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Root-associated aerobic methanotrophs play an important role in regulating methane emissions from the wetlands. However, the influences of the plant genotype on root-associated methanotrophic structures, especially on active flora, remain poorly understood. Transcription of the  pmo A gene, encoding particulate methane monooxygenase in methanotrophs, was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from root samples of three emergent macrophytes, including  Phragmites australis ,  Typha angustifolia , and  Schoenoplectus triqueter  (syn.  Scirpus triqueter  L.) from a eutrophic wetland. High-throughput sequencing of  pmo A based on DNA and cDNA was used to analyze the methanotrophic community. Sequencing of cDNA  pmo A amplicons confirmed that the structure of active methanotrophic was not always consistent with DNA. A type I methanotroph,  Methylomonas , was the most active group in  P. australis , whereas  Methylocystis,  a type II methanotroph, was the dominant group in  S. triqueter . In  T. angustifolia , these two types of methanotroph existed in similar proportions. However, at the DNA level,  Methylomonas  was predominant in the roots of all three plants. In addition, vegetation type could have a profound impact on root-associated methanotrophic community at both DNA and cDNA levels. These results indicate that members of the genera  Methylomonas  (type I) and  Methylocystis  (type II) can significantly contribute to aerobic methane oxidation in a eutrophic wetland.

Diversity of active root-associated methanotrophs of three emergent plants in a eutrophic wetland in northern China