Abstract
Aims: This study aimed at bioprospecting underexplored extreme habitats (Thar desert, India) for novel bio- and chemo-diversity.
Background: Bioactive metabolites from microorganisms, such as fungi from underexplored habitats, serve as basic skeletons of therapeutic agents, including antimicrobials, combating the effect of multidrug resistance of pathogens.
Objectives: The main objectives of the current study are (i) characterization of isolate TD-082 and (ii) metabolite fingerprinting of butanol extract showing antimicrobial compounds.
Methods: In search of novel antimicrobial drugs, a promising microcolonial fungus TD-082, obtained from the Thar Desert, India, was identified by ITS1–5.8S–ITS2 sequencing. Phenotypic characteristics were marked by microscopy. The fungus was investigated for antimicrobial activity against a panel of Gram-positive, Gram-negative bacteria and fungi. Butanol extract that showed the best antimicrobial activity was partially purified; fractions exhibiting antimicrobial activity were pooled and fingerprinted by GC-MS analysis.
Results: Sequencing data indicated that the isolate belonged to Aureobasidium sp. It showed 96% similarity to Aureobasidium iranianum and Kabatiella bupleuri, and 95 % to A. thailandense and A. subglaciale. Microscopy results confirmed that it belongs to Aurebasidium sp. Metabolite fingerprinting showed tentatively ten novel compounds belonging to three major categories, hydrocarbons, fatty acids, and peptides.
Conclusion: The study shows that understudied habitats, such as deserts, can provide skeletons for novel compounds from novel microorganisms. The study can be expanded to other niche habitats with higher chances of identifying more novel bioactive compounds.
Keywords: Desert, microcolonial, ITS, antimicrobial, metabolite fingerprinting, GC-MS
Graphical Abstract
[1]
Bérdy, J. Thoughts and facts about antibiotics: where we are now and where we are heading. J. Antibiot. (Tokyo), 2012, 65(8), 385-395.
[http://dx.doi.org/10.1038/ja.2012.27] [PMID: 22511224]
[http://dx.doi.org/10.1038/ja.2012.27] [PMID: 22511224]
[2]
Abdel-Razek, A.S.; El-Naggar, M.E.; Allam, A.; Morsy, O.M.; Othman, S.I. Microbial natural products in drug discovery. Processes (Basel), 2020, 8(4), 470.
[http://dx.doi.org/10.3390/pr8040470]
[http://dx.doi.org/10.3390/pr8040470]
[3]
Palmer, F.E.; Emery, D.R.; Stemmler, J.; Staley, J.T. Survival and growth of microcolonial rock fungi as affected by temperature and humidity. New Phytol., 1987, 107(1), 155-162.
[http://dx.doi.org/10.1111/j.1469-8137.1987.tb04889.x]
[http://dx.doi.org/10.1111/j.1469-8137.1987.tb04889.x]
[4]
Onofri, S.; Selbmann, L.; Zucconi, L.; Pagano, S. Antarctic microfungi as models for exobiology. Planet. Space Sci., 2004, 52(1-3), 229-237.
[http://dx.doi.org/10.1016/j.pss.2003.08.019]
[http://dx.doi.org/10.1016/j.pss.2003.08.019]
[5]
Egidi, E.; De Hoog, G.S.; Isola, D.; Onofri, S.; Quaedvlieg, W.; de Vries, M.; Verkley, G.J.M.; Stielow, J.B.; Zucconi, L.; Selbmann, L. Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies. Fungal Divers., 2014, 65(1), 127-165.
[http://dx.doi.org/10.1007/s13225-013-0277-y]
[http://dx.doi.org/10.1007/s13225-013-0277-y]
[6]
Gorbushina, A. Microcolonial fungi: survival potential of terrestrial vegetative structures. Astrobiology, 2003, 3(3), 543-554.
[http://dx.doi.org/10.1089/153110703322610636] [PMID: 14678663]
[http://dx.doi.org/10.1089/153110703322610636] [PMID: 14678663]
[7]
Zakharova, K.; Tesei, D.; Marzban, G.; Dijksterhuis, J.; Wyatt, T.; Sterflinger, K. Microcolonial fungi on rocks: a life in constant drought? Mycopathologia, 2013, 175(5-6), 537-547.
