Sustainable Building Engineering 2021/22

Environmental Chemistry and Biology

Environmental Biology

Lecture 1. Basics of environmental microbiology

Beata Mądrecka-Witkowska, PhD

Institute of Environmental Engineering and Building Installations
Faculty of Environmental Engineering and Energy
Poznan University of Technology
 Basic bibliography:
• Pepper I.L., Gerba C.P., Gentry T.J.,
Environmental Microbiology, 3rd Edition
• Yates M.V., Nakatsu C. H., Miller R.V., Pillai
S.D., 2016. Manual of Environmental
Microbiology, Fourth Edition (e-book;
KNOWEL Library)

Additional bibliography:
• Willey J., Sherwood L., Woolverton C.J., 2017. Prescott's Microbiology 8th Edition
• Harley J. Laboratory Exercises in Microbiology 10th Edition
• Brandt M. J., Johnson K. M., Elphinston A. J., Ratnayaka D. D. 2016. Twort's Water
Supply, 7th Edition, (e-book; KNOWEL Library)
Book in Polish – for Polish
students
 Environmental Microbiology - basic definitions

Environment – (in biology) the complex of physical, chemical, and biotic factors
that act upon an organism or an ecological community and ultimately determine
its form and survival (Encyclopedia Britannica);

UV-radiation
insolation

temperature

presence of other
organisms

wind

soil

precipitation
https://eige.europa.eu/gender-mainstreaming/policy-areas/environment-and-climate-
change?lang=es
 Environmental Microbiology - basic definitions
Environment – (in biology) the complex of physical, chemical, and biotic factors that
act upon an organism or an ecological community and ultimately determine its form
and survival (Encyclopedia Britannica);

Microbiology - study of microorganisms (microbes), a diverse group of generally

minute, simple life-forms that include bacteria, archaea, algae, fungi, protozoa,
and viruses. The field concerns the structure, function, and classification of such
organisms as well as ways of using and controlling their activities by human
(Encyclopedia Britannica).

Microbial ecology is the study of the interactions of microorganisms within an

environment such as soil, air or water.

Environmental microbiology is an applied field of science. Its main aim is to

understand the functioning of microorganisms in the environment – their beneficial
or detrimental impacts on human health and welfare.
Its aim is to improve the environment for benefit society. (Maier et al., 2000).
 Taxonomy of living organisms

Taxonomy – the science of biological classification; in broader sense it

consists of separated but interrelated parts: classification, nomenclature
and identification.
Taxon (p. taxa) - any unit used in the science of biological classification,
or taxonomy. Taxa are arranged in a hierarchy e.g. from kingdom to
subspecies, a given taxon ordinarily including several taxa of lower rank
(Encyclopedia Britannica).
Phylogenetics - in biology, the study of relatedness of groups of
organisms, whether alive or extinct (Encyclopedia Britannica)
(Maier et al., 2000)
 Taxonomy of living organisms

Phylogenetic tree based on Woese et al. rRNA analysis. The (Prescott et al., 2004)
vertical line at bottom represents the last universal common
ancestor (LUCA). Other lines represent the group or taxa
separation from the ancestor.
 Taxonomy of living organisms

Chatton (1925) defined two terms: Prokaryotes and Eucaryotes.

Eukaryotes

The word prokaryote comes from the Greek: Their name comes from the Greek:
πρό (pro) - "before" εὖ (eu) - "well" or "true” κάρυον (karyon) -
κάρυον (karyon) - "nut" or "kernel" "nut" or "kernel”
 Selected differences between 3 domains (Prescott et al., 2004)
Property Archaea Bacteria Eucarya
Membrane-enclosed nucleus - (nucleoid present) - (nucleoid present) +
Complex internal membranous - - +
organelles
Plasmids + + -
Cell wall Variety of types, no Almost always have No muramic acid
muramic acid peptydoglycan containing
muramic acid
Gas vesicles + + -
Size of ribosomes 70S 70S 80S (cytoplasmic
ribosomes)
Nitrogen fixation + + -
Chlorophyll-based - + +
photosynthesis
Chemolithotrophy + + -
Ability to live in extreme very common noted rare
environment
Pathogens not noted up to now + +
 Taxonomic ranks and names

Rank Example

Domain Bacteria

Phylum (pl. phyla) Proteobacteria

Class γ-Proteobacteria

Order Enterobacteriales

Family Enterobacteriaceae

Genus (pl. genera) Escherichia

Species (pl. species) Escherichia coli Escherichia coli

Subspecies ---

Strain Escherichia coli ATCC 11775

Serovar (serotype) Escherichia coli sv. O157:H7

 Taxonomic ranks and names

Strain – a population of organisms that is considered to have descended from a single

organism of pure culture isolate.

