Isolation and Screening of Soil Penicillium sp VIT-2012 Metabolites against Methicillin Resistant Staphylococcus aureus
Manjunath Sangappa, Dr. Padma Thiagarajan*
School of Biosciences and Technology (SBST), VIT University, Vellore, India. Vellore-632014
*Corresponding Author E-mail: p.padma@vit.ac.in
ABSTRACT:
Sixty one fungal colonies, belonging to five genera, viz., Penicillium, Fusarium, Aspergillus, Cladosporium and Trichoderma and ten species, were isolated from soil. Among them, Penicilliun sp were found to be dominant. Metabolites from 50% of the organisms were active against methicillin resistant Staphylococcus aureus (MRSA). Penicillium sp VIT-2012, with highest activity, was selected for study of effect of temperature and pH on production of metabolties and biomass of the fungus. The maximum biomass was noticed at 300C and pH 7.0 on Manju Kori Broth and highest anti-MRSA activity was noticed under the same conditions but at a pH of 6.0. Mass production of metabolites was carried using optimum conditions. The crude metabolites extracted were checked for minimum inhibitory concentrations (MIC) which was found to be 25µg and 12.5 µg against seven and three MRSA isolates respectively. FTIR indicated the peaks for carboxylate anion, C-H, C-C, C-O and carboxylic acid dimer. GC-MS analysis revealed the active principle to be either dibutyl phthalate, 1, 2-benzenedicarboxylic acid or butyl 2-methylpropyl ester or their derivatives. 28S rDNA gene of Penicillium sp VIT-2012 showed 99% similarity with Penicillium radicum.
KEYWORDS: Soil fungi, Penicillium sp VIT-2012, Drug resistant bacteria, Anti MRSA activity, MIC.
1.0 INTRODUCTION:
Drug resistance is a rapidly growing universal problem which is compounded by the short reproductive rates of microbes. Incomplete antibiotic treatment of patients and inappropriate usage of antimicrobials as food preservatives exacerbates this issue. Managing the use of medically important antibiotics in all kind of food products is very important to reduce risks from drug resistant pathogens. Frequent usage of antimicrobials in livestock may lead to the development of more virulent and multidrug resistant microbes which transmit from animals to humans1. National Antimicrobial Resistance Monitoring System (NARMS) retail meat report 2010 revealed that meat and poultry products are contaminated with multidrug-resistant bacteria belonging to the species Campylobacter, Salmonella, Enterococcus and Escherichia coli2. Staphylococcus aureus was found to be the most overriding multidrug resistant pathogen in 136 meat and poultry samples collected from five US cities3. A study conducted on the dissemination of drug resistant S.aureus in hospital wards, public places, both indoor and outdoor and poultry farms mainly revealed that air is the possible mode of transmission for these microbes 4-6.
Future world would be most treacherous if the problem of drug resistance is neglected. Hence search for strong antimicrobial compound(s) active against drug resistant pathogens, may possibly be the key for disease control. The genus Penicillium is known for the production of secondary metabolites that include drugs against MRSA 7, cancer 8 and malarial parasite 9. Both bacteria and fungi from marine environments have been reported to produce metabolites with anti-MRSA activity 10,11. In contrast, reports of anti-MRSA compounds isolated from soil environment, especially soil fungi, are very few. The present study involved the isolation and screening of soil fungal metabolites against clinical isolates of MRSA.
Clinical isolates:
10 clinical isolates of MRSA obtained from Narayani Hospital, Vellore, India. All experiments were conducted in triplicate and mean of three values were used for the graphical presentation and tabulation.
2.1 Collection of soil sample and its analyses:
Soil sample was collected using sterile techniques, during the month of July-August 2010, Vellore, India. Top soil vegetation was cleared and sample was collected from 20 cm depth. Subsequently, a thermometer was inserted in deep soil for 10 minutes and temperature was recorded. pH was determined in slurry of 10 grams soil prepared in 50 ml of distilled water. Chemical and biological properties of soil were analysed by Shri AMM Murugappa Chettiar Research Centre (MCRC), Taramani, Chennai by following an alternative analytical indigenous technology developed by them and IIT (M). Chemical analyses and estimations carried out were the total organic carbon, NPK, Ca, Mg, Na, Fe, Mn, Cu, Zn, B, Mo, Sulphate and humus along with total minerals. Chromatogram of soil sample was prepared at MCRC using recommendations from Bio-Dynamic association of India12, (http://www.biodynamics.in/ chrom.htm).
