Soil Metagenome of Tropical White Sand Heath Forests in Borneo: What Functional Traits Are Associated with an Extreme Environment Within the Tropical Rainforest?

• Published in: Pedosphere Vol. 29; no. 1; pp. 12 - 23
• Main Authors: KERFAHI, Dorsaf, TRIPATHI, Binu M., SLIK, Johan W. Ferry, SUKRI, Rahayu S., JAAFAR, Salwana, DONG, Ke, OGWU, Matthew Chidozie, KIM, Hyo-Ki, ADAMS, Jonathan M.
• Format: Journal Article
• Language: English
• Published: Beijing Elsevier Ltd 01.02.2019; Elsevier Science Ltd; Department of Biological Sciences, Seoul National University, Seoul 08826 Republic of Korea%Korea Polar Research Institute, 26 Songdomirae-ro, Yoonsu-gu, Incheon 21990 Republic of Korea%Faculty of Science, Universiti Brunei Darussalam, Gadong BE1410 Brunei Darussalam%College of Natural Sciences, Kyonggi University, Seoul 443-760 Republic of Korea%Celemics Inc.612 Avison Biomedical Research Center, Yonsei Medical Center, Seoul 120-752 Republic of Korea%Division of Agrifood and Environment, School of Water, Energy and Environment Building 52a, Cranfield University, Bedfordshire MK43 0AL UK
• Subjects: Abundance; Annotations; Antibiotic resistance; Antibiotics; biotic interaction; Deoxyribonucleic acid; DNA; DNA sequencing; Dormancy; Extreme environments; Forests; Genes; kerangas; microbial community; Microbiota; Microorganisms; Nutrients; Rainforests; Sand; Sandy soils; shotgun metagenomics; Soil investigations; Soil microorganisms; Species composition; Sporulation; Stress; stress tolerance; Subsystems; tropical forest; Tropical forests; Virulence; Viruses; Borneo; microbiota; kerangas; microbial community; stress tolerance; antibiotic resistance; tropical forest; biotic interaction; shotgun metagenomics
• ISSN: 1002-0160; 2210-5107
• DOI: 10.1016/S1002-0160(18)60054-2

White sand heath forests (WS) or kerangas, an unusual variant of tropical forests in Borneo, characterized by open scrubby vegetation, low productivity, and distinctive plant species composition and soil microbial community, are regarded as a stressful low-pH and/or nutrient environment. We investigated whether the functional soil metagenome also shows a predicted set of indicators of stressful conditions in WS. Based on stress-tolerant strategies exhibited by larger organisms, we hypothesized that genes for stress tolerance, dormancy, sporulation, and nutrient processing are more abundant in the soil microbiota of WS. We also hypothesized that there is less evidence of biotic interaction in white sand soils, with lower connectivity and fewer genes related to organismic interactions. In Brunei, we sampled soils from a WS and a normal primary dipterocarp forest, together with an inland heath, an intermediate forest type. Soil DNA was extracted, and shotgun sequencing was performed using Illumina HiSeq platform, with classification by the Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST). The results, on one hand, supported our hypothesis (on greater abundance of dormancy, virulence, and sporulation-related genes). However, some aspects of our results showed no significant difference (specifically in stress tolerance, antibiotic resistance, viruses, and clustered regularly interspaced short palindrome repeats (CRISPRs)). It appears that in certain respects, the extreme white sand environment produces the predicted strategy of less biotic interaction, but exhibits high soil microbiota connectivity and functional diversity.