Detection of Alpha-Amylase Activity from Soil Bacteria

IOSR Journal of Biotechnology and Biochemistry (IOSR-JBB)
e-ISSN: XXXX-XXXX, p-ISSN: XXXX-XXXX, Volume 1, Issue 6 (Sep. – Oct. 2015), PP 01-09
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Detection of Alpha-Amylase Activity from Soil Bacteria
1
Salihu, Y.,1
Saidu, A. Y., 2
Rabiu, G. A., 1
Umar A.A.,3
Zeynep, A., 3
Unzile, G.
1
Department of Biological Sciences, Faculty of Science, Federal University Dutse, Jigawa State-Nigeria.
2
School of Sciences, Department of Biology, Saadatu Rimi College of Education, Kunbotso, Kano State-Nigeria.
3
Department of Genetics and Bioengineering, School of Sciences and Engineering, Fatih University Istanbul,
Turkey.
Abstract:
Background: Alpha-amylase is one of the industrial enzymes that hydrolyze starch molecules into polymers
composed of glucose units. The enzyme has potential application in a wide number of industrial processes such
as food, textile, paper, detergent, fermentation and pharmaceutical industries. Alpha-amylase can be produced
by microorganisms, plants or animals.
Aim: The aim of this study is to detect the activity of alpha-amylase from bacteria isolated from soil
environment.
Method: Soil samples were inoculated onto the media that are rich in nutrient that favour the growth of the
bacteria and incubated for 24 hours at 37o
C after which the bacterial growth was detected in form of colonies.
In this study, bacterial species belonging to the genus Bacillus were identified through phylogenetic analysis
using 16s-ribosomal RNA sequencing for detection of the enzymatic activity. Effects of pH and temperature on
the enzymatic activity were observed using DNS activity assay method.
Results: Positive response to alpha-amylase activity by the soil bacteria was observed by the formation of clear
zone of inhibition shown by the colonies on the petri plates.
Conclusions: The optimal pH and temperature activities showed that the bacteria exhibit enzymatic activity at
mesophilic temperature and acidophilic or alkalophilic pH.
Keywords: Alpha-amylase, Bacillus, phylogenetic analysis, DNS activity assay.
I. Introduction
Microorganisms have become increasingly important producers of industrial enzymes. In view of their
biochemical diversity and the ease with which enzymes concentrations may be increased by environmental and
genetic manipulation, several attempts are now being made to replace enzymes, which traditionally have been
isolated from complex eukaryotes. Amylolytic enzymes capable of degrading starch are most important in
biotechnology industries with large application in food, fermentation, textile and paper industries [1].
Amylases can be obtained from several sources such as plants, animals and microorganisms [2]. The
microbial source of amylase is preferred to other sources of its plasticity and vast abundance. Amylase obtained
from microorganisms has almost surpassed the synthetic sources in different industries [1]. Amylolytic enzymes
are widely distributed in bacteria and fungi. They are categorized into exo-acting, endo-acting and debranching
enzymes. Among the amylases, beta-amylase is exo-acting, where alpha-amylase is endo-acting enzyme.
A vast number of organisms live in the soil [3], so great are microfloral number that dominate the
biomass in spite of the minute size of each organism [4]. Together with the earthworms, the microflora
monopolizes the metabolic activity in the soils. It is estimated that 60-80% of the soil metabolism is due to
microflora. Not only do they destroy plant residues but they function in the digestive tracts of animals and
eventually decompose the dead bodies of all organisms.
Alpha-amylases are hydrolytic enzymes that are widespread in nature being found in microorganisms,
plants and animals [5]. They are among the most important in present day biotechnology. The enzyme has found
numerous applications in commercial processes including thinning and liquefaction of starch alcohol, brewing
and sugar industries [6].
The genus Bacillus produces a large variety of extracellular enzymes of which amylases and proteases
are of significant industrial importance. Najafi et al [7] showed that the optimum pH and temperature of the
alpha-amylase from Bacillus subtilus were 6.0 and 55o
C respectively. The end products of soluble starch were
glucose (70-75%) and maltose (20-25%).
Demands for novel amylases worldwide are increasing day to day as these enzymes application spectra
are spreading in various industrial sectors [8]. This class of industrial enzyme constitutes approximately 25% of
the enzyme market covering many industrial processes [9].
This study is aimed at detecting alpha-amylase activity produced by some soil bacteria. The activity of
the bacterial enzyme was detected at different pH and temperatures after which the optimal activities were
obtained. The objectives of this study include: (1) Isolation and identification of the soil bacteria. (2) Gram’s

