Showing papers by "Institut national de la recherche agronomique published in 2001"

Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: A review

Abstract: In most soils, inorganic phosphorus occurs at fairly low concentrations in the soil solution whilst a large proportion of it is more or less strongly held by diverse soil minerals. Phosphate ions can indeed be adsorbed onto positively charged minerals such as Fe and Al oxides. Phosphate (P) ions can also form a range of minerals in combination with metals such as Ca, Fe and Al. These adsorption/desorption and precipitation/dissolution equilibria control the concentration of P in the soil solution and, thereby, both its chemical mobility and bioavailability. Apart from the concentration of P ions, the major factors that determine those equilibria as well as the speciation of soil P are (i) the pH, (ii) the concentrations of anions that compete with P ions for ligand exchange reactions and (iii) the concentrations of metals (Ca, Fe and Al) that can coprecipitate with P ions. The chemical conditions of the rhizosphere are known to considerably differ from those of the bulk soil, as a consequence of a range of processes that are induced either directly by the activity of plant roots or by the activity of rhizosphere microflora. The aim of this paper is to give an overview of those chemical processes that are directly induced by plant roots and which can affect the concentration of P in the soil solution and, ultimately, the bioavailability of soil inorganic P to plants. Amongst these, the uptake activity of plant roots should be taken into account in the first place. A second group of activities which is of major concern with respect to P bioavailability are those processes that can affect soil pH, such as proton/bicarbonate release (anion/cation balance) and gaseous (O2/CO2) exchanges. Thirdly, the release of root exudates such as organic ligands is another activity of the root that can alter the concentration of P in the soil solution. These various processes and their relative contributions to the changes in the bioavailability of soil inorganic P that can occur in the rhizosphere can considerably vary with (i) plant species, (ii) plant nutritional status and (iii) ambient soil conditions, as will be stressed in this paper. Their possible implications for the understanding and management of P nutrition of plants will be briefly addressed and discussed.

Soil moisture retrieval from space: the Soil Moisture and Ocean Salinity (SMOS) mission

Abstract: Microwave radiometry at low frequencies (L-band: 1.4 GHz, 21 cm) is an established technique for estimating surface soil moisture and sea surface salinity with a suitable sensitivity. However, from space, large antennas (several meters) are required to achieve an adequate spatial resolution at L-band. So as to reduce the problem of putting into orbit a large filled antenna, the possibility of using antenna synthesis methods has been investigated. Such a system, relying on a deployable structure, has now proved to be feasible and has led to the Soil Moisture and Ocean Salinity (SMOS) mission, which is described. The main objective of the SMOS mission is to deliver key variables of the land surfaces (soil moisture fields), and of ocean surfaces (sea surface salinity fields). The SMOS mission is based on a dual polarized L-band radiometer using aperture synthesis (two-dimensional [2D] interferometer) so as to achieve a ground resolution of 50 km at the swath edges coupled with multiangular acquisitions. The radiometer will enable frequent and global coverage of the globe and deliver surface soil moisture fields over land and sea surface salinity over the oceans. The SMOS mission was proposed to the European Space Agency (ESA) in the framework of the Earth Explorer Opportunity Missions. It was selected for a tentative launch in 2005. The goal of this paper is to present the main aspects of the baseline mission and describe how soil moisture will be retrieved from SMOS data.

The composite genome of the legume symbiont Sinorhizobium meliloti.

Abstract: The scarcity of usable nitrogen frequently limits plant growth. A tight metabolic association with rhizobial bacteria allows legumes to obtain nitrogen compounds by bacterial reduction of dinitrogen (N2) to ammonium (NH4+). We present here the annotated DNA sequence of the alpha-proteobacterium Sinorhizobium meliloti, the symbiont of alfalfa. The tripartite 6.7-megabase (Mb) genome comprises a 3.65-Mb chromosome, and 1.35-Mb pSymA and 1.68-Mb pSymB megaplasmids. Genome sequence analysis indicates that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution. The genome sequence will be useful in understanding the dynamics of interkingdom associations and of life in soil environments.

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Abstract: Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group. [The sequence data described in this paper has been submitted to the GenBank data library under accession no. AE005176.]

