Sains Malaysiana 49(10)(2020): 2335-2344

http://dx.doi.org/10.17576/jsm-2020-4910-01

 

Effects of Elevated Temperature on the Tropical Soil Bacterial Diversity

(Kesan Peningkatan Suhu terhadap Kepelbagaian Bakteria Tanah Tropika)

 

CHIN LAI MUN¹ & CLEMENTE MICHAEL WONG VUI LING^1,2*

 

¹Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia

 

²National Antarctic Research Centre, University of Malaya, 50603 Kuala Lumpur, Federal Territory, Malaysia

 

Received: 25 October 2019/Accepted: 22 April 2020

 

ABSTRACT

Bacteria are important biological components of soil that play pivotal roles in improving soil quality and maintaining a balanced ecosystem. However, global climate change may have severe impacts on biodiversity and ecosystems including species loss and extinction of plants and animals, including microbes. Thus, it is crucial to determine how elevated temperature may alter soil bacterial diversity and composition. In this study, an in vitro simulated temperature rise experiment was carried out on soils from three sampling sites, referring to S1, S2, and S3 around Sabah, Malaysia. Soils were incubated at 25 °C (control) and 27 °C (simulated warming) with constant parameters in a growth chamber up to 16 months. Total DNA was extracted from microbes in the soil and used for PCR amplification targeting the V3-V4 region of the 16S rRNA gene. These amplicons were sequenced using the MiSeq platform (Illumina, USA). Raw DNA sequences were trimmed, merged, and aligned against the 16S rRNA sequences in the NCBI 16S database. The results showed that the analyzed soils were mainly dominated by Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia. After 16 months of simulated warming, a net decrease of Proteobacteria, Acidobacteria, and Planctomycetes, and an increase of Actinobacteria and Chloroflexi were observed for all three soil samples, indicating that these phyla were highly affected by a temperature rise. At the genus level, Gaiella and Nocardioides exhibited a net increase while Bradyrhizobium, Mycobacterium, Tepidisphaera, and Paludibaculum demonstrated net decrease after 16 months of simulated warming. Knowledge on the changes of soil bacterial diversity patterns as a result of temperature elevation will contribute to select the best intervention strategy to overcome global warming issue in the future.

 

Keywords: 16S metagenomic sequencing; growth chamber; soil bacteria; temperature

 

ABSTRAK

Bakteria merupakan komponen biologi penting yang memainkan peranan dalam meningkatkan kualiti tanah dan mengekalkan keseimbangan ekosistem. Akan tetapi, perubahan iklim global mungkin akan memberi kesan buruk terhadapkepelbagaian bio dan ekosistem termasuk kehilangan spesies serta kepupusan haiwan, tumbuhan dan mikrob. Oleh itu, adalah penting untuk menentukan bagaimana peningkatan suhu akan menyebabkan perubahan kepelbagaian dan komposisi bakteria dalam tanah. Dalam kajian ini, uji kajisimulasi peningkatan suhu secarain vitro telah dijalankan ke atas tanah yang diperoleh dari tiga tapak pensampelan di sekitar Sabah, Malaysia. Tanah tersebut dieram pada suhu 25 °C (kawalan) dan 27 °C (simulasi) dengan parameter yang sama dalam kebuk pertumbuhan selama 16 bulan. DNA keseluruhan telah diekstrak daripada mikrob dalam tanah dan digunakan untuk amplifikasi PCR menyasarkan kawasan V3-V4 pada gen 16 SrRNA. Amplikon tersebut dijujuk dengan menggunakan platform Miseq (Illumina, USA). Data penjujukan telah dipangkas, digabungkan dan disejajarkan dengan jujukan 16 SrRNA pada pangkalan data 16S NCBI. Hasil kajian menunjukkan bahawa sampel tanah didominasi oleh Proteobacteria, Actinobacteria, Acidobacteria dan Verrucomicrobia. Selepas simulasi pemanasan selama 16 bulan, pengurangan bersih bagi Proteobacteria, Acidobacteria dan Planctomycetes serta peningkatan bagi Actinobacteria dan Chloroflexi dapat diperhatikan untuk ketiga-tiga sampel tanah. Pada peringkat genus, Gaiella dan Nocardioides menunjukkan peningkatan bersih manakala Bradyrhizobium, Mycobacterium, Tepidisphaera dan Paludibaculum menunjukkan penurunan bersih selepas 16 bulan. Pengetahuan corak perubahankepelbagaian bakteria dalam tanah akibat peningkatan suhu persekitaran akan dapat membantu dalam strategi intervensi ke atas tanah bagi menangani isu pemanasan global pada masa hadapan.

 

Kata kunci: Bakteria tanah; kebuk pertumbuhan; penjujukan metagenomik 16S; suhu

 

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*Corresponding author; email: michaelw@ums.edu.my