Biovars – are variants strains which differ biochemically or physiologically.

Morphovars (morphotype) – are variants of strains which differ morphologically.
Serovars (serotypes) - are variants of strains, which differ in antigenic (serological)
properties.

(Prescott et al., 2004)

 Domain: Archaea
Domain: Archaea (Greek archaios – ancient)
 This domain includes 2 phyla, 55 genera (Bergey’s manual of systematic bacteriology
2001-2012)
 Taxa belonged to Archea are often found in extreme aquatic and terrestrial habitats, they
are extremophiles e.g. in anaerobic, hypersaline, high temperature environments (even
above 100°C).
 This group is diverse in morphology and physiology (Gram-positive or Gram-negative;
different shape of cell; morphology: single cells, filaments or aggregates)
 Diameter from 0.1 to over 15 µm (some filaments grow up to 200 µm long).

Domain: Bacteria
 This domain includes: 23 phyla, 1227 genera (Bergey’s manual of systematic
bacteriology 2001-2012)
 It includes taxa with very diverse morphology, metabolism and ecology.

https://microbewiki.kenyon.edu/

The compendium of knowledge about the morphology, physiology and taxonomy of

index.php/File:Hydrothermal_vent.jpg

bacteria is a four-volume work:

„Bergey’s manual of systematic bacteriology” Second Edition, 2001-2012

(Prescott et al., 2004)
Size of bacterial cells is usually in the range: fractions of micrometers to
several micrometers.
Three main types of shape of bacterial cell are: spherical, rod-shaped and
spiral. Cell shapes and cell arrangements:

Coccus Diplococcus Tetrad Sarcina

Streptococcus Staphylococcus

Bacterium Bacillus Streptobacterium/Streptobacillus

Vibrio Spirillum Spirochete

 Cell structure of Prokaryotes

PROKARYOTIC CELL

Cell protoplasm Cell envelope Cell appendages

• Nucleoid • Cell membrane • Flagella (s. flagellum)

• Mezosomes • Cell wall • Fimbriae (s. fimbria)
• Ribosomes • Glycocalyx • Pili (s. pilus)
• Inclusion bodies
• Plasmids
• Cytoplasm

(Maier et al., 2000; Prescott et al., 2004)

 Cell structure of Prokaryotes
Nucleoid Plasmids
 dense area of DNA,  double-stranded DNA molecules,
 consists of a single circular molecule of  contain genes which encode the abilities
double-stranded DNA called bacterial useful for the bacterium in some specific
chromosome, environmental conditions but are not
required for the growth and survival e.g.:
 contains genes which encode
 Genes of heavy metal resistance,
information about cell structure,
 Genes of the ability of degradation
metabolism and other cell functions
potentially toxic compounds,
needed to bacterial survive such as
 Genes of antibiotic resistance.
replication.
 plasmids can be transferred from one
bacterial cell to another via horizontal
gene transfer.

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Mezosomes
 They are invaginations of the plasma membrane.
 They form vesicles, tubes or lamellae.
 The are probably involved in cell wall formation during division or in chromosome
replication and distribution to daughter cells.
Ribosomes
 They are located in cytoplasmic matrix and also may be attached to the plasma
membrane.
 They are small particles – about 20 nm in diameter.
 Their function is protein synthesis.
 They are composed of ribosomal ribonucleic acid (rRNA) (60%) and proteins (40%).

Inclusion bodies
 Granules of organic or inorganic material present in the cytoplasmic matrix - their
function is usually nutrients storage, e.g.
• carbon as glycogen (polymer of glucose) or poly-β-hydroxybutyrate (PHB);
• elemental sulfur – as sulfur granules (e.g. purple photosynthetic bacteria);
• phosphate - as polyphosphates or volutin granules.
(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Other types of inclusion bodies
Gas vesicles
 provide buoyancy regulation – e.g. organisms try to float at specific depth where they
benefit from optimal light intensity, oxygen concentration or nutrient level
 in aquatic bacteria (purple and green photosynthetic bacteria, in many cyanobacteria)

Endospores
 produced only by several genera e.g. Bacillus and Clostridium (only Gram-positive bacteria)
 develop within vegetative cells of bacteria
 they are capable of surviving adverse conditions and environmental stresses e.g. lack of
nutrients, heat, UV radiation, gamma radiation, chemical disinfectants, desiccation.
 spore formation is called sporulation or sporogenesis occurs when growth ceases due to
lack of nutrients
 endospores can have different location in cell – it depends on species
 in favourable environmental conditions spores can transform into active vegetative cells – it
occurs in 3 stages: activation, germination and outgrowth

