1. Mejice kot podpora biotski raznolikosti, ohranjanju tradicionalnega in izginjajočega kulturnega vzorca slovenskega podeželja ter zagotavljanju ekosistemskih storitev : priročnik dobre prakseTine Grebenc, Ajša Alagić, Nejc Suban, Benjamin Leskovec, Polona Urh, Jani Gačnik, Jure Štanta, Tamara Urbančič, Tine Božič, Matevž Podjed, Maja Košuta, 2024, slovar, enciklopedija, leksikon, priročnik, atlas, zemljevid Ključne besede: mejice, priročniki, ekosistemske storitve, kmetijsko gospodarstvo, praktični preskus, plodonosnost, gomoljke Objavljeno v DiRROS: 26.07.2024; Ogledov: 317; Prenosov: 125
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2. High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, Nina Gunde-Cimerman, Tine Grebenc, Cene Gostinčar, 2017, izvirni znanstveni članek Povzetek: The genetic platforms of Deinococcus species remain the only systems in which massive ionizing radiation (IR)-induced genome damage can be investigated in vivo at exposures commensurate with cellular survival. We report the whole genome sequence of the extremely IR-resistant rod-shaped bacterium Deinococcus ficus KS 0460 and its phenotypic characterization. Deinococcus ficus KS 0460 has been studied since 1987, first under the name Deinobacter grandis, then Deinococcus grandis. The D. ficus KS 0460 genome consists of a 4.019 Mbp sequence (69.7% GC content and 3894 predicted genes) divided into six genome partitions, five of which are confirmed to be circular. Circularity was determined manually by mate pair linkage. Approximately 76% of the predicted proteins contained identifiable Pfam domains and 72% were assigned to COGs. Of all D. ficus KS 0460 proteins, 79% and 70% had homologues in Deinococcus radiodurans ATCC BAA-816 and Deinococcus geothermalis DSM 11300, respectively. The most striking differences between D. ficus KS 0460 and D. radiodurans BAA-816 identified by the comparison of the KEGG pathways were as follows: (i) D. ficus lacks nine enzymes of purine degradation present in D. radiodurans, and (ii) D. ficus contains eight enzymes involved in nitrogen metabolism, including nitrate and nitrite reductases, that D. radiodurans lacks. Moreover, genes previously considered to be important to IR resistance are missing in D. ficus KS 0460, namely, for the Mn-transporter nramp, and proteins DdrF, DdrJ and DdrK, all of which are also missing in Deinococcus deserti. Otherwise, D. ficus KS 0460 exemplifies the Deinococcus lineage. Ključne besede: Deinococcus-Thermus, Deinococcaceae, Deinococcus ficus, radiation-resistant, rod-shaped, phenotype characterization, genome analysis, phylogenetic analysis Objavljeno v DiRROS: 25.07.2024; Ogledov: 125; Prenosov: 108
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3. Unearthing the soil-borne microbiome of land plantsRaúl Ochoa-Hueso, David J. Eldridge, Miguel Berdugo, Pankaj Trivedi, Blessing Sokoya, Concha Cano-Díaz, Sebastian Abades, Fernando D. Alfaro, Adebola R. Bamigboye, Felipe Bastida, Tine Grebenc, Tina Unuk Nahberger, 2024, izvirni znanstveni članek Povzetek: Plant–soil biodiversity interactions are fundamental for the functioning of terrestrial ecosystems. Yet, the existence of a set of globally distributed topsoil microbial and small invertebrate organisms consistently associated with land plants (i.e., their consistent soil-borne microbiome), together with the environmental preferences and functional capabilities of these organisms, remains unknown. We conducted a standardized field survey under 150 species of land plants, including 58 species of bryophytes and 92 of vascular plants, across 124 locations from all continents. We found that, despite the immense biodiversity of soil organisms, the land plants evaluated only shared a small fraction (less than 1%) of all microbial and invertebrate taxa that were present across contrasting climatic and soil conditions and vegetation types. These consistent taxa were dominated by generalist decomposers and phagotrophs and their presence was positively correlated with the abundance of functional genes linked to mineralization. Finally, we showed that crossing environmental thresholds in aridity (aridity index of 0.65, i.e., the transition from mesic to dry ecosystems), soil pH (5.5; i.e., the transition from acidic to strongly acidic soils), and carbon (less than 2%, the lower limit of fertile soils) can result in drastic disruptions in the associations between land plants and soil organisms, with potential implications for the delivery of soil ecosystem processes under ongoing global environmental change. Ključne besede: belowground networks, environmental thresholds, moss microbiome, plant microbiome, plant–soil interactions Objavljeno v DiRROS: 31.05.2024; Ogledov: 238; Prenosov: 149
