Microbial Ecology

, Volume 75, Issue 3, pp 761–770 | Cite as

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

  • Yo-Jin Shiau
  • Yuanfeng Cai
  • Yu-Te Lin
  • Zhongjun JiaEmail author
  • Chih-Yu ChiuEmail author
Soil Microbiology


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.


Methanotrophs Mangrove forest DNA stable isotope probing pmoA gene 16S rRNA gene 



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.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Data Availability

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

Supplementary material

248_2017_1080_MOESM1_ESM.docx (16 kb)
ESM 1 (DOCX 15.6 kb)
248_2017_1080_MOESM2_ESM.tif (486 kb)
ESM 2 Relative abundance of microbial community in the fresh mangrove forest soils (DOCX 485 kb).


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Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
  2. 2.State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of ScienceNanjingPeople’s Republic of China

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