1. 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, original scientific article Abstract: 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. Keywords: belowground networks, environmental thresholds, moss microbiome, plant microbiome, plant–soil interactions Published in DiRROS: 31.05.2024; Views: 277; Downloads: 166
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2. How beech provenance affects the structure of secondary xylem, leaf traits, and the ectomycorrhizal community under optimal growth conditionsTanja Mrak, Jožica Gričar, Tina Unuk Nahberger, Gregor Božič, Luka Krajnc, Peter Prislan, Domen Arnič, Tom Levanič, Hojka Kraigher, 2024, original scientific article Abstract: Beyond growth parameters and drought tolerance, comparatively little is known about the functioning of different beech (Fagus sylvatica L.) provenances. We investigated properties of leaves, stem secondary xylem, and ectomycorrhiza (ECM), and explored their interdependencies to identify the best performing beech provenance in optimal growth conditions. The study was conducted on 23-year-old trees in a provenance trial. The investigated provenances originated from Atlantic (Belgium—BE), Alpine (Italy—IT, Slovenia—SI), and continental climates (the Czech Republic—CZ). A significant effect of provenance was observed for stem vessel diameters and conductive area, as well as for foliar %C, δ13C, δ15N, and δ18O. δ13C as a proxy of intrinsic water use efficiency (iWUE) showed that the highest iWUE was achieved in BE provenance. Individuals with a better iWUE had wider growth rings regardless of provenance. Better iWUE was associated with lower specific leaf area (SLA). ECM community composition and diversity indices did not differ significantly among the provenances. Specific ECM taxa were associated with individuals with high SLA, δ13C, δ15N, and δ18O. In optimal growth conditions with no stress events, BE is a promising provenance due to an efficient water conducting system with high vessel diameters and conductive area, and high iWUE, while Alpine provenances showed an adaptation of their water conducting system to freezing conditions at their original locations. Integrating findings from different compartments improves our understanding of functioning of different beech provenances. Keywords: Fagus sylvatica, provenance trial, stable isotopes, specific leaf area, xylem vessels, ectomycorrhizal fungi Published in DiRROS: 19.04.2024; Views: 393; Downloads: 784
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3. 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, original scientific article Abstract: 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. Keywords: soil, ecosystem services, urban forests Published in DiRROS: 17.04.2024; Views: 359; Downloads: 173
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4. Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwideYu-Rong Liu, Marcel G. A. van der Heijden, Judith Riedo, Carlos Sanz-Lazaro, David J. Eldridge, Felipe Bastida, Eduardo Moreno-Jiménez, Xin-Quan Zhou, Hang-Wei Hu, Ji-Zheng He, Tine Grebenc, Tina Unuk Nahberger, 2023, original scientific article Abstract: Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing. Keywords: soil contamination, urban greenspaces Published in DiRROS: 28.03.2023; Views: 836; Downloads: 399
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5. Buckwheat milling waste effects on root morphology and mycorrhization of Silver fir seedlings inoculated with Black Summer Truffle (Tuber aestivum Vittad.)Tina Unuk Nahberger, Tine Grebenc, Daniel Žlindra, Tanja Mrak, Matevž Likar, Hojka Kraigher, Zlata Luthar, 2022, original scientific article Abstract: Large amounts of buckwheat waste are generated annually by the industry and are used in several different ways. To date, there has been little research regarding its suitability as a medium for growing seedlings in nurseries. The aim of this study was therefore to analyze the suitability of common and Tartary buckwheat wastes (brans and husks) as media used for raising seedlings. A pot experiment with five different treatments was carried out, in which silver fir root parameters were analyzed and compared 6 and 12 months after summer truffle-spore inoculation. A significantly higher concentration of the antioxidant rutin was confirmed in Tartary buckwheat bran compared to other buckwheat waste used. We also confirmed a significantly positive effect of added Tartary buckwheat husks on specific root length, root tip density, and specific root tip density compared to added common buckwheat husks or Tartary buckwheat bran, for which a significantly negative effect on branching density was confirmed. A significantly negative effect of added buckwheat husks and Tartary buckwheat bran was confirmed for summer truffle mycorrhization level. Keywords: buckwheat waste, root growth, summer truffle, forest nursery, silver fir, inoculation with ectomycorrhizal fungi Published in DiRROS: 09.02.2022; Views: 1148; Downloads: 752
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6. Potential link between ectomycorrhizal community composition and host tree phenologyTina Unuk Nahberger, Rok Damjanić, Hojka Kraigher, Tine Grebenc, 2021, original scientific article Abstract: The timing of leaf phenology tends to be crucial in controlling ecosystem processes such as the acquisition of carbon and water loss as well as in controlling tree nutrient cycling. To date, tree phenology has mostly been associated with environmental control (e.g., temperature and photoperiod) in a relationship with inheritance, while it has rarely been linked with ectomycorrhizal community compositional changes through the host tree’s phenological stages. Seasonal variations of fungal communities have been widely studied, but little is known about mycorrhiza community composition changes along phenological stages. Therefore, we analyzed ectomycorrhizal communities associated with silver fir and their compositional changes during the transition between phenological stages. The phenological stages of each individual tree and time of bud break were monitored weekly for two years and, at the same time, ectomycorrhiza was harvested from selected silver fir trees. In total, 60 soil cores were analyzed for differences in the ectomycorrhizal community between phenological stages using Sanger sequencing of individual ectomycorrhizal morphotypes. A significant difference in beta diversity for an overall ectomycorrhizal community was confirmed between analyzed time periods for both sampled years. Species-specific reactions to transitions between phenological stages were confirmed for 18 different ectomycorrhizal taxa, where a positive correlation of Russula ochroleuca, Russula illota, Tomentella sublilacina, and Tylospora fibrillosa was observed with the phenological stage of bud burst. Keywords: Abies alba (Mill.), ectomycorrhizal community, phenological stages Published in DiRROS: 20.12.2021; Views: 989; Downloads: 727
