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With the aim to characterize changes caused by grapevine leafroll-associated virus 3 (GLRaV-3) singly or in coinfection with other viruses and to potentially determine genotype-specific or common markers of viral infection, thirty-six parameters, including nutrient status, oxidative stress parameters, and primary metabolism as well as symptoms incidence were investigated in ‘Cabernet Franc,’ ‘Merlot,’ ‘Pinot Noir,’ and ‘Tribidrag’ grapevine varieties. Host responses were characterized by changes in cellular redox state rather than disturbances in nutrient status and primary metabolic processes. Superoxide dismutase, hydrogen peroxide, and proteins were drastically affected regardless of the type of isolate, the host, and the duration of the infection, so they present cellular markers of viral infection. No clear biological pattern could be ascertained for each of the GLRaV-3 genotypes. There is a need to provide a greater understanding of virus epidemiology in viticulture due to the increasing natural disasters and climate change to provide for global food production security. Finding grape varieties that will be able to cope with those changes can aid in this task. Among the studied grapevine varieties, autochthonous ‘Tribidrag’ seems to be more tolerant to symptoms development despite numerous physiological changes caused by viruses.

The decomposition process in wetlands is affected by various factors, among which hydrology and litter quality are very important. We studied the decomposition rate of Phragmites australis upper and lower leaf litter from the lake and the riparian sites at the intermittent Lake Cerknica (Slovenia), exposed to flooded and dry conditions. Xray fluorescence spectrometry revealed that leaf litter element composition was related to soil element composition. Fresh leaves also differed according to their age, especially regarding leaf silicon, which ranged from 2.8% to 6.1% dry matter, and leaf phosphorus, which ranged from 0.12% to 0.17% dry matter for the different leaf groups. According to factorial ANOVA, leaf litter decomposition rate was significantly affected by sampling site, exposure location, and leaf age (p ≤ 0.01). Decomposition rate was significantly lower at the dry location compared to the flooded location, and was not related to leaf silicon content. However, leaf sulphur, chlorine, and calcium contents had a significant positive impact on leaf litter decomposition rate at both the dry and the flooded locations. Leaf phosphorus significantly positively affected leaf litter decomposition rate only at the dry location.

Japanese knotweed (Fallopia japonica) (Houtt.) Ronse Decr. and Bohemian knotweed (F. ×bohemica) (Chrtek and Chrtková) J. P. Bailey are invasive plants in Slovenia. We studied the effects of aqueous extracts [0.5 %, 1 %, 2 %, 5 % and 10 % (w/v)] from rhizomes of F. japonica and F. ×bohemica on the seeds of radish (Raphanus sativus) and examined the morphological and biochemical changes during germination and early growth of seedlings. Germination and early growth of radish were monitored 3, 5 and 7 days after treatment. Extracts of these two knotweed taxa delayed seed germination and strongly reduced the length of the primary root, but had less effect on shoot growth. These extracts triggered stress-induced morphogenic responses in the treated radish seedlings, stimulating the formation of lateral roots at low concentrations and causing inhibition at high concentrations. The extract concentration and not the knotweed taxon influenced the biochemical markers of oxidative stress in the radish. Total antioxidative capacity was increased in treated radish seedlings. The extract of F. japonica had a greater impact on the radish morphology than that of F. ×bohemica, with similar influences on the biochemical parameters. High pressure liquid chromatography identified emodin, resveratrol, catechin and epicatechin in the rhizomes of both knotweed species. Their contents were species dependent.

Common buckwheat (Fagopyrum esculentum Moench, CB) and Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn., TB) are used in human nutrition. The idea to screen in the haploid phase for genes affecting low amylose concentration opens the possibility for the effective search of low amylose (waxy) genotypes in CB populations. Self-pollinated homozygous plants of TB might allow us to use a part of endosperm for screening of amylose content. Phenolic substances have a significant inhibitory effect on the digestion of CB and TB proteins, thus metabolites may have impact on protein digestibility. Digestion-resistant peptides are largely responsible for the bile acid elimination. Breeding to diminish polyphenols and anti-nutritional substances might have negative effects on the resistance of plants against pests, diseases and UV-radiation. Bread and pasta are popular CB and TB dishes. During dough making most of CB or TB rutin is degraded to quercetin by rutin-degrading enzymes. The new trace-rutinosidase TB variety makes possible making TB bread with considerable amount of rutin, preserving the initial rutin from flour. Breeding CB and TB for larger embryos would make it possible to increase protein, rutin, and essential minerals concentration in CB and TB grain.