Productivity overshadows temperature in determining soil and ecosystem respiration across European forests

Abstract: Summary This paper presents CO2 flux data from 18 forest ecosystems, studied in the European Union funded EUROFLUX project. Overall, mean annual gross primary productivity (GPP, the total amount of carbon (C) fixed during photosynthesis) of these forests was 1380 ± 330 gC m−2 y−1 (mean ±SD). On average, 80% of GPP was respired by autotrophs and heterotrophs and released back into the atmosphere (total ecosystem respiration, TER = 1100 ± 260 gC m−2 y−1). Mean annual soil respiration (SR) was 760 ± 340 gC m−2 y−1 (55% of GPP and 69% of TER). Among the investigated forests, large differences were observed in annual SR and TER that were not correlated with mean annual temperature. However, a significant correlation was observed between annual SR and TER and GPP among the relatively undisturbed forests. On the assumption that (i) root respiration is constrained by the allocation of photosynthates to the roots, which is coupled to productivity, and that (ii) the largest fraction of heterotrophic soil respiration originates from decomposition of young organic matter (leaves, fine roots), whose availability also depends on primary productivity, it is hypothesized that differences in SR among forests are likely to depend more on productivity than on temperature. At sites where soil disturbance has occurred (e.g. ploughing, drainage), soil espiration was a larger component of the ecosystem C budget and deviated from the relationship between annual SR (and TER) and GPP observed among the less-disturbed forests. At one particular forest, carbon losses from the soil were so large, that in some years the site became a net source of carbon to the atmosphere. Excluding the disturbed sites from the present analysis reduced mean SR to 660 ± 290 gC m−2 y−1, representing 49% of GPP and 63% of TER in the relatively undisturbed forest ecosystems.

Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake.

Abstract: Frequently, crop plants do not take up adequate amounts of iron from the soil, leading to chlorosis, poor yield and decreased nutritional quality. Extremely limited soil bioavailability of iron has led plants to evolve two distinct uptake strategies: chelation, which is used by the world's principal grain crops1,2; and reduction, which is used by other plant groups3,4,5. The chelation strategy involves extrusion of low-molecular-mass secondary amino acids (mugineic acids) known as ‘phytosiderophores’, which chelate sparingly soluble iron6. The Fe(iii)-phytosiderophore complex is then taken up by an unknown transporter at the root surface7,8. The maize yellow stripe1 (ys1) mutant is deficient in Fe(iii)-phytosiderophore uptake7,8,9,10, therefore YS1 has been suggested to be the Fe(iii)-phytosiderophore transporter. Here we show that ys1 is a membrane protein that mediates iron uptake. Expression of YS1 in a yeast iron uptake mutant restores growth specifically on Fe(iii)-phytosiderophore media. Under iron-deficient conditions, ys1 messenger RNA levels increase in both roots and shoots. Cloning of ys1 is an important step in understanding iron uptake in grasses, and has implications for mechanisms controlling iron homeostasis in all plants.

Skill-Biased Organizational Change? Evidence from A Panel of British and French Establishments

Abstract: This paper investigates the determination and consequences of organizational changes (OC) in a panel of British and French establishments. Organizational changes include the decentralization of authority, delayering of managerial functions, and increased multitasking. We argue that OC and skills are complements. We offer support for the hypothesis of "skill-biased" organizational change with three empirical findings. First, organizational changes reduce the demand for unskilled workers in both countries. Second, OC is negatively associated with increases in regional skill price differentials (a measure of the relative supply of skill). Third, OC leads to greater productivity increases in establishments with larger initial skill endowments. Technical change is also complementary with human capital, but the effects of OC is not simply due to its correlation with technological change but has an independent role.

DNA extraction from soils: old bias for new microbial diversity analysis methods.

Abstract: The impact of three different soil DNA extraction methods on bacterial diversity was evaluated using PCR-based 16S ribosomal DNA analysis. DNA extracted directly from three soils showing contrasting physicochemical properties was subjected to amplified ribosomal DNA restriction analysis and ribosomal intergenic spacer analysis (RISA). The obtained RISA patterns revealed clearly that both the phylotype abundance and the composition of the indigenous bacterial community are dependent on the DNA recovery method used. In addition, this effect was also shown in the context of an experimental study aiming to estimate the impact on soil biodiversity of the application of farmyard manure or sewage sludge onto a monoculture of maize for 15 years.