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8. Global homogenization of the structure and function in the soil microbiome of urban greenspacesManuel Delgado-Baquerizo, David J. Eldridge, Yu-Rong Liu, Blessing Sokoya, Jun-Tao Wang, Hang-Wei Hu, Ji-Zheng He, Felipe Bastida, José L. Moreno, Adebola R. Bamigboye, Tine Grebenc, Tina Unuk Nahberger, 2021, original scientific article Abstract: The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity, but support highly homogenized microbial communities worldwide. Urban greenspaces had a greater proportion of fast-growing bacteria, algae, amoebae, and fungal pathogens, but a lower proportion of ectomycorrhizal fungi than natural ecosystems. These urban ecosystems also showed higher proportions of genes associated with human pathogens, greenhouse gas emissions, faster nutrient cycling, and more intense abiotic stress than natural environments. City affluence, management practices, and climate were fundamental drivers of urban soil communities. Our work paves the way toward a more comprehensive global-scale perspective on urban greenspaces, which is integral to managing the health of these ecosystems and the well-being of human populations. Keywords: soil biodiversity, structural diversity, functional diversity, urban soils Published in DiRROS: 15.07.2021; Views: 1179; Downloads: 988
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9. Effect of earthworms on mycorrhization, root morphology and biomass of silver fir seedlings inoculated with black summer truffle (Tuber aestivum Vittad.)Tina Unuk Nahberger, Niccolo G. M. Benucci, Tine Grebenc, Hojka Kraigher, 2021, original scientific article Abstract: Species of the genus Tuber have gained a lot of attention in recent decades due to their aromatic hypogenous fruitbodies, which can bring high prices on the market. The tendency in truffle production is to infect oak, hazel, beech, etc. in greenhouse conditions. We aimed to show whether silver fir (Abies alba Mill.) can be an appropriate host partner for commercial mycorrhization with truffles, and how earthworms in the inoculation substrate would affect the mycorrhization dynamics. Silver fir seedlings inoculated with Tuber. aestivum were analyzed for root system parameters and mycorrhization, how earthworms affect the bare root system, and if mycorrhization parameters change when earthworms are added to the inoculation substrate. Seedlings were analyzed 6 and 12 months after spore inoculation. Mycorrhization with or without earthworms revealed contrasting effects on fine root biomass and morphology of silver fir seedlings. Only a few of the assessed fine root parameters showed statistically significant response, namely higher fine root biomass and fine root tip density in inoculated seedlings without earthworms 6 months after inoculation, lower fine root tip density when earthworms were added, the specific root tip density increased in inoculated seedlings without earthworms 12 months after inoculation, and general negative effect of earthworm on branching density. Silver fir was confirmed as a suitable host partner for commercial mycorrhization with truffles, with 6% and 35% mycorrhization 6 months after inoculation and between 36% and 55% mycorrhization 12 months after inoculation. The effect of earthworms on mycorrhization of silver fir with Tuber aestivum was positive only after 6 months of mycorrhization, while this effect disappeared and turned insignificantly negative after 12 months due to the secondary effect of grazing on ectomycorrhizal root tips. Keywords: mycorrhiza, truffles, silver fir, inoculation, earthworms, spore inoculation Published in DiRROS: 22.03.2021; Views: 1239; Downloads: 892
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10. PCR primers comparisons for a successful Tuber spp. DNA region amplification in routine identificationsTina Unuk Nahberger, Hojka Kraigher, Tine Grebenc, 2020, original scientific article Abstract: Since late 20th century DNA sequencing became the method of choice method in precision species identification. The ITS region is one of the official fungal barcoding DNA markers, although in some cases sequencing of the ITS re-gion may, due to misidentification, mislabeling or nomen-clature errors in public databases, lead to incorrect or insuf-ficient identification, as is currently a case in the genus Tu b e r. The aim of this study was to test, which ITS primer pairs are most appropriate and optimal for Tu b e r species DNA region amplification. Thereby we (1) compared ampli-fication success for different Tu b e r species using fungal spe-cific primer pair ITS1f and ITS4 and (2) compared amplifi-cation success using different ITS primer pair combinations in amplifying DNA region an example species Tuber aesti-vum. Based on results, Tuber aestivum was one of the most reluctant Tu b e r species in this study and in most cases failed to amplify with the above primer pair. After comparing dif-ferent ITS primer pairs, we conclude that the primer pair ITS5 and ITS7 is the most appropriate primer pair for ampli-fication DNA region of T. ae stiv um as it resulted in high am-plification success from ectomycorrhizal root tips. Based on sequences, gained from public databases, we found that ITS1f and ITS6 primers have a mismatch in one base pair compared to the target sequence of Tuber aestivum, thus re-sulting in poor or no amplification success. Although prim-er pair ITS5 and ITS7 in our study was proven to be the most appropriate primer pair in amplifying DNA region Tu b e r aestivum species, further analysis about appropriateness of it for a general barcoding and identification of ectomycorrhiza in complex community samples is needed. Keywords: Tuber spp., ITS region, PCR amplification, ITS primers Published in DiRROS: 30.07.2020; Views: 1886; Downloads: 1337
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