Exploring the Bacteriome Diversity and Use as a Proxy for Climate Change and Human Impacts on Groundwater in Temperate and Tropical Countries Oana Teodora Moldovan, Erika Levei, Rodrigo Lopes Ferreira, Marconi Souza Silva, Ionuț Cornel Mirea Microbial Ecology, 2025 This research investigates bacterial communities in various cave pool water and substrates from Brazil and Romania for their use as indicators of environmental impacts on groundwater. Regional and seasonal differences were observed even if, at the phylum level, common bacteria for both countries were found. Distinct patterns emerged at the genus level due to the different climates (tropical vs. temperate) and ecosystems. Chemoautotrophic conditions define an utterly different groundwater bacteriome than oligotrophic conditions independent of the temperature. Bacteria as a proxy for climate change were explored using seasonal changes in Romanian caves; specific genera become dominant in summer months, such as Acinetobacter, Paeniglutamicibacter, Polaromonas, and Saccharimonadales, indicating processes that occur during the low-water season. Climate change, particularly dryness, is expected to exacerbate these variations, threatening the stability of groundwater ecosystems. The research also identified anthropic pollution indicators (Vogesella, Cutibacterium) and potential decontaminants (Bacillus) in Brazilian cave waters. Anthropic pollution indicators, like Pseudoarthrobacter. were also found in Romanian caves. Other key bacteria genera, such as Flavobacterium, Pseudomonas, and Acinetobacter, are chemolithotrophs or involved in the nitrogen cycle, which is critical in supplying nutrients for the cave food web. Marked differences between water and substrate microbiomes within the same pools suggested that substrates may play a crucial, underexplored role in groundwater ecosystem processes. Our study found unassigned taxa, 3 phyla, 2 families, and 832 genera (> 40%) in the studied pools. The results underscore the need to further explore groundwater microbiomes as potentially crucial yet fragile ecosystems in the face of climate change and human impacts.
Assessment of Potentially Toxic Elements Pollution Pattern and Environmental Risk in Soils from Carpathian Areas Using a GIS-Based Approach and Pollution Indices Ana Moldovan, Ionuț-Cornel Mirea, Anamaria Iulia Torok, Maria Laura Tîrlă, Erika Andrea Levei, et al. Land, 2025 Understanding the occurrence and spatial variability of potentially toxic elements in soils is essential for tracing pollution origins, assessing ecological risks, and supporting sustainable land use management. This study investigates the soil pollution with Cd, Pb, Ni, Cu, Zn, Cr, As, Mn, Sr, and Fe, their spatial distribution, and environmental risks in two areas in southwestern Romania—Isverna and Tismana—using a combination of pollution indices and Geographic Information System (GIS)-based analyses. Results indicated predominantly low to moderate pollution across both areas, with localized hotspots of high to extreme pollution, particularly with Ni and Pb, near human settlements. In contrast, Tismana showed more uniform, generally lower pollution levels, suggesting the influence of natural (lithogenic) sources. Spatial distribution maps highlighted these differences, showing more heterogeneous localized hotspots in Isverna, likely linked to anthropogenic activities such as agricultural runoff and improper domestic waste disposal. The integrated use of pollution indices and GIS mapping proved effective in identifying contamination patterns and risk zones, providing valuable insights for environmental monitoring and sustainable management of rural land.
