Arable plant communities as a surrogate of crop rhizosphere microbiota.

Soil microbiota is a crucial component of agroecosystem biodiversity, enhancing plant growth and providing important services in agriculture. However, its characterization is demanding and relatively expensive. In this study, we evaluated whether arable plant communities can be used as a surrogate of bacterial and fungal communities of the rhizosphere of Elephant Garlic (Allium ampeloprasum L.), a traditional crop plant of central Italy. We sampled plant, bacterial, and fungal communities, i.e., the groups of such organisms co-existing in space and time, in 24 plots located in eight fields and four farms. At the plot level, no correlations in species richness emerged, while the composition of plant communities was correlated with that of both bacterial and fungal communities. As regards plants and bacteria, such correlation was mainly driven by similar responses to geographic and environmental factors, while fungal communities seemed to be correlated in species composition with both plants and bacteria due to biotic interactions. All the correlations in species composition were unaffected by the number of fertilizer and herbicide applications, i.e., agricultural intensity. Besides correlations, we detected a predictive relationship of plant community composition towards fungal community composition. Our results highlight the potential of arable plant communities to be used as a surrogate of crop rhizosphere microbial communities in agroecosystems.

Co-occurrence of true truffle mycelia in Tuber magnatum fruiting sites.

Tuber magnatum (the white truffle) is the most precious species of the genus Tuber which comprises the hypogeous ectomycorrhizal species called "true truffle." Despite its high economic value, the knowledge on its ecology is scant, principally due to the difficulty to find its mycorrhizas in the soil. The possibility to detect its mycelium by DNA extracted from soil has given a new chance for studying this truffle species. In this work, the co-occurrence of other Tuber species with T. magnatum mycelium was investigated by using species-specific primers in several productive areas located in central and northern Italy. Most (82%) of the examined soil samples showed at least one other Tuber species in addition to T. magnatum. The most common was T. maculatum (72% of soil samples) followed by T. borchii, T. rufum, T. brumale, T. dryophilum, T. macrosporum, and T. melanosporum (40%, 37%, 22%, 19%, 12%, and 1% of soil samples, respectively). Tuber aestivum was never detected in T. magnatum productive patches. Analysis of species co-occurrence showed that the pairwise associations between T. dryophilum-T. brumale, T. brumale-T. borchii, and T. borchii-T. dryophilum was significant. The results suggest that Tuber mycelial network in white truffle grounds is much more extensive than the distribution of their ectomycorrhizas and competitive exclusion between different Tuber species seems to take place only for root colonization.

Phylogenetic Comparison between Italian and Worldwide Hericium Species (Agaricomycetes).

A broad literature concerns the genus Hericium, mainly regarding the medicinal properties of H. erinaceus. Congeneric species of H. erinaceus have been poorly investigated. We collected basidiomata of H. alpestre, H. coralloides and H. erinaceus in Italy and isolated the corresponding mycelia in pure culture. Analysis of the respective internal transcribed spacer regions confirmed the morphological identification of the strains. Internal transcribed spacer sequences from the Italian strains were phylogenetically compared along with 64 other sequences available from Gen-Bank, the CBS Strain Database, and the European Nucleotide Archive (ENA) for the same Hericium . Geographic origin and host plant species were cross-checked using the above data banks. Bayesian phylogenetic analysis produced a phylogram that permitted good discrimination among Hericium species. It provides an updated phylogeny within the genus Hericium and a better understanding of affinity among the species analyzed. The main Hericium clade includes the following: the H. erinaceus group and the H. alpestre/H. coralloides group, where the two species cluster separately. This study also allowed us to differentiate the H. erinaceus group on a biogeographical basis. The phylogenetic comparison further confirms the importance of a joint morphological-molecular approach to avoid misidentification and to guarantee the quality of strains for further chemical and medicinal characterization.

Teamwork makes the dream work: Disentangling cross-taxon congruence across soil biota in black pine plantations.

