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INTRODUCTION
Antibiotics are the most important natural To overcome the problem of spread
secondary metabolites produced by the soil resistant microorganisms, there is an interest
microorganisms such as bacteria and fungi to discover novel antibiotics and new
and are important in medicine as well as in therapeutic agents by continuous screening of
economy. One of the most widely distributed secondary microbial products produced from
soil microbes in the earth are that belong to potential bacterial taxa (5). Therefore
the Order Actinomycetales. Actinomycetes searching for new Actinomycetales strains in
belong to the order Actinomycetales and a new habitat is a promising way to
produce wide range of secondary overcome the problem of spread of the
metabolites. Among these microorganisms, antibiotic resistant microorganisms. In
the actinomycetes are the largest source of addition; to our knowledge, no study on the
antibiotics, anti-tumor and immune investigation and survey of the antibiotic
suppressant agents (1). Also, this Order has producing bacteria were carried out in the
the most well-known genus Streptomyces Northern part of Saudi Arabia. As far as we
which includes the largest number of species know, only the isolation and characterization
and strains in the order Actinomycetales. The of several streptomycetes strains from
genus Streptomyces is an aerobic Gram- western region soil in Saudi Arabia were
positive, spore-forming actinomycetes carried out by Malibari (6) and Atta et al.(7).
belonging to the family Streptomycetaceae Therefore, the current study was designed to
(2). Approximately 80% of the naturally describe the isolation of an antibiotic
derived antibiotics, which are in clinical use, producing Actinomycetales strain isolated
were derived from Streptomyces genus alone from soil samples collected from different
(3,4).The specific/intra-specific relationships localities at Northern part of Saudi Arabia.
in the streptomycetes and the way they are Isolation, biochemical and molecular
reflected in the biosynthetic potential to characterization and identification of the
produce bioactive compounds could Actinomycetales strain were reported. Also,
significantly influence strategies for search the antimicrobial activity of the
and discovery, screening and bioprocess Actinomycetales strain was tested against
development. several Gram negative and Gram positive
bacteria and Fungi.
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In the present study five different soil sterile distilled water and shaken vigorously
samples were collected from different to make a stock solution. From this stock
localities at Rafha Governorate in the solution, 1ml was used to prepare the final
Northern Border Region, Kingdom of Saudi volume of 10-1, 10 -2, 10 -3, 10-4 and 10 -5 by
Arabia (KSA). Soil sample from each site serial dilution method. Finally, 0.1ml of soil
was taken from the top layer of the soil sample suspension from 10-1, 10 -2, 10 -3, 10 -4
surface (0-30 cm depth) and directly and 10-5 were used to spread on sterilized
transferred into polyethylene bags to starch nitrate agar medium (g/L): Soluble
Soil samples were subjected to three sterilization using 0.1 N NaOH or 0.1 N HCl
physical and chemical pretreatment methods solutions (9)and incubated at 37°C for 7
in order to facilitate the better isolation of days; triplicates were maintained for each
actinomycetes populations (8). These soil dilution. After 7 days, the plates were
samples were air-dried and subjected to heat observed for actinomycetes colonies. The
treatment up to 40-45°C for 15 h to kill the grown actinomycete colonies were purified
Gram negative bacteria, 1.4% of the phenol using the dilution plate technique. The
solution was mixed with one gram of soil obtained purified cultures were sub-cultured
sample and incubated at room temperature on starch casein agar slants and stored at 4°C
for 10 min to kill the normal bacteria, then an for further studies. For every 30 days the
equal amounts of soil sample and CaCO3 cultures were sub-cultured freshly for better
were mixed with sufficient amount of water bioactive production.
and incubated at room temperature for one 2.4. Screening for antimicrobial activity
week to enrich the soil for better isolation of of the isolated streptomycete
actinomycetes. Testing antimicrobial activity of the
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performed by diffusion plate methods (10), DNA was extracted according to the method
based on the observation of inhibition zone of Kumar et al.(14). The extracted total
