Environmental Science and Pollution Research

, Volume 26, Issue 1, pp 636–646 | Cite as

Methylococcaceae are the dominant active aerobic methanotrophs in a Chinese tidal marsh

  • Yongcui Deng
  • Qian Gui
  • Marc Dumont
  • Cheng Han
  • Huan Deng
  • Juanli Yun
  • Wenhui ZhongEmail author
Research Article


Although coastal marshes are net carbon sinks, they are net methane sources. Aerobic methanotrophs in coastal marsh soils are important methane consumers, but their activity and populations are poorly characterized. DNA stable-isotope probing followed by sequencing was used to determine how active methanotrophic populations differed in the main habitats of a Chinese coastal marsh. These habitats included mudflat, native plant-dominated, and alien plant-dominated habitats. Methylococcaceae was the most active methanotroph family across four habitats. Abundant methylotroph sequences, including methanotrophs and non-methane-oxidizing methylotrophs (Methylotenera and Methylophaga), constituted 50–70% of the 16S rRNA genes detected in the labeled native plant-dominated and mudflat soils. Methylotrophs were less abundant (~ 20%) in labeled alien plant-dominated soil, suggesting less methane assimilation into the target community or a different extent of carbon cross-feeding. Canonical correspondence analysis indicated a significant correlation between the active bacterial communities and soil properties (salinity, organic carbon, total nitrogen, pH, and available phosphorus). Importantly, these results highlight how changing vegetation or soil features in coastal marshes may change their resident active methanotrophic populations, which will further influence methane cycling.


Methanotrophs Methylococcaceae DNA-SIP Spartina alterniflora Tidal marsh Methane 



This work was supported by the Natural Science Foundation of Jiangsu Province, China [grant number BK20140923 and BK20181386], the National Natural Science Foundation of China [grant number 41401075], and the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11356_2018_3560_Fig5_ESM.png (32 kb)
Figure S1

Changes in the copy number of pmoA genes in soils of four marsh habitats (MF: mudflat, PA: Phragmites australis-, SS: Suaeda salsa-, and SA: Spartina alterniflora-dominated) incubated with 13CH4 or 12CH4 for 6 days. Error bars represent standard deviations (n = 3). (PNG 31 kb)

11356_2018_3560_MOESM1_ESM.eps (600 kb)
High resolution image (EPS 599 kb)
11356_2018_3560_Fig6_ESM.png (235 kb)
Figure S2

Bacterial 16S rRNA gene T-RFLP analysis of the DNA recovered from the CsCl gradient fractions. The three panels on the upper left of the figure, MF-1, MF-2, and MF-3 represent three replications of the heavy fractions of 13CH4-labeled mudflat (MF) soils, while panels in their left represent three replications of the light fractions of the 12CH4-incubated MF soil. The same principles were applied to Phragmites australis- (PA), Suaeda salsa- (SS), and Spartina alterniflora- (SA) dominated soils. The numbers accompanying the arrows point to each T-RF peak indicates the respective T-RF length (bp). The associated CsCl buoyant density (g ml-1) is listed at the center-top of each panel. (PNG 234 kb)

11356_2018_3560_MOESM2_ESM.eps (2.4 mb)
High resolution image (EPS 2415 kb)
11356_2018_3560_Fig7_ESM.png (146 kb)
Figure S3

Relative abundance of the major 16S rRNA gene-derived clusters in the Sanger sequencing datasets that were retrieved from the heavy fractions of the labeled soils (density = ~ 1.74 g ml–1). (PNG 145 kb)

11356_2018_3560_MOESM3_ESM.eps (733 kb)
High resolution image (EPS 733 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Yongcui Deng
    • 1
    • 2
    • 3
    • 4
  • Qian Gui
    • 1
  • Marc Dumont
    • 5
  • Cheng Han
    • 1
  • Huan Deng
    • 1
  • Juanli Yun
    • 6
  • Wenhui Zhong
    • 1
    • 3
    • 4
    Email author
  1. 1.School of Geography ScienceNanjing Normal UniversityNanjingChina
  2. 2.Key Laboratory of Virtual Geographic EnvironmentMinistry of EducationNanjingChina
  3. 3.Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and ApplicationNanjingChina
  4. 4.Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution ControlNanjingChina
  5. 5.Biological SciencesUniversity of SouthamptonSouthamptonUK
  6. 6.Institute of MicrobiologyChinese Academy of SciencesBeijingChina

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