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4. Urban greenspaces and nearby natural areas support similar levels of soil ecosystem servicesDavid J. Eldridge, Haiying Cui, Jingyi Ding, Miguel Berdugo, Tadeo Sáez-Sandino, Jorge Duran, Juan J. Gaitan, José L. Blanco-Pastor, Alexandra Rodríguez, César Plaza, Tine Grebenc, Tina Unuk Nahberger, 2024, izvirni znanstveni članek Povzetek: Greenspaces are important for sustaining healthy urban environments and their human populations. Yet their capacity to support multiple ecosystem services simultaneously (multiservices) compared with nearby natural ecosystems remains virtually unknown. We conducted a global field survey in 56 urban areas to investigate the influence of urban greenspaces on 23 soil and plant attributes and compared them with nearby natural environments. We show that, in general, urban greenspaces and nearby natural areas support similar levels of soil multiservices, with only six of 23 attributes (available phosphorus, water holding capacity, water respiration, plant cover, arbuscular mycorrhizal fungi (AMF), and arachnid richness) significantly greater in greenspaces, and one (available ammonium) greater in natural areas. Further analyses showed that, although natural areas and urban greenspaces delivered a similar number of services at low (>25% threshold) and moderate (>50%) levels of functioning, natural systems supported significantly more functions at high (>75%) levels of functioning. Management practices (mowing) played an important role in explaining urban ecosystem services, but there were no effects of fertilisation or irrigation. Some services declined with increasing site size, for both greenspaces and natural areas. Our work highlights the fact that urban greenspaces are more similar to natural environments than previously reported and underscores the importance of managing urban greenspaces not only for their social and recreational values, but for supporting multiple ecosystem services on which soils and human well-being depends. Ključne besede: soil, ecosystem services, urban forests Objavljeno v DiRROS: 17.04.2024; Ogledov: 328; Prenosov: 155
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5. Truffle mycorrhization in a pecan orchardMylla Trisha Mello Souza, Joice Aline Freiberg, Tine Grebenc, Marcelo Aloisio Sulzbacher, Diniz Fronza, Juliano Borela Magalhães, Vanessa da Rosa Gonçalves, Nathalie Caroline Hirt Kessler, Lucas Moura Somavilla, Zaida Ines Antoniolli, 2024, izvirni znanstveni članek Povzetek: The ectomycorrhizal association of Tuber spp. in orchards is essential for truffle production. In this sense, this study aimed to evaluate the ectomycorrhizal association of Tuber aestivum Vittad. and Tuber brumale Vittad. in pecan after five years of cultivation in an orchard. The experiment was conducted in Santa Maria – Rio Grande do Sul, Brazil, in a pecan orchard planted with seedlings inoculated with these two species of truffles. The orchard was characterized in terms of soil physical and chemical properties and soil type. Initially non-inoculated plants, plants inoculated with Tuber aestivum (TA), and plants inoculated with Tuber brumale (TB) were evaluated for the percentage (%) of roots colonized by Tuber spp., other ectomycorrhizae, and non-mycorrhizal roots. A reduction in the colonization of both truffle species was observed five years after transplanting the seedlings to the orchard but they have the potential to maintain the ectomycorrhizal association with pecan seedlings. Ključne besede: Carya illinoinensis, ectomycorrhiza, truffle, tuber Objavljeno v DiRROS: 26.03.2024; Ogledov: 394; Prenosov: 180
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6. The genus Fomitopsis (Polyporales, Basidiomycota) reconsideredViacheslav Spirin, K. Runnel, J. Vlasák, I. Viner, M.D. Barrett, L. Ryvarden, Annarosa Bernicchia, B. Rivoire, A.M. Ainsworth, Tine Grebenc, 2024, izvirni znanstveni članek Povzetek: Based on seven- and three-gene datasets, we discuss four alternative approaches for a reclassification of Fomitopsidaceae (Polyporales, Basidiomycota). After taking into account morphological diversity in the family, we argue in favour of distinguishing three genera only, viz. Anthoporia, Antrodia and Fomitopsis. Fomitopsis becomes a large genus with 128 accepted species, containing almost all former Fomitopsis spp. and most species formerly placed in Antrodia, Daedalea