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BackgroundCupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.ResultsThe 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.ConclusionsSTM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

This work aims to evaluate the potential of nickel (Ni), an essential micronutrient, as an oxidative stress inducer along with associated morphological and biochemical responses in different varieties of fenugreek (Trigonella foenum-graecum L.), a chief economically cultivated crop of India. Varietal differences in crop performance upon exposure to 0, 20, 40, 60 and 80 mg Ni kg− 1 soil reflects that Ni applied at 20 mg Ni kg− 1 soil offers growth-promoting effects, improved photosynthesis attributes, carbonic and nitrate reductase activities more profound in PEB followed by AFg2, AFg1 and UM185 variety. This study observed a dose-dependent reduction in all the above parameters. Maximum toxic effects were noticed at 80 mg kg− 1 Ni, manifested in the form of enhanced H2O2 and MDA contents, which were efficiently counteracted by augmentation in proline content, SOD, POX, CAT and APX activities in PEB over other varieties, suggesting that the Ni tolerance in fenugreek varieties can be organized as PEB > AFg2 > AFg1 > UM185. [ABSTRACT FROM AUTHOR]

In this study, nickel tolerance (NiSO4.7H2O) of some Turkish national barley (Hordeum vulgare L.) genotypes (Bülbül-89, Kalaycı-97, Karatay-94, Larende, Tarm-92, Tokak-157/37, Yesevi-93 and Zeynel Ağa) was investigated. Barley genotypes were exposed to different nickel concentrations [0 mM (control), 250, 500, 1000, 1500, and 2000 ppm]. Nickel toxicity significantly inhibited root and coleoptile growth in all barley genotypes in a concentration-dependent manner. However, root growth was much more inhibited by nickel applications in comparison with coleoptile growth, probably due to a higher level of sensitivity of root meristems against nickel toxicity or direct contact of roots with nickel ions in the growth medium. Root growth in the genotype Karatay-94 and coleoptile growth in the genotype Yesevi-93 was more remarkably reduced by nickel toxicity. Root and coleoptile growth in the genotypes Larende and Kalaycı-97 were less affected under nickel toxicity, respectively. In addition, nickel toxicity disturbed water relations in barley genotypes dependent on the organ type, as demonstrated by more severe inhibition in root fresh weight as compared to coleoptile fresh weight. These results could show that nickel toxicity reduced water uptake from growth medium in barley genotypes used in this study. Changes in dry weight of roots and coleoptiles indicated that nickel toxicity more severely decreased biomass accumulation in roots of barley genotypes. The calculated tolerance indices demonstrated that the genotype Kalaycı-97 is the most tolerant to nickel toxicity, while the genotype Karatay-94 is the most susceptible one.

In this work, endophytic bacteria from the nickel hyperaccumulating plant Leucocroton havanensis are characterized. Three strains belonging to Bacillus genus were used. It was evaluated the tolerance to Ni (II), the influence of temperature and pH in growth, as well as the influence of metal in the production of indolacetic acid, ammonia and in the biological fixation of dinitrogen. Bacterial solubilization of nickel was determined. The strains grew in temperature intervals of 30-50 °C, at pH values of 5- 9 and up to 10 mmol. L-1 Ni (II). The strains produce AIA, ammonia and fix dinitrogen in the presence of 5 mmol. L-1 of nickel. In addition, they solubilize more than 70% of the nickel incorporated in the culture medium in the form of nickel carbonate. Endophytic bacteria of L. havanensis present characteristics that make them interesting to be evaluated in phytoremediation alternatives.

In this study, nickel tolerance (NiSO4.7H2O) of some Turkish national barley (Hordeum vulgare L.) genotypes (Bülbül-89, Kalaycı-97, Karatay-94, Larende, Tarm-92, Tokak-157/37, Yesevi-93 and Zeynel Ağa) was investigated. Barley genotypes were exposed to different nickel concentrations [0 mM (control), 250, 500, 1000, 1500, and 2000 ppm]. Nickel toxicity significantly inhibited root and coleoptile growth in all barley genotypes in a concentration-dependent manner. However, root growth was much more inhibited by nickel applications in comparison with coleoptile growth, probably due to a higher level of sensitivity of root meristems against nickel toxicity or direct contact of roots with nickel ions in the growth medium. Root growth in the genotype Karatay-94 and coleoptile growth in the genotype Yesevi-93 was more remarkably reduced by nickel toxicity. Root and coleoptile growth in the genotypes Larende and Kalaycı-97 were less affected under nickel toxicity, respectively. In addition, nickel toxicity disturbed water relations in barley genotypes dependent on the organ type, as demonstrated by more severe inhibition in root fresh weight as compared to coleoptile fresh weight. These results could show that nickel toxicity reduced water uptake from growth medium in barley genotypes used in this study. Changes in dry weight of roots and coleoptiles indicated that nickel toxicity more severely decreased biomass accumulation in roots of barley genotypes. The calculated tolerance indices demonstrated that the genotype Kalaycı-97 is the most tolerant to nickel toxicity, while the genotype Karatay-94 is the most susceptible one. [ABSTRACT FROM AUTHOR]

