobic, mezophilic, G-,
enterobacteria
o intestinal tract, probiotic, indicators of faecal
pollution, pathogenic
o E. coli
 Mixed acid fermentation

Salmonella
o facultative anaerobic,
mezophilic, G-, enterobacteria
o intestinal tract, zoonotic
infection (transferred between
animals and human), food
o S. enterica

Proteus
o facultative anaerobic,
mezophilic, G-, enterobacteria
o intestinal tract, urinary infections
 Butanediol fermentation

pyruvate → acetoin → butanediol + ethanol + acids

Enterobacter, Serratia, Erwinia

o facultative anaerobic, mezophilic, G-,
enterobacteria
o intestinal tract
 Catabolism of Carbohydrates

polymers (starch, cellulose)

hydrolysis or phosphorolysis
monomers (glu, man, fru, gal)
glycolysis
pyruvate

fermentation respiration
 Aerobic respiration

pyruvate → acetyl-CoA → tricarboxylic acid

cycle → electon transport and oxidative
phosphorylation → CO2 + H2O

o 38 ATP from glucose

o aerobic process
o aerobic bacteria
o most of fungi
o electrons from organic
molecules are donated to
molecular O2 by way of an
electron transport chain
 Incomplete aerobic respiration

organic C-substrate → simpler organic molecule +

(CO2) + H2O + energy

o acetic fermentation
o citric acid fermentation
 Acetic fermentation

ethanol + O2 → acetic acid + H2O + energy (6 ATP)

Acetobacter
o aerobic, G- rods, acidophils
o vinegar
o spoilage of alcoholic beverages
 Citric acid fermentation

saccharides + O2 → citric acid + H2O + energy

Aspergillus niger
o ascomycetes
o citric acid production (preservation of
food and beverages, aroma)
 Anaerobic respiration
o aerobic – electrons from
organic molecules are donated
to molecular O2 by way of an
electron transport chain
o anaerobic – electron transport
chains that can operate with
inorganic electron acceptors
other than O2
o electron acceptor is an
oxidized inorganic molecule
o nitrates (reduction,
denitrification), sulphate
(desulfuration), CO2
(methanogens), ....
 Catabolism of polysaccharides

o hydrolysis
o secreting of
hydrolytic
enzymes
o assimilation of
smaller molecules
Disaccharide cleavage
Catabolism of polysaccharides

Anaerobic condition Aerobic condition

CO2 + H2O2
 Cellulose cleavage

o structure polymer of glucose in plants

cellulases
Aerobic condition
o soil, mineralisation of organic matter
o complex of cellulolytic bacteria: Cytophaga,
Sporocytophaga, Cellulomonas
o actinomycetes, micromycetes

Anaerobic condition
o butyric fermentation
o Clostridium
o waterlogged soil, bottoms of rivers and lakes
o mulch, compost, sludge digestion, production of
biogas
Cellulose cleavage in ruminants

o Fibrobacter
o Butyrivibrio
o Bacteroides
o Ruminococcus
o Clostridium
o anaerobic moulds
o in monogastric
animals – large
intestine
 Strarch cleavage

o reserve polymer of glucose

amylases
Aerobic condition
o moulds - Apergillus, Rhizopus
o bacteria - Bacillus, Pseudomonas, Streptomyces
o mineralization in soil, amylolytic enzymes, malt
production, synthetic sugars

Anaerobic condition
o butyric fermentation
o Clostridium
o intestinal tract, waterlogged soil
 Pectin cleavage

o polymer of galacturonic acid, plant

pectinases cell walls and tissues

Aerobic condition
o Bacillus, Mucor, Alternaria
o plant pathogens, soil

Anaerobic condition
o butyric fermentation, except of
galcturonic acid
o Clostridium
o soil, intestinal tract, sludge digestion,
production of biogas
Lipid catabolism

o energy source
o lipids = triacylglycerols
(esters of glycerol and fatty
acids)
o hydrolyzed by lipases
o glycerol is catabolised in
the glycolysis
o fatty acids are oxidized in
the β-oxidation pathway →
acetyl-CoA – fed into the
TCA cycle or used in
biosynthesis
Protein and amino acid catabolism

o source of carbon and energy

o some bacteria and fungi
o pathogenic, food spoilage, soil
microorganisms
aerobic
o Bacillus, Pseudomonas, Proteus,
moulds
o products: NH3, CO2
anaerobic
o Clostridium
o products: NH3, CO2, H2S, scatol,
indol, mercaptans, organic acids,...
Protein and amino acid catabolism

o proteases – hydrolysis of proteins

to amino acids – transported to the
cell and catabolised
o deamination – removal of the amino
group from AA → organic acids
o transamination – amino group is
transferred to an keto acid acceptor
o convertion of organic acids to
pyruvate, acetyl-CoA, TCA cycle
intermediate
o nitrogen is excreted as ammonium
Anabolism - biosynthesis
 The cell‘s energy cycle