The Arabidopsis TT2 Gene Encodes an R2R3 MYB Domain Protein That Acts as a Key Determinant for Proanthocyanidin Accumulation in Developing Seed

Abstract: In Arabidopsis, proanthocyanidins specifically accumulate in the endothelium during early seed development. At least three TRANSPARENT TESTA (TT) genes, TT2, TT8, and TTG1, are necessary for the normal expression of several flavonoid structural genes in immature seed, such as DIHYDROFLAVONOL-4-REDUCTASE and BANYULS (BAN). TT8 and TTG1 were characterized recently and found to code for a basic helix-loop-helix domain transcription factor and a WD-repeat–containing protein, respectively. Here the molecular cloning of the TT2 gene was achieved by T-DNA tagging. TT2 encoded an R2R3 MYB domain protein with high similarity to the rice OsMYB3 protein and the maize COLORLESS1 factor. A TT2–green fluorescent protein fusion protein was located mostly in the nucleus, in agreement with the regulatory function of the native TT2 protein. TT2 expression was restricted to the seed during early embryogenesis, consistent with BAN expression and the proanthocyanidin deposition profile. Finally, in gain-of-function experiments, TT2 was able to induce ectopic expression of BAN in young seedlings and roots in the presence of a functional TT8 protein. Therefore, our results strongly suggest that stringent spatial and temporal BAN expression, and thus proanthocyanidin accumulation, are determined at least partially by TT2.

Wood Formation in Trees

Abstract: Among the ecosystem services provided by forests, wood provisioning takes a central position. Wood and derived products have played a critical role in the evolution of human kind and demand for raw material is increasing in a foreseeable future. Wood is used for energy production, construction and a wide variety of products for which different properties are required. Anatomical, chemical and physical properties of wood are determined through a complex process called xylogenesis controlled by internal and external signals and occurring during the life of the tree. In this chapter we describe i/how wood is formed and ii/the different factors controlling this developmental process with emphasis on the molecular machinery involved, iii/the functions of wood and iv/the biotechnology approaches developed to improve wood biomass production and properties genetically.

RNA Silencing in Plants--Defense and Counterdefense

Abstract: RNA silencing is a remarkable type of gene regulation based on sequence-specific targeting and degradation of RNA. The term encompasses related pathways found in a broad range of eukaryotic organisms, including fungi, plants, and animals. In plants, it serves as an antiviral defense, and many plant viruses encode suppressors of silencing. The emerging view is that RNA silencing is part of a sophisticated network of interconnected pathways for cellular defense, RNA surveillance, and development and that it may become a powerful tool to manipulate gene expression experimentally.

Proteomic Analysis of Arabidopsis Seed Germination and Priming

Abstract: To better understand seed germination, a complex developmental process, we developed a proteome analysis of the model plant Arabidopsis for which complete genome sequence is now available. Among about 1,300 total seed proteins resolved in two-dimensional gels, changes in the abundance (up- and down-regulation) of 74 proteins were observed during germination sensu stricto (i.e. prior to radicle emergence) and the radicle protrusion step. This approach was also used to analyze protein changes occurring during industrial seed pretreatments such as priming that accelerate seed germination and improve seedling uniformity. Several proteins were identified by matrix-assisted laser-desorption ionization time of flight mass spectrometry. Some of them had previously been shown to play a role during germination and/or priming in several plant species, a finding that underlines the usefulness of using Arabidopsis as a model system for molecular analysis of seed quality. Furthermore, the present study, carried out at the protein level, validates previous results obtained at the level of gene expression (e.g. from quantitation of differentially expressed mRNAs or analyses of promoter/reporter constructs). Finally, this approach revealed new proteins associated with the different phases of seed germination and priming. Some of them are involved either in the imbibition process of the seeds (such as an actin isoform or a WD-40 repeat protein) or in the seed dehydration process (e.g. cytosolic glyceraldehyde-3-phosphate dehydrogenase). These facts highlight the power of proteomics to unravel specific features of complex developmental processes such as germination and to detect protein markers that can be used to characterize seed vigor of commercial seed lots and to develop and monitor priming treatments.

Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts.

