Recycling of polluted dredged sediment - Building new materials for plant growing

The worldwide concern is caused by a large quantity of dredged sediment. The issue becomes more severe when contaminated sediment has to be landfilled. Therefore, researchers involved in the dredged sediment management are increasingly motivated to improve circularity in sediment management processes. Prior to the dredged sediment usage in agriculture, its necessary to confirm conclusively its safety in the context of trace elements (TEs) levels. This study reports the use of different solidification/stabilization (S/S) sediment amendments (cement, clay, fly ash and green synthetized nano-zerovalent iron-nZVI) to remediate dredged sediment. The aim was to identify the effects of applied sediment S/S treatments on the growth and development of Brassica napus. The results showed that in all S/S mixtures TEs levels in the highly labile and bioavailable fraction were significantly decreased (less than 10%, while untreated sediment contained up to 36% of TEs). Simultaneously, the highest share of metals (69-92%) was in the residual fraction, which is considered as chemically stable and biologically inert fraction. Nevertheless, it was noticed that different S/S treatments trigger plants' functional traits indicating that plants' establishment in S/S treated sediment can be limited to certain extent. Besides, based on primary and secondary metabolites (elevated specific leaf area along with declined malondialdehyde content) it was concluded that Brassica plants employ a conservative resource use strategy aiming to buffer phenotypes against stress condition. Lastly, it was inferred that among all analyzed S/S treatments, green synthetized nZVI from oak leaves can effectively promote TEs stabilization in dredged sediment, concurrently enabling plant's establishment and fitness.

Evaluation of historical atmospheric pollution in an industrial area by dendrochemical approaches

We conducted a dendrochemical study in order to evaluate the exposure of territories and populations to different types of pollutants and to characterise the history of pollution in one of the most intensely industrialised areas of Europe: the industrial port zone of Fos, also heavily urbanised. To perform the study, two tree species have been selected, Pinus halepensis and Populus nigra, on a rural plot located roughly 20 km away from the industrial harbour, an urban plot located in the city of Fos-sur-Mer and an industrial plot. Our study indicated that poplar was a more relevant model for the dendrochemical studies, exhibiting a higher bioaccumulation capacity than pine except for Hg, Sb and Mn. Moreover, thanks to this work, we observed significant exposure of the trees in the urban and industrial areas to As, Cd, Co, Cu, Mo, Sb, Zn, Al, Ca, and Mg, highlighting the exposure of the territory and populations living in the vicinity of the industrial harbour. The temporal variability of the concentrations measured in the tree rings corresponds to the increasing industrialisation of the territory as well as to the evolution of the industrial processes. Thus, this project highlighted the exposure of the Gulf of Fos to atmospheric emissions (industrial, road and urban) of the industrial harbour as well as the changes over time. It also pointed out the relevance of using dendrochemistry to measure atmospheric exposure of metals and metalloids and its temporal variability.

Developing and validating a practical decision support tool (DST) for biomass selection on marginal land

Marginal, often contaminated, sites exist in large areas across the world as a result of historic activities such as industry, transportation and mineral extraction. Remediation, or other improvements, of these sites is typically only considered for sites with high exploitation pressure and those posing the highest risks to human health or the environment. At the same time there is increasing competition for land resources for different needs such as biofuel production. Potentially some of this land requirement could be met by production of biomass on brownfield or other marginal land, thereby improving the land while applying the crop cultivation as part of an integrated management strategy. The design and decision making for such a strategy will be site specific. A decision support framework, the Rejuvenate DST (decision support tool) has been developed with the aim of supporting such site specific decision making. This tool is presented here, and has been tested by applying it to a number of case study sites. The consequent SWOT (strength, weakness, opportunities and threats) analysis is discussed and evaluated. The DST was found to be systematic, transparent, and applicable for diverse sites in France, Romania and Sweden, in addition to the sites to which it was applied through its development. The DST is regarded as especially useful if applied as a checklist in an iterative way throughout the decision process, from identifying potential crops to identifying knowledge gaps, working/non-working management strategies and potential risks. The DST also provides a structure promoting effective stakeholder engagement.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Molecular characterization of two ammonium transporters from the ectomycorrhizal fungus Hebeloma cylindrosporum

