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Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments


Understanding temporal and spatial microbial community abundance and diversity variations is necessary to assess the functional roles played by microbial actors in the environment. In this study, we investigated spatial variability and temporal dynamics of two functional microbial sediment communities, methanogenic Archaea and methanotrophic bacteria, in Lake Bourget, France. Microbial communities were studied from 3 sites sampled 4 times over a year, with one core sampled at each site and date, and 5 sediment layers per core were considered. Microbial abundance in the sediment were determined using flow cytometry. Methanogens and methanotrophs community structures, diversity, and abundance were assessed using T-RFLP, sequencing, and real-time PCR targeting mcrA and pmoA genes, respectively. Changes both in structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics. Methanogen diversity was dominated by Methanomicrobiales (mainly Methanoregula) members, followed by Methanosarcinales and Methanobacteriales. For methanotrophs, diversity was dominated by Methylobacter in the deeper area and by Methylococcus in the shallow area. Organic matter appeared to be the main environmental parameter controlling methanogens, while oxygen availability influenced both the structure and abundance of the methanotrophic community.

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Data Availability

Sequences were deposited in GenBank under accession numbers KR011354 to KR011484 for partial mcrA gene sequences and from KR011489 to KR011714 for partial pmoA gene sequences.


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We thank Emmanuel Mallet and Jean-Philippe Jenny for field assistance, as well as Annie Millery and Cécile Pignol for sediment characterization analyses. We utilized the database from the observatory on perialpine lakes (reference article: as the source of complementary data on Lake Bourget; we thank OLA (Observatory on LAkes), © OLA-IS, AnaEE-France, INRAE Thonon-les-Bains, CISALB, and IS OLA Data (


Elodie Billard was supported by a Ph.D. fellowship from the French Ministère de l’Enseignement Supérieur et de la Recherche.

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E. Lyautey, E. Billard, and I. Domaizon conceived and designed the study; E. Billard, N. Tissot and S. Jacquet performed the experiments and analyzed the samples; E. Billard and N. Tissot conducted the bioinformatic and biostatistical analyses; E. Lyautey, E. Billard and I. Domaizon drafted the manuscript.

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Correspondence to Emilie Lyautey.

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Lyautey, E., Billard, E., Tissot, N. et al. Seasonal Dynamics of Abundance, Structure, and Diversity of Methanogens and Methanotrophs in Lake Sediments. Microb Ecol 82, 559–571 (2021).

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  • Archaea
  • Bacteria
  • Methane cycle
  • Benthic habitat