Community-level physiological profiling of carbon substrate metabolization by microbial communities associated to sediments and water in karstic caves from Romania Diana Felicia Panait, Andrei Marian Panait, Adorján Cristea, Erika Andrea Levei, Oana Teodora Moldovan, et al. Studia Universitatis Babes Bolyai Biologia, 2025 Cave ecosystems comprise specialized microbial communities that play essential roles in biogeochemical cycles; yet their metabolic capabilities and ecological functions are not fully understood. As conventional cultivation techniques provide limited insights into the metabolic capabilities, methods based on direct functionality screening may improve our knowledge of cave microbial activity. In this study, the Community-Level Physiological Profiling (CLPP) based on Biolog® EcoPlate™ approach was applied to assess carbon (C) substrate utilization by microbial communities associated with 36 environamental samples collected from five karstic caves (Cloșani, Ferice, Leșu, Muierilor, and Topolnița) in Romania. Principal Component Analysis (PCA) and Generalized Additive Models (GAMs) statistics were employed to infer the patterns of C substrate metabolization and their environmental drivers. Environmental variables such as sodium (Na) and electrical conductivity (EC) significantly impacted C substrate utilization capabilities as indicated by both PCA and GAM. The latter analysis elucidated non-linear relationships between variables, such as EC, Na, and Mg, and microbial metabolic diversity indices. However, distinct C substrate utilization patterns were detected among sampled sites and chemical types. Unlike moonmilk samples where associated microbial communities appeared as exhibiting low C substrate utilization, the highest activity was shown in cave pool water samples with the associated microbial communities extensively consuming D-galacturonic acid and Tween 80. Conversely, substrates like L-threonine and α-ketobutyric acid showed limited utilization across all cave samples. Average Well Color Development (AWCD) and Shannon diversity indices indicated that microbial communities associated to samples from Cloșani and Muierilor caves demonstrated the highest metabolic diversity. Our findings suggested that metabolic profiling using Biolog® EcoPlate™ method combined with multivariate statistical methods might prove a suitable analysis approach to effectively screen for cave microbial functionality and the probable environmental drivers. Besides, this work distinguishes from similar studies by relying on GAM analysis to predict the environmental factors governing the microbially-mediated organic carbon degradation in subterranean ecosystems. Article history: Received 28 February 2025; Revised 30 April 2025; Accepted 18 May 2025; Available online 25 June 2025
Linking rock outcrop size and distance to soil multifunctionality in mountain ecosystems Jiangnan Li, Sixing Chen, Xianwen Long, Peilei Hu, Dan Xiao, et al. Functional Ecology, 2025 Rock outcrops, prevalent in mountain ecosystems worldwide, occupy space and exhibit distinct physical and chemical properties compared with soil. Therefore, it is theorized that these properties significantly affect soil functions. However, previous studies have either overlooked rocks entirely or only considered the proportion of rock covered, leaving a gap in understanding rock outcrops' distance and size on soil ecological processes and ecosystem functions. To address this, we conducted a field study to evaluate the distance and size effects of rock outcrops on the surrounding soil multifunctionality. A total of 31 rock outcrops of varying sizes were selected and categorized into five diameter classes: 0–1 m, 1–2 m, 2–3 m, 3–4 m and 4–5 m. Plant litter and soil samples were collected at two distances (0–20 cm and 20–50 cm) to capture the direct influence of rock outcrops while minimizing interference from broader environmental factors. Five functions assessed soil multifunctionality: nutrient provisioning, microbial growth efficiency, soil organic matter (SOM) decomposition, nutrient cycling and plant‐microbe symbiosis. Our results suggested that soil multifunctionality and microbial growth efficiency were significantly greater at closer distances (0–20 cm) (approximately 17% and 24% higher, respectively) than at further distances (20–50 cm) from rock outcrops. Although plant litter increased with the increasing size of rocks, the effect of rock size on soil multifunctionality exhibited a convex hump‐shaped curve. Soil multifunctionality around medium‐sized rocks (i.e. 2–4 m) was approximately 40%–60% greater than that around smaller rocks (i.e. 0–1 m). Nutrient provisioning, microbial growth efficiency and SOM decomposition functions showed similar trends. Further analysis showed that exchangeable calcium and soil organic carbon emerged as the most important intermediary variables connecting rock size and distance to soil multifunctionality. Overall, the soil near rock outcrops benefits from extra resources such as plant litter, rainfall, atmospheric deposition and nutrients released from rock weathering, which may directly contribute to its high soil multifunctionality; however, excessively large rock outcrops may hinder these resources from contributing to soil multifunctionality. Future surveys and models of mountain ecosystem functions should incorporate factors such as rock size and distance from rocks to enhance assessment accuracy. Read the free Plain Language Summary for this article on the Journal blog.
