Sculpting the soil microbiota

Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota–plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota-based strategies to preserve natural resources and develop more environmentally friendly agricultural practices

Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam

Background: Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results: The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions: Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development

Plant microbiota controls an alternative root branching regulatory mechanism in plants

The establishment of beneficial interactions with microbes has helped plants to modulate root branching plasticity in response to environmental cues. However, how the plant microbiota harmonizes with plant roots to control their branching is unknown. Here, we show that the plant microbiota influences root branching in the model plant Arabidopsis thaliana. We define that the microbiota's ability to control some stages in root branching can be independent of the phytohormone auxin that directs lateral root development under axenic conditions. In addition, we revealed a microbiota-driven mechanism controlling lateral root development that requires the induction of ethylene response pathways. We show that the microbial effects on root branching can be relevant for plant responses to environmental stresses. Thus, we discovered a microbiota-driven regulatory pathway controlling root branching plasticity that could contribute to plant adaptation to different ecosystems

Functional characterization of genes regulated by the CROWN ROOT LESS 1 transcription factor involved in crown root initiation and development in rice

Le but de cette thèse est de préciser les mécanismes moléculaires agissant en aval du facteur de transcription CROWN ROOT LESS 1 (CRL1) qui régule la formation des racines coronaires (RC). Nous avons pu identifier dans un premier temps une nouvelle séquence d’ADN reconnue par CRL1 nommé CRL1-box différente de la LBD-box qui était le seul motif cis-régulateur précédemment décrit pour la famille des facteurs de transcription (FT) de type LATERAL ORGAN BOUNDARIES DOMAIN (LBD). Nous avons ensuite identifié un groupe de gènes régulés par CRL1, et avons montré l’implication de deux d’entre eux, OsROP et OsbHLH044, dans le développement des RC. OsbHLH044 est un facteur de transcription répresseur et semble être aussi impliqué dans la sénescence cellulaire ainsi que la réponse aux stress. Enfin, nous avons mis en évidence une cascade de régulation liant positivement CRL1 avec QUIESCENT-CENTER-SPECIFIC HOMEOBOX (QHB) un gène impliqué dans la différenciation et le maintien du centre quiescent via le facteur de transcription OsHOX14. En addition nous avons mis en évidence une boucle de rétroaction négative de QHB sur ses activateurs CRL1 et OsHOX14, qui pourrait être impliquée dans la structuration du primordia de racine coronaire.The aim of this thesis is to specify the molecular mechanisms acting downstream of the CROWN ROOT LESS 1 transcription factor (CRL1) that regulates coronary root (CR) formation. We were able to identify at first a new CRL1 recognized DNA sequence named CRL1-box different from the LBD-box which was the only cis-regulatory motif previously described for the LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor (TF) family. We then identified a group of genes regulated by CRL1, and showed the involvement of two of them, OsROP and OsbHLH044, in the development of CR. OsbHLH044 is a repressive transcription factor and appears to be also involved in cell senescence as well as stress response. Finally, we demonstrated a regulatory cascade linking CRL1 with QUIESCENT-CENTER-SPECIFICHOMEOBOX (QHB), a gene involved in the differentiation and maintenance of the quiescent center, via the OsHOX14 transcription factor. In addition we have demonstrated a negative feedback loop of QHB on its activators CRL1 and OsHOX14, which could be involved in structuring the coronary root primordi

Utilisation de l’indice de biodiversité potentielle

Entretenir sa forêt: Fiche techniquePeu de temps après la création de l’IBP en 2008, le CRPF Midi-Pyrénées a proposé cette méthode à un propriétaire tarnais qui réalisait son PSG et souhaitait mieux intégrer la biodiversité ordinaire dans sa gestion courante. C’est ce travail qui est ici relaté. Notons qu’en complément à l’IBP, le propriétaire a utilisé ultérieurement la démarche BIOFIL 1, développée par le CRPF Midi-Pyrénées et permettant notamment de mieux repérer à l’échelle de la forêt leséléments de biodiversité remarquables

Industrie et environnement : une nouvelle préoccupation, le management écologique

Industrial civilization is clearly the main responsable for environmental hazards. Therefore the growing ecological concept among industrialists lead to an ecological way of management. As far as possible they try to reduice the nuissances for the general well being. German industrialists made the first steps, opening the way with bäum association. Some firms, like madaus adopted strongly ecological concepts which became a full part of their firm culture.Si l'industrialisation est en grande partie responsable de la détérioration de l'environnement, la prise de conscience écologique est très forte chez les industriels qui, par un management écologique de leur entreprise essaient de maîtriser au mieux les nuisances, pour le bien de tous. Les industriels allemands sont les pionniers en la matière avec le mouvement B.A.U.M.. Certaines firmes, comme MADAUS, adoptent complètement les concepts écologiques qui sont intégrés dans la «culture d'entreprise».Biguet L., Gachelin Charles, Gonin Patrick, Mathieu B., Roussel Isabelle. Industrie et environnement : une nouvelle préoccupation, le management écologique. In: Hommes et Terres du Nord, 1991/4. Environnement. pp. 256-260

What Makes Adventitious Roots?

The spermatophyte root system is composed of a primary root that develops from an embryonically formed root meristem, and of different post-embryonic root types: lateral and adventitious roots. Adventitious roots, arising from the stem of the plants, are the main component of the mature root system of many plants. Their development can also be induced in response to adverse environmental conditions or stresses. Here, in this review, we report on the morphological and functional diversity of adventitious roots and their origin. The hormonal and molecular regulation of the constitutive and inducible adventitious root initiation and development is discussed. Recent data confirmed the crucial role of the auxin/cytokinin balance in adventitious rooting. Nevertheless, other hormones must be considered. At the genetic level, adventitious root formation integrates the transduction of external signals, as well as a core auxin-regulated developmental pathway that is shared with lateral root formation. The knowledge acquired from adventitious root development opens new perspectives to improve micropropagation by cutting in recalcitrant species, root system architecture of crops such as cereals, and to understand how plants adapted during evolution to the terrestrial environment by producing different post-embryonic root types