2.2 Isolation and identification of fungi and screening of their metabolites for anti-MRSA activity:
Soil fungi were isolated using the soil dilution method13. Colony characteristics were compared with data outlined in standard manuals14, literature reports15 and fungal database, available with International Mycological Association. Screening of metabolite’s antibacterial activity was carried out by growing fungi in Yeast Extract Sucrose broth (YESB) of pH 7.0 ± 0.2. In 5ml of sterile YESB, 8mm agar block of each fungus was inoculated and tubes were incubated at room temperature (280C) for ten days. After incubation period, 100µl of each YESB was taken and checked for antibacterial activity by agar well diffusion method 16. Based on these results, the fungus which showed the highest activity i.e., Penicillium sp VIT-2012, was selected for further studies.
2.3 Selection of medium, temperature and pH for production of biomass and anti-MRSA metabolites of Penicillium sp VIT-2012:
In order to select the best medium that support for synthesis of anti-MRSA metabolites , Penicillium sp VIT-2012 was grown in five fungal media viz., SDB, Malt Extract Broth (MEB), YESB, CYB and MKB. MKB was an artificially designed medium based on the soil analyses report. The tubes were incubated for 10 days at room temperature (300C) after which their antibacterial activity was assessed by agar well diffusion method. The medium in which highest anti-MRSA activity was found was considered as optimum medium. To determine the optimum temperature, 25ml of MKB was prepared in 100ml conical flasks and were inoculated with 1ml of 106conidia/ml of Penicillium sp VIT-2012. Flasks were incubated at 50C, 100C, 150C, 200C, 250C, 300 C, 350 C, 400C and 450C for 10 days. Determination of optimum pH was carried out at the optimum temperature. All conditions like quantity of inoculum, medium and incubation time were maintained similar to the temperature experiments and the pH was adjusted from 3.0 to 9.0 at one pH unit intervals. On 10th day, anti-MRSA activity, in terms of zone of inhibition and biomass (both wet and dry weights) were measured for temperature and pH experiments.
2.4 Mass production and determination of MIC of crude ethyl acetate extract of Penicillium sp VIT-2012:
2.5 UV, FT-IR and GC-MS Analyses of crude extract:
A small amount of the mat extract was pelletized with KBr and the spectrum was recorded for functional group analysis. Extract was also analysed by GCMS, after filteration through membrane (0.45µm pore size) and data was interpreted through computer software TurboMass ver. 5.4.2 and matched with NISTO2 2008 version library.
2.6 Phylogeny of Penicillium sp VIT-2012 based on 28S rDNA sequencing
Penicillium sp VIT-2012 was sequenced for 28S rDNA gene for identification17,18. Fungal DNA was isolated and amplified using the forward (LR0R-5’-ACCCGCTGAACTTAAGC-3’) and reverse (D1/D2-NL4–5’-GGTCCGTGTTTCAAGACGG-3’) universal primers of large subunit 28S rDNA gene. The resultant 718 nucleotide 28S rDNA sequence was matched with NCBI database in Blast and submitted to GenBank of NCBI.
RESULTS:
The temperature and pH of soil sample were found to be 300C and 7.0 ±0.2 respectively. Its chromatogram revealed a prominent inner zone of diameter 3.1cm and was pinkish brown. The middle zone of diameter of 2.2 cm was dark brown in colour. No outer zone was observed but small protrusion of spikes into it was seen (Fig.1). Among macronutrients and micronutrients, the amount of nitrogen and phosphorus were found to be at low and boron and molybdenum were not detected. On the other hand, the concentration of calcium, magnesium, iron, manganese, copper and humus were high. Optimum concentrations of organic carbon, zinc, potassium and sulphur were found (Table 1).
