Microbial communities play a pivotal role in the functioning of plants by influencing their physiology and development. While many members of the rhizosphere microbiome are beneficial to plant growth, also plant pathogenic microorganisms colonize the rhizosphere striving to break through the protective microbial shield and to overcome the innate plant defense mechanisms in order to cause disease. A third group of microorganisms that can be found in the rhizosphere are the true and opportunistic human pathogenic bacteria, which can be carried on or in plant tissue and may cause disease when introduced into debilitated humans. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, for the vast majority of rhizosphere microorganisms no knowledge exists. To enhance plant growth and health, it is essential to know which microorganism is present in the rhizosphere microbiome and what they are doing. Here, we review the main functions of rhizosphere microorganisms and how they impact on health and disease. We discuss the mechanisms involved in the multitrophic interactions and chemical dialogues that occur in the rhizosphere. Finally, we highlight several strategies to redirect or reshape the rhizosphere microbiome in favor of microorganisms that are beneficial to plant growth and health.

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

Summary: High-affinity iron acquisition is mediated by siderophore-dependent pathways in the majority of pathogenic and nonpathogenic bacteria and fungi. Considerable progress has been made in characterizing and understanding mechanisms of siderophore synthesis, secretion, iron scavenging, and siderophore-delivered iron uptake and its release. The regulation of siderophore pathways reveals multilayer networks at the transcriptional and posttranscriptional levels. Due to the key role of many siderophores during virulence, coevolution led to sophisticated strategies of siderophore neutralization by mammals and (re)utilization by bacterial pathogens. Surprisingly, hosts also developed essential siderophore-based iron delivery and cell conversion pathways, which are of interest for diagnostic and therapeutic studies. In the last decades, natural and synthetic compounds have gained attention as potential therapeutics for iron-dependent treatment of infections and further diseases. Promising results for pathogen inhibition were obtained with various siderophore-antibiotic conjugates acting as “Trojan horse” toxins and siderophore pathway inhibitors. In this article, general aspects of siderophore-mediated iron acquisition, recent findings regarding iron-related pathogen-host interactions, and current strategies for iron-dependent pathogen control will be reviewed. Further concepts including the inhibition of novel siderophore pathway targets are discussed.

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Siderophore-Based Iron Acquisition and Pathogen Control

Occurrence, classification, and biological function of hydrogenases: an overview.

Bacteria that colonize plant roots and promote plant growth are referred to as plant growth-promoting rhizobacteria (PGPR). PGPR are highly diverse and in this review we focus on rhizobacteria as biocontrol agents. Their effects can occur via local antagonism to soil-borne pathogens or by induction of systemic resistance against pathogens throughout the entire plant. Several substances produced by antagonistic rhizobacteria have been related to pathogen control and indirect promotion of growth in many plants, such as siderophores and antibiotics. Induced systemic resistance (ISR) in plants resembles pathogen-induced systemic acquired resistance (SAR) under conditions where the inducing bacteria and the challenging pathogen remain spatially separated. Both types of induced resistance render uninfected plant parts more resistant to pathogens in several plant species. Rhizobacteria induce resistance through the salicylic acid-dependent SAR pathway, or require jasmonic acid and ethylene perception from the plant for ISR. Rhizobacteria belonging to the genera Pseudomonas and Bacillus are well known for their antagonistic effects and their ability to trigger ISR. Resistance-inducing and antagonistic rhizobacteria might be useful in formulating new inoculants with combinations of different mechanisms of action, leading to a more efficient use for biocontrol strategies to improve cropping systems.

https://www.lume.ufrgs.br/bitstream/handle/10183/87984/000873412.pdf;sequence=1

Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents

Iron is an essential element for most organisms, including bacteria. The oxidized form is insoluble, and the reduced form is highly toxic for most macromolecules and, in biological systems, is generally sequestrated by iron- and heme-carrier proteins. Thus, despite its abundance on earth, there is practically no free iron available for bacteria whatever biotope they colonize. To fulfill their iron needs, bacteria have multiple iron acquisition systems, reflecting the diversity of their potential biotopes. The iron/heme acquisition systems in bacteria have one of two general mechanisms. The first involves direct contact between the bacterium and the exogenous iron/heme sources. The second mechanism relies on molecules (siderophores and hemophores) synthesized and released by bacteria into the extracellular medium; these molecules scavenge iron or heme from various sources. Recent genetic, biochemical, and crystallographic studies have allowed substantial progress in describing molecular mechanisms of siderophore and hemophore interactions with the outer membrane receptors, transport through the inner membrane, iron storage, and regulation of genes encoding biosynthesis and uptake proteins.

