National Institute of Biology

Beneath the Earth's surface lies a network of interconnected caves, voids, and systems of fissures forming in rocks of sedimentary, igneous, or metamorphic origin. Although largely inaccessible to humans, this hidden realm supports and regulates services critical to ecological health and human well-being. Subterranean ecosystems are integral to major biogeochemical cycles, sustain diverse surface habitats, and serve as the primary source of irrigation and drinking water. They also offer non-material benefits, including scientific discovery, education, and cultural practices. Yet, these contributions often go unrecognised, partly due to the lack of a unified synthesis of ecosystem services across terrestrial, freshwater, and marine subterranean compartments. This gap limits effective communication of their value to scientists, practitioners, and the public. Through a systematic expert-based review, we show that subterranean ecosystems contribute to up to 75% of classified ecosystem services. Notably, many of these contributions are described only qualitatively, lacking numerical or economic quantification. Next, we list examples of the main ecosystem services provided by subterranean systems to offer a global overview of their multifaceted value and vulnerability to environmental change. We believe this synthesis provides researchers and practitioners with concrete examples to communicate more effectively the importance of subterranean ecosystems to diverse audiences.

Abstract Motivation Long-read RNA-seq and phased reference genomes enable haplotype-resolved gene and isoform expression analysis. While methods and tools exist for diploid organisms, analysis tools for polyploids are lacking. Results We developed an end-to-end framework for allele-specific gene and isoform analysis in polyploids with three components: Syntelogfinder identifies syntenic genes in phased assemblies; longrnaseq quantifies transcripts, discovers novel isoforms, and performs quality control of long-read RNA-seq; and PolyASE analyzes differential allelic expression, differential isoform usage between conditions, and structural differences in major isoforms between haplotypes. We demonstrate the use of the framework on diploid rice and autotetraploid potato. Availability and Implementation Syntelogfinder and longrnaseq are implemented in Nextflow and available on GitHub. PolyASE is a Python package available on PyPI. The framework is fully documented and tutorials are provided. Contact Nadja.nolte.franziska@nib.si Supplementary information Supplementary data are available online and on Zenodo.

The molt cycle of Ligia italica was divided into four stages with altogether eight sub-stages. The average duration of the molt cycle was determined in laboratory animals. Males and non-breeding females molt every 15 days, breeding females molt every 34 days. Molt-related changes in the infrastructure of the anterior sternal integument and digestive system were investigated with scanning and transmission electron microscopy. Calcium storage and translocation in the integument and the midgut glands during the molt cycle were examined with cytochemical methods. The total calcium concentrations in the midgut glands and haemolymph were determined. Calcium is resorbed from the old cuticle prior to ecdysis and stored as calcium granules in the ecdysal space. In the intramolt animal the resorbed calcium is transported, via the haemolymph, to me posterior part of the integument for the mineralization of the new cuticle. The epithelial cells of the digestive tract with high glycogen content and variously shaped apical parts direct the differentiation of the cuticular structures in the foregut and the hindgut during the premolt stage. The ultrastructure of the midgut and midgut glands also changed during the molt cycle. Changes in the lipid content and distribution were observed in the large cells of the midgut glands throughout the molt cycle. Numerous calcium granules in the small cells of the hepatopancreas of premolt animals may be the source of calcium employed for the mineralization of the cuticle of the digestive tract.

This study presents the first comprehensive assessment of microalgal diversity in two Slovenian transitional waters (TWs): the shallow brackish lagoon of the Škocjanski Zatok Nature Reserve (SZNR) and the Rižana River estuary within the Port of Koper (PK) area. Between 2018 and 2021, water samples collected with a phytoplankton net were analyzed using light and scanning electron microscopy. In total, 240 species from 117 genera were identified in TW, dominated by diatoms and dinoflagellates, surpassing the diversity at a marine coastal station (91 species, 59 genera). Species richness was higher in PK (226) than in SZNR (154), mainly due to dinoflagellates and coccolithophores. Marine taxa predominated along the salinity gradient, with moderate contributions from brackish taxa and few freshwater forms, reflecting both natural and anthropogenic influences. Planktonic taxa dominated at all sites, while benthic forms were abundant in the lagoon, particularly in spring. Thirty-two taxa were recorded for the first time in Slovenian TW, mostly benthic or tychopelagic diatoms. The detection of Coolia monotis and five cyanobacterial genera with potentially harmful traits highlights the role of TW as an ecological interface. The taxonomic sufficiency analysis showed that the order level is sufficient to distinguish transitional from marine assemblages, beyond which ecological information is lost. Overall, this study highlights the importance of detailed taxonomic resolution for detecting microalgal diversity, including harmful and non-indigenous species to ensure robust ecological assessments under the WFD and MSFD directives.

