Short-term effects of rhizosphere microorganisms on fe uptake from microbial siderophores by maize and oat

Effects of rhizosphere microorganisms on Fe uptake by oat (Avena sativa) and maize (Zea mays) were studied in short-term (10 h) nutrient solution experiments. Fe was supplied either as microbial siderophores (pseudobactin [PSB] or ferrioxamine B [FOB]) or as phytosiderophores obtained as root exudates from barley (epi-3-hydroxy-mugineic acid [HMA]) under varied population densities of rhizosphere microorganisms (axenic, uninoculated, or inoculated with different microorganism cultures). When maize was grown under axenic conditions and supplied with FeHMA, Fe uptake rates were 100 to 300 times higher compared to those in plants supplied with Fe siderophores. Fe from both sources was taken up without the involvement of an extracellular reduction process. The supply of FeHMA enhanced both uptake rate and translocation rate to the shoot (more than 60% of the total uptake). However, increased density of microorganisms resulted in a decrease in Fe uptake rate (up to 65%), presumably due to microbial degradation of the FeHMA. In contrast, when FeFOB or FePSB was used as the Fe source, increased population density of microorganisms enhanced Fe uptake. The enhancement of Fe uptake resulted from the uptake of FeFOB and FePSB by microorganisms adhering to the rhizoplane or living in the free space of cortical cells. The microbial apoplastic Fe pool was not available for root to shoot transport or, thus, for utilization by the plants. These results, in addition to the low uptake rate under axenic conditions, are in contrast to earlier hypotheses suggesting the existence of a specific uptake system for Fe siderophores in higher plants. The bacterial siderophores PSB and FOB were inefficient as Fe sources for plants even when supplied by stem injection. It was concluded that microorganisms are involved in degradation processes of microbial siderophores, as well as in competition for Fe with higher plants.     

Bacterial siderophores : structure and NMR assignment of pyoverdins Pa,siderophores ofPseudomonas aeruginosa ATCC 15692

Summary In iron-deficient conditions,Pseudomonas aeruginosa ATCC 15692 synthesizes two major siderophores, pyoverdins Pa and pyoverdin Pa B. Two other compounds, pyoverdin Pa A (occurring from hydrolysis of pyoverdin Pa during the culture) and pyoverdin Pa C (occurring artifactually during the purification procedure) were also isolated. All these compounds possess the same partly cyclic peptide chain wherel-Orn(OH · HCO) isN -formyl,N -hydroxy-l-ornithine. The chain is bound to a chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline and having the (S) configuration. The four pyoverdins differ only in the acyl substituent bound to the nitrogen atom bound to carbon C3 of the chromophore. This is succinamide (pyoverdin Pa), succinic acid (pyoverdin Pa A), methyl succinate (pyoverdin Pa C) and 2-oxoglutaric acid (pyoverdin Pa B). The complete¹H- and¹³CNMR assignments, using two-dimensional total correlation NMR spectroscopy (TOCSY) and rotating-frame Overhauser enhancement spectroscopy (ROESY) procedures, as well as¹H-¹³C correlations, are reported. The complete sequence of the peptide using CH-NH correlations was achieved by NMR and confirmed the partly cyclic structure earlier reported using fast-atom-bombardment mass spectrometry (FAB-MS) on the siderophores and their dansylated fragments [Briskot G, Taraz K, Budzikiewicz H (1989)Liebigs Ann Chem: 375–384]. The use of these NMR procedures appears to be a tool of choice and a complementary approach to FAB-MS in the structure determination of some complex pyoverdins.Abbreviations Ser serine - Arg arginine - Thr ethreonine - Lys lysine - OHOrn N -hydroxyornithine - Chr chromophore     

