The Isolation Rate of Culturable Actinomycetes from Malaysian Borneo Forests and Their Activity Against Mammalian GSK-3β

Main Article Content

Fauze Mahmud
Salahaudin Maili
Dg. Nur Azierah Fachyuni Abdul Aziz
Levianita Marajin
Mary Jembun
Siew Eng How
Jualang Azlan Gansau
Hasidah Mohd. Sidek
Noor Embi
Ping-Chin Lee*

Abstract

More than ten types of forests can be found in Sabah, Malaysian Borneo. Studies comparing culturable actinomycetes potential in this region are relatively scarce. This study described a preliminary statistical comparison of culturable actinomycetes isolation rates and their biological activity against mammalian glycogen synthase kinase-3 (GSK-3β). We isolated 1049 isolates using standard isolation media for actinomycetes (HVA, ISP4 and AIA) with distinctive morphologies from the main forest types in Sabah; primary, secondary, mangrove, and beach forests. Isolate prevalence analysis revealed that secondary forests had the highest soil-to-isolate ratio (1:11). Interestingly, Kruskal-Wallis analysis revealed no significant differences in the overall isolation rates of actinomycetes, including non-sporulating strains, between forest types (P-value=0.142). The crude extracts of these isolates were assayed against GSK-3β, and we identified 19 active isolates; nine from primary and nine from secondary forests (no significant mean difference (P-value=0.558), one from beach forests, and none from mangrove forests. Overall, despite the different sampling locations and soil types, the isolation rates of culturable actinomycetes in Sabah did not vary significantly. However, both primary and secondary forests yielded more actinomycetes isolates that were active against mammalian GSK-3β than mangrove and beach forests. Hence, secondary forests are an attractive alternative to primary forests for exploring bioactive compounds from culturable actinomycetes in Sabah.


Keywords: actinomycetes; Sabah rainforests; statistical comparison; isolation rate; GSK-3β inhibitor


*Corresponding author: E-mail: leepc@ums.edu.my


 

Downloads

Download data is not yet available.