Heterologous expression of the yeast triple Mep mutant has enabled the first molecular characterization of AMT/MEP family members in an ectomycorrhizal fungus. External hyphae, which play a key role in nitrogen nutrition of trees, are considered as the absorbing structure of the ectomycorrhizal symbiosis and therefore molecular studies on ammonium transport in hyphae are urgently needed. The kinetic properties of AMT2 and AMT3 from Hebeloma cylindrosporum were studied in Saccharomyces cerevisiae. Expression of HcAmts in the yeast triple Mep mutant restored ammonium retention within cells. The HcAmts did not complement the ammonium sensing defect phenotype of Mep2Delta cells during pseudohyphal differentiation. Northern blot analysis in H. cylindrosporum showed that the HcAMTs were up-regulated upon nitrogen deprivation and down-regulated by ammonium.

Molecular cloning, characterization and regulation by cadmium of a superoxide dismutase from the ectomycorrhizal fungus Paxillus involutus

The gene encoding a superoxide dismutase (PiSOD) was cloned by suppressive subtractive hybridization from cDNA library of the ectomycorrhizal fungus, Paxillus involutus, grown under cadmium-stress conditions. The encoded protein was presumed to be localized in the peroxisomes because it contained a C-terminal peroxisomal localization peptide (SKL) and lacked an N-terminal mitochondrial transit peptide. Complementation of an Escherichia coli SOD null strain that is unable to grow in the presence of paraquat or cadmium indicated that cloned Pisod encoded a functional superoxide dismutase. Sensitivity of PiSOD activity to H2O2 but not KCN, and sequence homologies to other SODs strongly suggest that it is a manganese-containing superoxide dismutase. Monitoring PiSOD transcript, immunoreactive polypeptide and superoxide dismutase activity following cadmium stress suggests that the principal level of control is post-translational. This is, to our knowledge, the first insight in the characterization of molecular events that take place in an ectomycorrhizal fungus during exposure to heavy metals.

Carbon dioxide concentration and nitrogen input affect the C and N storage pools in Amanita muscaria-Picea abies mycorrhizae

We studied the influence of elevated atmospheric CO2 concentration ([CO2]) on the vacuolar storage pool of nitrogen-containing compounds and on the glycogen pool in the hyphal sheath of Amanita muscaria (L. ex Fr.) Hooker-Picea abies L. Karst. mycorrhizae grown with two concentrations of ammonium in the substrate. Mycorrhizal seedlings were grown in petri dishes on agar containing 5.3 or 53 mg N l(-1) and exposed to 350 or 700 microl CO2 l(-1) for 5 or 7 weeks, respectively. Numbers and area of nitrogen-containing bodies in the vacuoles of the mycorrhizal fungus were determined by light microscopy linked to an image analysis system. The relative concentration of nitrogen in the vacuolar bodies was measured by electron energy loss spectroscopy (EELS). Glycogen stored in the cytosol was determined at the ultrastructural level by image analysis after staining the sections (PATAg test). Shoot dry weight, net photosynthesis and relative amounts of N in vacuolar bodies were greater at the higher N and CO2 concentrations. The numbers and areas of vacuolar N-containing bodies were significantly greater at the higher N concentration only at ambient [CO2]. In the same treatment the percentage of hyphae containing glycogen declined to nearly zero. We conclude that, in the high N/low [CO2] treatment, the mycorrhizal fungus had an insufficient carbohydrate supply, partly because of increased amino acid synthesis by the non-mycorrhizal rootlets. When [CO2] was increased, the equilibrium between storage of glycogen and N-containing compounds was reestablished.