staining characteristics of the bacteria. (3) 16s ribosomal sequencing of the alpha-amylase producing bacteria.
(4) Enzymatic activity assay of the bacterial enzyme.
II. Material and Method
2.1 Study Site, Sample Collection and Media Preparation
This study was conducted in Fatih University Istanbul, Turkey. The soil samples were collected in
clean dry sterile containers from different soil environments as follows: Behind E-block and car-pack of Fatih
university, Istanbul; Buyucekmece Lake, Istanbul and Agricultural land of Bursa all in Turkey.
Upon soil samples collection, the culture media were prepared and the soil was inoculated onto the
plates containing the media that support the growth of the bacteria. The plates were put in an incubator at 37o
C
for 24 hours after which the bacterial growths were detected in form of colonies. Similarly, the bacterial samples
that showed positive response to alpha-amylase were grown in LB-medium and placed in an incubator at 37o
C
for 24 hours for the bacterial cell cultivation.
2.2 Preparation of Media and Regents
2.2.1 Alpha-amylase media
Two alpha-amylase media were prepared for the growth of soil bacteria. The media were enriched with
the starch as the substrate for alpha-amylase enzyme (table 2.1). Following the mixture of the chemicals, the
media were autoclaved at 121o
C for 15 minutes using autoclave (Nuve OT4060 steam sterilizer (Turkey)). They
were poured on to the clean and dry Petri plates and allowed to cool after which they solidified. The plate
containing the media were sealed with stretch film and stored at 4o
C before use. The preparation of the media
was performed under aseptic conditions.
2.2.2 LB-Medium
For the preparation of 500Ml LB-broth medium, 10g powder was suspended in 500ml of distilled
water. The media were autoclaved at 121o
C for 15 minutes, then cooled to 50o
C and stored at 4o
C before use.
2.3 Preparation of Buffers and Solutions
2.3.1 Phosphate buffer
Reagents used
Monobasic sodium phosphate: 2.78g of sodium dihydrogen phosphate was dissolved in 100ml
distilled water (Merck, Germany).
Dibasic sodium phosphate (0.2M): 5.3g of disodium hydrogen phosphate (Sigma-Aldrich, Germany)
was dissolved in 100ml distilled water.
Procedure
About 39ml of dihydrogen sodium phosphate (Merck, Germany) was mixed with 61ml of disodium
hydrogen phosphate. This made up to 200ml with distilled water which gives phosphate buffer (PO4)2 of 0.2M.
The pH was measured with pH meter which was standardized with standard buffer and its electrode
was washed with distilled water.
DNS Reagent
About 1g of dinitrosalicylic acid (DNS) (Merck, Germany) was dissolved in 50ml of distilled water. To
the solution, 30g of sodium tartarate tetrahydrate (Merck, Germany) was added in small lots, the solution turned
yellow in colour. 20ml of 2N NaOH (Merck, Germany) was then added, which turned solution to transparent
orange –yellow colour. The final volume was made to 100ml with the distilled water. The solution was stored in
an amber coloured bottle.
1% Starch solution
About 80cm3
of distilled water was heated in a beaker. 1 gram of starch was weighed, mixed with a
splash of distilled water. When the water was a near boiling, the starch was added to make up to 100cm3
and
brought to boil.
Biochemical activation of the colonies
The colonies that showed positive response to alpha-amylase were detected by the formation of clear
zone of inhibition. This shows that the bacteria were able to break down alpha-amylase. The colonies were sub-
cultured, stocked and stored at 40
C.

