Phosphorus deficiency affects the allocation of below-ground resources to combined cluster roots and nodules in Lupinus albus

Lupins can rely on both cluster roots and nodules for P acquisition and biological nitrogen fixation (BNF), respectively. The resource allocation (C, N and P) between cluster roots and nodules has been largely understudied during P-deficient conditions. The aim of this investigation was therefore to determine the changes in resource allocation between these organs during fluctuations in P supply. Lupinus albus was cultivated in sand culture for 3 weeks, with either sufficient (2 mM high) or limiting (0.1 mM low) P supply. Although variation on P supply had no effect on the total biomass, there were significant differences in specialised below-ground organ allocation to cluster roots and nodule formation. Cluster root formation and the associated C-costs increased during low P supply, but at sufficient P-supply the construction and growth respiration costs of cluster roots declined along with their growth. In contrast to the cluster root decline at high P supply, there was an increase in nodule growth allocation and corresponding C-costs. However, this was not associated with an increase in BNF. Since cluster roots were able to increase P acquisition under low P conditions, this below-ground investment may also have benefited the P nutrition of nodules. These findings provide evidence that when lupins acquire N via BNF in their nodules, there may be a trade-off in resource allocation between cluster roots and nodules.     

The value of 99mTc-MIBI scan in the detection of malignancy potential of hypermetabolic thyroid incidentalomas of 18F-FDG PET/CT

Aim of the studyIncreasingly use of PET/CT leads to discovery of incidental findings. Hypermetabolic thyroid nodules are one of the unexpected lesions in PET/CT imaging with an increased risk of thyroid cancers. Our study aims to determine the malignant potential of incidentally detected 18F-FDG avid thyroid nodules by using Tc-99m MIBI imaging.Materials and methodsPET/CT scans were performed for nonthyroidal purposes and were evaluated for the presence of hypermetabolic thyroid nodules. Tc-99m MIBI scans and ultrasonography-guided fine needle aspiration biopsies were subsequently performed for all patients.ResultsPrimary thyroid malignancies were identified in 25% of patients with increased focal FDG uptake at definitive diagnosis. Among the patients with FDG avid thyroid nodules, Tc-99m MIBI scan showed true-positive results in all thyroid carcinomas (n:7) with a 36.3% (4/11) false-positivity rate. In three patients with indeterminate cytology results, Tc-99m MIBI scan findings were also negative. The sensitivity, specificity, positive predictive value of Tc-99m MIBI scan in predicting the malignancy of FDG-positive thyroid nodules were 100%, 77%, 63.6%, respectively.ConclusionThe implementation of ^99mTc-MIBI scan performed by dual phase and SPECT/CT modality might be a helpful cost-effective approach in addition to FNAB in patients with ¹⁸F-FDG-positive thyroid nodules and indeterminate cytology to improve the patients’ prognosis and reduce unnecessary thyroid operations with associated use of FNAB.     

Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

Background

MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.

Results

We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.

Conclusions

We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N₂-fixing symbiotic nodules.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1639-5) contains supplementary material, which is available to authorized users.     

Metabolic changes of iron uptake in N2-fixing common bean nodules during iron deficiency

Iron is an important nutrient in N₂-fixing legume nodules. The demand for this micronutrient increases during the symbiosis establishment, where the metal is utilized for the synthesis of various iron-containing proteins in both the plant and the bacteroid. Unfortunately, in spite of its importance, iron is poorly available to plant uptake since its solubility is very low when in its oxidized form Fe(III). In the present study, the effect of iron deficiency on the activity of some proteins involved in Strategy I response, such as Fe-chelate reductase (FC-R), H⁺-ATPase, and phosphoenolpyruvate carboxylase (PEPC) and the protein level of iron regulated transporter (IRT1) and H⁺-ATPase proteins has been investigated in both roots and nodules of a tolerant (Flamingo) and a susceptible (Coco blanc) cultivar of common bean plants. The main results of this study show that the symbiotic tolerance of Flamingo can be ascribed to a greater increase in the FC-R and H⁺-ATPase activities in both roots and nodules, leading to a more efficient Fe supply to nodulating tissues. The strong increase in PEPC activity and organic acid content, in the Flamingo root nodules, suggests that under iron deficiency nodules can modify their metabolism in order to sustain those activities necessary to acquire Fe directly from the soil solution.     

Early colonization of red alder and Douglas fir by ectomycorrhizal fungi and Frankia in soils from the Oregon coast range

The potential for mycorrhizal formation and Frankia nodulation were studied in soils from six sites in the Pacific Northwest. The sites included young and old alder stands, a 1-year-old conifer clear-cut, a young conifer plantation, and rotation-aged and old-growth conifer stands. A bioassay procedure was used with both red alder and Douglas fir seedlings as hosts. After 6 weeks growth, seedlings of both hosts were harvested every 3 weeks for 21 weeks and numbers of nodules and ectomycorrhizal types estimated. Nodules formed on red alder and ectomycorrhizae formed on both alder and Douglas fir in soil from all sites. Nodulation potential was highest in soil from the alder stands and the conifer plantation. Seven morphologically distinct ectomycorrhizal types were recovered on Douglas fir and five on alder. Only Thelephora terrestris, a broad-host-range mycobiont, formed mycorrhizae on both hosts. New ectomycorrhizal types formed on both hosts throughout the bioassay. Ectomycorrhizal colonization of alder was greatest in the alder and clear-cut soils. Low ectomycorrhizal colonization on alder was found in soils from sites where conifers were actively growing. Ectomycorrhizal colonization of Douglas fir was highest in the young alder and conifer plantation soils and was low in the rotation-aged conifer soil. The highest diversity of ectomycorrhizal types was found on alder in the conifer clear-cut soil and on Douglas fir in the rotation-aged conifer soil. Effects of host specificity, nodulation and mycorrhiza-forming potential and nodule-mycorrhiza interactions on seedling establishment are discussed in relation to seral stage dynamics and attributes of pioneer ectomycorrhizal fungal species.     

