The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26T (= DSM 106348T = CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments.
Nodulin-26-like intrinsic proteins (NIPs) of the aquaporin family are involved in the transport of diverse solutes, but the mechanisms controlling the selectivity of transport substrates are poorly understood. The purpose of this study was to investigate how the aromatic/arginine (ar/R) selectivity filter influences the substrate selectivity of two NIP aquaporins; the silicic acid (Si) transporter OsLsi1 (OsNIP2;1) from rice and the boric acid (B) transporter AtNIP5;1 from Arabidopsis; both proteins are also permeable to arsenite. Native and site-directed mutagenized variants of the two genes were expressed in Xenopus oocytes and the transport activities for Si, B, arsenite, and water were assayed. Substitution of the amino acid at the ar/R second helix (H2) position of OsLsi1 did not affect the transport activities for Si, B, and arsenite, but that at the H5 position resulted in a total loss of Si and B transport activities and a partial loss of arsenite transport activity. Conversely, changes of the AtNIP5;1 ar/R selectivity filter and the NPA motifs to the OsLsi1 type did not result in a gain of Si transport activity. B transport activity was partially lost in the H5 mutant but unaffected in the H2 mutant of AtNIP5;1. In contrast, both the single and double mutations at the H2 and/or H5 positions of AtNIP5;1 did not affect arsenite transport activity. The results reveal that the residue at the H5 position of the ar/R filter of both OsLsi1 and AtNIP5;1 plays a key role in the permeability to Si and B, but there is a relatively low selectivity for arsenite.
The influence of soil properties on the bioavailability and toxicity of Co to barley (Hordeum vulgare L.) root elongation was investigated. Ten soils varying widely in soil properties were amended with seven doses of CoCl2. Soil properties greatly influenced the expression of Co toxicity. The effective concentration of added Co causing 50% inhibition (EC50) ranged from 45 to 863mgkg−1, representing almost 20-fold variation among soils. Furthermore, we investigated Co toxicity in relation to Co concentrations and free Co2+ activity in soil solution. The EC50 values showed variation among soils of 17- and 29-fold, based on the Co concentration in soil solution and free Co2+ activity, respectively. Single regressions were carried out between Co toxicity threshold values and selected soil properties. Models obtained showed that soil effective cation exchange capacity (eCEC) and exchangeable calcium were the most consistent single predictors of the EC50 values based on soil added Co.
Field experiments were carried out at three sites in England to investigate the effects of S fertilisation on breadmaking quality of three winter wheat varieties (Hereward, Rialto and Spark) in the 1996–1997 season. The soils at the three sites differed in extractable S contents. Depending on site, either 180 and 230 kg ha−1 N or 230 and 280 kg ha−1 N treatments were factorially combined with three S treatments (0, 20 and 100 kg ha−1 S). Addition of S increased loaf volume significantly at two sites where grain S concentration was also significantly increased and grain N:S ratio decreased. Application of the extra 50 kg ha−1 N increased grain protein concentration but did not increase loaf volume at any of the sites. Loaf volume was found to correlate more closely with grain S than with grain protein concentration. Addition of S generally decreased the elastic modulus of gel protein and dough resistance but increased dough extensibility. Despite considerable differences in their dough rheology, the responses in rheology and loaf volume to S were similar in all three varieties. Selected flour samples of Rialto from the Bridgets site were also analysed for the glutenin subunit distribution, showing that S addition increased the relative proportion of low-molecular-weight subunits at the expense of high-molecular-weight subunits of glutenin. This study therefore shows that the beneficial effects of S on breadmaking quality are associated with decreased dough elasticity and increased extensibility resulting from effects on the amount and composition of the glutenin polymers. The results also indicate that S fertilisation is required in some areas of England to maintain breadmaking quality. © 1999 Society of Chemical Industry
Thlaspi caerulescens J. & C. Presl is a hyperaccumulator of both Zn and Cd. A pot experiment was carried out to investigate whether T. caerulescens (the Ganges ecotype) could utilize Cd and Zn from insoluble sources. An uncontaminated soil was enriched with either insoluble Cd compounds (CdS or CdC03), or soluble Cd (CdS04) at a rate of 56 mg Cd kg-1 soil. In a separate experiment, soil was enriched with either ZnS04, Zn3(P04)2, or ZnS at a rate of 100 mg Zn kg-1. Neither soluble nor insoluble forms of Cd or Zn affected the growth of T. caerulescens . The Cd concentration of the shoots of the plants grown on the unenriched soil was 40 mg kg-1 dry wt., whereas the concentration in the case of the enriched soil reached 2,050 to 2,900 mg kg-1 dry wt. However, there were no significant differences in the shoot Cd concentration between the treatments with soluble or insoluble Cd compounds, even though the Cd concentration in the soil solution was in the order of CdS04 ≫CdC03 < CdS. T. caerulescens grown on the ZnS-enriched soil accumulated up to 6,900 mg kg-1 Zn in the shoots, although Zn accumulation was 1.5-fold higher with the addition of the more soluble compounds Zn3(P04)2 or ZnS04. These results indicate that the Ganges ecotype of T. caerulescens is able to utilize both insoluble Cd and Zn compounds.
