11 - Environmental and Applied Microbiology

Edaphon

A community of living organisms in the soil

Viruses

lead a strictly parasitic existence: they reproduce within bacteria, plants, animals, and human cells.

bacteriophages

most important kind of viruses in the soil environment are the viruses living in bacterial cells

Rhizobium

phages that attack the root nodule bacteria, which are the cause of the decline of papilionaceous plant crops.

Bacteria

• Basic mass of all soil microorganisms

• High metabolic activity

• Adheres to the surfaces of mineral molecules and soil

  colloids

Actinomycetes and Artherobacter

Largest group of soil bacteria

Fungi

• Eukaryotic organisms and absolute heterotrophs
  Obtain carbon and energy for cell building through the decomposition of organic compounds

• Lack chlorophyll and have cell walls containing chitin, glucans, and other polysaccharides

• Form symbiotic relationships with algae, insects, and higher plants, while some species are pathogenic to humans, plants, and animals

Fungi

Usually occur in the upper layers of the (acidic) soil, but can also be found in deeper layers of soil (~1 meter deep)

1. Penicillium

2. Aspergillus

3. Trichoderma

4. Verticillium

5. Fusarium

6. Rhizopus

7. Mucor

8. Zygorhynchus

9. Chaetomium

Common soil fungi

Humus

vital component that influences soil structure, sorption qualities, and organic compound richness. co-created by bacteria and fungi

T

T or F: Both bacteria and fungi co-create soil structure by producing humus

T

T or F: Bacteria and fungi contribute to the formation of crumb texture and a spongy soil structure through the production of mucous capsules and their filamentous growth forms.

Soil phytoedaphon

primarily consists of algae, with higher plants making a smaller contribution.

algae

abundant on the soil surface and can penetrate deeper through various means like ploughing, percolating water, and animal activity, existing asepiphytoedaphon and endophytoedaphon.

1. Nostoc

2. Anabaena

3. Scytonema

4. Tylopothrix

Blue-green algae that can fix atmospheric nitrogen, enriching the nitrogen content in soil significantly. They can colonize nitrogen and organic carbon-free soil due to their nitrogen and carbon assimilation abilities.

1. Blue-green algae

2. Green algae

3. Diatoms

4. Yellow-green algae

5. Euglenoids

6. Red algae

species of algae that occur in soil

Protozoans

The soil microfauna is represented by the ______, which mainly feed on bacteria.

• Their role is to conduct selection and rejuvenate and renew the population of soil bacteria.

1. Diplura (Wingless Insects with Antennae)

2. Protura (Wingless Insects with No Antennae)

3. Collembola (Springtails)

4. Myriapoda (Myriapods)

5. Acarina (Mites)

6. Lumbricus terrestris (Earthworms)

7. Nematoda (Eelworms)

8. Protozoans (e.g., Rhizopoda)

Main types of soil fauna

Mesofauna

category of soil fauna which includes nematodes, snails, insects, myriapods, mites, and others, which contribute to humus formation by feeding on dead organic matter.

Macrofauna

category of soil fauna which comprises earthworms, moles, and rodents, which break up soil material and transport it to deeper layers.

Earthworms

especially significant among invertebrates, consuming dead organic matter and mineral soil, and excreting coprolites (lumps) that enhance soil crumb texture and looseness.

coprolites

Excreted by earthworms, this enhances soil crumb texture and looseness

cellulose

Major component of plant cell walls composed of long unbrancehd chain of glucose

Cytophaga

Cellulolytic bacteria which aids in cellulose degradation

Trichoderma

Particular genus of fungi known to release highly active cellulase enzymes that facilitate cellulose breakdown

1. Acetovibrio

2. Bacteroides

3. Clostridium

4. Ruminococcus

Genera which conducts anaerobic decomposition of cellulose resulting in the production of CO2, H2, and CH4

F. Basic → acidic

T or F: Decomposition is faster in soils with neutral or slightly basic pH and slower in highly basic soils.

Lignin

• Major component of wood tissues alongside cellulose

• Can constitute up to 30% of plant biomass

• Polymer composed of phenylpropane units containing

  aromatic rings and methoxyl groups (–OCH3).
  

1. Basidiomycetes

   1. Trametes versicolor

   2. Phanerochaete chrysoporium

   3. Pleurotus ostreatus

   4. Lentinula edodses

2. Ascomycetes

   1. Xylaria

   2. Libertella

   3. Hypoxylon

Fungi causing rot of wood that are most efficient lignin degraders

Oxidoreductase

1. Laccase

2. Lignin peroxidase

enzyme complexes that breakdown lignin bonds using oxygen or hydrogen peroxide

Humus

Amorphous organic substance, usually dark, that makes up the colloidal system of a large surface area capable of adsorbing ions of water and gases.

C:N = 40:1

Ratio of organiz substances in dead plants’ residue

Fulvic, humic acids and humins

Composition of humus

Nitrification

Formed ammonium ions are utilized by the bacteria and plants for the synthesis of amino acids or undergo the process of ____.