Bacteria as paleoenvironmental proxies: the study of a cave Pleistocene profile Cătălina Haidău, Ionuţ Cornel Mirea, Silviu Constantin, Oana Teodora Moldovan Biogeosciences, 2025 Caves are well-known archives that preserve valuable information about the past, relevant for reconstructing past climates and environments. We sampled sediments from a 480 cm deep profile, and 16S ribosomal ribonucleic acid (rRNA) gene-based metabarcoding analyses were undertaken that complemented lithological logging, sedimentology, and optically stimulated luminescence (OSL) dating. These analyses revealed different sedimentation conditions along the profile with various water inputs. The OSL age of the sediments places the profile between 74.7 ± 12.3 to 56 ± 8 ka (base to top). However, the more recent Last Glacial Maximum (LGM) paleofloods might have occurred in the upper and lower passages of the cave. Bacterial compositions changed with depth, from soil bacteria (present in the upper part of the sediment profile) to thermophilic/sulfurous bacteria (abundant in the deeper samples of the profile). Considering the thermophilic bacteria, we could only assume their origin from a surface of hot sulfurous springs, old thermal springs, or sapropel sediments.
An Exploration of K-Mer Ranges for Megahit in the Context of Microbial Community-Wide Identification of Antimicrobial Resistance Genes and Biosynthetic Gene Clusters Alina Cărunta, Alexandru Eugeniu Mizeranschi, Cristina Cărunta, Horia Leonard Banciu, Oana Teodora Moldovan, et al. 2024 IEEE 24th International Conference on Bioinformatics and Bioengineering Bibe 2024, 2024 With the advent of genomics and next generation sequencing, metagenomics has become a discipline in its own right, enabling for the first time the study of complex microbial ecosystems containing species that cannot be cultured in the lab. Sequencing and characterizing these microbial genomes enables the identification of novel antimicrobial resistance genes (ARGs) and biosynthetic gene clusters (BGCs), with potential applications in industry. De novo sequence assembly, as a crucial step in metagenomics, is currently being implemented with tools such as MEGAHIT, which employ a multiple <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$k$</tex>-mer approach, where several intermediate assemblies are built from k-mers from a range of sizes and merged at the end. The objective of this study was to investigate the impact that this range of k-mer sizes could have on a range of quality metrics, including the number of identified ARGs and BGCs, using a series of assembly scenarios involving 7 samples collected from the Movile Cave in Romania We found that larger k-mer sizes and more fine-grained ranges of intermediate steps were associated with increased metrics, including larger numbers of identified BGCs. Future studies are required in order to better understand the role of the range of k-mer sizes in MEGAHIT in the context of microbial communitywide identification of ARGs and BGCs.
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database Nathanaelle Saclier, Louis Duchemin, Lara Konecny‐Dupré, Philippe Grison, David Eme, et al. Molecular Ecology Resources, 2024 Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species‐rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large‐scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade‐offs during groundwater colonization.
