evolution: new Archaea found (Introduction)

by David Turell , Tuesday, August 06, 2024, 16:21 (41 days ago) @ David Turell

In a California pool:

https://www.nature.com/articles/s41467-024-49872-z?utm_campaign=related_content&utm...

"Abstract
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.

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"Atabeyarchaeia and Freyarchaeia use different enzymes to produce pyruvate. Atabeyarchaeia encodes the oxygen-sensitive reversible enzyme, pyruvate:phosphate dikinase (PpdK), whereas Freyarchaeia encodes unidirectional pyruvate water dikinase/phosphoenolpyruvate synthase (PpS) and pyruvate kinase (Pk), producing phosphoenolpyruvate and pyruvate52, respectively. Pyruvate generated via the EMP pathway can then be converted to acetyl-CoA by pyruvate:ferredoxin oxidoreductase (PorABCDG) complex using a low-potential electron acceptor such as a ferredoxin. Alternatively, acetyl-CoA can also be generated via pyruvate formate-lyase (pflD) generating formate as a byproduct. The final step involves the conversion of acetyl-CoA to acetate via acetate-CoA ligase (ADP-forming), producing ATP via substrate-level phosphorylation, in a crucial energy-conserving step during the fermentation of carbon compounds in both lineages.

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"We manually curated three complete genomes for Asgard archaea from wetland soils, uncovering bidirectional replication and an unexpected abundance of introns in tRNA genes. These features suggest another facet of the evolutionary relationship between archaea and eukaryotes. Metabolic reconstruction and metatranscriptomic measurements of in situ activity revealed a non-methanogenic, acetogenic lifestyle and a diverse array of proteins likely involved in energy conservation. The genome analysis uncovered some metabolic similarities between soil and sediment-associated Asgard archaea. In addition, the unusual genomic features, such as high intron prevalence and the presence of ESPs call for deeper investigations into their biological significance and contribution to the adaptability and evolution of Asgard archaea. Overall, the findings point to metabolic flexibility and adaptation to soil conditions of wetlands. Finally, they contribute to the cycling of carbon compounds that are relevant for methane production by coexisting methanogenic archaea. Future studies should aim to explore the functional roles of the identified genes and pathways in situ, which will further elucidate the ecological impacts and evolutionary history of these enigmatic microorganisms." (my bold)

Comment: it is amazing to find how chemically active are these newly found Archaea. They hold a unique position as very ancient forms yet closely related to Eukaryotes. Their chemical activities helped transform the Earth soils into useful substrates for life to use.