Resonance Raman analysis of intracellular vitamin B₁₂ analogs in methanogenic archaea

Abstract

Methanogenic archaea (methanogens) are microorganisms that can synthesize methane. They are found in diverse environments ranging from paddy fields to animal digestive tracts to deep‐sea hydrothermal vents. Investigating their distribution and physiological activity is crucial for the detailed analysis of the dynamics of greenhouse gas generation and the search for the environmental limits of life. In methanogens, cobamide cofactors (vitamin B12 analogs) play a key role in methane synthesis and carbon fixation, thus serving as a marker compound that metabolically characterizes them. Here, we report on resonance Raman detection of cobamides in methanogenic cells without destroying cells and provide structural insights into those cobamides. We succeeded in detecting cobamides in four representative methanogens Methanosarcina mazei, Methanosarcina barkeri, Methanopyrus kandleri, and Methanocaldococcus jannaschii. The former two are mesophilic, cytochrome‐containing methanogens, whereas the latter two are hyperthermophilic, non‐cytochrome‐containing methanogens. The 532 nm‐excited Raman spectra of single or multiple cells of the four species all showed resonance Raman bands of cobamides arising mainly from the corrin ring, with the most intense one at ∼1500 cm−1. We envision that resonance Raman microspectroscopy could be useful for in situ, nondestructive identification of methanogenic cells that produce high levels of cobamides.

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its co-evolution history with the early Earth surface environment

“…Moreover, our other work also demonstrated that one Baizosediminiarchaeum species of the lignin-degrading clade employs a novel MT system to transfer the methyl groups from lignin-derived ArOCH 3 to H 4 MPT, which are either further oxidized to CO 2 or converted to acetate for energy production ( 45 ). This suggests that this Bathyarchaeia-specific MT system plays a key role in anaerobic lignin degradation, thus likely explaining their predominance in the lignin-enriched estuarine and nearshore sediments.…”

“…Accordingly, the presence of the cobalamin synthesis pathway in these two genera makes Bathyarchaeia the third archaeal lineage with this unusual capability, suggesting they could serve as a keystone species in the subseafloor microbial community by providing this essential cofactor for other members. In addition, some Baizosediminiarchaeum species could grow with lignin as the energy source ( 14 ) using a novel O-demethylation methyltransferase system that require cobalamin-binding corrinoid protein ( 45 ), while the growth of certain Baizomonas species (assigned to subgroup-6) was also significantly simulated by different lignin-derived aldehydes with methoxy groups in enrichments ( 15 ). Overall, the cobalamin synthesis capability might be one of the key factors in explaining the ubiquitous distribution and predominance of genera Baizomonas and Baizosediminiarchaeum (previously subgroups-6/-5bb and -8), even the whole class Bathyarchaeia, in global freshwater and marine sediments ( 25 ).…”

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

“…S5). Despite cobalamin being an essential cobalt-containing cofactor for all three domains of life, in the domain Archaea, only a few Thaumarchaeota and euryarchaeotal methanogens could de novo synthesize it, which might facilitate their key roles in seawater and the methane zone in deep sediments, respectively ( 36 , 37 ). Accordingly, the presence of the cobalamin synthesis pathway in these two genera makes Bathyarchaeia the third archaeal lineage with this unusual capability.…”