Article Details

Section
Research Articles

References

[1] Hussein, R.A. and El-Anssary, A.A., 2019. Plants secondary metabolites: The key drivers of the pharmacological actions of medicinal plants. In: P. Builders, ed. Herbal Medicine. London: IntechOpen Limited, pp. 11-30.
[2] Patin, N. V., Schorn, M., Aguinaldo, K., Lincecum, T., Moore, B.S. and Jensen, P.R., 2017. Effects of actinomycete secondary metabolites on sediment microbial communities. Applied and Environmental Microbiology, 83(4), https://doi.org/10.1128/AEM.02676-16.
[3] Zaynab, M., Fatima, M., Abbas, S., Sharif, Y., Umair, M., Zafar, M.H. and Bahadar, K., 2018. Role of secondary metabolites in plant defense against pathogens. Microbial Pathogenesis, 124, 198-202.
[4] Das, R., Romi, W., Das, R., Sharma, H.K. and Thakur, D., 2018. Antimicrobial potentiality of actinobacteria isolated from two microbiologically unexplored forest ecosystems of Northeast India. BMC Microbiology, 18(1), 71, https://doi.org/10.1186/s12866-018-1215-7.
[5] Lichota, A. and Gwozdzinski, K., 2018. Anticancer activity of natural compounds from plant and marine environment. International Journal of Molecular Sciences, 9(11), 3533, https://doi.org/10.3390/ijms19113533.
[6] Morales-Hidalgo, D., Oswalt, S.N. and Somanathan, E., 2015. Status and trends in global primary forest, protected areas, and areas designated for conservation of biodiversity from the global forest resources assessment 2015. Forest Ecology and Management, 352, 68-77.
[7] Potapov, P., Hansen, M.C., Laestadius, L., Turubanova, S., Yaroshenko, A., Thies, C., Smith, W., Zhuravleva, I., Komarova, A., Minnemeyer, S. and Esipova, E., 2017. The last frontiers of wilderness: Tracking loss of intact forest landscapes from 2000 to 2013. Science Advances, 3(1), e1600821, https://doi.org/10.1126/sciadv.1600821.
[8] Zeng, Z., Estes, L., Ziegler, A.D., Chen, A., Searchinger, T., Hua, F., Guan, K., Jintrawet, A. and Wood, E.F., 2018. Highland cropland expansion and forest loss in Southeast Asia in the twenty-first century. Nature Geoscience, 11, 556-562.
[9] Khan, M.A.W., Bohannan, B.J.M., Nüsslein, K., Tiedje, J.M., Tringe, S.G., Parlade, E., Barberán, A. and Rodrigues, J.L.M., 2019. Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils. FEMS Microbiology Ecology, 95(2), 1-12.
[10] Payne, J., 2011. Wild Sabah: The Magnificent Wildlife and Rainforests of Malaysian Borneo, Oxford: John Beaufoy Publishing.
[11] Bryan, J.E., Shearman, P.L., Asner, G.P., Knapp, D.E., Aoro, G. and Lokes, B., 2013. Extreme differences in forest degradation in Borneo: Comparing practices in Sarawak, Sabah, and Brunei. PLoS ONE, 8(7), e69679, https://doi.org/10.1371/journal.pone.0069679.
[12] Crouzeilles, R., Ferreira, M.S., Chazdon, R.L., Lindenmayer, D.B., Sansevero, J.B.B., Monteiro, L., Iribarrem, A., Latawiec, A.E. and Strassburg, B.B.N., 2017. Ecological restoration success is higher for natural regeneration than for active restoration in tropical forests. Science Advances, 3(11), e1701345, https://doi.org/10.1126/sciadv.1701345.
[13] Ang, C.C., O'Brien, M.J., Ng, K.K.S., Lee, P.C., Hector, A., Schmid, B. and Shimizu, K.K., 2016. Genetic diversity of two tropical tree species of the Dipterocarpaceae following logging and restoration in Borneo: high genetic diversity in plots with high species diversity. Plant Ecology and Diversity, https://doi.org/10.1080/17550874.2016.1270363.
[14] Queiroz, C., Beilin, R ., Folke, C. and Lindborg, R., 2014. Farmland abandonment: Threat or opportunity for biodiversity conservation? A global review. Frontiers in Ecology and the Environment, 12(5), 288-296.
[15] Basham, E.W., González del Pliego, P., Acosta-Galvis, A.R., Woodcock, P., Medina Uribe, C.A., Haugaasen, T., Gilroy, J.J. and Edwards, D.P., 2016. Quantifying carbon and amphibian co-benefits from secondary forest regeneration in the Tropical Andes. Animal Conservation, 19(6), 1-13.
[16] Zakaria, M. and Rajpar, M.N., 2015. Assessing the fauna diversity of Marudu Bay mangrove forest, Sabah, Malaysia, for future conservation. Diversity, 7(2), 137-148.
[17] Mohd-Azlan, J., Nurul-Asna, H., Jailan, T.S., Tuen, A.A., Engkamat, L., Abdillah, D.N., Zainudin, R. and Brodie, J.F., 2018. Camera trapping of terrestrial animals in Tanjung Datu National Park, Sarawak, Borneo. Raffles Buletin on Zoology, 66, 587-594.