Development of nodules of Glycine max infected with an ineffective strain of Rhizobium japonicum

Bacteroids in ineffective (nitrogenase negative) nodules of Glycine max, infected with Rhizobium japonicum 61-A-24, as compared to those in effective nodules are characterized by reduced specific activities of alanine dehydrogenase to 15%, of 3-hydroxybutyrate dehydrogenase to 50%, and an increase of glutamine synthetase to 400%. In the plant cytoplasm of ineffective nodules, glutamine synthetase activity is reduced to 10–30%, glutamate dehydrogenase to 50–70%, and the aspartate aminotransferase and alanine aminotransferase are enhanced to 120–200%, depending on the age of the nodules. The total pool of soluble amino acids is reduced to 52 mol per g nodule fresh weight, as compared to 186 mol in effective nodules, with a replacement of asparagine (42 mol% of the amino acids) by an unknown amino compound. This compound is absent in nitrogenase, repressed and derepressed, free-living Rhizobium japonicum cells and in the uninfected root tissue. In nitrogenase derepressed, as compared to the repressed free-living cells of Rhizobium japonicum 61-A-101, arginine shows the most obvious change with a reduction to less than one tenth. The ultrastructure of the ineffective nodule is different from the effective organ even in the early stages. The membrane envelopes of the infection vacuoles are decomposing in heavily infected cells within 18 to 20 d after infection. In lightly infected cells very large vacuoles develop with only a few bacteroids inside. No close associations of cristae-rich mitochondria with amyloplasts are observed as in effective nodules. The uninfected cells keep their large starch granules even 40 d after infection. Some poly--hydroxybutyrate accumulation in the bacteroids is observed but only in the early stages, and it is almost absent in old nodules (40 d). At this age the infected cells are obviously compressed by uninfected cells, whereas in effective nodules with nitrogenase activity and leghaemoglobin formation, the infected cells have a much higher osmotic pressure than the neighbouring uninfected cells.Abbreviations PHBA poly--hydroxybutyric acid Prof. Dr. A. Pirson on the occasion of his 70th birthday     

Mutants of Rhizobium japonicum defective in nodulation

Several mutants defective in nodulation were isolated from Rhizobium japonicum strains 3I1b110 and 61A 76. Mutants of class I do not form nodules after incubation with soybean [Glycine max (L.) Merrill] for 17 days, but will do so by 28 days. When host plants other than G. max are infected with several of these strains, there is no detectable difference in the time of nodulation or size of nodules as compared to the wild type. Two mutants of class I (i. e., SM1 and SM2) have been shown previously to be altered in the lipopolysaccharide portion of their cell wall. Mutants of class II are not slow to nodulate but form fewer nodules than the wild type on all the host plants tested. Mutants of class III are unable to form nodules. Some bacteriophage-resistant mutants, altered in cell surface structure, fall into this class. Two mutants of class III do not bind to soybean roots.     

气候因子对三种豆科树种固氮的影响

研究了气候因子对台湾相思(Acacia confusa)、大叶相思(A．awriculaeformis)和南岭黄檀(Dalbergia balansae)根瘤固氮酶和吸氢酶活性的影响。3种树木根瘤均具有吸氢酶活性,外源H：可提高固氮酶活性,表明吸氢酶有助于固氮效率的提高。3树种根瘤的固氮活性有明显季节变化,夏秋活性较高,早春及冬季活性较低。离体根瘤固氮和吸H2活性表达的最适温度为25—30℃。光照强度及土壤湿度均显著影响根瘤固氮和吸H2活性。     

Effect of applied nitrate on enzymes of ammonia assimilation in nodules ofCicer arietinum L.

Summary The relationship between N₂-fixation, nitrate reductase and various enzymes of ammonia assimilation was studied in the nodules and leaves ofC. arietinum. In the nodules of the plants growing on atmospheric nitrogen, maximum activities of glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), asparagine synthetase (AS) and aspartate aminotransferase (AAT) were recorded just prior to maximum activity of nitrogenase. In nitrate fed plants, the first major peak of GDH and AS coincided with that of nitrate reductase in the nodules. With the exception of AS, application of nitrate decreased the activities of all these enzymes in nodules but not in leaves. Activities of GS, GOGAT and AAT were affected to much greater extent than that of GDH. On comparing the plants grown without nitrate and those with nitrate, the ratios of the activities of GDH/GS and GDH/GOGAT in nitrate given plants, increased by 4 and 12 fold, respectively. The results presented in this paper suggest that in nodules of nitrate fed plants, assimilation of ammonia via GDH assumes much greater importance.     

Distribution of spore-positive and spore-negative nodules in stands ofAlnus glutinosa andAlnus incana in Finland

Summary The distribution of spore positive (Sp⁺) and spore negative (Sp⁻) nodules on the two native alder species (A. incana andA. glutinosa) in Finland was investigated. Nodules were collected throughout the country from different ecosystems (forests, swamps, lake- sea- and riversides, old pastures and fields as well as from alder plantations). OnA. incana Sp⁺ nodules predominated, whereas onA. glutinosa the vast majority of the nodules were of the Sp⁻ type. Sp⁺ nodules onA. glutinosa were found only at sites where the two alder species grew close together. This distribution pattern indicates an association of nodule type with alder species, the reasons for which are discussed. Indications of saprophytic growth in the Sp⁻ strain were also found.