Sains Malaysiana 51(2)(2022): 451-460

http://doi.org/10.17576/jsm-2022-5102-10

Tropical Soil Bacterial Diversity in Sabah, Malaysia

(Kepelbagaian Bakteria Tanah Tropika di Sabah, Malaysia)

CHIN LAI MUN & CLEMENTE MICHAEL WONG VUI LING*

Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia

Diserahkan: 15 September 2020/Diterima: 27 Mei 2021

ABSTRACT

Bacteria are an essential biological component of soil function that plays fundamental roles in biogeochemical cycling, soil quality improvement, habitat-shaping, and ecosystem conservation. It is therefore important to have a good record of soil bacteria in the tropics in order to monitor future changes that may occur due to global warming and other factors. However, extremely limited data are available on the diversity of bacteria in soils in some tropical Borneo regions such as Sabah, Malaysia. This research, therefore, was undertaken to determine the bacterial diversity of soils from various locations in Sabah, Malaysia. Ten soil samples (n=10) were collected around Sabah. 16S rDNA of bacterial DNA extracted from soils were amplified and analysed using the Denaturing Gradient Gel Electrophoresis (DGGE). A total of 100 dominant and well-defined DNA fragments observed in the DGGE gel were extracted, sequenced, and aligned. The results indicated that 93 different bacterial operational taxonomic units (OTUs) representing bacteria from 8 different phyla were present. The most abundant phyla in the analysed Sabah soils were Proteobacteria followed by Acidobacteria, Firmicutes, Actinobacteria, Planctomycetes, Verrucomicrobia, Chloroflexi, and Bacteroidetes. The examined soils of Sabah and Peninsular Malaysia had similar dominant phyla in general, except that the most dominant phylum in Peninsular Malaysia soils is the Acidobacteria instead of Proteobacteria. These baseline data generated from this work are important and can be used to track bacterial diversity shifts due to soil or environmental changes in the future.

Keywords: 16S rDNA; bacterial diversity; DGGE; Sabah; tropics

ABSTRAK

Bakteria adalah komponen biologi penting dalam fungsi tanah yang memainkan peranan asas seperti pengitaran biogeokimia, peningkatan kualiti tanah, pembentukan habitat dan pemuliharaan ekosistem. Oleh itu, rekod yang baik mengenai bakteria tanah di kawasan tropika adalah penting untuk diperoleh bagi memantau perubahan pada masa akan datang yang mungkin berlaku akibat pemanasan global dan faktor lain. Walau bagaimanapun, jumlah data tentang kepelbagaian bakteria dalam tanah dari kawasan tropika Borneo tertentu seperti Sabah, Malaysia adalah sangat terhad. Oleh itu, projek ini dijalankan untuk menentukan kepelbagaian bakteria tanah dari pelbagai lokasi di Sabah, Malaysia. Sebanyak 10 sampel tanah (n=10) dikumpulkan dari sekitar Sabah. 16S rDNA daripada DNA bakteria yang diekstrak diamplifikasikan dan dianalisis menggunakan Penyahaslian Gradien Gel Elektroforesis(DGGE). Sebanyak 100 fragmen DNA yang dominan dan jelas dicerap dalam gel DGGE telah diekstrak, dijujuk dan dijajarkan. Keputusan menunjukkan bahawa 93 unit operasi taksonomi (OTU) bakteria yang berbeza mewakili bakteria daripada 8 filum yang berbeza telah dijumpai. Filum yang paling banyak dalam tanah dari Sabah yang telah dianalisis adalah Proteobakteria diikuti oleh Asidobakteria, Firmikutes, Aktinobakteria, Planktomisetes, Verrukomikrobia, Klorofleksi dan Bakteroidetes. Tanah di Sabah dan Semenanjung Malaysia yang diperiksa mempunyai filum dominan yang serupa pada umumnya, kecuali filum yang paling dominan dalam tanah di Semenanjung Malaysia iaitu Asidobakteria dan bukannya Proteobakteria. Data asas yang direkodkan dalam kajian ini adalah penting dan boleh digunakan untuk mengesan perubahan kepelbagaian bakteria yang disebabkan oleh perubahan tanah atau persekitaran pada masa akan datang.

Kata kunci: 16S rDN; DGGE; kepelbagaian bakteria; Sabah; tropika

RUJUKAN

Ahmad, N., Johri, S., Abdin, M.Z. & Qazi, G.N. 2009. Molecular characterization of bacterial population in the forest soil of Kashmir, India. World Journal of Microbiology and Biotechnology 25(1): 107-113.

Aislable, J., Deslippe, J.R. & Dymond, J. 2013. Soil microbes and their contribution to soil services. In Ecosystem Services in New Zealand–Conditions and Trends, edited by Dymond, J. Lincoln: Manaaki Whenua Press. pp. 143-161.

Bergmann, G.T., Bates, S.T., Eilers, K.G., Lauber, C.L., Caporaso, J.G., Walters, W.A., Knight, R. & Fierer, N. 2011. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology and Biochemistry 43(7): 1450-1455.

Clark, D.A. & Norris, P.R. 1996. Acidimicrobium ferrooxidans gen. nov., sp. nov.: Mixed-culture ferrous iron oxidation with Sulfobacillus species. Microbiology 142(4): 785-790.

Dunbar, J., Ticknor, L.O. & Kuske, C.R. 2000. Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Applied and Environmental Microbiology 66(7): 2943-2950.

Fierer, N. & Jackson, R.B. 2006 The diversity and biogeography of soil bacterial communities. In Proceedings of the National Academy of Sciences of the United States of America. PNAS. pp. 626-631.