Table 1: Chemical properties of soil sample:
Soil property |
OC |
HA |
N |
P |
K |
Ca |
Mg |
Na |
Fe |
Mn |
Cu |
Zn |
Sulfate |
Conc. |
0.77 |
161 |
110.2 |
10.74 |
94.87 |
433 |
170 |
124 |
14 |
11.5 |
2.2 |
0.76 |
14.22 |
Rec. level MCRC |
0.75-1.5 |
18 -31 |
113-182 |
18-36 |
60-138 |
>300 |
10-15 |
- |
6-8 |
1.2-2.5 |
0.3-1 |
1.5-1 |
10-15 |
[Note: Organic Carbon (OC ) in %, humus (HA) to K in Kg/acre of soil, Ca to Sulfate in Mg/Kg of soil]
Table 2: Enzymatic and microbial properties of soil sample:
Soil property |
Protease (µgs Tyr/g/hr) |
Cellulase (µgs Tyr/g/hr) |
Invertase (µgs Tyr/g/hr) |
Bacteria (109cfu/gm) |
Actinomycetes (106cfu/gm) |
Rhizobium (106cfu/gm) |
Fungi (106cfu/gm) |
Conc. |
49.5 |
0.371 |
0.178 |
20 |
0.8 |
100 |
23 |
Bacteria were the dominant microbial flora in soil sample, especially those of Rhizobium species. This may be due to association of Rhizobium with roots of the vegetation. The second largest population was that of fungi. Among the soil enzymes, protease activity was found to be the maximum followed by that of cellulase and invertase (Table 2).
From the soil sample, sixty one fungal colonies, belonging to five genera viz., Penicillium, Fusarium, Aspergillus, Cladosporium and Trichoderma were isolated. Among these, ten species were identified, of which Penicillium sp and Fusarium sp were dominant followed by Aspergillus sp Cladosporium sp and Trichoderma sp. The metabolites from five isolates were found to be active. Genus Penicillium, comprising of 30%, showed highest activity, followed by Aspergillus (10%) and Trichoderma (10%) (Fig. 2).
Fig 1: Showing chromatogram of soil sample.
Fig 2: Total number of fungal species isolated from soil sample and anti-MRSA activity.
The zone of inhibition (in mm), of these metabolites against MRSA, for growth between 4th to 20th day, is shown in (Table 3).
Table 3: Anti-MRSA activity of soil fungi screened from 4th day to 20th day.
[a Mean value of three, b Days of incubation]
Soil sample |
The organisms |
Zone of inhibition (mma) |
||||
4b |
8b |
12b |
16b |
20b |
||
02VITLB |
Aspergillus niger |
Nil |
Nil |
10 |
Nil |
Nil |
02VITLB |
Penicillium sp1 |
Nil |
Nil |
Nil |
05 |
08 |
02VITLB |
Penicillium sp VIT-2012 |
Nil |
08 |
10 |
16 |
18 |
02VITLB |
Penicillium sp4 |
Nil |
Nil |
Nil |
Nil |
08 |
02VITLB |
Trichoderma sp1 |
Nil |
Nil |
Nil |
Nil |
05 |
Among Penicillium isolates, only one species i.e., Penicillium sp VIT-2012 showed maximum and constant activity from 8th to 20th day of growth . Hence this isolate was selected for further studies. The metabolites of Penicillium sp VIT-2012 showed the maximum anti-MRSA activity on MKB compared to rest of the media (Fig. 3).
Fig 3: AntiMRSA activity and medium selection of Penicillium sp VIT-2012.
Penicillium sp VIT-2012 was identified by growing on different fungal media and also by SEM and 28S rDNA sequencing. Three point inoculation of Penicillium sp VIT-2012, on three fungal media, indicated colony morphology resembling that of its close relavtive Penicillium radicum19. On CYA , colony morphology showed cottony white mycelium with a yellow center. Yellowish green colour mycelia were observed on MEA surrounded by yellow colour vegetative mycelia. Light pigmentation was seen at the backside of the colony on CYA and MEA. However, the colony on SBD was yellow in colour, and contained constrictions radiating from its centre. SEM results of Penicillium sp VIT-2012 indicated the long stipe containing terverticillium metulae. Each matula contained conical shaped shrunken philides and was brush like in appearance. Conidia were arranged in chains which grew from each philide. The shape of the conidia were ellipsoidal, wrinkled and shruken with smooth surface (Fig. 4).
