Biology subjects

Torok, P.

Publications and source records attributed to Torok, P..

10 recordsLinked to original sources

bioRxiv2025

Morphology-guided convolutional Graph Neural Network decodes optically barcoded nanoparticles for one-pot, purification-,amplification-, and enzyme-free femtomolar nucleic-acid diagnostics

Affordable, accurate, and rapid point-of-care diagnostic tests remain elusive due to inherent trade-offs between performance and cost. Conventional nucleic acid tests offer high sensitivity but require complex, expensive steps such as amplification and purification, whereas lateral flow assays are simple and low-cost but lack the necessary sensitivity for many applications. To bridge this gap, we present a miniaturized and simplified chip-based platform that combines three components into a single diagnostic pipeline: we use (i) spectrally distinct silver and gold nanoparticles that form analyte-dependent clusters with unique spectral fingerprints, (ii) a one-pot, enzyme- and purification-free assay on a chip integrated with a high-throughput automated low-cost microscope, and (iii) a morphology-guided convolutional Graph Neural Network that embeds morphology information into convolutional kernels and performs graph-based relational learning across particle-level features. This integration captures spectral, spatial, and morphological quantification at the particle level, rather than relying on bulk spectral shifts, thereby overcoming the limitations of contemporary nanoparticle assays and image-level deep learning approaches. Processing up to 5000 particles per image using only <5 GB GPU memory, Mc-GNN achieves femtomolar sensitivity with 98.2% recall for synthetic DNA and 94.8% for SARS-CoV-2 RNA from whole virus, despite variations in nanoparticle selection and sample complexity. By embedding morphological information into the biosensing pipeline, our diagnostic platform is computationally efficient, smartphone-compatible and is readily extensible to new analytes and multiplexing, offering a scalable solution for a fieldable diagnostic tool.

bioengineering↗

bioRxiv2024

Origin of plant trait data matters: Shared species of Northwestern Europe and the Pannonian Ecoregion have different trait values in the two regions

Trait-based ecology considerably increased our comprehension of various fields related to ecology and evolution. As measuring traits can be time-consuming and costly, analyses regularly gather trait data from databases instead of carrying out new measurements. However, intraspecific trait variability can cause considerable differences between the trait values of different population and regions. Here we evaluated whether intraspecific trait variability causes considerable differences in trait values measured in two different regions of Europe. We tested whether regionally measured trait data from the Pannonian Ecoregion differ from trait data of the same species originating from Northwestern Europe, by comparing data from the Pannonian Database of Plant Traits (PADAPT) and the LEDA Traitbase. We evaluated six traits of the same set of species: thousand-seed mass (TSM), seed bank persistence index (SBPI), leaf area (LA), leaf dry matter content (LDMC), specific leaf area (SLA), and leaf dry mass. We found that trait data from the two databases significantly differed for TSM, SBPI, SLA, and LDMC. Our results indicate that the markedly different climate of the two regions can cause substantial intraspecific trait variation, therefore, the geographical origin of trait data matters in trait-based analyses. The findings corroborate the assumption that regionally measured trait data and building regional databases are essential for reliable regional-scale trait-based studies. We conclude that for studies analysing traits in the Pannonian Ecoregion (and possibly in Easter and Central Europe in general), it is advisable to use PADAPT instead of databases compiling data from regions with markedly different climatic conditions.

ecology↗

bioRxiv2023

Alkaline and loess grasslands with contrasting richness and biomass patterns are not separated on the CSR strategy spectrum.

Studying the relationship between biodiversity patterns and processes in vegetation has been at the centre of interest in vegetation ecology for several decades. By studying the biomass of loess and alkaline grasslands along a water and salinity gradient, we aimed to analyse species diversity and CSR functional type patterns. We aimed to test the following hypotheses: i) The biomass and species richness scores and the species composition are significantly different between the sampled grassland community types. ii) The sampled communities are well separated based on the CSR strategy spectrum. iii) The amount of green biomass and litter are positively correlated with competitiveness and negatively with stress tolerance. The biomass and species richness scores and the species composition of the sampled communities along the sampled gradients were significantly different; the highest species richness, evenness and Shannon diversity values were found in loess grasslands. The highest level of litter accumulation was found in alkaline meadows. The communities were well separated in the ordinations but surprisingly, calculation of coordinates for CSR strategy types have not shown clear separation of the grassland community types. Based on the results we can conclude that the current CSR classification is too robust to delineate grassland communities in alkaline landscapes which are markedly different in composition. We point out that the CSR classification is based on the magnitude of stress, and it is not able to differentiate between the various forms of stress which might be responsible for the marked compositional differences. Therefore, developing an index focusing specifically on the functional characterisation of stressed communities and able to differentiate between different forms of stress (e.g., water and/or salinity stress) would be highly beneficial for future studies.

ecology↗

bioRxiv2021

Sand dropseed (Sporobolus cryptandrus) - A new pest in Eurasian sand areas?