The current study inventoried remaining populations of wild grapevine [Vitis vinifera subsp. sylvestris (Gmel.) Hegi] in territories of south-east Europe encompassing Croatia, Slovenia and Bosnia and Herzegovina. Morphological and genetic traits of wild grapevine specimens were evaluated. The inventory started in 2015, confirming several historical populations in eastern Adriatic regions. In addition, some new ones not recorded until now were discovered. During prospection, wild grapevines were found at six geographically distant locations in this territory. Each observed individual was considered to meet truly morphological criteria (dioecism and leaf morphology) for sylvestris. Eighty-two sylvestris individuals belonging to six populations and 23 cultivated grapevines have been analyzed at 20 nuclear simple sequence repeat (SSR) loci to detect genetic diversity. Principal coordinate analysis and model-based cluster analysis differentiated among wild and cultivated grapevines, highlighting clearly two different groups. The results demonstrated the high genetic diversity of wild grapevine, and the existence of hidden alleles that could be of interest for breeding programs. The study provides necessary information for conservation management and further characterization of wild grapevine.

The data presented in this article are related to the research article entitled “Root-associated community composition and co-occurrence patterns of fungi in wild grapevine”. This dataset documents the diversity of endophytic and rhizoplane fungi found on the roots of 38 wild grapevine plants growing at four locations (Krka, Neretva, Psunj and Paklenica) in Croatia and Bosnia and Herzegovina. We record here 48 identified fungal operational taxonomic units (OTUs) from 3 phyla, 23 families and 30 genera. The material in this Data in Brief paper comprised the data on the identification of OTUs with their corresponding ecological niche, abundance distribution of each fungal OTU recorded in each of the host and location, restrictedness and with fit to the Sloan neutral community model.

Crops’ wild relatives host a wide range of microorganisms, including some beneficial species that are not found or are under-represented in the domesticated crops. Our goal was to study the underexplored composition of root-associated fungal communities in endangered wild grapevines. We found high taxonomic diversity representing multiple trophic guilds that include beneficial symbiotrophs and endophytes. Soil factors explain a relatively small part of their overall variability. In contrast, the majority of the associated fungal taxa shows a close fit to the neutral model for prediction of their distributions. Only beneficial arbuscular mycorrhizal fungi and the pathogenic Ilyonectria depart from the neutral distribution model and form intimate interactions with the plant host. In addition, pathogenic fungi rarely occurred in samples that included ectomycorrhizal fungi, which suggested potentially applicable inter-microorganism interactions. High abundance and diversity of fungal endophytes on the wild grapevine roots highlight the need for their careful consideration in future studies.

Additional file 1 Fig. S1. Growth of Brassica oleracea accessions (C6 and F103) cultivated hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P) and 0.25 mM P (High P). Fig. S2. Root (a), shoot (b) and plant (c) phosphorus (P) content of two Brassica oleracea accessions (C6 and F103) grown hydroponically for 2 weeks in solutions containing 0.025 mM P (Low P; LP) and 0.25 mM P (High P; HP). Data are means (n = 5–6) and standard errors. Asterisks indicate statistically significant differences (two-way analysis of variance followed by Holm-Sidak post hoc test at P

