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Insights into the Phylogeny and Metabolic Potential of a Primary Tropical Peat Swamp Forest Microbial Community by Metagenomic Analysis

  • Environmental Microbiology
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Abstract

A primary tropical peat swamp forest is a unique ecosystem characterized by long-term accumulation of plant biomass under high humidity and acidic water-logged conditions, and is regarded as an important terrestrial carbon sink in the biosphere. In this study, the microbial community in the surface peat layer in Pru Toh Daeng, a primary tropical peat swamp forest, was studied for its phylogenetic diversity and metabolic potential using direct shotgun pyrosequencing of environmental DNA, together with analysis of 16S rRNA gene library and key metabolic genes. The community was dominated by aerobic microbes together with a significant number of facultative and anaerobic microbial taxa. Acidobacteria and diverse Proteobacteria (mainly Alphaproteobacteria) constituted the major phylogenetic groups, with minor representation of archaea and eukaryotic microbes. Based on comparative pyrosequencing dataset analysis, the microbial community showed high metabolic versatility of plant polysaccharide decomposition. A variety of glycosyl hydrolases targeting lignocellulosic and starch-based polysaccharides from diverse bacterial phyla were annotated, originating mostly from Proteobacteria, and Acidobacteria together with Firmicutes, Bacteroidetes, Chlamydiae/Verrucomicrobia, and Actinobacteria, suggesting the key role of these microbes in plant biomass degradation. Pyrosequencing dataset annotation and direct mcrA gene analysis indicated the presence of methanogenic archaea clustering in the order Methanomicrobiales, suggesting the potential on partial carbon flux from biomass degradation through methanogenesis. The insights on the peat swamp microbial assemblage thus provide a valuable approach for further study on biogeochemical processes in this unique ecosystem.

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Acknowledgement

This project was supported by a research grant from the National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (BT-B-02-LG-BA-5106). Manuscript proofreading by Dr. Philip J. Shaw is much appreciated.

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Authors and Affiliations

  1. National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, 113 Thailand Science Park, Paholyothin Road, Klong Luang, Pathumthani, 12120, Thailand

    Pattanop Kanokratana, Tanaporn Uengwetwanit, Ukrit Rattanachomsri, Benjarat Bunterngsook, Thidarat Nimchua, Sithichoke Tangphatsornruang, Vethachai Plengvidhya, Verawat Champreda & Lily Eurwilaichitr

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  1. Pattanop Kanokratana
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  2. Tanaporn Uengwetwanit
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Correspondence to Verawat Champreda.

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Figure S1

Neighbor-joining tree showing the phylogeny of bacterial 16S rRNA gene sequences from the Pru Toh Daeng peat swamp forest. Sequences were aligned (1,501 nt) with Clustal X and distances were calculated with the maximum likelihood model. Sequences named “PW” are those from this study. Bootstrap values (1,000 replicates) above 50% are shown. Bar, 10% sequence divergence. Aquifex pyrophillus was used as outgroup taxa. Acidobacteria sequences were grouped for simplicity. The potential new taxa are marked with an asterisk. (PDF 35 kb)

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Kanokratana, P., Uengwetwanit, T., Rattanachomsri, U. et al. Insights into the Phylogeny and Metabolic Potential of a Primary Tropical Peat Swamp Forest Microbial Community by Metagenomic Analysis. Microb Ecol 61, 518–528 (2011). https://doi.org/10.1007/s00248-010-9766-7

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