Effects of heavy metals on nitrogen uptake by Paxillus involutus and mycorrhizal birch seedlings

The effects of the heavy metals Cu, Cd, Ni, Pb and Zn on [(14)C]methylamine and [(14)C]aminoisobutyric acid uptake were studied in the free-living fungus Paxillus involutus and in mycorrhizal and non-mycorrhizal birch roots. The uptake of both N sources by P. involutus was inhibited by the five metals tested. However, Cu(2+) and Pb(2+) had a greater inhibitory effect. Non-competitive inhibitions were determined between heavy metals and [(14)C]methylamine uptake. [(14)C]Methylamine uptake was reduced by one third by 2 µM Cd(2+) and Cu(2+) in non-mycorrhizal roots, whereas that of mycorrhizal roots was not affected. However, it was reduced by 30 to 80% by 200 µM Cd(2+) and Cu(2+) irrespective of the mycorrhizal status. [(14)C]Aminoisobutyric acid uptake in mycorrhizal roots was not significantly affected by Cd(2+) and Cu(2+), whereas that of non-mycorrhizal roots was decreased by 77% at 200 µM Cu(2+). [(14)C]Aminoisobutyric acid uptake was 4.5 to 6 fold higher in mycorrhizal roots, compared with non-mycorrhizal roots, even under metal exposure. The high efficiency of N acquisition by mycorrhizal birch seedlings under metal exposure might be regarded as a mechanism of stress avoidance.

Ammonium and methylamine transport by the ectomycorrhizal fungus Paxillus involutus and ectomycorrhizas

Using [(14)C]methylamine as an analogue of ammonium, the kinetics and the energetics of NH(4)(+) transport were studied in the ectomycorrhizal fungus, Paxillus involutus (Batsch) Fr. The apparent half-saturation constant (K(m)) and the maximum uptake rate (V(max)) for the carrier-mediated transport derived from the Eadie-Hofstee transformation were 180 µM and 380 nmol (mg dry wt)(-1) min(-1,) respectively. Both pH dependence and inhibition by protonophores indicate that methylamine transport in P. involutus was dependent on the electrochemical H(+) gradient. Both long-term and short-term uptake experiments were consistent with regulation of ammonium/methylamine transport processes by the presence of an organic nitrogen source. Analysis of methylamine uptake by different P. involutus isolates revealed no obvious trend in the uptake capacities in relation to N deposition at the collection site. Kinetic parameters were determined in P. involutus/Betula pendula (Roth.) axenic association and in detached mycorrhizal roots isolated from forest sites. Enhanced methylamine uptake in the presence of the fungal symbiont was demonstrated. Homogeneous V(max) values were found for axenic and detached mycorrhizas, whereas K(m) values showed greater variations.

Effects of nitrogen source on growth and activity of nitrogen-assimilating enzymes in Douglas-fir seedlings

Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) seedlings were grown for 68 days in a growth chamber in nutrient solutions with ammonium, nitrate or ammonium nitrate as the nitrogen source. Among the nitrogen sources tested, whole-seedling biomass, relative growth rate (RGR), root and shoot elongation, and number of lateral roots, were greatest in seedlings grown with ammonium. In the absence of nitrogen, plant growth and formation of lateral roots were poor. Initially, glutamine synthetase, NAD-glutamate dehydrogenase and aspartate aminotransferase activities were high in young roots and shoots, but all three enzymatic activities decreased after one month of culture. In root apices, glutamine synthetase and aspartate aminotransferase activities were higher than NAD-glutamate dehydrogenase activity. Enzymatic activities were often higher in ammonium-fed seedlings than in seedings supplied with the other forms of nitrogen. Activities of all three enzymes were significantly reduced in seedlings grown in the absence of nitrogen. The beneficial effect of ammonium is discussed on the basis of its involvement in the assimilation pathways of Douglas-fir.

Physiology of organic nitrogen acquisition by ectomycorrhizal fungi and ectomycorrhizas

Ectomycorrhizal fungi are symbiotically associated microorganisms which ecological importance has been repeatedly demonstrated. There has been a considerable amount of research aimed at assessing the ability of ectomycorrhizal fungi and ectomycorrhizas to utilize organic nitrogen sources. The fate of soil proteins, peptides and amino acids has been studied from a number of perspectives. Exocellular hydrolytic enzymes have been detected and characterized in a number of ectomycorrhizal and ericoid fungi. Studies on amino acid transport through the plasma membrane have demonstrated the ability of ectomycorrhizal fungi to take up the products of proteolytic activities. Investigations on intracellular metabolism of amino acids have allowed the identification of the metabolic pathways involved. Possible intracellular compartmentation of amino acids will be examined by immunocytochemistry. Further translocation of amino acids in symbiotic tissues has been established by experiments using isotopic tracers, although the exact nature of the nitrogenous compounds transferred at the symbiotic interface remained unclear. One of the main future challenges in the physiology of organic nitrogen acquisition is to determine the nature, the regulation and the location of N-compound transporters at the soil-fungus and fungus-plant interfaces. The molecular approach which is just emerging in this particular research area will greatly improve our knowledge. Future research should also address the extent of competition between different ectomycorrhizal species and between different microbial populations for organic nitrogen.