For the effective control of an invasive species, gathering as much information as possible on its ecology, establishment and persistence in the subjected communities is of utmost importance. We aimed to review the current distribution and characteristics of Sporobolus cryptandrus (sand dropseed), an invasive C4 grass species of North American origin recently discovered in Hungary. We aimed to provide information on (i) its current distribution paying special attention to its invasion in Eurasia; (ii) the characteristics of the invaded habitats in Central Europe; (iii) seed bank formation and germination characteristics, crucial factors in early establishment; and (iv) the effects of its increasing cover on vegetation composition. Finally, we aimed to (v) point out further research directions that could enable us to understand the invasion success of this potential invasive species. Field surveys uncovered large stands of the species in Central and Eastern Hungary with most of the locations in the former, especially the Kiskunsag region. The species invaded disturbed stands of dry and open sand grasslands, closed dune slack grasslands and it also penetrates into natural open sand grasslands from neighbouring disturbed habitats. Increasing cover of Sporobolus cryptandrus caused a decline in species richness and abundance of subordinate species both in the vegetation and seed banks, but a low density of Sporobolus cryptandrus can even have a weak positive effect on these characteristics. Viable seeds of Sporobolus were detected from all soil layers (2.5 cm layers measured from the surface to 10 cm in depth), which indicates that the species is able to form a persistent seed bank (1,114 to 3,077 seeds/m2 with increasing scores towards higher abundance of the species in vegetation). Germination of Sporobolus cryptandrus was negatively affected by both litter cover and 1 cm deep soil burial. To sum up, Sporobolus cryptandrus can be considered as a transformer invasive species, whose spread forms a high risk for dry sand and steppe grasslands in Eurasia. We can conclude that for the effective suppression of the species it is necessary: (i) to clarify the origin of the detected populations; (ii) to assess its competitive ability including its potential allelopathic effects; (iii) to assess its seed bank formation potential in habitats with different abiotic conditions; and (iv) to assess the possibility of its suppression by natural enemies and management techniques such as mowing or livestock grazing.

ecology↗

bioRxiv2020

Oak regeneration at the arid boundary of the temperate deciduous forest biome: insights from a seeding and watering experiment

Temperate deciduous forests dominated by oaks cover extensive areas in European lowlands. These ecosystems have been under intense anthropogenic use for millennia, thus their natural dynamics, and their regeneration in particular, is still not well understood. Previous studies found that pedunculate oak (Quercus robur), one of the most widespread and abundant species in European deciduous forests, regenerates in open habitats and forest edges, but not in closed forest interiors. However, these observations usually come from the core areas of the biome, and much less is known about such processes at its arid boundary, where limiting factors may be different, and climate change may first exert its effects. In a full factorial field experiment, we tested the effects of different habitats and increased growing season precipitation on the early regeneration of pedunculate oak in a forest-steppe ecosystem in Central Hungary, at the arid boundary of temperate deciduous forests. We planted acorns into three neighbouring habitats (grassland, forest edge, forest interior) and studied seedling emergence and plant performance under ambient weather and additional watering for four years. In the grassland habitat, seedling emergence was very low, and no seedlings survived by the fourth year. In contrast, seedling emergence was high and similar at forest edges and forest interiors, and was not affected by water addition. Most seedlings survived until the fourth year, with no difference between forest edge and forest interior habitats in numbers, and only minor or transient differences in size (leaf number, height). The lack of oak regeneration in the grassland contradicts previous reports on successful oak regeneration in open habitats, and may be related to a shift from light limitation to other limiting factors, such as moisture or microclimatic extremes, when moving away from the core of the deciduous forest biome towards its arid boundary. The similar number and performance of seedlings in forest edges and forest interiors may also be related to the decreasing importance of light limitation. The above-average precipitation in the year of seedling emergence (2016) might be a reason why watering had no effect on oak regeneration. Overall, our results highlight that oak regeneration and thus forest dynamics may be limited by different factors at a biome boundary compared to its core areas. Indeed, this very simple mechanism (inability of oak regeneration in grassland habitats) may contribute to the opening up of the closed forest biome, and the emergence of a biome transition zone.

ecology↗

bioRxiv2020

Turning old foes into new allies - harnessing drainage canals for biodiversity conservation in desiccated novel ecosystems

