The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.

The processes involved in the formation of primordia on the shoor apex are those controlling (1) growth rate, (2) division plane. (3) surface microstructure, and (4) extensibility of the surface. Changes in growth rate and division planes may accompany primordium formation but are considered as probably not in themselves being causal. Changes in surface microstructure may be necessary to delimit the position and area occupied by an incipient primordium. However, attention is directed to changes in surface extensibility as perhaps being the overriding factor in primordium formation. Nevertheless, the position and form of the primordia will also depend on growth rate, division plane, and surface microstructurc being permissive. The relative importance of these four sets of processes may differ from species to species and from one stage of development to another. Chemical and metabolic changes within the apex may first be necessary to determine whether the surface can extend sufficiently for any primordia to form at all, but their positions and time of initiation may depend more on the other factors. The surface microstructure may become more important when patterning is detailed and precise as it is in the developing flower, whereas a less precise mechanism dependent on localized induction of synthesis of a morphogen (auxin?) may provide sufficient information to determine the general position and liming of primordium initiation in vegetative apices. In determining the pattern of primordia on the apex, primordial area at initiation is important and reasons for believing that auxin may be involved in determining this are summarised. The different developmental pathways of primordia seem to diverge from the moment of initiation. Developmental fate of primordia is determined by the hamcotic genes which may in fact be heterochronic genes. How these regulatory genes control the processes involved in differentiation of different types of primordia is so far unknown. Contents Summary 1 I. Introduction 2 II. The mechanism of primordium formation: what causes an outgrowth of the apical surface? 2 III. The positions of successive primordia: what determines their size and localization, so giving rise to pattern? 11 IV. What determines the developmental pathways of the primordia once initiated? 13 V. Conclusions 15 VI. Acknowledgements 16 VII. References 16.

Plant hormone biology is an ever-evolving field and as such, novel avenues of research must always be sought. Technological and theoretical advancement can also allow for previously dismissed research to yield equally interesting insights into processes now that they are better understood. The auxin phenylacetic acid (PAA) is an excellent example of this. PAA is a plant auxin that also possesses substantial antimicrobial activity. It has a broad distribution and has been studied in bacteria, fungi, algae and land plants. Research on this compound in plants was prominent in the 1980s, where its bioactivity and broad distribution were frequently examined. Unfortunately, due to the strong interest in the quintessential auxin, indole-3-acetic acid (IAA), research on PAA quickly petered out. Recently, several groups have resumed investigations on this hormone in plants, yet, little is known about PAA biology and its physiological role is unclear. PAA biosynthesis from the amino acid Phe invites direct comparisons with previously studied IAA biosynthesis pathways, and recent work has shown that PAA metabolism and signaling appears to be similar to that of IAA. However, given the large gap between previous work and recent investigations, a historical review of this auxin is required to renew our understanding of PAA. Here, previous work on PAA is reassessed in light of recent research in plants and serves as a synthesis of current knowledge on PAA biology.

The rhizobia-legume symbiosis is a mutualistic association in which bacteria provide plants with nitrogen compounds and the plant provides bacteria with carbon sources. A successful symbiotic interaction relies on a molecular dialog between the plant and the bacteria, and generally involves rhizobial lipo-chitooligosaccharide signals called Nod factors (NFs). In most cases, specific NF perception is required for rhizobia to enter root cells through newly formed intracellular structures called infection threads (ITs). Concomitantly to IT formation in root hairs, root cortical cells start to divide to create a new root organ called the nodule, which will provide the bacteria with a specific micro-environment required for symbiotic nitrogen fixation. During all these steps of plant-bacteria interaction, new plant cellular compartments and developmental programs are activated. This interaction is costly for the plant that tightly controls symbiosis establishment and functioning. Phytohormones are key regulators of cellular and developmental plasticity in plants, and they are influential endogenous signals that rapidly control plant responses. Although early symbiotic responses were known for decades to be linked to phytohormone-related responses, new data reveal the molecular mechanisms involved and links between phytohormones and the control of early symbiotic events. Reciprocally, NF signaling also targets phytohormone signaling pathways. In this review, we will focus on the emerging notion of NF and phytohormone signaling crosstalk, and how it could contribute to the tight control of symbiosis establishment in legume host plants.

The growing problem of remediation of contaminated sediments dredged from harbor channels needs to be resolved by a cost effective and sustainable technology. Phytoremediation, by ex situ remediation plants, seems to have the potential to replace traditional methods in case of moderately contaminated sediments. On the other side, the need to mix sediments with soil and/or sand to allow an easier establishment of most employed species causes an increase of the volume of the processed substrate up to 30%. Moreover the majority of phytoremediating species are natives of temperate climate belt. Mangroves, with a special focus on the genus Avicennia - a salt secreting species - should represent an effective alternative in terms of adaptation to salty, anoxic sediments and an opportunity to develop ex situ phytoremediation plants in tropical and subtropical regions. The use of humic acid to increase root development, cell antioxidant activity and the potential attenuation of the \"heavy metals exclusion strategy\" to increase phytoextraction potentials of mangroves will be reviewed.

Auxin is a key regulator of virtually every aspect of plant growth and development from embryogenesis to senescence. Previous studies have indicated that auxin regulates these processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs). ARFs are likely components that confer specificity to auxin response through selection of target genes as transcription factors. They bind to auxin response DNA elements (AuxRE) in the promoters of auxin-regulated genes and either activate or repress transcription of these genes depending on a specific domain in the middle of the protein. Genetic studies have implicated various ARFs in distinct developmental processes through loss-of-function mutant analysis. Recent advances have provided information on the regulation of ARF gene expression, the role of ARFs in growth and developmental processes, protein-protein interactions of ARFs and target genes regulated by ARFs in plants. In particular, protein interaction and structural studies of ARF proteins have yielded novel insights into the molecular basis of auxin-regulated transcription. These results provide the foundation for predicting the contributions of ARF genes to the biology of other plants.