Isolation and characterization of the colonies
In order to isolate and identify the group of bacteria that were responsible for alpha-activity, the
colonies that showed positive response to alpha-amylase were subjected to microbial characterization via
Gram’s staining and microscopy.
Gram’s staining
Gram’s staining technique was employed for the characterization of the colonies so as to know the
nature of the bacterial cell-wall based on Gram’s reactions. Clean dried slides were used for fixing the smears.
After fixing the smears on the slides using fire flame, the fixed smears on the slides were subjected to Gram’s
staining steps as follows:
Staining Techniques
The slides were flooded with the crystal violet solution (primary stain) for 1 minute and then washed
with water not five seconds and drained. The slides were flooded with Gram’s iodine solutions (modant) for
about 1 minute, washed with water and drained. The slides were flooded with 95% alcohol (decolourizer) for 10
seconds, washed with water and drained. The slides were flooded with safranin (counterstain) for 30 seconds,
washed with water and drained. All the slides were examined under the microscope using Nikon Labophot-2
Electric Microscope (Germany) with oil immersion lens (times 100 magnifications).
Microscopy
Following Gram’s staining, the stained slides were observed microscopically under oil immersion lens.
The colonies Gram’s stain characteristics which include their morphologies and nature of Gram’s stain reaction
were observed and recorded.
Phylogenetic analysis
In order to identify the species of bacteria isolated from the soil environment that showed positive
response to alpha-amylase activity, the samples were sent to MACROGEN (Korea) and REFGEN (Ankara) for
phylogentic analysis using 16s ribosomal RNA sequencing technique.
16S ribosomal RNA is a component of the 30s small prokaryotic ribosomes subunit. It is 1.542kb (or
1542 nucleotide) in length. The genes coding for it are referred to as 16s rDNA and are used in constructing
phylogenies. It is highly conserved between different species of bacteria and archea.
The result of a phylogentic analysis is expressed in a phylogenetic tree where closely related organisms have a
high degree of agreement in the molecular structure of DNA, RNA and proteins.
Alpha –amylase activity assay procedure
Following identification of bacterial species that showed positive response to alpha-amylase activity,
the samples were subjected to activity assay via DNS method. The bacterial samples were grown in LB-medium
overnight at 37o
C.
Upon the overnight growth of the bacterial samples in LB-medium, the samples were centrifuged for
10 minutes using a centrifuge (Beckman counter (Germany)) and the pellets were collected after discarding the
supernatants. The cells were suspended in 1000ul phosphate buffer (pH 7). The cells were subjected to
sonication for lyses using a sonicator (Bendelin electronic (Germany)). Following cell lyses, the samples were
further centrifuged for 10 minutes after which the supernatants were collected.
Having collected the supernatant after centrifugation, DNS method was employed for the bacterial enzymatic
assay as described below:
DNS Activity Assay Method for Alpha-amylase:
 250ul of the enzyme solutions (supernatants) were mixed with 250ul of starch solutions (at pH 6, 7 and 8)
and incubated at different temperature (25o
C, 37o
C and 80o
C) for 10 minutes.
 500ul of DNS reagents were added to the mixture.
 The solutions were boiled in a boiling water bath for 5 minutes.
 The solutions were cooled in a running tap water.
 1ml of deionised distilled water was added to each solution.
 A blank was prepared without enzyme.
 The absorbance was read at 540nm using UV-Vis spectrophotometer (Nano-Drop, Thermo (U.S.A).

III. Result
Biochemical Activation of the Colonies
Following the overnight incubation of the culture media, the bacteria were able to degrade the media
there by producing a clear zone of inhibition. The larger the zone of inhibition, the more active is the bacteria!
The diameter of the zone of inhibition and that of the colonies were measured.
Table: 1 Biochemical Activation of the colonies.
Gram’s stain Result
Following Gram’s stain reaction, microscopic examination showed that the bacteria are Gram-positive
(appear purple in colour). Also, the morphological examination showed that the bacteria are rod in shape
(bacilli).
The result shows that the bacteria are Gram-positive and appear rod in shape (Bacilli). It was observed
under electrical microscope at 100 times magnification (under oil immersion lens).
Phylogenetic Analysis Result
Based on the nature of 16s ribosomal RNA, the colonies that were identified from Gram’s stain
reaction and microscopic examination were sequenced and the sequence analysis showed that the bacteria
belonged to the family Bacillaceae as can be seen from the phylogenetic tree. The analysis was carried out using
computer programme as follows:
First, a blast search for the contig sequence was made. In the blast search, about 10 species were picked
from the top. Then, their fasta formats were saved. After saving, they were copied and pasted on ClustalW2
programme for the alignment between the species. In the ClustalW2 programme, a tree construction link was
used for the automatic construction of the phylogenetic tree after the alignment between the species.
The phylogenetic trees for the three bacterial species are as follows:
Figure: 5 Phylogenetic tree of Bacillus mojavensus.
The figure: 5 shows the phylogeny of the bacteria after the blast search using ClustalW2 programme. It
shows a Bacillus mojavensus and related member of the family (Bacillus pumilus).
Sample no. Colony diameter
(mm)
Zone diameter (mm) Enzymatic index
A1.3.S2.1 7 17 2.42
A1.3.S2.2 6 16 2.66
A1.3.S2.3 5 16 3.2
A1.5.S3.2 7 14 2
A1.5.S3.2 7 14 2
a
c

