{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T15:56:17Z","timestamp":1790610977115,"version":"4.1.0"},"reference-count":24,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T00:00:00Z","timestamp":1790553600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Deep groundwater ecosystems are energy-limited microbial habitats in which hydrochemical conditions, hydrogeological structure, and habitat isolation jointly influence community assembly. However, the relative importance of environmental filtering and hydrogeological compartmentalization in structuring subsurface microbial communities remains poorly understood. We characterized hydrochemistry, bacterial communities, and archaeal signatures across two contrasting groundwater systems in Qu\u00e9bec, Canada: a shallow permeable groundwater system at pointe-du-lac (PDL) and deep fractured formation waters (1,460\u20131,690\u202fm) at saint-Flavien (SF). Hydrochemical analyses, bacterial and archaeal amplicon sequencing, occupancy-based approaches, and multivariate statistical analyses were used to evaluate patterns of community composition, persistence, and environmental association. The two groundwater systems differed markedly in hydrochemical composition, with PDL enriched in major ions and SF characterized by elevated trace element concentrations. Despite these differences, bacterial communities were structured primarily at the scale of individual wells rather than by groundwater system. Well identity explained a substantially larger fraction of community variation than hydrochemistry, indicating strong hydrogeological compartmentalization. PDL supported a larger recurrent bacterial component, stronger taxon\u2013environment relationships, and repeated methanogen-associated archaeal signatures, whereas SF contained a smaller persistent community fraction and a greater contribution from localized taxa. Across both systems,\n                    <jats:italic>Acetobacterium<\/jats:italic>\n                    was the dominant bacterial genus and was largely represented by a single recurrent lineage distributed across multiple wells and hydrochemically distinct habitats. Recurrent taxa in PDL were enriched in anaerobic and sulfur-associated lineages, while SF was characterized by a smaller set of persistent groundwater-associated taxa. Methanogen-associated archaea were largely restricted to PDL and included both methylotrophic and hydrogenotrophic lineages. These results demonstrate that hydrogeological compartmentalization outweighs hydrochemistry in structuring microbial communities across contrasting subsurface habitats. The persistence of recurrent bacterial lineages, together with localized archaeal assemblages, suggests that deep groundwater ecosystems are shaped by the combined effects of hydrogeological compartmentalization, environmental filtering, and adaptation to long-term energy limitation.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1919949","type":"journal-article","created":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T15:10:16Z","timestamp":1790608216000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Hydrogeological compartmentalization outweighs hydrochemistry in structuring microbial communities across contrasting subsurface habitats"],"prefix":"10.3389","volume":"17","author":[{"given":"Cassandre Sara","family":"Lazar","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al (UQAM)","place":["Montreal, QC, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Betti","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al (UQAM)","place":["Montreal, QC, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Coralie","family":"Rolland","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Universit\u00e9 du Qu\u00e9bec \u00e0 Montr\u00e9al (UQAM)","place":["Montreal, QC, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-S\u00e9bastien","family":"Marcil","sequence":"additional","affiliation":[{"name":"Derena G\u00e9osciences","place":["Quebec City, QC, Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,28]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"wrae091","DOI":"10.1093\/ismejo\/wrae091","article-title":"Microbial ecology of the deep terrestrial subsurface","volume":"18","author":"Beaver","year":"2024","journal-title":"ISME J."