[18] Hughes, A.C., 2017. Understanding the drivers of Southeast Asian biodiversity loss. Ecosphere, https://doi.org/10.1002/ecs2.1624.
[19] Miyashita, N.T., Iwanaga, H., Charles, S., Diway, B., Sabang, J. and Chong, L., 2013. Soil bacterial community structure in five tropical forests in Malaysia and one temperate forest in Japan revealed by pyrosequencing analyses of 16S rRNA gene sequence variation. Genes and Genetic Systems, 88, 93-103.
[20] Png, K.K. and Lee, P.-C., 2020. Isolation and classification of antimicrobial producing microroganisms from mangroves in Sabah. International Journal of Agriculture, Forestry and Plantation, 10, 202-208.
[21] Muramatsu, H., Shahab, N., Tsurumi, Y. and Hino, M., 2003. A comparative study of Malaysian and Japanese Actinomycetes using a simple identification method based on partial 16S rDNA sequence. Actinomycetologica, 17, 33-43.
[22] Hackl, E., Pfeffer, M., Donat, C., Bachmann, G. and Zechmeister-Boltenstern, S., 2005. Composition of the microbial communities in the mineral soil under different types of natural forest. Soil Biology and Biochemistry, 37(4), 661-671.
[23] Abdelmohsen, U.R., Grkovic, T., Balasubramanian, S., Kamel, M.S., Quinn, R.J. and Hentschel, U., 2015. Elicitation of secondary metabolism in actinomycetes. Biotechnology Advances, 33(6 Pt 1), 798-811.
[24] Lewis, K., Epstein, S., D’Onofrio, A. and Ling, L.L., 2010. Uncultured microorganisms as a source of secondary metabolites. Journal of Antibiotics (Tokyo), 63(8), 468-476.
[25] Shin, L.N., Yung, C.V.L., Daim, S., Wai, L.C., Ling, K.C., Koon, L.B., Ching, L.A., Chahil, J.K., Janim, J. and Choke, H.C., 2009. Screening for eukaryotic signal transduction and Mycobacterium isocitrate lyase inhibitor from actinomycetes and fungi of dipterocarp rain forests at Imbak Valley, Sabah, Malaysia. Journal of Tropical Biology and Conservation, 5, 87-117.
[26] Ho, W.., Chan, K.., Vui, B., Lim, S.., Ngao, W.., Tong, M.., Teh, S.., Vun, S.., Mak, K., L.J, R., Fay, J.., Deosing, F., Peter, J., Hew, C.., Lai, N.., Lee, P.. and Ho, C., 2009. Screening for potential microbial inhibitors against prokaryotic and eukaryotic signal transduction and isocitrate lyase in Mycobacterium from Danum Valley, Sabah. Sabah Society Journal, 26, 1-91.
[27] Cheenpracha, S., Zhang, H., Mar, A.M.N., Foss, A.P., Sek, H.F., Ngit, S.L., Jap, M.J., Heng, F.S., Coy, C.H. and Leng, C.C., 2009. Yeast glycogen synthase kinase-3β pathway inhibitors from an organic extract of Streptomyces sp. Journal of Natural Products, 72(8), 1520-1523.
[28] Dahari, D.E., Salleh, R.M., Mahmud, F., Chin, L.P., Embi, N. and Sidek, H.M., 2016. Anti-malarial activities of two soil actinomycete isolates from sabah via inhibition of glycogen synthase kinase 3β. Tropical Life Sciences Research, 27(2), 53-71.
[29] Goh, L.P.W., Mahmud, F. and Lee, P.-C., 2021. Draft genome sequence data of Streptomyces sp. FH025. Data in Brief, 36, 107128, https://doi.org/10.1016/j.dib.2021.107128.
[30] Domoto, T., Pyko, I.V., Furuta, T., Miyashita, K., Uehara, M., Shimasaki, T., Nakada, M. and Minamoto, T., 2016. Glycogen synthase kinase-3b is a pivotal mediator of cancer invasion and resistance to therapy. Cancer Science, 107(10), 1363-1372.
[31] Embi, N., Rylatt, D.B. and Cohen, P., 1980. Glycogen synthase kinase‐3 from rabbit skeletal muscle: Separation from cyclic‐AMP‐dependent protein kinase and phosphorylase kinase. European Journal of Biochemistry, 107(2), 519-527.
[32] Rockenstein, E., Torrance, M., Adame, A., Mante, M., Bar-on, P., Rose, J.B., Crews, L. and Masliah, E., 2007. Neuroprotective effects of regulators of the glycogen synthase kinase-3β signaling pathway in a transgenic model of Alzheimer's disease are associated with reduced amyloid precursor protein phosphorylation. Journal of Neuroscience, 27(8), 1981-1991.
[33] Zhu, Q., Yang, J., Han, S., Liu, J., Holzbeierlein, J., Thrasher, J.B. and Li, B., 2011. Suppression of glycogen synthase kinase 3 activity reduces tumor growth of prostate cancer in vivo. Prostate, 17(8), 835-845.