Life histories in groundwater organisms Michael Venarsky, Matthew L. Niemiller, Cene Fišer, Nathanaelle Saclier, Oana Teodora Moldovan Groundwater Ecology and Evolution, 2023
Brazilian cave heritage under siege Rodrigo Lopes Ferreira, Enrico Bernard, Francisco William da Cruz Júnior, Luis Beethoven Piló, Allan Calux, Marconi Souza-Silva, Jos Barlow, Paulo S. Pompeu, Pedro Cardoso, Stefano Mammola, Alejandro Martínez García, William R. Jeffery, William Shear, Rodrigo A. Medellín, J. Judson Wynne, Paulo A. V. Borges, Yoshitaka Kamimura, Tanja Pipan, Nadja Zupan Hajna, Alberto Sendra, Stewart Peck, Bogdan P. Onac, David C. Culver, Hannelore Hoch, Jean-François Flot, Fabio Stoch, Martina Pavlek, Matthew L. Niemiller, Shirish Manchi, Louis Deharveng, Danté Fenolio, José-María Calaforra, Jill Yager, Christian Griebler, Fadi Henri Nader, William F. Humphreys, Alice C. Hughes, Brock Fenton, Paolo Forti, Francesco Sauro, George Veni, Amos Frumkin, Efrat Gavish-Regev, Cene Fišer, Peter Trontelj, Maja Zagmajster, Teo Delic, Diana M. P. Galassi, Ilaria Vaccarelli, Marjan Komnenov, Guilherme Gainett, Valeria da Cunha Tavares, Ľubomír Kováč, Ana Z. Miller, Kazunori Yoshizawa, Tiziana Di Lorenzo, Oana T. Moldovan, David Sánchez-Fernández, Soumia Moutaouakil, Francis Howarth, Helena Bilandžija, Tvrtko Dražina, Nikolina Kuharić, Valerija Butorac, Charles Lienhard, Steve J. B. Cooper, David Eme, André Menezes Strauss, Mattia Saccò, Yahui Zhao, Paul Williams, Mingyi Tian, Krizler Tanalgo, Kyung-Sik Woo, Miran Barjakovic, Gary F. McCracken, Nancy B Simmons, Paul A. Racey, Derek Ford, José Ayrton Labegalini, Nivaldo Colzato, Maria João Ramos Pereira, Ludmilla M. S. Aguiar, Ricardo Moratelli, Gerhard Du Preez, Abel Pérez-González, Ana Sofia P. S. Reboleira, John Gunn, Ann Mc Cartney, Paulo E. D. Bobrowiec, Dmitry Milko, Wanja Kinuthia, Erich Fischer, Melissa B. Meierhofer, Winifred F Frick Science, 2022
Diversity of cultivable heterotrophic bacteria from three Romanian karst caves Studia Universitatis Babes Bolyai Biologia, 2021
The dilemma of self-citation in taxonomy Douglas Zeppelini, Ana Dal Molin, Carlos J. E. Lamas, Carlos Sarmiento, Cristina A. Rheims, Daniell R. R. Fernandes, Elison F. B. Lima, Evandro N. Silva, Fernando Carvalho-Filho, Ľubomír Kováč, James Montoya-Lerma, Oana T. Moldovan, Pedro G. B. Souza-Dias, Peterson R. Demite, Rodrigo M. Feitosa, Sarah L. Boyer, Wanda M. Weiner, William C. Rodrigues Nature Ecology and Evolution, 2021
Beetles Oana Teodora Moldovan Encyclopedia of Caves, 2012
The North American continental copepods in Chappuis' legacy and redescription of three species of the genus Moraria T. & A. Scott 1893 (Crustacea: Copepoda: Harpacticoida) Zoological Studies, 2012
Oribatid mite fossils from quaternary and pre-quaternary sediments in Slovenian caves I. two new genera and two new species of the family oppiidae from the Early Pleistocene Acta Musei Nationalis Pragae Series B Historia Naturalis, 2012
Assessing the contents of arsenic and of some heavy metals in surface flows and in the hyporheic zone of the arieş stream catchment area, Romania Carpathian Journal of Earth and Environmental Sciences, 2010
Reconsidering Pholeuon C. Hampe (Coleoptera: Leiodidae: Cholevinae), with the description of a new subgenus Zootaxa, 2007
Adaptation of the mouthparts in some subterranean Cholevinae (Coleoptera, Leiodidae) Natura Croatica, 2004
An early modern human from the Peştera cu Oase, Romania Erik Trinkaus, Oana Moldovan, ştefan Milota, Adrian Bîlgăr, Laurenţiu Sarcina, et al. Proceedings of the National Academy of Sciences of the United States of America, 2003