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Cytoplasm
It is a substance lying between the plasma membrane and the nucleoid
- consists mainly of water, metabolites, nutrients, enzymes

.Cell wall
 It is the outer cover of the cell.
 It protects the cell against external environmental factors (physical and chemical) e.g.:
changes in osmotic pressure, detergents, mechanical damage, against other
microorganisms.
 It gives the cell a shape.
 It occurs in all bacteria. (The exception are Mycoplasmatales).
 Characteristic compound for bacteria cell wall is peptidoglycan (murein). The layer of
peptidoglican is the support structure of the cell wall. Other chemical compounds of
the cell wall are connected with peptidoglycan, e.g. lipoproteins, lipopolysaccharides,
proteins.
 There are 2 main types of the cell wall structure and based on it, two main groups of
bacteria are distinguished: Gram-positive and Gram-negative.

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Cell wall – differences between Gram-negative and Gram-positive bacteria

Feature Gram-negative bacteria Gram-positive bacteria

Presence of outer membrane + -
Peptidoglycan thin (1-3 layers) thick (approx. 40 layers)
<10% of dry weight of cell wall 50-90% of dry weight of cell
wall
Teichoic acids, lipoteichoic acids - +
Lipopolysaccharide (LPS) + -
Resistance to high pH worse better
Resistance to high temperature worse better
Resistance to high osmotic worse better
pressure
Resistance to antibiotics better worse
Resistance to detergents better worse
Color in Gram-staining pink-red blue-purple
procedure

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Cell membrane
 It is composed of phospholipids and proteins;
 The cytoplasm is surrounded by plasma membrane.
 The cell wall of Gram-negative bacteria consists of two membrane: interior cell
membrane and outer cell membrane. The outer cell membrane contains
lipopoliysaccharide (LPS) – this layer is responsible for the antigenic properties and can
exhibits toxic properties (it is called endotoxin associated with Gram-negative bacteria)

Glycocalyx
 It is a coating (layer) of macromolecules (usually polysaccharides), external to plasma
membrane. It is not observed in all bacterial taxa.
 Its functions are: cell protection from water and nutrient loss or other environmental
stresses e.g. heavy metal toxicity. It helps to resist phagocytosis by host phagocytes.
 The slime layer is build of loose, diffuse and unorganized material.
 The capsule - the layer of glycocalyx is rigid and well organized. Cells with
capsules produce gummy, mucoid colonies.

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Cell appendages
Flagellum (p. flagella)
 It is a complex appendage that improves motility of cells.
 It allows to move through an aqueous environment.

a) If the bacterial cells move in chemically homogeneous environment, their movement is chaotic.
They tumble often and they don’t move long in one direction
b) If the cells are in environment with a gradient of environmental factor they move in specific
direction – towards or against this factor. It is called taxis.

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
 Positive taxis – movement toward attractant. The factor has a positive impact on cell. It
attracts bacteria.
 Negative taxis – movement against repellent. The factor has a negative impact on the
cell. It repels bacteria.
Types of taxis:
 Chemotaxis - movement of a bacterium in response to chemical factors, either towards
the factor (positive chemotaxis) or away from it (negative chemotaxis)
 Phototaxis – movement of a bacterium in response to light, either towards the source
of light (positive phototaxis) or away from it (negative phototaxis)
 Aerotaxis - movement of a bacterium in response to oxygen concentration (positive or
negative)
 Thermotaxis - movement of a bacterium in response to thermal factor (positive or
negative)
 Magnetotaxis - movement of a bacterium in response to the magnetic field (positive or
negative)

(Maier et al., 2000; Prescott et al., 2004; Libudzisz et al., 2007; Baj and Markiewicz, 2015)
 Cell structure of Prokaryotes
Cell appendages
Fimbria (p. fimbriae)
 They are short surface appendages, sometimes very numerous.
 They are not involved in motility but they are used cell in attachment to surfaces e.g.
formation biofilms in pipes, colonization of soil particles.

Pilus (p. pili)

 This is appendage longer than fimbria.
 They are typical only for Gram-negative bacteria
 They are involved in a mating process between cells known as conjugation.
This is a process of DNA transfer from donor cell to recipient cell
(usually plasmids, rarely bacterial chromosome). Pilus forms a connection between two
cells.
This process is a type of horizontal gene transfer (HGT). Other types of horizontal gene transfer are
https://www.britannica.com/science/pilus
transformation and transduction. HGT increases the diversity of microorganisms, which allows
better adaptation of the bacterial population to the environment.

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Bacterial physiology

Most of bacteria reproduce asexually by binary fission.