of bacterial growth on agar media. genomic DNA was used as a template for
2.5. Taxonomic characterization of the PCR reactions.
most active streptomycete NBR isolate 2.4.2.2. PCR Amplification & Sequencing
2.5.1. Conventional taxonomy The 16S rRNA of the isolate was
The characterization of isolated amplified by the following primers 10F; 5’-
streptomycetewas carried out according to AGTTTGATCCTGGCTC-3’and 1525R; 5’-
the guidelines adopted by International AAGGAGGTGATCCAGCC-, using the
Streptomyces Project (11). The cultural TopTaq Master Mix Kit (Qiagen) following
characteristics were studied according to the the manufacturer’s instruction. The PCR was
guidelines established by the ISP carried out by Gene AMP PCR System 9700
(11),colours were assessed on the scale from PE Applied Biosystems (Perkin Elmer,
indicated by Kutzner et al. (12). Micro- Ohio, USA). PCR mixture conditions were
morphological studies were carried out using performed according to El-Naggar (15). The
light and scanning electron microscope PCR products were purified using a
(JEOL JSM 5300, JEOL Technics Ltd., QIAquick PCR purification kit (Qiagen,
Japan). Diaminopimelic acid isomers in the Hilden, Germany) and were detected using a
cell-wall and whole cell sugar pattern were gel documentation system, (Alpha-Imager
analyzed using the method of Becker et 2200, CA, USA) then the purified PCR
al.(13). The physiological and biochemical product was sequenced with BigDye
characteristics; melanin pigment production, Terminator using an ABI PRISM 377 DNA
utilization of carbon and nitrogen sources, sequencer and ABI PRISM Cycle
enzymatic activities and other physiological Sequencing (Perkin Elmer, Ohio, U.S.). The
characters were also studied (11, 12). nucleotide sequence data was aligned using
2.5.2. Molecular characterization the ClustalW. A multiple sequence
2.4.2.1. DNA Extraction alignment, molecular phylogenetic analyses
The culture of the streptomycete and the phylogenetic tree were carried out by
strain NBR was inoculated into 50 ml of the DNASTAR Lasergene (V.7.1) program.
starch nitrate broth and incubated at 200 rpm RESULTS AND DISCUSSION
and 28 °C for 72 hours. The total genomic
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morphology of colonies and the texture of the Bergy's Manual of Systematic Bacteriology
aerial mycelium. The production of different more than 500 streptomycete strains; from
pigments has been widely used in these strains only 5, 15 and 14 streptomycete
classification and identification, but it is strains produce lipase, pectinase and H2S
important to mention that colony morphology respectively. This means that the production
is too variable for use as a taxonomic of lipase, pectinase as well as hydrogen
character (2). sulfide might need special environmental
2.6.2. Physiological and biochemical conditions or might be in extreme
properties environments. So we suggest that our strain
The physiological and biochemical was free from lipase, pectinase and hydrogen
characteristics of the Streptomyces strain sulfide production because it was isolated
NBR are indicated in (Table: 3). The carbon from a normal habitat.
sources utilization by this Streptomyces strain The optimum temperature for the
NBR were found positive for all carbon growth of the NBR strain was 30 oC-40 oC,
sources except for sucrose, D-galactose and but no growth was found at the high
L-rhamnose that showed no growth. temperature 50oC, as well as, lower
However, in the case of nitrogen sources temperatures 10-25oC. These results
utilization, the growth of this isolate was suggesting that our strain belongs to the
abundant and much better than the presence group of mesophilic bacteria. It is known that
of the carbon source (Table: 3). So we can the optimum growth temperature for most
conclude that the growth of the NBR isolate actinomycetes is 23-37°C (21, 22). However
can be influenced by the type of carbon and there are also thermotolerant and
nitrogen sources (7, 18-20). thermophilic actinomycetes (23).
The enzymatic activities of this The NBR strain was tolerant to the
isolate were positive with all tested enzymes NaCl concentration till 7% with good
except for lipase, pectinase and H2S growth, however there was a weak and no
production as shown in (Table: 3). growth observed at 8% and 9% NaCl
Generally, it is known that very few strains concentration respectively. Atta et al.(7) and
from streptomycetes are able to produce Das et al.(24) reported the inhibition in
lipase, pectinase and hydrogen sulfide. growth of some streptomycetes strains at
Goodfellow listed in the latest edition of the NaCl concentration higher than 7%. The
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growth pH was best at pH 7, but no growth of the 16S rRNA gene which is highly
was observed in both of the highly acidic and conserved among species, it is easily to use
highly alkaline media. These results for discrimination at species level. We were
indicated that our strain is a neutrophil (2, able to reconfirm the identity of the
25). Streptomycetes are known to prefer streptomycete strain NBR. So the 16S rRNA
neutral to alkaline environmental pH, the gene of the NBR isolate was amplified by
optimal growth pH range being 6.5 to 8.0. PCR method with total size of approximately
Kumar et al.(26) reported an isolate that has 1.5kpb (Fig. 3). Then a partial sequencing of
a pH range from 4 -12. In addition, the 16S rRNA gene was sequenced and then
acidophilic and alkalophilic streptomycetes sent to DNA database for homology search
have also been found (20, 24, 27). and FASTA analysis. Multiple sequence
In addition the NBR isolate was alignment was done using sequences of the
sensitive to the growth inhibitors sodium 16S rRNA genes of 25 Streptomyces and
azide (0.02%) and thallus acetate (0.001%). actinomyces strains from the DNA Data
Previous studies were carried out by Atta et Bank in addition to our NBR isolate.