The genetic diversity and relationship between wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi and cultivated (V. vinifera L. subsp. vinifera) grapevine in the western Balkan region and Central Europe have not been studied together previously, although this area has a rich viticultural past. Here, we studied wild grapevine populations sampled from their natural habitats in several countries of the western Balkan region and Central Europe. Their genetic diversity and structure were compared to cultivars that are traditionally in use in this region. A sample set of 243 accessions was genotyped at 20 nuclear microsatellite loci, including 167 sylvestris and 76 diverse vinifera cultivars. The genetic diversity of the wild grapevines was lower than that of cultivars by all genetic parameters. Both hierarchical and nonhierarchical clustering methods differentiated two main groups, indicating clear separation between wild and cultivated vines but also revealed clear gene flow between the cultivated and wild gene pools through overlaps and admixed ancestry values in the graphs. There was greater affinity to the wild grapes in Central European cultivars than in Balkan cultivars. Fine arrangement of the structure among cultivated grapevines showed differentiation among Central European and Balkan cultivars. These results confirm the divergence of wild grapes from vinifera and highlight the &ldquo, crossroad&rdquo, role of the western Balkan peninsula in the broader context of European viticulture.

In the present study, the genetic relationships and ergot-alkaloid production of the fungus Claviceps purpurea on grasses were investigated, to determine any associations between grass host specificity, ergot-alkaloid production, and geographic origin. C. purpurea sclerotia were obtained from wild and cultivated grasses along a 300-km climatic gradient, from sub-Mediterranean to continental climates. Twenty-one infected grass samples provided 39 sclerotia for analysis of the ergot alkaloids ergometrine, ergosine, ergotamine, ergocornine, ergocryptine, and ergocristine, and their “-inine” epimers, using liquid chromatography–tandem mass spectrometry. C. purpurea ribosomal DNA underwent molecular classification to determine any grass host or geographic specificity of ergot-alkaloid composition for the different operational taxonomic units. Molecular analysis of sclerotia ribosomal DNA showed three genetic groups, with some associations with specific grass host taxonomic groups. The ergot-alkaloid composition data were in agreement with the data obtained by molecular methods. The most frequent ergot-alkaloid epimers were ergocristine, and ergosine. The total ergot-alkaloid concentrations in sclerotia varied from 59 to 4,200 mg kg–1, which corresponds to 0.059 to 4.2 mg kg–1 in animal feed (assuming ergot alkaloids at 1,000 mg kg–1 sclerotia). Therefore, grasses can be associated with significant levels of ergot alkaloids. In addition, the ergot-alkaloid compositions of C. purpurea sclerotia can be different for infections with different C. purpurea genetic groups, because these show different ergot-alkaloid compositions.

The new ecological approach to viticulture emphasises ecologically sound grape production and recognizes the importance of grapevine ( Vitis vinifera ) interactions with soil microbial communities. Due to different viticulture measures, distinctly different microbial communities can form, which affects the potentially beneficial interactions with the grapevines. Therefore, the objective of the present study was to identify differences in the community structures of fungal and bacterial soil communities on a landscape scale, and to relate these to the type and duration of soil management, and to within vineyard habitats. Soil fungal and bacterial communities were screened in vineyards with different soil management (ecological, conventional) and ages (3, 10, 35 years). In each vineyard, 35 rhizosphere soil samples were acquired from beneath the grapevines and between the rows, using a grid covering of 240 m 2 per vineyard. Automated ribosomal intergenic spacer analysis of the microbial soil samples was carried out, with the microbial lifeforms compared among the vineyards (bacteria vs. fungi). There was high variability in the local microbial diversity for all of the sampled plots, with significant differences among the vineyards under ecological and conventional soil management. In comparison to fungi, soil management and age of vineyard had significantly greater impact on bacteria. Microbial communities showed no general overlap in diversity spots or simultaneous changes in community composition along the sampling grids. These results suggest that the microbial communities reflect the influences of highly localised biogeographic factors and vineyard management, with the most profound effects observed after deep tillage. Furthermore, fungal and bacterial communities forming in the vineyard soils appear to be influenced by different sets of environmental factors.