Physiology of organic nitrogen acquisition by ectomycorrhizal fungi and ectomycorrhizas

Ectomycorrhizal fungi are symbiotically associated microorganisms which ecological importance has been repeatedly demonstrated. There has been a considerable amount of research aimed at assessing the ability of ectomycorrhizal fungi and ectomycorrhizas to utilize organic nitrogen sources. The fate of soil proteins, peptides and amino acids has been studied from a number of perspectives. Exocellular hydrolytic enzymes have been detected and characterized in a number of ectomycorrhizal and ericoid fungi. Studies on amino acid transport through the plasma membrane have demonstrated the ability of ectomycorrhizal fungi to take up the products of proteolytic activities. Investigations on intracellular metabolism of amino acids have allowed the identification of the metabolic pathways involved. Possible intracellular compartmentation of amino acids will be examined by immunocytochemistry. Further translocation of amino acids in symbiotic tissues has been established by experiments using isotopic tracers, although the exact nature of the nitrogenous compounds transferred at the symbiotic interface remained unclear. One of the main future challenges in the physiology of organic nitrogen acquisition is to determine the nature, the regulation and the location of N-compound transporters at the soil-fungus and fungus-plant interfaces. The molecular approach which is just emerging in this particular research area will greatly improve our knowledge. Future research should also address the extent of competition between different ectomycorrhizal species and between different microbial populations for organic nitrogen.

Respiration of [14C]alanine by the ectomycorrhizal fungus Paxillus involutus

The ectomycorrhizal fungus Paxillus involutus efficiently took up exogenously supplied [14C]alanine and rapidly converted it to pyruvate, citrate, succinate, fumarate and to CO2, thus providing direct evidence for the utilisation of alanine as a respiratory substrate. [14C]alanine was further actively metabolised to glutamate, glutamine and aspartate. Exposure to aminooxyacetate completely suppressed 14CO2 evolution and greatly reduced the flow of carbon from [14C]alanine to tricarboxylic acid cycle intermediates and amino acids, suggesting that alanine aminotransferase plays a pivotal role in alanine metabolism in Paxillus involutus.

Purification and Characterization of Glutamine Synthetase and NADP-Glutamate Dehydrogenase from the Ectomycorrhizal Fungus Laccaria laccata

Glutamine synthetase (GS) and NADP-dependent glutamate dehydrogenase (NADP-GDH) play a key role in nitrogen assimilation in the ectomycorrhizal fungus Laccaria laccata (Scop. ex Fr. Cke) strain S 238. The two enzymes were purified to apparent electrophoretic homogeneity by a three-step procedure involving diethylaminoethyl (DEAE)-Trisacryl and affinity chromatography, and DEAE-5PW fast protein liquid chromatography. This purification scheme resulted in a 23 and 62% recovery of the initial activity for GS and NADP-GDH, respectively. Purified GS had a specific activity of 713 nanomoles per second per milligram protein and a pH optimum of 7.2. Michaelis constants (millimolar) for the substrates were NH(4) (+) (0.024), glutamate (3.2), glutamine (30), ATP (0.18), and ADP (0.002). The molecular weight (M(r)) of native GS was approximately 380,000; it was composed of eight identical subunits of M(r) 42,000. Purified NADP-GDH had a specific activity of 4130 nanomoles per second per milligram protein and a pH optimum of 7.2 (amination reaction). Michaelis constants (millimolar) for the substrates were NH(4) (+) (5), 2-oxoglutarate (1), glutamate (26), NADPH (0.01), and NADP (0.03). Native NADP-GDH was a hexamer with a M(r) of about 298,000 composed of identical subunits with M(r) 47,000. Polyclonal antibodies were produced against purified GS and NADP-GDH. Immunoprecipitation tests and immunoblot analysis showed the high reactivity and specificity of the immune sera against the purified enzymes.