Bacterial Iron Sources: From Siderophores to Hemophores

Iron is essential to virtually all organisms, but poses problems of toxicity and poor solubility. Bacteria have evolved various mechanisms to counter the problems imposed by their iron dependence, allowing them to achieve effective iron homeostasis under a range of iron regimes. Highly efficient iron acquisition systems are used to scavenge iron from the environment under iron-restricted conditions. In many cases, this involves the secretion and internalisation of extracellular ferric chelators called siderophores. Ferrous iron can also be directly imported by the G protein-like transporter, FeoB. For pathogens, host–iron complexes (transferrin, lactoferrin, haem, haemoglobin) are directly used as iron sources. Bacterial iron storage proteins (ferritin, bacterioferritin) provide intracellular iron reserves for use when external supplies are restricted, and iron detoxification proteins (Dps) are employed to protect the chromosome from iron-induced free radical damage. There is evidence that bacteria control their iron requirements in response to iron availability by down-regulating the expression of iron proteins during iron-restricted growth. And finally, the expression of the iron homeostatic machinery is subject to iron-dependent global control ensuring that iron acquisition, storage and consumption are geared to iron availability and that intracellular levels of free iron do not reach toxic levels.

Bacterial iron homeostasis

Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis.

FtnA is the major iron-storage protein of Escherichia coli accounting for < or = 50% of total cellular iron. The FtnA gene (ftnA) is induced by iron in an Fe(2+)-Fur-dependent fashion. This effect is reportedly mediated by RyhB, the Fe(2+)-Fur-repressed, small, regulatory RNA. However, results presented here show that ftnA iron induction is independent of RyhB and instead involves direct interaction of Fe(2+)-Fur with an 'extended' Fur binding site (containing five tandem Fur boxes) located upstream (-83) of the ftnA promoter. In addition, H-NS acts as a direct repressor of ftnA transcription by binding at multiple sites (I-VI) within, and upstream of, the ftnA promoter. Fur directly competes with H-NS binding at upstream sites (II-IV) and consequently displaces H-NS from the ftnA promoter (sites V-VI) which in turn leads to derepression of ftnA transcription. It is proposed that H-NS binding within the ftnA promoter is facilitated by H-NS occupation of the upstream sites through H-NS oligomerization-induced DNA looping. Consequently, Fur displacement of H-NS from the upstream sites prevents cooperative H-NS binding at the downstream sites within the promoter, thus allowing access to RNA polymerase. This direct activation of ftnA transcription by Fe(2+)-Fur through H-NS antisilencing represents a new mechanism for iron-induced gene expression.

Induction of the ferritin gene (ftnA) of Escherichia coli by Fe2+–Fur is mediated by reversal of H-NS silencing and is RyhB independent