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"1457","DOI":"10.3389\/fmicb.2015.01457","article-title":"Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths","volume":"6","author":"Ben Maamar","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1769","DOI":"10.1093\/gbe\/evt128","article-title":"Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis","volume":"5","author":"Borrel","year":"2013","journal-title":"Genome Biol. Evol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"104926","DOI":"10.1016\/j.jconhyd.2026.104926","article-title":"Microbial community characteristics in a major groundwater supply source of a water-Scarce City in North Anhui, China: composition and driving factors","volume":"279","author":"Chen","year":"2026","journal-title":"J. Contam. Hydrol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"fiz160","DOI":"10.1093\/femsec\/fiz160","article-title":"Selection imposed by local environmental conditions drives differences in microbial community composition across groundwater aquifers","volume":"95","author":"Fillinger","year":"2019","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1111\/j.1365-2427.2008.02013.x","article-title":"Microbial biodiversity in groundwater ecosystems","volume":"54","author":"Griebler","year":"2009","journal-title":"Freshw. Biol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"1846","DOI":"10.1038\/ismej.2015.2","article-title":"Aquifer environment selects for microbial species cohorts in sediment and groundwater","volume":"9","author":"Hug","year":"2015","journal-title":"ISME J."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1007\/s100400050003","article-title":"Microbial communities in the deep subsurface","volume":"8","author":"Krumholz","year":"2000","journal-title":"Hydrogeol. J."},{"key":"ref9","doi-asserted-by":"crossref","DOI":"10.4095\/288027","volume-title":"Rock-Eval\/TOC Data from Cambrian-Ordovician of the Saint Lawrence Platform and Humber Zone, and Silurian-Devonian of the Gasp\u00e9 Belt Successions","author":"Lavoie","year":"2011"},{"key":"ref10","volume-title":"G\u00e9ologie et potentiel en hydrocarbures des bassins s\u00e9dimentaires du sud du Qu\u00e9bec","author":"Lavoie","year":"2014"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"284","DOI":"10.3389\/fmicb.2011.00284","article-title":"Acetogenesis in the energy-starved deep biosphere \u2013 a paradox","volume":"2","author":"Lever","year":"2012","journal-title":"Front. Microbiol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1093\/femsre\/fuv020","article-title":"Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations","volume":"39","author":"Lever","year":"2015","journal-title":"FEMS Microbiol. Rev."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-018-0488-2","article-title":"Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages","volume":"6","author":"Liu","year":"2018","journal-title":"Microbiome"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1196\/annals.1419.019","article-title":"Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea","volume":"1125","author":"Liu","year":"2008","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1038\/s41561-018-0221-6","article-title":"The biomass and biodiversity of the continental subsurface","volume":"11","author":"Magnabosco","year":"2018","journal-title":"Nat. Geosci."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1755","DOI":"10.1128\/AEM.00197-08","article-title":"The genome of Polaromonas sp. JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium","volume":"10","author":"Mattes","year":"2008","journal-title":"Environ. Microbiol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1111\/1574-6941.12196","article-title":"Weighing the deep continental biosphere","volume":"87","author":"McMahon","year":"2014","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1038\/ismej.2017.94","article-title":"Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community","volume":"11","author":"Momper","year":"2017","journal-title":"ISME J."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"8773","DOI":"10.1128\/AEM.71.12.8773-8783.2005","article-title":"Desulfotomaculum and Methanobacterium spp. dominate a 4- to 5-kilometer-deep fault","volume":"71","author":"Moser","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"4056","DOI":"10.1128\/AEM.00882-16","article-title":"Energetics and application of heterotrophy in acetogenic bacteria","volume":"82","author":"Schuchmann","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1038\/s43247-025-02680-9","article-title":"Groundwater microbiomes balance resilience and vulnerability to hydroclimatic extremes","volume":"6","author":"Wang","year":"2025","journal-title":"Commun. Earth Environ."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1139\/w11-004","article-title":"Microbial diversity of active-layer and permafrost environments and the ecological versatility of Polaromonas spp","volume":"57","author":"Wilhelm","year":"2011","journal-title":"Can. J. Microbiol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1093\/femsre\/fuy023","article-title":"Bathyarchaeota: globally distributed metabolic generalists in anoxic environments","volume":"42","author":"Zhou","year":"2018","journal-title":"FEMS Microbiol. Rev."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1919949\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T15:10:17Z","timestamp":1790608217000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1919949\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,28]]},"references-count":24,"alternative-id":["10.3389\/fmicb.2026.1919949"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1919949","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,28]]},"article-number":"1919949"}}