Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2025
Authors
Sonja G. Keel Alice Budai Lars Elsgaard Brieuc Hardy Florent Levavasseur Liang Zhi Claudio Mondini César Plaza Jens LeifeldAbstract
The potential for soil carbon (C) sequestration strongly depends on the availability of plant biomass inputs, making its efficient use critical for designing net zero strategies. Here, we compared different biomass processing pathways and quantified the long-term effect of the resulting exogenous organic materials (EOMs) to that of direct plant residue input on soil organic carbon (SOC) storage. We estimated C losses during feed digestion of plant material, storage of manure, composting and anaerobic digestion of plant material and manure, and pyrolysis of plant material, using values reported in the literature. We then applied an extended version of the widely used SOC model RothC with newly developed parameters to quantify the SOC storage efficiency, that is, accounting for both processing losses off-site and decomposition losses of the different EOMs in the soil. Based on simulations for a 39-year long cropland trial in Switzerland, we found that the SOC storage efficiency is higher for plant material directly added to the soil (16%) compared to digestate and manure (3% and 5%, respectively). For compost, the effect was less clear (2% ̶ 18%; mean: 10%) due to a high uncertainty in C-losses during composting. In the case of biochar, 43% of the initial plant C remained in the soil, due to its high intrinsic stability despite C-losses of 54% during pyrolysis. To provide robust recommendations for optimal biomass use, it is essential to consider additional factors such as nutrient availability of EOMs, environmental impacts of soil application, and life cycle assessments for the entire production processes.
Authors
Lucía D. Moreyra Alfonso Susanna Juan Antonio Calleja Jennifer R. Ackerfield Turan Arabacı Carme Blanco-Gavaldà Christian Brochmann Tuncay Dirmenci Kazumi Fujikawa Mercè Galbany-Casals Tiangang Gao Abel Gizaw Seid Iraj Mehregan Roser Vilatersana Juan Viruel Bayram Yıldız Frederik Leliaert Alexey P. Seregin Cristina RoquetAbstract
Widely distributed plant genera offer insights into biogeographic processes and biodiversity. The Carduus-Cirsium group, with over 600 species in eight genera, is diverse across the Holarctic regions, especially in the Mediterranean Basin, Southwest Asia, Japan, and North America. Despite this diversity, evolutionary and biogeographic processes within the group, particularly for the genus Cirsium, remain underexplored. This study examines the biogeographic history and diversification of the group, focusing on Cirsium, using the largest molecular dataset for the group (299 plants from 251 taxa). Phylogenomic analyses based on 350 nuclear loci, derived from target capture sequencing, revealed highly resolved and consistent phylogenetic trees, with some incongruences likely due to hybridization and incomplete lineage sorting. Ancestral range estimations suggest that the Carduus-Cirsium group originated during the Late Miocene in the Western Palearctic, particularly in the Mediterranean, Eastern Europe, or Southwest Asia. A key dispersal event to tropical eastern Africa around 10.7 million years ago led to the genera Afrocarduus and Afrocirsium, which later diversified in the Afromontane region. The two subgenera of Cirsium—Lophiolepis and Cirsium—began diversifying around 7.2–7.3 million years ago in the Western Palearctic. During the Early Pliocene, diversification rates increased, with both subgenera dispersing to Southwest Asia, where extensive in situ diversification occurred. Rapid radiations in North America and Japan during the Pleistocene were triggered by jump-dispersals events from Asia, likely driven by geographic isolation and ecological specialization. This added further layers of complexity to the already challenging taxonomic classification of Cirsium.Keywords: Biogeography; Carduinae; Cirsium; Diversification; North Hemisphere; Target-enrichment; Taxonomy.