The rapid evolution of bioinformatics and data-driven life sciences necessitates widespread, effective training solutions capable of transcending geographical and institutional boundaries. ELIXIR, as a pan-European bioinformatics research infrastructure, has strategically embraced e-learning methodologies to meet this challenge. This white paper systematically reviews the current landscape of e-learning initiatives across various ELIXIR Nodes and Communities, detailing both historical developments and contemporary practices. It identifies core attributes and desirable features of effective e-learning, presenting an analysis of diverse educational platforms and the deployment of Learning Management Systems (LMS) within ELIXIR's framework. Emphasis is placed on the interactive, open-access, and sustainable nature of these resources, exemplified by platforms such as the Training e-Support System (TeSS) and the ELIXIR-SI eLearning Platform (EeLP). The paper highlights critical advancements toward standardization and interoperability through initiatives such as the adoption of SCORM protocols, facilitating resource reuse across Nodes. Additionally, the integration of e-learning into broader educational strategies-such as hybrid learning environments and structured learning paths-is examined. Finally, future directions are discussed, including strategies for integrating e-learning with traditional training methods, enhancing trainer expertise, and further expanding the availability and FAIRification of bioinformatics training resources.

In September 2023, symptoms of bacterial wilt were observed in ginger (Zingiber officinale) plants in two greenhouses in Zreče, Savinjska region, Slovenia. Affected plants exhibited symptoms such as leaf yellowing, wilting, and stem browning, eventually progressing to dieback. Rhizomes exhibited brown vascular discoloration, with tissue softening and maceration, and milky-white exudates. In one greenhouse, an incidence of up to 80% of the plants was observed. Bulk samples (three plants per greenhouse) were surface disinfected with 70% ethanol. Extracts were prepared separately from rhizomes and stems, plated on a modified SMSA medium (mSMSA; Elphinstone et al., 1996) and incubated at 28 °C for three days. Colonies characteristic of the Ralstonia solanacearum species complex (RSSC) on mSMSA were isolated from all samples. Four isolates were purified and characterized on mSMSA, TSBA (BD Difco ™ , Cat. No. 211768), and SPA (Hayward, 1960) media. Real-time PCR (Vreeburg et al., 2016) was employed to confirm the identity of the strain as RSSC, and conventional PCR using primers Rs-1-F/Rs-3-R (Pastrik et al., 2002) was used to identify the pathogen as Ralstonia pseudosolanacearum Safni et al., 2014. Sequevar determination using egl gene sequencing (EPPO, 2021) showed 100% identity with 100% coverage to strain RUN 6824 from ginger in Germany (GenBank OQ753212), confirming phylotype I, sequevar 30 (Cellier et al., 2023). The sequences were deposited in GenBank (accessions: PV358607–PV358610). The pathogenicity of two selected ginger isolates was assessed by inoculating five tomato (Solanum lycopersicum cv. Moneymaker) plants per isolate. The stems were pricked with a sterile needle dipped in 24-h-old cultures grown on CPG medium (Schaad et al., 2001). Positive controls (R. solanacearum NCPPB 4156 and R. pseudosolanacearum GBBC 1112 (ILVO Plant Clinic, Merelbeke, Belgium) and a negative control (sterile needle) were included in the study. Wilting symptoms appeared within 2 days. Ginger isolates caused partial to complete wilting by 14 days post-inoculation. Plants were incubated in a growth chamber at 28°C (day), 25°C (night), and 80% humidity. Ginger isolates NIB Z 3683 and NIB Z 3685, from this study, initially induced more severe wilting than positive controls. Fourteen days post inoculation (pricking) positive controls caused plant death, while ginger isolates led to partial or complete wilting, affecting most leaves except the top parts of the inoculated plants. The negative control remained asymptomatic. The pathogen was successfully reisolated from infected plants and identified by real-time PCR (Vreeburg et al., 2016). This is the first report of R. pseudosolanacearum causing bacterial wilt of ginger in Slovenia. Traceability analysis suggests indirect introduction via imported rhizomes from Peru. Official eradication measures were taken, including destruction of all plants, disinfection, and a three-year host-plant ban. Ongoing annual monitoring is conducted in and around the affected area. As the cultivation of ginger is constantly increasing in Europe, this report underscores the need for vigilant monitoring and phytosanitary control of imported rhizomes to prevent further spread of this regulated pathogen.

Layered double hydroxides (LDHs) are low-cost and versatile materials, many of which are well-established water oxidation electrocatalysts. A simple MgFe-LDH variant, synthesized as size-tunable nanosheets, was successfully decorated on the surface of hematite (α-Fe2O3) nanorods to structure an integrating photoanode for improved photoelectrochemical (PEC) water oxidation. Combined XPS and SEM analysis showed that MgFe-LDH decoration does not interfere with the nanostructure of the light-harvesting α-Fe2O3. However, intensified Raman bands for the decorated α-Fe2O3 pointed to enhanced interactions between MgFe-LDH and α-Fe2O3. Optimization of the surface amount for MgFe-LDH can lead to a 340mV cathodic shift in the onset potential at 0.1mA cm-2. Mott-Schottky analysis and electrochemical impedance spectroscopy further revealed that LDH decoration enhances the photogenerated charge-carrier separation and efficiently consumes holes accumulating at the electrode surface. Furthermore, density functional theory (DFT) calculations suggest a lower Gibbs free energy (ΔG) value of 1.35eV for MgFe-LDH/α-Fe2O3 contrasted to pristine α-Fe2O3 (ΔG of1.46eV) for the rate-determining step (RDS), further indicating that the MgFe-LDH co-catalyst lowers the activation energy barrier for the OER. This work offers a promising method for designing high-efficiency and low-cost hematite-based photoanodes for solar-fuel devices relying on noncritical elements.