[http://dx.doi.org/10.1007/s11046-012-9592-1] [PMID: 23073825]
[http://dx.doi.org/10.1007/s11046-012-9592-1] [PMID: 23073825]
[8]
Coleine, C.; Stajich, J.E.; de Los Ríos, A.; Selbmann, L. Beyond the extremes: Rocks as ultimate refuge for fungi in drylands. Mycologia, 2021, 113(1), 108-133.
[http://dx.doi.org/10.1080/00275514.2020.1816761] [PMID: 33232202]
[http://dx.doi.org/10.1080/00275514.2020.1816761] [PMID: 33232202]
[9]
Alqaisi, A.Q.I.; Mbekeani, A.J.; Llorens, M.B.; Elhammer, A.P.; Denny, P.W. The antifungal Aureobasidin A and an analogue are active against the protozoan parasite Toxoplasma gondii but do not inhibit sphingolipid biosynthesis. Parasitology, 2018, 145(2), 148-155.
[http://dx.doi.org/10.1017/S0031182017000506] [PMID: 28486997]
[http://dx.doi.org/10.1017/S0031182017000506] [PMID: 28486997]
[10]
Price, N.P.; Bischoff, K.M.; Leathers, T.D.; Cossé, A.A.; Manitchotpisit, P. Polyols, not sugars, determine the structural diversity of anti-streptococcal liamocins produced by Aureobasidium pullulans strain NRRL 50380. J. Antibiot. (Tokyo), 2017, 70(2), 136-141.
[http://dx.doi.org/10.1038/ja.2016.92] [PMID: 27436607]
[http://dx.doi.org/10.1038/ja.2016.92] [PMID: 27436607]
[11]
Mohamed, A.; Abdel-Wahab, Ali H.; Abdallah, M.; Elgorban, E.B.; Gareth, J. High-throughput amplicon sequencing of fungi and microbial eukaryotes associated with the seagrass Halophila stipulacea (Forssk.) Asch. from Al-Leith mangroves, Saudi Arabia. Mycol. Prog., 2021, 20(10), 1365-1381.
[http://dx.doi.org/10.1007/s11557-021-01744-2]
[http://dx.doi.org/10.1007/s11557-021-01744-2]
[12]
Pridham, T.G.; Gottlieb, D. The utilization of carbon compounds by some actinomycetales as an aid for species determination. J. Bacteriol., 1948, 56(1), 107-114.
[http://dx.doi.org/10.1128/jb.56.1.107-114.1948] [PMID: 16561537]
[http://dx.doi.org/10.1128/jb.56.1.107-114.1948] [PMID: 16561537]
[13]
White, T.J.; Bruns, T.D.; Lee, S.B. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications; , 1990; pp. 315-322.
[http://dx.doi.org/10.1016/B978-0-12-372180-8.50042-1]
[http://dx.doi.org/10.1016/B978-0-12-372180-8.50042-1]
[14]
Jukes, T.H.; Cantor, C.R. Evolution of protein molecules. In: Mammalian protein metabolism; Elsevier, 1969; pp. 21-132.
[http://dx.doi.org/10.1016/B978-1-4832-3211-9.50009-7]
[http://dx.doi.org/10.1016/B978-1-4832-3211-9.50009-7]
[15]
Tamura, K.; Stecher, G.; Peterson, D.; Filipski, A.; Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol., 2013, 30(12), 2725-2729.
[http://dx.doi.org/10.1093/molbev/mst197] [PMID: 24132122]
[http://dx.doi.org/10.1093/molbev/mst197] [PMID: 24132122]
[16]
Bauer, A.W.; Kirby, W.M.; Sherris, J.C.; Turck, M. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clin. Pathol., 1966, 45(4), 493-496.
[http://dx.doi.org/10.1093/ajcp/45.4_ts.493] [PMID: 5325707]
[http://dx.doi.org/10.1093/ajcp/45.4_ts.493] [PMID: 5325707]
[17]
Nielsen, M.T.; Ranberg, J.A.; Christensen, U.; Christensen, H.B.; Harrison, S.J.; Olsen, C.E.; Hamberger, B.; Møller, B.L.; Nørholm, M.H. Microbial synthesis of the forskolin precursor manoyl oxide in an enantiomerically pure form. Appl. Environ. Microbiol., 2014, 80(23), 7258-7265.