Abstract Background Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems. Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance. Conclusions STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

Excessive heavy metals in medicinal plants cause critical health issues to humans. Therefore, in the present study, the effect of soil amendment with chitosan (0, 0.125, 0.25, 0.5, and 1%) on bioavailability and tolerance of nickel in Calendula tripterocarpa grown in a soil spiked with Ni (100 and 150 mg/kg soil) was investigated. The results showed that Ni toxicity significantly reduced plant growth and content of chlorophyll a, b but increased carotenoid levels, lipid peroxidation, and catalase (CAT) and superoxide dismutase (SOD) activities in roots and shoots. The Ni bioaccumulation was significantly higher in shoots than roots. The soil amendment with chitosan reduced Ni bioavailability in soil, as well as lowered the biological accumulation of Ni in roots and shoots, and Ni transfer to leaves. The chitosan application also increased growth parameters and levels of chlorophyll a, b and carotenoids under both normal and Ni stress conditions. Furthermore, chitosan reduced the level of malondialdehyde and the activities of SOD and CAT in roots and shoots under Ni stress. In conclusion, results indicated that chitosan through lowering bioavailability of Ni in soils can remarkably relieve adverse effects of Ni toxicity in C. tripterocarpa. [ABSTRACT FROM AUTHOR]

Ultramafic soils are usually marginal in macronutrients (nitrogen (N), phosphorus (P), potassium (K) and calcium (Ca)) for growth of crop plants. Commercial nickel (Ni) agromining is dependent on attaining high yield and high Ni concentration in harvestable biomass of Ni hyperaccumulator species. We previously reported on the biomass responses of two promising tropical 'metal crops' (Phyllanthus rufuschaneyi and Rinorea cf. bengalensis) to rates of N, P, and K fertilisers. Calcium, sulphur (S) and organic matter amendments have varied effects on the biomass production and Ni uptake in temperate Ni hyperaccumulator species used in agromining, but the trends in tropical 'metal crops' are not reported to-date. We investigated the effects of these amendments on the growth performance and the Ni (and other elements) uptake in P. rufuschaneyi and R. cf. bengalensis The experiments consisted of a large 12-month randomised growth trial in large pots in Sabah (Malaysia) using ultramafic soils under different treatment levels of soluble Ca and S, and organic matter amendments. We found that Ca and S additions had no significant effects on the growth of P. rufuschaneyi and R. cf. bengalensis. Organic matter amendments had strong positive effect on the growth of R. cf. bengalensis (p < 0.05), but we recorded significant negative growth response in P. rufuschaneyi. Whereas Ca and S additions improved the Ni uptake in these species, organic matter amendments significantly reduced the shoot Ni concentrations in both species. Our findings indicate that Ca and S additions are important in the agronomy of tropical 'metal crops' to be used in economic Ni agromining, but organic matter amendments may not be useful. • Calcium and sulphur amendments in the form of CaSO 4 are essential for viable tropical agromining. • Organic matter amendments reduces nickel uptake in tropical 'metal crops'. • Calcium and Sulphur additions have no significant effect on biomass of tropical 'metal crops'. • The effect of organic matter on biomass of tropical 'metal crops' is species-dependent. [ABSTRACT FROM AUTHOR]

Abstract R.communis L. has high capability to accumulate nickel which is a trace nutrient for higher plants and also an environmental contaminant causes toxicity related symptoms at higher concentrations. MicroRNAs (miRNAs) are known to be important modulators of responses against heavy metal stress for detoxification of the metal. In this study, we experimentally measured and validated the transcript levels of the seven heavy metal stress response-related miRNAs and the expression levels of target genes in both leaf and root tissues of R. communis L. subjected to three different concentrations of nickel stress via qRT-PCR quantification. The results demonstrated differential regulations of heavy metal stress-responsive miRNAs and their putative targets in both tissues in same stress treatments. This dynamic regulation suggest that regulatory processes differ between the tissues under nickel stress. Our data suggest that, miR838 was the most responsive to the Ni2+ stress. miR398 target gene Cu-Zn/SOD was found to be up-regulated in both root and leaf tissues. The relations between TCP and expression levels of miR159 and miR319 were also found statistically significant exclusive to leaf tissues. In leaf tissue, changes in miR395 level and its putative target genes, sulphate transporter and sulphate adenyltransferase gene were found in relation whereas, only expression level of sulphate transporter represented a statistically significant relation in root tissue. The sharp decrease in transcript levels of 2r3 myb gene at lower nickel dose suggest to investigate the role of r2r3 myb and the all MYB family members in primary and secondary metabolisms against nickel stress. Highlights • Castor bean plants were subjected to 0, 0.05 mM, 0.1 mM and 0.2 mM NiCl 2 stress. • Altered levels of miRNAs were accompanied by the levels of target genes in both leaf and root tissues. • Differential regulations of selected miRNAs and their putative targets were observed. • r2r3 myb gene showed a sharp decrease in transcript levels at lower nickel dose. • TCP expression related to growth was restricted due to increasing nickel stress.Results are given as the mean values of three independent [ABSTRACT FROM AUTHOR]

