Tree roots in a changing world

Globally, forests cover 4 billion hectares or 30% of the Earth's land surface, and 20%-40% of the forest biomass is made up of roots. Roots play a key role for trees: they take up water and nutrients from the soil, store carbon (C) compounds, and provide physical stabilization. Estimations from temperate forests of Central Europe reveal that C storage in trees accounts for about 110 t C ha−1, of which 26 t C ha−1 is in coarse roots and 1.2 t C ha−1 is in fine roots. Compared with soil C, which is about 65 t C ha−1 (without roots), the contribution of the root C to the total belowground C pool is about 42%. Flux of C into soils by plant litter (stemwood excluded) compared with the total soil C pool, however, is relatively small (4.4 t C ha−1 year−1) with the coarse and fine roots each contributing about 20%. Elevated CO2 concentrations and N depositions lead to increased plant biomass, including that of roots. Recent analysis in experiments with elevated CO2 concentrations have shown increases of the forest net primary productivity by about 23%, and, in the case of poplars, an increase of the standing root biomass by about 62%. The turnover of fine roots is also positively influenced by elevated CO2 concentrations and can be increased in poplars by 25%-45%. A recently established international platform for scientists working on woody root processes, COST action E38, allows the exchange of information, ideas, and personnel, and it has the aim to identify knowledge gaps and initiate future collaborations and research activitie

Contribution of Ectomycorrhizal Fungi to Cadmium Uptake of Poplars and Willows from a Heavily Polluted Soil

Phytoextraction has been proposed in recent years as an environmentally and cost-efficient treatment technique for the remediation of heavy-metal contaminated sites. In particular, plants that are fast growing, metal accumulating, and economically interesting, such as sunflowers or trees, recently became more important in research on phytoextraction. Heavy metal uptake of trees can be strongly influenced by ectomycorrhizal fungi. We investigated the possibility of enhancing phytoextraction of Cd by willows (Salix viminalis) and poplars (Populus canadensis) in association with three well known ectomycorrhizal fungi (Hebeloma crustuliniforme, Paxillus involutus and Pisolithus tinctorius). A pot experiment was conducted using Cd polluted soil from a contaminated site. Four replicates of each combination of fungus and tree species, and controls without fungal inoculum, were set up. After a growth period of 11weeks, yields and Cd concentrations in roots, stems, and leaves were measured. In addition, the total Cd uptake, the transfer to roots, and the translocation to stems and leaves were calculated. The association of P. canadensis with P. involutus led to a highly significant increase of Cd concentrations, in particular in the leaves, which contained 2.74 ± 0.34mg Cd per kg dry matter. Compared to the control this is an enhancement of nearly 100%. The fungi also significantly enhanced the translocation from the roots to the leaves, leading to a concentration ratio (leaves/roots) of 0.32 ± 0.06 compared to 0.20 ± 0.02 of the control plants. Additionally, P. involutus significantly enhanced the total Cd extraction by P. canadensis. Similar effects were not observed by other fungi or in association with S. viminali

Does low soil base saturation affect fine root properties of European beech ( Fagus sylvatica L.)?

It is generally believed that high soil solution Al3+ in acidic soils with low base saturation (BS), negatively influences the properties of fine roots. Fine roots from European beech (Fagus sylvatica L.) trees growing in highly acidic soils with very low BS and potentially high Al3+ concentration in the soil solution were analysed and the dependency of fine root properties on soil BS was measured. The fine roots were sampled down to 1m depth at seven forest sites located on the Swiss Plateau. These sites varied in their BS from 1.4 to 11.4% in the mineral layers. We evaluated relationships between the BS of these mineral layers and fine root properties, such as ratio between bio- and necromass (live/dead ratio), specific root length (SRL), root tip abundance (RTA), root branching abundance (RBA), O2-consumption, and the Ca/Al molar ratio in the fine root tissue. The fine root properties were compared not only with the BS of the soil, but also with the Ca/Al molar ratio in the fine root tissues. Significant relations of fine root properties occurred when the soils of the seven sites were grouped into two BS groups (<5 and 5-10%). The live/dead ratio, the RTA, the RBA, the O2-consumption, and Ca/Al molar ratio were lower in the group of BS <5% than in the group 5-10%. Decreases in the morphological properties and in the O2-consumption were related to decrease in the Ca/Al molar ratio of the fine root tissues. There is evidence that the fine root properties are negatively influenced, nevertheless, fine root systems of mature European beech in their natural ecological environment seem to be able to compensate adverse effects of low B

Pattern of Elemental Release During the Granite Dissolution Can Be Changed by Aerobic Heterotrophic Bacterial Strains Isolated from Damma Glacier (Central Alps) Deglaciated Granite Sand

Colonisation and weathering of freshly deglaciated granite are key processes in initial soil formation and development. We have obtained 438 isolates from granite sand covering glacial toe, 284 isolates at 22°C and 154 at 4°C incubation temperatures, respectively, to obtain cultures for the investigation of their weathering capabilities under laboratory conditions. The isolation of bacteria from granite sand was performed on rich-, intermediate- and low-nutrient-content solid media. Isolates were identified by 16S rRNA gene sequencing. According to the genera-associated weathering capabilities described in the literature and according to their abundance in our culture collection, we selected eight strains to analyse their effects on the weathering dynamics of granite sand during the batch culture experiment. Analysis of culturable bacteria showed higher species richness among isolates from 22°C than from 4°C incubations. In the R2A and 1/100 Ravan media, we observed the highest species richness of isolates obtained at 22°C and 4°C incubation temperatures, respectively. The obtained 16S rRNA sequences revealed the presence of alpha-, beta- and gamma-proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The most numerous group of isolates was distantly related to Collimonas representatives, and according to the sequences of the 16S rRNA genes, they can form a new genus. Isolates from this group had the capability of causing increased dissolution rates for Fe, W, Ni and Rb. In general, at each sampling during the 30-day experiment, every strain showed a unique weathering profile resulting from differential rates of the dissolution and the precipitation of different minerals in the batch culture. Consequently, the presence of different strains, their growth stage and changes in proportions of strains in the bacterial community can affect further soil development and the successive colonisation by plant

Detection of silver nanoparticles inside leaf of European beech (Fagus sylvatica L.)

