Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites

Abstract

Background Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth’s ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen. Methods In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort. Results The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites. Conclusions Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders.

Strain-level profiling of viable microbial community by selective single-cell genome sequencing

“…PMA-coupled metagenomics has been employed for assessing the composition of viable bacteria. While this method has also been utilized to prevent misinterpretation of bacterial composition and activity due to dead bacteria in samples, metagenome-assembled genome (MAG) acquisition from uncultured viable microorganisms has not been well validated 36 , 37 . In particular, single-cell sequencing has been proposed to acquire SAGs from microorganisms active in the bacterial community in combination with BONCAT or Raman spectroscopy 33 , 35 , but PMA and single-cell sequencing combined with the acquisition of viable SAGs has not yet been reported.…”

Microbial Metabolism of Amino Acids—Biologically Induced Removal of Glycine and the Resulting Fingerprint as a Potential Biosignature

“…In summary, these data suggest that the individual fingerprints of the amino acids alanine, aspartic acid, valine, leucine, isoleucine and phenylalanine can vary, i.e., increase or decrease, depending on the composition of the microbial community. Cultivation and subsequent isolation has shown that the microbial communities from these two samples vary significantly (Cockell et al, 2017;Bashir et al, 2021). Although these complexities do not rule out such amino acid degradation patterns as biosignatures, they suggest that further investigation would be needed on any given sample, including its geological and temporal context, to determine if the differential changes in the amino acids in different communities can be disentangled from the expected abiotic degradation processes and attributed to a potential metabolic influence.…”

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

“…Applications of metagenomics are not only restricted to humans, industries, or the earth, but also beyond the earth’s atmosphere. In the last few years, metagenomics has been applied towards safety and space exploration to understand the taxonomic and functional characteristics of microbiomes in extreme conditions and anoxic sites [ 66 ]. Metagenomics study has revealed how the minimal genomes and genome plasticity of Pseudomonas can thrive under severe nutrient stress conditions [ 67 ].…”