Figure: 6 Phylogenetic Tree of Bacillus subtilus.
The figure: 6 above shows the phylogeny of Bacillus subtilus after the blast search using ClustalW2
programme. A2.11.S1.2 is the sample number of the bacterial specie.
Figure: 7 Phylogenetic tree of Paenibacillus sp B3a.
The figure above shows the phylogeny of Paenibacillus sp B3a after the blast search using ClustalW2
programme. L.18.S1.2 is the sample number of the bacterial specie.
Alpha-amylase Activity Assay Results
Dinitrosalicylic (DNS) method was employed for the alpha-amylase activity assay. Absorbance of the
enzyme was measured sphectrophotometrically and the effects of pH and temperature were determined. The
enzymatic activities of the enzyme differ with respect to the bacterial species in relation to pH and temperature
dependent as can be seen in the tables below:
Table: 2 Alpha-amylase Activity Result for Bacillus mojavensus.
Table: 3Alpha-amylase Activity Result for Bacillus subtilus.
pH TEMPERATURE (o
C) ABSORBANCE (nm)
6 80 0.765
6 37 0.769
6 25 0.778
7 80 0.447
7 37 0.452
7 25 0.483
8 80 0.325
8 37 0.336
8 25 0.369
pH TEMPERATURE (o
C) ABSORBANCE (nm)
6 80 0.272
6 37 0.250
6 25 0.249
7 80 0.291
7 37 0.289
7 25 0.251
8 80 0.239
8 37 0.636
8 25 0.262

Table : 4 Alpha-amylase Activity Result for Paenibacillus sp B3a.
Bacillus mojavensus
Figure: 8 Graph of pH gradient with respect to relative enzymatic activity for Bacillus mojavensus.
The figure: 8 above shows the bacterial amylase activity when studied at different pH gradients. The
maximum activity of the enzyme was obtained at pH 8. The enzymatic activity was studied under alkaline
condition not acidic because the activity was low at acidic medium.
Figure: 9 Graph of temperature gradient with respect to relative enzymatic activity for Bacillus mojavensus.
The figure above shows the maximum activity of bacterial alpha-amylase when studied at temperature
gradients. 37o
C was found to be the maximum temperature. Other temperatures show little activity. In the
conclusion, the maximum enzymatic activity was found to be at 37o
C and pH 8.2 Bacillus subtilus
0
10
20
30
40
50
60
70
80
90
100
25 30 37 45 55 70 80
Relativeactivity(%)
Temperature C
relative activity
pH TEMPERATURE (o
C) ABSORBANCE (nm)
6 80 0.351
6 37 0.409
6 25 0.483
7 80 0.369
7 37 0.819
7 25 0.803
8 80 0.325
8 37 0.323
8 25 0.793
0
10
20
30
40
50
60
70
80
90
100
3 4 5 6 7 8 9
Relativeactivity(%)
pH
relative activity

Figure: 10 Graph of pH gradient with respect to relative enzymatic activity for Bacillus subtilus.
The figure above shows the bacterial alpha-amylase activity assay at different pH gradients using DNS
alpha-amylase activity assay. Our enzyme shows maximum activity at pH 6.
Figure: 11 Graph of temperature gradient with respect to relative enzymatic activity for Bacillus subtilus.
The figure: 11 above shows the bacterial alpha-amylase activity at different temperature using DNS
alpha-amylase activity assay method. The enzyme shows maximum activity at 30o
C. In the conclusion, our
enzyme shows maximum activity at pH 6 and 30o
C temperature.
Paenibacillus sp B3a
Figure:12 Graph of pH gradient with respect to relative enzymatic activity for Paenibacillus sp B3a
0
20
40
60
80
100
120
3 4 5 6 7 8 9
Relativeactivity(%)
pH
relative activity
relative activity
0
20
40
60
80
100
0 20 40 60 80 100
Relativeactivity(%)
Temperature C
relative activity
relative activity
0
20
40
60
80
100
120
0 2 4 6 8 10
Relativeactivity(%)
ph
relative activity
relative activity
pH

