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GROUP
: 5
EXPERIMENT
DATE PERFORMED
: 15 SEPTEMBER 2015
SEMESTER
: 5
PROGRAMME CODE
: EH242 5E
SUBMIT TO
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Title
Abstract/Summary
Introduction
Aims
Theory
Apparatus
Methodology/Procedure
Results
Calculations
Discussion
Conclusion
Recommendations
Reference
Appendices
TOTAL
Allocated Marks
5
5
5
5
5
10
10
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100
Marks
Remarks:
Checked by:
Rechecked by:
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Date:
Date:
1
Table of Contents
NO.
TITLE
PAGES
Abstract
Introduction
Objectives
Theory
Apparatus
Methodology/Procedure
Results
11
Calculations
17
Discussion
17
10
Conclusion
20
11
Recommendations
21
12
Reference
21
13
Appendices
22
Abstract
In this experiment the study is for the growth kinetics of microorganisms in shake flask. E.coli is
grown in a LB and TB broth mediums and being fermented for 24 hours at 350 rpm and 370C.
Throughout the fermentation, the cell culture is taken out every 1 hours from 0 hour to 4th hour
and continued with every 2 hour until 20th hour and the absorbance analysis, glucose analysis
and cell dry weight are being performed. As for the optical density analysis, the absorbance
reading from the spectrophotometer is taken while for the glucose test, the reading of glucose
level is taken from the YSI 2700 Select Biochemical Analyzer. These substrate concentration
values will then being plotted on graph with growth rate. The cell dry weight, in the other hand, is
taken after the mass concentration is being dried overnight in the oven. The weight of the tube
which contains the biomass before and after the drying process is recorded to get the cell dry
weight. For the optical density of the cell, the absorbance value showed an increment which
indicating that the cell was growing and number of cell is increased in the shake flask. The growth
rate, however, cannot be determined as the absorbance values were increased and decreased
unevenly and calculation of rate of microbial growth cannot be made as the data for cell dry weight
concentration, X are not consistent giving some of the results negative value thus some of the
rate of growth, and substrate constant, Ks cannot be calculated. Supposedly, as the number of
cell increased inside the shake flask, the cell dry weight also should be increased. Therefore no
conclusion can be made about the cell growth rate in the shake flask. Another reason because
the electronic weight balance shows different reading when weighted twice.
Introduction
There are many ways to carried out Fermentation process such as batch, continuous and fedbatch processes. In this experiment, we decided to use the shake flask fermentation. The shake
flask fermentation is an example of batch fermentation. In shake flask, the culture flask usually
Erlenmeyer flask is being used to place and growing the microorganisms. It is a small scale
equipment which equivalent to stirred tank bioreactor and it is also the cheapest and easiest way
to culture microorganism aerobically, in small volumes of nutrient broth.
To ensure the prevention of any contamination to the culture, shake flask must be plugged.
Different plug can be made of cotton-wool, glass wool, polyurethane foam, gauze or synthetic
fibrous material. In this experiment, we used cotton plugged. The plug function to prevent airborne
microorganism from getting into the medium while at the same time allowing free flow of air enter
the flask.
The cultures are incubated at certain temperature 37o C and shaking frequency 350 rpm for 4
hours in an incubator shaker to achieve a required growth rate. The shaking agitates the medium
and the culture to keep the mixture relatively homogeneous and also to ensure aeration, creating
an aerobic condition. In batch culture, it is closed environment that means there is neither input
supplied nor output generated throughout the fermentation. The medium culture is initially
inoculated with the microorganism. The growth keeps increasing until at certain extent, the growth
is inhibited because of the decreasing substrate concentration and the presence of toxic
metabolites.
The microorganism that we used to study in this experiment is E.coli. There are many specific
media for growth of E.coli but in this experiment we used Luria Bertani (LB) a Terrific Broth (TB)
media because it is the most commonly used medium in molecular biology for E. coli cell culture.
The relationship between the specific growth rate () of a microbial population and the substrate
concentration (s), is an indispensable tool in all fields of microbiology, be it physiology, genetics,
ecology, or biotechnology, and therefore it is an important part of the basic teaching of
microbiology (Kovrov-Kovar. K, et. al, 1998)
Objectives
To construct a growth curve including lag, log, stationary and death phases
Theory
Shake flask fermentation is one of the examples of batch fermentation. Batch culture is an
example of a closed culture system which contains an initial, limited amount of nutrient. The
inoculated culture will pass through a number of phases. After an inoculation there is a period
during which no growth appears to take place. This period is referred as the lag phase and may
be considered as a time of adaptation. In a commercial process, the length of the lag phase should
be reduced as much as possible. Following a period during which the cell gradually increases,
the cell grows at constant, maximum rate and this period is known as the exponential phase. The
exponential phase may be described by the equation below:
= x -------------------1
where
x is the concentration of microbial biomass
t is the time, in hours
is the specific growth rate, in hour -1
on integration, equation (1) gives
= ------------------2
where
is the original biomass concentration
is the biomass concentration after time interval, t hours
During the exponential phase, the organism is growing at its maximum specific growth rate,
for the prevailing conditions.