[http://dx.doi.org/10.1128/AEM.02301-14] [PMID: 25239892]
[http://dx.doi.org/10.1128/AEM.02301-14] [PMID: 25239892]
[18]
Babushok, V.I.; Linstrom, P.J.; Zenkevich, I.G. Retention Indices for frequently reported compounds of plant essential oils. J. Phys. Chem. Ref. Data, 2011, 40(4), 043101.
[http://dx.doi.org/10.1063/1.3653552]
[http://dx.doi.org/10.1063/1.3653552]
[19]
Jiang, H.; Liu, N.N.; Liu, G.L.; Chi, Z.; Wang, J.M.; Zhang, L.L.; Chi, Z.M. Melanin production by a yeast strain XJ5-1 of Aureobasidium melanogenum isolated from the Taklimakan desert and its role in the yeast survival in stress environments. Extremophiles, 2016, 20(4), 567-577.
[http://dx.doi.org/10.1007/s00792-016-0843-9] [PMID: 27290725]
[http://dx.doi.org/10.1007/s00792-016-0843-9] [PMID: 27290725]
[20]
Sterflinger, K.; Tesei, D.; Zakharova, K. Fungi in hot and cold deserts with particular reference to microcolonial fungi. Fungal Ecol., 2012, 5(4), 453-462.
[http://dx.doi.org/10.1016/j.funeco.2011.12.007]
[http://dx.doi.org/10.1016/j.funeco.2011.12.007]
[21]
Raja, H.A.; Miller, A.N.; Pearce, C.J.; Oberlies, N.H. Fungal identification using molecular tools: A primer for the natural products research community. J. Nat. Prod., 2017, 80(3), 756-770.
[http://dx.doi.org/10.1021/acs.jnatprod.6b01085] [PMID: 28199101]
[http://dx.doi.org/10.1021/acs.jnatprod.6b01085] [PMID: 28199101]
[22]
Arzanlou, M. Aureobasidium iranianum, a new species on bamboo from Iran. Mycosphere, 2012, 3(4), 404-408.
[http://dx.doi.org/10.5943/mycosphere/3/4/2]
[http://dx.doi.org/10.5943/mycosphere/3/4/2]
[23]
Bills, G.F.; Menéndez, V.G.; Platas, G. Kabatiella bupleuri sp. nov. (Dothideales), a pleomorphic epiphyte and endophyte of the Mediterranean plant Bupleurum gibraltarium (Apiaceae). Mycologia, 2012, 104(4), 962-973.
[http://dx.doi.org/10.3852/12-003] [PMID: 22495450]
[http://dx.doi.org/10.3852/12-003] [PMID: 22495450]
[24]
Peterson, S.W.; Manitchotpisit, P.; Leathers, T.D. Aureobasidium thailandense sp. nov. isolated from leaves and wooden surfaces. Int. J. Syst. Evol. Microbiol., 2013, 63(Pt 2), 790-795.
[http://dx.doi.org/10.1099/ijs.0.047613-0] [PMID: 23178722]
[http://dx.doi.org/10.1099/ijs.0.047613-0] [PMID: 23178722]
[25]
Zalar, P.; Gostinčar, C.; de Hoog, G.S.; Ursic, V.; Sudhadham, M.; Gunde-Cimerman, N. Redefinition of Aureobasidium pullulans and its varieties. Stud. Mycol., 2008, 61, 21-38.
[http://dx.doi.org/10.3114/sim.2008.61.02] [PMID: 19287524]
[http://dx.doi.org/10.3114/sim.2008.61.02] [PMID: 19287524]
[26]
Jiang, H.; Liu, G-L.; Chi, Z.; Hu, Z.; Chi, Z.M. Genetics of trehalose biosynthesis in desert-derived Aureobasidium melanogenum and role of trehalose in the adaptation of the yeast to extreme environments. Curr. Genet., 2018, 64(2), 479-491.
[http://dx.doi.org/10.1007/s00294-017-0762-z] [PMID: 29018921]
[http://dx.doi.org/10.1007/s00294-017-0762-z] [PMID: 29018921]
[27]
Wajda, Ł.; Wyderka, M.; Polak, Z.; Duda-Chodak, A.; Makarewicz, M. Examination of novel Aureobasidium pullulans isolates dominating apple microflora and assessing their potential for apple juice spoilage. World J. Microbiol. Biotechnol., 2018, 34(8), 115.
