Microbial community patterns in two geochemically contrasting zones within the alkaline lake Bagno dell'Acqua (Pantelleria Island, Italy)

Agnese Piacentini¹Stefano Amalfitano²Barbara Casentini²Andrea Butturini³Ilaria Mazzini⁴Marco Seminara⁵Emanuele Colica⁶F. G. Falese⁷F. L. Chiocci⁸Cristina Mazzoni^1*Stefano Fazi^9*

• ¹Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
• ²CNR-Water Research Institute (IRSA), ARRM1, Montelibretti, Rome, Italy, Istituto di Ricerca sulle Acque Consiglio Nazionale delle Ricerche, Rome, Italy
• ³Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain, Rome, Italy
• ⁴CNR-Institute of Environmental Geology and Geoengineering (IGAG), ARRM1, Montelibretti, Rome, Italy, Montelibretti, Italy
• ⁵Department of Environmental Biology, Sapienza University of Rome, 00185, Rome, Italy, Rome, Italy
• ⁶Department of Geosciences, University of Malta, MSD 2080 Msida, Malta, Msida, Malta
• ⁷CNR-Institute of Environmental Geology and Geoengineering (IGAG), c/o Department of Earth Sciences, Sapienza University of Rome, 00185, Rome, Italy, Rome, Italy
• ⁸Department of the Earth Sciences, Sapienza University of Rome, 00185, Rome, Italy, Rome, Italy
• ⁹CNR-Water Research Institute (IRSA), ARRM1, Montelibretti, Rome, Italy, Montelibretti, Italy

Alkaline lakes are natural laboratories for studying microbial adaptation to extreme conditions, due to their high pH and often multiple co-occurring stressors. The Lake Bagno dell'Acqua (Pantelleria Island, Italy) is an alkaline crater lake influenced by hydrothermal fluids, which create steep geochemical gradients. We investigated the spatial heterogeneity of the lake's microbial communities and geochemical conditions by sampling both the hydrothermal inflow at different distances from the shore and the water column at the center of the lake in two different seasons (spring and late summer). Using 16S rRNA gene amplicon sequencing, we characterized the aquatic microbial diversity and inferred the microbial metabolic potential, complementing detailed physicochemical analyses and flow cytometric quantification of microbial abundances. Microbial communities differed markedly between water column and the hydrothermally influenced area along the observed environmental gradient. Water column community was dominated by Actinomycetota, Cyanobacteriota, and Chloroflexota, whereas sediments hosted distinct populations including notable archaeal lineages, such as Thermoplasmatota and Nanoarcheaota. During the spring season, a unique mat dominated by Planctomycetota was observed above the sediment. The area influenced by thermal fluids showed elevated cell abundance and increased taxonomic diversity, consistent with the coexistence of microbial lineages that reflected inputs from both water sources. These findings provide new insights into the distribution and ecological structuring of microbial communities in alkaline–hydrothermal environments and highlights the value of Bagno dell'Acqua as a model for extreme microbial ecosystems.