In this process a parent cell divides into two daughter cells. All cells are genetically
identical. This is vertical gene transfer.

2n= N

n- number of divisions,
N – number of cells after n divisions

Cells of Escherichia coli divide every hour.

Every hour a new generation of cells is formed.
If in the initial number of bacterial cells in the culture is 10000, after one day there may be:

224 = 167 772 160 000 cells

 Bacterial physiology

Colony – is an assemblage of microorganisms growing on a solid medium which occurs as

a result of binary fission of one cell or cell arrangement. It can be visible and use in
microbiological diagnostic, because a colony morphology is often typical for the taxon.

At microbiological laboratory conditions microorganisms grow on special media.

Culture medium – is a liquid or solid preparation use to grow, transport and store
microorganisms. It must contain nutrients required for the growth of studied bacteria.
Liquid media – do not contain any solidifying agent. They are used in flasks or test tubes.
Solid media - contain solidifying agent – usually agar. They are used for surface cultivation
of microorganisms on Petri dishes, (sometimes also in flasks or test tubes).

(Prescott et al., 2004; Michałkiewicz and Fischer, 2007)

 Bacterial physiology

 In natural environment most of bacteria grow in aggregation called biofilm.

 Biofilm – is a surface association of microorganisms that are strongly attached through
the production of extracellular polymeric substances (EPS) (usually polysaccharides).
 It grows on solid materials that have permanent or temporary contact with water or in
moist environments.
 Biofilm consist of single layer of microorganisms or can be very complex structure.
Biofilms can consist of single species or mixed communities.

 Many pathogens are capable to form biofilms: Escherichia coli, Salmonella,

Pseudomonas, Bacillus, Streptococcus, Staphylococcus aureus, Staphylococcus
epidermidis, Listeria monocytogenes, Legionella pneumophila.
 Biofilms occur e.g. in natural environments: rocks, submerged leaves of aquatic plants,
and in human environments: drinking water installations, food industry installations,
tooth enamel, dialysis units.

(Prescott et al., 2004)

 Bacterial physiology

Bacteria in biofilms can communicate. This process is called quorum sensing.

In Gram-negative bacteria it operates by the production of small signal molecules called

autoinducers. The concentration of these molecules is correlated with the number of
bacteria.
The sufficient number of cells (a quorum) must be present to cause specific gene
expression in bacteria.
This expression may involve genes resposible for biofilm formation, flagella loss and EPS
production and biofilm destruction
This process enables the bacteria to get information about size of the population and its
metabolic state. It helps coordinate the population density and cell number in relation to
environmental conditions e.g. availability of nutrients.

(Encyclopaedia Britannica; Libudzisz et al., 2007)

 Bacterial physiology

https://www.dovepress.com/chronic-tonsillitis-and-biofilms-a-brief-overview-of-treatment-modalit-peer-reviewed-fulltext-article-JIR
 Bacterial physiology

Micororganisms benefit from being part of a biofilm:

- Extracellular maxtrix protects against dessication, changes in pH or temperature,
predators.
- Biofilm cells are more resistant to antibacterial substances such as antibiotics or
disinfectants.

Biofilms are used in systems of purifying water from municipal sewage or in biologically
active carbon filter beds using in drinking water purification. Bacteria remove organic
matter and various contaminants.

Biofilms cause tooth decay and grow on medical implants what may results in hospital-
borne infections.

Biofilms growing in various pipes (water or sewage) lower the flow capacity, decrease
heat-exchange efficiency and catalyze corrosion in case of metal pipes.

(Encyclopaedia Britannica; Libudzisz et al., 2007)

 Bacterial ecology
The influence of environmental factors on bacterial growth
1) Osmotic pressure - the amount of pressure needed to stop the flow of a liquid through
a membrane (= cell covering).
Osmosis - is the spontaneous movement of solvent molecules through a selectively
permeable membrane into a region of higher solute concentration, in the direction
that tends to equalize the solute concentrations on the two sides of membrane.