Mercury (Hg) – plant – fungal interactions are only poorly studied. Hg speciation and ligand environment in maize roots inoculated with arbuscular mycorrhizal (AM) fungi were investigated in order to better understand the role of AM in Hg soil to root transfer. The maize plants were grown in Hg polluted substrate (50 μg g −1 as dissolved HgCl 2 ) and inoculated with AM fungi originating from: a) highly Hg polluted environment of a former Hg smelting site in Idrija, Slovenia, ( Glomus sp. – sample AmI), and b) non-polluted environment (commercial AM inoculum Symbivit ® – sample AmC). Hg speciation and ligand environment in maize roots was studied by Hg-L 3 XANES and EXAFS with emphasis on XAS methodology – modelling and fitting the XAFS spectra to extract in a reliable way as much information on Hg coordination as possible. The AmI plants developed more arbuscules and less vesicles than the AmC plants, and also accumulated more Hg in the roots. A clear difference in Hg coordination between the AM (AmC & AmI) and the control (ConC & ConI) plants is recognized in Hg L 3 -edge EXAFS analysis: in the ConC & ConI maize roots 73–80% of Hg is attached between two sulphur atoms at the distance of 2.34 A. The remaining ligand is nitrogen at 2.04 A. In AmI & AmC roots another Hg-S attachment encompassing four thiol groups at the S-distance of ∼2.50 A are identified, accounting for 21–26%. AM fungi can modify Hg ligand environment in plant roots, thus playing an important role in biogeochemical cycling of Hg in terrestrial ecosystems.

The aim of this paper is to review principles and potential application of micro-proton induced X-ray emission (micro-PIXE), synchrotron-based micro-X-ray fluorescence (micro-XRF) and inductively coupled plasma-mass spectrometry (ICP-MS) hyphenated with pulsed laser ablation (LA) for analysing plants and plant materials to elucidate feature of constituensts of nutritional value. These are required in order to develop novel high-quality functional and other food products in view of the variability of properties of plant tissues and products.

Soil borne microorganisms such as mycorrhizal fungi and plant growth-promoting rhizobacteria help plants to overcome abiotic and biotic stress. Mechanisms used in this situtations are: growth promotion and induced resistance. Beneficial soil microorganisms also interact with foliar insects (herbivores, natural enemies and pollinators). This kind of interactions are getting more and more important in different ecosystems, especially in agriculture. A better knowledege of these systems would certainly help to deepen the understanding of multitrophic interactions.

Six Monascus purpureus (red mould) strains were cultivated on brown rice and millet as substrates. They underwent strain selection for high lovastatin and pigment production, and low citrinin mycotoxin production, with particular reference to potential for millet as substrate. For most of these strains, substrate dry matter loss was 54–60% on rice and 46–48% on millet, although the ‘MOPU GS1’ strain showed 18% and 17% dry matter loss, respectively. ‘MOPU GS1’ was also the only strain with detectable levels of lovastatin (1.3 and 1.6 mg lovastatin/g substrate dry weight [dw], respectively) and citrinin under the limit of detection. In the other strains, citrinin varied from 0.3 to 18.2 mg/g substrate dw. Among the six strains, ‘EBY3’ provided high pigment production when grown on rice, although it produced 1.1 mg citrinin/g substrate dw. Millet showed good potential as an alternative substrate to rice, due to higher lovastatin and lower citrinin production; however, rice was the better substrate for production of M. purpureus pigments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13197-019-03820-8) contains supplementary material, which is available to authorized users.

Common buckwheat (Fagopyrum esculentum Moench) and Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) are sources of many bioactive compounds, such as rutin, quercetin, emodin, fagopyrin and other (poly)phenolics. In damaged or milled grain under wet conditions, most of the rutin in common and Tartary buckwheat is degraded to quercetin by rutin-degrading enzymes (e.g., rutinosidase). From Tartary buckwheat varieties with low rutinosidase activity it is possible to prepare foods with high levels of rutin, with the preserved initial levels in the grain. The quercetin from rutin degradation in Tartary buckwheat grain is responsible in part for inhibition of α-glucosidase in the intestine, which helps to maintain normal glucose levels in the blood. Rutin and emodin have the potential for antiviral effects. Grain embryos are rich in rutin, so breeding buckwheat with the aim of producing larger embryos may be a promising strategy to increase the levels of rutin in common and Tartary buckwheat grain, and hence to improve its nutritional value.

