Public Abstract

DE-SC0025661: Ecophysiology of non-Euryarchaeotal methanogens and their impact on carbon cycling

Award Status: Active

Institution: Montana State University, Bozeman, MT
UEI: EJ3UF7TK8RT5
DUNS: 625447982

Most Recent Award Date: 09/20/2024
Number of Support Periods: 1
PM: Wawrik, Boris

Current Budget Period: 09/01/2024 - 08/31/2025
Current Project Period: 09/01/2024 - 08/31/2028
PI: Hatzenpichler, Roland

Supplement Budget Period: N/A

Public Abstract

Methane plays an essential role in Earth’s biogeochemical carbon cycle and understanding its sources and sinks is a crucial endeavor in microbiology, environmental sciences, and biogeochemistry. Methane is the second highest contributor to global warming and has a 28-times higher warming potential than carbon dioxide. Since the year 1900 methane has contributed approximately 0.5 ºC to global warming. The microbes that will be studied in this project are methanogens, i.e. anaerobic archaea that produce methane as their metabolic end-product. Methanogens are the primary producers of biogenic methane and are responsible for ca. 60% of methane emissions into the atmosphere. Since their first description in the 1930s all cultured methanogens were found to affiliate to the archaeal super-phylum Euryarchaeota. In the past decade, the discovery of methanogenesis marker genes on metagenome-assembled genomes obtained from diverse anoxic habitats has led to the proposal that other phylum-level lineages within the Archaea might also engage in anaerobic methane cycling. However, until recently, all predictions of novel methanogens outside the Euryarchaeota lacked experimental validation; it all has been conjecture from metagenomics. Our lab recently established enrichment cultures of methanogens belonging to the candidate class Methanomethylcia (formerly Verstraetearchaeota), a member of the phylum Thermoproteota (formerly TACK superphylum). This the first-time that a methanogen from outside the Euryarchaeota has been cultured. In collaboration with researchers at the Joint Genome Institute and Environmental Molecular Sciences Laboratory we will study the physiology of these novel methanogens both in vitro and in situ. We will address under which conditions cells engage in methanogenesis vs. other energy-conserving metabolisms and study which gene products they express. To achieve these goals, we will combine growth experiments of our enrichment culture with metatranscriptomics and metabolomics. Using genome-resolved metatranscriptomics and detailed geochemical measurements we will study which mode of energy conservation these archaea employ in their native habitats, i.e. cow rumen, wastewater sludge, soil, and sediments. We will address to what extent results from culture-based experiments are translatable to their native habitat. This work will be complemented with nano-scale secondary ion mass spectrometry experiments that will quantify the uptake of isotope labeled substrates into individual cells. This work will generate foundational knowledge on a group of methanogens that have hitherto (unknowingly) been ignored and evaluate to what extend these microorganisms contribute to methane emissions in diverse anoxic habitats. Understanding the biological processes controlling methane emissions, studying patterns of biogeochemical carbon cycling, and revealing the microbial drivers of elemental cycling are core objectives of the DOE Biological Environmental Research program as well as the two national laboratories that will collaborate on this research, the Joint Genome Institute and Environmental Molecular Sciences Laboratory.

Methane plays an essential role in Earth’s biogeochemical carbon cycle and understanding its sources and sinks is a crucial endeavor in microbiology, environmental sciences, and biogeochemistry. Methane is the second highest contributor to global warming and has a 28-times higher warming potential than carbon dioxide. Since the year 1900 methane has contributed approximately 0.5 ºC to global warming. The microbes that will be studied in this project are methanogens, i.e. anaerobic archaea that produce methane as their metabolic end-product. Methanogens are the primary producers of biogenic methane and are responsible for ca. 60% of methane emissions into the atmosphere.

Since their first description in the 1930s all cultured methanogens were found to affiliate to the archaeal super-phylum Euryarchaeota. In the past decade, the discovery of methanogenesis marker genes on metagenome-assembled genomes obtained from diverse anoxic habitats has led to the proposal that other phylum-level lineages within the Archaea might also engage in anaerobic methane cycling. However, until recently, all predictions of novel methanogens outside the Euryarchaeota lacked experimental validation; it all has been conjecture from metagenomics. Our lab recently established enrichment cultures of methanogens belonging to the candidate class Methanomethylcia (formerly Verstraetearchaeota), a member of the phylum Thermoproteota (formerly TACK superphylum). This the first-time that a methanogen from outside the Euryarchaeota has been cultured.

In collaboration with researchers at the Joint Genome Institute and Environmental Molecular Sciences Laboratory we will study the physiology of these novel methanogens both in vitro and in situ. We will address under which conditions cells engage in methanogenesis vs. other energy-conserving metabolisms and study which gene products they express. To achieve these goals, we will combine growth experiments of our enrichment culture with metatranscriptomics and metabolomics. Using genome-resolved metatranscriptomics and detailed geochemical measurements we will study which mode of energy conservation these archaea employ in their native habitats, i.e. cow rumen, wastewater sludge, soil, and sediments. We will address to what extent results from culture-based experiments are translatable to their native habitat. This work will be complemented with nano-scale secondary ion mass spectrometry experiments that will quantify the uptake of isotope labeled substrates into individual cells.

This work will generate foundational knowledge on a group of methanogens that have hitherto (unknowingly) been ignored and evaluate to what extend these microorganisms contribute to methane emissions in diverse anoxic habitats. Understanding the biological processes controlling methane emissions, studying patterns of biogeochemical carbon cycling, and revealing the microbial drivers of elemental cycling are core objectives of the DOE Biological Environmental Research program as well as the two national laboratories that will collaborate on this research, the Joint Genome Institute and Environmental Molecular Sciences Laboratory.