[34] Amaral, A.C., Perez-Nievas, B.G., Chong, M.S.T., Gonzalez-Martinez, A., Argente-Escrig, H., Rubio-Guerra, S., Commins, C., Muftu, S., Eftekharzadeh, B., Hudry, E., Fan, Z., Ramanan, P., Takeda, S., Frosch, M.P., Wegmann, S. and Gomez-Isla, T., 2021. Isoform-selective decrease of glycogen synthase kinase-3-beta (GSK-3 ) reduces synaptic tau phosphorylation, transcellular spreading, and aggregation. iScience, 24(2), 102058, https://doi.org/10.1016/j.isci.2021.102058.
[35] June, C.C., Wen, L.H., Sani, H.A., Latip, J., Gansau, J.A., Chin, L.P., Embi, N. and Sidek, H.M., 2012. Hypoglycemic effects of Gynura procumbens fractions on streptozotocin- induced diabetic rats involved phosphorylation of GSK3β (Ser-9) in liver. Sains Malaysiana, 41(8), 969-975.
[36] Wong, S.K., Jann, M.L.S., Sudi, S., Hassan, W.R.B.M., Chin, L.P., Embi, N. and Sidek, H.M., 2015. Anti-malarial and anti-inflammatory effects of Gynura procumbens are mediated by kaempferol via inhibition of glycogen synthase kinase-3β (GSK3β). Sains Malaysiana, 44(10), 1489-1500.
[37] Hayakawa, M. and Nonomura, H., 1987. Humic acid-vitamin agar, a new medium for the selective isolation of soil Actinomycetes. Journal of Fermentation Technology, 65, 501-509.
[38] Katili, A.S., Retnowati, Y., 2017. Isolation of Actinomycetes from mangrove ecosystem in Torosiaje, Gorontalo, Indonesia. Biodiversitas 18, 826-833.
[39] Andoh, T., Hirata, Y. and Kikuchi, A., 2000. Yeast glycogen synthase kinase 3 is involved in protein degradation in cooperation with Bul1, Bul2, and Rsp5. Molecular and Cellular Biology, 20(18), 6712-6720.
[40] Aziz, D.N.A.F.A., Mahmud, F., Sidek, H., Embi, N., Andoh, T.T. and Lee, P.C., 2017. Assessment of the inhibitory mechanism of action for a yeast cell-based screening system targeting glycogen synthase kinase-3α (GSK-3α). Journal of Biological Sciences, 17(1), 47-51.
[41] Naik, B.S., Shashikala, J. and Krishnamurthy, Y.L., 2009. Study on the diversity of endophytic communities from rice (Oryza sativa L.) and their antagonistic activities in vitro. Microbiological Research, 164(3), 290-296.
[42] Ghorbani-Nasrabadi, R., Greiner, R., Alikhani, A.H., Hamedi, J. and Yakhchali, B., 2013. Distribution of actinomycetes in different soil ecosystems and effect of media composition on extracellular phosphatase activity. Journal of Soil Science and Plant Nutrition, 13(1), 223-236.
[43] Yuan, C.-M., Liu, W.-Y., Tang, C.Q. and Li, X.-S., 2009. Species composition, diversity, and abundance of lianas in different secondary and primary forests in a subtropical mountainous area, SW China. Ecological Research, 24, 1361-1370.
[44] Jiang, Y., Li, Q., Chen, X. and Jiang, C., 2016. Isolation and cultivation methods of Actinobacteria. In: D. Dharumadurai and Y. Jiang, eds. Actinobacteria: Basics and Biotechnological Applications. Rijeka: InTech, pp. 39-58.
[45] Hayakawa, M., Sadakata, T., Kajiura, T. and Nonomura, H., 1991. New methods for the highly selective isolation of Micromonospora and Microbispora from soil. Journal of Fermentation and Bioengineering, 72(5), 320-326.
[46] Viaene, T., Langendries, S., Beirinckx, S., Maes, M. and Goormachtig, S., 2016. Streptomyces as a plant's best friend? FEMS Microbiology Ecology, 92(8), https://doi.org/10.1093/femsec/ fiw119.
[47] Badri, D.V. and Vivanco, J.M., 2009. Regulation and function of root exudates. Plant, Cell and Environment, 32(6), 666-681.
[48] Moni, C., Derrien, D., Hatton, P.J., Zeller, B. and Kleber, M., 2012. Density fractions versus size separates: Does physical fractionation isolate functional soil compartments? Biogeosciences, 9(12), 5181-5197.
[49] Van Veen, J.A. and Kuikman, P.J., 1990. Soil structural aspects of decomposition of organic matter by microorganisms. Biogeochemistry, 11, 213-233.
[50] Plaza-Bonilla, D., Álvaro-Fuentes, J. and Cantero-Martínez, C., 2014. Identifying soil organic carbon fractions sensitive to agricultural management practices. Soil and Tillage Research, 139, 19-22.
[51] Berkelmann, D., Schneider, D., Engelhaupt, M., Heinemann, M., Christel, S., Wijayanti, M., Meryandini, A. and Daniel, R., 2018. How rainforest conversion to agricultural systems in Sumatra (Indonesia) affects active soil bacterial communities. Frontiers in Microbiology, 9(2381), https://doi.org/10.3389/fmicb.2018.02381.