Background Phosphorus (P) deficiency limits crop production worldwide. Crops differ in their ability to acquire and utilise the P available. The aim of this study was to determine root traits (root exudates, root system architecture (RSA), tissue-specific allocation of P, and gene expression in roots) that (a) play a role in P-use efficiency and (b) contribute to large shoot zinc (Zn) concentration in Brassica oleracea. Results Two B. oleracea accessions (var. sabellica C6, a kale, and var. italica F103, a broccoli) were grown in a hydroponic system or in a high-throughput-root phenotyping (HTRP) system where they received Low P (0.025 mM) or High P (0.25 mM) supply for 2 weeks. In hydroponics, root and shoot P and Zn concentrations were measured, root exudates were profiled using both Fourier-Transform-Infrared spectroscopy and gas-chromatography-mass spectrometry and previously published RNAseq data from roots was re-examined. In HTRP experiments, RSA (main and lateral root number and lateral root length) was assessed and the tissue-specific distribution of P was determined using micro-particle-induced-X-ray emission. The C6 accession had greater root and shoot biomass than the F103 accession, but the latter had a larger shoot P concentration than the C6 accession, regardless of the P supply in the hydroponic system. The F103 accession had a larger shoot Zn concentration than the C6 accession in the High P treatment. Although the F103 accession had a larger number of lateral roots, which were also longer than in the C6 accession, the C6 accession released a larger quantity and number of polar compounds than the F103 accession. A larger number of P-responsive genes were found in the Low P treatment in roots of the F103 accession than in roots of the C6 accession. Expression of genes linked with “phosphate starvation” was up-regulated, while those linked with iron homeostasis were down-regulated in the Low P treatment. Conclusions The results illustrate large within-species variability in root acclimatory responses to P supply in the composition of root exudates, RSA and gene expression, but not in P distribution in root cross sections, enabling P sufficiency in the two B. oleracea accessions studied.

High levels of arbuscular mycorrhizal fungi colonisation of 90% to 100%, as well as high vesicular and arbuscular colonisation were found in the roots of the rare and endangered wild grapevine (Vitis vinifera subsp. sylvestris) along the Neretva River in southwestern Bosnia and Herzegovina, surpassing colonisation in region vineyads.

We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.

Viticulture is an important agronomic sector that has the potential to greatly benefit by improvements in our understanding of grapevine cultivation. Although conventional viticulture relies to a great extent on pesticide and fertilizer application, more sustainable approaches involve management practices that favor plant–fungus interactions that have positive effects on the nutritional quality of the grapes and reduce production costs (i.e., of pesticides and fertilizers) and thus reduce the negative effects on the environment. Fungal endophytes that colonize grapevines belong to different taxa, with the majority of reports focusing on fungi that form arbuscular mycorrhizal associations. These fungal endophytes have been demonstrated to confer beneficial growth and nutrition effects to their plant hosts via improved exploitation of the substrate and improved tolerance of the grapevine to abiotic and biotic stresses. Here, we review current knowledge on the importance and potential of these diverse fungal groups for grapevine production and expose the gaps in our understanding of possible functions of fungal groups that are currently little studied. In addition, we underline the effects of sustainable agricultural practices on fungal communities, to boost the progress in different viticultural techniques on the interactions between fungal endophytes and grapevines.

Plant essential oils are potential food preservatives due to their inhibitory effects on bacterial and fungal growth. Antifungal activities of common thyme (Thymus vulgaris) essential oil were tested against endophytic fungi grown from wheat (Triticum aestivum) grain, molecularly identified as Alternaria alternata, Alternaria infectoria, Aspergillus flavus, Epicoccum nigrum and Fusarium poae. Their susceptibility to thyme essential oil was tested in vitro, and ranged from fungicidal to fungistatic. Treatment combinations of prior grain surface sterilization with hypochlorite and direct/indirect treatment with the essential oil were used, which showed strong effects on infection incidence and germination. Direct soaking of the wheat grain in the essential oil was particularly effective, but inhibited both fungal growth and seed germination. In contrast, indirect treatment of the grain with the essential oil (i.e., fumigation) inhibited fungal growth without negative effects on seed germination. In combination with grain surface sterilization with hypochlorite, indirect treatment with thyme essential oil reduced these fungal infections even more. Since thyme essential oil is safe for plants and consumers, in the form of fumigation it could be used as a protectant of storage containers for wheat grain intended for sowing and for food production.