Water flow out of the cell. No change in The cell interior

The protoplast shrinks cell volume accumulates water
(plasmolysis)
 Most of micoorganisms live under hypotonic and isotonic conditiones
 Osmotolerant – grows over wide range of osmotic pressure (Staphylococcus aureus)

(Prescott et al., 2004)

 Bacterial ecology

2) Salinity
 Halophiles – optimal growth is noted if the concentration of NaCl or other
salt is above 0.2 mol/l.
 Extreme or obligate halophiles - require very high salt concentrations (20 to
30%). (Bacteria in Dead Sea)
 Facultative halophiles - do not require high salt concentrations for growth,
but tolerate 2% salt or more.
3) pH
 Acidophiles – growth optimum between pH 0 and 5.5 (Picrophilus)
 Neutrophiles - growth optimum between pH 5.5 and 8.0 (Escherichia)
 Alkalophiles - growth optimum between pH 8.0 and 11.5 (Bacillus
alcalophilus)
4) Pressure
 Barotolerant – the increase of pressure does not affect them negatively
 Barophilic – their growth is faster if the pressure is high

(Prescott et al., 2004)

 Bacterial ecology
5) Temperature
Group of Minimum Optimum growth Maximum Examples
microorganisms temparature
Psychrophiles 0°C or lower 15°C or lower 20°C Bacillus psychrophilus

Psychrotrophs ~0°C 20-30°C 35°C Listeria monocytogenes

Pseudomonas fluorescens
(facultative
psychrophiles)
Mesophiles 15-20°C 20-45°C 45°C or lower most of human pathogens
(37°C), Escherichia coli

Thermophiles ~45°C 55-65°C Thermus aquaticus

Hyperthermophiles 80-113°C Pyrococcus

(Prescott et al., 2004)

 Bacterial ecology

6) Oxygen concentration
 Aerobes – organisms able to grow in the presence of atmospheric oxygen;
 Obligate aerobes – completely dependent on atmospheric O2 (e.g. Micrococcus
luteus);
 Microaerophiles – require O2 concentration between 2 to 10% (less than in the
atmosphere) (e.g. Campylobacter, Treponema pallidum);

 Anaerobes – organisms that can grow only in the absence of atmospheric oxygen.
 Obligate anaerobes – die in the presence of O2 (e.g. Clostridium);
 Aerotolerant anaerobes – grow equally well whether O2 is present or not (e.g.
Streptococcus pyogenes);
 Facultative anaerobes – do not require O2 for growth, but they grow better if ithe
oxygen is present (e.g. Escherichia, Enterococcus);

(Prescott et al., 2004)

 Microbial Metabolism
Every living cell need organic compounds for build their structure and for various living
processes. There are various sources of carbon, energy and electrons for metabolic
processes:
1. Carbon sources
• Autotrophs – CO2 is sole or principal inorganic carbon source for biosynthesis; They
convert it into organic compounds. They are not depended form other organisms.
• Heterotrophs – they obtain carbon in an organic form; they reduce preformed, organic
molecules from other organisms e.g. lipids, proteins, carbohydrates.

2. Energy sources
• Phototrophs – capture radiant energy from sun light, they photosynthesize.
• Chemotrophs – they gain energy from chemical compounds; they oxidize organic
(chemoorganotrophs) or inorganic compounds (chemolitotrophs).

Chemolitotrophs – e.g. iron-oxidizing bacteria

2 Fe2+ + 0.5 O2 + 2 H+ → 2 Fe3+ + H2O + e- + energy

Chemoorganotrophs - mostly nonphotosynthetic bacteria

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy

(Maier et al., 2000; Prescott et al., 2004; Baj and Markiewicz, 2015)
 Viruses

Virus – a small infectious agent.

It is simple, acellular entity consisting of
one or more molecules of DNA or RNA
enclosed in coat of protein (capsid) and
sometimes in addition substances such
as lipids and carbohydrates and other
proteins (outer membrane).
They can reproduce only within living
cells and are obligatory intracellular
parasites.

Size range is about 10-300 (400) nm in

diameter. (The smallest viruses are a
little larger than ribosomes). Extracellular form of virus is called viron.

(Maier et al., 2000; Prescott et al., 2004)

 Viruses
Structure:
• nucleocapsid core – composed of a
nucleic acid (either DNA or RNA) held
within a capsid.
• capsid - protein coat protect viral
genetic material.
(Maier et al., 2000; Prescott et al., 2004)

Tail

https://asknature.org/idea/virus-battery/#jp-carousel-5447

Helical virus Bacteriophage – virus that infects

bacteria
 References
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Warszawa.
• Bobrowski M. M., 2002. Podstawy Biologii Sanitarnej. Wydawnictwo Ekonomia i Środowisko,
Białystok.
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McGraw-Hill Companies.
• Kunicki-Goldfinger W., 2006. Życie bakterii. PWN, Warszawa.
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środowiska ich występowania. Tom1., PWN, Warszawa.
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Wydawnictwo Politechniki Poznańskiej.
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Warszawa.
• Prescott L. M.; Harley J.P., Klein D.A., 2004. Microbiology 6th edition. McGraw-Hill Science.
• Schlegel H.G., 2005. Mikrobiologia ogólna. PWN, Warszawa.