1. First, ammonia is oxidized to nitrite by nitroso bacteria

2. nitrite is further oxidized to nitrate by nitro bacteria

Two stages of nitrification

Aspergillus flavus

Penicillium

Heterotrophic microorganisms that can also conduct nitrification

Denitrification

conversion of nitrate into molecular nitrogen, primarily occurring in oxygen-free environments where nitrates serve as terminal electron acceptors during respiration.

1. Achromobacter

2. Bacillus

3. Micrococcus

Heterotrophic bacteria that are key players in denitrification

chemoautotropic bacteria

1. Thiobacillus denitrificans

Contribute to denitrification by oxidizing sulfur compounds while reducing nitrates

Underground waters

oligotrophic and host a sparse microflora with few species and little plant or animal life.

Surface waters

support a diverse flora and fauna, including microorganisms from soil habitats and sewage, influenced by living and industrial pollution

botton sediments

oxygen-free and host anaerobic decomposition processes. Fosters anaerobic putrefying microflora, cellulolytic bacteria, and anaerobic chemoautotrophs, releasing hydrogen sulfide and methane into the water

mineral and thermal springs

example of underground waters

streams, rivers, lakes and seas

example of surface waters

transitional habitat between soil and waters

example of bottom sediments

plankton / bioseston

group of organisms that passively float in water not being able to resist the movement and the flow of water mass

Phytoplankton / Plant plankton

• Usually microscopic algae and blue-green algae

• Very small (<50μm)

Sea phytoplanktons — diatoms, dinophyta

Freshwater phytoplanktons — cryptophytes, diatoms, green algae, blue-green algae

sea phytoplanktons vs freshwater phytoplanktons

zooplankton / animal plankton

Rotifers, brachiopods, and copepods

• Consists of protozoa in open water zones

• Main consumers of bacteria

Protozoa plankton

planktons which are flagellates and ciliates

bacterioplankton

Occupy waters abundant in organic compounds

virus plankton

• Smallest percentage of planktons

• Usually found in fresh and seawater habitats

• Crucial factor in bacteria mortality

a. gram-negative rods

b. cocci

Polluted waters are primarily occupied by a. while clean waters like rivers and streams contain a sparse microflora with b dominance.

• Filiform green bacteria (Chloroflexaceae)

• Sulfuric green bacteria (Chlorobiaceae)

• Sulfuric purple bacteria (Chromatiaceae and Ectothiorhodaceae)

• Non-sulfuric purple bacteria (Rhodospirillaceae)

• Heliobacteria (Heliobacteriaceae)

examples of photoautotrophs (photosynthesizing bacteria)

• Nitrifying Bacteria

• Ferruginous Bacteria (Leptothrix ochracea and Crenothrixpolyspora)

• Sulfuric Bacteria

  • Bacteria that move in sliding motions (Beggiatoa alba) and fixed to the bottom (Thiothrix nivea)

example of chemoautotrophs (chemosynthesizing bacteria)

• Genus Hydrogenomonas

• Micrococcus denitrificans

• Desulfovibrio desulfuricans

example of hydrogen bacteria

allochthonous bacteria

• High fertility and heavily polluted surface waters harbor saprophytic and parasitic bacteria, including Gram-negative intestinal rods

• Gram-positive rods (bacilli) which are washed into bodies of water from soil during heavy rainfall, are also prevalent.

• Municipal waste serves as a primary source of pathogenic bacteria, with soil bacteria entering water during infiltration and surface runoff.

• Air plays a significant role in water contamination, especially in densely populated urban and industrial areas.

Gram-negative intestinal rods	Escherichia coli
	Proteus
	Klebsiella
	Enterobacter
	Pseudomonas aeruginosa
	Arthrobacter
Gram-positive rods (bacilli)	Bacillus
	Corynebacterium
	Clostridium

examples of allochthonous bacteria

Oomycota	Leptomitus lacteus
	Phytophthora
Zygomycota	Mucor
	Rhizopus
Ascomycota
Deuteromycota

examples of water fungi

thalli

Algae exist as single cells or form multicellular bodies known as ____ (single = thallus), which can take various shapes such as threads, spheres, or multilayer clusters.

T

T or F: The composition of algae communities varies significantly based on the quality and quantity of mineral salt content and pollutant characteristics of the water body.

Blue-green algae

• They exhibit various forms including unicellular, colonial, and filamentous forms.

• Unlike other bacteria, they can conduct oxygen photosynthesis, containing chlorophyll as well as other photosynthetic pigments like phycocyanin and allophycocyanin.

Anabaena

example of blue-green algae

F. Sensitive → resilient

T or F: Blue-green algae are sensitive to extreme environmental conditions and are found ubiquitously, even in deserts and hot springs.

microbial antagonism

In the 19th century, Pasteur’s experiments demonstrated _____________ , where common bacteria inhibited anthrax.

• Vitamins

• Amino Acids

• Dextrans

• Iron-chelating agents

• Enzymes

Microorganisms contribute to the synthesis of various medicinal agent such as:

iron dextran solution

containing iron hydroxide complexes with dextrans, treat iron-deficiency anemia.