Maize root residues that remain in the field after harvesting are a source of water-soluble compounds, which can inhibit growth of succeeding maize crops through autotoxicity. The aim of this study was to test whether the formation of symbiosis between maize and arbuscular mycorrhizal fungi (AMF) alleviates negative effects of autotoxicity. Maize root extracts containing water-soluble compounds were used to simulate the release of autotoxic compounds from decomposing root residues in soil under experimental conditions and were applied at increasing concentrations to maize seedlings. The 0.15% (w/v) root extract treatment decreased root biomass and increased guaiacol peroxidase (G-POD) activity and concentrations of the major water-soluble compound benzoxazinone 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) in roots of maize seedlings. As such, 0.15% concentration was used in subsequent inoculation experiment. The effects of maize root extracts seen in non-inoculated seedlings were lost in AMF-inoculated maize, even though the AMF colonization was reduced in the root extract-treated seedlings. These data indicate that AMF can alleviate the negative effects induced in maize seedlings by water-soluble compounds from maize roots and show potential importance of AMF in extensive agricultural practice.

Dark septate endophyte (DSE) fungi are the most frequent colonists on the roots of Salix caprea in highly metal-contaminated soils. The present study was performed to obtain insights into the physiology and potential role(s) of DSE fungi for Salix caprea growing in metal-enriched sites. Fungal isolates from S. caprea roots were identified using molecular methods, and tested for their tolerance and metal accumulation in axenic cultures. In addition, an inoculation experiment was performed to monitor the effects of the fungi on the metal uptake by the plant host. Fitness of S. caprea cuttings was assessed by photosynthetic pigment quantification and measurements of transpiration. Fungal isolates were identified as members of the Phialophora/Cadophora complex. They showed different levels of metal tolerance and maintained growth on metal-enriched media. In comparison to non-inoculated cuttings, the DSE-inoculated cuttings had lower leaf Cd content, and for isolates DB146 and DB148, also lower Zn concentrations. All DSE isolates increased the chlorophyll levels of the cuttings, with isolate DB146 also positively affecting the transpiration rate of S. caprea. Our findings suggest that DSE reduced the metal uptake by the S. caprea cuttings, thus suggesting a beneficial role for S. caprea in metal-enriched soils.

Background Arbuscular mycorrhizal fungi (AMF) are among the most important beneficial fungal root endophytes, and are known to colonise the roots of the majority of land plants, including grapevines. Similar to other plant species with low root densities or with relatively coarse fine roots, grapevines appear to be reliant on AMF colonisation for normal growth and development, which is especially important in organic vineyards that follow low-input practices, as these support higher AMF spore abundance and diversity. Key results and discussion The comparison of the AMF communities on the roots of grapevines from East Adriatic Karst region showed that the fungal communities associated with grapevine roots seem to be relatively stable, with inter-vineyard variability comparable to intra-vineyard variability. Some of the changes in the fungal communities were attributed to environmental factors (eg. plant-available P) and geographical location of the vineyard. The majority of the AMF belonged to various representatives of genus Glomus, with some species that are less frequently observed in studies on AMF (eg. Glomus sinuosum and Glomus indicum). Screening of vineyard weeds belonging to 11 plant families and showed varying level of fungal colonization and seemed to promote different sets of dominant AMF, potentially providing a wider spectrum of AMF for colonizing grapevine roots. This indicates the value of encouraging host plant diversity in vineyards. In deed herbaceous weed Tanacetum cinerariifolium was shown to improve colonization of grapevine plants in a pot culture experiment. In the next stage of our studies, we were starting to focus on the other aspects of “terroir” (vineyard management) and its consequences on the fungal endophyte communities. AMF spore abundance greatly increased in organic vineyards, as has been seen for different agricultural systems, including vineyards. In contrast, vineyard management had no effect on the overall diversity of AMF colonizing grapevine roots. Our results confirm that the production vineyard harbor well formed AMF communities that are greatly affected by the vineyard management. Change towards more sustainable vineyard practices improves the abundance and diversity of AMF that can result in positive effects on the mineral nutrition of grapevines due to modified nutrient availability related to changes in the abiotic and biotic characteristics of the soil.