Equation 2 predicts that growth will continue indefinitely. However, growth results in the
consumption of nutrients and the excretion of microbial products. Thus after a certain time the cell
growth rate will decrease until growth ceases. The cessation of growth may be due to the
depletion of some essential nutrient in the medium when there is limitation in substrate.
The decrease in growth rate and the cessation of growth due to the depletion of substrate may
be described by the relationship between and the residual growth-limiting substrate as follows:
where
Figure 4.1: The graph showing the relationship between the parameter of the Monod equation.
The stationary phase in batch culture is the point where the growth rate has declined to zero. In
the other word the growth rate is equivalent to the death rate. The cell death is might due to the
nutrient limitations due to their incorporation into cells during log-phase growth or a build-up of
toxins due to their release of fermentation products also during log-phase growth.
6
The death phase is the result of the inability of the bacteria to carry out further reproduction as
condition in the medium become less and less supportive of cell division. The nutrient is extremely
insufficient for the growth of the microorganism. Eventually, the number of viable bacterial cells
begins to decline at an exponential rate. Industrial fermentation is usually interrupted at the end
of the exponential growth phase or before the death phase begins.
Apparatus
Cuvettes (spectrophotometer)
Incubator Shaker
Refrigerated Centrifuge
Spectrophotometer
Biochemical Analyzer
Cotton plugged
pH meter
Procedure
a)
b)
Phosphate buffer
Concentration
components
1
K2HPO4
8 g/l
KH2PO4
3 g/l
a)
b)
Main experiment
1. 10% of inoculum to the main experiment media is transferred using aseptic technique.
(For instance, if the working volume is 150ml, therefore, 10% of inoculum would be
15mL of seed culture needed).
2. The shake flask is then capped (cotton plugged) and swabbed with 70% ethanol before
incubation in a thermostated rotary shaker at required rotational speed and
temperature for 24 hours.
(iii)
Sampling
1. Required amount of sample is transferred into the sampling tube with interval time for
every hour or every 2 or 3 hours.
2. 5 mL of sample is withdrawn every time sampling is done during fermentation for
measuring optical density (OD), glucose analysis and total cell number (biomass
concentration: g/L).
3. Table below is referred for planned usage of sample volume:
Table 6.2: Sampling
No.
Sample Name
OD
1000
CDW
1000
1500
Glucose Analysis
iv)
Volume (uL)
Use for
v)
10
vi)
Results
Luria Bertani Results
Time
(h)
OD
(nm)
M1
(g)
M2
(g)
X
(g/L)
ln X
(g/L)
(M2-M1)
S
(g/L)
(1/h)
Ln (X/X0)
0.188
1.084
1.031
-26.5
8.71
0.000
0.189
1.076
1.085
4.5
1.504
8.82
0.307
1.076
1.243
83.5
4.401
8.70
2.897
0.806
1.097
1.091
-3
7.92
-2.179
0.853
1.103
1.095
-4
1.386
8.09
-1.891
0.655
1.098
1.098
5.79
0.757
1.097
1.078
-9.5
5.72
-1.026
10
0.783
1.093
1.093
4.83
12
0.802
1.098
1.109
5.5
1.705
4.21
-0.2695
10
14
0.282
1.104
1.155
25.5
3.239
3.89
0.767
11
16
0.406
1.089
1.091
3.47
-1.609
12
18
0.409
1.098
1.104
1.099
3.30
0.549
13
20
0.498
1.113
1.095
-9
2.90
-1.080
11
Absorbance
(nm)
0.6
0.4
0.2
0
0
10
15
20
25
Time(h)
Figure 7.1: The growth curve of E.coli plotted using absorbance optical density.
ln X against Time
5
4.5
4
3.5
3
ln X
2.5
2
1.5
1
0.5
0
0
10
15
20
Time (h)
Figure 7.2: Graph of ln X against time which is plotted to construct the growth curve of the cell
by using cell dry weight
12
By referring Figure 7.2, it show that the exponential phase may be between at 1th and 14th hour.
This is because at 1st to 2nd hour at 12th and 14th hour shows an increasing data. Thus, the data
between one of this period will be used to find the value max. I take period of 1st to 2nd hour.