and Laccocephalum. Genera Buglossoporus, Cartilosoma, Daedalea, Melanoporia, Neolentiporus, alongside twenty others, are treated as synonyms of Fomitopsis. This generic scheme allows for morphologically distinct genera in Fomitopsidaceae, unlike other schemes we considered. We provide arguments for retaining Fomitopsis and suppressing earlier (Daedalea, Caloporus) or simultaneously published generic names (Piptoporus) considered here as its synonyms. Taxonomy of nine species complexes in the genus is revised based on ITS, ITS + TEF1, ITS + TEF1 + RPB1 and ITS + TEF1 + RPB2 datasets. In total, 17 species are described as new to science, 26 older species are reinstated and 26 currently accepted species names are relegated to synonymy. A condensed identification key for all accepted species in the genus is provided. Ključne besede: brown-rot fungi, new taxa, phylogeny, polypores, taxonomy Objavljeno v DiRROS: 28.02.2024; Ogledov: 541; Prenosov: 338
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7. Description, identification, and growth of Tuber borchii Vittad. mycorrhized Pinus sylvestris L. seedlings on different lime contentsTanja Mrak, Tine Grebenc, Silke Friedrich, Babette Münzenberger, 2024, izvirni znanstveni članek Povzetek: Tuber borchii forms ectomycorrhiza with oaks, hazel, and pines, including Pinus sylvestris. However, its ectomycorrhiza morphotype with P. sylvestris was not comprehensively described so far, and molecular analyses are missing despite a high danger of misidentification of T. borchii ectomycorrhiza with other closely related and less valuable truffle species. We described for the first time the morphology and anatomy of T. borchii-P. sylvestris ectomycorrhiza using differential interference contrast technique and semi-thin sections in combination with molecular confirmation of identity. Color of ectomycorrhiza is reddish to dark brown, and morphotypes are unevenly but densely covered by warts-bearing pin-like cystidia. All layers of the hyphal mantle are pseudoparenchymatous with outer mantle layer formed of epidermoid cells. T. borchii ectomycorrhiza was identified by a molecular comparison with fruitbodies used for inoculation and its respective ectomycorrhizae. T. borchii has a wide ecological amplitude. To get a better insight in mycorrhization requirements, we investigated growth of P. sylvestris and its ectomycorrhiza infection rate with T. borchii in substrate with different lime content. The mycorrhization of P. sylvestris with T. borchii in the mycorrhization substrate and cultivation in greenhouse conditions was successful, with colonization of P. sylvestris varying between 36.5 and 48.1%. There was no significant correlation of mycorrhization to applied lime contents, and consequently to pH in substrate, while the increased levels of lime improved growth of the P. sylvestris seedlings. Ključne besede: root anatomy, ectomycorrhiza, Limestone content, molecular identification, Pinus sylvestris, Tuber borchii Objavljeno v DiRROS: 22.01.2024; Ogledov: 608; Prenosov: 386
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8. Tehnične smernice za ohranjanje in rabo genskih virov : trepetlika in beli topol = Populus tremula, populus alba : SloveniaRobert Brus, Aleksander Marinšek, Tine Grebenc, Gregor Božič, 2012, strokovni članek Ključne besede: genski viri, drevesne vrste, tehnične smernice, trepetlika, beli topol, Populus tremula, Populus alba, Slovenija Objavljeno v DiRROS: 20.12.2023; Ogledov: 446; Prenosov: 126
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9. Evropski pravi kostanj v Sloveniji - tehnične smernice za ohranjanje in rabo genskih virov ter vpetost v okolje : Castanea sativa :SlovenijaTine Grebenc, Zoran Grecs, Dušan Jurc, Robert Brus, 2012, strokovni članek Ključne besede: genski viri, drevesne vrste, tehnične smernice, evropski pravi kostanj, Castanea sativa, Slovenija Objavljeno v DiRROS: 20.12.2023; Ogledov: 584; Prenosov: 122
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10. Designing innovative business models for the wild food products sector in several Mediterranean countriesAnže Japelj, Marta Rovira, Miriam Piqué, José Antonio Bonet, Daniel Oliach, Enrico Vidale, Nicola Andrighetto, José Guilherme Borges, Inês Conceição, Ibtissem Taghouti, Mariem Khalfaoui, Kaja Plevnik, Tine Grebenc, 2023, objavljeni znanstveni prispevek na konferenci Ključne besede: wild food products, Mediterranean, business model, innovation, living labs Objavljeno v DiRROS: 06.10.2023; Ogledov: 590; Prenosov: 198
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