The figure above shows the bacterial alpha-amylase activity at different ph gradients using DNS alpha-
amylase activity assay method. The enzyme shows maximum activity at pH 7.
Figure:13 Graph of temperature gradient with respect to relative enzymatic activity for Paenibacillus sp B3a.
The figure: 13 above shows alpha-amylase activity at different temperature gradients using DNS alpha-
amylase activity assay method. The maximum enzymatic activity is at 37o
C. In the conclusion, our enzyme
shows maximum activity at pH 7 and 37o
C.
IV. Discussion
Different types of soil favour the growth of alpha-amylase producing microorganisms such as fungi
and bacteria. In this study, we were able to isolate and identify three bacterial species that are capable of
producing alpha-amylase activity from different soil environments. Our investigation shows that, the alpha-
amylase producing bacteria grow best in a soil that is rich in nutrients that favour the growth and survival of
these bacteria. Growth and survival of soil bacteria is attributed to the possession of spores that help them to
resist adverse environmental conditions in the soil such as severe heat, cold and drying. To cope with the
adverse environmental conditions mentioned above, these bacteria have the ability to produce endospore as the
cell envelope. The nutrients that favour the growth of these bacteria in the soil originated from decayed leaves,
kitchen- wastes or dead organic matters. Sasnita Mishra and Niranjar Behera were able to isolate and identify
bacteria that show amylase activity from soil receiving kitchen wastes [10]. Similarly, Oseini, O.A. and
Ekperigin M.M., isolated and identified bacterial strains from soil in the forest that show alpha-amylase activity
[11].
As it is obtained from the result, majority of the soil bacteria that show alpha-amylase activity belong
to the genus Bacillus. They belong to the family Bacillaceae that are Gram-positive, spore-forming, aerobic or
facultative anaerobe and rod in shape. Following Gram’s staining technique; the colonies that show alpha-
amylase activities are Gram-positive and appear rod in shape morphologically.
Furthermore, phylogenetic analysis based on 16s ribosomal RNA sequence, shows that Bacillus
mojavensus, Bacillus subtilus and Paenibacillus sp B3a were the identified bacterial species that showed
positive response to alpha-amylase activity. Many researchers have reported the isolation and identification of
these bacteria from different soil environments as the major producers of alpha-amylase. For example, Noomen
et al isolated and identified Bacillus mojavensus from the soil of marine water as an organism that produces
alpha-amylase [12].
On the basis of their temperature requirement, bacteria are classified into psychrophilic, mesophilic and
thermophilic type. Similarly, bacteria can also be classified into acidophilic, alkalophilic and neutrophilic on the
basis of their pH requirement. Therefore, pH and temperature play a vital role in the growth and survival of
bacteria in different environment. Also ezymatic activity can be altered by these parameters. For this reason, the
effects of pH and temperature on the alpha-amylase activity shown by these bacteria were studied
spectrophotometrically using DNS activity assay method. As it is obtained from the result, the enzymatic
activity varies with respect to the bacterial specie. Bacillus mojavensus shows maximum activity at 37o
C and pH
8. Bacillus subtilus shows maximum amylase activity at 30o
C and pH 6. Finally, Paenibacillus sp B3a shows the
maximum enzymatic activity at pH 7 and 37o
C. Therefore, the results show that the bacterial species identified
show alpha-amylase activity at the pH range of 6 to 8 and temperature range of 30o
C to 37o
C. The variation in
the pH and temperature can be attributed to the type of bacteria and the soil type. In contrary to this research,
some researchers were able to isolate and identify bacteria that produce thermostable alpha-amylase. It means
the enzyme produced by the bacteria is at higher temperature (40o
C to above). Example, Vasakaran, S. et al
0
20
40
60
80
100
120
0 20 40 60 80 100
Relativeactivity(%)
Temperature C
relative activity
relative activity

reported the isolation and identification of bacterial strain that are capable of producing thermostable alpha-
amylase [13]. Similarly, some researchers have reported the isolation and identification of halophilic alpha-
amylase producing bacteria. Prakash et al reported the isolation, purification and characterization of two
extremely halotolerant, thermostable and alkali-stable alpha-amylase from chromohalobacter sp TVSP 101.
[14].
Generally, all the bacterial species identified, show optimal alpha-amylase activity at mesophilic
temperature (30o
C to 37o
C) out of which two species (Bacillus mojavensus and Paenibacillus sp B3a) show
maximum alpha-amylase activity at 37o
C while, the other specie (Bacillus subtilus) shows 30o
C as maximum
enzymatic activity. In terms of pH, both Bacillus mojavensus and Paenibacillus sp B3a show the maximum
alpha-amylase activity at alkalophilic pH (7 and 8) while Bacillus subtilus show the maximum enzymatic
activity at acidophilic pH.
V. Conclusion
Phylogenetic analysis based on 16s ribosomal RNA sequence showed that species of bacteria
belonging to the family Bacillaceae were responsible for showing alpha-amylase activity, also it can be
concluded that, alpha-amylase activity can be detected from different species of soil dwelling microorganisms
particularly bacteria.
Competing Interests
Authors have declared that no Competing interest exist.
Reference
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Detection of Alpha-Amylase Activity from Soil Bacteria

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