Serpentine soils promote ectomycorrhizal fungal diversity

Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia)

The Island of Borneo is a major biodiversity hotspot, and in the Malaysian state of Sabah, ultramafic soils are extensive and home to more than 31 endemic nickel hyperaccumulator plants. The aim of this study was to characterize the structure and the diversity of the rhizosphere bacterial communities of several of these nickel hyperaccumulator plants and factors that affect these bacterial communities in Sabah. The most abundant phyla were Proteobacteria, Acidobacteria and Actinobacteria. At family level, Burkholderiaceae and Xanthobacteraceae (Proteobacteria phylum) were the most abundant families in the hyperaccumulator rhizospheres. Redundancy analysis based on soil chemical analyses and relative abundances of the major bacterial phyla showed that abiotic factors of the studied sites drove the bacterial diversity. For all R. aff. bengalensis rhizosphere soil samples, irrespective of studied site, the bacterial diversity was similar. Moreover, the Saprospiraceae family showed a high representativeness in the R. aff. bengalensis rhizosphere soils and was linked with the nickel availability in soils. The ability of R. aff. bengalensis to concentrate nickel in its rhizosphere appears to be the major factor driving the rhizobacterial community diversity unlike for other hyperaccumulator species.

Ectomycorrhizal Communities Associated with the Legume Acacia spirorbis Growing on Contrasted Edaphic Constraints in New Caledonia

This study aims to characterize the ectomycorrhizal (ECM) communities associated with Acacia spirorbis, a legume tree widely spread in New Caledonia that spontaneously grows on contrasted edaphic constraints, i.e. calcareous, ferralitic and volcano-sedimentary soils. Soil geochemical parameters and diversity of ECM communities were assessed in 12 sites representative of the three mains categories of soils. The ectomycorrhizal status of Acacia spirorbis was confirmed in all studied soils, with a fungal community dominated at 92% by Basidiomycota, mostly represented by/tomentella-thelephora (27.6%), /boletus (15.8%), /sebacina (10.5%), /russula-lactarius (10.5%) and /pisolithus-scleroderma (7.9%) lineages. The diversity and the proportion of the ECM lineages were similar for the ferralitic and volcano-sedimentary soils but significantly different for the calcareous soils. These differences in the distribution of the ECM communities were statistically correlated with pH, Ca, P and Al in the calcareous soils and with Co in the ferralitic soils. Altogether, these data suggest a high capacity of A. spirorbis to form ECM symbioses with a large spectrum of fungi regardless the soil categories with contrasted edaphic parameters.

Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo

The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges. We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect). Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model. We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect.

Ectomycorrhizal fungal diversity associated with endemic Tristaniopsis spp. (Myrtaceae) in ultramafic and volcano-sedimentary soils in New Caledonia

New Caledonian serpentine (ultramafic) soils contain high levels of toxic heavy metals, in particular nickel, (up to 20 g kg^-1) and are deficient in essential elements like carbon, nitrogen and phosphorus while having a high magnesium/calcium ratio. Although previous studies showed that ectomycorrhizal symbioses could play an important role in the adaptation of the endemic plants to ultramafic soils (FEMS Microbiol Ecol 72:238-49, 2010), none of them have compared the diversity of microbial communities from ultramafic vs non-ultramafic soils in New Caledonia. We explored the impact of edaphic characteristics on the diversity of ectomycorrhizal (ECM) fungi associated with different endemic species of Tristaniopsis (Myrtaceae) growing under contrasting soil conditions in the natural ecosystems of New Caledonia. ECM root tips were thus sampled from two different ultramafic sites (Koniambo massif and Desmazures forest) vs two volcano-sedimentary ones (Arama and Mont Ninndo). The molecular characterization of the ECM fungi through partial sequencing of the ITS rRNA gene revealed the presence of different dominant fungal genera including, both soil types combined, Cortinarius (36.1%), Pisolithus (18.5%), Russula (13.4%), Heliotales (8.2%) and Boletellus (7.2%). A high diversity of ECM taxa associated with Tristaniopsis species was found in both ultramafic and volcano-sedimentary soils but no significant differences in ECM genera distribution were observed between both soil types. No link could be established between the phylogenetic clustering of ECM taxa and their soil type origin, thus suggesting a possible functional-rather than taxonomical-adaptation of ECM fungal communities to ultramafic soils.

Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard

Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.

Shading and litter mediate the effects of soil fertility on the performance of an understorey herb

BACKGROUND AND AIMS

Soil fertility and topographic microclimate are common determinants of plant species distributions. However, biotic conditions also vary along these abiotic gradients, and may mediate their effects on plants. In this study, we investigated whether soils and topographic microclimate acted directly on the performance of a focal understorey plant, or indirectly via changing biotic conditions.

METHODS

We examined direct and indirect relationships between abiotic variables (soil fertility and topographic microclimate) and biotic factors (overstorey and understorey cover, litter depth and mycorrhizal colonization) and the occurrence, density and flowering of a common understorey herb, Trientalis latifolia, in the Klamath-Siskiyou Mountains, Oregon, USA.