10
15
20
25
-0.5
y = 0.0554x - 2.0291
R = 0.5576
-1
ln X/X0
-1.5
-2
-2.5
Time (h)
Figure 7.3: Graph of ln X/X0 against time is plotted to find the value of max
From Figure 7.3, the value of max which is equal to the slope of the graph is 0.0554.
Thus, the doubling time is 12.51 h.
1.5
1
0.5
0
-0.5 0
10
-1
-1.5
-2
13
From Figure 7.4 we cannot find the Ks we lack the value of thus make the graph uncomplete.
The value of Ks can be determined if the graph complete by using max. By using Monod
Equation Ks value can be determined.
Terrific Broth Results
Seed culture preparation (inoculum)
Initial OD : 0.168
Final OD : 1.203
Table 7.2: Absorbance value at 600 nm obtained using Terrific Broth as medium
(fermentation)
No.
Time (h)
Absorbance Optical
Density (nm)
0.191
0.442
0.763
1.541
0.888
0.991
0.994
10
1.110
12
1.103
10
14
1.129
11
16
1.526
12
18
1.178
13
20
1.068
14
Absorbance
(nm)
1.4
1.2
1
0.8
0.6
0.4
0.2
0
0
10
15
20
25
Time(h)
Figure 7.5: The growth curve of E.coli plotted using absorbance optical density.
Table 7.3: Results of Cell Dry Weight (CDW) obtained using Terrific Broth as medium
No.
Time
Empty
Empty tube +
Cell dry
Cell mass
(h)
tube +
sticker + cell
weight (g)
concentration,
sticker (g),
(g), m2
(m2 m1)
X (g/L)
ln x
ln X/X0
m1
1
1.10991
1.10
0.0009
0.45
-0.7985
0.000
1.1030
1.11
0.0070
3.50
1.2528
2.0513
1.0946
1.09
-0.0046
2.30
0.8329
1.6314
1.0861
1.09
0.0039
1.95
0.6678
1.4663
1.1064
1.11
0.0036
1.80
0.5878
1.3863
1.1021
1.11
0.0079
3.95
1.3737
2.1722
1.0983
1.11
0.0117
5.85
1.7664
2.5649
10
1.1032
1.11
0.0068
3.40
1.2238
2.0223
12
1.1106
1.13
0.0194
9.70
2.2721
3.0707
10
14
1.1005
1.11
0.0095
4.75
1.5581
2.3567
11
16
1.0920
1.10
0.0080
4.00
1.3863
2.1848
12
18
1.1029
1.11
0.0071
3.55
1.2669
2.0655
13
20
1.1025
1.11
0.0075
3.75
1.3218
2.1203
15
ln X against Time
2.5
2
1.5
ln X
1
0.5
0
0
10
15
20
25
Time (h)
Figure 7.6: Graph of ln X against time which is plotted to construct the growth curve of the cell
by using cell dry weight
By referring Figure 7.6, it show that the exponential phase may at between at 4th and 12th hour.
Thus, the data between that particular times will be used to find the value max.
3
2.5
2
ln X/X0
Y-Values
1.5
Linear (Y-Values)
1
0.5
0
0
10
15
Time (h)
Figure 7.7: Graph of ln X/X0 against time is plotted to find the value of max
From Figure 7.7, the value of max which is equal to the slope of the graph is 0.1997.
Thus, the doubling time is 3.4709.
16
Calculations
Cell dry weight, X
final weight initial weight
Volume of Sample
X=
1.085 g 1.076 g
0.009 g
Growth Rate,
=
ln x1 ln x0
Time1 Time0
ln 83.5 ln 4.5
21
2.897 1/h
Yield of substrate, (Y )
Y = -
(g cells/ g substrate)
- 25.5 5.5
3.89 4.21
Within that period, the biomass/cell sample is taken out for every 1 hours from 0 hour to 4 hour
and continued every 2 hour from 4 hour to 20 hour. This is done to analyze the concentration of
the cell (g/L), the cell dry weight and the glucose concentration.
In order to analyze the concentration of the cell inside the flask, absorbance reading for the optical
density is taken from the spectrophotometer. The higher the absorbance reading means higher
number of cell presence inside the flask at a particular time. As for this experiment, the
absorbance reading for LB is increase from the beginning of the experiment until the 6th hour and
decrease slightly until the 8th hour then increase back before decrease until 20th hour. It can be
explained that the number of cell increase and decrease inconsistently throughout the cultivation.