Authors
Szymon Rusinowski Jacek Krzyżak Krzysztof Sitko Alicja Szada-Borzyszkowska Jacek Borgulat Paulina Janota Radosław Stec Hans Martin Hanslin Marta PogrzebaAbstract
Green roofs and walls offer many benefits, not only in terms of the ecosystem services, but also in terms of improving building performance. The growing medium is the most important component of green roofs and walls. It should ensure stable plant growth with minimal maintenance and the proper choice is crucial for the survival and performance of the vegetation. In the study, we investigated how the source and supply of nutrients affects plant performance in a designed substrate for green walls and roofs. Topsoil from the site of plant origin mixed with sand and compost supplemented with mineral fertilizer was used to study the growth of Trifolium medium L. and Potentilla reptans L., element contents, oxidative stress level and photosynthetic efficiency. P. reptans was in most cases insensitive to mineral fertilization, but an adequate dose of compost improved its growth. T. medium was very sensitive to excessive mineral fertilization, which significantly impaired the growth and physiological status of the plants. Compost as the sole source of additional nutrients in a topsoil-based substrate seems to be the appropriate choice when legumes are used in a green wall or green roof. From the results obtained, we can conclude that calcareous grassland species can be successfully used in designing of green urban infrastructure.
Authors
Paul Eric Aspholm Carmen Rizzo Gabriella Caruso Giovanna Maimone Luisa Patrolecco Marco Termine Marco Bertolino Stefania Giannarelli Alessandro Ciro Rappazzo Josef Elster Alessio Lena Maria Papale Tanita Pescatore Jasmin Rauseo Rosamaria Soldano Francesca Spataro Maurizio Azzaro A Lo GiudiceAbstract
No abstract has been registered
Abstract
Mitochondrial genomes (mitogenomes) display relatively rapid mutation rates, low sequence recombination, high copy numbers, and maternal inheritance patterns, rendering them valuable blueprints for mapping lineages, uncovering historical migration patterns, understanding intraspecific population dynamics, and investigating how environmental pressures shape traits underpinned by genetic variation. Here, we present the bioinformatic pipeline and code used to assemble and annotate the complete mitogenomes of five houndsharks (Chondrichthyes: Triakidae) and compare them to the mitogenomes of other closely related species. We demonstrate the value of a combined assembly approach for detecting deviations in mitogenome structure and describe how to select an assembly approach that best suits the sequencing data. The datasets required to run our analyses are available on the GitHub and Dryad repositories
Abstract
The limited standards for the rigorous and objective use of mitochondrial genomes (mitogenomes) can lead to uncertainties regarding the phylogenetic relationships of taxa under varying evolutionary constraints. The mitogenome exhibits heterogeneity in base composition, and evolutionary rates may vary across different regions, which can cause empirical data to violate assumptions of the applied evolutionary models. Consequently, the unique evolutionary signatures of the dataset must be carefully evaluated before selecting an appropriate approach for phylogenomic inference. Here, we present the bioinformatic pipeline and code used to expand the mitogenome phylogeny of the order Carcharhiniformes (groundsharks), with a focus on houndsharks (Chondrichthyes: Triakidae). We present a rigorous approach for addressing difficult-to-resolve phylogenies, incorporating multi-species coalescent modelling (MSCM) to address gene/species tree discordance. The protocol describes carefully designed approaches for preparing alignments, partitioning datasets, assigning models of evolution, inferring phylogenies based on traditional site-homogenous concatenation approaches as well as under multispecies coalescent and site heterogenous models, and generating statistical data for comparison of different topological outcomes. The datasets required to run our analyses are available on GitHub and Dryad repositories.
Authors
Tatsiana EspevigAbstract
No abstract has been registered
Abstract
• Conventional forest operations can exert significant impacts on the hydrology and water quality of downstream aquatic environments. • Few research results have been published on the impacts of continuous cover forestry (CCF) on water quality. • CCF could be useful for reducing nutrient, carbon, and suspended solid exports in waterways. • CCF may be a better alternative to rotation forestry (RF) on mineral soils and drained peatlands. • Further research is needed on the many processes controlling nutrient and carbon exports in CCF and RF.
Authors
Erik J. JonerAbstract
No abstract has been registered
Abstract
No abstract has been registered