海洋微生物宏基因组工程进展与展望

据初步统计,生活于海洋环境包括大洋深处的微生物有100万种以上,构成了一个动态的遗传基因库,其中绝大多数微生物或者从来没有经过实验室培养,或者至今无法培养,因而其分类地位及其生态学功能尚未为人类所认识。随着16S rRNA序列分析与系统分类学的广泛应用,海洋微生物多样性研究领域已经发生了很可观的改变,这些变化极大的丰富了人们对的微生物多样性及其生态功能的认识和理解。这里结合笔者近十年来的工作实践,讨论近年来在海洋微生物资源开发利用方面的研究进展,提出一个带有自动化特征的宏基因组功能表达平台,探讨海洋微生物资源利用的新途径。可以预见在不久的将来,海洋环境宏基因组工程研究将在一定程度上使得传统未培养海洋微生物基因资源及其功能产物能够为人类所开发和利用。     

Root-microbial effects on plant iron uptake from siderophores and phytosiderophores

Collaborative experiments were conducted to determine whether microbial populations associated with plant roots may artifactually affect the rates of Fe uptake and translocation from microbial siderophores and phytosiderophores. Results showed nonaxenic maize to have 2 to 34-fold higher Fe-uptake rates than axenically grown plants when supplied with 1 μM Fe as either the microbial siderophore, ferrioxamine B (FOB), or the barley phytosiderophore, epi-hydroxymugineic acid (HMA). In experiments with nonsterile plants, inoculation of maize or oat seedlings with soil microorganisms and amendment of the hydroponic nutrient solutions with sucrose resulted in an 8-fold increase in FOB-mediated Fe-uptake rates by Fe-stressed maize and a 150-fold increase in FOB iron uptake rates by Fe-stressed oat, but had no effect on iron uptake by Fe-sufficient plants. Conversely, Fe-stressed maize and oat plants supplied with HMA showed decreased uptake and translocation in response to microbial inoculation and sucrose amendment. The ability of root-associated microorganisms to affect Fe-uptake rates from siderophores and phytosiderophores, even in short-term uptake experiments, indicates that microorganisms can be an unpredictable confounding factor in experiments examining mechanisms for utilization of microbial siderophores or phytosiderophores under nonsterile conditions.     

Receptor uptake arrays for vitamin B12, siderophores,and glycans shape bacterial communities

Molecular variants of vitamin B₁₂, siderophores, and glycans occur. To take up variant forms, bacteria may express an array of receptors. The gut microbe Bacteroides thetaiotaomicron has three different receptors to take up variants of vitamin B₁₂ and 88 receptors to take up various glycans. The design of receptor arrays reflects key processes that shape cellular evolution. Competition may focus each species on a subset of the available nutrient diversity. Some gut bacteria can take up only a narrow range of carbohydrates, whereas species such as B. thetaiotaomicron can digest many different complex glycans. Comparison of different nutrients, habitats, and genomes provides opportunity to test hypotheses about the breadth of receptor arrays. Another important process concerns fluctuations in nutrient availability. Such fluctuations enhance the value of cellular sensors, which gain information about environmental availability and adjust receptor deployment. Bacteria often adjust receptor expression in response to fluctuations of particular carbohydrate food sources. Some species may adjust expression of uptake receptors for specific siderophores. How do cells use sensor information to control the response to fluctuations? This question about regulatory wiring relates to problems that arise in control theory and artificial intelligence. Control theory clarifies how to analyze environmental fluctuations in relation to the design of sensors and response systems. Recent advances in deep learning studies of artificial intelligence focus on the architecture of regulatory wiring and the ways in which complex control networks represent and classify environmental states. I emphasize the similar design problems that arise in cellular evolution, control theory, and artificial intelligence. I connect those broad conceptual aspects to many testable hypotheses for bacterial uptake of vitamin B₁₂, siderophores, and glycans.     

Molecular genetics of fungal siderophore biosynthesis and uptake: the role of siderophores in iron uptake and storage

To acquire iron, all species have to overcome the problems of iron insolubility and toxicity. In response to low iron availability in the environment, most fungi excrete ferric iron-specific chelators--siderophores--to mobilize this metal. Siderophore-bound iron is subsequently utilized via the reductive iron assimilatory system or uptake of the siderophore-iron complex. Furthermore, most fungi possess intracellular siderophores as iron storage compounds. Molecular analysis of siderophore biosynthesis was initiated by pioneering studies on the basidiomycete Ustilago maydis, and has progressed recently by characterization of the relevant structural and regulatory genes in the ascomycetes Aspergillus nidulans and Neurospora crassa. In addition, significant advances in the understanding of utilization of siderophore-bound iron have been made recently in the yeasts Saccharomyces cerevisiae and Candida albicans as well as in the filamentous fungus A. nidulans. The present review summarizes molecular details of fungal siderophore biosynthesis and uptake, and the regulatory mechanisms involved in control of the corresponding genes.     