RESULTS

We found that the positive effects of soil fertility on Trientalis occurrence were mediated by greater overstorey shading and deeper litter. However, we did not find any effects of topographic microclimate on Trientalis distribution that were mediated by the biotic variables we measured. The predictive success of Trientalis species distribution models with soils and topographic microclimate increased by 12 % with the addition of the biotic variables.

CONCLUSIONS

Our results reinforce the idea that species distributions are the outcome of interrelated abiotic gradients and biotic interactions, and suggest that biotic conditions, such as overstorey density, should be included in species distribution models if data are available.

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits

Microbial species richness and assemblages across ultramafic ecosystems were investigated to assess the relationship between their distributional patterns and environmental traits. The structure of microorganism communities in the Koniambo massif, New Caledonia, was investigated using a metagenetic approach correlated with edaphic and floristic factors. Vegetation cover and soil properties significantly shaped the large phylogenetic distribution of operational taxonomic unit within microbial populations, with a mean per habitat of 3.477 (±317) for bacteria and 712 (±43) for fungi. Using variance partitioning, we showed that the effect of aboveground vegetation was the most significant descriptor for both bacterial and fungal communities. The floristic significant predictors explained 43% of the variation for both the bacterial and fungal community structures, while the edaphic significant predictors explained only 32% and 31% of these variations, respectively. These results confirm the previous hypothesis that the distribution of microorganisms was more structured by the vegetation cover rather than the edaphic characteristics and that microbial diversity is not limited in ultramafic ecosystems.

Facilitation allows plant coexistence in Cuban serpentine soils

Serpentine soils represent stressful habitats where plants have to cope with heavy metals, moisture limitation and low nutrient availability. We propose that facilitation is an important mechanism structuring plant communities under such stressful conditions. Facilitation has been shown to generate the spatial association of species, forming discrete vegetation patches of phylogenetically distant species. We measured these spatial and phylogenetic signatures left by facilitation in a serpentine plant community of central Cuba. Our results show that seedlings preferentially grow under plants of different species, and that adults are significantly aggregated into vegetation patches. In these patches, adults tend to co-occur with distant relatives, ultimately forming phylogenetically diverse neighbourhoods. We discuss possible mechanisms explaining how species adapted to serpentine areas may be acting as nurses, reducing the stressful conditions for the establishment of other species.

Ectomycorrhizal Pisolithus albus inoculation of Acacia spirorbis and Eucalyptus globulus grown in ultramafic topsoil enhances plant growth and mineral nutrition while limits metal uptake

Ectomycorrhizal fungi (ECM) isolates of Pisolithus albus (Cooke and Massee) from nickel-rich ultramafic topsoils in New Caledonia were inoculated onto Acacia spirorbis Labill. (an endemic Fabaceae) and Eucalyptus globulus Labill. (used as a Myrtaceae plant host model). The aim of the study was to analyze the growth of symbiotic ECM plants growing on the ultramafic substrate that is characterized by high and toxic metal concentrations i.e. Co, Cr, Fe, Mn and Ni, deficient concentrations of plant essential nutrients such as N, P, K, and that presents an unbalanced Ca/Mg ratio (1/19). ECM inoculation was successful with a plant level of root mycorrhization up to 6.7%. ECM symbiosis enhanced plant growth as indicated by significant increases in shoot and root biomass. Presence of ECM enhanced uptake of major elements that are deficient in ultramafic substrates; in particular P, K and Ca. On the contrary, the ECM symbioses strongly reduced transfer to plants of element in excess in soils; in particular all metals. ECM-inoculated plants released metal complexing molecules as free thiols and oxalic acid mostly at lower concentrations than in controls. Data showed that ECM symbiosis helped plant growth by supplying uptake of deficient elements while acting as a protective barrier to toxic metals, in particular for plants growing on ultramafic substrate with extreme soil conditions. Isolation of indigenous and stress-adapted beneficial ECM fungi could serve as a potential tool for inoculation of ECM endemic plants for the successful restoration of ultramafic ecosystems degraded by mining activities.

Phylogenetic structure of ectomycorrhizal fungal communities of western hemlock changes with forest age and stand type

On Vancouver Island, British Columbia, fertilization with nitrogen (N) and phosphorus (P) following clearcutting increases growth of western hemlock. To explore whether fertilization also resulted in ectomycorrhizal fungal communities that were more or less similar to neighboring unlogged stands, we sampled roots from western hemlock from three replicate plots from each of five different, well-characterized, forest stand types that differed in site type, and in logging and fertilization history. We harvested four samples of 100 ectomycorrhizal root tips from each plot, a total of 60 samples per stand type. From each sample, we analyzed fungal ribosomal internal transcribed spacers and 28S DNA, sequencing 15-29 clones per sample and 60-116 clones per plot. We detected 147 fungal operational taxonomic units among a total of 1435 sequences. Craterellus tubaeformis was frequently present and resulted in a pattern of phylogenetic overdispersion in the fungal communities. Fungal species composition was strongly correlated with foliar nitrogen concentration. However, other site quality factors were also important because the fertilized regenerating hemlock and mature hemlock-amabilis fir forests had similar foliar nitrogen content but little overlap in fungal species. Compared with unfertilized regenerating forests, fungal communities in N + P-fertilized regenerating forests had significantly more species overlap with old growth forests. However, the fungal communities of all regenerating forest were similar to one another and all differed significantly from older forests. By correlating fungal clades with habitats, this research improves understanding of how forest management can contribute to maintaining diverse ectomycorrhizal fungal communities across a landscape.

