94% of researchers rate our articles as excellent or good
Learn more about the work of our research integrity team to safeguard the quality of each article we publish.
Find out more
ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Extreme Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1533115
This article is part of the Research Topic Rising Stars in Geomicrobiology: Microbial Life in Subsurface, Seep and Hydrothermal Ecosystems View all articles
Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers
Provisionally accepted- 1 Ben-Gurion University of the Negev, Be'er Sheva, Israel
- 2 Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Beer-Sheva, Southern District, Israel
- 3 Department of Marine Biology, National Institute of Oceanography, Israel Oceanographic and Limnological Research (IOLR), Haifa, Haifa, Israel
- 4 Heidelberg University, Heidelberg, Baden-Württemberg, Germany
Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the attached microbial communities is of paramount importance, especially in the context of biofouling.However, obtaining samples of attached microbes that thrive under natural (undisturbed) conditions is challenging. Our study addresses this by retrieving sessile microbes on-site. We installed columns filled with site-specific rock cuttings at the wellhead, allowing fresh groundwater to flow continuously for approximately 60 days. We hypothesized that the attached microbial communities would differ structurally from planktonic microbes due to the aquifer's lithological and mineralogical composition.This study involved an exploratory examination of the microbial communities in different aquifers with distinct mineralogies, including quartzitic sandstone, calcareous, chert, and highly heterogeneous (clastic) aquifers in Israel's Negev Desert. Metagenomic analysis revealed both shared and distinct microbial communities among attached and planktonic forms in the various environments, likely shaped by the aquifers' physical, lithological, and mineralogical properties. A wealth of carbon-fixation pathways and energy-conservation strategies in the attached microbiome provide evidence for the potential productivity of these biofilms. We identified widespread genetic potential for biofilm formation (e.g., via pili, flagella, and extracellular polymeric substance production) and the interactome (e.g., quorum-sensing genes). Our assessment of these functions provides a genomic framework for groundwater management and biofouling treatment.
Keywords: deep subsurface, Deep aquifers, Groundwater, attached-sessile communities, Biofilm
Received: 23 Nov 2024; Accepted: 06 Mar 2025.
Copyright: © 2025 Atencio, Malavin, Ram, Rubin-Blum, Adar and Ronen. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Zeev Ronen, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Southern District, Israel
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.