Metagenomic insights into the metabolism of microbial communities that mediate iron and methane cycling in Lake Kinneret sediments

Abstract. Complex microbial communities facilitate iron and methane transformations in anoxic ‎methanic sediments of freshwater lakes, such as Lake Kinneret (The Sea of Galilee, Israel). The ‎phylogenetic and functional diversity of these consortia are not fully understood, and it is not ‎clear which lineages perform iron reduction, anaerobic oxidation of methane (AOM) or both ‎‎(Fe-AOM). Here, we investigated microbial communities from both natural Lake Kinneret ‎sediments and iron-amended slurry incubations using metagenomics, focusing on functions ‎associated with iron reduction and methane cycling. Analyses of the phylogenetic and ‎functional diversity indicate that consortia of archaea (mainly Bathyarchaeia, ‎Methanomicrobia, Thermoplasmata, and Thermococci) and bacteria (mainly Chloroflexi ‎‎(Chloroflexota), Nitrospirae (Nitrospirota) and Proteobacteria) perform key metabolic ‎reactions such as amino acid uptake and dissimilation, organic matter fermentation, and ‎methanogenesis. The intrinsic Deltaproteobacteria, especially Desulfuromondales ‎‎(Desulfuromonadota), have the potential to transfer electrons extracellularly either to iron ‎mineral particles or to microbial syntrophs, including methanogens. This is likely via ‎transmembrane cytochromes, outer membrane hexaheme c-type cytochrome (OmcS) in ‎particular, or pilin monomer, PilA, which were attributed to this lineage. The bonafide ‎anaerobic oxidizers of methane (ANME) and denitrifying methanotrophs Methylomirabilia ‎‎(NC10) were scarce, and we consider the role of the lineage Methanothrix (Methanothrichales) ‎in Fe-AOM. We show that putative aerobes, such as methane-oxidizing bacteria Methylomonas ‎and their methylotrophic synthrophs Methylotenera are found among the anaerobic lineages in ‎Lake Kinneret iron amended slurries and can be involved in the oxidation of methane or its ‎intermediates, as suggested previously. We propose a reaction model for metabolic interactions ‎in the lake sediments, linking the potential players that interact via intricate metabolic ‎tradeoffs and direct electron transfer between species. Our results highlight the metabolic ‎complexity of microbial communities in an energy-limited environment, where aerobe and ‎anaerobe communities may co-exist and facilitate Fe-AOM as one strategy for survival.‎