In the other hand, the decrease in cell number in
6th
has been interrupted maybe because there are contamination occur to the sample. The
absorbance reading for TB shows increasing until 10th hour then it decrease a bit before increase
until 18th hour. For TB media, the results shows better reading maybe there are no contamination
occur during conducting the experiment. When there is other microorganism in the culture, the
growth will be interrupted thus the growth of E. coli started to slow down. When there are different
microorganism during the growth they will compete each other to keep living. Only the strong
microorganism can withstand starvation. There is much turnover of protein for the culture to cope
with this period of low substrate availability. In cell growth, the cell will go through several phases
like lag, exponential, deceleration, stationary and death phase. We can say the absorbance
experiment is fail due to inconsistence result.
In cell cultivation, the cells themselves need food or carbon sources like glucose for growth. In
batch fermentation for example in this experiment, the glucose can be the limiting factor for the
cell growth or we called it as substrate limiting growth. For this condition, the Monod equation can
be used to predict the growth rate and the cell concentration inside the shake flask. In addition,
the glucose concentration can be known by testing the cell sample into the glucose analyzer and
the direct glucose concentration can be obtained. The LB media experiment, there are glucose
concentration in there and the reading was obtained by using glucose analyzer. From the results
of substrate concentration, we manage to get what we suppose to get which is the reading will
decrease against time. Although the starting reading is lower than the second reading, the third
until the last reading shows decreasing.
18
For the graph ln X against time, we also fail to get the estimated result. This graph is plotted to
determine the gradient of exponential phase which is the max. The estimated exponential phase
for LB media is from 1st hour until 14th hour. The graph shows decreasing at 2nd hour might be
because of contamination. The reason why I estimate the exponential growth until 14th hour
because the growth occur until that hour. The max for this period is 0.0554. For TB media, the
estimated exponential phase may at between at 4th and 12th hour thus, the data between that
particular times will be used to find the value max which is 0.1997. The graph below shows the
result that we should achieved but we fail due to so many error.
Conclusion
After conducting the experiment we can ensure that, E.coli is suitable to be fermented inside a
shake flask and it is a simple method to investigate the growth kinetics of the microorganism.
Knowledge of microbial growth kinetics is essential to determine when to harvest the culture for
different purposes. Although we fail to achieve the objectives due to some errors during
conducting the experiment, we try to learn our mistake for next experiment.
Microorganism will go through several phases in their growth, several analyses on the cell
need to be done to know the growth kinetics of the cell and the duration for each phase. This
includes the cell concentration, glucose concentration and also the cell dry weight analyses. This
method can be done in the laboratory before the fermentation or the cultivation of microbes in
large scale is performed. Growth kinetics deals with the rate of cell growth and how it is affected
by various chemical and physical conditions. During the course of growth, the cells is continuously
changing and adapting itself in the media environment, which is also continuously changing in
physical and chemical conditions.
In conclusion, the microbial culture in batch culture system that is shake flask system goes
through a lag phase, exponential growth phase, decelerating growth phase, stationary phase and
sometimes the death phase depends on the end product desired. The substrate concentration in
the culture medium and growth parameters, such as glucose concentration changes
correspondingly throughout the growth phases. Thus, the physiology of the microorganisms is
always in a transient stage, subjected to a continually changing culture conditions. Consequently,
product formation is confined to a certain period of cultivation, for example antibiotics would only
be produced in the decelerating and stationary growth phases.
The batch culture system is still widely used in certain industrial processes for example
brewery industry because of its easy management of feed stocks. These advantages allow the
use of unskilled labor and low risk of financial loss. Low level of microbial contamination in
fermented products is at time tolerable, as long as the microbial contaminants are not pathogenic
and do not alter the desired properties of the product, such as taste, color and texture.
20
Recommendation
Aseptic technique must be practised when handling biomass concentration to avoid any
contamination.
Cuvette must be wiped cleanly to prevent any scratch that would affect the
spectrophotometer reading during protein test.
Disinfect the work area with 70% alcohol before handling the culture.
The cap of the viral must be opened to fasten the drying process of the biomass in the
oven.
The supernatant of cell concentration should be taken out carefully without any taking out
of the biomass.
This experiment must be carried out under the laminar flow to prevent any contamination
to the culture.
References
Ardestani, F., (2011). Investigation of the Nutrient Uptake and Cell Growth Kinetics with Monod
and Moser Models for Penicillium brevicompactum ATCC 16024 in Batch Bioreactor.
culture, Iranica Journal of Energy and Environment (IJEE), 2(2): 117-121
Crueger W and Crueger A., (1990). Biotechnology: A Textbook of Industrial Microbiology. Sinauer
Associates, Sunderland Massachusetts.
Kovrov-Kovar, K., & Egli, T. (1998). Growth Kinetics of Suspended Microbial Cells: From
Single-Substrate-Controlled Growth to Mixed-Substrate Kinetics. Retrieved on October 4,
2015 from http://mmbr.asm.org/content/62/3/646.full
21
Appendix
22