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Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides

  • Soil Microbiology
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Abstract

Methanotrophs are important microbial communities in coastal ecosystems. They reduce CH4 emission in situ, which is influenced by soil conditions. This study aimed to understand the differences in active aerobic methanotrophic communities in mangrove forest soils experiencing different inundation frequency, i.e., in soils from tidal mangroves, distributed at lower elevations, and from dwarf mangroves, distributed at higher elevations. Labeling of pmoA gene of active methanotrophs using DNA-based stable isotope probing (DNA-SIP) revealed that methanotrophic activity was higher in the dwarf mangrove soils than in the tidal mangrove soils, possibly because of the more aerobic soil conditions. Methanotrophs affiliated with the cluster deep-sea-5 belonging to type Ib methanotrophs were the most dominant methanotrophs in the fresh mangrove soils, whereas type II methanotrophs also appeared in the fresh dwarf mangrove soils. Furthermore, Methylobacter and Methylosarcina were the most important active methanotrophs in the dwarf mangrove soils, whereas Methylomonas and Methylosarcina were more active in the tidal mangrove soils. High-throughput sequencing of the 16S ribosomal RNA (rRNA) gene also confirmed similar differences in methanotrophic communities at the different locations. However, several unclassified methanotrophic bacteria were found by 16S rRNA MiSeq sequencing in both fresh and incubated mangrove soils, implying that methanotrophic communities in mangrove forests may significantly differ from the methanotrophic communities documented in previous studies. Overall, this study showed the feasibility of 13CH4 DNA-SIP to study the active methanotrophic communities in mangrove forest soils and revealed differences in the methanotrophic community structure between coastal mangrove forests experiencing different tide frequencies.

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Acknowledgements

We thank Ms. Yu-Shiuan Huang from the Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, and Ms. Dongmei Wang from the Nanjing Soil Research Institute, Chinese Academy of Science, Nanjing, PRC, for the laboratory work.

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  1. Biodiversity Research Center, Academia Sinica, No. 128, Academia Road Section II, Nangang, Taipei, 11529, Taiwan

    Yo-Jin Shiau, Yu-Te Lin & Chih-Yu Chiu

  2. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Science, No. 71 East Beijing Road, Nanjing, 210008, People’s Republic of China

    Yuanfeng Cai & Zhongjun Jia

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All of the pmoA and 16S rRNA gene sequences obtained from Miseq sequencing have been deposited in NCBI with accession codes SRP111433.

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Relative abundance of microbial community in the fresh mangrove forest soils (DOCX 485 kb).

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Shiau, YJ., Cai, Y., Lin, YT. et al. Community Structure of Active Aerobic Methanotrophs in Red Mangrove (Kandelia obovata) Soils Under Different Frequency of Tides. Microb Ecol 75, 761–770 (2018). https://doi.org/10.1007/s00248-017-1080-1

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