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

D. Ghezzi, F. Sauro, A. Columbu, C. Carbone, Pei-Ying Hong, F. Vergara, J. De Waele, M. Cappelletti

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9 Scopus citations


AbstractThe 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.
Original languageEnglish (US)
JournalScientific Reports
Issue number1
StatePublished - Feb 16 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-02-23
Acknowledgements: We acknowledge the Rector Prof. Francesco Ubertini, the Vice-Rector for Research Prof. A. Rotolo and the Governing Academic Bodies of the University of Bologna (UNIBO) for the financial support of the research project and the PhD scholarship for Daniele Ghezzi. Funding for part of the microbial analyses was provided by Europlanet 2020 17-EPN3-026 grant. Europlanet 2020 RI has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654208. Our gratitude also goes to Prof. Christine Moissl-Eichinger, Dr. Kaisa Koskinen, Dr. Alexander Mahnert, Dr. Slave Trajanoski and Dr. Manuela Pausan at the Medical University of Graz (Austria) for their help with sample preparation for Illumina sequencing, qPCR and data analysis. We thank Prof. Leonardo Piccini for his contribution in the sample collection. Many thanks to Dr. Hosam Zowawi for supporting contacts with KAUST and for further advancement of the research project in the last years, and Dr. Laura Negretti for technical assistance in SEM and FESEM analyses. We acknowledge the agencies and associations involved in granting the permit for the speleological expeditions and samples collection: Instituto National de Parques and the patronage of the Government of Bolivar State from Venezuela, the Embassy of the Bolivarian Republic of Venezuela in Italy. Finally, we are grateful to Dr. Andrea Firrincieli for his support about theoretical aspects of EMIRGE algorithm and the UNIBO students Lisa Foschi, Andrea Gozzi and Alessandro Caprini for their precious contribution in the experimental work. This article has been developed in the framework of the Rolex Award of Enterprise supporting Francesco Sauro in research and exploration on the tepui highlands of South America.


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