Academia Journal of Scientific Research 1(1): 006-009, February 2013

DOI: http://dx.doi.org/10.15413/ajsr.2012.0107
ISSN: 2315-7712
©2013 Academia Publishing

Research Paper

Microbial analysis of different top soil samples of selected sites in Gilgit, Gilgit-
Baltistan, Pakistan

Accepted 5th January, 2013

ABSTRACT

Syed Aftab Hussain Shah* and Khalil
Ahmed
Department of Biological Science,
Karakoram International University,
Gilgit, Gilgit-Baltistan, Pakistan.
*Corresponding author.
Email:aftab.yarkhoon@gmail.com.
Tel: +92-342-5070-718
The research was carried out from November 2010 to April, 2011, during which
soil samples of three selected sites that is Gilgit city (GLTC), Jutial (JTL) and
Danyor (DNR) were analyzed. Five samples were taken from each site from a
depth of 1.3 cm with the help of sterilized spatulas in sterilized jam jars and
analyzed within four hour in laboratory.15 bacteria and 7 fungi were isolated
throughout the selected sites. Mean total bacterial count (TBC) was 13.8x105
cfu/g of soil, 8.5x105cfu/g of soil and 19.4x105cfu/g of soil for DNR, GLTC and JTL
respectively and Escherichia coli was the most dominant bacteria across the
different sampling locations. Mean total fungal count (TFC) was1.7x105 cfu/g of
soil, 2x105 cfu/g of soil and 7x104 cfu/g of soil for DNR, GLTC and JTL respectively
dominated by Rhizopus oryzae. Although some isolates were common to all
sampling location but many were exclusive to these specific locations, this was
due to different agricultural practices like different types of fertilizers and water
of different quality used for irrigation.
Key words: Top soil, bacteria, fungi.

INTRODUCTION

Soil is the surface on the earth’s crust where geology and
biology meet and the land surface that provides a home to
plant, animal and microbial life (Pelczar et al., 1993). Soil
offers various types of habitats like aerobic, anaerobic and
“mini” aquatic (Prescott et al., 2005), that is why soil
sustains an immense diversity of microbes (Anderson and
Cairney, 2004), it is estimated that one gram of soil contains
bacteria 3.0 x 106 – 5.0 x 108, actinomycetes 1.0 x 106 – 2.0 x
107, fungi 5.0 x 103 – 9.0 x 106, yeast (I.0 x 103 – 1.0 x 106),
algae and protozoa 1.0 x 103- 5.0 x 105, nematodes 50 –
200 counts per gram of soil (Ogunmonye et al., 2008).
Despite this large diversity most of the microorganisms
have remained unexplored, moreover our understanding
about soil fungi is poor as compared to bacteria (Anderson
and Cairney, 2004), due to limitation of culture-based
techniques to study them (Cheryl et al., 1997). It is
estimated that only 1% of bacteria and less than 1% fungi
can be cultured by standard laboratory techniques (Jennifer
et al., 2004; Sharma et al., 2008; Torsvik and Ovreas, 2002)
due to the selective nature of the media (Garland and Mills
1991). Although soil sustains an immense diversity
nevertheless the individual genera present in soil depends
upon various factors like plant roots; that releases various
types of chemicals like ethylene, sugars, amino acids,
organic acids vitamins and polysaccharides in their root
zones which greatly effects the diversity of microbes
(Garbeva et al. 2004), seasonal fluctuation, spatial
variation, fertilizers (Torsvik et al., 2002) and soil type
(Baudoin et al 2002; Duineveld et al., 2001; Latour et al.,
1996; Buyer et al., 1999). In this study isolated bacteria and
fungi samples were taken from three selected sites,
although the study has been carried out within limited
 Academia Journal of Scientific Research; Shah and Ahmed 007

Table 1. Bacterial isolates and their distribution among the three selected sites.

Occurrence Mean Total Count X105

Bacteria
DNR GLTC JTL DNR GLTC JTL
Aeromonas salmonicida - + - - 12 -
Citrobacter rodentium - + - 9 -
Escherichia coli + + + 30 16 5
Moraxella boevrei + + + 4 2 33
Moraxella catarrhalis - - + - - 35
Moraxella lacunata - + - - 12 -
Neisseria canis + - + 4 - 23
Neisseria elongat glycolytica + - - 7 - -
Neisseria lactamica - - + - - 6
Neisseria polysaccharea - - + - - 17
Providencia stutzeri - + - - 6.4 -
Pseudomonas flavescens - - + - - 17
Pseudomonas pseudoalcaligenes + - - 10 - -
Staphylococcus aureus + + - 28 3 -
Yersinia mollaretii - + - - 1.4 -
DNR, Danyor; GLTC, Gilgit city; JTL, Jutial; - = absent and + = present.

laboratory resources due to which many species might
remain unexplored but still this study will provide an
insight about the soil microbial diversity of the region.
MATERIAL AND METHODS
Sterilization techniques
2006). A small well of depth 6 cm and width 8 cm were
decked in the four corners and in the centre, soil from the
side and bottom of the well were taken with the help of
sterilized spatula in sterilized jam jars and transferred
immediately to the laboratory where analysis was carried
out within four hour.