O_LIDrainage canals are ubiquitous components of agricultural landscapes worldwide. Although canals have greatly contributed to biodiversity loss by desiccating wetlands, they have recently attracted conservation attention due to their potential to function as refugia for native wetland-dependent species in intensively managed landscapes. However, their conservation role in complex landscapes comprising a mosaic of agricultural and desiccated semi-natural habitats, on which canals still pose a heavy burden, is unknown. Improved understanding of drainage canals and related biodiversity in these landscapes could help unlock their potential and support synergistic land management for nature conservation and water management. C_LIO_LIWe applied a multitaxon approach, including plants, butterflies, true bugs, spiders and birds, to (1) assess the conservation value of drainage canals in a heavily drained European lowland region, (2) to test landscape-level and local canal parameters for aiding prioritization among canal types, and (3) to propose a reconciliation-based management framework that suits the interest of all stakeholders. C_LIO_LIWe found that drainage canals concentrate more species across most taxa than adjacent semi-natural habitats, owing to the micro-environmental heterogeneity and the comparatively low management intensity in the canals. The species-concentrating capacity is particularly high in canals that traverse semi-natural habitats, although agricultural canals also support remarkable species diversity. However, agricultural canals are important dispersal corridors for invasive plants, which may negatively affect native species. Canal size has little effect on biodiversity but habitat stress is an important determinant. The higher the stress (due to sandiness and salinity), the higher is the added value of canals to landscape-wide biodiversity. C_LI Synthesis and applicationsWe provide evidence that drainage canals can harbour surprisingly high levels of biodiversity and should therefore be recognized as important novel ecosystems with high conservation value, even within semi-natural habitats. Canals have previously been considered detrimental to nature conservation due to their association with loss of wetlands. However, by reducing water loss with reversible obstructions, controlling invasive species and applying specific conservation measures, they may be turned into conservation allies without compromising long-term interests of water management and agricultural land use.

ecology↗

bioRxiv2020

Establishment gaps in species-poor grasslands: artificial biodiversity hotspots to support the colonization of target species

Sowing of grass seed mixtures is a feasible and cost-effective method for landscape-scale grassland restoration. However, sowing only grasses usually leads to species-poor and dense grass sward, where the establishment of target forbs is hampered both by microsite and propagule limitation. To overcome these limitations and increase the diversity of species-poor sown grasslands we developed a novel method by creating establishment gaps. We used tillage to open gaps of 1 m2, 4 m2 and 16 m2 size in the dense grass sward of six species-poor sown grasslands in the Great Hungarian Plain. We sowed high-diversity seed mixtures of 35 native species into all gaps. We analyzed vegetation development during the first five years after setting up the trial. We also studied the colonization dynamics of the sown species along four 20-m transects around each gap, resulting in a total of 1440 plots of 1 m2 size that were studied. Our results indicated that most of the sown species were able to establish permanently in the establishment gaps. The total cover and the cover of perennial sown species increased independently of gap size. Meanwhile the cover of short-lived sown species decreased during the five years. There was only a moderate level of weed abundance in the gaps, and weed cover decreased over the years. The sown target species started to colonize the species-poor grasslands surrounding the establishment gaps within five years. The highest number of species and individuals dispersed from the 4 m2-sized gaps, as they had a more stable development than small gaps and were exposed to lower grazing pressure than large ones. Implications for practiceO_LIEstablishment gaps are widely applicable tools to increase the diversity of species-poor grasslands. Gaps of 4 m2 represent a more feasible solution compared to larger openings also for the farmers, because there is only a moderate level of weed encroachment and smaller soil disturbance occurs during their creation. C_LIO_LIWe recommend sowing high-diversity seed mixtures containing both short-lived species that can establish in the first year and perennial species, which guarantee a high cover of target species later on. C_LIO_LIGaps sown with high-diversity seed mixture are highly resistant to unfavorable climatic conditions: increasing grass abundance in dry years does not hamper the recovery of target grassland species in the following years. C_LI

ecology↗

bioRxiv2020

Vegetation and seed bank dynamics highlight the importance of post-restoration management in sown grasslands