Phylogenetic tree analysis of experimental isolate constructed based on 28S rRNA gene sequence indicated its close relation with P. radicum. The Blast results showed 99% homology with P. radicum and a new isolate had emerged in lower clad as a separate branch, indicating new isolate19.The 718 nucleotide sequence was deposited in the GenBank database in NCBI with Accession No JX908779 (Fig. 5).
On this most favorable medium, i.e. MKB, neither growth nor activity were noticed between 00C to 200C and 400C and 450C. However, activity was observed at 250C and 350C in terms of zone of inhibition. The maximum activity was seen at 300C. Growth of the organism commenced from 150C with maximum growth being observed at 300C, measured in terms of wet and dry biomass. The growth decreased beyond this temperature. Penicillium spVIT-2012 was found to grow at a wide range of pH, and growth, as well as anti-MRSA activity, of its metabolites was observed at almost all pH values, i.e., from 3.0 to 9.0. Activity was found to be comparable between pH 4 and 9 with significantly higher values being observed at pH 6.
However, maximum biomass was produced at pH 7.0 (Fig. 6).
Mass production of anti-MRSA metabolites on MKB, at optimum temperature 30OC and pH 6 yielded 280 milligrams broth extract and 2.156 grams of mat extract. Both extracts showedstrong anti-MRSA activity against ten clinical isolates checked at mg/ml concentration. But the highest antiMRSA activity found in mat extract in contrast to broth extracts. Further the MIC values of mat extract were found to be 25µg against seven isolates and 12.5µg against three isolates in comparison to 1.6 µg MIC value of standard drug vancomycin (Table 4).
Fig 4: Colony morphology dentification of Penicillium sp VIT-2012 on different media. (A- CYA, B-MEA, C- SDB, D-SEM )
Fig.5: Phylogenetic tree constructed based on 28S rDNA sequence data of Penicillium sp VIT-2012 using neighbour-joining method.
Fig. 6: Effect of temperature and pH on (a) anti-MRSA activity (b) growth of Penicillium sp VIT-2012.
Table 4: MIC values of crude extract of Pencillium sp VIT-2012 and vancomycin tested against 10 cliniical MRSA isolates.
[M- Methicillin resistant Staphylococcus aureus]
Clinical isolates |
M1 |
M2 |
M3 |
M4 |
M5 |
M6 |
M7 |
M8 |
M9 |
M10 |
Crude extract (µg) |
25 |
25 |
12.5 |
25 |
25 |
12.5 |
12.5 |
25 |
25 |
25 |
Vancomycin (µg) |
1.6 |
1.6 |
1.6 |
1.6 |
1.6 |
1.6 |
1.6 |
1.6 |
1.6 |
1.6 |
The FTIR analysis indicated the peaks at 1633, 1452,1402, 1259, 1080,933 and 744 cm-1. Highest percentage of transmittance was observed at for 1633 cm-1 (Fig. 7).
Fig7: FTIR spectra of crude extract of Penicillium sp VIT-2012.
GC analysis produced retention times, varying from 14.29 to 16.74 minutes, for ten components whose relative abundance spanned between 100% to 5% (Fig. 8).
Fig 8: GC analysis of crude extract of Penicillium sp VIT-2012.