Iron binding to Azotobacter salinestris melanin,iron mobilization and uptake mediated by siderophores

Iron-sufficient Azotobacter salinestris cells bound large amounts of ⁵⁵Fe to cell-associated catechol melanin in an energy-independent manner. Iron was mobilized from the cell surface by citric acid and transported into the cell in a process that was inhibited by azide, carbonyl cyanide m-chlorophenyl-hydrazone (CCCP), KCl or RbCl, the latter two known to inhibit Na⁺-dependent activities in A. salinestris. Iron-limited cells produced a hydroxamate compound (HDX) which promoted ⁵⁵Fe-uptake into iron-limited cells in a two step process. Initial uptake was inhibited by azide or CCCP, but not by KCl, while subsequent uptake was blocked by all inhibitors. Citric acid also mediated energy-dependent ⁵⁵Fe-uptake in iron-limited cells, but initial iron-uptake was less sensitive to CCCP than HDX-mediated iron-uptake. The results show that melanin serves as an iron trap, probably to protect the cells from oxidative damage mediated by H₂O₂ and the Fenton reaction. A model for HDX siderophore-mediated iron-uptake is proposed which requires energy to concentrate iron in the periplasm and H⁺/Na⁺-dependent events to bring iron into the cell.     

Iron uptake by plants from microbial siderophores : a study with 7-nitrobenz-2 oxa-1,3-diazole-desferrioxamine as fluorescent ferrioxamine B analog

The synthetically produced fluorescent siderophore NBD-desferrioxamine B (NBD-DFO), an analog of the natural siderophore ferrioxamine B, was used to study iron uptake by plants. Short-term (10-hour) ⁵⁵Fe uptake rates by cotton (Gossypium spp.) and maize (Zea mays L.) plants from the modified siderophore were similar to those of the natural one. In longer-term uptake experiments (3 weeks), both siderophore treatments resulted in similar leaf chlorophyll concentration and dry matter yield. These results suggest that the synthetic derivative acts similarly to the natural siderophore. The NBD-DFO is fluorescent only when unferrated and can thus be used as a probe to follow iron removal from the siderophore. Monitoring of the fluorescence increase in a nutrient solution containing Fe³⁺-NBD-DFO showed that iron uptake by plants occurs at the cell membrane. The rate of iron uptake was significantly lower in both plant species in the presence of antibiotic agent, thus providing evidence for iron uptake by rhizosphere microbes that otherwise could have been attributed to plant uptake. Confocal fluorescence microscopy revealed that iron was taken up from the complex by cotton plants, and to a much lesser extent by maize plants. The active cotton root sites were located at the main and lateral root tips. Significant variations in the location and the intensity of the uptake were noticed under nonaxenic conditions, which suggested that rhizosphere microorganisms play an important role in NBD-DFO-mediated iron uptake.     

Role of two siderophores in Ustilago sphaerogena: Regulation of biosynthesis and uptake mechanisms

Under iron-deficient conditions the smut fungus Ustilago sphaerogena produces two kinds of siderophores, ferrichrome and ferrichrome A. Regulation of ligand biosyntheses and uptake mechanisms of the iron chelates were studied to determine the role of each chelate in U. sphaerogena. The biosynthesis of each ligand was differentially regulated. Ferrichrome A, the more effective chelate, was preferentially synthesized under more extreme conditions of iron stress, but completely repressed when the cell was supplied with sufficient iron. In contrast, biosynthesis of ferrichrome was strongly but not completely repressed by iron. The mechanism of repression was examined using a newly developed in vivo synthesis assay. Chromium and gallium-containing siderophore analogs had no effect on siderophore ligand biosynthesis. Iron, added as siderophores, resulted in increased oxygen uptake and amino acid transport, which was soon followed by decreased ligand biosynthesis, suggesting that regulation may be indirect and related to oxidative metabolism. Uptake experiments were used to rule out a ligand-exchange mechanism for ferrichrome A-iron transport. The data suggest that ferrichrome A-iron is taken up at a specific site that results in a rapid distribution of iron inside the cell.     