Nickel (Ni) and copper (Cu) are the most prevalent metals found in the Greater Sudbury Region ecosystems. The main objectives of this study are to (1) assess silver maple(Acer saccharinum) tolerance to different doses of Ni and (2) determine the translocation pattern of metals inA. sacharinum. This study revealed thatA. sacharinumis highly tolerant to high doses of NI (1600 and 9200 mg/kg). Growth chamber screening trials revealed that Ni is stored in roots and does not translocate to other plant parts. Analysis of samples fromA. sacharinumgrowing for >30 years in soil contaminated with metals also showed that the levels of iron (Fe), manganese (Mn), Ni, and zinc (Zn) were significantly higher in roots compared with soils and aerial parts. On the other hand, the amount of Cu was higher in soil compared with roots and other plant parts. In fact, the bioaccumulation factors (BFs) were 0.29, 2.00, 3.6, 1.9, and 4.0 for Cu, Fe, Mn, Ni, and Zn, respectively. The translocation from roots to aerial parts showed an insignificant level of movement of Cu, Fe, and Ni. Hence,A. saccharinumis classified as excluder for Fe, Mn, Ni, and Zn, and avoider for Cu. [ABSTRACT FROM AUTHOR]

Aims: To assess the importance of Ni and drought tolerance in serpentine adaptation, the effects of Ni and polyethylene glycol (PEG)-simulated drought, alone and in combination, on growth, water-status, photosynthetic pigments, osmoprotectants, stress markers, and ROS-scavenging enzymes were compared between the serpentine endemic Cleome heratensis and the closely related non-serpentinophyte C. foliolosa. Methods: C. heratensis and C. foliolosa were exposed to combinations of Ni (0, or 20 μM) and PEG (0, −0.3, or −0.9 MPa) in a full factorial, replicated randomized block design. Results were analyzed using 3-way ANOVA. Results: Ni improved growth, enhanced osmoprotectant synthesis, and decreased oxidative stress in C. heratensis, but had insignificant, or deleterious effects on the same parameters in C. foliolosa. The second order Ni*PEG*species interactions were usually significant, demonstrating that the species responded distinctly to combined exposure to PEG and excess Ni. In most cases this was due to additive deleterious effects of Ni in PEG-treated C. foliolosa, i.e. on growth, shoot water status and stress markers, and beneficial effects or no effects of Ni in PEG-treated C. heratensis. Conclusions: In the absence of Ni exposure, the species were approximately equally tolerant to PEG-simulated drought. Under PEG exposure, Ni positively affected the performance of C. heratensis, but had additive deleterious effects in C. foliolosa. C. heratensis does not only exhibit Ni hypertolerance, associated with a strongly decreased root-to-shoot translocation, but also an enhanced requirement for Ni, particularly when under PEG exposure, in comparison with C. foliolosa. [ABSTRACT FROM AUTHOR]

New Caledonian serpentine (ultramafic) soils contain high levels of toxic heavy metals, in particular nickel, (up to 20 g kg) 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. [ABSTRACT FROM AUTHOR]

Compared with serpentine floras of Southeast Asia, the serpentine vegetation of Sri Lanka is impoverished in regard to serpentine endemics and nickel hyperaccumulators. All species so far documented from the serpentine outcrops of Sri Lanka also have non-serpentine populations; it is unclear whether the serpentine populations are physiologically distinct and deserve ecotypic recognition. We conducted a preliminary study to examine whether serpentine and non-serpentine populations of Fimbristylis ovata represent locally adapted ecotypes by investigating their growth and potential for nickel uptake and tolerance under greenhouse conditions. Although both populations of F. ovata showed a similar growth pattern in serpentine soil during short-term exposure (21 days), the non-serpentine population was unable to survive in serpentine soil under long-term exposure (4 months). Both populations were able to uptake nickel from serpentine soil during short-term exposure (21 days). The serpentine population, however, translocated significantly more nickel from its roots to shoots (translocation factor 0.43) than the non-serpentine population (translocation factor 0.29). Our preliminary investigations suggest that the serpentine and non-serpentine populations of F. ovata may be locally adapted to their respective soils. However, additional studies are required to determine whether the populations deserve ecotypic recognition. We conducted a study to examine whether serpentine and non-serpentine populations of Fimbristylis ovata represent locally adapted ecotypes by investigating their growth and potential for nickel uptake and tolerance under greenhouse conditions. The serpentine population showed significantly better growth and nickel tolerance than did the non-serpentine population. Our preliminary investigations suggest that the serpentine and non-serpentine populations may be locally adapted to their respective soils; however, additional studies are required to determine whether the populations deserve ecotypic recognition. [ABSTRACT FROM AUTHOR]