Table 5: Most probable compounds identified in crude ethyl acetate extract of Penicillium sp VIT-2012 by GC-MS analysis
REV |
for |
Compound Name |
M.W |
Formula |
934 |
924 |
Dibutyl Phthalate |
278 |
C16H22O4 |
928 |
903 |
1,2-Benzenedicarboxylic Acid, Butyl 2-Methylpropyl Ester |
278 |
C16H22O4 |
916 |
892 |
Dibutyl Phthalate |
278 |
C16H22O4 |
915 |
871 |
Dibutyl Phthalate |
278 |
C16H22O4 |
901 |
871 |
1,2-Benzenedicarboxylic Acid, Bis(2-Methylpropyl) Ester |
278 |
C16H22O4 |
884 |
855 |
Phthalic Acid, Butyl Hexyl Ester |
306 |
C18H26O4 |
876 |
848 |
1,2-Benzenedicarboxylic Acid, Butyl Cyclohexyl Ester |
304 |
C18H24O4 |
870 |
838 |
Phthalic Acid, Isobutyl 2-Pentyl Ester |
292 |
C17H24O4 |
869 |
818 |
Phthalic Acid, Butyl Non-5-Yn-3-YL Ester |
344 |
C21H28O4 |
864 |
832 |
Phthalic Acid, Butyl 2-Pentyl Ester |
292 |
C17H24O4 |
858 |
830 |
1,2-Benzenedicarboxylic Acid, Bis(2-Methylpropyl) Ester |
278 |
C16H22O4 |
853 |
818 |
Phthalic Acid, Isobutyl 4-Octyl Ester |
334 |
C20H30O4 |
852 |
788 |
Phthalic Acid, Butyl 4-Nitrophenyl Ester |
343 |
C18H17O6N |
850 |
820 |
1,2-Benzenedicarboxylic Acid, Bis(2-Methylpropyl) Ester |
278 |
C16H22O4 |
850 |
818 |
Phthalic Acid, Butyl Isoporpyl Ester |
264 |
C15H20O4 |
849 |
783 |
Phthalic Acid, Butyl Hex-2-YN-4-YL Ester |
302 |
C18H22O4 |
848 |
828 |
1,2-Benzenedicarboxylic Acid, Butyl 2-Ethylhexyl Ester |
334 |
C20H30O4 |
846 |
813 |
1,2-Benzenedicarboxylic Acid, Butyl Octyl Ester |
334 |
C20H30O4 |
842 |
812 |
Phthalic Acid, Isobutyl Non-5-YN-3-YL Ester |
344 |
C21H28O4 |
838 |
803 |
Phthalic Acid, Butyl Nonyl Ester |
348 |
C21H32O4 |
3.0 DISCUSSION:
Resistance to MRSA is emerging as a life threatening issue the world over, and the search for new compounds, to combat this problem, forms an important area of active research. These compounds may emerge from a wide variety of natural habitats, comprising of plant and microbial populations, and one such relatively under explored environs is the soil and its fungal population. Hence the current study was aimed to isolate and screen specific soil fungal metabolites for their activity against MRSA. Certain fungi, under favourable conditions of growth, may not produce an anti MRSA compound, but at times, due to fluctuations in physical and chemical nature of soil, they may present with altered physiology as a natural adaptation. This may lead to the production of specific secondary metabolites which otherwise may not be formed under regular conditions of growth. Temperature is a key environmental factor in the biosynthesis of secondary metabolites as reported for fumonisins and moniliformin by Fusarium oxysporum and ergosterol by Fusarium proliferatum20. pH also plays an important role in their production as reported for Penicillium caseifulvum21. In our study, the fungus, Penicillium sp VIT-2012 was found to grow best at 300C in laboratory conditions with the same temperature being observed in the area of sampling also, which is otherwise a high temperate region. However, the sampling temperature was 300C as monsoon had set in during soil collection. The soil pH of 7.0, found during collection is probably due to even distribution of its acidic and basic constituents like humus, proteins, etc. The fungus was found to be thriving at this pH, although in general, fungi as known to be largely acidophilic. An adaptation may probably be the cause for the same.
