Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment

Abstract

The orthoquartzite Imawarì Yeuta cave hosts exceptional silica speleothems and represents a unique model system to study the geomicrobiology associated to silica amorphization processes under aphotic and stable physical–chemical conditions. In this study, three consecutive evolution steps in the formation of a peculiar blackish coralloid silica speleothem were studied using a combination of morphological, mineralogical/elemental and microbiological analyses. Microbial communities were characterized using Illumina sequencing of 16S rRNA gene and clone library analysis of carbon monoxide dehydrogenase (coxL) and hydrogenase (hypD) genes involved in atmospheric trace gases utilization. The first stage of the silica amorphization process was dominated by members of a still undescribed microbial lineage belonging to the Ktedonobacterales order, probably involved in the pioneering colonization of quartzitic environments. Actinobacteria of the Pseudonocardiaceae and Acidothermaceae families dominated the intermediate amorphous silica speleothem and the final coralloid silica speleothem, respectively. The atmospheric trace gases oxidizers mostly corresponded to the main bacterial taxa present in each speleothem stage. These results provide novel understanding of the microbial community structure accompanying amorphization processes and of coxL and hypD gene expression possibly driving atmospheric trace gases metabolism in dark oligotrophic caves.

Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations

“…This suggests that Ktedonobacteria members appear to prevail in oligotrophic and extreme environments, implying these strains may have evolved versatile metabolic pathways to cope with extreme conditions. For instance, the potential to oxidise carbon monoxide (CO) has been reported for Ktedonobacteria members [46].…”

“…Hot springs from different regions host different cox encoding communities [53]. The Ktedonobacteria genome also includes the reductive TCA cycle along with multiple copies of cox operons, conferring CO oxidation potential to this taxa, allowing it to predominate the microbial community [46] under the influence of CO-rich gas vents, hydrothermal springs, and soil environments [41,54,55]. Other high abundant taxa have evolved diverse strategies, for instance, most Anaerolineaceae species metabolise various organic carbon sources under anaerobic conditions through fermentative metabolism [56].…”

Insights into the microbial life in silica-rich subterranean environments: microbial communities and ecological interactions in an orthoquartzite cave (Imawarì Yeuta, Auyan Tepui, Venezuela)

“…The PCR reaction mixture contained 10 ng of total DNA, 1x Takara Ex Taq buffer with MgCl 2 (10x; Takara Bio Inc., Tokyo, Japan), primers 300 nM, BSA (Roche Life Science, Basel, Switzerland) 1 mg mL −1 , dNTP mix 200 μM, Takara Ex Taq Polymerase 0.5 U, and water (Lichrosolv ® ; Merck, Darmstadt, Germany) up to a total volume of 50 μl. After shearing PCR amplicons using restriction endonucleases, libraries were prepared using NEB Next Ultra II FS DNA Library Prep Kit (New England Biolabs; Ghezzi et al, 2021b). Paired-end Illumina sequencing was performed at the Core Facility Molecular Biology of the Medical University of Graz (Austria).…”

“…Quartzite caves in Venezuelan tepuis (i.e., orthoquartzite table mountains), represent an excellent natural laboratory to investigate microbe-mineral interactions in dark, low-temperature Si-rich environments. In particular, Imawarì Yeuta cave is composed of 98% of silica in the form of α-quartz and minor amounts of amorphous silica, i.e., opal-A, opal-G (Sauro et al, 2018;Ghezzi et al, 2021b). The cave was discovered in the Auyan Tepui in 2013 and is considered one of the most ancient caves in the world (Sauro et al, 2013).…”

“…Thus, the interaction between microbes and the orthoquartzite rocky substrates seems to contribute to this impressive speleothem formation process. In this regard, our previous works described the shifting of the composition/ structure of microbial communities associated with some speleothems characterized by distinct silica amorphization phases (Sauro et al, 2018;Ghezzi et al, 2021b). Imawarì Yeuta provides a unique window to further investigate the microbial ecology of quartz/silica-rich environments under aphotic and non-thermal conditions.…”