Aug 2026· International Journal of Molecular Sciences· Vol 27, pp. 6905· 0 citations· 52 references
Medicine
TL;DR
The El Tatio geothermal field is identified as a rich source of putative hydrolase-encoding genes for future biochemical and biotechnological exploration and expands current knowledge of microbial diversity and functional potential in high-altitude geothermal ecosystems.
Abstract
Geothermal ecosystems constitute important reservoirs of thermophilic microorganisms and their associated metabolic functions; however, the genome-resolved diversity and enzymatic potential of high-altitude geothermal systems remain poorly characterized. Here, we applied shotgun metagenomics and genome-resolved approaches to investigate thermophilic microbial communities inhabiting geothermal sediments from the El Tatio geothermal field, a polyextreme hydrothermal system located at ~4300 m above sea level in the Andean Altiplano of northern Chile. Genome reconstruction yielded 657 metagenome-assembled genomes (MAGs), including 190 near-complete and 273 high-quality genomes, providing a comprehensive genome-resolved view of microbial diversity in this environment. Taxonomic analyses revealed diverse archaeal and bacterial communities dominated by members of Thermoproteota, Methanobacteriota, Deinococcota, and Actinomycetota. Functional screening identified 612 high-confidence putative hydrolase-encoding genes distributed across multiple thermophilic lineages, including genes associated with esterases, lipases, proteases, and glycoside hydrolases. Notably, several candidates were recovered from archaeal MAGs affiliated with Thermoproteus, Sulfolobales, Pyrobaculum, and Acidilobaceae, expanding the genomic repertoire of putative hydrolytic functions in thermophilic archaea. Sequence-based thermostability prediction identified proteins with estimated melting temperatures exceeding 80 °C, with the highest predicted value reaching 87.6 °C. Collectively, these results expand current knowledge of microbial diversity and functional potential in high-altitude geothermal ecosystems and identify El Tatio as a rich source of putative hydrolase-encoding genes for future biochemical and biotechnological exploration.
Introduction Microbial communities from deep subsurface petroleum reservoirs are adapted to hydrocarbon-rich, oxygen-limited, and physicochemically extreme environments. However, genome-resolved knowledge of petroleum reservoir microbiomes from Pakistan remains largely unexplored. Methods Shotgun metagenomic sequencing was used to investigate the functional and metabolic potential of microbial communities inhabiting deep subsurface petroleum reservoir cores from the Nashpa Oil Field, Pakistan, at depths of 3,770–4,315 m. Metagenome-assembled genomes (MAGs) were reconstructed and functionally annotated to assess taxonomic composition and predicted metabolic capabilities. Results A total of 402 metagenome-assembled genomes (MAGs) were recovered, of which 216 were high-quality MAGs (≥90% completeness and ≤5% contamination). Taxonomic analysis showed dominance of Pseudomonadota and Actinobacteriota,, including genera such as Alcanivorax, Marinobacter, Pseudomonas, Rhodococcus, and Thermohalobaculum. Functional annotation revealed genes involved in hydrocarbon transformation, nitrate-linked respiration, oxygen-limited metabolism, oxidative phosphorylation, aromatic compound degradation, and cellular stress-response systems. However, markers of hydrocarbon degradation were detected only in a small subset of MAGs, suggesting taxon-specific metabolic specialization rather than broad community-wide enrichment. Genes associated with nitrate reduction and microaerophilic or anaerobic respiration suggested metabolic flexibility under the variable oxygen conditions typical of deep petroleum reservoirs. Stress-associated genes, including molecular chaperones and heat-shock proteins, further indicated putative adaptation to reservoir-associated environmental stress, although thermotolerance was not experimentally confirmed. Discussion This study provides one of the first genome-resolved insights into deep petroleum reservoir microbiomes from Pakistan and identifies candidate microbial lineages carrying MEOR-relevant genomic traits for future functional validation.
Sajida Tayyaba, Arshia Amin, Sobia Zulfiqar et al.· Frontiers in Microbiology· 0 citations
Geothermal environments harbor abundant microbial diversity, yet rare lineages remain poorly resolved, limiting understanding of ecosystem function and evolutionary innovation under energy limitation. Here, we describe Candidatus Vitaminotrophota, a previously unrecognized bacterial phylum represented by 35 metagenome-assembled genomes (MAGs) from Tengchong hot spring sediments, China. Phylogenomic analyses support a coherent internal taxonomy comprising one order, two families and four candidate genera. Metabolic reconstruction indicates a predominantly anaerobic, mixotrophic lifestyle, with widespread carbon fixation potential via the Wood-Ljungdahl pathway and a noncanonical CODH/ACS architecture featuring divergent acsA paralogs. Nitrogenase structural genes (nifHDK) occur in two genera, suggesting diazotrophic potential in part of the lineage. All MAGs encode complete or near-complete cobalamin and pantothenate biosynthesis pathways, and most retain conserved thiamine pathway components, alongside transport systems consistent with corrinoid and metal acquisition. Ca. Vitaminotrophota dominated community-level cobalamin biosynthetic potential in several samples, reaching 99.11% and accounting for >50% in nearly half of the samples. Conserved flagellar and chemotaxis gene sets suggest capacity to navigate steep physicochemical gradients. These findings expand the phylogenetic and functional landscape of geothermal bacteria and identify Ca. Vitaminotrophota as a candidate contributor to carbon fixation and vitamin-mediated metabolic interactions in nutrient-limited hot springs.
