METHODS IN ENVIRONMENTAL MICROBIOLOGY:

Jennifer Julizar November 6th , 2014BIOL 351 Section 906

Environmental Microbiology Introduction
Soil and water are parts of the environment that humans and other organisms
encounter every day. Therefore, it is important to understand the importance of
microorganisms living in the soil. The purpose of performing this
environmental microbiology lab exercise is to gain knowledge of which
microorganisms exist in environments of soil and water and to understand what
effect they have on these environments (1, 2, 3). The soil microbial count
experiment determines the concentration of microorganisms living in soil (2). The
multiple tube fermentation experiment tests the effect of microorganisms on the
quality of water (3). Lastly, the ammonification experiment indicates how
concentrated ammonia becomes in the soil after microorganisms have modified the
overall soil chemistry
(1). Microorganisms can play either beneficial or pathogenic roles on the soil (2).
Because they also have different ways of adapting to their environments,
microorganisms need to be grown in different media that will fulfill their specific
needs. The soil microbial countexperiment is performed to determine the
concentrations of actinomycetes, bacteria, and fungi collected from the soil. There
are also environmental factors that influence these soil residents. Actinomycetes
are grown in Glycerol Yeast Extract Agar, while bacteria are grown in Nutrient
Agar, and fungi are grown in Sabouraud Dextrose Agar (2).
Each of those media contain different compositions that fulfill particular
microorganisms` needs in order to grow and perform particular functions. In this
experiment, a sample of soil solution is diluted several times by performing the
pour plate technique and then transferred to three different media, which is
followed by incubation. While performing this experiment, three different colonies
of microorganisms are grown in their respective media and their populations are
counted (2).

Jennifer Julizar November 6th , 2014BIOL 351 Section 906

Other than soil, water is another environment where microorganisms will
live. The multiple tube fermentation method can be performed to measure the
density of coliform and Escherichia coli which are present in water. In this
experiment, a water sample is diluted with sterile water followed by serial dilution.
Evolution of bubbles indicates a positive result for water contamination (3).
Transferring the sample water to tubes containing Lauryl Tryptose Broth(LTB) is a
presumptive test for water contamination. Tubes with bubbles produced then are
transferred to tubes containing Brilliant Green Lactose Bile (BGLB) Broth
as confirmation of coliform contamination in water. The ones that produce bubbles
in BGLB are then transferred to EC broth for confirmation of contamination by
the Escherichia coli confirmation test.
The quality of water can be judged through this method, which can be used to
determine whether orn ot contamination has prevented the water sample from
being drinkable. An increase in the percentage of tubes which produce bubbles
with every dilution indicates that more coliform or Escherichia coli exists in the
water (3). Some bacteria and fungi are capable of decomposing dead matter and
nitrogenous wastes to produce ammonia. Ammonia can also be produced by
deamination of amino acids. Plants are capable of recycling ammonia as an
essential source of nitrogen (1). Without bacteria and fungi, plants would have
more difficulty recycling ammonia in order to have a source of nitrogen. The
ammonification experiment is performed to determine the relative prevalence of
ammonia in the soil. In this experiment, soil is put into a tube containing peptone
water, incubated, and then added with a drop of Ammonia Reagent. The degree of
color change will provide an approximation of how concentrated
available ammonia is within the soil. A darker green color indicates a higher
concentration of ammonia is in the sample soil (1).

Drinking Water test

Researchers targeted E. coli -- the culprit in a deadly outbreak in Walkerton, Ontario in
2000 -- because it is an indicator organism of water contamination.
The bottom of the paper strip developed by Mitra and his colleagues is laced with sugar,
which begins to dissolve when placed in water. E. coli bacteria are attracted by the
resulting sugar trail and get trapped in the porous paper when they come in contact with
it.
As water enters the paper, it carries the trapped bacteria into an area of the strip
containing a mixture of chemicals. The E. coli react with those chemicals and turn the
strip pinkish red to signify a positive test.
With high levels of contamination, a result is produced in just 30 minutes. Low levels of
contamination take up to 180 minutes. Work is underway to reduce test times.

TITLES OF METHODS USED IN ENVIRONMENTAL MICROBIOLOGY:

1 The Needle in a Haystack: Detection of Microbes in Source and Drinking

Water by Molecular Methods- Keya Sen

2. Taking the Hay Out of the Haystack: Collecting and Processing Water
Samples

3. The Coming Together of the Sciences: Biosensors for the Detection of

Waterborne Pathogens Using Antibodies and Gene-Based Recognition
Chemistries

4. Simple, Powerful, and Smart: Using LAMP (for Low Cost Screening of
Multiple Waterborne Pathogens on loop-mediated isothermal amplification

5. Challenges of Multiplexed Detection: Detection of Pathogens in Water and

Wastewater Using Microarrays

6. Discovering New Pathogens: Amoebae as Tools to Isolate Amoeba-

resisting Microorganisms from Environmental Samples

7. Identity and Function of Single Microbial Cells Within a Community by

Raman Microspectroscopy and Related Single-cell Techniques

8. Are They Alive? Detection of Viable Organisms and Functional Gene

Expression Using Molecular Techniques

9. Characterization of Microbial Community Structures in Recreational Waters

and Primary Sources of Fecal Pollution with a Next-Generation Sequencing
Approach

10. Microbial Source Tracking: Current and Future Molecular Tools in Microbial
Water Quality Forensics

11. Dynamics of Microbes in the Natural Setting: Development of the Geochip