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https://doi.org/10.5194/bg-2020-329
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-2020-329
© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

  10 Sep 2020

10 Sep 2020

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This preprint is currently under review for the journal BG.

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

Michal Elul1, Maxim Rubin-Blum2, Zeev Ronen3, Itay Bar-Or4, Werner Eckert5, and Orit Sivan1 Michal Elul et al.
  • 1Department of Earthand Environmental Science,Ben-Gurion University of the Negev, Beer Sheva, Israel
  • 2Israel Limnology and Oceanography Research, Haifa, Israel
  • 3Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer, Israel
  • 4Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
  • 5Israel Oceanographic & Limnological Research, The Yigal Allon Kinneret Limnological Laboratory, Migdal, Israel

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.‎

Michal Elul et al.

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Status: final response (author comments only)
Status: final response (author comments only)
AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

Michal Elul et al.

Data sets

S.DB.2| Microbial composition of Lake Kinneret sediments and slurry incubations based on MAR (MARine) database Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, Orit Sivan https://doi.org/10.6084/m9.figshare.11800875

S.DB.1| Microbial composition of Lake Kinneret sediments and slurry incubations based on ‎SILVA (V132) database -Taxonomic classification (up until genus level) and abundance (in ‎percentage) based on metagenomic reads to SILVA (V132) database. Eukar Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, Orit Sivan https://doi.org/10.6084/m9.figshare.12933863

S.DB.3| Abundance and classification of genes in Lake Kinneret sediments and slurry incubations ‎based on KEGG orthology (in units of counts per million (CPM)). ‎ Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, Orit Sivan https://doi.org/10.6084/m9.figshare.12933893

S.DB.4| ANME‏2‏d Multiheme c-type cytochromes (MHC)sequences used as a query for BLASTing ‎against Lake Kinneret sediment metagenome. ‎ Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, Orit Sivan https://doi.org/10.6084/m9.figshare.12933905

S.DB.5| Abundance (in units of counts per million (CPM)) of genes encoding for ‎F420:methanophenazine dehydrogenase complex (fpoABCDHIJKLMNO) in Lake Kinneret ‎sediments and slurry incubations. ‎ Michal Elul, Maxim Rubin-Blum, Zeev Ronen, Itay Bar-Or, Werner Eckert, Orit Sivan https://doi.org/10.6084/m9.figshare.12933908

Michal Elul et al.

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