Yuan-Guo Xie, Xing-Ru Cao, Yanling Qi et al.· npj Biofilms and Microbiomes· 0 citations
ABSTRACT Polyethylene terephthalate (PET) waste represents a major environmental challenge due to limited recycling solutions. Thermophilic bacteria from geothermal environments harbor diverse enzymatic machinery adapted to extreme conditions, offering promising biocatalysts for plastic degradation; however, biological resources from Peru and other South American countries remain scarce. We characterized four bacterial strains isolated from two geothermal sites in Cajamarca, Peru, screened for PET hydrolysis at 50°C. Whole‐genome sequencing using hybrid assembly achieved near‐complete circular genomes. GTDB‐Tk classification identified three species: Neobacillus thermocopriae (strain 19A), Bacillus licheniformis (strains 16P and BI2), and Brevibacillus agri (strain BI8). Quantitative assays revealed that strain 16P achieved the highest mass loss (0.598%), followed by strain BI8 (0.449%). ATR‐FTIR analysis of the incubated sheets showed a significant reduction of the ester carbonyl index in strains 16P, 19A, and BI8 relative to both non‐incubated PET and an abiotic control, whereas strain BI2 did not differ from the controls, indicating preferential modification of ester bonds at the sheet surface. Genome mining and structure‐based homology searches identified multiple candidate enzymes similar to validated PETases and carboxylesterases, including PETase46‐like homologs in strains BI8 and 16P and a terephthalate‐active carboxylesterase homolog in strain 16P. Molecular docking supported the conservation of catalytic geometry and substrate‐binding sites in these candidates. This work represents one of the first systematic genomic and structural characterizations of putative PET‐hydrolases in Peruvian geothermal bacteria, expanding knowledge of extremophile diversity and advancing thermostable enzymes for sustainable plastic waste management.
Marco A Rivera-Jacinto, Claudia Rodríguez-Ulloa, Sara R Briones-Ramírez et al.· MicrobiologyOpen· 0 citations
Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes.
The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including
Candidatus
Bipolaricaulota and
Candidatus
Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the
Candidatus
Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage.
This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.
M. Macey, Velislava Ilieva, B. Stephens et al.· Environmental Microbiome· 0 citations
Ancient DNA and metagenomic studies provide valuable insights into microbial evolution, host–microbe interactions, and the ecology of ancient microbial communities; however, data from urban archaeological contexts remain limited. This study investigated microbial DNA preserved in paired petrous bone and adjacent sediment samples recovered from the Bath–Gymnasium complex of Stratonikeia, a Hellenistic–Roman city in western Anatolia, to characterize microbial diversity and functional gene profiles in an archaeological context. DNA was extracted under contamination-controlled conditions and analysed using high-throughput shotgun metagenomic sequencing. Bioinformatic analyses included taxonomic profiling, microbial diversity assessment, differential abundance analysis, and characterization of virulence-associated and antimicrobial resistance-related genes. The RH1MK1 (Tepidarium) samples exhibited greater microbial diversity and a higher relative abundance of bacterial taxa with recognized pathogenic potential, including Escherichia coli, Shigella flexneri, Vibrio cholerae, and Clostridioides difficile, compared with the SRH1PPG (Palaestra) samples. Virulence-associated genes, including Shiga toxin-, cholera toxin-, and type III secretion system-related sequences, together with antimicrobial resistance-associated genes, were more abundant in RH1MK1, consistent with differences in depositional and microenvironmental conditions between the two archaeological contexts. Comparative analyses revealed both shared and site-specific microbial profiles relative to other Anatolian archaeological sites. These findings demonstrate the potential of shotgun metagenomics for investigating preserved microbial DNA in archaeological materials while emphasizing that the detected microbial taxa and functional genes should be interpreted within their archaeological and depositional context rather than as direct evidence of ancient infectious diseases or epidemic events.
AIMS
Methanogenic archaea are key players in anaerobic digestion, driving methane production in biogas reactors. This study aimed to assess the diversity of methanogenic archaea in full-scale anaerobic digesters using genome-resolved metagenomics and to systematically evaluate the taxonomic coverage of commonly used mcrA-targeted qPCR primer sets against this genomic framework.
METHODS AND RESULTS
Methanogenic diversity was assessed using 113 dereplicated archaeal metagenome-assembled genomes (MAGs) recovered from 109 full-scale anaerobic digesters treating diverse substrates. Genome-resolved analyses revealed a diverse archaeal community spanning multiple phyla, dominated by Halobacteriota and Methanobacteriota, with additional representatives from Methanobacteriota_B, Thermoplasmatota, and Thermoproteota. The presence of the mcrA gene was identified in a subset 55 MAGs, which were subsequently used as the genomic framework to evaluate six commonly used mcrA qPCR primer sets in silico. This subset clustered into nine phylogenetic groups and formed the basis for the primer coverage analysis. The evaluation revealed marked differences in taxonomic coverage among primer sets. Most primers preferentially detected Methanobacteriales and Methanosarcinales, while underrepresenting or excluding other methanogenic lineages, including H₂-dependent methylotrophic Methanomassiliicoccaceae.
CONCLUSIONS
Commonly used mcrA primer sets differ substantially in their ability to capture methanogenic diversity, with some showing broad representation of reactor-associated methanogens and others exhibiting strong lineage-specific biases. Genome-resolved metagenomics provides an effective framework for benchmarking primer performance and supports the selection and improvement of molecular tools for more accurate monitoring of anaerobic digestion systems.
C. Callejas, P. Bovio-Winkler, C. Etchebehere· Journal of Applied Microbiol...· 0 citations