All the material used in this research work like jam jars,
spatulas, beakers, test tubes, pipettes, distilled water (used
for media preparation) and media were sterilized in
autoclave at 121Co for 25 min.
Media preparation
Muller-Hinton agar (MHA) was used for the culture of
bacteria while Potato Dextrose Agar (PDA) was used for the
culture of fungus; both were prepared by dissolving the
media powder in sterilized distilled water according to the
manufacturer instruction. PDA was added with
streptomycin 30g/l (Iram et al., 2009) to inhibit bacterial
growth.
Microbiological analyses
In the laboratory soil samples were mixed and the coarser
particles removed, one gram of soil was suspended in 100
ml water and then serially diluted to five fold that was used
for the microbial analysis. This method is called pore-plate
dilution described by Cappuccino and Sherman (2005).
After solidification of media, they were incubated at 37oC
for 24 and 48 h for bacteria and fungi respectively, then
colonies were counted and isolates were identified on the
basis of cultural, microscopic, and biochemical charac-
teristics with reference to Bergey’s manual of systematic
bacteriology for bacteria, and Talbot (1978) for fungi.
RESULTS

Sample collection Total bacterial count (TBC)

Three sites selected for the analysis were Gilgit City (GLTC),
Jutial (JTL) and Danyore (DNR). Five samples were taken
from each site; for the collection of each sample 5 x 5m
quadrate was selected (Ogunmonye et al., 2008). Surface
soil of 1.30 cm was removed so as to ease the removal of
plant and any coarse material (Al-Yemeni and Hashem,
A total of fifteen bacterial species are isolated and identified
during this research (Table 1), mean total bacterial count
was 13.8x105 cfu/g of soil, 8.5x105cfu/g of soil and
19.4x105cfu/g of soil for DNR, GLTC and JTL respectively
while number of species isolated from each site was 6, 8
and 7 for DNR, GLTC and JTL respectively. TBC was highest
 Academia Journal of Scientific Research; Shah and Ahmed 008

20
18

Count x 10⁵ cfu/g of soil

16
14
12
10 19
8
13.8
6
4 8.5
2
0
DNR GLTC JTL
Sampling locations
Figure 1. Average total bacterial count of Sampling locations.
DNR, Danyor; GLTC, Gilgit city; JTL, Jutial.

Table 2. Fungal isolates and their distribution among the three selected sites.

Occurrence Mean Total

Fungi
DNR GLTC JTL DNR GLTC JTL
Alterneria - + - - 2 -
Aspergillur niger - + + - 1 0.3
Aspergillus flavus + - - 2 - -
Fusavium spp + - - 1 - -
Microsprum spp - - + - - 0.9
Rhizopus oryzae + + + 3 3 -
Sclerotium spp + + + 1 2 1
DNR, Danyor; GLTC, Gilgit city; JTL, Jutial; - = absent and + = present.

in JTL and lowest in GLTC (Figure 1). TBC for Escherichia
coli was high as 35x105 while that of Yersinia mollaretii was
lowest as 1.4x105.
Total fungal count (TFC)
Seven fungi were isolated across the three sites (Table 2),
mean total fungal count (TFC) was 1.7x105 cfu/g of soil,
2x105 cfu/g of soil and 7x104 cfu/g of soil for DNR, GLTC
and JTL respectively (Figure 2), while number of species
isolated were 4, 4 and 3 for DNR, GLTC and JTL
respectively. TFC was highest in GTLC and lowest in JTL.
TFC for Rhizopus oryzae was highest as 3x105 and lowest
for Microsprum spp as 9x104.
of 104-105 likewise total fungal count was lesser then total
bacterial count, all these results were similar to that shown
by Ogunmwonyi et al. (2008) and Ingham et al. (1989).
Bacterial isolates throughout the regions were significant
though some species were common to all sampling
locations; this difference was due to the different
agricultural practices. These results corroborate with
findings of Torsvik et al. (2002). The dominant bacterial
isolates were Protobacteria; these finding corroborate with
that of Sessitsch et al. (2001). Both bacterial and fungal
isolates were similar to those which were previously
reported by other workers, but some bacterial isolates
especially species belonging to genus Moraxella were
newer to soil, these finding indicates that this region (Gilgi-
Baltistan) may harbor some distinct microbial diversity.

DISCUSSION Conclusion

Total bacterial count observed during this study was in the The results of this study shows that the soil of these
range of 105-107 while total fungal count was in the range selected locations has a large diversity which have simi-
 Academia Journal of Scientific Research; Shah and Ahmed
2.5
Count x 10⁵ cfu/g of soil
2
1.5
1 2
1.7
0.5
0
DNR
Sampling Locations
Figure 2. Average total fungal count of sampling locations.
DNR, Danyor; GLTC Gilgit city; JTL, Jutial.
larities with that of other regions of the world but these
finding cannot be considered as exhaustive because of the
limited resources of the laboratory due to which there is a
possibility of missing of certain species and other location
of the same sites may have larger diversity than the
sampling location. Some bacterial isolates were newer; that
indicates that there may be many species that are exclusive
to this region of the world but more research are needed in
this regard, as this will open doors for new research.
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Cite this article as:
Syed AHS and Khalil A (2013). Microbial analysis of
different top soil samples of selected sites in Gilgit, Gilgit-
Baltistan, Pakistan. Acad. J. Sci. Res. 1(1): 006-009.
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