Sowing grass seeds generally supports the rapid development of a closed perennial vegetation, which makes the method universally suitable for fast and effective landscape-scale restoration of grasslands. However, sustaining the recovered grasslands, and increasing their diversity is a challenging task. Understanding the role of seed bank compositional changes and vegetation dynamics contributes to designating management regimes that support the establishment of target species and suppress weeds. Our aim was to reveal the effect of post-restoration management on the vegetation and seed bank dynamics in grasslands restored in one of the largest European landscape-scale restoration projects. Eight years after restoration we sampled the vegetation and seed bank in a total of 96 plots located in 12 recovered grasslands in the Great Hungarian Plain. In each recovered grassland stand we designated a mown (mown from Year 1 to Year 8) and an abandoned sample site (mown from Year 1 to Year 3 then abandoned from Year 4 to Year 8). Mown and abandoned sites showed divergent vegetation and seed bank development. Abandonment led to the decline of sown grasses and higher cover of weeds, especially in the alkaline grasslands. Our study confirmed that seed bank has a limited contribution to the maintenance of biodiversity in both grassland types. We found that five years of abandonment had a larger effect on the seed bank than on the vegetation. We stress that long-term management is crucial for controlling the emergence of the weeds from their dense seed bank in restored grasslands. Implications for practiceO_LISeed sowing of grass mixtures can be a feasible tool for restoring grasslands at large scales. However, the developed vegetation usually has low biodiversity and a high seed density of weeds is typical in the soil seed bank even several years after the restoration. Therefore, post-restoration management is necessary for suppressing weeds both aboveground and belowground. C_LIO_LIWe recommend to design the long-term management of the sites subjected to grassland restoration already in the planning phase of the restoration projects and ensure that the management plan is ecologically and economically feasible. C_LIO_LIWe recommend to complement the monitoring of vegetation with the analysis of soil seed bank for evaluating restoration success. C_LI

ecology↗

bioRxiv2020

Underground deserts below fertility islands? - Woody species desiccate lower soil layers in sandy drylands

Woody plants in water-limited ecosystems affect their environment on multiple scales: locally, natural stands can create islands of fertility for herb layer communities compared to open habitats, but afforestation has been shown to negatively affect regional water balance and productivity. Despite these contrasting observations, no coherent multiscale framework has been developed for the environmental effects of woody plants in water-limited ecosystems. To link local and regional effects of woody species in a spatially explicit model, we simultaneously measured site conditions (microclimate, nutrient availability and topsoil moisture) and conditions of regional relevance (deeper soil moisture), in forests with different canopy types (long, intermediate and short annual lifetime) and adjacent grasslands in sandy drylands. All types of forests ameliorated site conditions compared to adjacent grasslands, although natural stands did so more effectively than managed ones. At the same time, all forests desiccated deeper soil layers during the vegetation period, and the longer the canopy lifetime, the more severe the desiccation in summer and more delayed the recharge after the active period of the canopy. We conclude that the site-scale environmental amelioration brought about by woody species is bound to co-occur with the desiccation of deeper soil layers, leading to deficient ground water recharge. This means that the cost of creating islands of fertility for sensitive herb layer organisms is an inevitable negative impact on regional water balance. The canopy type or management intensity of the forests affects the magnitude but not the direction of these effects. The outlined framework of the effects of woody species should be considered for the conservation, restoration, or profit-oriented use of forests as well as in forest-based carbon sequestration and soil erosion control projects in water-limited ecosystems.

ecology↗

bioRxiv2020

Beyond the forest-grassland dichotomy: the gradient-like organization of habitats in forest-steppes

Featuring a transitional zone between closed forests and treeless steppes, forest-steppes cover vast areas and have outstanding conservation importance. The components of this mosaic ecosystem can conveniently be classified into two basic types, forests and grasslands. However, this dichotomic classification may not fit reality as habitat organization can be much more complex. In this study, our aim was to find out if the main habitat types can be grouped into two distinct habitat categories (which would support the dichotomic description), or a different paradigm better fits this complex ecosystem. We selected six main habitats of sandy forest-steppes, and, using 176 releves, we compared their vegetation based on species composition (NMDS ordination, number of common species of the studied habitats), relative ecological indicator values (mean indicators for temperature, soil moisture, and light availability), and functional species groups (life-form categories, geoelement types, and phytosociological preference groups). According to the species composition, we found a well-defined gradient, with the following habitat order: large forest patches - medium forest patches - small forest patches - north-facing edges - south-facing edges - grasslands. A considerable number of species were shared among all habitats, while the number of species restricted to certain habitat types was also numerous, especially for north-facing edges. The total (i.e., pooled) number of species peaked near the middle of the gradient, in north-facing edges. The relative ecological indicator values and functional species groups showed mostly gradual changes from the large forest patches to the grasslands. Our results indicate that the widely used dichotomic categorization of forest-steppe habitats into forest and grassland patches is too simplistic, potentially resulting in a considerable loss of information. We suggest that forest-steppe vegetation better fits the gradient-based paradigm of landscape structure, which is able to reflect continuous variations.

plant biology↗