Abstract: The nodC and nifH genes were characterized in a collection of 83 rhizobial strains which represented 23 recognized species distributed in the genera Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, as well as unclassified rhizobia from various host legumes. Conserved primers were designed from available nucleotide sequences and were able to amplify nodC and nifH fragments of about 930 bp and 780 bp, respectively, from most of the strains investigated. RFLP analysis of the PCR products resulted in a classification of these rhizobia which was in general well-correlated with their known host range and independent of their taxonomic status. The nodC and nifH fragments were sequenced for representative strains belonging to different genera and species, most of which originated from Phaseolus vulgaris nodules. Phylogenetic trees were constructed and revealed close relationships among symbiotic genes of the Phaseolus symbionts, irrespective of their 16S-rDNA-based classification. The nodC and nifH phylogenies were generally similar, but cases of incongruence were detected, suggesting that genetic rearrangements have occurred in the course of evolution. The results support the view that lateral genetic transfer across rhizobial species and, in some instances, across Rhizobium and Sinorhizobium genera plays a role in diversification and in structuring the natural populations of rhizobia.

Dynamical model development and parameter identification for an anaerobic wastewater treatment process

Abstract: This paper deals with the development and the parameter identification of an anaerobic digestion process model. A two-step (acidogenesis-methanization) mass-balance model has been considered. The model incorporates electrochemical equilibria in order to include the alkalinity, which has to play a central role in the related monitoring and control strategy of a treatment plant. The identification is based on a set of dynamical experiments designed to cover a wide spectrum of operating conditions that are likely to take place in the practical operation of the plant. A step by step identification procedure to estimate the model parameters is presented. The results of 70 days of experiments in a 1-m(3) fermenter are then used to validate the model. (C) 2001 John Wiley & Sons, Inc.

The digestion rate of protein is an independent regulating factor of postprandial protein retention

Abstract: To evaluate the importance of protein digestion rate on protein deposition, we characterized leucine kinetics after ingestion of “protein” meals of identical amino acid composition and nitrogen con...

Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.

Abstract: Rhizobia described so far belong to three distinct phylogenetic branches within the alpha-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, "Methylobacterium nodulans," within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the alpha subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that "M. nodulans" is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that "M. nodulans" NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer.

Post-transcriptional gene silencing in plants

Abstract: Post-transcriptional gene silencing (PTGS) in plants is an RNA-degradation mechanism that shows similarities to RNA interference (RNAi) in animals. Indeed, both involve double-stranded RNA (dsRNA), spread within the organism from a localised initiating area, correlate with the accumulation of small interfering RNA (siRNA) and require putative RNA-dependent RNA polymerases, RNA helicases and proteins of unknown functions containing PAZ and Piwi domains. However, some differences are evident. First, PTGS in plants requires at least two genes--SGS3 (which encodes a protein of unknown function containing a coil-coiled domain) and MET1 (which encodes a DNA-methyltransferase)--that are absent in C. elegans and thus are not required for RNAi. Second, all Arabidopsis mutants that exhibit impaired PTGS are hypersusceptible to infection by the cucumovirus CMV, indicating that PTGS participates in a mechanism for plant resistance to viruses. Interestingly, many viruses have developed strategies to counteract PTGS and successfully infect plants--for example, by potentiating endogenous suppressors of PTGS. Whether viruses can counteract RNAi in animals and whether endogenous suppressors of RNAi exist in animals is still unknown.

Towards a better understanding of the genetic and physiological basis for nitrogen use efficiency in maize

Abstract: To enhance our understanding of the genetic basis of nitrogen use efficiency in maize (Zea mays), we have developed a quantitative genetic approach by associating metabolic functions and agronomic traits to DNA markers. In this study, leaves of vegetative recombinant inbred lines of maize, already assessed for their agronomic performance, were analyzed for physiological traits such as nitrate content, nitrate reductase (NR), and glutamine synthetase (GS) activities. A significant genotypic variation was found for these traits and a positive correlation was observed between nitrate content, GS activity and yield, and its components. NR activity, on the other hand, was negatively correlated. These results suggest that increased productivity in maize genotypes was due to their ability to accumulate nitrate in their leaves during vegetative growth and to efficiently remobilize this stored nitrogen during grain filling. Quantitative trait loci (QTL) for various agronomic and physiological traits were searched for and located on the genetic map of maize. Coincidences of QTL for yield and its components with genes encoding cytosolic GS and the corresponding enzyme activity were detected. In particular, it appears that the GS locus on chromosome 5 is a good candidate gene that can, at least partially, explain variations in yield or kernel weight. Because at this locus coincidences of QTLs for grain yield, GS, NR activity, and nitrate content were also observed, we hypothesize that leaf nitrate accumulation and the reactions catalyzed by NR and GS are coregulated and represent key elements controlling nitrogen use efficiency in maize.

Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut.

Abstract: We have shown that bacterial mutation rates change during the experimental colonization of the mouse gut. A high mutation rate was initially beneficial because it allowed faster adaptation, but this benefit disappeared once adaptation was achieved. Mutator bacteria accumulated mutations that, although neutral in the mouse gut, are often deleterious in secondary environments. Consistently, the competitiveness of mutator bacteria is reduced during transmission to and re-colonization of similar hosts. The short-term advantages and long-term disadvantages of mutator bacteria could account for their frequency in nature.

AtSPO11‐1 is necessary for efficient meiotic recombination in plants

Abstract: The Saccharomyces cerevisiae Spo11 protein catalyses DNA double-strand breaks (DSBs) that initiate meiotic recombination. The model plant Arabidopsis thaliana possesses at least three SPO11 homologues. T-DNA and ethyl-methane sulfonate mutagenesis allowed us to show that meiotic progression is altered in plants in which the AtSPO11-1 gene is disrupted. Both male and female meiocytes formed very few bivalents. Furthermore, no fully synapsed chromosomes were observed during prophase I. Later, in meiosis I, we observed that chromosomes segregated randomly, leading to the production of a large proportion of non-functional gametes. These meiotic aberrations were associated with a drastic reduction in meiotic recombination. Thus, our data show that initiation of meiotic recombination by SPO11- induced DSBs is a mechanism conserved in plants. Furthermore, unlike Drosophila and Caenorhabditis elegans, but like fungi, SPO11 is necessary for normal synapsis in plants.

Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Booroola Mérino ewes

Abstract: Ewes from the Booroola strain of Australian Merino sheep are characterized by high ovulation rate and litter size. This phenotype is due to the action of the FecB(B) allele of a major gene named FecB, as determined by statistical analysis of phenotypic data. By genetic analysis of 31 informative half-sib families from heterozygous sires, we showed that the FecB locus is situated in the region of ovine chromosome 6 corresponding to the human chromosome 4q22-23 that contains the bone morphogenetic protein receptor IB (BMPR-IB) gene encoding a member of the transforming growth factor-beta (TGF-beta) receptor family. A nonconservative substitution (Q249R) in the BMPR-IB coding sequence was found to be associated fully with the hyperprolificacy phenotype of Booroola ewes. In vitro, ovarian granulosa cells from FecB(B)/FecB(B) ewes were less responsive than granulosa cells from FecB(+)/FecB(+) ewes to the inhibitory effect on steroidogenesis of GDF-5 and BMP-4, natural ligands of BMPR-IB. It is suggested that in FecB(B)/FecB(B) ewes, BMPR-IB would be inactivated partially, leading to an advanced differentiation of granulosa cells and an advanced maturation of ovulatory follicles.

Effects of grass feeding systems on ruminant meat colour and flavour. A review

Abstract: Grass feeding has been reported to affect several meat quality characteristics, in particular colour and flavour. In this paper we have reviewed some differences in meat colour and flavour between ruminants fed concentrates and animals allowed to graze pasture. The possible factors influ- encing the differences have been also examined. We have examined a total of 35 experiments which report the effect of pasture vs concentrate finishing systems on beef meat colour. Meat from cattle raised on pasture is reported to be darker than meat from animals raised on concentrates if measured by objec- tive (P < 0.001) as well as subjective ( P < 0.05) methods. Several factors, not a specific one are responsible for this difference, variations in ultimate-pH and in intramuscular fat content between ani- mals finished at pasture and those finished on concentrates, seem to play a major role. Diet also affects meat flavour in both sheep and cattle but the components involved seem to be different. In sheep pastoral flavour is mostly determined by the branched-chain fatty acids and 3-methylindole (ska- tole). An important role seems to be played also by some products of oxidation of linolenic acid and its derivates. In cattle the role of skatole seems to be less important than sheep because of the lack of the branched-chain fatty acids. The pastoral flavour seems to be mostly determined by products of oxidation of linolenic acid and its derivates which derives substantially from grass. grass feeding / meat colour / meat flavour / ruminants