In a greenhouse experiment, silver nanoparticles (Ag-NPs) were applied on European beech (Fagus sylvatica L.) leaves using the droplet application method. Scanning electron microscopy (SEM) analyses showed that after 24 h silver nanoparticles were mostly present in aggregates or as single particles on the surface of the leaf, surrounding or covering the stomata. Analyses of cross sections of the leaf revealed that some silver nanoparticles were adhering to the cell walls of the mesophyll and palisade cells, most likely after penetration into the leaf through the stomata as particles and not as Ag ions. Our preliminary results showed evidence of foliar uptake of silver nanoparticles in European beech. This opens new insights on the ability of trees to take up solid nanosized particles, eventually contained in raindrops, through their leaves, and potentially transport them to other parts of the tree. This study would be helpful for investigating the role of trees in atmospheric ultrafine particle mitigation

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil

Seasonal variations of throughfall chemistry in pure and mixed stands of Oriental beech (Fagus orientalis Lipsky) in Hyrcanian forests (Iran)

International audienceAbstractKey messageThroughfall nutrient fluxes were generally higher in a mixed stand than in a pure stand of Oriental beech. Throughfall fluxes were higher than bulk precipitation fluxes except for nitrogen and indicate higher canopy uptake of this element in the pure stand compared to the mixed stand.ContextOriental beech is an economically relevant tree species for Iran and adjacent countries. Yet little is known about nutrient cycling in Oriental beech stands and the influence of the degree of mixture with other species.AimsWe assessed the effect of seasons on nutrient fluxes in precipitation and whether throughfall chemistry differed between pure and mixed stands.MethodsBulk precipitation in the open field and throughfall were sampled during one whole month within each season from August 2013 to May 2014 in a pure (81 % of beech trees on average) and a mixed stand (57 % of beech trees) of Oriental beech. Samples were analysed for pH, nitrate (NO3−), ammonium (NH4+), phosphorus (P), calcium (Ca2+), magnesium (Mg2+) and potassium (K+).ResultsNutrient concentrations were generally higher in the growing season than in the dormant season, both in bulk precipitation and in throughfall. Nutrient fluxes were higher in fall and these peaks coincided with higher amounts of precipitation. The concentrations and fluxes of NH4+, NO3−, P, Ca2+, Mg2+ and K+ were generally higher in the mixed stand than in the pure stand in all seasons. Compared to the open field, throughfall fluxes were usually higher, except for NO3− and NH4+, indicating direct canopy uptake of nitrogen.ConclusionCanopy composition in Oriental beech stands (owing to differences in foliage chemistry) and seasons (owing to differences in precipitation regime and phenological stages) have a significant effect on throughfall nutrient fluxes

Bacterial, Archaeal and Fungal Succession in the Forefield of a Receding Glacier

Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the T-RFLP profiles, bacteria showed a high Shannon diversity index (H) (ranging from 2.3 to 3.4) with no trend along the forefield. The major bacterial lineages were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Cyanobacteria. An interesting finding was that Euryarchaeota were predominantly colonizing young soils and Crenarchaeota mainly mature soils. Fungi shifted from an Ascomycota-dominated community in young soils to a more Basidiomycota-dominated community in old soils. Redundancy analysis indicated that base saturation, pH, soil C and N contents and plant coverage, all related to soil age, correlated with the microbial succession along the forefiel

The plastisphere microbiome in alpine soils alters the microbial genetic potential for plastic degradation and biogeochemical cycling

Plastic is exceedingly abundant in soils, but little is known about its ecological consequences for soil microbiome functioning. Here we report the impacts of polyethylene and biodegradable Ecovio and BI-OPL plastic films buried in alpine soils for 5 months on the genetic potential of the soil microbiome using shotgun metagenomics. The microbiome was more affected by Ecovio and BI-OPL than by polyethylene. Fungi, α- and β-Proteobacteria dominated on the biodegradable films. Ecovio and BI-OPL showed signs of degradation after the incubation, whereas polyethylene did not. Genes involved in cellular processes and signaling (intracellular trafficking, secretion, vesicular transport), as well as metabolism (carbohydrate, lipid and secondary metabolism), were enriched in the plastisphere. Several α/β-hydrolase gene families (cutinase_like, polyesterase-lipase-cutinase, carboxylesterase), which encode enzymes essential to plastic degradation, and carbohydrate-active genes involved in lignin and murein degradation increased on Ecovio and BI-OPL films. Enriched nitrogen fixation and organic N degradation and synthesis genes and decreased nitrification genes on Ecovio altered the biogeochemical cycling, leading to higher ammonium concentrations and depletion of nitrite and nitrate in the soil. Our results indicate that plastics affect the alpine soil microbiome and its functions and suggest that the plastisphere has an untapped microbial potential for plastic biodegradation. + Graphical Abstrac

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula)

ABSTRACT: BACKGROUND: Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. RESULTS: Treatment of the aspen roots with 500 uM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE. CONCLUSION: Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms