Karol Ciuchcinski

Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.

Heavy metal pollution poses a major environmental challenge, with microbial resistance to heavy metals offering potential solutions through bioremediation. Additionally, the presence and diversity of microbial metal resistance genes (MMRGs) could contribute to an ecosystem’s ability to adapt and recover from heavy metal contamination by maintaining essential microbial functions and promoting the cycling of nutrients under stress conditions. Thus, MMRGs may serve not only as markers of contamination but also as indicators of an ecosystem’s self-purification capacity and resilience to environmental disturbances. Here we present MetHMMDB, a database containing 254 profile Hidden Markov Models representing 121 MMRGs. Unlike traditional sequence-based resources, MetHMMDB relies on HMMs to improve detection sensitivity and functional specificity across microbial communities. Created through iterative database searches, sequence clustering, structural prediction, and manual annotation, MetHMMDB emphasizes functional annotation rather than gene classification. The database outperforms sequence-based approaches, identifying over twice as many MMRGs in metagenomic datasets, including those from extreme environments. Analysis of agricultural soil revealed distinct resistance profiles correlating with soil quality. MetHMMDB advances our understanding of microbial adaptation to heavy metal contamination while supporting environmental management strategies through improved identification and characterization of metal resistance mechanisms. Database URL: https://github.com/Haelmorn/MetHMMDB .

Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools - PlasX, GeNomad and PLASMe – on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multi-approach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analyzing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin-antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.

Cultural heritage objects constitute a very diverse environment, inhabited by various bacteria and fungi. The impact of these microorganisms on the degradation of artworks is undeniable, but at the same time, some of them may be applied for the efficient biotreatment of cultural heritage assets. Interventions with microorganisms have been proven to be useful in restoration of artworks, when classical chemical and mechanical methods fail or produce poor or short-term effects. The path to understanding the impact of microbes on historical objects relies mostly on multidisciplinary approaches, combining novel meta-omic technologies with classical cultivation experiments, and physico-chemical characterization of artworks. In particular, the development of metabolomic- and metatranscriptomic-based analyses associated with metagenomic studies may significantly increase our understanding of the microbial processes occurring on different materials and under various environmental conditions. Moreover, the progress in environmental microbiology and biotechnology may enable more effective application of microorganisms in the biotreatment of historical objects, creating an alternative to highly invasive chemical and mechanical methods.

There is no standardized protocol for the assessment of microbial air contamination in museums and other cultural heritage sites. Therefore, most museums conduct such assessments based on their own guidelines or good practices. Usually, microbial air contamination is assessed using only classical microbiology methods with the application of a single growth medium. Therefore, this medium should be carefully selected to limit any selective cultivation bias. Metabarcoding, i.e., a next-generation sequencing (NGS)-based method, combined with classical microbiological culturing was used to assess the effectiveness of various media applications in microbiological screening at the Museum of King John III’s Palace at Wilanow (Warsaw, Poland). The obtained results indicated that when using a classical microbiology approach to assess the microbial air contamination at the museum, the selection of a proper growth medium was critical. It was shown that the use of rich media (commonly applied by museum conservators) introduced significant bias by severely underreporting putative human pathogens and the bacterial species involved in biodeterioration. Therefore, we recommend the use of other media, such as Frazier or Reasoner’s 2A (R2A) medium, as they could yield more diverse communities and recovered the highest number of genera containing human pathogens, which may be suitable for public health assessments.