Paper Chromatography was done here to detect the minerals, organic carbon, humus and protein which were separated into different layers or zones. The colour intensity and diameter of each zone indicates the concentration of respective chemical constituents in soil. Pinkish brown colour of inner zone and its diameter size revealed that the soil sample is rich in minerals (except for nitrogen and phosphorus) which are evenly distributed and this fact is supported by soil analysis report (Table 1). The dark brown colour of middle zone shows the presence of acidic humus and organic compound (starch) present in the sample. The improper protrusion of blunt spikes into the outer zone reveals the presence of low amount of proteins. The maximum population was seen for Rhizobium sp which is associated with grass roots and this may be because the soil was collected from grassland area.
In many fungi, macroelements and microelements were found to be gene regulators, not only for synthesis of bioactive compounds, but also for carrying out other cellular activities. In Aspergillus flavus and Fusarium graminearum, Zn2+, Cu+2, Fe+2 are known to regulate the growth, development and production of aflatoxin and zearalenone by metal modulated gene expression phenomenon22. The appropriate combination and concentration of elements seem to play an important role in secondary metabolite production. Combination of K2HPO4, KCl and MgSO4 and sodium nitrate-nitrogen (0.24-0.48 g/l) are ideal to enhance the sclerotium formation and production of carotenoid by Penicillium sp. PT95 23. Soil sample in the present study had metals like Mg, Fe, Mn, Cu in high concentrations along with humus and low amount of N and P. However their influence on growth and anti-MRSA activity of Penicillium sp VIT-2012 metabolites needs further analyses. Fungal diversity is reported to be different between seasons24. Though different categories of secondary metabolites have been isolated from marine fungi, soil fungi were also found to be equally potent producers of secondary metabolites including that of anti-MRSA compounds. In the soil sample under study, Penicillium and Fusarium were the dominant organisms. Genus Penicillium is well known for the production of antibacterial secondary metabolites. Due to their versatility in nutrient requirements and production of a number of secondary metabolites active against many bacteria and fungi, they would have surpassed the remaining soil fungi in growth.
The UV absorption peaks obtained for the components of the extract corresponds to the different components of secondary metabolites. Thirteen peaks are seen which infers that at least this many groups of compounds are present in the crude extract and any of these may have the antibacterial activity. The maximum OD is obtained at 207nm but this may or may not be the active compound.
The strong symmetrical stretching band of FTIR at 1633 cm and weaker peak at 1402cm corresponds to carboxylate anion. The moderately intense band at 744cm in the low frequency region indicates presence of carboxylic acid dimer and also indicates C-H bending of aromatic compounds. The peak at 1452 may indicate the presence of aromatic skeleton (1600-1300) and this is supported by the lack of strong band at a low frequency area (900-650). From these results it may be inferred that phthalic acid, benzenedicarboxylic acid and or its derivatives may be present as part of the metabolites. 1452 band also reveals the presence of cyclohexane which is evident for hexyl derivative of phthalic acid (Phthalic acid, Butyl Hex-2-YN-4-YL Ester) shown in Table 4. Presence of Butyl 2-Methylpropyl Ester may be supported by C-H bending for CH3 at 1452, C-C stretching vibration at 1080 and 933. The peak 1259 is due to C-H bending vibration (overtone) 28. On the TLC sheet, four spots of crude extract designated the four groups of the metabolites. Each spot may have different types of components. The MS analysis of highest peak of GC i.e., 15.23 (100% relative abundance) corresponds to phthalate, 1, 2-benzenedicarboxylic acid, butyl 2-methylpropyl ester or butyl ester and their derivatives. No reports of their anti-MRSA activity are available in the literature. However the type, potentialilty and toxicity of the compound can be justified based on the futher purification of the crude extract.
However, it is expected from this study that a metabolite synthesised from Penicillium sp VIT-2012 may be a unknown compound as understood from the preliminary analysis of its crude extract by GC-MS studies. Further purification and structural elucidation of the pure compound from Penicillium sp VIT-2012, which is under progress, may confirm this inference.
4.0 ACKNOWLEDGEMENT:
The authors acknowledge VIT University, Vellore, India, for providing the infrastructure and financial support for carrying out this research work.
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Received on 20.09.2013 Modified on 21.10.2013
Accepted on 30.10.2013 © RJPT All right reserved
Research J. Pharm. and Tech. 6(12): Dec. 2013; Page 1340-1349