[52] Barlow, J., Gardner, T.A., Araujo, I.S., Ávila-Pires, T.C., Bonaldo, A.B., Costa, J.E., Esposito, M.C., Ferreira, L. V., Hawes, J., Hernandez, M.I.M., Hoogmoed, M.S., Leite, R.N., Lo-Man-Hung, N.F., Malcolm, J.R., Martins, M.B., Mestre, L.A.M., Miranda-Santos, R., Nunes-Gutjahr, A.L., Overal, W.L., Parry, L., Peters, S.L., Ribeiro, M.A., Da Silva, M.N.F., Da Silva Motta, C. and Peres, C.A., 2007. Quantifying the biodiversity value of tropical primary, secondary, and plantation forests. Proceedings of the National Academy of Sciences of the United States of America, 104(47), 18555-18560.
[53] Gibson, L., Lee, T.M., Koh, L.P., Brook, B.W., Gardner, T.A., Barlow, J., Peres, C.A., Bradshaw, C.J.A., Laurance, W.F., Lovejoy, T.E. and Sodhi, N.S., 2011. Primary forests are irreplaceable for sustaining tropical biodiversity. Nature, 478, 378-381.
[54] Guo, X., Qiu, D., Ruan, J. and Huang, Y., 2011. Actinophytocola xinjiangensis sp. nov., isolated from virgin forest soil. International Journal of Systematic and Evolutionary Microbiology, 61(12), 2928-2932.
[55] Jiang, Y., Chen, X., Cao, Y. and Ren, Z., 2013. Diversity of cultivable Actinomycetes in tropical rainy forest of Xishuangbanna, China. Open Journal of Soil Science, 3(1), 9-14.
[56] Lanoue, A., Burlat, V., Henkes, G.J., Koch, I., Schurr, U. and Röse, U.S.R., 2010. De novo biosynthesis of defense root exudates in response to Fusarium attack in barley. New Phytologist, 185(2), 577-588.
[57] Saw, L.G., Chua, L.S.L., Suhaida, M., Yong, W.S.Y. and Hamidah, M., 2010. Conservation of some rare and endangered plants from Peninsular Malaysia. Kew Bulletin, 65(4), 681-689.
[58] Hossain, M.D. and Nuruddin, A.A., 2016. Soil and mangrove: A review. Journal of Environmental Science and Technology, 9(2), 198-207.
[59] Diem, H.G., Duhoux, E., Zaid, H. and Arahou, M., 2000. Cluster roots in Casuarinaceae: Role and relationship to soil nutrient factors. Annals of Botany, 85(6), 929-936.
[60] van der Meij, A., Worsley, S.F., Hutchings, M.I. and van Wezel, G.P., 2017. Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiology Reviews, 41(3), 392-416.
[61] Strehmel, N., Böttcher, C., Schmidt, S. and Scheel, D., 2014. Profiling of secondary metabolites in root exudates of Arabidopsis thaliana. Phytochemistry, 108, 35-46.
[62] Carvalhais, L.C., Dennis, P.G., Badri, D.V., Kidd, B.N., Vivanco, J.M. and Schenk, P.M., 2015. Linking Jasmonic acid signaling, root exudates, and rhizosphere microbiomes. Molecular Plant-Microbe Interactions, 28(9), 1049-1058.
[63] Geml, J., Morgado, L., Semenova‐Nelsen, T. and Schilthuizen, M., 2017. Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo. New Phytologist, 215(1), 454-468.
[64] Hanya, G., Kanamori, T., Kuze, N., Wong, S.T. and Bernard, H., 2020. Habitat use by a primate community in a lowland dipterocarp forest in Danum Valley, Borneo. American Journal of Primatology, 82(8), e23157, https://doi.org/10.1002/ajp.23157.
[65] Nakagawa, M. and Nakashizuka, T., 2004. Relationship between physical and chemical characteristics of dipterocarp seeds. Seed Science Research, 14(04), 363-369.
[66] Dilworth, L., Riley, C. and Stennett, D., 2017. Plant constituents: Carbohydrates, oils, resins, balsams, and plant hormones. In: S. Badal and R. Delgoda, eds. Pharmacognosy: Fundamentals, Applications and Strategies. London: Academic Press, pp. 61-80.
[67] Wu, Y., Bai, J., Zhong, K., Huang, Y., Qi, H., Jiang, Y. and Gao, H., 2016. Antibacterial activity and membrane-disruptive mechanism of 3-p-trans-coumaroyl-2-hydroxyquinic acid, a novel phenolic compound from pine needles of Cedrus deodara, against Staphylococcus aureus. Molecules, 21(8), 1084, https://doi.org/10.3390/molecules21081084.
[68] Devadass, B., Paulraj, M., Ignacimuthu, S., Theoder, P.A. and Dhabi, N.A., 2016. Antimicrobial activity of soil Actinomycetes isolated from western ghats in Tamil Nadu, India. Journal of Bacteriology & Mycology: Open Access, 3(2), 224-232.
[69] Berry, N.J., Phillips, O.L., Lewis, S.L., Hill, J.K., Edwards, D.P., Tawatao, N.B., Ahmad, N., Magintan, D., Khen, C.V., Maryati, M., Ong, R.C. and Hamer, K.C., 2010. The high value of logged tropical forests: Lessons from northern Borneo. Biodiversity and Conservation, 19(4), 985-997.