Selenium (Se) is an essential micronutrient for many organisms, including plants, animals and humans. As plants are the main source of dietary Se, plant Se metabolism is therefore important for Se nutrition of humans and other animals. However, the concentration of Se in plant foods varies between areas, and too much Se can lead to toxicity. As we discuss here, plant Se uptake and metabolism can be exploited for the purposes of developing high-Se crop cultivars and for plant-mediated removal of excess Se from soil or water. Here, we review key developments in the current understanding of Se in higher plants. We also discuss recent advances in the genetic engineering of Se metabolism, particularly for biofortification and phytoremediation of Se-contaminated environments.
Methylation of arsenic in soil influences its environmental behavior and accumulation by plants, but little is known about the factors affecting As methylation. As speciation was determined in the pore waters of six soils from diverse geographical locations over 54 days of incubation under flooded conditions. The concentration of methylated As (monomethylarsonic acid, MMA, and dimethylarsinic acid, DMA) varied from 0 to 85 μg L(-1) (0 - 69% of the total As in pore water). Two Bangladeshi paddy soils contaminated by irrigation of As-laden groundwater produced large concentrations of inorganic As but relatively little methylated As. Two contaminated paddy soils from China produced a transient peak of DMA during the early phase of incubation. Methylated As represented considerable proportions of the total soluble As in the two uncontaminated soils from the UK and U.S. The copy number of the microbial arsenite methyltransferase gene (arsM) correlated positively with soil pH. However, pore-water methylated As correlated negatively with pH or arsM copy number, and positively with dissolved organic C. GeoChip assay revealed considerable arsM diversity among the six soils, with 27-35 out of 66 sequences in the microarray being detected. As speciation in rice plants grown in the soils generally mirrored that in the pore water. The results suggest that methylated As species in plants originated from the soil and As methylation in soil was influenced strongly by the soil conditions.
150 lines of bread wheat representing diverse origin and 25 lines of durum, spelt, einkorn and emmer wheat species were analysed for variation in micronutrient concentrations in grain. A subset of 26 bread wheat lines was grown at six sites or seasons to identify genetically determined differences in micronutrient concentrations. Substantial variation among the 175 lines existed in grain Fe, Zn and Se concentrations. Spelt, einkorn and emmer wheats appeared to contain higher Se concentration in grain than bread and durum wheats. Significant differences between bread wheat genotypes were found for grain Fe and Zn, but not Se concentration; the latter was influenced more by the soil supply. Grain Zn, but not Fe, concentration correlated negatively with grain yield, and there was a significant decreasing trend in grain Zn concentration with the date of variety release, suggesting that genetic improvement in yield has resulted in a dilution of Zn concentration in grain. Both grain Zn and Fe concentrations also correlated positively and significantly with grain protein content and P concentration, but the correlations with kernel size, kernel weight or bran yield were weak. The results from this study are useful for developing micronutrient biofortification strategies.
No abstract is provided for this article.
No abstract is provided for this article.
The entry of Cd into the food chain is of concern as it can cause chronic health problems. To investigate the relationship between soil properties and the concentration of Cd in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) grain, we analyzed 162 wheat and 215 barley grain samples collected from paired soil and crop surveys in Britain, and wheat and barley samples from two long-term sewage sludge experiments. Cadmium concentrations were much lower in barley grain than in wheat grain under comparable soil conditions. Multiple regression analysis showed that soil total Cd and pH were the significant factors influencing grain Cd concentrations. Significant cultivar differences in Cd uptake were observed for both wheat and barley. Wheat grain Cd concentrations could be predicted reasonably well from soil total Cd and pH using the following model: log(grain Cd) = a + b log(soil Cd) − c(soil pH), with 53% of the variance being accounted for. The coefficients obtained from the data sets of the paired soil and crop surveys and from long-term sewage sludge experiments were similar, suggesting similar controlling factors of Cd bioavailability in sludge-amended or unamended soils. For barley, the model was less satisfactory for predicting grain Cd concentration (22% of variance accounted for). The model can be used to predict the likelihood of wheat grain Cd exceeding the new European Union (EU) foodstuff regulations on the maximum permissible concentration of Cd under different soil conditions, particularly in relation to the existing Directive and the proposed new Directive on land applications of sewage sludge.