Among four cultivars ofBrassica junceaL., viz., TM-4, TM-2, RH-30, and T-59, cv. T-59 was relatively more tolerant to nickel (Ni) toxicity based on the growth parameters, seedling vigor index, and metal tolerance index. Nickel application inhibited the activity of the nitrate-assimilating enzyme nitrate reductase in the roots, stem, and leaves, whereas the total organic nitrogen, proline, and activity of a polyamine-metabolizing enzyme, diamine oxidase, increased in this tolerant cultivar (T-59). It accumulated a good amount of Ni from the soil in its root and shoot (i.e., 6.0–6.51 μg Ni g−1dry weight) during 2 months of cultivation with an 8.0 mM Ni supply in the soil. The data presented in this paper indicate that Ni tolerance and its removal by Indian mustard from subtropical Indian soil is cultivar dependent, possibly due to different genetic and physiological adaptations of the cultivars. [ABSTRACT FROM PUBLISHER]

Aims: Heavy-metal tolerance is a widespread phenotype in bacteria, particularly occurring in strains isolated from heavy-metal contaminated sites. Concerning nickel tolerance, the nre system is one of the most common. An ortholog of the nreB gene is present in the alfalfa symbiont Sinorhizobium meliloti also, which stir the attention on its functional role in such Ni-sensitive species and on the evolutionary relationships with Ni-resistant strain orthologs. Methods: Phylogenetic reconstruction and comparative genomics were performed to analyze the phylogenetic relationships of nreB orthologs, as well aa nreB deletion mutant S. meliloti strain was constructed and subjected to phenotypic analysis. Results: Phylogenetic analysis of nreB genes indicated horizontal gene transfer events, possibly mediated via mobile genetic elements. Phenotype Microarray, biochemical and symbiotic analyses of the deletion mutant strain (Δ nreB) showed that in S. meliloti nreB is involved in the tolerance to several stresses other than Ni (mainly urea and copper), possibly partially mediated through the modulation of urease and hydrogenase activities. Conclusions: Obtained results allowed us to speculate that nreB is a highly mobile gene cassette, spread in the bacterial phylogenetic tree via many HGT events, which could have been recruited to confer nickel-tolerance in strains thriving in contaminated environments, by small changes linked to its basic functions (e.g. modulation of urease and hydrogenase activity). [ABSTRACT FROM AUTHOR]

Difference in Ni tolerance/accumulation in plant genotypes might be used to identify or develop plants for remediation of high Ni soils. Ryegrass was shown to be more sensitive to Ni toxicity and accumulated much more Ni in shoots than maize. The objectives of this study were to examine the relationship of organic acids to Ni accumulation andxylem transport of Ni in ryegrass (Lolium perenne L.) and maize (Zeamays L.). The results showed that accumulation of Ni in shoots was 5to 7 fold higher in ryegrass than in maize grown at 20 to 80 5M Ni, whereas Ni concentration in ryegrass roots was only 1 to 2 fold higher at 0.1 to 40 5M Ni and 1.5-fold lower at 80 5M Ni than that of maize roots. Xylem transport rates of Ni increased with increasing Ni supply for both species, and were about 2 to 7 times higher in ryegrass than in maize. Shoot concentrations of citric, malic, oxalic and cis-aconitic acids increased at Ni levels above 20 5M, and were about 2 to 6 times higher in ryegrass than in maize. Whereas, maize roots accumulated greater amount of malic, oxalic, and cis-aconitic acids than ryegrass roots, especially at Ni levels of 40-80 5M. The rate of Ni exudation by roots in the two species was significantly correlated with root Ni concentrations. It could be concluded that high Ni accumulation in shoots was closely related to high xylem transport rates of Ni and that the accumulation of organic acids, citric and malic acid in particular. A high root exudate rate of Ni and the enhanced accumulation of organic acids, malic acid in particular, in roots might be among the important factors which are associated with the tolerance ofcrops to toxic Ni levels. [ABSTRACT FROM AUTHOR]