ABSTRACT In this study, the adsorption performance of poly(2‐acrylamido‐2‐methylpropanesulfonic acid) (PAMPS)‐based polymerized high internal phase emulsion (polyHIPE) for the removal of Zn 2+ , Fe 3+ , and Al 3+ ions from water is investigated. The triple‐factor analysis includes the role of shape, porosity, and sulfonate group density. By systematically comparing different forms of PAMPS, that is, polyHIPE beads and monoliths (shape effect), PAMPS homopolymers and copolymers (SO 3 − group density effect), and porous polyHIPEs compared to commercially available gel‐type, non‐macroporous beads (porosity effect), we determine how structure–function relationships govern metal ion uptake. The results show ion‐specific effects: The high charge density of Fe 3+ and Al 3+ generates a strong electrostatic driving force for multipoint binding to SO 3 − groups, which leads to fast adsorption. In contrast, Zn 2+ adsorption is slower due to its lower charge density and the relatively stable hydration sphere. It therefore appears to be diffusion‐limited compared to Fe 3+ and Al 3+ . These results show how the polymer architecture can be tuned to optimize adsorption efficiency, selectivity, and robustness. Such a design principle of PAMPS‐based polyHIPEs demonstrates a strategy to customize adsorbents for advanced water treatment applications.

To understand the relative importance of cis and trans effects on regulation, we crossed multi-parent recombinant-inbred lines (RILs) to a common tester and measured allele-specific gene expression in the offspring. Testing the difference of allelic imbalance between two RIL × Tester crosses is a test of cis or trans, depending on the RIL alleles compared. The study design also enables to separation of two sources of trans variation, genetic and environmental, detected via interactions with cis effects. We demonstrate the effectiveness of this approach in a long-read RNA-seq experiment in female abdominal tissue at two time points in Drosophila melanogaster. Among the 40% of all loci that show evidence of genetic variation in cis, trans effects due to environment are detectable in 31% of loci and trans effects due to genetic background in 19%, with little overlap in sources of trans variation. The genes identified in this study are associated with genes previously reported to exhibit genetic variation in gene expression. Eleven genes in a QTL for thermotolerance, previously shown to differ in expression based on temperature, have evidence for regulation of gene expression regardless of the environment, including the cuticular protein Cpr67B, suggesting a functional role for standing variation in gene expression. This study provides a blueprint for identifying regulatory variation in gene expression, as the tester design maximizes cis variation and enables the efficient assessment of all pairs of RIL alleles relative to the tester, a much smaller study compared to the pairwise direct assessment.

BackgroundAquatic plants play key roles in ecosystems, serving as primary producers and providing habitat for other aquatic life. While many are ecologically important, some invasive species, often introduced through the ornamental plant trade, pose threats to various aquatic ecosystems. Although viral infections have been documented to some extent in aquatic crops, the viral diversity in wild and ornamental aquatic plants remains largely unexplored. Investigating the viral communities of aquatic plants is important, as their direct contact with water allows for the potential long-distance transmission of stable viruses released from infected individuals. Invasive aquatic plants exacerbate this issue by introducing novel microbes, including viruses, to new regions, increasing the potential threat to native plant populations.ResultsHere, we investigated the viral communities of diverse aquatic plants by mining publicly available transcriptome data of 79 wild aquatic species and sequencing the RNA from 14 plant species (some of them of different ornamental varieties), sourced from hobby aquascaping stores. Plant viruses from various families were detected in taxonomically diverse aquatic plants, ranging from algae to angiosperms. Alongside sequences of known crop pathogens, such as turnip yellows virus, cucumber mosaic virus, and lettuce chlorosis virus, we identified contigs of putative novel viral species belonging to several plant-infecting viral families. Most notably, we discovered sequences of known and novel begomoviruses, which may be causing observed ornamental phenotypes in two different aquatic plants. Further, we identified a novel potyvirus that appears to be globally present in multiple ornamental plants from the genus Sagittaria. We detected it in three plants sourced from online stores in Slovenia, as well as six plants intercepted during the import process into the UK.ConclusionsOur findings expand on the so far limited knowledge of aquatic plant viruses, revealing known and putative novel plant viral species across diverse aquatic plant taxa. The detection of crop viruses, including regulated pathogens, in ornamental aquatic plants highlights the risks associated with their unregulated global trade. Further research into viruses of aquatic plants may provide insights into their role in ecosystems as well as their potential impact on agriculture.Supplementary InformationThe online version contains supplementary material available at 10.1186/s40793-025-00783-6.