[http://dx.doi.org/10.1007/s11274-018-2497-5] [PMID: 29998388]
[http://dx.doi.org/10.1007/s11274-018-2497-5] [PMID: 29998388]
[28]
Srivastava, N.; Nandi, I.; Ibeyaima, A.; Gupta, S.; Sarethy, I.P. Microbial diversity of a Himalayan forest and characterization of rare actinomycetes for antimicrobial compounds. 3 Biotech, 2019, 9, 27.
[29]
Ibeyaima, A.; Dwivedi, A.K.; Saini, N.; Gupta, S.; Sarethy, I.P. Saccharothrix sp. TD-093 from the Thar Desert, India: metabolite fingerprinting of antimicrobial compounds and in silico analysis. Curr. Microbiol., 2017, 74(3), 334-343.
[http://dx.doi.org/10.1007/s00284-016-1183-9] [PMID: 28120024]
[http://dx.doi.org/10.1007/s00284-016-1183-9] [PMID: 28120024]
[30]
Shortt, J.; Hsu, A.K.; Martin, B.P.; Doggett, K.; Matthews, G.M.; Doyle, M.A.; Ellul, J.; Jockel, T.E.; Andrews, D.M.; Hogg, S.J.; Reitsma, A.; Faulkner, D.; Bergsagel, P.L.; Chesi, M.; Heath, J.K.; Denny, W.A.; Thompson, P.E.; Neeson, P.J.; Ritchie, D.S.; McArthur, G.A.; Johnstone, R.W. The drug vehicle and solvent N-methylpyrrolidone is an immunomodulator and antimyeloma compound. Cell Rep., 2014, 7(4), 1009-1019.
[http://dx.doi.org/10.1016/j.celrep.2014.04.008] [PMID: 24813887]
[http://dx.doi.org/10.1016/j.celrep.2014.04.008] [PMID: 24813887]
[31]
Casella, S.; Leonardi, M.; Melai, B.; Fratini, F.; Pistelli, L. The role of diallyl sulfides and dipropyl sulfides in the in vitro antimicrobial activity of the essential oil of garlic, Allium sativum L., and leek, Allium porrum L. Phytother. Res., 2013, 27(3), 380-383.
[http://dx.doi.org/10.1002/ptr.4725] [PMID: 22610968]
[http://dx.doi.org/10.1002/ptr.4725] [PMID: 22610968]
[32]
Mends, T.M.; Yu, E.; Strobel, G.A. An endophytic Nodulisporium sp. producing volatile organic compounds having bioactivity and fuel potential. J. Pet. Environ. Biotechnol., 2012, 3(3), 1-8.
[http://dx.doi.org/10.4172/2157-7463.1000117]
[http://dx.doi.org/10.4172/2157-7463.1000117]
[33]
Idowu, O.T.; Ojo, O.A. Antimicrobial Activity and Fatty Acids from Ipomea ochraceae. Med. Chem., 2017, 7, 10.
[34]
Sivakumar, R.; Jebanesan, A.; Govindarajan, M.; Rajasekar, P. Larvicidal and repellent activity of tetradecanoic acid against Aedes aegypti (Linn.) and Culex quinquefasciatus (Say.) (Diptera:Culicidae). Asian Pac. J. Trop. Med., 2011, 4(9), 706-710.
[http://dx.doi.org/10.1016/S1995-7645(11)60178-8] [PMID: 21967693]
[http://dx.doi.org/10.1016/S1995-7645(11)60178-8] [PMID: 21967693]
[35]
Zin, N.M.; Remali, J.; Nasrom, M.N.; Ishak, S.A.; Baba, M.S.; Jalil, J. Bioactive compounds fractionated from endophyte Streptomyces SUK 08 with promising ex-vivo antimalarial activity. Asian Pac. J. Trop. Biomed., 2017, 7(12), 1062-1066.
[http://dx.doi.org/10.1016/j.apjtb.2017.10.006]
[http://dx.doi.org/10.1016/j.apjtb.2017.10.006]
[36]
Hameed, R.H.; Al-Shareefi, E.; Hameed, I.H. Determination of anti-microbial activity and characterization of metabolites produced by Neisseria gonorrhea. Indian J. Public Health Res. Dev., 2018, 9(5), 487.
[http://dx.doi.org/10.5958/0976-5506.2018.00491.6]
[http://dx.doi.org/10.5958/0976-5506.2018.00491.6]
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