Crop responses to ozone: uptake, modes of action, carbon assimilation and partitioning

The inhibitory effects of tropospheric O₃ on crop photosynthesis, growth, and yield have been documented in numerous studies over the past 35 years. In large part, the results of this research supported governmental regulations designed to limit tropospheric O₃ levels to concentrations that affected crop production at economically acceptable levels. Recent studies have brought into question the efficacy of these concentration-based O₃ standards compared with flux-based approaches that incorporate O₃ uptake along with environmental and biotic factors that influence plant responses. In addition, recent studies provide insight into the biochemical mechanisms of O₃ injury to plants. Current interpretations suggest that upon entry into the leaf intercellular space O₃ rapidly reacts with components of the leaf apoplast to initiate a complex set of responses involving the formation of toxic metabolites and generation of plant defence responses that constitute variably effective countermeasures. Plant species and cultivars exhibit a range of sensitivity to O₃, evident as heritable characteristics, that must reflect identifiable biochemical and molecular processes that affect sensitivity to O₃ injury, although their exact makeup remains unclear. Ozone clearly impairs photosynthetic processes, which might include the effects on electron transport and guard cell homeostasis as well as the better-documented effects on carbon fixation via decreased Rubisco activity. Translocation of photosynthate could be inhibited by O₃ exposure as well. Further, the influence of tropospheric O₃ needs to be considered when assessing potential effects of rising concentrations of atmospheric CO₂ on crop production. Advances in O₃ flux modelling and improved understanding of biochemical and molecular effects of O₃ on photosynthetic gas exchange and plant defence processes are leading to more complete, integrated assessments of O₃ impacts on crop physiology that continue to support the rationale for maintaining or improving current O₃ air quality standards as well as providing a basis for development of more O₃-tolerant crop lines.     

Identification of siderophores and siderophore-mediated uptake of iron in Stemphylium botryosum

Under iron-deficient conditions Stemphylium botryosum f. sp. lycopersici produces three major siderophores; dimerum acid, coprogen B and an unidentified monohydroxamate siderophore designated as A. The system of siderophores mediating uptake of iron was characterized. It exhibits active transport, saturation kinetics and an optimum at pH 6 and 30°. The rate of iron uptake via dimerum acid and coprogen B was four times higher than siderophore A. S. botryosum was capable of taking up iron from hydroxamate siderophores produced by other fungi, e.g. ferrichrome, fusigen, rhodotorulic acid but not ferrioxamine B. Double labelling experiments suggest that ferric coprogen B accumulates in mycelial cells as an intact chelate.     

Structure and membrane affinity of new amphiphilic siderophores produced by Ochrobactrum sp. SP18

The coastal α-proteobacterium Ochrobactrum sp. SP18 produces a suite of three citrate-derived, cell-associated amphiphilic siderophores, ochrobactins A–C. The ochrobactins are composed of a citric acid backbone amide-linked to two lysine residues. Each ε-amine of lysine is hydroxylated and acylated forming two hydroxamic acid moieties. One of the acylated appendages of each ochrobactin is (E)-2-decenoic acid. The other acylated appendages for ochrobactins A–C are (E)-2-octenoic acid, octanoic acid and (E)-2-decenoic acid, respectively. The ferric ochrobactin complexes are photoreactive in UV light, producing an oxidized ligand with loss of 46 mass units that can still coordinate Fe(III). The relative partitioning of the apo-ochrobactins, Fe(III) ochrobactins and Fe(III) photoproducts into 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles is presented. The ochrobactins are the first example of aerobactin-based siderophores with two fatty acid appendages produced in a suite with varying acyl appendage lengths.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing

The microbial taxonomic composition of the three domains of life in two coastal plankton samples was assessed by random total community metagenomic sequencing and PCR-based rDNA amplicon deep-sequencing in order to compare the resulting diversity and investigate possible limitations and complementarities of each method. The various universal primer sets, used to amplify different hypervariable rDNA regions, revealed the same major high-level taxonomic groups in Bacteria and unicellular Eukaryota, and showed a scarce Archaea apparent richness. However, significant differences were found between the different primer sets (p-value < 0.05, with the Kolmogorov–Smirnov test), regarding both operational taxonomic unit (OTU) richness and relative abundance of the major high-level taxonomic groups detected. Based on the metagenomic approach, the phylum Bacteroidetes dominated the prokaryotic community, followed by Proteobacteria, while the detected eukaryotic unicellular taxa belonged to the groups of Alveolata, Fungi, Chlorophyta, Stramenopiles and Phaeophyceae. These groups were found to carry genes typically found in microbial communities, which are linked to DNA, RNA and protein metabolism and the synthesis of nucleotides, amino acids, carbohydrates and vitamins. Although our findings suggest that the total community metagenomic approach can provide a more comprehensive picture of the planktonic microbial community structure, a number of issues associated with this approach emerged. These issues include the still relatively high cost compared to amplicon sequencing, the possible low coverage of the full marine diversity, the insufficiency of databases for other gene markers than the small subunit gene, and the bias towards bacterial sequences because of their higher abundance relative to eukaryotes in marine environments.     

Bacterial siderophores: structure elucidation, and 1H, 13C and 15N two-dimensional NMR assignments of azoverdin and related siderophores synthesized by Azomonas macrocytogenes ATCC 12334

Two major azoverdins were isolated from the cultures of Azomonas macrocytogenes ATCC 12334 grown in irondeficient medium. Their structures have been established using fast atom bombardment-mass spectroscopy, homonuclear and heteronuclear two-dimensional ¹⁵N, ¹³C and ¹H NMR, and circular dichroism techniques. These siderophores are chromopeptides possessing at the N-terminal end of their peptide chain the chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline common to pyoverdins. The linear peptide chain (l)-Hse-(d)-AcOHOrn-(d)-Ser-(l)-AcOHOrn-(d)-Hse-(l)-CTHPMD has at its C-terminal end a new natural amino acid which is the result of the condensation of 1 mol of homoserine and 1 mol of 2,4-diaminobutyric acid forming a cyclic amidine belonging to the tetrahydropyrimidine family: 2-homoseryl-4-carboxyl-3,4,5,6-tetrahydropyrimidine. The azoverdins differ only by a substitutent bound to the nitrogen on C-3 of the chromophore: azoverdin, the most abundant one, possesses a succinamide moiety, whereas azoverdin A bears a succinic acid moiety. ¹⁵N-labelled azoverdin afforded readily, after the complete assignment of the ¹⁵N spectrum of the siderophore, a sequence determination of the peptidic part of the molecule and gave evidence for the presence of two tetrahydropyrimidine groups on the molecule: one on the chromophore and the second at the C-terminal end of the siderophore.     

Coupled biogeochemical cycling of iron and manganese as mediated by microbial siderophores

Siderophores, biogenic chelating agents that facilitate Fe(III) uptake through the formation of strong complexes, also form strong complexes with Mn(III) and exhibit high reactivity with Mn (hydr)oxides, suggesting a pathway by which Mn may disrupt Fe uptake. In this review, we evaluate the major biogeochemical mechanisms by which Fe and Mn may interact through reactions with microbial siderophores: competition for a limited pool of siderophores, sorption of siderophores and metal–siderophore complexes to mineral surfaces, and competitive metal-siderophore complex formation through parallel mineral dissolution pathways. This rich interweaving of chemical processes gives rise to an intricate tapestry of interactions, particularly in respect to the biogeochemical cycling of Fe and Mn in marine ecosystems.     

Strontium as a tracer for calcium: uptake,transport and partitioning within tomato plants

Plant and Soil - Calcium (Ca2+) is a major structural plant nutrient whose low mobility in the phloem causes deleterious nutritional disorders in non-transpiring organs. Since strontium (Sr2+) and...