Soil plays a fundamental role in many ecological processes, throughout a complex network of above- and below-ground interactions. This has aroused increasing interest in the use of correlates for biodiversity assessment and has demonstrated their reliability with respect to proxies based on environmental data alone. Although co-variation of species richness and composition in forests has been discussed in the literature, only a few studies have explored these elements in forest plantations, which are generally thought to be poor in biodiversity, being aimed at timber production. Based on this premise our aims were 1) to test if cross-taxon congruence across different groups of organisms (bacteria, vascular plants, mushrooms, ectomycorrhizae, mycelium, carabids, microarthropods, nematodes) is consistent in artificial stands; 2) to evaluate the strength of relationships due to the existing environmental gradients as expressed by abiotic and biotic factors (soil, spatial-topographic, dendrometric variables). Correlations between groups were studied with Mantel and partial Mantel tests, while variance partition analysis was applied to assess the relative effect of environmental variables on the robustness of observed relationships. Significant cross-taxon congruence was observed across almost all taxonomic groups pairs. However, only bacteria/mycelium and mushrooms/mycelium correlations remained significant after removing the environmental effect, suggesting that a strong abiotic influence drives species composition. Considering variation partitioning, the results highlighted the importance of bacteria as a potential indicator: bacteria were the taxonomic group with the highest compositional variance explained by the predictors used; furthermore, they proved to be involved in the only cases where the variance attributed solely to the pure effect of biotic or abiotic predictors was significant. Remarkably, the co-dependent effect of all predictors always explained the highest portion of total variation in all dependent taxa, testifying the intricate and dynamic interplay of environmental factors and biotic interactions in explaining cross-taxon congruence in forest plantations.

Spatio-temporal dynamic of Tuber magnatum mycelium in natural truffle grounds.

Tuber magnatum produces the world's most expensive truffle. This fungus produces very rare ectomycorrhizas which are difficult or even impossible to detect in the field. A "real-time" PCR assay was recently developed to quantify and to track T. magnatum mycelium in soil. Here, this technique was used to investigate the spatial distribution of T. magnatum extra-radical mycelium in soil productive patches and its dynamic across seasons. This study was carried out in four different natural T. magnatum truffle grounds located in different Italian regions. During the fruiting seasons, the amount of T. magnatum mycelium was significantly higher around the fruiting points and decreased going farther away from them. Moreover, T. magnatum mycelium inside the productive patches underwent seasonal fluctuations. In early spring, the amount of T. magnatum mycelium was significantly higher than in summer. In summer, probably due to the hot and dry season, T. magnatum mycelium significantly decreased, whereas in autumn it increased again and was concentrated at the putative fruiting points. These results give new insights on T. magnatum ecology and are useful to plan the most appropriate sampling strategy for evaluating the management of a truffle ground.

Development and validation of a real-time PCR assay for detection and quantification of Tuber magnatum in soil.

BACKGROUND: Tuber magnatum, the Italian white truffle, is the most sought-after edible ectomycorrhizal mushroom. Previous studies report the difficulties of detecting its mycorrhizas and the widespread presence of its mycelium in natural production areas, suggesting that the soil mycelium could be a good indicator to evaluate its presence in the soil. In this study a specific real-time PCR assay using TaqMan chemistry was developed to detect and quantify T. magnatum in soil. This technique was then applied to four natural T. magnatum truffières located in different regions of Italy to validate the method under different environmental conditions. RESULTS: The primer/probe sets for the detection and quantification of T. magnatum were selected from the ITS rDNA regions. Their specificity was tested in silico and using qualitative PCR on DNA extracted from 25 different fungal species. The T. magnatum DNA concentration was different in the four experimental truffières and higher in the productive plots. T. magnatum mycelium was however also detected in most of the non-productive plots. Ascoma production during the three years of the study was correlated with the concentration of T. magnatum DNA. CONCLUSIONS: Taken together, these results suggest that the specific real-time PCR assay perfected in this study could be an useful tool to evaluate the presence and dynamics of this precious truffle in natural and cultivated truffières.