Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes

Abstract

The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived, especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in clusters of orthologous groups (COG) categories L (replication, recombination and repair) and S (function unknown) were relatively high in metagenome-assembled genomes representing Methylococcales clearly thriving below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. By contrast, genes in COG category N (cell motility) were relatively high in metagenome-assembled genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface.

Anaerobic oxidation of methane in sediments of a nitrate-rich, oligo-mesotrophic boreal lake

“…The quality assessment of the raw sequence reads, merging of paired end reads, alignment, chimera removal, preclustering, taxonomic classification (and removal of chloroplast, mitochondria, and eukaryote sequences) and division of 16S rRNA gene sequences into operational taxonomic units (OTUs) at 97 % similarity level was conducted as previously described (Rissanen et al 2020). Singleton OTUs (OTUs with only 1 sequence) were removed, and the data were then normalized by subsampling to the same size, 77340 sequences.…”

“…Methylococcales in the study lake) (Fig. S1), include members that harbored genetic potential for denitrification in the hypoxic and anoxic water columns of closely located Lake Alinen-Mustajärvi (within 20 km from the study lake) and Lake Lovojärvi (within 4 km) (Rissanen et al 2018(Rissanen et al , 2020. In addition, Methylobacter in boreal lake sediments have genetic potential for denitrification, as indicated by our functional annotation analysis (Prokka, version 1.14.5, Seemann 2014) finding genes coding for dissimilatory nitrate and nitrite reduction in two MAGs representing genus Methylobacter in sediments of Lake Alinen Mustajärvi (NCBI accession no.…”

“…Furthermore, recent evidence suggests that some members of Methylococcales transfer electrons from CH4 to Fe 3+ minerals and organic EAs while oxidizing CH4 in hypoxic and anoxic conditions (Oswald et al 2016;Zheng et al 2020). Accordingly, genetic potential for extracellular electron transfer to metal minerals and organic EAs has been found in MAGs of Methylococcales in lake water columns (He et al 2019;Rissanen et al 2020). Furthermore, our functional annotation analysis (using FeGenie, Garber et al 2020) of the aforementioned Methylobacter -MAGs from the sediments of Lake Alinen Mustajärvi found genetic potential for extracellular electron transfer in one of them (GCA_903870475.1).…”

Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

“…Numerous environmental studies employing stable isotope probing (SIP) or mRNA-based analyses, showed that gammaproteobacterial methanotrophs are predominant and thrive at oxic-anoxic interfaces with rapid oxygen fluctuations (e.g., lake sediments, mangrove sediments, rice paddies, and peatlands; He et al, 2012;Reim et al, 2012;Shiau et al, 2018;Kaupper et al, 2020Kaupper et al, , 2021. For instance, vertical stratification along an oxygen gradient in a stratified lake has been observed, supported by metagenomic analysis revealing the genetic potential for aerobic methane oxidation under micro-oxic conditions, with the gammaproteobacterial methanotrophs (e.g., Methylobacter) present at the oxic-anoxic interface, and alphaproteobacterial methanotrophs present and stratified at the oxic water layer (Blees et al, 2014;Rissanen et al, 2018Rissanen et al, , 2020.…”

Methane oxidation in the waters of a humic-rich boreal lake stimulated by photosynthesis, nitrite, Fe(III) and humics

“…The majority of lacustrine CH 4 is produced by anaerobic methanogenic archaea as the end product of remineral-S. van Grinsven et al: Methane oxidation in Lake Lovojärvi ization of organic matter in anoxic sediments (Bartlett and Harriss, 1993;Rudd, 1980). From the sediments, CH 4 can diffuse into the water column and may be emitted to the atmosphere at the water-air interface.…”