Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil

Abstract

Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.

Response of Methanogenic Archaea from Siberian Permafrost and Non-permafrost Environments to Simulated Mars-like Desiccation and the Presence of Perchlorate

“…The adaptations aim to preserve the membrane fluidity, cover the necessities for metabolism, and regulate it in response to environmental changes (Cavicchioli et al, 2000). Previous studies indicate that the permafrost and non-permafrost strains in this study have a different chemical composition in terms of aliphatic chain composition of lipids, aromatic amino acids, and carbohydrates among others (Serrano et al, 2015), which may be related to cold adaptive mechanisms and therefore a differential postfreezing recovery in the two groups. This is in accordance with a newly described fatty acid that regulates the temperature adaptation in a coldadapted bacterium isolated from an Antarctic ice-free oasis (Bajerski et al, 2017;Mangelsdorf et al, 2017).…”

“…Methanogenic archaea from Siberian permafrost meet many of the preconditions for survival in the martian subsurface, showing a remarkable resistance against desiccation, osmotic stress, low temperatures, starvation, radiation, and thermophysical martian conditions as compared to non-permafrost strains Morozova et al, , 2015Morozova et al, 2015;Mickol et al, 2017). They are also a subject of astrobiological interest for future planetary exploration missions that involve life detection (de Vera et al, 2012;Serrano et al, 2014Serrano et al, , 2015Mickol et al, 2018;Taubner et al, 2018). Schuerger et al (2012) discussed the biotoxicity of multiple martian soils and concluded that they are not likely to be overtly toxic to terrestrial microorganisms.…”

Machine learning-assisted single-cell Raman fingerprinting for in situ and nondestructive classification of prokaryotes

“…Archaea are found predominantly in extreme environments such as hot/cold, acidic/basic, highly saline, and high-pressure environments ( Baker et al., 2020 ), but microbiome analysis reveals the abundance of archaea in soil and freshwater and their unique ecological roles (e.g., in the nitrogen cycle ( Adair and Schwartz, 2008 )). It is thus crucial to include archaeal species in the list of microorganisms to classify, although there are much fewer Raman studies on archaea ( Fendrihan et al., 2009 ; Jehlička et al., 2013 ; Marshall et al., 2007 ; Serrano et al., 2015 ; Spang et al., 2012 ) than on bacteria.

Figure 1 Workflow of the prokaryotic classification method developed in this study, using single-cell Raman microspectroscopy and RF algorithm (A) Acquisition of the Raman spectra of single prokaryotic cells in aqueous solution (PBS) using an optical tweezer achieved by the same laser beam at 632.8 nm as that used for the Raman excitation (see STAR Methods ).

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Raman spectroscopy and determination of soil yeasts

“…Promene u izgledu Raman spektara dve izabrane vrste kvasca se ne odnose samo na promene u sadržaju lipida, već i na promene u Raman odgovoru aromatičnih aminokiselina i nukleotidnih baza, što je prikazano na slici 2. Pik koji se u našim spektrima zapaža u oblasti oko 15811584 cm -1 se u literaturi pripisuje vibracijama unutar aromatičnih aminokiselina i nukleotidnih baza (prvenstveno adenina i guanina) [16,19]. Pored toga, pikovi na  747 cm -1 i 1002 cm -1 se pripisuju primarno aromatičnim aminokiselinama triptofanu i fenilalaninu respektivno, kao i vibracijama pojedinih veza koje u proteinima grade neke komponente sa bočnim ostacima ovih aminokiselina [14,16,20].…”

“…C. guilliermondii se zapaža složeni pik sastavljen od više Raman linija, koji pokazuje oblik karakterističan za dominantan odziv frakcije lipida[17,19], dok kod kvasca C. utilis nema nikakvih naznaka diferencijacije ovog pika na pojedine Raman mode. Pik na  2725 cm-1 , za koji se iz literaturnih podataka može zaključiti da takođe karakteriše lipide[17], prisutan je kod oba kvasca, ali je izraženiji kod C. guilliermondii.…”