The Williams–Beuren syndrome (WBS, MIM 194050) is a genetic disorder caused by a microdeletion at 7q11.23 that involves the ELN (Elastin) and LIMK1 amongst other genes [Meng et al., 1998]. Its frequency varies from 1:13,700 to 1: 25,000 [Udwin, 1990] with an equal proportion amongst both sexes. The main phenotypic features are: distinctive face, cardiovascular malformations, fundamentally supravalvular aortic stenosis with or without supravalvular pulmonary stenosis, and a typical growth pattern with a precocious puberty in a subgroup of affected women. They can also present with anomalies in the kidneys, as well as radio-ulnar synostosis. Generally they have mild to moderate mental retardation with an outgoing personality, hyperacousia, and attention deficit hyperactivity disorder (ADHD) [Osborne, 1999]. The causative hemizygotic deletion in 7q11.23 was described first by Ewart et al. [1993] in 1993. The West ‘‘syndrome’’ (WS), although not a syndrome in the true genetic sense, is an age-dependent epileptic encephalopathy that is characterized by a clinical triad of epileptic spasms, psychomotor delay, and hypsarrhythmia. It is a symptom complex of multiple etiology due to the inadequate response of an immature brain to a variety of causes [Watanabe, 1998]. Its frequency is estimated to be 2–5:10,000, with equal proportions between both sexes [Wong and Trevathan, 2001]. Although the WS has been considered inside the refractory epilepsy, its prognosis varies extensively according to its etiology. It can be classified in prenatal, perinatal, and postnatal, depending on the period in which the cerebral damage is produced. According to the ‘‘International Classification of Epilepsies and Epileptic Syndromes,’’ the WS can be also classified as symptomatic and cryptogenic. The symptomatic group are those in which it is possible to recognize or to suspect an underlying pathogenesis of the central nervous system, while in the cryptogenic group, the underlying cause is not known [Commission on Classification and Terminology of the International League against Epilepsy, 1989]. Our propositus is a 3-year-old Arabian male of Egyptian origin born of a third pregnancy with a premature delivery at the 7th month. There was no family history of developmental or psychomotor delay. His parents were healthy and nonconsanguineous, and they have previously had two healthy children. He was born at 42 weeks of gestational age by a delivery complicated with dystocia, a stained amniotic fluid and a weight of 3,350 g. His Apgar score was 9 at the min, and 10 at 5 min of life, respectively. At 3 weeks a heart murmur was observed and diagnosed as an interventricular communication that had been followed by the Cardiology Service. The psychomotor development was retarded: he smiled at 2.5 months, laughed spontaneously at 3 months, kept his head upright at 6 months, sat with tripod at 10 months, stood up at 13 months, and began to walk at 2 years. He emitted his first vocalizations at 2 months and monosyllabic words at 1 year. At 5 months he was referred to the pediatrician because of generalized spasms, and he was evaluated subsequently in Egypt by a neurologist who performed him a cranial CAT that was normal and began treatment with piracetam and vincamyn. We evaluated him at 7.5 months because of a psychomotor delay. He had an OFC of 45.5 cm (50 centile), and had the anterior fontanel opened. His weight was 9,200 g (50– 75 centile). He was alert but irritable, with a lack of visual responsiveness. He had a lively and hoarse cry, could not grip objects, and could not sit unsupported. We observed hypotonia of the extremities and also axial hypotonia with a light retraction of the aquileus and isquiotibial muscles, although he did not present parachuting. No anomalies were found in the strength, sensation, and reflexes. A distinctive facial phenotype was observed including large ears, thick lips, and upturned nose, all suggestive of WBS (Fig. 1). Genomic DNA was obtained from the patient and his parents by standard methods [Miller et al., 1988]. Polymerase chain reaction (PCR) for the amplification of the markers D7S672, D7S613, ELN-i-1, ELN-i-18, D7S1870, D7S2490, D7S2518, D7S2421, and D7S634 were performed as described in the Genome data bank (http://www.gdb.org). The PCR products were analyzed on nondenaturant 8% and 10% polyacrylamyde gel slabs (19:1). This molecular genetic study comprising the WBS critical region at 7q11.23 with polymorphic markers intra and extradeletion, showed a de novo deletion of paternal origin (Fig. 2). The following studies showed as normal: abdominal echography, cranial MRI, biochemistry (muscular enzymes included), and standard karyotype. Nevertheless the trunk evoked auditory potentials showed a cochlear bilateral hypoacusia of 50 db. In the visual potentials the only finding of interest was their low amplitude, and in the EEG a pattern of hypsarrhythmia was appreciated. The patient was re-evaluated subsequently at 11 and 19 months and at 2 years we verified slow progression of his motor and cognitive capacities. He was derived to the Hypoacusia Unit where they prescribed him audiphones. He still does not pronounce any word albeit he has received physiotherapy and early stimulation. The EEGs of control became normal, and the antiepileptic treatment was withdrawn. We present here a new case of WS associated with WBS. The WBS has been confirmed by the presence of the hemizygotic deletion of the critical region of WBS, analyzed with microsatellites intra and extradeletion (Fig. 2). The pattern of interictal hypsarrhythmia in the EEG and the presence of spasms were pathognomonic of WS. The patient did not have SVAS, but did have an interventricular communication. He did not present episodes of hypercalcemia. *Correspondence to: Miguel Fernández-Burriel Tercero, Laboratorio de Genética Molecular, Hospital Universitario MaternoInfantil de Canarias, Avda, Marı́tima del Sur s/n, 35016-Las Palmas de Gran Canaria, Canary Islands, Spain. E-mail: mferter@gobiernodecanarias.org

Francisco Rodríguez-Quiñones

Papers

Bacterial iron homeostasis

Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis.

Induction of the ferritin gene (ftnA) of Escherichia coli by Fe2+–Fur is mediated by reversal of H-NS silencing and is RyhB independent

Williams–Beuren syndrome and West “syndrome:” Causal association or contiguous gene deletion syndrome?