Strong coupling of plant and fungal community structure across western Amazonian rainforests

The Amazon basin harbors a diverse ecological community that has a critical role in the maintenance of the biosphere. Although plant and animal communities have received much attention, basic information is lacking for fungal or prokaryotic communities. This is despite the fact that recent ecological studies have suggested a prominent role for interactions with soil fungi in structuring the diversity and abundance of tropical rainforest trees. In this study, we characterize soil fungal communities across three major tropical forest types in the western Amazon basin (terra firme, seasonally flooded and white sand) using 454 pyrosequencing. Using these data, we examine the relationship between fungal diversity and tree species richness, and between fungal community composition and tree species composition, soil environment and spatial proximity. We find that the fungal community in these ecosystems is diverse, with high degrees of spatial variability related to forest type. We also find strong correlations between α- and β-diversity of soil fungi and trees. Both fungal and plant community β-diversity were also correlated with differences in environmental conditions. The correlation between plant and fungal richness was stronger in fungal lineages known for biotrophic strategies (for example, pathogens, mycorrhizas) compared with a lineage known primarily for saprotrophy (yeasts), suggesting that this coupling is, at least in part, due to direct plant-fungal interactions. These data provide a much-needed look at an understudied dimension of the biota in an important ecosystem and supports the hypothesis that fungal communities are involved in the regulation of tropical tree diversity.

Fungal diversity is not determined by mineral and chemical differences in serpentine substrates

The physico-chemical properties of serpentine soils lead to strong selection of plant species. Whereas many studies have described the serpentine flora, little information is available on the fungal communities dwelling in these sites. Asbestos minerals, often associated with serpentine rocks, can be weathered by serpentine-isolated fungi, suggesting an adaptation to this substrate. In this study, we have investigated whether serpentine substrates characterized by the presence of rocks with distinct mineral composition could select for different fungal communities. Both fungal isolation and 454 pyrosequencing of amplicons obtained from serpentine samples following direct DNA extraction revealed some fungal taxa shared by the four ophiolitic substrates, but also highlighted several substrate-specific taxa. Bootstrap analysis of 454 OTU abundances indicated weak clustering of fungal assemblages from the different substrates, which did not match substrate classification based on exchangeable macronutrients and metals. Intra-substrate variability, as assessed by DGGE profiles, was similar across the four serpentine substrates, and comparable to inter-substrate variability. These findings indicate the absence of a correlation between the substrate (mineral composition and available cations) and the diversity of the fungal community. Comparison of culture-based and culture-independent methods supports the higher taxonomic precision of the former, as complementation of the better performance of the latter.

Trace metal contents in wild edible mushrooms growing on serpentine and volcanic soils on the island of Lesvos, Greece

The objectives of this survey were (1) to assess for the first time the Cd, Cu, Cr, Fe, Mn, Ni, Pb and Zn contents in wild edible mushrooms (Russula delica, Lactarius sanguifluus, Lactarius semisanguifluus, Lactarius deliciosus, Suillus bellinii) from the island of Lesvos, (2) to investigate the metals' variability among the species, as well as in relation to the chemical composition of the underlying soil, comparing mushrooms collected from volcanic and serpentine substrates and (3) to estimate metal intake by the consumption of the mushrooms under consideration. The trace metals in 139 samples were determined by flame or flameless atomic absorption spectroscopy. The median metal concentrations were as follows: Cd: 0.14; Cr: 0.10; Cu: 8.51; Fe: 30.3; Mn: 5.26; Ni: 0.34; Pb: 0.093 and Zn: 64.50, all in mgkg(-1) dry weight. The observed concentrations are among the lowest reported for mushrooms from Europe or Turkey, while Pb and Cd values did not exceed the limits set by the European Union. Significant species- and substrate-related differences in the metal contents were found, but the variability did not follow a uniform pattern for all the metals in all mushroom species. As a general trend, the mushrooms growing in serpentine sites contained higher Cd, Cr and Ni than those from volcanic sites. The calculated bioconcentration factors (BCFs) showed that none of the mushrooms can be regarded as a metal bioaccumulator, although BCF values slightly above unity were found for Zn in the three Lactarius species, and for Cu in R. delica. The studied mushrooms could supply considerable amounts of essential metals such as Zn and Cr. On the other hand, the consumption of R. delica collected from volcanic soils could provide 12% of the Cd daily tolerable intake and as high as 53% when collected from serpentine soils. Nonetheless, our results indicate that the regular consumption of wild edible mushrooms from Lesvos is quite safe for human health.