Foong, C.P., Ling, C.M.W.V. & González, M. 2010. Metagenomic analyses of the dominant bacterial community in the Fildes Peninsula, King George Island (South Shetland Islands). Polar Science 4(2): 263-273.

Gafan, G.P., Lucas, V.S., Roberts, G.J., Petrie, A., Wilson, M. & Spratt, D.A. 2005. Statistical analyses of complex denaturing gradient gel electrophoresis profiles. Journal of Clinical Microbiology 43(8): 3971-3978.

Garrity, G.M., Bell, J.A. & Lilburn, T.G. 2004. Taxonomic outline of the prokaryotes. In Bergey’s Manual of Systematic Bacteriology, edited by Whitman, W.B., Goodfellow, M., Kämpfer, P., Busse, H., Trujillo, M.E., Ludwig, W. & Suzuki, K. New York: Springer.

Hashim, G.M. 2003. Salt-affected soils of Malaysia. In Proceedings of the Workshop on Soil Science in Malaysia towards 2020. Malaysian Society of Soil Science.

Hayat, R., Ali, S., Amara, U., Khalid, R. & Ahmed, I. 2010. Soil beneficial bacteria and their role in plant growth promotion: A review. Annals of Microbiology 60(4): 579-598.

Holmes, A.J., Bowyer, J., Holley, M.P., O'donoghue, M., Montgomery, M. & Gillings, M.R. 2000. Diverse, yet-to-be-cultured members of the Rubrobacter subdivision of the Actinobacteria are widespread in Australian arid soils. FEMS Microbiology Ecology 33(2): 111-120.

Hugenholtz, P., Goebel, B.M. & Pace, N.R. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180(18): 4765-4774.

Janssen, P.H. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Applied and Environmental Microbiology 72(3): 1719-1728.

Jones, R.T., Robeson, M.S., Lauber, C.L., Hamady, M., Knight, R. & Fierer, N. 2009. A comprehensive survey of soil Acidobacterial diversity using pyrosequencing and clone library analyses. The ISME Journal 3(4): 442-453.

Kerfahi, D., Tripathi, B.M., Dong, K., Go, R. & Adams, J.M. 2016. Rainforest conversion to rubber plantation may not result in lower soil diversity of bacteria, fungi, and nematodes. Microbial Ecology 72(2): 1-13.

Kim, M., Kim, W.S., Tripathi, B.M. & Adams, J. 2014. Distinct bacterial communities dominate tropical and temperate zone leaf litter. Microbial Ecology 67(4): 837-848.

Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M. & Glöckner, F.O. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next generation sequencing-based diversity studies. Nucleic Acids Research 41(1): 1-11. 

Kobabe, S., Wagner, D. & Pfeiffer, E.M. 2004. Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation. FEMS Microbiology Ecology 50(1): 13-23.

Kuramae, E.E., Yergeau, E., Wong, L.C., Pijl, A.S., van Veen, J.A. & Kowalchuk, G.A. 2012. Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiology Ecology 79(1): 12-24.

Makhalanyane, T.P., Valverde, A., Gunnigle, E., Frossard, A., Ramond, J.B. & Cowan, D.A. 2015. Microbial ecology of hot desert edaphic systems. FEMS Microbiology Reviews 39(2): 203-221.

Miyashita, N.T. 2015. Contrasting soil bacterial community structure between phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests. Genes and Genetic Systems 90(2): 61-77. 

Rappé, M.S. & Giovannoni, S.J. 2003. The uncultured microbial majority. Annual Reviews in Microbiology 57(1): 369-394.

Rinnan, R., Michelsen, A., Bååth, E. & Jonasson, S. 2007. Fifteen years of climate change manipulations alter soil microbial communities in a subarctic heath ecosystem. Global Change Biology 13(1): 28-39.

Roszak, D.B. & Colwell, R.R. 1987. Survival strategies of bacteria in the natural environment. Microbiological Reviews 51(3): 365.

Schutter, M., Sandeno, J. & Dick, R. 2001. Seasonal, soil type, and alternative management influences on microbial communities of vegetable cropping systems. Biology and Fertility of Soils 34(6): 397-410.

Teo, J.K.C. & Wong, C.M.V.L. 2014. Analyses of soil bacterial diversity of the Schirmacher Oasis, Antarctica. Polar Biology 37(5): 631-640.

Tripathi, B.M., Lee-Cruz, L., Kim, M., Singh, D., Go, R., Shukor, N.A., Husni, M.H.A., Chun, J. & Adams, J.M. 2014. Spatial scaling effects on soil bacterial communities in Malaysian tropical forests. Microbial Ecology 68(2): 247-258.

Vásquez-Dean, J., Maza, F., Morel, I., Pulgar, R. & González, M. 2020. Microbial communities from arid environments on a global scale. A systematic review. Biological Research 53(1): 1-12.

Ward, N.L., Challacombe, J.F., Janssen, P.H., Henrissat, B., Coutinho, P.M., Wu, M., Xie, G., Haft, D.H., Sait, M., Badger, J. & Barabote, R.D. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and Environmental Microbiology 75(7): 2046-2056.

Woese, C.R. 1987. Bacterial evolution. Microbiological Reviews 51(2): 221.

Xue, D., Yao, H.Y., Ge, D.Y. & Huang, C.Y. 2008. Soil microbial community structure in diverse land use systems: A comparative study using biolog, DGGE, and PLFA analyses. Pedosphere 18(5): 653-663.

Yergeau, E. & Kowalchuk, G.A. 2008. Responses of Antarctic soil microbial communities and associated functions to temperature and freeze-thaw cycle frequency. Environmental Microbiology 10(9): 2223-2235.

*Pengarang untuk surat-menyurat; email: michaelw@ums.edu.my