Grapevine ( Vitis vinifera L.) and two selected weeds from Mediterranean Croatian vineyards (Plantago lanceolata L. and Tanacetum cinerariifolium (Trevir.) Sch.Bip.) were examined in pot culture experiments, individually or when combined, to see whether multiple hosts influenced the formation of the symbiosis with arbuscular mycorrhizal fungi (AMF). The results after six-month period showed that plant identity and density significantly influenced development of mycorrhizal intra- and extraradical mycelium and/or sporulation. Grapevine and T. cinerariifolium individually and in combination resulted in a greater development of arbuscular mycorrhizae in terms of spore production, extraradical mycelium length and root colonization compared with pots containing P. lanceolata. Herbaceous weed species seemed to promote a different set of dominant AMF, potentially providing a wider spectrum of AMF for colonising grapevine roots. This indicates the value of encouraging host plant diversity in vineyards. AMF sequences obtained in this study are the first data reported for soils in Croatia.

Fungal endophytes can affect the heavy metal uptake of their host plants and increase the tolerance of their host plants to heavy metal stress. Therefore, in the present study, a wide-range screening of the fungal endophyte communities was conducted to determine the fungal distribution and diversity on S. caprea roots on a metal polluted site. Fungal communities were screened using amplification with the 5.8S-ITS2-28S part of the rDNA operon, with the resulting amplicons analysed by temporal temperature gradient gel electrophoresis (TTGE) and sequencing. This technique is reproducible and shows good coverage of ascomycete and basidiomycete taxa, as 68% and 32% of all of the sequences, respectively. No clear shift in fungal ITS-TTGE profiles from S. caprea roots was seen along the secondary succession stages. Ascomycetes dominated the more polluted plots, while there was a greater diversity of basidiomycetes in the less polluted and control plots, suggesting greater tolerance of ascomycetes in comparison with basidiomycete fungi. The high diversity of DSEs was confirmed at the highly metal-enriched locations, with species belonging to the genera Phialophora, Phialocephala and Leptodontidium. Furthermore, the DSE colonisation of S. caprea roots and the frequency of the sequences showing affinity towards DSE genus Phialophora, showed good correspondence with soil Pb, Cd and plant-available P concentrations, possibly indicating that DSEs improve metal tolerance of willows to high heavy metal contamination.

Goat willow (Salix caprea L.) was selected in a previous vegetation screening study as a potential candidate for the later-stage phytostabilisation efforts at a heavily metal polluted site in Slovenia. The aims of this study were to identify the fungi colonising roots of S. caprea along the gradient of vegetation succession and to estimate their colonisation levels in relation to metal pollution in order to reveal its mycorrhizal status at the site. Additionally the metal accumulation capacity of S. caprea and photosynthetic pigments were analysed as indications of its fitness at four differentially polluted plots. Despite high concentrations of leaf accumulated Cd, no significant differences in photosynthetic pigment concentrations were observed. The roots were colonised by arbuscular mycorrhizal (AM) fungi, ectomycorrhizal (EM) fungi, and dark septate endophytes (DSE), with EM as the dominant type on all the plots. Molecular characterisation showed poor correlation of the root EM community with the above-ground sporocarp diversity. Members of Sordariaceae were the most frequent colonisers with an average colonisation of 21% of all root tips, followed by Thelephoraceae with 10%. DSE colonisation increased with increasing Pb concentrations and decreasing organic matter (OM).