Catabolism Anabolism
The Construction of Cells

heterotrophs

autotrophs
 The Organization
of Anabolism

o biosynthetic products (in

blue) are derived from
intermediates
o CO2 fixation (in red)
 Fixation of CO2

o only autothrops
Photosynthesis
high need for energy:
o photosynthesis
o oxidation of reduced inorganic
molecules
incorporation of CO2:
o Calvin cycle
o reductive pentose phosphate cycle
carboxysomes:
o site for CO2 fixation
o thiobacilly
o cyanobacteria
o nitrifying bacteria
 Synthesis of Saccharides

gluconeogenesis:
o reversed glycolytic pathway
o pyruvate synthesis, glucose or fructose, converted to other sugars
synthesis of polysaccharides:
Synthesis of proteins

o amino acids joined by

peptide bonds
o different proteins have
different amino acid
sequences and structure

amino acids
o amination
o transamination
 Synthesis of lipids

fatty acids:
o straight chained or branched
o fatty acid synthetase

glycerol:
o arises from the reduction of the
glycolytic intermediates

phospholipids
Nitrogen cycle
Ammonification
 Ammonification

o mineralization, mainly in soil

o proteins, amino acids, nucleic acids, urea, chitin,
uric acid, peptidoglycan, etc. → NH3, NH4+
The use of NH4+
o source of N for biosynthesis
o source of energy through nitrification
o volatisation (outflow into the atmosphere)
o sorption on soil complex
o leaching into underground and surface water
Nitrification
 Nitrification
o aerobic!
o oxidation of ammonium in two steps
o chemolitothrophic autotrophs
o source of energy for nitrifying
bacteria (source of C usually CO2)
Nitritation
NH4+ + O2 → NO2- + 2H+ + H2O + E
Nitrosomonas, Nitrosococcus,
Nitrosolobus…
Nitratation
NO2- + O2 → NO3- + E
Nitrobacter, Nitrococcus…
Significance of Nitrification

o source of energy for nitrifying bacteria

o NO3- is main source of N for plants
o NO3- is used in denitrification
o NO3- is not stable
o losses of N by leaching
→ limitation for use water as drinking
→ eutrophisation of surface water →
developing of algae
o undesirable oxidation of NH4+ in farmyard
mature (→ N losses by leaching)
Denitrification
 Denitrification

o NO3- + H+ → N2 + H2O + E + O2
o (NO3- → NO2- → NO → N2O → N2)
o respiration chain in which O from nitrates
is an acceptor of H+
o source of energy for denitrifying bacteria
o anaerobic
o Pseudomonas, Paracoccus,
Propionibacterium, Thiobacillus
o losses of N from soil
o removing of NO3- from drinking water
Assimilatory nitrate reduction
Assimilatory nitrate reduction

o NO3- + H+ → NH4+ + H2O + E

o anerobic respiration
o O2 from NO3-
o source of energy and N for
synthesis of amino acids and
proteins
N2 Fixation
 N2 Fixation

o returning N2 from athmosphere to soil

o nitrogenases
o high need for energy
o anaerobic or aerobic proces
o N = N → HN=NH → H2N-NH2 → 2 NH3 → 2 NH4+ → AK
o N2 + 8e- + 16 ATP + 10 H+ → 2NH3 + H2 + 16ADP + 16 Pi
N2 Fixation - Diazotrophic bacteria

o soil free living bacteria: Clostridium, Azotobacter

o associative bacteria: Azospirillum (G- curved rods)
o symbiotic bacteria: Frankia (G+ filamentous),
Rhizobium, Bradyrhizobium (G- rods)

Frankia Bradyrhizobium
 N2 Fixation - Diazotrophic bacteria

Clostridium
o G+ sporeforming anaerobic rods
o acidic waterlogged soils
o fixation 5 kg/ha/year
o only in absence of other sources
 N2 Fixation - Diazotrophic bacteria

Azotobacter
o G- nonsporeforming aerobic
rods (nonfixing stage) x cocci
(fixing stage)
o neutral, high quality soils
o fixation 5-10 kg/ha/year
o only in absence of other sources
 N2 Fixation - Diazotrophic bacteria

Rhizobium
o G- nonsporeforming aerobic
pleomorphic rods
o straight in soil and media, branched in
root nodules = bacteroids (shape „Y“)
o fixation only in the roots if the content
of N in soil is low (50-150 kg/ha/year)
o symbiosis with Fabaceae
o plants give sugars, rhizobia N
o to improve fixation seeds could be
inoculated before sowing
Sulphur cycle