4.2 Article

16S rRNA gene sequences of Candidatus Methylumidiphilus (Methylococcales), a putative methanotrophic genus in lakes and ponds

Journal

AQUATIC MICROBIAL ECOLOGY
Volume 88, Issue -, Pages 25-30

Publisher

INTER-RESEARCH
DOI: 10.3354/ame01983

Keywords

Candidatus Methylumidiphilus; Methanotroph; 16S rRNA gene; Metagenome; Lake; Pond

Funding

  1. Kone Foundation [201803224]
  2. Science for Life Laboratory biodiversity program
  3. SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) [SNIC snic2020-5-19]
  4. SciLifeLab fellows program

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A putative novel methanotrophic genus, Candidatus Methylumidiphilus, was found to be ubiquitous and abundant in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it may have been missed in previous studies due to insufficient database coverage. By screening metagenome-assembled genomes (MAGs), researchers discovered two unique 16S rRNA gene sequences belonging to this genus, which could enhance its detection in environmental samples.
A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with Ca. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG data set. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5 %) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we found 5 MAGs, each containing one 1532 bp sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in 2 unique 16S rRNA gene sequences. These sequences represented 2 different putative species: Ca. Methylumidiphilus alinenensis (GenBank accession OK236221) and another unnamed species of Ca. Methylumidiphilus (GenBank accession OK236220). We suggest that including these 2 sequences in reference databases will enhance 16S rRNA gene-based detection of members of this genus from environmental samples.

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