Nuclear ribosomal sequences and Cd, Zn, Pb and Fe accumulation of different populations of the recently discovered Cd/Zn-hyperaccumulating species Thlaspi praecox Wulfen (Noccaea) were studied to reveal their relationships to other representatives of the genus and especially to the well known hyperaccumulator T. caerulescens; comparisons of their accumulating properties were also made. Internal transcribed spacer (ITS) rDNA sequences from eight T. praecox populations from Slovenia showed 99% similarity and formed a sister group to T. caerulescens. Divergence estimates from the ITS rDNA support the origins of T. praecox in the Early Pleistocene, with further fragmentation of T. praecox populations in Slovenia since the Middle Pleistocene. Cd-hyperaccumulating features (>100 mg Cd kg−1 in the above-ground biomass) of T. praecox were seen for two populations collected at polluted sites (Žerjav and Mežica) and one population collected at a non-polluted site (Lokovec). The variability of the Cd concentrations in shoots was almost completely explained by the soil Cd concentrations, and were positively correlated with shoot Zn and Pb concentrations. The results from this molecular and metal accumulation characterisation of T. praecox populations provide new insights into the taxonomic affinities and accumulation potential of this hyperaccumulating species.

Secovlje salterns are an important protected area of biotic diversity in the Mediterranean. They represent an extreme environment with high salinity and drought that severely influence the growth of organisms. In the present study, diversity of plant halophytes and their mycorrhizal status were screened at eight different locations, which were mostly dikes and salt ponds, and which were deliberately selected for their distinct properties (e.g. soil salinity ranging from 105 to 2627 μS cm−1, vegetation type and management practice of the salterns). Twelve different halophytic plant species were recorded, of which eleven are designated as vulnerable. With few exceptions, they were found at the abandoned (Fontanigge) and sustained (Lera) locations of the Secovlje salterns, distributed according to their tolerance to the salinity and waterlogging. The highest diversity of halophytes was listed at Fontanigge, in the abandoned, periodically flooded and gradually overgrown salt ponds. All of the examined species were colonised with either arbuscular mycorrhizal fungi (AMF) and/or dark septate endophytes (DSEs). High levels of colonisation were however detected only for species belonging to the Asteraceae and Plantaginaceae families. Higher root colonisation frequencies were generally seen for plants growing in the abandoned parts, when compared to the managed parts, whereas there was little correlation of the colonisation parameters with physicochemical parameters of rhizospheric soil properties. Molecular analysis by temporal temperature gradient gel electrophoresis (TTGE) of roots of halophytic plant species with confirmed AMF colonisation (arbuscules present) revealed the occurrence of at least six different AMF species, related to Glomus geosporum, Glomus caledonium and Glomus intraradices, and to different Glomus sp. clades and the Diversispora clade. This is to the best of our knowledge the first report of AMF and DSE mycorrhizal status of most of the halophyte plant species examined and of the brother scale identification of AMF species based on molecular analyses of roots of diverse halophytes from high saline environments.

Interactions between plants and microorganisms can significantly affect plant health and productivity as well as ecosystem functioning. Detailed knowledge of the tripartite relationships between plants, fungi, and bacteria, and their environment is still limited. In the present study, the soils adjacent to three plant species (Cruciata laevipes, Mentha piperita, Equisetum arvense) in the Ljubljana Marsh and the bulk, plant-free soil were analyzed for their bacterial community structure in June and October 2006. The terminal restriction fragment length polymorphism analysis indicated a different bacterial community structure in the rhizosphere and in bulk soil, however, with almost no seasonal changes between late spring and autumn samples and no apparent impact of the three plant species. In addition, root colonization of the three plant species by arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) was microscopically assessed monthly from May until October 2006. A presumably accidental correlation between monthly precipitation and the degree of arbuscule formation, with the latter lagging 1 month, was noted for M. piperita, the most heavily colonized of the three plant species. With all three plants, the phosphorus content in roots correlated positively with most AMF structures. Microsclerotia of DSE were mainly abundant in autumn samples. Fungal diversity in roots was estimated using temporal temperature gradient gel electrophoresis separation of the fungal polymerase chain reaction products obtained for both 18S-rDNA and the 5.8S-ITS2-28S rDNA segments. No specific effects of either plant species or seasonal changes on mycorrhizal community structure were discernible.