Dextran sodium sulfate

with anticoagulant properties comparable to heparin, is formulated for intravenous use

dextran

• polysaccharides primarily produced by lactic acid bacteria, notably Leuconostoc species, from sucrose fermentation.

• Large fermenters are used for growth, with low nitrogen and high carbohydrate media.

• of defined molecular weight are crucial for laboratory and clinical applications, obtained through methods like acid hydrolysis or polymerization using templates.

• serve as plasma expanders for intravenous injection to maintain or restore blood volume and are used in wound care to form a hydrophilic layer.

vitamin B2 or riboflavin

• B group vitamin found in various foods like milk, liver, cereals, and vegetables, and is synthesized by intestinal flora in carbohydrate-rich diets.

• Deficiency can lead to symptoms such as inflamed tongue, dermatitis, and bone marrow injury, often accompanying other vitamin deficiencies in cases of malnutrition.

B2 or riboflavin

B group vitamin found in various foods like milk, liver, cereals, and vegetables, and is synthesized by intestinal flora in carbohydrate-rich diets.

Deficiency can lead to inflamed tongue, dermatitis, and bone marrow injury, often accompanying other vitamin deficiencies in cases of malnutrition.

B12 or cyanocobalamin

can be obtained from liver or as a by-product of microbial metabolism

Treatment for pernicious anemia

Biotin or Vit H

B family vitamin found in similar food sources and essential for metabolic functions and bacterial growth.

Chemical synthesis identical to that found in yeasts and other cells, facilitating practical applications.

Amino acids

• utilized as components of infusion solutions for parenteral nutrition and for treating specific conditions individually.

• They are produced through fermentation processes similar to those used for antibiotics or in cell-free extracts using enzymes isolated from bacteria.

citric and lactic acids

widely utilized in the food, drink, and plastics industries.

Gluconic acid

a metal-chelating agent and finds applications in detergent products.

siderophores

low-molecular weight iron-chelating agents

Desferrioxamine B

• a siderophore produced by Streptomyces pilosus, is highly effective in treating acute iron poisoning.

inhibition zone

The diameter of the _________ correlates with the antibiotic concentration in the reservoir.

Radioenzymatic assays

• rely on specific enzymes associated with bacterial resistance to aminoglycosides (e.g., gentamicin, tobramycin, amikacin, and neomycin) and chloramphenicol.

• These enzymes render antibiotics inactive by acetylating, adenylating, or phosphorylating them.

• Radioenzymatic assays use radio-labeled cofactors to label the drug being assayed, and the amount of radioactivity extracted is directly proportional to the drug's concentration.

1. AAC / acetyltransferase

2. AAD / adenylyltransferase

3. ANT / nucleotidyl transferases

4. APH / phosphotransferases

enzymes that target aminoglycosides

CAT / acetyltransferase

enzymes that target chloramphenicol

a. phosphocellulose paper

b. organic solvent

Aminoglycosides are typically separated using a. , while chloramphenicol is extracted using an b. .

Agar diffusion assays

measure the response of a growing population of microorganisms to antimicrobial agents

Firefly luciferase

measure ATP levels in bacterial cultures, have been studied for antibiotic sensitivity testing.

Growth exhibition

Microbiological bioassays for growth factors like vitamins and amino acids are based on ________.

high-performance liquid chromatography (HPLC) and enzyme-linked immunosorbent assay (ELISA)

modern methods which has replaced microbiological bioassays

Phenylketonuria

• a genetic disorder (an inborn error in metabolism) where the body cannot convert surplus phenylalanine (PA) to tyrosine due to a deficiency in the liver enzyme phenylalanine hydroxylase.

• leads to elevated levels of both PA and phenylpyruvic acid (PPVA) in the blood and excessive excretion of PPVA.

carcinogen

causes living tissues to develop malignant tumors.

• Forward mutation changes the wild-type organism from a natural to a more stringent form.

• Reverse mutation restores a mutant strain to the wild-type form, returning the original function of the gene.

forward vs. reverse mutation

1. Frame-shift mutations alter the gene by adding or deleting 1 or more bases, modifying the reading frame.

2. Base-pair mutations change a single base, modifying the reading frame.

types of reverse mutatioin

liver homogenates / s9 fraction

used to refine ames test

T

T or F: Ames test require histidine-requiring mutants to detect mutagens

Reverse mutation

In Ames test, this signifies that a sample is mutagenic

probiotics

live cultures of beneficial bacteria intended to survive stomach transit and colonize the intestinal mucosa, replacing diminished microflora or displacing pathogens.

7 (A-G)

how many serotypes does botox have

Bacteriophage

Listeria monocytogenes E. coli O157:H7 Salmonella Shigella

undergo lytic replication, causing cell death, or lysogenic replication, where viral DNA integrates into the host bacterium's genome and replicates during cell division, potentially shifting to a lytic cycle under certain triggers like UV radiation.

dysentery and typhoid fever.

Bacteriophage

Pseudomonas aeruginosa

bacteriophage used against cystic fibrosis

Probiotics

Bifidobacteria Lactobacillus

dairy products like yogurts, sometimes combined with prebiotics to promote probiotic growth

preventing and treating various types of diarrhea and in managing conditions like ulcerative colitis