al.(7) on Actinomycete isolate and showed Computer assisted DNA similarly searches
the inhibition of the bacterial growth at against bacterial database revealed that 16S
(0.001%) thallus acetate. However a normal rRNA sequence was 97% similar to
growth was observed in case of other growth Streptomyces coeruleorubidus strain NSWG-
inhibitors such as phenol, crystal violet as 20 (accession number JX905302). A
well as low concentration from sodium azide phylogenetic tree was constructed by the
(0.01%). Finally, this strain was resistant to DNASTAR Lasergene (V.7.1) program using
the antibiotics norfloxacin (30 µg/ml) and the nucleotide sequence of the 16S rRNA
rifampicin (50 µg/ml), however, it was gene of NBR strain as well as another 25
sensitive to erythromycin, penicillin and Streptomycesand Actinomyces strains and
others as shown in (Table: 3). showed that NBR strain is grouped with
2.6.3. Molecular and phylogenetic Streptomyces coeruleorubidus strain NSWG-
identification 20 in the same clade which indicate that our
The molecular techniques give better strain might be a new Streptomyces
and accurate identification at species-level. coeruleorubidusstrain (Fig. 4).
One of these important methods is the using
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(a) (b)
Figure (2): a; Phase-contrast micrograph of the aerial mycelium showing spiral shaped mycelium (x600) b; Scanning
electron microscopy (SEM) showing a smooth spore surface (x7500) of actinomycete isolate, NBR grown on inorganic
salts-starch agar (ISP-4) for 21 days.
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Aerial Diffusible
Medium Growth Substrate mycelium
mycelium pigments
Tryptone-yeast extract broth (ISP– Dark yellow White
Weak None
1) (ISCC-NBS 88) (ISCC-NBS 263)
Pinkish Gray Moderate gray Gray red purple
Yeast -malt extract agar (ISP–2) Good
(ISCC-NBS 10) (ISCC-NBS 265) (SCC-NBS 245)
Oatmeal agar Slightly purple Pinkish Gray Very deep red purple
Good
(ISP–3) (ISCC-NBS 218) (ISCC-NBS 10) (SCC-NBS 243)
Inorganic-trace salt- starch agar Pinkish gray Pinkish gray Very deep red purple
Good
(ISP–4) (ISCC-NBS 10) (ISCC-NBS 10 (ISCC-NBS 243)
Pinkish gray (ISCC- White Very deep red purple
Glycerol-asparagine agar (ISP–5) Good
NBS 10) (ISCC-NBS 263) (ISCC-NBS 243)
Peptone-yeast extract iron agar Dark yellow Deep gray Deep olive brown
Moderate
(ISP–6) ISCC-NBS 88) (ISCC-NBS 266) (ISCC-NBS 96)
Tyrosine agar -
No growth - -
(ISP–7)
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a
(-) = Negative or no growth, b(+) = Positive or moderate growth, c(+++) = Abundant (Very good growth), d(++) = Good
growth, e(wg) = Weak growth.
Table (4): Antimicrobial activities of the culture filtrate from Streptomycessp strain NBR
Test organism Mean diameter of inhibition zone (mm)
Bacteria
Bacillus subtilis (ATCC 6633) 27.00
Staphylococcus aureus (ATCC 6538) 18.00
Escherichia coli (ATCC 7839) 19.00
Pseudomonas aeruginosa (ATCC 9027) 14.00
Yeasts
Candida albicans (ATCC 10231) 22.0
1.5
Figure (3): Amplified fragment of 16S rRNA gene, (M): 100 bp DNA
Ladder
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Figure (4): The phylogenetic tree of Streptomyces sp.strain NBR was constructed using the neighbor-joining method with
aid of DNASTAR Lasergene (V.7.1).
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